# If you add titratable residues to getData, also add them here. EXP_PKAS is only # used to screen residues based on maxpKa and minpKa. flags. TITRATABLE = "AS4 GL4 HIP TYR LYS CYS DAP DCP DG DT AP CP G U " EXP_PKAS = "4.0 4.4 6.5 9.6 10.4 8.5 3.9 4.3 2.1 9.7 3.9 4.3 2.1 9.3" # This python file is used by cpinutil.py and has all of the data for # each titratable residue for each value of igb that is desired. def getData(residue, igb, has_water=False, neighbor_right='none', neighbor_left='none'): import sys, math # Factors to adjust TI energies KB = 0.00199 # kcal/mol * K LN_TO_LOG = math.log(10) TEMP = 300 data = [] charges = [] if residue == "AS4": pKa = 4.0 # set the relative energies for the different igb choices if igb == 2: if has_water: relene = 26.6047496 + KB * LN_TO_LOG * TEMP * pKa else: relene = 26.8894581 + KB * LN_TO_LOG * TEMP * pKa elif igb == 5: if has_water: relene = 26.1881636 + KB * LN_TO_LOG * TEMP * pKa else: relene = 26.5980488 + KB * LN_TO_LOG * TEMP * pKa elif igb == 8: relene = 26.3448911 + KB * LN_TO_LOG * TEMP * pKa else: relene = 0.0 return [ [ 0, # Relative energy STATE 0 Deprotonated 0, # Relative protonation -0.4157, # N 0.2719, # H 0.0341, # CA 0.0864, # HA -0.1783, # CB -0.0122, # HB2 -0.0122, # HB3 0.7994, # CG -0.8014, # OD1 -0.8014, # OD2 0.0000, # HD21 0.5973, # C -0.5679, # O 0.0000, # HD22 0.0000, # HD11 0.0000 ], # HD12 [ relene, # Relative energy STATE 1 Protonated syn O2 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0341, # CA 0.0864, # HA -0.0316, # CB 0.0488, # HB2 0.0488, # HB3 0.6462, # CG -0.5554, # OD1 -0.6376, # OD2 0.4747, # HD21 0.5973, # C -0.5679, # O 0.0000, # HD22 0.0000, # HD11 0.0000 ], # HD12 [ relene, # Relative energy STATE 2 Protonated anti O2 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0341, # CA 0.0864, # HA -0.0316, # CB 0.0488, # HB2 0.0488, # HB3 0.6462, # CG -0.5554, # OD1 -0.6376, # OD2 0.0000, # HD21 0.5973, # C -0.5679, # O 0.4747, # HD22 0.0000, # HD11 0.0000 ], # HD12 [ relene, # Relative energy STATE 3 Protonated syn O1 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0341, # CA 0.0864, # HA -0.0316, # CB 0.0488, # HB2 0.0488, # HB3 0.6462, # CG -0.6376, # OD1 -0.5554, # OD2 0.0000, # HD21 0.5973, # C -0.5679, # O 0.0000, # HD22 0.4747, # HD11 0.0000 ], # HD12 [ relene, # Relative energy STATE 4 Protonated anti O1 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0341, # CA 0.0864, # HA -0.0316, # CB 0.0488, # HB2 0.0488, # HB3 0.6462, # CG -0.6376, # OD1 -0.5554, # OD2 0.0000, # HD21 0.5973, # C -0.5679, # O 0.0000, # HD22 0.0000, # HD11 0.4747 ] ] # HD12 if residue == "GL4": pKa = 4.4 if igb == 2: if has_water: relene = 8.0464682 + KB * TEMP * LN_TO_LOG * pKa else: relene = 8.4057785 + KB * TEMP * LN_TO_LOG * pKa elif igb == 5: if has_water: relene = 7.6690995 + KB * TEMP * LN_TO_LOG * pKa else: relene = 8.0855764 + KB * TEMP * LN_TO_LOG * pKa elif igb == 8: relene = 8.3493469 + KB * TEMP * LN_TO_LOG * pKa else: relene = 0.0 return [ [ 0, # Relative energy STATE 0 Deprotonated 0, # Relative protonation -0.4157, # N 0.2719, # H 0.0145, # CA 0.0779, # HA -0.0398, # CB -0.0173, # HB2 -0.0173, # HB3 0.0136, # CB -0.0425, # HG2 -0.0425, # HG3 0.8054, # CD -0.8188, # OE1 -0.8188, # OE2 0.0000, # HE21 0.5973, # C -0.5679, # O 0.0000, # HE22 0.0000, # HE11 0.0000 ], # HE12 [ relene, # Relative energy STATE 1 Protonated syn O2 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0145, # CA 0.0779, # HA -0.0071, # CB 0.0256, # HB2 0.0256, # HB3 -0.0174, # CB 0.0430, # HG2 0.0430, # HG3 0.6801, # CD -0.5838, # OE1 -0.6511, # OE2 0.4641, # HE21 0.5973, # C -0.5679, # O 0.0000, # HE22 0.0000, # HE11 0.0000 ], # HE12 [ relene, # Relative energy STATE 2 Protonated anti O2 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0145, # CA 0.0779, # HA -0.0071, # CB 0.0256, # HB2 0.0256, # HB3 -0.0174, # CB 0.0430, # HG2 0.0430, # HG3 0.6801, # CD -0.5838, # OE1 -0.6511, # OE2 0.0000, # HE21 0.5973, # C -0.5679, # O 0.4641, # HE22 0.0000, # HE11 0.0000 ], # HE12 [ relene, # Relative energy STATE 3 Protonated syn O1 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0145, # CA 0.0779, # HA -0.0071, # CB 0.0256, # HB2 0.0256, # HB3 -0.0174, # CB 0.0430, # HG2 0.0430, # HG3 0.6801, # CD -0.6511, # OE1 -0.5838, # OE2 0.0000, # HE21 0.5973, # C -0.5679, # O 0.0000, # HE22 0.4641, # HE11 0.0000 ], # HE12 [ relene, # Relative energy STATE 4 Protonated anti O1 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0145, # CA 0.0779, # HA -0.0071, # CB 0.0256, # HB2 0.0256, # HB3 -0.0174, # CB 0.0430, # HG2 0.0430, # HG3 0.6801, # CD -0.6511, # OE1 -0.5838, # OE2 0.0000, # HE21 0.5973, # C -0.5679, # O 0.0000, # HE22 0.0000, # HE11 0.4641 ] ] # HE12 if residue == "TYR": pKa = 9.6 if igb == 2: if has_water: relene = -65.003415 - KB * TEMP * LN_TO_LOG * pKa else: relene = -65.113428 - KB * TEMP * LN_TO_LOG * pKa elif igb == 5: if has_water: relene = -64.047229 - KB * TEMP * LN_TO_LOG * pKa else: relene = -64.166385 - KB * TEMP * LN_TO_LOG * pKa elif igb == 8: relene = -61.3305355 - KB * TEMP * LN_TO_LOG * pKa else: relene = 0.0 return [ [ 0, # Relative energy STATE 0 TYR (prot) 1, # Relative protonation -0.4157, # N 0.2719, # H -0.0014, # CA 0.0876, # HA -0.0152, # CB 0.0295, # HB2 0.0295, # HB3 -0.0011, # CG -0.1906, # CD1 0.1699, # HD1 -0.2341, # CE1 0.1656, # HE1 0.3226, # CZ -0.5579, # OH 0.3992, # HH -0.2341, # CE2 0.1656, # HE2 -0.1906, # CD2 0.1699, # HD2 0.5973, # C -0.5679 ], # O [ relene, # Relative energy STATE 1 TYM (deprot) 0, # Relative protonation -0.4157, # N 0.2719, # H -0.0014, # CA 0.0876, # HA -0.0858, # CB 0.0190, # HB2 0.0190, # HB3 -0.2130, # CG -0.1030, # CD1 0.1320, # HD1 -0.4980, # CE1 0.1320, # HE1 0.7770, # CZ -0.8140, # OH 0.0000, # HH -0.4980, # CE2 0.1320, # HE2 -0.1030, # CD2 0.1320, # HD2 0.5973, # C -0.5679 ] ] # O if residue == "HIP": pKa1 = 6.5 pKa2 = 7.1 if igb == 2: if has_water: relene1 = -2.77641 - KB * TEMP * LN_TO_LOG * pKa1 relene2 = -6.71562 - KB * TEMP * LN_TO_LOG * pKa2 else: relene1 = -2.84183 - KB * TEMP * LN_TO_LOG * pKa1 relene2 = -6.58793 - KB * TEMP * LN_TO_LOG * pKa2 elif igb == 5: if has_water: relene1 = -2.90517 - KB * TEMP * LN_TO_LOG * pKa1 relene2 = -6.82684 - KB * TEMP * LN_TO_LOG * pKa2 else: relene1 = -2.86001 - KB * TEMP * LN_TO_LOG * pKa1 relene2 = -6.70726 - KB * TEMP * LN_TO_LOG * pKa2 elif igb == 8: relene1 = -3.4000 - KB * TEMP * LN_TO_LOG * pKa1 relene2 = -6.3190 - KB * TEMP * LN_TO_LOG * pKa2 else: relene1 = 0.0 relene2 = 0.0 return [ [ 0, # Relative energy STATE 0 HIP 2, # Relative Protonation -0.3479, # N 0.2747, # H -0.1354, # CA 0.1212, # HA -0.0414, # CB 0.0810, # HB2 0.0810, # HB3 -0.0012, # CG -0.1513, # ND1 0.3866, # HD1 -0.0170, # CE1 0.2681, # HE1 -0.1718, # NE2 0.3911, # HE2 -0.1141, # CD2 0.2317, # HD2 0.7341, # C -0.5894 ], # 0 [ relene1, # Relative energy STATE 1 HID 1, # Relative Protonation -0.3479, # N 0.2747, # H -0.1354, # CA 0.1212, # HA -0.1110, # CB 0.0402, # HB2 0.0402, # HB3 -0.0266, # CG -0.3811, # ND1 0.3649, # HD1 0.2057, # CE1 0.1392, # HE1 -0.5727, # NE2 0.0000, # HE2 0.1292, # CD2 0.1147, # HD2 0.7341, # C -0.5894 ], # 0 [ relene2, # Relative energy STATE 2 HIE 1, # Relative Protonation -0.3479, # N 0.2747, # H -0.1354, # CA 0.1212, # HA -0.1012, # CB 0.0367, # HB2 0.0367, # HB3 0.1868, # CG -0.5432, # ND1 0.0000, # HD1 0.1635, # CE1 0.1435, # HE1 -0.2795, # NE2 0.3339, # HE2 -0.2207, # CD2 0.1862, # HD2 0.7341, # C -0.5894 ] ] # 0 if residue == "LYS": pKa = 10.4 if igb == 2: if has_water: relene = -15.1417977 + KB * TEMP * LN_TO_LOG * pKa else: relene = -15.2423959 + KB * TEMP * LN_TO_LOG * pKa elif igb == 5: if has_water: relene = -14.3162107 + KB * TEMP * LN_TO_LOG * pKa else: relene = -14.5392838 + KB * TEMP * LN_TO_LOG * pKa elif igb == 8: relene = -18.393654 + KB * TEMP * LN_TO_LOG * pKa else: relene = 0.0 return [ [ relene, # Relative energy STATE 0 LYS 3, # Relative protonation -0.3479, # N 0.2747, # H -0.2400, # CA 0.1426, # HA -0.0094, # CB 0.0362, # HB2 0.0362, # HB3 0.0187, # CG 0.0103, # HG2 0.0103, # HG3 -0.0479, # CD 0.0621, # HD2 0.0621, # HD3 -0.0143, # CE 0.1135, # HE2 0.1135, # HE3 -0.3854, # NZ 0.3400, # HZ1 0.3400, # HZ2 0.3400, # HZ3 0.7341, # C -0.5894 ], # O [ 0, # Relative energy STATE 1 LYN 2, # Relative protonation -0.3479, # N 0.2747, # H -0.2400, # CA 0.1426, # HA -0.10961, # CB 0.0340, # HB2 0.0340, # HB3 0.06612, # CG 0.01041, # HG2 0.01041, # HG3 -0.03768, # CD 0.01155, # HD2 0.01155, # HD3 0.32604, # CE -0.03358, # HE2 -0.03358, # HE3 -1.03581, # NZ 0.0000, # HZ1 0.38604, # HZ2 0.38604, # HZ3 0.7341, # C -0.5894 ] ] # O if residue == "CYS": pKa = 8.5 if igb == 2: if has_water: relene = 77.5680281 + KB * TEMP * LN_TO_LOG * pKa else: relene = 77.4666763 + KB * TEMP * LN_TO_LOG * pKa elif igb == 5: if has_water: relene = 76.2827217 + KB * TEMP * LN_TO_LOG * pKa else: relene = 76.2588331 + KB * TEMP * LN_TO_LOG * pKa elif igb == 8: relene = 71.5804519 + KB * TEMP * LN_TO_LOG * pKa else: relene = 0.0 return [ [ relene, # Relative energy STATE 0 CYS 1, # Relative protonation -0.4157, # N 0.2719, # H 0.0213, # CA 0.1124, # HA -0.1231, # CB 0.1112, # HB2 0.1112, # HB3 -0.3119, # SG 0.1933, # HG 0.5973, # C -0.5679 ], # O [ 0, # Relative energy STATE 1 CYM 0, # Relative protonation -0.4157, # N 0.2719, # H 0.0213, # CA 0.1124, # HA -0.3593, # CB 0.1122, # HB2 0.1122, # HB3 -0.8844, # SG 0.0000, # HG 0.5973, # C -0.5679 ] ] # O if residue == "DAP": pKa = 3.9 if igb == 2: relene = -19.8442 - KB * TEMP * LN_TO_LOG * pKa elif igb == 5: relene = -19.8442 - KB * TEMP * LN_TO_LOG * pKa else: relene = 0.0 return [ [ relene, # Relative energy STATE 0 DA 1, # Relative protonation 1.1659, # P -0.7761, # O1P -0.7761, # O2P -0.4954, # O5' -0.0069, # C5' 0.0754, # H5'1 0.0754, # H5'2 0.1629, # C4' 0.1176, # H4' -0.3691, # O4' 0.0431, # C1' 0.1838, # H1' -0.0268, # N9 0.1607, # C8 0.1877, # H8 -0.6175, # N7 0.0725, # C5 0.6897, # C6 -0.9123, # N6 0.4167, # H61 0.4167, # H62 -0.7624, # N1 0.5716, # C2 0.0598, # H2 -0.7417, # N3 0.3800, # C4 0.0713, # C3' 0.0985, # H3' -0.0854, # C2' 0.0718, # H2'1 0.0718, # H2'2 -0.5232, # O3' 0.0000 ] , # H1 [ 0, # Relative energy STATE 1 DAP 2, # Relative protonation 1.1659, # P -0.7761, # O1P -0.7761, # O2P -0.4954, # O5' -0.0069, # C5' 0.0754, # H5'1 0.0754, # H5'2 0.1629, # C4' 0.1176, # H4' -0.3691, # O4' 0.0431, # C1' 0.1838, # H1' 0.0944, # N9 0.1617, # C8 0.2281, # H8 -0.5674, # N7 0.1358, # C5 0.5711, # C6 -0.8251, # N6 0.4456, # H61 0.4456, # H62 -0.5750, # N1 0.4251, # C2 0.1437, # H2 -0.5611, # N3 0.3421, # C4 0.0713, # C3' 0.0985, # H3' -0.0854, # C2' 0.0718, # H2'1 0.0718, # H2'2 -0.5232, # O3' 0.4301 ] ] # H1 if residue == "DCP": pKa = 4.3 if igb == 2: relene = -40.526 - KB * TEMP * LN_TO_LOG * pKa elif igb == 5: relene = -40.526 - KB * TEMP * LN_TO_LOG * pKa else: relene = 0.0 return [ [ relene, # Relative energy STATE 0 DC 1, # Relative protonation 1.1659, # P -0.7761, # O1P -0.7761, # O2P -0.4954, # O5' -0.0069, # C5' 0.0754, # H5' 0.0754, # H5' 0.1629, # C4' 0.1176, # H4' -0.3691, # O4' -0.0116, # C1' 0.1963, # H1' -0.0339, # N1 -0.0183, # C6 0.2293, # H6 -0.5222, # C5 0.1863, # H5 0.8439, # C4 -0.9773, # N4 0.4314, # H41 0.4314, # H42 -0.7748, # N3 0.7959, # C2 -0.6548, # O2 0.0713, # C3' 0.0985, # H3' -0.0854, # C2' 0.0718, # H2' 0.0718, # H2' -0.5232, # O3' 0.0000 ] , # H3 [ 0, # Relative energy STATE 1 DCP 2, # Relative protonation 1.1659, # P -0.7761, # O1P -0.7761, # O2P -0.4954, # O5' -0.0069, # C5' 0.0754, # H5' 0.0754, # H5' 0.1629, # C4' 0.1176, # H4' -0.3691, # O4' -0.0116, # C1' 0.1963, # H1' 0.2167, # N1 -0.0282, # C6 0.2713, # H6 -0.4162, # C5 0.2179, # H5 0.6653, # C4 -0.8590, # N4 0.4598, # H41 0.4598, # H42 -0.4956, # N3 0.5371, # C2 -0.5028, # O2 0.0713, # C3' 0.0985, # H3' -0.0854, # C2' 0.0718, # H2' 0.0718, # H2' -0.5232, # O3' 0.4108 ] ] # H3 if residue == "DG": pKa = 9.2 if igb == 2: relene = -90.0011 - KB * TEMP * LN_TO_LOG * pKa elif igb == 5: relene = -90.0011 - KB * TEMP * LN_TO_LOG * pKa else: relene = 0.00 return [ [ 0, # Relative energy STATE 0 DG 1, # Relative protonation 1.1659, # P -0.7761, # O1P -0.7761, # O2P -0.4954, # O5' -0.0069, # C5' 0.0754, # H5' 0.0754, # H5' 0.1629, # C4' 0.1176, # H4' -0.3691, # O4' 0.0358, # C1' 0.1746, # H1' 0.0577, # N9 0.0736, # C8 0.1997, # H8 -0.5725, # N7 0.1991, # C5 0.4918, # C6 -0.5699, # 06 -0.5053, # N1 0.3520, # H1 0.7432, # C2 -0.9230, # N2 0.4235, # H21 0.4235, # H22 -0.6636, # N3 0.1814, # C4 0.0713, # C3' 0.0985, # H3' -0.0854, # C2' 0.0718, # H2' 0.0718, # H2' -0.5232 ] , # O3' [ relene, # Relative energy STATE 1 DGD 0, # Relative protonation 1.1659, # P -0.7761, # O1P -0.7761, # O2P -0.4954, # O5' -0.0069, # C5' 0.0754, # H5' 0.0754, # H5' 0.1629, # C4' 0.1176, # H4' -0.3691, # O4' 0.0358, # C1' 0.1746, # H1' -0.0507, # N9 0.0779, # C8 0.1516, # H8 -0.6122, # N7 0.0806, # C5 0.7105, # C6 -0.7253, # 06 -0.8527, # N1 0.0000, # H1 0.9561, # C2 -0.9903, # N2 0.3837, # H21 0.3837, # H22 -0.8545, # N3 0.2528, # C4 0.0713, # C3' 0.0985, # H3' -0.0854, # C2' 0.0718, # H2' 0.0718, # H2' -0.5232 ] ] # O3' if residue == "DT": pKa = 9.7 if igb == 5: relene = -56.7729 - KB * TEMP * LN_TO_LOG * pKa elif igb == 2: relene = -56.7729 - KB * TEMP * LN_TO_LOG * pKa else: relene = 0. return [ [ 0, # Relative energy STATE 0 DT 1, # Relative protonation 1.1659, # P -0.7761, # O1P -0.7761, # O2P -0.4954, # O5' -0.0069, # C5' 0.0754, # H5' 0.0754, # H5' 0.1629, # C4' 0.1176, # H4' -0.3691, # O4' 0.0680, # C1' 0.1804, # H1' -0.0239, # N1 -0.2209, # C6 0.2607, # H6 0.0025, # C5 -0.2269, # C7 0.0770, # H71 0.0770, # H72 0.0770, # H73 0.5194, # C4 -0.5563, # O4 -0.4340, # N3 0.3420, # H3 0.5677, # C2 -0.5881, # O2 0.0713, # C3' 0.0985, # H3' -0.0854, # C2' 0.0718, # H2' 0.0718, # H2' -0.5232 ] , # O3' [ relene, # Relative energy STATE 1 DTD 0, # Relative protonation 1.1659, # P -0.7761, # O1P -0.7761, # O2P -0.4954, # O5' -0.0069, # C5' 0.0754, # H5' 0.0754, # H5' 0.1629, # C4' 0.1176, # H4' -0.3691, # O4' 0.0680, # C1' 0.1804, # H1' -0.2861, # N1 -0.1874, # C6 0.2251, # H6 -0.1092, # C5 -0.2602, # C7 0.0589, # H71 0.0589, # H72 0.0589, # H73 0.8263, # C4 -0.7396, # O4 -0.9169, # N3 0.0000, # H3 0.9167, # C2 -0.7722, # O2 0.0713, # C3' 0.0985, # H3' -0.0854, # C2' 0.0718, # H2' 0.0718, # H2' -0.5232 ] ] # O3' if residue == "AP": pKa = 3.9 if igb == 5: relene = 15.903 + KB * TEMP * LN_TO_LOG * pKa elif igb == 2: relene = 55.1918 + KB * TEMP * LN_TO_LOG * pKa else: relene = 0. return [ [ 0, # Relative energy STATE 0 A 1, # Relative protonation 1.1662, # P -0.7760, # O1P -0.7760, # O2P -0.4989, # O5' 0.0558, # C5' 0.0679, # H5'1 0.0679, # H5'2 0.1065, # C4' 0.1174, # H4' -0.3548, # O4' 0.0394, # C1' 0.2007, # H1' -0.0251, # N9 0.2006, # C8 0.1553, # H8 -0.6073, # N7 0.0515, # C5 0.7009, # C6 -0.9019, # N6 0.4115, # H61 0.4115, # H62 -0.7615, # N1 0.5875, # C2 0.0473, # H2 -0.6997, # N3 0.3053, # C4 0.2022, # C3' 0.0615, # H3' 0.0670, # C2' 0.0972, # H2'1 -0.6139, # O2' 0.4186, # HO'2 -0.5246, # O3' 0.0000 ] , # H1 [ relene, # Relative energy STATE 1 AP 2, # Relative protonation 1.1662, # P -0.7760, # O1P -0.7760, # O2P -0.4989, # O5' 0.0558, # C5' 0.0679, # H5'1 0.0679, # H5'2 0.1065, # C4' 0.1174, # H4' -0.3548, # O4' 0.0394, # C1' 0.2007, # H1' 0.0961, # N9 0.2011, # C8 0.1965, # H8 -0.5569, # N7 0.1136, # C5 0.5845, # C6 -0.8152, # N6 0.4403, # H61 0.4403, # H62 -0.5776, # N1 0.4435, # C2 0.1307, # H2 -0.5201, # N3 0.2681, # C4 0.2022, # C3' 0.0615, # H3' 0.0670, # C2' 0.0972, # H2'1 -0.6139, # O2' 0.4186, # HO'2 -0.5246, # O3' 0.4310 ] ] # H1 if residue == "CP": pKa = 4.3 if igb == 5: relene = 40.1407 + KB * TEMP * LN_TO_LOG * pKa elif igb == 2: relene = 40.1407 + KB * TEMP * LN_TO_LOG * pKa else: relene = 0. return [ [ 0, # Relative energy STATE 0 C 1, # Relative protonation 1.1662, # P -0.7760, # O1P -0.7760, # O2P -0.4989, # O5' 0.0558, # C5' 0.0679, # H5'1 0.0679, # H5'2 0.1065, # C4' 0.1174, # H4' -0.3548, # O4' 0.0066, # C1' 0.2029, # H1' -0.0484, # N1 0.0053, # C6 0.1958, # H6 -0.5215, # C5 0.1928, # H5 0.8185, # C4 -0.9530, # N4 0.4234, # H41 0.4234, # H42 -0.7584, # N3 0.7538, # C2 -0.6252, # O2 0.2022, # C3' 0.0615, # H3' 0.0670, # C2' 0.0972, # H2'1 -0.6139, # O2' 0.4186, # HO'2 -0.5246, # O3' 0.0000 ] , # H3 [ relene, # Relative energy STATE 1 CP 2, # Relative protonation 1.1662, # P -0.7760, # O1P -0.7760, # O2P -0.4989, # O5' 0.0558, # C5' 0.0679, # H5'1 0.0679, # H5'2 0.1065, # C4' 0.1174, # H4' -0.3548, # O4' 0.0066, # C1' 0.2029, # H1' 0.1954, # N1 0.0028, # C6 0.2366, # H6 -0.4218, # C5 0.2253, # H5 0.6466, # C4 -0.8363, # N4 0.4518, # H41 0.4518, # H42 -0.4871, # N3 0.5039, # C2 -0.4753, # O2 0.2022, # C3' 0.0615, # H3' 0.0670, # C2' 0.0972, # H2'1 -0.6139, # O2' 0.4186, # HO'2 -0.5246, # O3' 0.4128 ] ] # H3 if residue == "G": pKa = 9.2 if igb == 5: relene = -96.0454 - KB * TEMP * LN_TO_LOG * pKa elif igb == 2: relene = -96.0454 - KB * TEMP * LN_TO_LOG * pKa else: relene = 0.00 return [ [ 0, # Relative energy STATE 0 G 1, # Relative protonation 1.1662, # P -0.7760, # O1P -0.7760, # O2P -0.4989, # O5' 0.0558, # C5' 0.0679, # H5'1 0.0679, # H5'2 0.1065, # C4' 0.1174, # H4' -0.3548, # O4' 0.0191, # C1' 0.2006, # H1' 0.0492, # N9 0.1374, # C8 0.1640, # H8 -0.5709, # N7 0.1744, # C5 0.4770, # C6 -0.5597, # O6 -0.4787, # N1 0.3424, # H1 0.7657, # C2 -0.9672, # N2 0.4364, # H21 0.4364, # H22 -0.6323, # N3 0.1222, # C4 0.2022, # C3' 0.0615, # H3' 0.0670, # C2' 0.0972, # H2'1 -0.6139, # O2' 0.4186, # HO'2 -0.5246 ] , # O3' [ relene, # Relative energy STATE 1 GD 0, # Relative protonation 1.1662, # P -0.7760, # O1P -0.7760, # O2P -0.4989, # O5' 0.0558, # C5' 0.0679, # H5'1 0.0679, # H5'2 0.1065, # C4' 0.1174, # H4' -0.3548, # O4' 0.0191, # C1' 0.2006, # H1' -0.0623, # N9 0.1479, # C8 0.1137, # H8 -0.6127, # N7 0.0488, # C5 0.7137, # C6 -0.7191, # O6 -0.8557, # N1 0.0000, # H1 0.9976, # C2 -1.0387, # N2 0.3969, # H21 0.3969, # H22 -0.8299, # N3 0.1992, # C4 0.2022, # C3' 0.0615, # H3' 0.0670, # C2' 0.0972, # H2'1 -0.6139, # O2' 0.4186, # HO'2 -0.5246 ] ] # O3' if residue == "U": pKa = 9.3 if igb == 5: relene = -134.883 - KB * TEMP * LN_TO_LOG * pKa elif igb == 2: relene = -134.883 - KB * TEMP * LN_TO_LOG * pKa else: relene = 0.00 return [ [ 0, # Relative energy STATE 0 U 1, # Relative protonation 1.1662, # P -0.7760, # O1P -0.7760, # O2P -0.4989, # O5' 0.0558, # C5' 0.0679, # H5'1 0.0679, # H5'2 0.1065, # C4' 0.1174, # H4' -0.3548, # O4' 0.0674, # C1' 0.1824, # H1' 0.0418, # N1 -0.1126, # C6 0.2188, # H6 -0.3635, # C5 0.1811, # H5 0.5952, # C4 -0.5761, # O4 -0.3549, # N3 0.3154, # H3 0.4687, # C2 -0.5477, # O2 0.2022, # C3' 0.0615, # H3' 0.0670, # C2' 0.0972, # H2'1 -0.6139, # O2' 0.4186, # HO'2 -0.5246 ] , # O3' [ relene, # Relative energy STATE 1 UD 0, # Relative protonation 1.1662, # P -0.7760, # O1P -0.7760, # O2P -0.4989, # O5' 0.0558, # C5' 0.0679, # H5'1 0.0679, # H5'2 0.1065, # C4' 0.1174, # H4' -0.3548, # O4' 0.0674, # C1' 0.1824, # H1' -0.2733, # N1 0.0264, # C6 0.1501, # H6 -0.5820, # C5 0.1560, # H5 0.9762, # C4 -0.7808, # O4 -0.9327, # N3 0.0000, # H3 0.8698, # C2 -0.7435, # O2 0.2022, # C3' 0.0615, # H3' 0.0670, # C2' 0.0972, # H2'1 -0.6139, # O2' 0.4186, # HO'2 -0.5246 ] ] # O3' return -1