# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 13:29:37 2021
#   Inital geometry file: a 112 line input string
#   Ligand name: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-9H-purin-6-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)n2cnc3c(O)ncnc23
#
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
 ITT  ITT  9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-9H-purin-6-ol  ligand  46  31  .  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_ITT
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
 ITT  PG    P  P     0   1.472  48.7147  59.3804  33.7621
 ITT  O1G   O  O     0  -0.677  48.9675  58.5654  34.9572
 ITT  O2G   O  OH1   0  -0.728  47.2498  59.9258  33.5076
 ITT  O3G   O  OH1   0  -0.712  49.1238  58.7732  32.3579
 ITT  PB    P  P     0   1.486  49.5367  62.0637  34.6855
 ITT  O1B   O  O     0  -0.685  50.8747  62.4816  35.1503
 ITT  O2B   O  OH1   0  -0.740  48.6760  63.0880  33.8835
 ITT  O3B   O  O2    0  -0.671  49.5358  60.7896  33.7270
 ITT  PA    P  P     0   1.494  48.7562  62.1374  37.4253
 ITT  O1A   O  O     0  -0.651  47.7334  61.6151  38.3350
 ITT  O2A   O  OH1   0  -0.738  50.2305  61.8123  37.9040
 ITT  O3A   O  O2    0  -0.696  48.6113  61.5444  35.9206
 ITT  O5'   O  O2    0  -0.602  48.6936  63.6905  37.0610
 ITT  C5'   C  CH2   0  -0.184  49.3238  64.7221  37.8196
 ITT  C4'   C  CH1   0  -0.028  49.1204  66.0044  37.0358
 ITT  O4'   O  O2    0  -0.491  49.7499  67.0581  37.7614
 ITT  C3'   C  CH1   0   0.012  49.7771  66.0316  35.6480
 ITT  O3'   O  OH1   0  -0.690  48.9854  65.5425  34.5996
 ITT  C2'   C  CH1   0  -0.057  50.1150  67.5202  35.4868
 ITT  O2'   O  OH1   0  -0.653  49.0196  68.2416  34.9929
 ITT  C1'   C  CH1   0   0.146  50.4843  67.8994  36.9225
 ITT  N9    N  NR5   0  -0.537  51.9085  67.7199  37.1757
 ITT  C8    C  CR15  0   0.112  52.5473  66.7659  37.9213
 ITT  N7    N  N     0  -0.441  53.8379  66.9170  37.9637
 ITT  C5    C  CR56  0   0.008  54.0739  68.0362  37.2119
 ITT  C6    C  CR6   0   0.463  55.2197  68.7552  36.8635
 ITT  O6    O  OH1   0  -0.584  56.4064  68.3605  37.2800
 ITT  N1    N  N     0  -0.467  55.1065  69.8357  36.1133
 ITT  C2    C  CR16  0   0.052  53.8959  70.2204  35.7029
 ITT  N3    N  N     0  -0.439  52.7413  69.6359  35.9587
 ITT  C4    C  CR56  0   0.497  52.8824  68.5541  36.7152
 ITT  H2G   H  HOH1  0   0.512  46.5430  59.3281  33.7891
 ITT  H3G   H  HOH1  0   0.511  49.8977  58.1925  32.3783
 ITT  H2B   H  HOH1  0   0.519  48.7778  64.0503  34.1619
 ITT  H2A   H  HOH1  0   0.498  50.9319  61.9957  37.2542
 ITT  H5'1  H  HCH2  0   0.237  50.3901  64.5112  37.9372
 ITT  H5'2  H  HCH2  0   0.282  48.8742  64.7994  38.8114
 ITT  H4'   H  HCH1  0   0.277  48.0453  66.2061  36.9531
 ITT  H3'   H  HCH1  0   0.281  50.6969  65.4392  35.6502
 ITT  H1    H  HOH1  0   0.478  48.2971  66.1846  34.3759
 ITT  H2'   H  HCH1  0   0.302  50.9398  67.6782  34.7918
 ITT  H3    H  HOH1  0   0.469  48.3652  68.4107  35.6809
 ITT  H1'   H  HCH1  0   0.305  50.2475  68.9452  37.1362
 ITT  H8    H  HCR5  0   0.303  52.0110  65.9800  38.4277
 ITT  HO6   H  HOH1  0   0.486  57.0818  68.9762  36.9608
 ITT  H2    H  HCR6  0   0.267  53.8649  71.1144  35.0919

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
 ITT  PG   O1G   double    1.468  0.020  1.468
 ITT  PG   O2G   single    1.584  0.020  1.584
 ITT  PG   O3G   single    1.584  0.020  1.584
 ITT  PG   O3B   single    1.631  0.020  1.631
 ITT  O2G  H2G   single    0.850  0.020  0.980
 ITT  O3G  H3G   single    0.850  0.020  0.980
 ITT  PB   O1B   double    1.477  0.020  1.477
 ITT  PB   O2B   single    1.560  0.020  1.560
 ITT  PB   O3B   single    1.594  0.020  1.594
 ITT  PB   O3A   single    1.628  0.020  1.628
 ITT  O2B  H2B   single    0.850  0.020  0.980
 ITT  PA   O1A   double    1.465  0.020  1.465
 ITT  PA   O2A   single    1.584  0.020  1.584
 ITT  PA   O3A   single    1.624  0.020  1.624
 ITT  PA   O5'   single    1.597  0.020  1.597
 ITT  O2A  H2A   single    0.850  0.020  0.980
 ITT  O5'  C5'   single    1.427  0.020  1.427
 ITT  C5'  C4'   single    1.517  0.020  1.517
 ITT  C5'  H5'1  single    0.970  0.020  1.090
 ITT  C5'  H5'2  single    0.970  0.020  1.090
 ITT  C4'  O4'   single    1.426  0.020  1.426
 ITT  C4'  C3'   single    1.536  0.020  1.536
 ITT  C4'  H4'   single    0.970  0.020  1.090
 ITT  O4'  C1'   single    1.397  0.020  1.397
 ITT  C3'  O3'   single    1.402  0.020  1.402
 ITT  C3'  C2'   single    1.535  0.020  1.535
 ITT  C3'  H3'   single    0.970  0.020  1.090
 ITT  O3'  H1    single    0.850  0.020  0.980
 ITT  C2'  O2'   single    1.402  0.020  1.402
 ITT  C2'  C1'   single    1.530  0.020  1.530
 ITT  C2'  H2'   single    0.970  0.020  1.090
 ITT  O2'  H3    single    0.850  0.020  0.980
 ITT  C1'  N9    single    1.458  0.020  1.458
 ITT  C1'  H1'   single    0.970  0.020  1.090
 ITT  N9   C8    aromatic  1.369  0.020  1.369
 ITT  N9   C4    aromatic  1.363  0.020  1.363
 ITT  C8   N7    aromatic  1.300  0.020  1.300
 ITT  C8   H8    single    0.930  0.020  1.080
 ITT  N7   C5    aromatic  1.369  0.020  1.369
 ITT  C5   C6    aromatic  1.397  0.020  1.397
 ITT  C5   C4    aromatic  1.391  0.020  1.391
 ITT  C6   O6    single    1.318  0.020  1.318
 ITT  C6   N1    aromatic  1.320  0.020  1.320
 ITT  O6   HO6   single    0.850  0.020  0.980
 ITT  N1   C2    aromatic  1.335  0.020  1.335
 ITT  C2   N3    aromatic  1.319  0.020  1.319
 ITT  C2   H2    single    0.930  0.020  1.080
 ITT  N3   C4    aromatic  1.328  0.020  1.328

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
 ITT  O3B   PG   O3G   100.49  3.000
 ITT  O3B   PG   O2G    99.48  3.000
 ITT  O3G   PG   O2G   103.21  3.000
 ITT  O3B   PG   O1G   114.22  3.000
 ITT  O3G   PG   O1G   117.67  3.000
 ITT  O2G   PG   O1G   118.76  3.000
 ITT  H2G   O2G  PG    114.60  3.000
 ITT  H3G   O3G  PG    114.71  3.000
 ITT  O3A   PB   O3B   101.58  3.000
 ITT  O3A   PB   O2B   106.61  3.000
 ITT  O3B   PB   O2B   102.44  3.000
 ITT  O3A   PB   O1B   111.50  3.000
 ITT  O3B   PB   O1B   114.57  3.000
 ITT  O2B   PB   O1B   118.42  3.000
 ITT  H2B   O2B  PB    115.44  3.000
 ITT  PB    O3B  PG    132.66  3.000
 ITT  O5'   PA   O3A    98.06  3.000
 ITT  O5'   PA   O2A   107.77  3.000
 ITT  O3A   PA   O2A   106.75  3.000
 ITT  O5'   PA   O1A   117.46  3.000
 ITT  O3A   PA   O1A   112.51  3.000
 ITT  O2A   PA   O1A   112.89  3.000
 ITT  H2A   O2A  PA    115.48  3.000
 ITT  PA    O3A  PB    122.39  3.000
 ITT  C5'   O5'  PA    124.37  3.000
 ITT  H5'2  C5'  H5'1  108.52  3.000
 ITT  H5'2  C5'  C4'   110.76  3.000
 ITT  H5'1  C5'  C4'   110.46  3.000
 ITT  H5'2  C5'  O5'   110.63  3.000
 ITT  H5'1  C5'  O5'   110.38  3.000
 ITT  C4'   C5'  O5'   106.09  3.000
 ITT  H4'   C4'  C3'   110.35  3.000
 ITT  H4'   C4'  O4'   109.58  3.000
 ITT  C3'   C4'  O4'   104.95  3.000
 ITT  H4'   C4'  C5'   109.02  3.000
 ITT  C3'   C4'  C5'   115.14  3.000
 ITT  O4'   C4'  C5'   107.61  3.000
 ITT  C1'   O4'  C4'   111.82  3.000
 ITT  H3'   C3'  C2'   109.90  3.000
 ITT  H3'   C3'  O3'   106.70  3.000
 ITT  C2'   C3'  O3'   112.59  3.000
 ITT  H3'   C3'  C4'   110.38  3.000
 ITT  C2'   C3'  C4'   101.90  3.000
 ITT  O3'   C3'  C4'   115.35  3.000
 ITT  H1    O3'  C3'   110.07  3.000
 ITT  H2'   C2'  C1'   112.31  3.000
 ITT  H2'   C2'  O2'   106.98  3.000
 ITT  C1'   C2'  O2'   113.06  3.000
 ITT  H2'   C2'  C3'   111.97  3.000
 ITT  C1'   C2'  C3'   101.24  3.000
 ITT  O2'   C2'  C3'   111.36  3.000
 ITT  H3    O2'  C2'   111.66  3.000
 ITT  H1'   C1'  N9    107.19  3.000
 ITT  H1'   C1'  C2'   111.60  3.000
 ITT  N9    C1'  C2'   111.61  3.000
 ITT  H1'   C1'  O4'   110.17  3.000
 ITT  N9    C1'  O4'   109.59  3.000
 ITT  C2'   C1'  O4'   106.70  3.000
 ITT  C4    N9   C8    106.09  3.000
 ITT  C4    N9   C1'   124.35  3.000
 ITT  C8    N9   C1'   129.52  3.000
 ITT  H8    C8   N7    124.28  3.000
 ITT  H8    C8   N9    122.13  3.000
 ITT  N7    C8   N9    113.58  3.000
 ITT  C5    N7   C8    104.37  3.000
 ITT  C4    C5   C6    114.96  3.000
 ITT  C4    C5   N7    110.66  3.000
 ITT  C6    C5   N7    134.37  3.000
 ITT  N1    C6   O6    120.12  3.000
 ITT  N1    C6   C5    119.52  3.000
 ITT  O6    C6   C5    120.37  3.000
 ITT  HO6   O6   C6    109.48  3.000
 ITT  C2    N1   C6    119.23  3.000
 ITT  H2    C2   N3    116.74  3.000
 ITT  H2    C2   N1    115.92  3.000
 ITT  N3    C2   N1    127.33  3.000
 ITT  C4    N3   C2    112.24  3.000
 ITT  N3    C4   C5    126.72  3.000
 ITT  N3    C4   N9    127.99  3.000
 ITT  C5    C4   N9    105.29  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
 ITT  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 ITT  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 ITT  CONST_03  C6   C5   C4   N9   180.00   0.0  0
 ITT  CONST_04  C2   N3   C4   N9   180.00   0.0  0
 ITT  CONST_05  C5   C4   N9   C8     0.00   0.0  0
 ITT  CONST_06  N3   C4   N9   C8   180.00   0.0  0
 ITT  CONST_07  C6   C5   N7   C8   180.00   0.0  0
 ITT  CONST_08  C4   C5   N7   C8     0.00   0.0  0
 ITT  CONST_09  C4   N9   C8   N7     0.00   0.0  0
 ITT  CONST_10  N1   C6   C5   N7   180.00   0.0  0
 ITT  CONST_11  N3   C4   C5   N7   180.00   0.0  0
 ITT  CONST_12  C2   N1   C6   C5     0.00   0.0  0
 ITT  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 ITT  CONST_14  N3   C4   C5   C6     0.00   0.0  0
 ITT  CONST_15  N3   C2   N1   C6     0.00   0.0  0
 ITT  CONST_16  C4   C5   C6   N1     0.00   0.0  0
 ITT  CONST_17  C4   N3   C2   N1     0.00   0.0  0
 ITT  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 ITT  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 ITT  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 ITT  CONST_21  O6   C6   C5   N7     0.00   0.0  0
 ITT  CONST_22  C4   C5   C6   O6   180.00   0.0  0
 ITT  CONST_23  C2   N1   C6   O6   180.00   0.0  0
 ITT  CONST_24  H8   C8   N9   C1'    0.00   0.0  0
 ITT  CONST_25  H2   C2   N1   C6   180.00   0.0  0
 ITT  Var_01    C4'  C5'  O5'  PA   174.38  30.0  3
 ITT  Var_02    O1B  PB   O3B  PG   128.02  30.0  1
 ITT  Var_03    O1A  PA   O3A  PB   174.36  30.0  1

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
 ITT  chir_03  C4'  C5'  O4'  C3'  negativ
 ITT  chir_04  C3'  O3'  C4'  C2'  positiv
 ITT  chir_05  C2'  O2'  C3'  C1'  positiv
 ITT  chir_06  C1'  O4'  N9   C2'  negativ
 ITT  chir_07  PB   O2B  O3B  O3A  both
 ITT  chir_08  PA   O2A  O3A  O5'  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
 ITT  plan-1  C1'  0.020
 ITT  plan-1  N9   0.020
 ITT  plan-1  C8   0.020
 ITT  plan-1  N7   0.020
 ITT  plan-1  C5   0.020
 ITT  plan-1  C6   0.020
 ITT  plan-1  O6   0.020
 ITT  plan-1  N1   0.020
 ITT  plan-1  C2   0.020
 ITT  plan-1  N3   0.020
 ITT  plan-1  C4   0.020
 ITT  plan-1  H8   0.020
 ITT  plan-1  H2   0.020

