# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 09:57:15 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7-methyl-3H-imidazo[4,5-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 QTP  QTP  3-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7-methyl-3H-imidazo[4,5-b]pyridine  ligand  48  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QTP
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 QTP  O2A  O  OH1   0  -0.727  -0.2289  -12.8578  50.1404
 QTP  PA   P  P     0   1.517  -1.1154  -12.7838  48.8291
 QTP  O1A  O  O     0  -0.655  -0.7346  -13.5773  47.6567
 QTP  O3A  O  O2    0  -0.690  -2.5286  -13.3100  49.4354
 QTP  PB   P  P     0   1.530  -3.7044  -12.6910  50.3214
 QTP  O1B  O  O     0  -0.660  -4.4267  -11.5561  49.7263
 QTP  O2B  O  OH1   0  -0.724  -2.9646  -12.4612  51.6975
 QTP  O3B  O  O2    0  -0.666  -4.6673  -13.9539  50.4839
 QTP  PG   P  P     0   1.480  -4.5646  -15.3378  51.3415
 QTP  O3G  O  O     0  -0.667  -5.5416  -16.3150  50.8464
 QTP  O2G  O  OH1   0  -0.727  -4.7349  -14.7475  52.7988
 QTP  O1G  O  OH1   0  -0.728  -3.0314  -15.7419  51.2929
 QTP  O5'  O  O2    0  -0.588  -1.3328  -11.2547  48.4787
 QTP  C5'  C  CH2   0  -0.225  -1.2604  -10.1516  49.3939
 QTP  C4'  C  CH1   0   0.003  -1.7898   -8.9132  48.7191
 QTP  C3'  C  CH1   0   0.011  -3.1627   -9.0155  48.0414
 QTP  O3'  O  OH1   0  -0.686  -4.2381   -8.8934  48.9212
 QTP  C2'  C  CH2   0  -0.535  -3.0728   -7.8453  47.0746
 QTP  C1'  C  CH1   0   0.184  -1.6031   -7.8612  46.6602
 QTP  O4'  O  O2    0  -0.495  -0.9000   -8.5059  47.6882
 QTP  N9   N  NR5   0  -0.528  -1.3617   -8.5793  45.4176
 QTP  C4   C  CR56  0   0.469  -1.3572   -8.0147  44.1696
 QTP  C5   C  CR56  0   0.060  -1.1146   -9.0734  43.2842
 QTP  N7   N  N     0  -0.461  -0.9773  -10.2458  43.9831
 QTP  C8   C  CR15  0   0.109  -1.1318   -9.9087  45.2325
 QTP  N3   N  N     0  -0.434  -1.5401   -6.7431  43.8650
 QTP  C2   C  CR16  0  -0.084  -1.4702   -6.4930  42.5634
 QTP  C1   C  CR16  0  -0.394  -1.2333   -7.4624  41.5835
 QTP  C6   C  CR6   0   0.125  -1.0460   -8.7986  41.9188
 QTP  C7   C  CH3   0  -0.725  -0.7918   -9.8684  40.9092
 QTP  H1   H  HOH1  0   0.514   0.7266  -12.8044  49.9912
 QTP  H2   H  HOH1  0   0.517  -3.4348  -11.9077  52.3390
 QTP  H3   H  HOH1  0   0.513  -4.9024  -15.4059  53.4880
 QTP  H4   H  HOH1  0   0.510  -2.7897  -16.3291  50.5624
 QTP  H5   H  HCH2  0   0.245  -1.8510  -10.3365  50.2924
 QTP  H6   H  HCH2  0   0.284  -0.2249  -10.0019  49.7048
 QTP  H7   H  HCH1  0   0.252  -1.8437   -8.1399  49.4982
 QTP  H8   H  HCH1  0   0.227  -3.2223   -9.9508  47.4697
 QTP  H9   H  HOH1  0   0.460  -4.3960   -9.7664  49.3130
 QTP  H10  H  HCH2  0   0.266  -3.2911   -6.9139  47.6024
 QTP  H11  H  HCH2  0   0.281  -3.7483   -7.9184  46.2233
 QTP  H12  H  HCH1  0   0.272  -1.2173   -6.8515  46.5019
 QTP  H13  H  HCR5  0   0.290  -1.0732  -10.5965  46.0611
 QTP  H14  H  HCR6  0   0.260  -1.6113   -5.4608  42.2648
 QTP  H15  H  HCR6  0   0.261  -1.1982   -7.1533  40.5466
 QTP  H16  H  HCH3  0   0.254   0.1490  -10.3812  41.1131
 QTP  H17  H  HCH3  0   0.255  -1.5782  -10.6240  40.9370
 QTP  H18  H  HCH3  0   0.251  -0.7465   -9.4617  39.9009

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 QTP  C7   C6   single    1.493  0.020  1.493
 QTP  C1   C6   aromatic  1.390  0.020  1.390
 QTP  C1   C2   aromatic  1.399  0.020  1.399
 QTP  C6   C5   aromatic  1.394  0.020  1.394
 QTP  C2   N3   aromatic  1.327  0.020  1.327
 QTP  C5   N7   aromatic  1.372  0.020  1.372
 QTP  C5   C4   aromatic  1.401  0.020  1.401
 QTP  N3   C4   aromatic  1.320  0.020  1.320
 QTP  N7   C8   aromatic  1.303  0.020  1.303
 QTP  C4   N9   aromatic  1.370  0.020  1.370
 QTP  C8   N9   aromatic  1.362  0.020  1.362
 QTP  N9   C1'  single    1.455  0.020  1.455
 QTP  C1'  C2'  single    1.527  0.020  1.527
 QTP  C1'  O4'  single    1.402  0.020  1.402
 QTP  C2'  C3'  single    1.520  0.020  1.520
 QTP  O1A  PA   double    1.466  0.020  1.466
 QTP  O4'  C4'  single    1.421  0.020  1.421
 QTP  C3'  C4'  single    1.534  0.020  1.534
 QTP  C3'  O3'  single    1.395  0.020  1.395
 QTP  O5'  PA   single    1.584  0.020  1.584
 QTP  O5'  C5'  single    1.435  0.020  1.435
 QTP  O3A  PA   single    1.625  0.020  1.625
 QTP  O3A  PB   single    1.597  0.020  1.597
 QTP  O1B  PB   double    1.471  0.020  1.471
 QTP  PA   O2A  single    1.585  0.020  1.585
 QTP  C4'  C5'  single    1.506  0.020  1.506
 QTP  O3G  PG   double    1.468  0.020  1.468
 QTP  O3B  PB   single    1.596  0.020  1.596
 QTP  O3B  PG   single    1.631  0.020  1.631
 QTP  PB   O2B  single    1.579  0.020  1.579
 QTP  PG   O1G  single    1.586  0.020  1.586
 QTP  PG   O2G  single    1.582  0.020  1.582
 QTP  O2A  H1   single    0.850  0.020  0.980
 QTP  O2B  H2   single    0.850  0.020  0.980
 QTP  O2G  H3   single    0.850  0.020  0.980
 QTP  O1G  H4   single    0.850  0.020  0.980
 QTP  C5'  H5   single    0.970  0.020  1.090
 QTP  C5'  H6   single    0.970  0.020  1.090
 QTP  C4'  H7   single    0.970  0.020  1.090
 QTP  C3'  H8   single    0.970  0.020  1.090
 QTP  O3'  H9   single    0.850  0.020  0.980
 QTP  C2'  H10  single    0.970  0.020  1.090
 QTP  C2'  H11  single    0.970  0.020  1.090
 QTP  C1'  H12  single    0.970  0.020  1.090
 QTP  C8   H13  single    0.930  0.020  1.080
 QTP  C2   H14  single    0.930  0.020  1.080
 QTP  C1   H15  single    0.930  0.020  1.080
 QTP  C7   H16  single    0.970  0.020  1.090
 QTP  C7   H17  single    0.970  0.020  1.090
 QTP  C7   H18  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 QTP  H1   O2A  PA   114.95  3.000
 QTP  O5'  PA   O3A  106.01  3.000
 QTP  O3A  PA   O1A  110.42  3.000
 QTP  O5'  PA   O1A  112.41  3.000
 QTP  O3A  PA   O2A   99.36  3.000
 QTP  O5'  PA   O2A  107.75  3.000
 QTP  O1A  PA   O2A  119.42  3.000
 QTP  PB   O3A  PA   136.19  3.000
 QTP  O3B  PB   O2B  108.00  3.000
 QTP  O2B  PB   O1B  118.05  3.000
 QTP  O3B  PB   O1B  110.82  3.000
 QTP  O2B  PB   O3A  101.24  3.000
 QTP  O3B  PB   O3A  101.18  3.000
 QTP  O1B  PB   O3A  115.85  3.000
 QTP  H2   O2B  PB   115.64  3.000
 QTP  PG   O3B  PB   133.37  3.000
 QTP  O1G  PG   O2G  103.14  3.000
 QTP  O2G  PG   O3G  119.19  3.000
 QTP  O1G  PG   O3G  117.60  3.000
 QTP  O2G  PG   O3B   99.26  3.000
 QTP  O1G  PG   O3B  105.12  3.000
 QTP  O3G  PG   O3B  110.22  3.000
 QTP  H3   O2G  PG   114.89  3.000
 QTP  H4   O1G  PG   114.77  3.000
 QTP  C5'  O5'  PA   126.45  3.000
 QTP  H6   C5'  H5   107.59  3.000
 QTP  H6   C5'  C4'  110.38  3.000
 QTP  H5   C5'  C4'  108.54  3.000
 QTP  H6   C5'  O5'  109.57  3.000
 QTP  H5   C5'  O5'  111.57  3.000
 QTP  C4'  C5'  O5'  109.17  3.000
 QTP  H7   C4'  O4'  110.07  3.000
 QTP  H7   C4'  C3'  108.43  3.000
 QTP  O4'  C4'  C3'  105.00  3.000
 QTP  H7   C4'  C5'  106.15  3.000
 QTP  C3'  C4'  C5'  117.23  3.000
 QTP  O4'  C4'  C5'  109.90  3.000
 QTP  H8   C3'  C2'  109.14  3.000
 QTP  H8   C3'  O3'  111.17  3.000
 QTP  C2'  C3'  O3'  112.29  3.000
 QTP  H8   C3'  C4'  109.60  3.000
 QTP  O3'  C3'  C4'  113.91  3.000
 QTP  C2'  C3'  C4'  100.17  3.000
 QTP  H9   O3'  C3'  107.55  3.000
 QTP  H11  C2'  H10  108.11  3.000
 QTP  H11  C2'  C1'  112.58  3.000
 QTP  H10  C2'  C1'  109.41  3.000
 QTP  H11  C2'  C3'  114.12  3.000
 QTP  H10  C2'  C3'  109.70  3.000
 QTP  C1'  C2'  C3'  102.80  3.000
 QTP  H12  C1'  N9   105.89  3.000
 QTP  H12  C1'  O4'  110.73  3.000
 QTP  N9   C1'  O4'  108.41  3.000
 QTP  H12  C1'  C2'  111.69  3.000
 QTP  O4'  C1'  C2'  106.76  3.000
 QTP  N9   C1'  C2'  113.36  3.000
 QTP  C1'  O4'  C4'  110.46  3.000
 QTP  C8   N9   C4   106.14  3.000
 QTP  C8   N9   C1'  128.74  3.000
 QTP  C4   N9   C1'  125.11  3.000
 QTP  N3   C4   C5   127.29  3.000
 QTP  N3   C4   N9   127.35  3.000
 QTP  C5   C4   N9   105.36  3.000
 QTP  C6   C5   N7   131.48  3.000
 QTP  N7   C5   C4   109.95  3.000
 QTP  C6   C5   C4   118.57  3.000
 QTP  C8   N7   C5   104.80  3.000
 QTP  H13  C8   N7   124.41  3.000
 QTP  H13  C8   N9   121.82  3.000
 QTP  N7   C8   N9   113.76  3.000
 QTP  C2   N3   C4   113.61  3.000
 QTP  H14  C2   C1   119.29  3.000
 QTP  H14  C2   N3   116.28  3.000
 QTP  C1   C2   N3   124.43  3.000
 QTP  H15  C1   C6   120.07  3.000
 QTP  H15  C1   C2   118.60  3.000
 QTP  C6   C1   C2   121.33  3.000
 QTP  C7   C6   C1   123.27  3.000
 QTP  C1   C6   C5   114.77  3.000
 QTP  C7   C6   C5   121.96  3.000
 QTP  H18  C7   H17  108.21  3.000
 QTP  H18  C7   H16  108.24  3.000
 QTP  H17  C7   H16  106.94  3.000
 QTP  H18  C7   C6   111.46  3.000
 QTP  H17  C7   C6   110.88  3.000
 QTP  H16  C7   C6   110.94  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 QTP  CONST_01  C6   C5   C4   N9    180.00   0.0  0
 QTP  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 QTP  CONST_03  C2   N3   C4   N9    180.00   0.0  0
 QTP  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 QTP  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 QTP  CONST_06  C8   N7   C5   C4      0.00   0.0  0
 QTP  CONST_07  C1   C2   N3   C4      0.00   0.0  0
 QTP  CONST_08  N7   C8   N9   C4      0.00   0.0  0
 QTP  CONST_09  C2   C1   C6   C5      0.00   0.0  0
 QTP  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 QTP  CONST_11  C8   N9   C4   C5      0.00   0.0  0
 QTP  CONST_12  C1   C6   C5   N7    180.00   0.0  0
 QTP  CONST_13  N3   C4   C5   N7    180.00   0.0  0
 QTP  CONST_14  C6   C5   N7   C8    180.00   0.0  0
 QTP  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 QTP  CONST_16  C6   C1   C2   N3      0.00   0.0  0
 QTP  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 QTP  CONST_18  C5   C4   N9   C1'   180.00   0.0  0
 QTP  CONST_19  N3   C4   N9   C1'     0.00   0.0  0
 QTP  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 QTP  CONST_21  C7   C6   C5   C4    180.00   0.0  0
 QTP  CONST_22  C7   C6   C5   N7      0.00   0.0  0
 QTP  CONST_23  C7   C6   C1   C2    180.00   0.0  0
 QTP  CONST_24  H13  C8   N9   C1'     0.00   0.0  0
 QTP  CONST_25  H14  C2   N3   C4    180.00   0.0  0
 QTP  CONST_26  H15  C1   C6   C5    180.00   0.0  0
 QTP  Var_01    H16  C7   C6   C5    -57.78  30.0  2
 QTP  Var_02    C4'  C5'  O5'  PA   -169.05  30.0  3
 QTP  Var_03    O1B  PB   O3A  PA     62.42  30.0  3
 QTP  Var_04    O5'  PA   O3A  PB    -34.02  30.0  3
 QTP  Var_05    O3G  PG   O3B  PB   -164.23  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 QTP  chir_03  C4'  O4'  C3'  C5'  negativ
 QTP  chir_04  C3'  O3'  C4'  C2'  positiv
 QTP  chir_05  C1'  O4'  N9   C2'  negativ
 QTP  chir_06  PA   O5'  O3A  O2A  both
 QTP  chir_07  PB   O1B  O3B  O2B  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 QTP  plan-1  C1'  0.020
 QTP  plan-1  N9   0.020
 QTP  plan-1  C4   0.020
 QTP  plan-1  C5   0.020
 QTP  plan-1  N7   0.020
 QTP  plan-1  C8   0.020
 QTP  plan-1  N3   0.020
 QTP  plan-1  C2   0.020
 QTP  plan-1  C1   0.020
 QTP  plan-1  C6   0.020
 QTP  plan-1  C7   0.020
 QTP  plan-1  H13  0.020
 QTP  plan-1  H14  0.020
 QTP  plan-1  H15  0.020

