# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 15:20:21 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: 1-{5-tert-butyl-3-[(5-oxo-1,4-diazepan-1-yl)carbonyl]thiophen-2-yl}-3-naphthalen-1-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1sc(NC(=O)Nc2cccc3ccccc23)c(c1)C(=O)N4CCNC(=O)CC4
#
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
 P7B  P7B  1-{5-tert-butyl-3-[(5-oxo-1,4-diazepan-1-yl)carbonyl]thiophen-2-yl}-3-naphthalen-1-ylurea  ligand  61  33  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P7B
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
 P7B  C1    C  CR5   0  -0.095   2.0458  -2.4157  -0.3490
 P7B  S2    S  S2    0   0.234   0.3381  -2.3540  -0.0123
 P7B  C3    C  CR5   0   0.084   0.3728  -0.6368   0.1521
 P7B  C4    C  CR5   0  -0.077   1.6475  -0.1386   0.0114
 P7B  C5    C  CR15  0  -0.249   2.5842  -1.1755  -0.2985
 P7B  C6    C  CT    0  -0.172   2.7007  -3.7360  -0.6690
 P7B  C7    C  CH3   0  -0.659   4.2002  -3.5314  -0.8861
 P7B  C8    C  CH3   0  -0.634   2.4985  -4.7212   0.4892
 P7B  C9    C  CH3   0  -0.628   2.0884  -4.3200  -1.9497
 P7B  C10   C  C     0   0.550   1.9337   1.3102   0.0593
 P7B  O11   O  O     0  -0.507   1.0954   2.1109  -0.3568
 P7B  N12   N  NH1   0  -0.757  -0.7557   0.1107   0.3777
 P7B  C13   C  C     0   0.734  -2.0035  -0.4163   0.5778
 P7B  O14   O  O     0  -0.493  -2.1972  -1.6189   0.6236
 P7B  N15   N  NH1   0  -0.795  -2.9766   0.5228   0.7170
 P7B  C16   C  CR6   0   0.298  -4.3407   0.2031   0.8579
 P7B  C17   C  CR16  0  -0.291  -4.7763  -0.5544   1.9132
 P7B  C18   C  CR16  0  -0.267  -6.1435  -0.8555   2.0616
 P7B  C19   C  CR16  0  -0.318  -7.0609  -0.3743   1.1700
 P7B  C20   C  CR66  0   0.095  -6.6464   0.4151   0.0730
 P7B  C21   C  CR66  0   0.086  -5.2655   0.6974  -0.1047
 P7B  C22   C  CR16  0  -0.310  -7.5780   0.9178  -0.8659
 P7B  C23   C  CR16  0  -0.256  -7.1631   1.6561  -1.9395
 P7B  C24   C  CR16  0  -0.251  -5.7909   1.9181  -2.1268
 P7B  C25   C  CR16  0  -0.307  -4.8649   1.4508  -1.2338
 P7B  N26   N  NT    0  -0.460   3.1338   1.7174   0.5425
 P7B  C27   C  CH2   0  -0.338   3.9527   0.9479   1.4593
 P7B  C28   C  CH2   0  -0.302   5.3650   0.6871   0.9522
 P7B  N29   N  NH1   0  -0.611   6.2543   1.8248   1.0516
 P7B  C30   C  C     0   0.507   6.1295   3.0029   0.4135
 P7B  C31   C  CH2   0  -0.576   4.8809   3.1996  -0.4195
 P7B  C32   C  CH2   0  -0.327   3.5585   3.0904   0.3472
 P7B  O33   O  O     0  -0.497   6.9799   3.8786   0.5082
 P7B  H5    H  HCR5  0   0.261   3.6234  -0.9793  -0.5163
 P7B  H7    H  HCH3  0   0.232   4.6887  -3.1394   0.0079
 P7B  H7A   H  HCH3  0   0.242   4.6701  -4.4864  -1.1258
 P7B  H7B   H  HCH3  0   0.233   4.4015  -2.8485  -1.7130
 P7B  H8    H  HCH3  0   0.228   1.4420  -4.9155   0.6838
 P7B  H8A   H  HCH3  0   0.233   2.9687  -5.6777   0.2520
 P7B  H8B   H  HCH3  0   0.234   2.9445  -4.3435   1.4105
 P7B  H9    H  HCH3  0   0.233   2.2064  -3.6324  -2.7885
 P7B  H9A   H  HCH3  0   0.232   2.5815  -5.2587  -2.2086
 P7B  H9B   H  HCH3  0   0.227   1.0232  -4.5290  -1.8346
 P7B  HN12  H  HNH1  0   0.426  -0.6279   1.1094   0.2669
 P7B  HN15  H  HNH1  0   0.414  -2.7382   1.4945   0.5864
 P7B  H17   H  HCR6  0   0.267  -4.0700  -0.9115   2.6504
 P7B  H18   H  HCR6  0   0.263  -6.4624  -1.4570   2.9024
 P7B  H19   H  HCR6  0   0.259  -8.1147  -0.5916   1.2935
 P7B  H22   H  HCR6  0   0.259  -8.6300   0.7033  -0.7214
 P7B  H23   H  HCR6  0   0.260  -7.8840   2.0338  -2.6526
 P7B  H24   H  HCR6  0   0.262  -5.4676   2.4877  -2.9882
 P7B  H25   H  HCR6  0   0.248  -3.8159   1.6515  -1.4061
 P7B  H27   H  HCH2  0   0.272   4.0161   1.4927   2.4071
 P7B  H27A  H  HCH2  0   0.286   3.4679   0.0017   1.6833
 P7B  H28   H  HCH2  0   0.282   5.8023  -0.0986   1.5654
 P7B  H28A  H  HCH2  0   0.251   5.3338   0.3054  -0.0731
 P7B  HN29  H  HNH1  0   0.399   7.0901   1.7060   1.6040
 P7B  H31   H  HCH2  0   0.277   4.9448   4.1976  -0.8516
 P7B  H31A  H  HCH2  0   0.274   4.8724   2.4928  -1.2554
 P7B  H32   H  HCH2  0   0.283   2.7918   3.6125  -0.2168
 P7B  H32A  H  HCH2  0   0.254   3.6381   3.5941   1.3157

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
 P7B  C1   S2    aromatic  1.742  0.020  1.742
 P7B  C1   C5    aromatic  1.353  0.020  1.353
 P7B  C1   C6    single    1.508  0.020  1.508
 P7B  S2   C3    aromatic  1.725  0.020  1.725
 P7B  C3   C4    aromatic  1.376  0.020  1.376
 P7B  C3   N12   single    1.372  0.020  1.372
 P7B  C4   C5    aromatic  1.431  0.020  1.431
 P7B  C4   C10   single    1.478  0.020  1.478
 P7B  C6   C7    single    1.529  0.020  1.529
 P7B  C6   C8    single    1.534  0.020  1.534
 P7B  C6   C9    single    1.535  0.020  1.535
 P7B  C10  O11   double    1.232  0.020  1.232
 P7B  C10  N26   single    1.356  0.020  1.356
 P7B  N12  C13   single    1.369  0.020  1.369
 P7B  C13  O14   double    1.219  0.020  1.219
 P7B  C13  N15   single    1.359  0.020  1.359
 P7B  N15  C16   single    1.408  0.020  1.408
 P7B  C16  C17   aromatic  1.370  0.020  1.370
 P7B  C16  C21   aromatic  1.423  0.020  1.423
 P7B  C17  C18   aromatic  1.408  0.020  1.408
 P7B  C18  C19   aromatic  1.367  0.020  1.367
 P7B  C19  C20   aromatic  1.414  0.020  1.414
 P7B  C20  C21   aromatic  1.421  0.020  1.421
 P7B  C20  C22   aromatic  1.415  0.020  1.415
 P7B  C21  C25   aromatic  1.415  0.020  1.415
 P7B  C22  C23   aromatic  1.367  0.020  1.367
 P7B  C23  C24   aromatic  1.410  0.020  1.410
 P7B  C24  C25   aromatic  1.369  0.020  1.369
 P7B  N26  C27   single    1.450  0.020  1.450
 P7B  N26  C32   single    1.450  0.020  1.450
 P7B  C27  C28   single    1.523  0.020  1.523
 P7B  C28  N29   single    1.447  0.020  1.447
 P7B  N29  C30   single    1.346  0.020  1.346
 P7B  C30  C31   single    1.514  0.020  1.514
 P7B  C30  O33   double    1.224  0.020  1.224
 P7B  C31  C32   single    1.533  0.020  1.533
 P7B  C5   H5    single    0.930  0.020  1.080
 P7B  C7   H7    single    0.970  0.020  1.090
 P7B  C7   H7A   single    0.970  0.020  1.090
 P7B  C7   H7B   single    0.970  0.020  1.090
 P7B  C8   H8    single    0.970  0.020  1.090
 P7B  C8   H8A   single    0.970  0.020  1.090
 P7B  C8   H8B   single    0.970  0.020  1.090
 P7B  C9   H9    single    0.970  0.020  1.090
 P7B  C9   H9A   single    0.970  0.020  1.090
 P7B  C9   H9B   single    0.970  0.020  1.090
 P7B  N12  HN12  single    0.860  0.020  1.020
 P7B  N15  HN15  single    0.860  0.020  1.020
 P7B  C17  H17   single    0.930  0.020  1.080
 P7B  C18  H18   single    0.930  0.020  1.080
 P7B  C19  H19   single    0.930  0.020  1.080
 P7B  C22  H22   single    0.930  0.020  1.080
 P7B  C23  H23   single    0.930  0.020  1.080
 P7B  C24  H24   single    0.930  0.020  1.080
 P7B  C25  H25   single    0.930  0.020  1.080
 P7B  C27  H27   single    0.970  0.020  1.090
 P7B  C27  H27A  single    0.970  0.020  1.090
 P7B  C28  H28   single    0.970  0.020  1.090
 P7B  C28  H28A  single    0.970  0.020  1.090
 P7B  N29  HN29  single    0.860  0.020  1.020
 P7B  C31  H31   single    0.970  0.020  1.090
 P7B  C31  H31A  single    0.970  0.020  1.090
 P7B  C32  H32   single    0.970  0.020  1.090
 P7B  C32  H32A  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
 P7B  C6    C1   C5   129.61  3.000
 P7B  C6    C1   S2   119.86  3.000
 P7B  C5    C1   S2   110.52  3.000
 P7B  C3    S2   C1    91.95  3.000
 P7B  N12   C3   C4   125.56  3.000
 P7B  N12   C3   S2   122.77  3.000
 P7B  C4    C3   S2   111.67  3.000
 P7B  C10   C4   C5   126.20  3.000
 P7B  C10   C4   C3   122.09  3.000
 P7B  C5    C4   C3   111.48  3.000
 P7B  H5    C5   C4   122.82  3.000
 P7B  H5    C5   C1   122.82  3.000
 P7B  C4    C5   C1   114.31  3.000
 P7B  C9    C6   C8   109.45  3.000
 P7B  C9    C6   C7   108.89  3.000
 P7B  C8    C6   C7   108.81  3.000
 P7B  C9    C6   C1   109.69  3.000
 P7B  C8    C6   C1   110.17  3.000
 P7B  C7    C6   C1   109.81  3.000
 P7B  H7B   C7   H7A  107.57  3.000
 P7B  H7B   C7   H7   108.26  3.000
 P7B  H7A   C7   H7   107.55  3.000
 P7B  H7B   C7   C6   111.86  3.000
 P7B  H7A   C7   C6   109.67  3.000
 P7B  H7    C7   C6   111.76  3.000
 P7B  H8B   C8   H8A  108.09  3.000
 P7B  H8B   C8   H8   107.86  3.000
 P7B  H8A   C8   H8   107.44  3.000
 P7B  H8B   C8   C6   111.18  3.000
 P7B  H8A   C8   C6   109.99  3.000
 P7B  H8    C8   C6   112.12  3.000
 P7B  H9B   C9   H9A  107.53  3.000
 P7B  H9B   C9   H9   107.89  3.000
 P7B  H9A   C9   H9   108.11  3.000
 P7B  H9B   C9   C6   111.97  3.000
 P7B  H9A   C9   C6   110.18  3.000
 P7B  H9    C9   C6   111.01  3.000
 P7B  N26   C10  O11  121.83  3.000
 P7B  N26   C10  C4   118.51  3.000
 P7B  O11   C10  C4   119.64  3.000
 P7B  HN12  N12  C13  120.69  3.000
 P7B  HN12  N12  C3   114.54  3.000
 P7B  C13   N12  C3   124.32  3.000
 P7B  N15   C13  O14  124.33  3.000
 P7B  N15   C13  N12  113.67  3.000
 P7B  O14   C13  N12  122.01  3.000
 P7B  HN15  N15  C16  117.41  3.000
 P7B  HN15  N15  C13  118.87  3.000
 P7B  C16   N15  C13  123.15  3.000
 P7B  C21   C16  C17  120.42  3.000
 P7B  C21   C16  N15  118.88  3.000
 P7B  C17   C16  N15  120.70  3.000
 P7B  H17   C17  C18  119.46  3.000
 P7B  H17   C17  C16  119.99  3.000
 P7B  C18   C17  C16  120.55  3.000
 P7B  H18   C18  C19  120.32  3.000
 P7B  H18   C18  C17  119.15  3.000
 P7B  C19   C18  C17  120.52  3.000
 P7B  H19   C19  C20  119.07  3.000
 P7B  H19   C19  C18  120.53  3.000
 P7B  C20   C19  C18  120.39  3.000
 P7B  C22   C20  C21  119.10  3.000
 P7B  C22   C20  C19  121.35  3.000
 P7B  C21   C20  C19  119.54  3.000
 P7B  C25   C21  C20  118.73  3.000
 P7B  C25   C21  C16  122.72  3.000
 P7B  C20   C21  C16  118.55  3.000
 P7B  H22   C22  C23  120.42  3.000
 P7B  H22   C22  C20  118.71  3.000
 P7B  C23   C22  C20  120.86  3.000
 P7B  H23   C23  C24  119.74  3.000
 P7B  H23   C23  C22  120.25  3.000
 P7B  C24   C23  C22  120.01  3.000
 P7B  H24   C24  C25  119.80  3.000
 P7B  H24   C24  C23  119.64  3.000
 P7B  C25   C24  C23  120.56  3.000
 P7B  H25   C25  C24  119.26  3.000
 P7B  H25   C25  C21  120.02  3.000
 P7B  C24   C25  C21  120.72  3.000
 P7B  C32   N26  C27  114.97  3.000
 P7B  C32   N26  C10  119.69  3.000
 P7B  C27   N26  C10  124.44  3.000
 P7B  H27A  C27  H27  106.30  3.000
 P7B  H27A  C27  C28  109.47  3.000
 P7B  H27   C27  C28  108.64  3.000
 P7B  H27A  C27  N26  109.91  3.000
 P7B  H27   C27  N26  108.41  3.000
 P7B  C28   C27  N26  113.83  3.000
 P7B  H28A  C28  H28  106.71  3.000
 P7B  H28A  C28  N29  110.85  3.000
 P7B  H28   C28  N29  106.37  3.000
 P7B  H28A  C28  C27  110.19  3.000
 P7B  H28   C28  C27  107.98  3.000
 P7B  N29   C28  C27  114.34  3.000
 P7B  HN29  N29  C30  116.08  3.000
 P7B  HN29  N29  C28  117.00  3.000
 P7B  C30   N29  C28  126.77  3.000
 P7B  O33   C30  C31  121.50  3.000
 P7B  O33   C30  N29  121.68  3.000
 P7B  C31   C30  N29  116.82  3.000
 P7B  H31A  C31  H31  106.80  3.000
 P7B  H31A  C31  C32  109.23  3.000
 P7B  H31   C31  C32  108.32  3.000
 P7B  H31A  C31  C30  110.04  3.000
 P7B  H31   C31  C30  106.80  3.000
 P7B  C32   C31  C30  115.29  3.000
 P7B  H32A  C32  H32  106.84  3.000
 P7B  H32A  C32  C31  110.31  3.000
 P7B  H32   C32  C31  108.38  3.000
 P7B  H32A  C32  N26  109.74  3.000
 P7B  H32   C32  N26  108.57  3.000
 P7B  C31   C32  N26  112.80  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
 P7B  CONST_01  C4    C3   S2   C1      0.00   0.0  0
 P7B  CONST_02  C3    C4   C5   C1      0.00   0.0  0
 P7B  CONST_03  C4    C5   C1   S2      0.00   0.0  0
 P7B  CONST_04  C5    C4   C3   S2      0.00   0.0  0
 P7B  CONST_05  C5    C1   S2   C3      0.00   0.0  0
 P7B  CONST_06  C19   C18  C17  C16     0.00   0.0  0
 P7B  CONST_07  C19   C20  C21  C16     0.00   0.0  0
 P7B  CONST_08  C22   C20  C21  C16   180.00   0.0  0
 P7B  CONST_09  C24   C25  C21  C16   180.00   0.0  0
 P7B  CONST_10  C20   C21  C16  C17     0.00   0.0  0
 P7B  CONST_11  C25   C21  C16  C17   180.00   0.0  0
 P7B  CONST_12  C20   C19  C18  C17     0.00   0.0  0
 P7B  CONST_13  C21   C16  C17  C18     0.00   0.0  0
 P7B  CONST_14  C21   C20  C19  C18     0.00   0.0  0
 P7B  CONST_15  C22   C20  C19  C18   180.00   0.0  0
 P7B  CONST_16  C25   C21  C20  C19   180.00   0.0  0
 P7B  CONST_17  C23   C22  C20  C19   180.00   0.0  0
 P7B  CONST_18  C24   C25  C21  C20     0.00   0.0  0
 P7B  CONST_19  C24   C23  C22  C20     0.00   0.0  0
 P7B  CONST_20  C23   C22  C20  C21     0.00   0.0  0
 P7B  CONST_21  C23   C24  C25  C21     0.00   0.0  0
 P7B  CONST_22  C25   C21  C20  C22     0.00   0.0  0
 P7B  CONST_23  C25   C24  C23  C22     0.00   0.0  0
 P7B  CONST_24  N12   C3   S2   C1    180.00   0.0  0
 P7B  CONST_25  C10   C4   C5   C1    180.00   0.0  0
 P7B  CONST_26  C10   C4   C3   S2    180.00   0.0  0
 P7B  CONST_27  C6    C1   S2   C3    180.00   0.0  0
 P7B  CONST_28  C6    C1   C5   C4    180.00   0.0  0
 P7B  CONST_29  N12   C3   C4   C5    180.00   0.0  0
 P7B  CONST_30  C18   C17  C16  N15   180.00   0.0  0
 P7B  CONST_31  C20   C21  C16  N15   180.00   0.0  0
 P7B  CONST_32  C25   C21  C16  N15     0.00   0.0  0
 P7B  CONST_33  H5    C5   C1   S2    180.00   0.0  0
 P7B  CONST_34  H18   C18  C17  C16   180.00   0.0  0
 P7B  CONST_35  H25   C25  C21  C16     0.00   0.0  0
 P7B  CONST_36  H19   C19  C18  C17   180.00   0.0  0
 P7B  CONST_37  H17   C17  C18  C19   180.00   0.0  0
 P7B  CONST_38  H22   C22  C20  C19     0.00   0.0  0
 P7B  CONST_39  H23   C23  C22  C20   180.00   0.0  0
 P7B  CONST_40  H24   C24  C25  C21   180.00   0.0  0
 P7B  CONST_41  C13   N12  C3   S2      0.00   0.0  0
 P7B  CONST_42  C13   N12  C3   C4    180.00   0.0  0
 P7B  CONST_45  HN12  N12  C3   S2    180.00   0.0  0
 P7B  CONST_47  O14   C13  N12  C3      0.00   0.0  0
 P7B  CONST_48  C16   N15  C13  O14     0.00   0.0  0
 P7B  CONST_49  N15   C13  N12  C3    180.00   0.0  0
 P7B  CONST_50  C16   N15  C13  N12   180.00   0.0  0
 P7B  Var_01    N26   C10  C4   C3    149.05  30.0  2
 P7B  Var_02    C7    C6   C1   S2   -178.43  30.0  2
 P7B  Var_03    H7    C7   C6   C1     61.31  30.0  3
 P7B  Var_04    H8    C8   C6   C1     60.20  30.0  3
 P7B  Var_05    H9    C9   C6   C1     58.26  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
 P7B  plan-1  C1    0.020
 P7B  plan-1  S2    0.020
 P7B  plan-1  C3    0.020
 P7B  plan-1  C4    0.020
 P7B  plan-1  C5    0.020
 P7B  plan-1  C6    0.020
 P7B  plan-1  C10   0.020
 P7B  plan-1  N12   0.020
 P7B  plan-1  H5    0.020
 P7B  plan-2  N15   0.020
 P7B  plan-2  C16   0.020
 P7B  plan-2  C17   0.020
 P7B  plan-2  C18   0.020
 P7B  plan-2  C19   0.020
 P7B  plan-2  C20   0.020
 P7B  plan-2  C21   0.020
 P7B  plan-2  C22   0.020
 P7B  plan-2  C23   0.020
 P7B  plan-2  C24   0.020
 P7B  plan-2  C25   0.020
 P7B  plan-2  H17   0.020
 P7B  plan-2  H18   0.020
 P7B  plan-2  H19   0.020
 P7B  plan-2  H22   0.020
 P7B  plan-2  H23   0.020
 P7B  plan-2  H24   0.020
 P7B  plan-2  H25   0.020
 P7B  plan-3  C3    0.020
 P7B  plan-3  N12   0.020
 P7B  plan-3  C13   0.020
 P7B  plan-3  O14   0.020
 P7B  plan-3  N15   0.020
 P7B  plan-3  C16   0.020
 P7B  plan-3  HN12  0.020
 P7B  plan-3  HN15  0.020
 P7B  plan-4  C28   0.020
 P7B  plan-4  N29   0.020
 P7B  plan-4  C30   0.020
 P7B  plan-4  C31   0.020
 P7B  plan-4  O33   0.020
 P7B  plan-4  HN29  0.020
 P7B  plan-5  C4    0.020
 P7B  plan-5  C10   0.020
 P7B  plan-5  O11   0.020
 P7B  plan-5  N26   0.020
 P7B  plan-5  C27   0.020
 P7B  plan-5  C32   0.020

