# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 19:27:30 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: N-(2-aminoethyl)-4'-{[(4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)sulfanyl]methyl}[1,1'-biphenyl]-4-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN[S](=O)(=O)c1ccc(cc1)c2ccc(CSC3=NC4=C(CCC4)C(=O)N3)cc2
#
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
 8O7  8O7  N-(2-aminoethyl)-4'-{[(4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)sulfanyl]methyl}[1,1'-biphenyl]-4-sulfonamide  ligand  55  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8O7
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
 8O7  C1   C  CH2   0  -0.291  -7.8828  -3.0782   0.2024
 8O7  N1   N  NH2   0  -0.801  -7.4366  -4.0332   1.2006
 8O7  C2   C  CH2   0  -0.286  -7.1669  -1.7534   0.4198
 8O7  N3   N  NC1   0  -0.727  -7.5743  -0.8052  -0.6132
 8O7  S4   S  S     0   1.374  -7.2113   0.7867  -0.4246
 8O7  O5   O  OS    0  -0.658  -7.6241   1.4435  -1.6539
 8O7  O6   O  OS    0  -0.655  -7.7695   1.2084   0.8494
 8O7  C7   C  CR6   0  -0.217  -5.4471   0.8935  -0.2987
 8O7  C8   C  CR16  0  -0.214  -4.8435   0.9403   0.9501
 8O7  C9   C  CR16  0  -0.300  -3.4615   0.9673   1.0338
 8O7  C10  C  CR6   0   0.104  -2.6707   0.9450  -0.1154
 8O7  C11  C  CR16  0  -0.299  -3.3035   0.9040  -1.3605
 8O7  C12  C  CR16  0  -0.218  -4.6828   0.8780  -1.4588
 8O7  C13  C  CR6   0   0.082  -1.1991   0.9584  -0.0167
 8O7  C14  C  CR16  0  -0.291  -0.5500   0.2820   1.0172
 8O7  C15  C  CR16  0  -0.264   0.8314   0.2889   1.1106
 8O7  C16  C  CR6   0   0.081   1.6024   0.9784   0.1797
 8O7  C17  C  CR16  0  -0.266   0.9597   1.6519  -0.8544
 8O7  C18  C  CR16  0  -0.292  -0.4222   1.6440  -0.9511
 8O7  C19  C  CH2   0  -0.623   3.0981   0.9663   0.2741
 8O7  S20  S  S2    0   0.083   3.6690  -0.4764  -0.6837
 8O7  C21  C  CR6   0   0.346   5.3981  -0.3984  -0.4309
 8O7  N22  N  N     0  -0.454   5.9318   0.5305   0.2957
 8O7  C23  C  CR56  0   0.248   7.2823   0.4765   0.4051
 8O7  C24  C  CR56  0  -0.148   8.0815  -0.4593  -0.1723
 8O7  C25  C  CR6   0   0.521   7.5016  -1.4981  -0.9613
 8O7  N26  N  NR16  0  -0.688   6.1112  -1.3709  -1.0440
 8O7  O27  O  O     0  -0.471   8.0737  -2.4160  -1.5281
 8O7  C28  C  CH2   0  -0.477   9.5228  -0.2568   0.1703
 8O7  C29  C  CH2   0  -0.466   9.5251   1.1699   0.7607
 8O7  C30  C  CH2   0  -0.500   8.0833   1.4404   1.2245
 8O7  H1   H  HCH2  0   0.205  -7.7259  -3.4105  -0.8337
 8O7  H2   H  HCH2  0   0.235  -8.9559  -2.9192   0.3219
 8O7  H3   H  HNH2  0   0.355  -8.0305  -4.8512   1.1771
 8O7  H4   H  HNH2  0   0.345  -6.5066  -4.3601   0.9705
 8O7  H6   H  HCH2  0   0.258  -7.4451  -1.3554   1.3950
 8O7  H7   H  HCH2  0   0.236  -6.0814  -1.9081   0.4175
 8O7  H8   H  HNC1  0   0.410  -7.3779  -1.1224  -1.5575
 8O7  H9   H  HCR6  0   0.287  -5.4360   0.9687   1.8543
 8O7  H10  H  HCR6  0   0.271  -2.9995   1.0268   2.0108
 8O7  H11  H  HCR6  0   0.271  -2.7139   0.8721  -2.2674
 8O7  H12  H  HCR6  0   0.286  -5.1476   0.8416  -2.4352
 8O7  H13  H  HCR6  0   0.263  -1.1247  -0.2728   1.7478
 8O7  H14  H  HCR6  0   0.263   1.3147  -0.2484   1.9174
 8O7  H15  H  HCR6  0   0.263   1.5424   2.1967  -1.5872
 8O7  H16  H  HCR6  0   0.263  -0.8970   2.1969  -1.7517
 8O7  H17  H  HCH2  0   0.309   3.5410   1.8655  -0.1501
 8O7  H18  H  HCH2  0   0.309   3.4378   0.8582   1.3025
 8O7  H19  H  HCH2  0   0.248   9.8556  -0.9983   0.9031
 8O7  H20  H  HCH2  0   0.243  10.2502   1.2853   1.5646
 8O7  H21  H  HCH2  0   0.260   7.7687   2.4745   1.0771
 8O7  H5   H  HNR6  0   0.430   5.6291  -2.0712  -1.5960
 8O7  H22  H  HCH2  0   0.250  10.1853  -0.3479  -0.6918
 8O7  H23  H  HCH2  0   0.245   9.7905   1.8821  -0.0219
 8O7  H24  H  HCH2  0   0.262   7.9425   1.2142   2.2864

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
 8O7  O5   S4   double    1.454  0.020  1.454
 8O7  S4   O6   double    1.453  0.020  1.453
 8O7  S4   N3   single    1.644  0.020  1.644
 8O7  S4   C7   single    1.772  0.020  1.772
 8O7  C8   C7   aromatic  1.388  0.020  1.388
 8O7  C8   C9   aromatic  1.385  0.020  1.385
 8O7  O27  C25  double    1.221  0.020  1.221
 8O7  N3   C2   single    1.460  0.020  1.460
 8O7  C7   C12  aromatic  1.389  0.020  1.389
 8O7  C9   C10  aromatic  1.395  0.020  1.395
 8O7  N26  C25  single    1.399  0.020  1.399
 8O7  N26  C21  single    1.353  0.020  1.353
 8O7  C12  C11  aromatic  1.383  0.020  1.383
 8O7  C25  C24  single    1.428  0.020  1.428
 8O7  C10  C13  single    1.475  0.020  1.475
 8O7  C10  C11  aromatic  1.397  0.020  1.397
 8O7  S20  C21  single    1.749  0.020  1.749
 8O7  S20  C19  single    1.823  0.020  1.823
 8O7  C14  C13  aromatic  1.396  0.020  1.396
 8O7  C14  C15  aromatic  1.385  0.020  1.385
 8O7  C13  C18  aromatic  1.395  0.020  1.395
 8O7  C2   C1   single    1.521  0.020  1.521
 8O7  C21  N22  double    1.294  0.020  1.294
 8O7  C15  C16  aromatic  1.392  0.020  1.392
 8O7  C18  C17  aromatic  1.385  0.020  1.385
 8O7  C1   N1   single    1.452  0.020  1.452
 8O7  C16  C17  aromatic  1.391  0.020  1.391
 8O7  C16  C19  single    1.499  0.020  1.499
 8O7  C24  C28  single    1.495  0.020  1.495
 8O7  C24  C23  double    1.359  0.020  1.359
 8O7  C28  C29  single    1.544  0.020  1.544
 8O7  N22  C23  single    1.356  0.020  1.356
 8O7  C23  C30  single    1.497  0.020  1.497
 8O7  C29  C30  single    1.539  0.020  1.539
 8O7  C1   H1   single    0.970  0.020  1.090
 8O7  C1   H2   single    0.970  0.020  1.090
 8O7  N1   H3   single    0.890  0.020  1.040
 8O7  N1   H4   single    0.890  0.020  1.040
 8O7  C2   H6   single    0.970  0.020  1.090
 8O7  C2   H7   single    0.970  0.020  1.090
 8O7  N3   H8   single    0.890  0.020  1.040
 8O7  C8   H9   single    0.930  0.020  1.080
 8O7  C9   H10  single    0.930  0.020  1.080
 8O7  C11  H11  single    0.930  0.020  1.080
 8O7  C12  H12  single    0.930  0.020  1.080
 8O7  C14  H13  single    0.930  0.020  1.080
 8O7  C15  H14  single    0.930  0.020  1.080
 8O7  C17  H15  single    0.930  0.020  1.080
 8O7  C18  H16  single    0.930  0.020  1.080
 8O7  C19  H17  single    0.970  0.020  1.090
 8O7  C19  H18  single    0.970  0.020  1.090
 8O7  C28  H19  single    0.970  0.020  1.090
 8O7  C29  H20  single    0.970  0.020  1.090
 8O7  C30  H21  single    0.970  0.020  1.090
 8O7  N26  H5   single    0.860  0.020  1.020
 8O7  C28  H22  single    0.970  0.020  1.090
 8O7  C29  H23  single    0.970  0.020  1.090
 8O7  C30  H24  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
 8O7  H2   C1   H1   106.71  3.000
 8O7  H2   C1   C2   108.67  3.000
 8O7  H1   C1   C2   109.31  3.000
 8O7  H2   C1   N1   108.83  3.000
 8O7  H1   C1   N1   113.91  3.000
 8O7  C2   C1   N1   109.27  3.000
 8O7  H4   N1   H3   105.85  3.000
 8O7  H4   N1   C1   109.78  3.000
 8O7  H3   N1   C1   109.61  3.000
 8O7  H7   C2   H6   107.83  3.000
 8O7  H7   C2   N3   111.49  3.000
 8O7  H6   C2   N3   108.95  3.000
 8O7  H7   C2   C1   110.04  3.000
 8O7  H6   C2   C1   109.02  3.000
 8O7  N3   C2   C1   109.46  3.000
 8O7  H8   N3   S4   111.51  3.000
 8O7  H8   N3   C2   113.64  3.000
 8O7  S4   N3   C2   119.09  3.000
 8O7  C7   S4   O6   107.62  3.000
 8O7  C7   S4   O5   108.40  3.000
 8O7  O6   S4   O5   120.08  3.000
 8O7  C7   S4   N3   106.64  3.000
 8O7  O6   S4   N3   107.26  3.000
 8O7  O5   S4   N3   106.13  3.000
 8O7  C12  C7   C8   120.83  3.000
 8O7  C12  C7   S4   119.19  3.000
 8O7  C8   C7   S4   119.93  3.000
 8O7  H9   C8   C9   119.71  3.000
 8O7  H9   C8   C7   121.00  3.000
 8O7  C9   C8   C7   119.28  3.000
 8O7  H10  C9   C10  120.16  3.000
 8O7  H10  C9   C8   118.79  3.000
 8O7  C10  C9   C8   121.03  3.000
 8O7  C13  C10  C11  120.78  3.000
 8O7  C11  C10  C9   118.54  3.000
 8O7  C13  C10  C9   120.68  3.000
 8O7  H11  C11  C12  118.90  3.000
 8O7  H11  C11  C10  120.06  3.000
 8O7  C12  C11  C10  121.03  3.000
 8O7  H12  C12  C11  119.56  3.000
 8O7  H12  C12  C7   121.16  3.000
 8O7  C11  C12  C7   119.28  3.000
 8O7  C18  C13  C14  118.38  3.000
 8O7  C18  C13  C10  121.01  3.000
 8O7  C14  C13  C10  120.61  3.000
 8O7  H13  C14  C15  119.13  3.000
 8O7  H13  C14  C13  120.09  3.000
 8O7  C15  C14  C13  120.77  3.000
 8O7  H14  C15  C16  119.79  3.000
 8O7  H14  C15  C14  119.54  3.000
 8O7  C16  C15  C14  120.67  3.000
 8O7  C19  C16  C17  120.78  3.000
 8O7  C19  C16  C15  120.45  3.000
 8O7  C17  C16  C15  118.76  3.000
 8O7  H15  C17  C18  119.49  3.000
 8O7  H15  C17  C16  119.85  3.000
 8O7  C18  C17  C16  120.66  3.000
 8O7  H16  C18  C17  119.09  3.000
 8O7  H16  C18  C13  120.13  3.000
 8O7  C17  C18  C13  120.76  3.000
 8O7  H18  C19  H17  108.86  3.000
 8O7  H18  C19  S20  108.66  3.000
 8O7  H17  C19  S20  108.75  3.000
 8O7  H18  C19  C16  111.83  3.000
 8O7  H17  C19  C16  112.02  3.000
 8O7  S20  C19  C16  106.61  3.000
 8O7  C21  S20  C19  101.44  3.000
 8O7  N26  C21  N22  123.57  3.000
 8O7  N22  C21  S20  121.38  3.000
 8O7  N26  C21  S20  115.06  3.000
 8O7  C23  N22  C21  115.30  3.000
 8O7  C30  C23  C24  111.17  3.000
 8O7  C30  C23  N22  123.45  3.000
 8O7  C24  C23  N22  125.36  3.000
 8O7  C28  C24  C25  128.08  3.000
 8O7  C28  C24  C23  112.09  3.000
 8O7  C25  C24  C23  119.79  3.000
 8O7  O27  C25  N26  120.44  3.000
 8O7  N26  C25  C24  111.73  3.000
 8O7  O27  C25  C24  127.82  3.000
 8O7  H5   N26  C25  116.24  3.000
 8O7  H5   N26  C21  119.52  3.000
 8O7  C25  N26  C21  124.24  3.000
 8O7  H22  C28  H19  106.73  3.000
 8O7  H22  C28  C29  112.23  3.000
 8O7  H19  C28  C29  111.69  3.000
 8O7  H22  C28  C24  113.14  3.000
 8O7  H19  C28  C24  110.78  3.000
 8O7  C29  C28  C24  102.37  3.000
 8O7  H23  C29  H20  107.36  3.000
 8O7  H23  C29  C30  109.24  3.000
 8O7  H20  C29  C30  112.51  3.000
 8O7  H23  C29  C28  109.23  3.000
 8O7  H20  C29  C28  112.41  3.000
 8O7  C30  C29  C28  106.04  3.000
 8O7  H24  C30  H21  106.85  3.000
 8O7  H24  C30  C29  112.12  3.000
 8O7  H21  C30  C29  113.34  3.000
 8O7  H24  C30  C23  109.21  3.000
 8O7  H21  C30  C23  112.46  3.000
 8O7  C29  C30  C23  102.89  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
 8O7  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 8O7  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 8O7  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 8O7  CONST_04  C13  C10  C9   C8    180.00   0.0  0
 8O7  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 8O7  CONST_06  C12  C7   C8   C9      0.00   0.0  0
 8O7  CONST_09  C12  C11  C10  C9      0.00   0.0  0
 8O7  CONST_10  C15  C14  C13  C10   180.00   0.0  0
 8O7  CONST_11  C17  C18  C13  C10   180.00   0.0  0
 8O7  CONST_14  C13  C10  C11  C12   180.00   0.0  0
 8O7  CONST_15  C16  C15  C14  C13     0.00   0.0  0
 8O7  CONST_16  C16  C17  C18  C13     0.00   0.0  0
 8O7  CONST_17  C17  C18  C13  C14     0.00   0.0  0
 8O7  CONST_18  C17  C16  C15  C14     0.00   0.0  0
 8O7  CONST_19  C18  C13  C14  C15     0.00   0.0  0
 8O7  CONST_20  C18  C17  C16  C15     0.00   0.0  0
 8O7  CONST_21  C24  C25  N26  C21     0.00   0.0  0
 8O7  CONST_22  C25  N26  C21  N22     0.00   0.0  0
 8O7  CONST_23  N26  C21  N22  C23     0.00   0.0  0
 8O7  CONST_24  C9   C8   C7   S4    180.00   0.0  0
 8O7  CONST_25  C11  C12  C7   S4    180.00   0.0  0
 8O7  CONST_26  C19  C16  C15  C14   180.00   0.0  0
 8O7  CONST_27  C19  C16  C17  C18   180.00   0.0  0
 8O7  CONST_28  C25  N26  C21  S20   180.00   0.0  0
 8O7  CONST_29  C23  N22  C21  S20   180.00   0.0  0
 8O7  CONST_30  O27  C25  N26  C21   180.00   0.0  0
 8O7  CONST_31  H10  C9   C8   C7    180.00   0.0  0
 8O7  CONST_32  H11  C11  C12  C7    180.00   0.0  0
 8O7  CONST_33  H12  C12  C7   C8    180.00   0.0  0
 8O7  CONST_34  H9   C8   C9   C10   180.00   0.0  0
 8O7  CONST_35  H13  C14  C13  C10     0.00   0.0  0
 8O7  CONST_36  H16  C18  C13  C10     0.00   0.0  0
 8O7  CONST_37  H14  C15  C14  C13   180.00   0.0  0
 8O7  CONST_38  H15  C17  C18  C13   180.00   0.0  0
 8O7  CONST_39  H5   N26  C21  N22   180.00   0.0  0
 8O7  Var_01    C29  C30  C23  N22  -167.18  30.0  1
 8O7  Var_02    C29  C28  C24  C23   -13.99  30.0  1
 8O7  Var_03    C28  C29  C30  C23   -22.34  30.0  1
 8O7  Var_04    C30  C29  C28  C24    22.13  30.0  1
 8O7  Var_05    C8   C7   S4   N3    -96.16  30.0  2
 8O7  Var_06    S20  C19  C16  C15    89.17  30.0  2
 8O7  Var_07    N26  C21  S20  C19  -179.81  30.0  3
 8O7  Var_08    C7   S4   N3   C2     59.24  30.0  1
 8O7  Var_09    S4   N3   C2   C1    166.65  30.0  2
 8O7  Var_10    N3   C2   C1   N1    177.84  30.0  2
 8O7  Var_11    H3   N1   C1   C2    169.16  30.0  3

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
 8O7  plan-1  S4   0.020
 8O7  plan-1  C7   0.020
 8O7  plan-1  C8   0.020
 8O7  plan-1  C9   0.020
 8O7  plan-1  C10  0.020
 8O7  plan-1  C11  0.020
 8O7  plan-1  C12  0.020
 8O7  plan-1  C13  0.020
 8O7  plan-1  H9   0.020
 8O7  plan-1  H10  0.020
 8O7  plan-1  H11  0.020
 8O7  plan-1  H12  0.020
 8O7  plan-2  C10  0.020
 8O7  plan-2  C13  0.020
 8O7  plan-2  C14  0.020
 8O7  plan-2  C15  0.020
 8O7  plan-2  C16  0.020
 8O7  plan-2  C17  0.020
 8O7  plan-2  C18  0.020
 8O7  plan-2  C19  0.020
 8O7  plan-2  H13  0.020
 8O7  plan-2  H14  0.020
 8O7  plan-2  H15  0.020
 8O7  plan-2  H16  0.020
 8O7  plan-3  S20  0.020
 8O7  plan-3  C21  0.020
 8O7  plan-3  N22  0.020
 8O7  plan-3  C23  0.020
 8O7  plan-3  C24  0.020
 8O7  plan-3  C25  0.020
 8O7  plan-3  N26  0.020
 8O7  plan-3  O27  0.020
 8O7  plan-3  C28  0.020
 8O7  plan-3  C30  0.020
 8O7  plan-3  H5   0.020

