# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun  6 03:04:00 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: 6-methyl-9-[(5E)-5,6,7-trideoxy-7-{[(4'-fluoro-4,5-dihydroxybiphenyl-3-yl)carbonyl]amino}-beta-D-ribo-hept-5-enofuranosyl]-9H-purine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncnc2n(cnc12)[C@@H]3O[C@H](\C=C\CNC(=O)c4cc(cc(O)c4O)c5ccc(F)cc5)[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
 637  637  6-methyl-9-[(5E)-5,6,7-trideoxy-7-{[(4'-fluoro-4,5-dihydroxybiphenyl-3-yl)carbonyl]amino}-beta-D-ribo-hept-5-enofuranosyl]-9H-purine  ligand  62  38  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_637
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
 637  C1    C  CR15  0   0.154  -3.6908  -1.9315   0.5857
 637  C2    C  CR15  0  -0.034  -4.4498  -2.0960  -0.7282
 637  O3    O  OH1   0  -0.661  -5.5347  -2.9407  -0.4623
 637  C4    C  CR15  0  -0.023  -3.3946  -2.7837  -1.5925
 637  O5    O  OH1   0  -0.661  -3.9942  -3.4779  -2.6446
 637  C6    C  CR15  0   0.002  -2.6891  -3.6898  -0.5623
 637  C7    C  CH3   0  -0.732  -1.5479   3.8014   1.1726
 637  N8    N  N     0  -0.457  -1.2381   0.7635   0.4030
 637  C9    C  CR15  0   0.139  -1.6248  -0.4684   0.2541
 637  N10   N  NR5   0  -0.538  -2.9263  -0.6873   0.6174
 637  C11   C  CR56  0   0.493  -3.4051   0.5194   1.0321
 637  C12   C  CR56  0   0.083  -2.3410   1.4149   0.8937
 637  O13   O  O     0  -0.487  -2.8282  -3.0201   0.6880
 637  C14   C  C1    0  -0.258  -1.2544  -3.9396  -0.8893
 637  C15   C  C1    0  -0.234  -0.2275  -3.7485  -0.0696
 637  C16   C  CH2   0  -0.361   1.2054  -3.9164  -0.4726
 637  N17   N  NH1   0  -0.649   1.9089  -2.6512  -0.3543
 637  C18   C  C     0   0.623   2.6125  -2.2880   0.7199
 637  O19   O  O     0  -0.535   2.8249  -3.0705   1.6577
 637  C20   C  CR6   0  -0.141   3.1617  -0.9086   0.7628
 637  C21   C  CR16  0  -0.403   2.7043   0.1196  -0.0673
 637  C22   C  CR6   0   0.102   3.2463   1.3918   0.0000
 637  C23   C  CR16  0  -0.407   4.2765   1.6357   0.9153
 637  C24   C  CR6   0   0.071   2.7429   2.4762  -0.8664
 637  C25   C  CR16  0  -0.291   3.6171   3.3994  -1.4417
 637  C26   C  CR16  0  -0.399   3.1516   4.4185  -2.2589
 637  C27   C  CR16  0  -0.319   1.3774   2.6037  -1.1274
 637  C28   C  CR16  0  -0.409   0.8956   3.6148  -1.9455
 637  C29   C  CR6   0   0.518   1.7941   4.5056  -2.4992
 637  F30   F  F     0  -0.316   1.3345   5.4870  -3.2929
 637  C31   C  CR6   0   0.240   4.1626  -0.6403   1.7023
 637  O32   O  OH1   0  -0.644   4.6305  -1.5409   2.5729
 637  C33   C  CR6   0   0.328   4.7352   0.6420   1.7546
 637  O34   O  OH1   0  -0.632   5.7144   0.9241   2.6347
 637  C35   C  CR6   0   0.233  -2.5801   2.7316   1.2715
 637  N38   N  N     0  -0.435  -3.7927   3.0397   1.7287
 637  C39   C  CR16  0   0.033  -4.7270   2.0935   1.8086
 637  N40   N  N     0  -0.426  -4.6117   0.8153   1.4804
 637  H1    H  HCR5  0   0.293  -4.3701  -1.9007   1.4409
 637  H2    H  HCR5  0   0.268  -4.7664  -1.1316  -1.1426
 637  HO3   H  HOH1  0   0.460  -5.9008  -3.2450  -1.3001
 637  H4    H  HCR5  0   0.247  -2.6924  -2.0294  -1.9704
 637  HO5   H  HOH1  0   0.469  -3.3402  -3.6493  -3.3287
 637  H6    H  HCR5  0   0.265  -3.2288  -4.6446  -0.5190
 637  H7    H  HCH3  0   0.265  -1.6454   4.3292   0.2214
 637  H7A   H  HCH3  0   0.263  -1.6726   4.5321   1.9693
 637  H7B   H  HCH3  0   0.255  -0.5412   3.3901   1.2140
 637  H9    H  HCR5  0   0.291  -0.9957  -1.2655  -0.1130
 637  H14   H  H     0   0.266  -1.0762  -4.2968  -1.9012
 637  H15   H  H     0   0.268  -0.3895  -3.4121   0.9500
 637  H16   H  HCH2  0   0.271   1.7049  -4.6541   0.1540
 637  H16A  H  HCH2  0   0.275   1.2860  -4.2547  -1.5054
 637  HN17  H  HNH1  0   0.419   1.7999  -2.0039  -1.1173
 637  H21   H  HCR6  0   0.248   1.9121  -0.0626  -0.7820
 637  H23   H  HCR6  0   0.270   4.7083   2.6259   1.0013
 637  H25   H  HCR6  0   0.264   4.6826   3.3189  -1.2672
 637  H26   H  HCR6  0   0.280   3.8366   5.1259  -2.7077
 637  H27   H  HCR6  0   0.302   0.6684   1.9266  -0.6637
 637  H28   H  HCR6  0   0.274  -0.1649   3.7120  -2.1387
 637  HO32  H  HOH1  0   0.484   4.0558  -2.3423   2.4845
 637  HO34  H  HOH1  0   0.476   5.9014   0.1559   3.1885
 637  H39   H  HCR6  0   0.261  -5.6922   2.4071   2.1887

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
 637  C1   C2    single    1.526  0.020  1.526
 637  C1   N10   single    1.461  0.020  1.461
 637  C1   O13   single    1.393  0.020  1.393
 637  C2   O3    single    1.400  0.020  1.400
 637  C2   C4    single    1.528  0.020  1.528
 637  C4   O5    single    1.396  0.020  1.396
 637  C4   C6    single    1.543  0.020  1.543
 637  C6   O13   single    1.425  0.020  1.425
 637  C6   C14   single    1.493  0.020  1.493
 637  C7   C35   single    1.490  0.020  1.490
 637  N8   C9    aromatic  1.300  0.020  1.300
 637  N8   C12   aromatic  1.372  0.020  1.372
 637  C9   N10   aromatic  1.369  0.020  1.369
 637  N10  C11   aromatic  1.363  0.020  1.363
 637  C11  C12   aromatic  1.398  0.020  1.398
 637  C11  N40   aromatic  1.321  0.020  1.321
 637  C12  C35   aromatic  1.391  0.020  1.391
 637  C14  C15   double    1.328  0.020  1.328
 637  C15  C16   single    1.498  0.020  1.498
 637  C16  N17   single    1.453  0.020  1.453
 637  N17  C18   single    1.334  0.020  1.334
 637  C18  O19   double    1.240  0.020  1.240
 637  C18  C20   single    1.485  0.020  1.485
 637  C20  C21   aromatic  1.398  0.020  1.398
 637  C20  C31   aromatic  1.399  0.020  1.399
 637  C21  C22   aromatic  1.385  0.020  1.385
 637  C22  C23   aromatic  1.399  0.020  1.399
 637  C22  C24   single    1.476  0.020  1.476
 637  C23  C33   aromatic  1.379  0.020  1.379
 637  C24  C25   aromatic  1.395  0.020  1.395
 637  C24  C27   aromatic  1.396  0.020  1.396
 637  C25  C26   aromatic  1.387  0.020  1.387
 637  C26  C29   aromatic  1.381  0.020  1.381
 637  C27  C28   aromatic  1.387  0.020  1.387
 637  C28  C29   aromatic  1.381  0.020  1.381
 637  C29  F30   single    1.343  0.020  1.343
 637  C31  O32   single    1.337  0.020  1.337
 637  C31  C33   aromatic  1.405  0.020  1.405
 637  C33  O34   single    1.346  0.020  1.346
 637  C35  N38   aromatic  1.332  0.020  1.332
 637  N38  C39   aromatic  1.332  0.020  1.332
 637  C39  N40   aromatic  1.325  0.020  1.325
 637  C1   H1    single    0.970  0.020  1.090
 637  C2   H2    single    0.970  0.020  1.090
 637  O3   HO3   single    0.850  0.020  0.980
 637  C4   H4    single    0.970  0.020  1.090
 637  O5   HO5   single    0.850  0.020  0.980
 637  C6   H6    single    0.970  0.020  1.090
 637  C7   H7    single    0.970  0.020  1.090
 637  C7   H7A   single    0.970  0.020  1.090
 637  C7   H7B   single    0.970  0.020  1.090
 637  C9   H9    single    0.930  0.020  1.080
 637  C14  H14   single    0.930  0.020  1.080
 637  C15  H15   single    0.930  0.020  1.080
 637  C16  H16   single    0.970  0.020  1.090
 637  C16  H16A  single    0.970  0.020  1.090
 637  N17  HN17  single    0.860  0.020  1.020
 637  C21  H21   single    0.930  0.020  1.080
 637  C23  H23   single    0.930  0.020  1.080
 637  C25  H25   single    0.930  0.020  1.080
 637  C26  H26   single    0.930  0.020  1.080
 637  C27  H27   single    0.930  0.020  1.080
 637  C28  H28   single    0.930  0.020  1.080
 637  O32  HO32  single    0.850  0.020  0.980
 637  O34  HO34  single    0.850  0.020  0.980
 637  C39  H39   single    0.930  0.020  1.080

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
 637  H1    C1   O13  110.46  3.000
 637  H1    C1   N10  106.52  3.000
 637  O13   C1   N10  109.88  3.000
 637  H1    C1   C2   111.58  3.000
 637  O13   C1   C2   106.68  3.000
 637  N10   C1   C2   111.76  3.000
 637  H2    C2   C4   112.44  3.000
 637  H2    C2   O3   112.25  3.000
 637  C4    C2   O3   111.78  3.000
 637  H2    C2   C1   111.97  3.000
 637  C4    C2   C1   101.07  3.000
 637  O3    C2   C1   106.66  3.000
 637  HO3   O3   C2   108.65  3.000
 637  H4    C4   C6   109.94  3.000
 637  H4    C4   O5   110.92  3.000
 637  C6    C4   O5   114.06  3.000
 637  H4    C4   C2   109.11  3.000
 637  C6    C4   C2   101.68  3.000
 637  O5    C4   C2   110.71  3.000
 637  HO5   O5   C4   109.43  3.000
 637  H6    C6   C14  109.61  3.000
 637  H6    C6   O13  109.04  3.000
 637  C14   C6   O13  111.39  3.000
 637  H6    C6   C4   108.21  3.000
 637  C14   C6   C4   113.05  3.000
 637  O13   C6   C4   105.38  3.000
 637  H7B   C7   H7A  109.39  3.000
 637  H7B   C7   H7   107.36  3.000
 637  H7A   C7   H7   107.63  3.000
 637  H7B   C7   C35  111.53  3.000
 637  H7A   C7   C35  110.74  3.000
 637  H7    C7   C35  110.06  3.000
 637  C12   N8   C9   104.59  3.000
 637  H9    C9   N10  121.74  3.000
 637  H9    C9   N8   124.42  3.000
 637  N10   C9   N8   113.83  3.000
 637  C11   N10  C9   105.86  3.000
 637  C11   N10  C1   125.23  3.000
 637  C9    N10  C1   128.91  3.000
 637  N40   C11  C12  125.85  3.000
 637  N40   C11  N10  128.51  3.000
 637  C12   C11  N10  105.65  3.000
 637  C35   C12  C11  116.67  3.000
 637  C35   C12  N8   133.25  3.000
 637  C11   C12  N8   110.08  3.000
 637  C6    O13  C1   111.31  3.000
 637  H14   C14  C15  119.65  3.000
 637  H14   C14  C6   114.60  3.000
 637  C15   C14  C6   125.74  3.000
 637  H15   C15  C16  115.48  3.000
 637  H15   C15  C14  120.59  3.000
 637  C16   C15  C14  123.89  3.000
 637  H16A  C16  H16  107.53  3.000
 637  H16A  C16  N17  108.17  3.000
 637  H16   C16  N17  108.72  3.000
 637  H16A  C16  C15  111.13  3.000
 637  H16   C16  C15  111.09  3.000
 637  N17   C16  C15  110.10  3.000
 637  HN17  N17  C18  119.49  3.000
 637  HN17  N17  C16  116.48  3.000
 637  C18   N17  C16  123.92  3.000
 637  C20   C18  O19  120.06  3.000
 637  C20   C18  N17  118.10  3.000
 637  O19   C18  N17  121.83  3.000
 637  C31   C20  C21  119.45  3.000
 637  C31   C20  C18  117.53  3.000
 637  C21   C20  C18  123.01  3.000
 637  H21   C21  C22  118.25  3.000
 637  H21   C21  C20  120.51  3.000
 637  C22   C21  C20  121.25  3.000
 637  C24   C22  C23  120.45  3.000
 637  C24   C22  C21  120.86  3.000
 637  C23   C22  C21  118.69  3.000
 637  H23   C23  C33  118.52  3.000
 637  H23   C23  C22  120.30  3.000
 637  C33   C23  C22  121.15  3.000
 637  C27   C24  C25  118.37  3.000
 637  C27   C24  C22  120.68  3.000
 637  C25   C24  C22  120.94  3.000
 637  H25   C25  C26  118.68  3.000
 637  H25   C25  C24  120.06  3.000
 637  C26   C25  C24  121.25  3.000
 637  H26   C26  C29  120.57  3.000
 637  H26   C26  C25  120.82  3.000
 637  C29   C26  C25  118.60  3.000
 637  H27   C27  C28  118.70  3.000
 637  H27   C27  C24  120.16  3.000
 637  C28   C27  C24  121.11  3.000
 637  H28   C28  C29  120.52  3.000
 637  H28   C28  C27  120.74  3.000
 637  C29   C28  C27  118.73  3.000
 637  F30   C29  C28  119.05  3.000
 637  F30   C29  C26  119.02  3.000
 637  C28   C29  C26  121.93  3.000
 637  C33   C31  O32  116.60  3.000
 637  C33   C31  C20  119.44  3.000
 637  O32   C31  C20  123.95  3.000
 637  HO32  O32  C31  106.50  3.000
 637  O34   C33  C31  120.78  3.000
 637  O34   C33  C23  119.26  3.000
 637  C31   C33  C23  119.95  3.000
 637  HO34  O34  C33  110.44  3.000
 637  N38   C35  C12  117.96  3.000
 637  N38   C35  C7   119.17  3.000
 637  C12   C35  C7   122.87  3.000
 637  C39   N38  C35  119.65  3.000
 637  H39   C39  N40  116.34  3.000
 637  H39   C39  N38  116.11  3.000
 637  N40   C39  N38  127.56  3.000
 637  C39   N40  C11  112.32  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
 637  CONST_01  C11   N10  C9   N8      0.00   0.0  0
 637  CONST_02  N10   C11  C12  N8      0.00   0.0  0
 637  CONST_03  N40   C11  C12  N8    180.00   0.0  0
 637  CONST_04  N38   C35  C12  N8    180.00   0.0  0
 637  CONST_05  C11   C12  N8   C9      0.00   0.0  0
 637  CONST_06  C35   C12  N8   C9    180.00   0.0  0
 637  CONST_07  C12   C11  N10  C9      0.00   0.0  0
 637  CONST_08  N40   C11  N10  C9    180.00   0.0  0
 637  CONST_09  C12   N8   C9   N10     0.00   0.0  0
 637  CONST_10  C35   C12  C11  N10   180.00   0.0  0
 637  CONST_11  C39   N40  C11  N10   180.00   0.0  0
 637  CONST_12  N38   C35  C12  C11     0.00   0.0  0
 637  CONST_13  N38   C39  N40  C11     0.00   0.0  0
 637  CONST_14  C39   N40  C11  C12     0.00   0.0  0
 637  CONST_15  C39   N38  C35  C12     0.00   0.0  0
 637  CONST_16  C23   C22  C21  C20     0.00   0.0  0
 637  CONST_17  C24   C22  C21  C20   180.00   0.0  0
 637  CONST_18  C23   C33  C31  C20     0.00   0.0  0
 637  CONST_19  C33   C31  C20  C21     0.00   0.0  0
 637  CONST_20  C33   C23  C22  C21     0.00   0.0  0
 637  CONST_23  C31   C20  C21  C22     0.00   0.0  0
 637  CONST_24  C31   C33  C23  C22     0.00   0.0  0
 637  CONST_25  C26   C25  C24  C22   180.00   0.0  0
 637  CONST_26  C28   C27  C24  C22   180.00   0.0  0
 637  CONST_29  C33   C23  C22  C24   180.00   0.0  0
 637  CONST_30  C29   C26  C25  C24     0.00   0.0  0
 637  CONST_31  C29   C28  C27  C24     0.00   0.0  0
 637  CONST_32  C28   C27  C24  C25     0.00   0.0  0
 637  CONST_33  C28   C29  C26  C25     0.00   0.0  0
 637  CONST_34  C27   C24  C25  C26     0.00   0.0  0
 637  CONST_35  C27   C28  C29  C26     0.00   0.0  0
 637  CONST_36  N40   C11  C12  C35     0.00   0.0  0
 637  CONST_37  N40   C39  N38  C35     0.00   0.0  0
 637  CONST_38  N8    C9   N10  C1    180.00   0.0  0
 637  CONST_39  C12   C11  N10  C1    180.00   0.0  0
 637  CONST_40  N40   C11  N10  C1      0.00   0.0  0
 637  CONST_41  N8    C12  C35  C7      0.00   0.0  0
 637  CONST_42  C11   C12  C35  C7    180.00   0.0  0
 637  CONST_43  C39   N38  C35  C7    180.00   0.0  0
 637  CONST_44  C22   C21  C20  C18   180.00   0.0  0
 637  CONST_45  C33   C31  C20  C18   180.00   0.0  0
 637  CONST_46  O34   C33  C31  C20   180.00   0.0  0
 637  CONST_47  O32   C31  C20  C21   180.00   0.0  0
 637  CONST_48  O34   C33  C23  C22   180.00   0.0  0
 637  CONST_49  O32   C31  C33  C23   180.00   0.0  0
 637  CONST_50  F30   C29  C26  C25   180.00   0.0  0
 637  CONST_51  F30   C29  C28  C27   180.00   0.0  0
 637  CONST_52  H9    C9   N10  C1      0.00   0.0  0
 637  CONST_53  H39   C39  N40  C11   180.00   0.0  0
 637  CONST_54  H23   C23  C22  C21   180.00   0.0  0
 637  CONST_55  H25   C25  C24  C22     0.00   0.0  0
 637  CONST_56  H27   C27  C24  C22     0.00   0.0  0
 637  CONST_57  H21   C21  C22  C23   180.00   0.0  0
 637  CONST_58  H26   C26  C25  C24   180.00   0.0  0
 637  CONST_59  H28   C28  C27  C24   180.00   0.0  0
 637  CONST_60  C20   C18  N17  C16   180.00   0.0  0
 637  CONST_61  HN17  N17  C18  C20     0.00   0.0  0
 637  CONST_62  O19   C18  N17  C16     0.00   0.0  0
 637  Var_01    C21   C20  C18  N17    17.19  30.0  2
 637  Var_02    H7    C7   C35  C12    93.64  30.0  2
 637  Var_03    C16   C15  C14  C6   -175.30   0.0  2
 637  Var_04    N17   C16  C15  C14   117.39  30.0  3
 637  Var_05    C18   N17  C16  C15    94.82  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
 637  chir_01  C1  C2   N10  O13  positiv
 637  chir_02  C2  O3   C4   C1   positiv
 637  chir_03  C4  O5   C2   C6   negativ
 637  chir_04  C6  O13  C14  C4   positiv

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
 637  plan-1  C18   0.020
 637  plan-1  C20   0.020
 637  plan-1  C21   0.020
 637  plan-1  C22   0.020
 637  plan-1  C23   0.020
 637  plan-1  C24   0.020
 637  plan-1  C31   0.020
 637  plan-1  O32   0.020
 637  plan-1  C33   0.020
 637  plan-1  O34   0.020
 637  plan-1  H21   0.020
 637  plan-1  H23   0.020
 637  plan-2  C22   0.020
 637  plan-2  C24   0.020
 637  plan-2  C25   0.020
 637  plan-2  C26   0.020
 637  plan-2  C27   0.020
 637  plan-2  C28   0.020
 637  plan-2  C29   0.020
 637  plan-2  F30   0.020
 637  plan-2  H25   0.020
 637  plan-2  H26   0.020
 637  plan-2  H27   0.020
 637  plan-2  H28   0.020
 637  plan-3  C1    0.020
 637  plan-3  C7    0.020
 637  plan-3  N8    0.020
 637  plan-3  C9    0.020
 637  plan-3  N10   0.020
 637  plan-3  C11   0.020
 637  plan-3  C12   0.020
 637  plan-3  C35   0.020
 637  plan-3  N38   0.020
 637  plan-3  C39   0.020
 637  plan-3  N40   0.020
 637  plan-3  H9    0.020
 637  plan-3  H39   0.020
 637  plan-4  C16   0.020
 637  plan-4  N17   0.020
 637  plan-4  C18   0.020
 637  plan-4  O19   0.020
 637  plan-4  C20   0.020
 637  plan-4  HN17  0.020
 637  plan-5  C6    0.020
 637  plan-5  C14   0.020
 637  plan-5  C15   0.020
 637  plan-5  C16   0.020
 637  plan-5  H14   0.020
 637  plan-5  H15   0.020

