# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 07:46:04 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (4R)-1-(2'-chloro[1,1'-biphenyl]-3-yl)-4-[4-(1,3-thiazole-2-carbonyl)piperazin-1-yl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1c2cccc(c2)N3C[C@@H](CC3=O)N4CCN(CC4)C(=O)c5sccn5
#
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
 9JX  9JX  (4R)-1-(2'-chloro[1,1'-biphenyl]-3-yl)-4-[4-(1,3-thiazole-2-carbonyl)piperazin-1-yl]pyrrolidin-2-one  ligand  55  32  .  2022-07-24  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_9JX
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
 9JX  C4   C   CR16  0  -0.171   6.8488   0.9510  -1.7210
 9JX  C5   C   CR16  0  -0.231   5.2228   2.0331   0.6267
 9JX  C6   C   CR16  0  -0.252   2.9079   1.9793   1.2841
 9JX  C7   C   CR16  0  -0.277   7.8148  -1.5784  -1.1668
 9JX  C8   C   CR16  0  -0.271   3.8466   0.1496   0.0326
 9JX  C10  C   CR15  0  -0.403  -8.7944  -0.7461  -2.1908
 9JX  C13  C   CR6   0   0.329   2.7569   0.7345   0.6727
 9JX  C15  C   CR5   0   0.044  -6.8824   0.2112  -1.0744
 9JX  C20  C   CH2   0  -0.339  -4.4956  -0.4070   0.6664
 9JX  C21  C   CH2   0  -0.291  -2.5113   1.5408   0.1619
 9JX  C22  C   CH2   0  -0.267  -3.0822  -0.7669   0.2357
 9JX  C24  C   CH1   0  -0.075  -0.7826  -0.1034   0.2266
 9JX  C1   C   CR16  0  -0.290   7.9255   0.4537  -2.4390
 9JX  C2   C   CR16  0  -0.188   8.4081  -0.8185  -2.1617
 9JX  C3   C   CR16  0  -0.317   4.1353   2.6208   1.2553
 9JX  C9   C   CR15  0  -0.070  -8.0951  -1.5934  -1.3851
 9JX  C11  C   CR6   0  -0.034   5.0808   0.7913   0.0121
 9JX  C12  C   CR6   0   0.051   6.2257   0.2032  -0.7194
 9JX  C14  C   CR6   0  -0.067   6.7374  -1.0678  -0.4599
 9JX  C16  C   C     0   0.604   1.2594  -1.2145   0.7612
 9JX  C18  C   CH2   0  -0.635  -0.2364  -1.4115   0.7900
 9JX  C19  C   CH2   0  -0.300  -3.9112   1.9171   0.6109
 9JX  C23  C   CH2   0  -0.310   0.2659   0.8999   0.7004
 9JX  N25  N   N     0  -0.305  -7.0195  -1.0387  -0.7633
 9JX  N26  N   NT    0  -0.591   1.4934   0.1212   0.6562
 9JX  N27  N   NT    0  -0.490  -4.8672   0.9082   0.1777
 9JX  N28  N   NT    0  -0.477  -2.1208   0.2313   0.6646
 9JX  O30  O   O     0  -0.537  -6.0784   2.3752  -1.0439
 9JX  S31  S   S2    0   0.078  -8.0836   0.8019  -2.1666
 9JX  CL1  CL  CL    0  -0.126   6.0704  -2.0438   0.8099
 9JX  H1   H   HCR6  0   0.272   6.4643   1.9377  -1.9460
 9JX  H2   H   HCR6  0   0.270   6.1804   2.5373   0.6174
 9JX  H3   H   HCR6  0   0.290   2.0702   2.4519   1.7788
 9JX  H4   H   HCR6  0   0.264   8.1920  -2.5656  -0.9366
 9JX  H5   H   HCR6  0   0.313   3.7287  -0.7910  -0.4851
 9JX  H7   H   HCH2  0   0.240  -5.1849  -1.1630   0.3103
 9JX  H8   H   HCH2  0   0.275  -4.5488  -0.3904   1.7589
 9JX  H9   H   HCH2  0   0.249  -2.4646   1.5814  -0.9404
 9JX  H10  H   HCH2  0   0.263  -1.8273   2.3018   0.5432
 9JX  H11  H   HCH2  0   0.228  -2.8865  -1.7248   0.7035
 9JX  H12  H   HCH2  0   0.272  -3.0633  -0.9103  -0.8590
 9JX  H13  H   HCH1  0   0.226  -0.7204  -0.1434  -0.8753
 9JX  H14  H   HCR6  0   0.238   8.3817   1.0560  -3.2136
 9JX  H15  H   HCR6  0   0.272   9.2469  -1.2227  -2.7138
 9JX  H16  H   HCR6  0   0.233   4.2441   3.5861   1.7325
 9JX  H17  H   HCR5  0   0.304  -8.3364  -2.6333  -1.2174
 9JX  H18  H   HCH2  0   0.286  -0.5449  -1.5431   1.8337
 9JX  H19  H   HCH2  0   0.310  -0.5223  -2.3071   0.2385
 9JX  H20  H   HCH2  0   0.254  -3.9441   1.9768   1.7023
 9JX  H21  H   HCH2  0   0.283  -4.1809   2.8907   0.2116
 9JX  H22  H   HCH2  0   0.278   0.3469   1.7769   0.0591
 9JX  H23  H   HCH2  0   0.283   0.0350   1.2326   1.7178
 9JX  O29  O   O     0  -0.548   2.1115  -2.0777   0.8402
 9JX  C17  C   C     0   0.536  -5.8842   1.2339  -0.6329
 9JX  H6   H   HCR5  0   0.317  -9.6767  -0.9645  -2.7746

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
 9JX  C10  C9   aromatic  1.362  0.020  1.362
 9JX  C10  S31  aromatic  1.703  0.020  1.703
 9JX  C9   N25  aromatic  1.361  0.020  1.361
 9JX  S31  C15  aromatic  1.728  0.020  1.728
 9JX  N25  C15  aromatic  1.295  0.020  1.295
 9JX  C15  C17  single    1.496  0.020  1.496
 9JX  C17  O30  double    1.229  0.020  1.229
 9JX  C17  N27  single    1.341  0.020  1.341
 9JX  C19  N27  single    1.456  0.020  1.456
 9JX  C19  C21  single    1.518  0.020  1.518
 9JX  N27  C20  single    1.451  0.020  1.451
 9JX  C21  N28  single    1.456  0.020  1.456
 9JX  C1   C2   aromatic  1.389  0.020  1.389
 9JX  C1   C4   aromatic  1.386  0.020  1.386
 9JX  C2   C7   aromatic  1.385  0.020  1.385
 9JX  C20  C22  single    1.521  0.020  1.521
 9JX  N28  C22  single    1.451  0.020  1.451
 9JX  N28  C24  single    1.447  0.020  1.447
 9JX  C4   C12  aromatic  1.397  0.020  1.397
 9JX  C7   C14  aromatic  1.386  0.020  1.386
 9JX  C23  C24  single    1.527  0.020  1.527
 9JX  C23  N26  single    1.454  0.020  1.454
 9JX  C14  C12  aromatic  1.394  0.020  1.394
 9JX  C14  CL1  single    1.735  0.020  1.735
 9JX  C12  C11  single    1.480  0.020  1.480
 9JX  C24  C18  single    1.525  0.020  1.525
 9JX  C8   C11  aromatic  1.391  0.020  1.391
 9JX  C8   C13  aromatic  1.393  0.020  1.393
 9JX  C11  C5   aromatic  1.393  0.020  1.393
 9JX  N26  C13  single    1.405  0.020  1.405
 9JX  N26  C16  single    1.360  0.020  1.360
 9JX  C18  C16  single    1.509  0.020  1.509
 9JX  C13  C6   aromatic  1.395  0.020  1.395
 9JX  C5   C3   aromatic  1.387  0.020  1.387
 9JX  C16  O29  double    1.215  0.020  1.215
 9JX  C6   C3   aromatic  1.385  0.020  1.385
 9JX  C4   H1   single    0.930  0.020  1.080
 9JX  C5   H2   single    0.930  0.020  1.080
 9JX  C6   H3   single    0.930  0.020  1.080
 9JX  C7   H4   single    0.930  0.020  1.080
 9JX  C8   H5   single    0.930  0.020  1.080
 9JX  C10  H6   single    0.930  0.020  1.080
 9JX  C20  H7   single    0.970  0.020  1.090
 9JX  C20  H8   single    0.970  0.020  1.090
 9JX  C21  H9   single    0.970  0.020  1.090
 9JX  C21  H10  single    0.970  0.020  1.090
 9JX  C22  H11  single    0.970  0.020  1.090
 9JX  C22  H12  single    0.970  0.020  1.090
 9JX  C24  H13  single    0.970  0.020  1.090
 9JX  C1   H14  single    0.930  0.020  1.080
 9JX  C2   H15  single    0.930  0.020  1.080
 9JX  C3   H16  single    0.930  0.020  1.080
 9JX  C9   H17  single    0.930  0.020  1.080
 9JX  C18  H18  single    0.970  0.020  1.090
 9JX  C18  H19  single    0.970  0.020  1.090
 9JX  C19  H20  single    0.970  0.020  1.090
 9JX  C19  H21  single    0.970  0.020  1.090
 9JX  C23  H22  single    0.970  0.020  1.090
 9JX  C23  H23  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
 9JX  H1   C4   C12  118.59  3.000
 9JX  H1   C4   C1   119.68  3.000
 9JX  C12  C4   C1   121.72  3.000
 9JX  H2   C5   C11  120.12  3.000
 9JX  H2   C5   C3   120.02  3.000
 9JX  C11  C5   C3   119.86  3.000
 9JX  H3   C6   C3   119.57  3.000
 9JX  H3   C6   C13  120.43  3.000
 9JX  C3   C6   C13  120.00  3.000
 9JX  H4   C7   C14  119.91  3.000
 9JX  H4   C7   C2   120.28  3.000
 9JX  C14  C7   C2   119.81  3.000
 9JX  H5   C8   C11  119.44  3.000
 9JX  H5   C8   C13  120.05  3.000
 9JX  C11  C8   C13  120.48  3.000
 9JX  H6   C10  S31  122.15  3.000
 9JX  H6   C10  C9   127.81  3.000
 9JX  S31  C10  C9   110.04  3.000
 9JX  N26  C13  C8   121.00  3.000
 9JX  N26  C13  C6   119.48  3.000
 9JX  C8   C13  C6   119.45  3.000
 9JX  S31  C15  N25  114.09  3.000
 9JX  N25  C15  C17  131.26  3.000
 9JX  S31  C15  C17  114.64  3.000
 9JX  H8   C20  H7   107.94  3.000
 9JX  H8   C20  N27  108.07  3.000
 9JX  H7   C20  N27  111.02  3.000
 9JX  H8   C20  C22  109.37  3.000
 9JX  H7   C20  C22  109.46  3.000
 9JX  N27  C20  C22  110.91  3.000
 9JX  H10  C21  H9   107.26  3.000
 9JX  H10  C21  N28  109.77  3.000
 9JX  H9   C21  N28  111.49  3.000
 9JX  H10  C21  C19  107.56  3.000
 9JX  H9   C21  C19  108.99  3.000
 9JX  N28  C21  C19  111.60  3.000
 9JX  H12  C22  H11  108.06  3.000
 9JX  H12  C22  N28  111.79  3.000
 9JX  H11  C22  N28  111.16  3.000
 9JX  H12  C22  C20  109.11  3.000
 9JX  H11  C22  C20  104.75  3.000
 9JX  N28  C22  C20  111.67  3.000
 9JX  H13  C24  N28  111.24  3.000
 9JX  H13  C24  C23  107.15  3.000
 9JX  N28  C24  C23  112.90  3.000
 9JX  H13  C24  C18  108.49  3.000
 9JX  C23  C24  C18  101.72  3.000
 9JX  N28  C24  C18  114.68  3.000
 9JX  H14  C1   C2   120.42  3.000
 9JX  H14  C1   C4   119.90  3.000
 9JX  C2   C1   C4   119.68  3.000
 9JX  H15  C2   C1   120.64  3.000
 9JX  H15  C2   C7   119.55  3.000
 9JX  C1   C2   C7   119.81  3.000
 9JX  H16  C3   C6   119.53  3.000
 9JX  H16  C3   C5   119.93  3.000
 9JX  C6   C3   C5   120.54  3.000
 9JX  H17  C9   N25  119.86  3.000
 9JX  H17  C9   C10  125.14  3.000
 9JX  N25  C9   C10  114.99  3.000
 9JX  C12  C11  C8   120.67  3.000
 9JX  C8   C11  C5   119.68  3.000
 9JX  C12  C11  C5   119.56  3.000
 9JX  C14  C12  C11  123.63  3.000
 9JX  C11  C12  C4   119.12  3.000
 9JX  C14  C12  C4   117.25  3.000
 9JX  CL1  C14  C12  120.53  3.000
 9JX  CL1  C14  C7   117.70  3.000
 9JX  C12  C14  C7   121.74  3.000
 9JX  O29  C16  N26  125.59  3.000
 9JX  O29  C16  C18  126.94  3.000
 9JX  N26  C16  C18  107.47  3.000
 9JX  H19  C18  H18  108.01  3.000
 9JX  H19  C18  C16  110.95  3.000
 9JX  H18  C18  C16  108.23  3.000
 9JX  H19  C18  C24  115.08  3.000
 9JX  H18  C18  C24  110.72  3.000
 9JX  C16  C18  C24  103.65  3.000
 9JX  H21  C19  H20  108.09  3.000
 9JX  H21  C19  N27  110.41  3.000
 9JX  H20  C19  N27  108.37  3.000
 9JX  H21  C19  C21  110.02  3.000
 9JX  H20  C19  C21  109.67  3.000
 9JX  N27  C19  C21  110.24  3.000
 9JX  H23  C23  H22  108.54  3.000
 9JX  H23  C23  N26  111.65  3.000
 9JX  H22  C23  N26  110.51  3.000
 9JX  H23  C23  C24  110.07  3.000
 9JX  H22  C23  C24  113.42  3.000
 9JX  N26  C23  C24  102.61  3.000
 9JX  C9   N25  C15  111.55  3.000
 9JX  C23  N26  C16  112.23  3.000
 9JX  C16  N26  C13  125.64  3.000
 9JX  C23  N26  C13  121.67  3.000
 9JX  C19  N27  C20  111.08  3.000
 9JX  C20  N27  C17  128.16  3.000
 9JX  C19  N27  C17  120.65  3.000
 9JX  C24  N28  C22  111.35  3.000
 9JX  C24  N28  C21  110.58  3.000
 9JX  C22  N28  C21  109.82  3.000
 9JX  C15  S31  C10   89.33  3.000
 9JX  O30  C17  N27  123.22  3.000
 9JX  N27  C17  C15  121.24  3.000
 9JX  O30  C17  C15  115.53  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
 9JX  CONST_01  C7   C2   C1   C4     0.00   0.0  0
 9JX  CONST_02  C7   C14  C12  C4     0.00   0.0  0
 9JX  CONST_06  C13  C8   C11  C5     0.00   0.0  0
 9JX  CONST_07  C13  C6   C3   C5     0.00   0.0  0
 9JX  CONST_08  C11  C8   C13  C6     0.00   0.0  0
 9JX  CONST_09  C11  C5   C3   C6     0.00   0.0  0
 9JX  CONST_10  C11  C12  C14  C7   180.00   0.0  0
 9JX  CONST_12  C3   C5   C11  C8     0.00   0.0  0
 9JX  CONST_13  C3   C6   C13  C8     0.00   0.0  0
 9JX  CONST_14  C15  N25  C9   C10    0.00   0.0  0
 9JX  CONST_15  N25  C15  S31  C10    0.00   0.0  0
 9JX  CONST_16  C12  C11  C8   C13  180.00   0.0  0
 9JX  CONST_17  C9   C10  S31  C15    0.00   0.0  0
 9JX  CONST_18  C14  C7   C2   C1     0.00   0.0  0
 9JX  CONST_19  C14  C12  C4   C1     0.00   0.0  0
 9JX  CONST_20  C11  C12  C4   C1   180.00   0.0  0
 9JX  CONST_21  C12  C4   C1   C2     0.00   0.0  0
 9JX  CONST_22  C12  C14  C7   C2     0.00   0.0  0
 9JX  CONST_23  C12  C11  C5   C3   180.00   0.0  0
 9JX  CONST_24  S31  C15  N25  C9     0.00   0.0  0
 9JX  CONST_25  S31  C10  C9   N25    0.00   0.0  0
 9JX  CONST_26  N26  C13  C6   C3   180.00   0.0  0
 9JX  CONST_27  N26  C13  C8   C11  180.00   0.0  0
 9JX  CONST_28  C18  C16  N26  C13  180.00   0.0  0
 9JX  CONST_29  C23  N26  C16  C18    0.00   0.0  0
 9JX  CONST_30  CL1  C14  C12  C4   180.00   0.0  0
 9JX  CONST_31  C17  C15  S31  C10  180.00   0.0  0
 9JX  CONST_32  C9   N25  C15  C17  180.00   0.0  0
 9JX  CONST_33  CL1  C14  C7   C2   180.00   0.0  0
 9JX  CONST_34  CL1  C14  C12  C11    0.00   0.0  0
 9JX  CONST_35  C19  N27  C17  C15  180.00   0.0  0
 9JX  CONST_36  C20  N27  C17  C15    0.00   0.0  0
 9JX  CONST_37  O29  C16  N26  C13    0.00   0.0  0
 9JX  CONST_38  O29  C16  N26  C23  180.00   0.0  0
 9JX  CONST_39  H15  C2   C1   C4   180.00   0.0  0
 9JX  CONST_40  H5   C8   C11  C5   180.00   0.0  0
 9JX  CONST_41  H3   C6   C3   C5   180.00   0.0  0
 9JX  CONST_42  H2   C5   C3   C6   180.00   0.0  0
 9JX  CONST_43  H14  C1   C2   C7   180.00   0.0  0
 9JX  CONST_44  H16  C3   C6   C13  180.00   0.0  0
 9JX  CONST_45  H6   C10  S31  C15  180.00   0.0  0
 9JX  CONST_46  H17  C9   N25  C15  180.00   0.0  0
 9JX  CONST_47  H4   C7   C2   C1   180.00   0.0  0
 9JX  CONST_48  H1   C4   C1   C2   180.00   0.0  0
 9JX  CONST_49  O30  C17  N27  C20  180.00   0.0  0
 9JX  CONST_50  O30  C17  N27  C19    0.00   0.0  0
 9JX  Var_01    C23  N26  C13  C6    27.33  30.0  2
 9JX  Var_02    C24  C23  N26  C13  162.90  30.0  1
 9JX  Var_03    C21  C19  N27  C20   56.32  30.0  1
 9JX  Var_04    C21  N28  C22  C20  -55.95  30.0  1
 9JX  Var_05    C19  N27  C20  C22  -55.76  30.0  1
 9JX  Var_06    C19  C21  N28  C22   56.87  30.0  1
 9JX  Var_07    N26  C16  C18  C24   18.33  30.0  1
 9JX  Var_08    N28  C21  C19  N27  -57.26  30.0  1
 9JX  Var_09    N28  C22  C20  N27   55.95  30.0  1
 9JX  Var_10    N27  C17  C15  N25    3.70  30.0  2

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
 9JX  chir_01  C24  N28  C23  C18  negativ

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
 9JX  plan-1  C10  0.020
 9JX  plan-1  C15  0.020
 9JX  plan-1  C9   0.020
 9JX  plan-1  N25  0.020
 9JX  plan-1  S31  0.020
 9JX  plan-1  H17  0.020
 9JX  plan-1  C17  0.020
 9JX  plan-1  H6   0.020
 9JX  plan-2  C5   0.020
 9JX  plan-2  C6   0.020
 9JX  plan-2  C8   0.020
 9JX  plan-2  C13  0.020
 9JX  plan-2  C3   0.020
 9JX  plan-2  C11  0.020
 9JX  plan-2  C12  0.020
 9JX  plan-2  N26  0.020
 9JX  plan-2  H2   0.020
 9JX  plan-2  H3   0.020
 9JX  plan-2  H5   0.020
 9JX  plan-2  H16  0.020
 9JX  plan-3  C4   0.020
 9JX  plan-3  C7   0.020
 9JX  plan-3  C1   0.020
 9JX  plan-3  C2   0.020
 9JX  plan-3  C11  0.020
 9JX  plan-3  C12  0.020
 9JX  plan-3  C14  0.020
 9JX  plan-3  CL1  0.020
 9JX  plan-3  H1   0.020
 9JX  plan-3  H4   0.020
 9JX  plan-3  H14  0.020
 9JX  plan-3  H15  0.020
 9JX  plan-4  C15  0.020
 9JX  plan-4  C20  0.020
 9JX  plan-4  C19  0.020
 9JX  plan-4  N27  0.020
 9JX  plan-4  O30  0.020
 9JX  plan-4  C17  0.020
 9JX  plan-5  C13  0.020
 9JX  plan-5  C16  0.020
 9JX  plan-5  C18  0.020
 9JX  plan-5  C23  0.020
 9JX  plan-5  N26  0.020
 9JX  plan-5  O29  0.020

