# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 21:12:43 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: (2S,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl 2-(1H-indol-3-yl)ethyl hydrogen (S)-phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H](O[P](O)(=O)OCCc4c[nH]c5ccccc45)[C@H](O)[C@H]3O
#
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
 V1N  V1N  '(2S,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl 2-(1H-indol-3-yl)ethyl hydrogen (S)-phosphate'  ligand  54  33  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V1N
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
 V1N  C27   C  CR16  0  -0.263  -26.3233  25.0291  -1.6744
 V1N  C28   C  CR16  0  -0.275  -25.1614  24.2494  -1.7865
 V1N  C26   C  CR16  0  -0.377  -26.3613  26.1312  -0.8417
 V1N  C29   C  CR16  0  -0.296  -24.0199  24.5543  -1.0704
 V1N  C22   C  CR15  0  -0.080  -23.6352  27.2819   1.2416
 V1N  C4    C  CR16  0   0.044  -26.8537  21.1218  -0.4621
 V1N  C9    C  CR15  0   0.113  -23.3875  22.5047   1.7141
 V1N  C25   C  CR56  0   0.056  -25.2226  26.4601  -0.0998
 V1N  C21   C  CR5   0   0.005  -24.9236  27.4964   0.8423
 V1N  C7    C  CR56  0  -0.000  -24.2986  21.4313   0.1412
 V1N  C24   C  CR56  0   0.365  -24.0674  25.6589  -0.2233
 V1N  C6    C  CR56  0   0.517  -25.3395  21.9630   0.8820
 V1N  C2    C  CR6   0   0.459  -24.6589  20.6983  -1.0025
 V1N  C32   C  CH1   0  -0.021  -24.9224  23.1710   4.3422
 V1N  C30   C  CH1   0  -0.044  -25.3685  24.4611   5.0073
 V1N  C11   C  CH1   0   0.163  -25.4046  23.4127   2.9096
 V1N  C13   C  CH1   0   0.272  -25.2217  25.4894   3.8674
 V1N  C20   C  CH2   0  -0.571  -25.8648  28.5807   1.2520
 V1N  C19   C  CH2   0  -0.205  -25.4358  29.3990   2.4524
 V1N  N5    N  N     0  -0.456  -26.6374  21.8322   0.6311
 V1N  N3    N  N     0  -0.476  -25.9616  20.5609  -1.2740
 V1N  N8    N  N     0  -0.449  -23.0863  21.7830   0.6786
 V1N  N23   N  NR15  0  -0.697  -23.1192  26.1897   0.5983
 V1N  N10   N  NR5   0  -0.548  -24.7390  22.6400   1.9077
 V1N  O16   O  O     0  -0.695  -27.7638  28.4082   4.1708
 V1N  O12   O  O2    0  -0.448  -25.1467  24.7792   2.6789
 V1N  O33   O  OH1   0  -0.649  -25.4846  22.0536   4.9536
 V1N  O31   O  OH1   0  -0.657  -24.5967  24.7279   6.1377
 V1N  O14   O  O2    0  -0.593  -26.3744  26.3246   3.7945
 V1N  O18   O  O2    0  -0.593  -25.2283  28.6206   3.6448
 V1N  O17   O  OH1   0  -0.741  -25.8694  27.6213   5.8217
 V1N  P15   P  P     0   1.494  -26.4212  27.8236   4.3373
 V1N  H27   H  HCR6  0   0.236  -27.1985  24.7608  -2.2528
 V1N  H28   H  HCR6  0   0.240  -25.1587  23.3950  -2.4507
 V1N  H26   H  HCR6  0   0.234  -27.2624  26.7288  -0.7655
 V1N  H29   H  HCR6  0   0.248  -23.1285  23.9458  -1.1533
 V1N  H22   H  HCR5  0   0.275  -23.0268  27.8257   1.9469
 V1N  H23   H  HNR5  0   0.399  -22.1981  25.8177   0.7519
 V1N  H4    H  HCR6  0   0.250  -27.8922  20.9730  -0.7377
 V1N  H9    H  HCR5  0   0.300  -22.6681  22.9645   2.3747
 V1N  H201  H  HCH2  0   0.261  -25.9964  29.2979   0.4338
 V1N  H202  H  HCH2  0   0.243  -26.8631  28.1652   1.4232
 V1N  H11N  H  HNH2  0   0.403  -24.0550  19.6326  -2.6300
 V1N  H12N  H  HNH2  0   0.410  -22.7741  20.2304  -1.6389
 V1N  H32   H  HCH1  0   0.252  -23.8239  23.1357   4.3583
 V1N  H30   H  HCH1  0   0.252  -26.4366  24.3706   5.2515
 V1N  H11   H  HCH1  0   0.269  -26.4721  23.1809   2.8249
 V1N  H33   H  HOH1  0   0.466  -24.9882  21.2716   4.6936
 V1N  H13   H  HCH1  0   0.250  -24.3184  26.0974   3.9750
 V1N  H31   H  HOH1  0   0.459  -25.0096  25.4403   6.6362
 V1N  H191  H  HCH2  0   0.252  -24.4791  29.8857   2.2674
 V1N  H192  H  HCH2  0   0.259  -26.1737  30.1774   2.6518
 V1N  H17   H  HOH1  0   0.506  -25.7675  28.4315   6.3402
 V1N  N1    N  NH2   0  -0.819  -23.7588  20.1515  -1.8217

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
 V1N  C27  C28   aromatic  1.404  0.020  1.404
 V1N  C27  C26   aromatic  1.382  0.020  1.382
 V1N  C28  C29   aromatic  1.382  0.020  1.382
 V1N  C26  C25   aromatic  1.398  0.020  1.398
 V1N  C29  C24   aromatic  1.393  0.020  1.393
 V1N  C22  C21   aromatic  1.366  0.020  1.366
 V1N  C22  N23   aromatic  1.369  0.020  1.369
 V1N  C4   N5    aromatic  1.322  0.020  1.322
 V1N  C4   N3    aromatic  1.330  0.020  1.330
 V1N  C9   N8    aromatic  1.298  0.020  1.298
 V1N  C9   N10   aromatic  1.372  0.020  1.372
 V1N  C25  C21   aromatic  1.432  0.020  1.432
 V1N  C25  C24   aromatic  1.411  0.020  1.411
 V1N  C21  C20   single    1.493  0.020  1.493
 V1N  C7   C6    aromatic  1.384  0.020  1.384
 V1N  C7   C2    aromatic  1.405  0.020  1.405
 V1N  C7   N8    aromatic  1.372  0.020  1.372
 V1N  C24  N23   aromatic  1.362  0.020  1.362
 V1N  C6   N5    aromatic  1.328  0.020  1.328
 V1N  C6   N10   aromatic  1.368  0.020  1.368
 V1N  C2   N3    aromatic  1.338  0.020  1.338
 V1N  C2   N1    single    1.334  0.020  1.334
 V1N  C32  C30   single    1.518  0.020  1.518
 V1N  C32  C11   single    1.531  0.020  1.531
 V1N  C32  O33   single    1.392  0.020  1.392
 V1N  C30  C13   single    1.542  0.020  1.542
 V1N  C30  O31   single    1.394  0.020  1.394
 V1N  C11  N10   single    1.430  0.020  1.430
 V1N  C11  O12   single    1.410  0.020  1.410
 V1N  C13  O12   single    1.387  0.020  1.387
 V1N  C13  O14   single    1.425  0.020  1.425
 V1N  C20  C19   single    1.515  0.020  1.515
 V1N  C19  O18   single    1.439  0.020  1.439
 V1N  O16  P15   double    1.474  0.020  1.474
 V1N  O17  P15   single    1.596  0.020  1.596
 V1N  O14  P15   single    1.595  0.020  1.595
 V1N  O18  P15   single    1.593  0.020  1.593
 V1N  C27  H27   single    0.930  0.020  1.080
 V1N  C28  H28   single    0.930  0.020  1.080
 V1N  C26  H26   single    0.930  0.020  1.080
 V1N  C29  H29   single    0.930  0.020  1.080
 V1N  C22  H22   single    0.930  0.020  1.080
 V1N  N23  H23   single    0.860  0.020  1.020
 V1N  C4   H4    single    0.930  0.020  1.080
 V1N  C9   H9    single    0.930  0.020  1.080
 V1N  C20  H201  single    0.970  0.020  1.090
 V1N  C20  H202  single    0.970  0.020  1.090
 V1N  N1   H11N  single    0.860  0.020  1.020
 V1N  N1   H12N  single    0.860  0.020  1.020
 V1N  C32  H32   single    0.970  0.020  1.090
 V1N  C30  H30   single    0.970  0.020  1.090
 V1N  C11  H11   single    0.970  0.020  1.090
 V1N  O33  H33   single    0.850  0.020  0.980
 V1N  C13  H13   single    0.970  0.020  1.090
 V1N  O31  H31   single    0.850  0.020  0.980
 V1N  C19  H191  single    0.970  0.020  1.090
 V1N  C19  H192  single    0.970  0.020  1.090
 V1N  O17  H17   single    0.850  0.020  0.980

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
 V1N  H27   C27  C26   119.82  3.000
 V1N  H27   C27  C28   119.26  3.000
 V1N  C26   C27  C28   120.92  3.000
 V1N  H28   C28  C29   119.36  3.000
 V1N  H28   C28  C27   119.32  3.000
 V1N  C29   C28  C27   121.32  3.000
 V1N  H26   C26  C25   120.67  3.000
 V1N  H26   C26  C27   120.33  3.000
 V1N  C25   C26  C27   119.00  3.000
 V1N  H29   C29  C24   121.37  3.000
 V1N  H29   C29  C28   121.10  3.000
 V1N  C24   C29  C28   117.52  3.000
 V1N  H22   C22  N23   119.81  3.000
 V1N  H22   C22  C21   130.10  3.000
 V1N  N23   C22  C21   110.10  3.000
 V1N  H4    C4   N3    115.41  3.000
 V1N  H4    C4   N5    116.15  3.000
 V1N  N3    C4   N5    128.44  3.000
 V1N  H9    C9   N10   121.88  3.000
 V1N  H9    C9   N8    124.78  3.000
 V1N  N10   C9   N8    113.34  3.000
 V1N  C24   C25  C21   107.30  3.000
 V1N  C24   C25  C26   119.12  3.000
 V1N  C21   C25  C26   133.57  3.000
 V1N  C20   C21  C25   125.06  3.000
 V1N  C20   C21  C22   128.94  3.000
 V1N  C25   C21  C22   106.00  3.000
 V1N  N8    C7   C2    132.77  3.000
 V1N  N8    C7   C6    110.88  3.000
 V1N  C2    C7   C6    116.31  3.000
 V1N  N23   C24  C25   107.21  3.000
 V1N  N23   C24  C29   130.70  3.000
 V1N  C25   C24  C29   122.09  3.000
 V1N  N10   C6   N5    128.26  3.000
 V1N  N10   C6   C7    105.15  3.000
 V1N  N5    C6   C7    126.58  3.000
 V1N  N1    C2   N3    119.36  3.000
 V1N  N1    C2   C7    122.71  3.000
 V1N  N3    C2   C7    117.93  3.000
 V1N  H32   C32  O33   111.80  3.000
 V1N  H32   C32  C11   109.48  3.000
 V1N  O33   C32  C11   114.24  3.000
 V1N  H32   C32  C30   108.33  3.000
 V1N  O33   C32  C30   111.77  3.000
 V1N  C11   C32  C30   100.56  3.000
 V1N  H30   C30  O31   111.92  3.000
 V1N  H30   C30  C13   108.16  3.000
 V1N  O31   C30  C13   114.77  3.000
 V1N  H30   C30  C32   108.22  3.000
 V1N  O31   C30  C32   110.79  3.000
 V1N  C13   C30  C32   102.41  3.000
 V1N  H11   C11  O12   111.75  3.000
 V1N  H11   C11  N10   106.57  3.000
 V1N  O12   C11  N10   108.91  3.000
 V1N  H11   C11  C32   110.23  3.000
 V1N  O12   C11  C32   104.39  3.000
 V1N  N10   C11  C32   115.08  3.000
 V1N  H13   C13  O14   110.31  3.000
 V1N  H13   C13  O12   108.92  3.000
 V1N  O14   C13  O12   107.46  3.000
 V1N  H13   C13  C30   112.11  3.000
 V1N  O14   C13  C30   110.58  3.000
 V1N  O12   C13  C30   107.29  3.000
 V1N  H202  C20  H201  104.81  3.000
 V1N  H202  C20  C19   109.84  3.000
 V1N  H201  C20  C19   105.79  3.000
 V1N  H202  C20  C21   110.01  3.000
 V1N  H201  C20  C21   110.25  3.000
 V1N  C19   C20  C21   115.54  3.000
 V1N  H192  C19  H191  107.83  3.000
 V1N  H192  C19  O18   109.39  3.000
 V1N  H191  C19  O18   104.82  3.000
 V1N  H192  C19  C20   109.80  3.000
 V1N  H191  C19  C20   110.83  3.000
 V1N  O18   C19  C20   113.91  3.000
 V1N  C6    N5   C4    111.66  3.000
 V1N  C2    N3   C4    119.07  3.000
 V1N  C7    N8   C9    104.48  3.000
 V1N  H23   N23  C24   125.86  3.000
 V1N  H23   N23  C22   124.68  3.000
 V1N  C24   N23  C22   109.39  3.000
 V1N  C11   N10  C6    126.06  3.000
 V1N  C11   N10  C9    127.65  3.000
 V1N  C6    N10  C9    106.13  3.000
 V1N  C13   O12  C11   110.27  3.000
 V1N  H33   O33  C32   108.98  3.000
 V1N  H31   O31  C30   108.91  3.000
 V1N  P15   O14  C13   123.85  3.000
 V1N  P15   O18  C19   121.52  3.000
 V1N  H17   O17  P15   115.38  3.000
 V1N  O17   P15  O18   102.05  3.000
 V1N  O18   P15  O14   107.47  3.000
 V1N  O17   P15  O14   100.79  3.000
 V1N  O18   P15  O16   115.76  3.000
 V1N  O14   P15  O16   111.17  3.000
 V1N  O17   P15  O16   118.05  3.000
 V1N  H12N  N1   H11N  118.41  3.000
 V1N  H12N  N1   C2    121.15  3.000
 V1N  H11N  N1   C2    120.43  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
 V1N  CONST_01  C24   C29  C28  C27     0.00   0.0  0
 V1N  CONST_02  C21   C25  C26  C27   180.00   0.0  0
 V1N  CONST_03  C24   C25  C26  C27     0.00   0.0  0
 V1N  CONST_04  C25   C26  C27  C28     0.00   0.0  0
 V1N  CONST_05  C25   C24  C29  C28     0.00   0.0  0
 V1N  CONST_06  N23   C24  C29  C28   180.00   0.0  0
 V1N  CONST_07  C29   C28  C27  C26     0.00   0.0  0
 V1N  CONST_08  C22   C21  C25  C26   180.00   0.0  0
 V1N  CONST_09  C29   C24  C25  C26     0.00   0.0  0
 V1N  CONST_10  N23   C24  C25  C26   180.00   0.0  0
 V1N  CONST_11  C21   C25  C24  C29   180.00   0.0  0
 V1N  CONST_12  C22   N23  C24  C29   180.00   0.0  0
 V1N  CONST_13  C24   C25  C21  C22     0.00   0.0  0
 V1N  CONST_14  C25   C24  N23  C22     0.00   0.0  0
 V1N  CONST_15  C7    C6   N5   C4      0.00   0.0  0
 V1N  CONST_16  N10   C6   N5   C4    180.00   0.0  0
 V1N  CONST_17  C7    C2   N3   C4      0.00   0.0  0
 V1N  CONST_18  C6    C7   N8   C9      0.00   0.0  0
 V1N  CONST_19  C2    C7   N8   C9    180.00   0.0  0
 V1N  CONST_20  C7    C6   N10  C9      0.00   0.0  0
 V1N  CONST_21  N5    C6   N10  C9    180.00   0.0  0
 V1N  CONST_22  N23   C22  C21  C25     0.00   0.0  0
 V1N  CONST_23  C24   N23  C22  C21     0.00   0.0  0
 V1N  CONST_24  N23   C24  C25  C21     0.00   0.0  0
 V1N  CONST_25  N10   C9   N8   C7      0.00   0.0  0
 V1N  CONST_26  N3    C2   C7   C6      0.00   0.0  0
 V1N  CONST_27  N3    C4   N5   C6      0.00   0.0  0
 V1N  CONST_28  N8    C9   N10  C6      0.00   0.0  0
 V1N  CONST_29  N5    C6   C7   C2      0.00   0.0  0
 V1N  CONST_30  N10   C6   C7   C2    180.00   0.0  0
 V1N  CONST_31  N5    C4   N3   C2      0.00   0.0  0
 V1N  CONST_32  N8    C7   C6   N5    180.00   0.0  0
 V1N  CONST_33  N8    C7   C2   N3    180.00   0.0  0
 V1N  CONST_34  N10   C6   C7   N8      0.00   0.0  0
 V1N  CONST_35  C11   N10  C6   C7    180.00   0.0  0
 V1N  CONST_36  N8    C9   N10  C11   180.00   0.0  0
 V1N  CONST_37  N5    C6   N10  C11     0.00   0.0  0
 V1N  CONST_38  C20   C21  C25  C26     0.00   0.0  0
 V1N  CONST_39  N1    C2   N3   C4    180.00   0.0  0
 V1N  CONST_40  C20   C21  C25  C24   180.00   0.0  0
 V1N  CONST_41  N1    C2   C7   C6    180.00   0.0  0
 V1N  CONST_42  N23   C22  C21  C20   180.00   0.0  0
 V1N  CONST_43  N1    C2   C7   N8      0.00   0.0  0
 V1N  CONST_44  H29   C29  C28  C27   180.00   0.0  0
 V1N  CONST_45  H26   C26  C27  C28   180.00   0.0  0
 V1N  CONST_46  H28   C28  C27  C26   180.00   0.0  0
 V1N  CONST_47  H27   C27  C28  C29   180.00   0.0  0
 V1N  CONST_48  H23   N23  C24  C29     0.00   0.0  0
 V1N  CONST_49  H22   C22  C21  C25   180.00   0.0  0
 V1N  CONST_50  H9    C9   N8   C7    180.00   0.0  0
 V1N  CONST_51  H4    C4   N5   C6    180.00   0.0  0
 V1N  CONST_52  H11N  N1   C2   C7    180.00   0.0  0
 V1N  CONST_53  H12N  N1   C2   C7      0.00   0.0  0
 V1N  Var_01    C19   C20  C21  C22   -12.57  30.0  2
 V1N  Var_02    O18   C19  C20  C21   -58.49  30.0  3
 V1N  Var_03    O16   P15  O14  C13  -177.65  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
 V1N  chir_01  C32  C30  C11  O33  positiv
 V1N  chir_02  C30  O31  C13  C32  negativ
 V1N  chir_03  C11  O12  N10  C32  negativ
 V1N  chir_04  C13  O12  O14  C30  negativ
 V1N  chir_05  P15  O17  O14  O18  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
 V1N  plan-1  C27   0.020
 V1N  plan-1  C28   0.020
 V1N  plan-1  C26   0.020
 V1N  plan-1  C29   0.020
 V1N  plan-1  C22   0.020
 V1N  plan-1  C25   0.020
 V1N  plan-1  C21   0.020
 V1N  plan-1  C24   0.020
 V1N  plan-1  C20   0.020
 V1N  plan-1  N23   0.020
 V1N  plan-1  H27   0.020
 V1N  plan-1  H28   0.020
 V1N  plan-1  H26   0.020
 V1N  plan-1  H29   0.020
 V1N  plan-1  H22   0.020
 V1N  plan-1  H23   0.020
 V1N  plan-2  C4    0.020
 V1N  plan-2  C9    0.020
 V1N  plan-2  C7    0.020
 V1N  plan-2  C6    0.020
 V1N  plan-2  C2    0.020
 V1N  plan-2  C11   0.020
 V1N  plan-2  N5    0.020
 V1N  plan-2  N3    0.020
 V1N  plan-2  N8    0.020
 V1N  plan-2  N10   0.020
 V1N  plan-2  H4    0.020
 V1N  plan-2  H9    0.020
 V1N  plan-2  N1    0.020
 V1N  plan-3  C2    0.020
 V1N  plan-3  H11N  0.020
 V1N  plan-3  H12N  0.020
 V1N  plan-3  N1    0.020

