# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:15:12 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)pyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@]1(CCN(C1=O)c2ccc3NC(=O)CCc3c2)C(=O)NCc4cc(F)cc(Cl)c4
#
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
 HZK  HZK  (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)pyrrolidine-3-carboxamide  ligand  49  30  .  2022-07-25  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_HZK
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
 HZK  C1   C   CR6   0   0.086  -4.3956   0.5268   0.3235
 HZK  C2   C   CR16  0  -0.269  -3.5483  -0.3525  -0.3379
 HZK  C3   C   CR6   0  -0.006  -3.9983  -1.6303  -0.6386
 HZK  C8   C   CR6   0   0.358   3.0388   1.0073  -0.1445
 HZK  C10  C   CH2   0  -0.291   1.9559   3.2405   0.2175
 HZK  C11  C   CH2   0  -0.466   0.5280   3.5969   0.6172
 HZK  C12  C   CT    0  -0.021  -0.3195   2.5640  -0.1123
 HZK  C13  C   C     0   0.549   0.6290   1.3625  -0.2321
 HZK  C15  C   C     0   0.537  -1.5443   2.1322   0.6906
 HZK  C19  C   CH2   0  -0.326  -3.9734   1.9306   0.6983
 HZK  C21  C   CR16  0  -0.372   3.1071  -0.2617   0.4255
 HZK  C22  C   CR16  0  -0.321   5.2796   0.7333  -0.9764
 HZK  C24  C   CR66  0   0.365   5.3370  -0.5360  -0.4159
 HZK  C27  C   C     0  -0.594   5.2460  -3.2963   0.0706
 HZK  N29  N   NR16  0  -0.733   6.4896  -1.3123  -0.5350
 HZK  C4   C   CR16  0  -0.386  -5.2690  -2.0633  -0.3037
 HZK  C5   C   CR6   0   0.550  -6.0842  -1.1612   0.3548
 HZK  C6   C   CR16  0  -0.444  -5.6791   0.1165   0.6752
 HZK  CL7  CL  CL    0  -0.114  -2.9352  -2.7214  -1.4607
 HZK  N9   N   NT    0  -0.582   1.8833   1.7997   0.0054
 HZK  O14  O   OH1   0  -0.655  -0.6135   3.0342  -1.4036
 HZK  O16  O   O     0  -0.455   0.2850   0.2466  -0.5682
 HZK  N17  N   NH1   0  -0.636  -2.7302   2.3520   0.1133
 HZK  O18  O   O     0  -0.472  -1.3959   1.6059   1.7819
 HZK  F20  F   F     0  -0.310  -7.3217  -1.5503   0.6885
 HZK  C23  C   CR16  0  -0.311   4.1348   1.5015  -0.8414
 HZK  C25  C   CR66  0   0.070   4.2477  -1.0358   0.2998
 HZK  C26  C   C     0  -0.491   4.3958  -2.3820   0.9424
 HZK  C28  C   CR6   0   0.506   6.5494  -2.6563  -0.3364
 HZK  O30  O   O     0  -0.467   7.5809  -3.2805  -0.5099
 HZK  H1   H   HCR6  0   0.268  -2.5475  -0.0602  -0.6251
 HZK  H2   H   HCH2  0   0.261   2.2630   3.7553  -0.6954
 HZK  H3   H   HCH2  0   0.278   0.4106   3.4821   1.6941
 HZK  H4   H   HCH2  0   0.286  -4.7488   2.6317   0.3895
 HZK  H5   H   HCH2  0   0.278  -3.8997   2.0014   1.7846
 HZK  H6   H   HCR6  0   0.265   2.2744  -0.6500   0.9972
 HZK  H7   H   HCR6  0   0.274   6.1252   1.1243  -1.5285
 HZK  H8   H   H     0   0.281   5.4634  -4.2358   0.5763
 HZK  H9   H   H     0   0.283   4.7057  -3.5452  -0.8496
 HZK  H10  H   HNR6  0   0.407   7.3234  -0.8674  -0.8935
 HZK  H11  H   HCR6  0   0.301  -5.6171  -3.0583  -0.5454
 HZK  H12  H   HCR6  0   0.282  -6.3550   0.7866   1.1926
 HZK  H13  H   HOH1  0   0.462  -0.8308   2.2949  -1.9852
 HZK  H14  H   HNH1  0   0.410  -2.7548   2.8138  -0.7822
 HZK  H15  H   HCR6  0   0.274   4.1036   2.4841  -1.2937
 HZK  H16  H   H     0   0.271   3.4212  -2.8348   1.1239
 HZK  H17  H   H     0   0.265   4.8725  -2.2636   1.9211
 HZK  H18  H   HCH2  0   0.281   0.2562   4.6167   0.3500
 HZK  H19  H   HCH2  0   0.271   2.6786   3.4715   0.9986

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
 HZK  F20  C5   single    1.339  0.020  1.339
 HZK  C6   C1   aromatic  1.393  0.020  1.393
 HZK  C6   C5   aromatic  1.378  0.020  1.378
 HZK  C19  C1   single    1.513  0.020  1.513
 HZK  C19  N17  single    1.437  0.020  1.437
 HZK  C1   C2   aromatic  1.389  0.020  1.389
 HZK  C5   C4   aromatic  1.383  0.020  1.383
 HZK  C4   C3   aromatic  1.384  0.020  1.384
 HZK  C2   C3   aromatic  1.388  0.020  1.388
 HZK  C3   CL7  single    1.731  0.020  1.731
 HZK  O18  C15  double    1.221  0.020  1.221
 HZK  N17  C15  single    1.337  0.020  1.337
 HZK  C15  C12  single    1.527  0.020  1.527
 HZK  O16  C13  double    1.215  0.020  1.215
 HZK  O14  C12  single    1.405  0.020  1.405
 HZK  C12  C13  single    1.535  0.020  1.535
 HZK  C12  C11  single    1.522  0.020  1.522
 HZK  C13  N9   single    1.349  0.020  1.349
 HZK  C11  C10  single    1.525  0.020  1.525
 HZK  N9   C8   single    1.409  0.020  1.409
 HZK  N9   C10  single    1.458  0.020  1.458
 HZK  C23  C8   aromatic  1.390  0.020  1.390
 HZK  C23  C22  aromatic  1.385  0.020  1.385
 HZK  C8   C21  aromatic  1.393  0.020  1.393
 HZK  C22  C24  aromatic  1.389  0.020  1.389
 HZK  C21  C25  aromatic  1.384  0.020  1.384
 HZK  C24  C25  aromatic  1.396  0.020  1.396
 HZK  C24  N29  single    1.395  0.020  1.395
 HZK  C25  C26  single    1.499  0.020  1.499
 HZK  N29  C28  single    1.360  0.020  1.360
 HZK  C27  C26  single    1.523  0.020  1.523
 HZK  C27  C28  single    1.508  0.020  1.508
 HZK  C28  O30  double    1.218  0.020  1.218
 HZK  C2   H1   single    0.930  0.020  1.080
 HZK  C10  H2   single    0.970  0.020  1.090
 HZK  C11  H3   single    0.970  0.020  1.090
 HZK  C19  H4   single    0.970  0.020  1.090
 HZK  C19  H5   single    0.970  0.020  1.090
 HZK  C21  H6   single    0.930  0.020  1.080
 HZK  C22  H7   single    0.930  0.020  1.080
 HZK  C27  H8   single    0.970  0.020  1.090
 HZK  C27  H9   single    0.970  0.020  1.090
 HZK  N29  H10  single    0.860  0.020  1.020
 HZK  C4   H11  single    0.930  0.020  1.080
 HZK  C6   H12  single    0.930  0.020  1.080
 HZK  O14  H13  single    0.850  0.020  0.980
 HZK  N17  H14  single    0.860  0.020  1.020
 HZK  C23  H15  single    0.930  0.020  1.080
 HZK  C26  H16  single    0.970  0.020  1.090
 HZK  C26  H17  single    0.970  0.020  1.090
 HZK  C11  H18  single    0.970  0.020  1.090
 HZK  C10  H19  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
 HZK  C6   C1   C19  117.91  3.000
 HZK  C19  C1   C2   122.36  3.000
 HZK  C6   C1   C2   119.74  3.000
 HZK  H1   C2   C3   119.43  3.000
 HZK  H1   C2   C1   121.33  3.000
 HZK  C3   C2   C1   119.24  3.000
 HZK  CL7  C3   C4   118.80  3.000
 HZK  CL7  C3   C2   118.96  3.000
 HZK  C4   C3   C2   122.25  3.000
 HZK  C23  C8   N9   120.01  3.000
 HZK  C23  C8   C21  119.38  3.000
 HZK  N9   C8   C21  120.60  3.000
 HZK  H19  C10  H2   108.24  3.000
 HZK  H19  C10  N9   110.30  3.000
 HZK  H2   C10  N9   110.99  3.000
 HZK  H19  C10  C11  112.57  3.000
 HZK  H2   C10  C11  111.85  3.000
 HZK  N9   C10  C11  102.85  3.000
 HZK  H18  C11  H3   108.33  3.000
 HZK  H18  C11  C12  112.27  3.000
 HZK  H3   C11  C12  110.01  3.000
 HZK  H18  C11  C10  112.85  3.000
 HZK  H3   C11  C10  109.59  3.000
 HZK  C12  C11  C10  103.72  3.000
 HZK  O14  C12  C15  114.20  3.000
 HZK  O14  C12  C13  108.62  3.000
 HZK  C15  C12  C13  108.38  3.000
 HZK  C13  C12  C11  102.97  3.000
 HZK  O14  C12  C11  109.26  3.000
 HZK  C15  C12  C11  112.74  3.000
 HZK  O16  C13  N9   127.55  3.000
 HZK  N9   C13  C12  107.88  3.000
 HZK  O16  C13  C12  124.42  3.000
 HZK  O18  C15  N17  124.38  3.000
 HZK  N17  C15  C12  115.97  3.000
 HZK  O18  C15  C12  119.64  3.000
 HZK  H5   C19  H4   106.75  3.000
 HZK  H5   C19  N17  109.14  3.000
 HZK  H4   C19  N17  108.15  3.000
 HZK  H5   C19  C1   109.01  3.000
 HZK  H4   C19  C1   109.15  3.000
 HZK  N17  C19  C1   114.37  3.000
 HZK  H6   C21  C25  118.78  3.000
 HZK  H6   C21  C8   120.36  3.000
 HZK  C25  C21  C8   120.84  3.000
 HZK  H7   C22  C23  119.65  3.000
 HZK  H7   C22  C24  120.24  3.000
 HZK  C23  C22  C24  120.11  3.000
 HZK  C25  C24  N29  119.30  3.000
 HZK  N29  C24  C22  120.56  3.000
 HZK  C25  C24  C22  120.13  3.000
 HZK  H9   C27  H8   107.00  3.000
 HZK  H9   C27  C28  107.21  3.000
 HZK  H8   C27  C28  108.60  3.000
 HZK  H9   C27  C26  109.99  3.000
 HZK  H8   C27  C26  111.33  3.000
 HZK  C28  C27  C26  112.48  3.000
 HZK  H10  N29  C28  116.78  3.000
 HZK  H10  N29  C24  117.84  3.000
 HZK  C28  N29  C24  125.02  3.000
 HZK  H11  C4   C5   121.12  3.000
 HZK  H11  C4   C3   121.97  3.000
 HZK  C5   C4   C3   116.90  3.000
 HZK  F20  C5   C6   118.88  3.000
 HZK  C6   C5   C4   122.84  3.000
 HZK  F20  C5   C4   118.28  3.000
 HZK  H12  C6   C5   120.07  3.000
 HZK  H12  C6   C1   120.89  3.000
 HZK  C5   C6   C1   119.04  3.000
 HZK  C13  N9   C10  113.08  3.000
 HZK  C10  N9   C8   122.03  3.000
 HZK  C13  N9   C8   124.15  3.000
 HZK  H13  O14  C12  110.15  3.000
 HZK  H14  N17  C19  118.36  3.000
 HZK  H14  N17  C15  118.72  3.000
 HZK  C19  N17  C15  122.91  3.000
 HZK  H15  C23  C22  119.12  3.000
 HZK  H15  C23  C8   120.65  3.000
 HZK  C22  C23  C8   120.23  3.000
 HZK  C26  C25  C24  117.66  3.000
 HZK  C26  C25  C21  123.00  3.000
 HZK  C24  C25  C21  119.30  3.000
 HZK  H17  C26  H16  106.58  3.000
 HZK  H17  C26  C25  109.21  3.000
 HZK  H16  C26  C25  110.86  3.000
 HZK  H17  C26  C27  109.49  3.000
 HZK  H16  C26  C27  110.20  3.000
 HZK  C25  C26  C27  110.42  3.000
 HZK  O30  C28  N29  121.52  3.000
 HZK  O30  C28  C27  123.57  3.000
 HZK  N29  C28  C27  114.89  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
 HZK  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 HZK  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 HZK  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 HZK  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 HZK  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 HZK  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 HZK  CONST_07  C24  C22  C23  C8      0.00   0.0  0
 HZK  CONST_08  C24  C25  C21  C8      0.00   0.0  0
 HZK  CONST_09  C22  C23  C8   C21     0.00   0.0  0
 HZK  CONST_10  C22  C24  C25  C21     0.00   0.0  0
 HZK  CONST_11  C25  C21  C8   C23     0.00   0.0  0
 HZK  CONST_12  C25  C24  C22  C23     0.00   0.0  0
 HZK  CONST_13  N9   C8   C23  C22   180.00   0.0  0
 HZK  CONST_14  C25  C21  C8   N9    180.00   0.0  0
 HZK  CONST_15  C12  C13  N9   C8    180.00   0.0  0
 HZK  CONST_16  C12  C13  N9   C10     0.00   0.0  0
 HZK  CONST_17  C27  C28  N29  C24     0.00   0.0  0
 HZK  CONST_18  F20  C5   C6   C1    180.00   0.0  0
 HZK  CONST_19  CL7  C3   C2   C1    180.00   0.0  0
 HZK  CONST_20  F20  C5   C4   C3    180.00   0.0  0
 HZK  CONST_21  C19  C1   C2   C3    180.00   0.0  0
 HZK  CONST_22  C5   C6   C1   C19   180.00   0.0  0
 HZK  CONST_23  CL7  C3   C4   C5    180.00   0.0  0
 HZK  CONST_24  O16  C13  N9   C8      0.00   0.0  0
 HZK  CONST_25  O16  C13  N9   C10   180.00   0.0  0
 HZK  CONST_26  O30  C28  N29  C24   180.00   0.0  0
 HZK  CONST_27  H12  C6   C1   C2    180.00   0.0  0
 HZK  CONST_28  H11  C4   C3   C2    180.00   0.0  0
 HZK  CONST_29  H7   C22  C23  C8    180.00   0.0  0
 HZK  CONST_30  H15  C23  C8   C21   180.00   0.0  0
 HZK  CONST_31  H6   C21  C25  C24   180.00   0.0  0
 HZK  CONST_32  H1   C2   C3   C4    180.00   0.0  0
 HZK  CONST_33  H10  N29  C28  C27   180.00   0.0  0
 HZK  CONST_34  C19  N17  C15  C12   180.00   0.0  0
 HZK  CONST_35  H14  N17  C15  C12     0.00   0.0  0
 HZK  CONST_36  O18  C15  N17  C19     0.00   0.0  0
 HZK  Var_01    C11  C10  N9   C8   -168.22  30.0  1
 HZK  Var_02    C23  C8   N9   C10   -37.44  30.0  2
 HZK  Var_03    N9   C10  C11  C12   -29.95  30.0  1
 HZK  Var_04    C27  C26  C25  C21   146.82  30.0  1
 HZK  Var_05    C28  N29  C24  C22  -162.43  30.0  1
 HZK  Var_06    C26  C27  C28  N29   -33.96  30.0  1
 HZK  Var_07    C28  C27  C26  C25    51.01  30.0  1
 HZK  Var_08    N17  C19  C1   C2     10.42  30.0  3
 HZK  Var_09    C15  N17  C19  C1    -88.34  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
 HZK  chir_01  C12  O14  C13  C11  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
 HZK  plan-1  C1   0.020
 HZK  plan-1  C2   0.020
 HZK  plan-1  C3   0.020
 HZK  plan-1  C19  0.020
 HZK  plan-1  C4   0.020
 HZK  plan-1  C5   0.020
 HZK  plan-1  C6   0.020
 HZK  plan-1  CL7  0.020
 HZK  plan-1  F20  0.020
 HZK  plan-1  H1   0.020
 HZK  plan-1  H11  0.020
 HZK  plan-1  H12  0.020
 HZK  plan-2  C8   0.020
 HZK  plan-2  C21  0.020
 HZK  plan-2  C22  0.020
 HZK  plan-2  C24  0.020
 HZK  plan-2  N29  0.020
 HZK  plan-2  N9   0.020
 HZK  plan-2  C23  0.020
 HZK  plan-2  C25  0.020
 HZK  plan-2  C26  0.020
 HZK  plan-2  H6   0.020
 HZK  plan-2  H7   0.020
 HZK  plan-2  H15  0.020
 HZK  plan-3  C12  0.020
 HZK  plan-3  C15  0.020
 HZK  plan-3  C19  0.020
 HZK  plan-3  N17  0.020
 HZK  plan-3  O18  0.020
 HZK  plan-3  H14  0.020
 HZK  plan-4  C24  0.020
 HZK  plan-4  C27  0.020
 HZK  plan-4  N29  0.020
 HZK  plan-4  C28  0.020
 HZK  plan-4  O30  0.020
 HZK  plan-4  H10  0.020
 HZK  plan-5  C8   0.020
 HZK  plan-5  C10  0.020
 HZK  plan-5  C12  0.020
 HZK  plan-5  C13  0.020
 HZK  plan-5  N9   0.020
 HZK  plan-5  O16  0.020

