# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 10:09:37 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (1R,2R)-N-(1-cyanocyclopropyl)-2-{[4-(4-fluorophenyl)piperazin-1-yl]carbonyl}cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)N2CCN(CC2)C(=O)[C@@H]3CCCC[C@H]3C(=O)NC4(CC4)C#N
#
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
 0LB  0LB  (1R,2R)-N-(1-cyanocyclopropyl)-2-{[4-(4-fluorophenyl)piperazin-1-yl]carbonyl}cyclohexanecarboxamide  ligand  56  29  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0LB
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
 0LB  N29  N  NS    0  -0.267   0.9447   3.5850   1.9194
 0LB  C28  C  CSP   0   0.115   1.8004   3.3786   1.1773
 0LB  C25  C  CT    0   0.084   2.8723   3.1084   0.2480
 0LB  C27  C  CH2   0  -0.471   3.8580   4.2175  -0.0195
 0LB  C26  C  CH2   0  -0.451   2.8528   3.8694  -1.0543
 0LB  N24  N  NH1   0  -0.670   3.3511   1.7753   0.2645
 0LB  C22  C  C     0   0.603   2.6227   0.7616  -0.2635
 0LB  O23  O  O     0  -0.465   1.5377   0.9573  -0.7820
 0LB  C18  C  CH1   0  -0.374   3.2858  -0.5978  -0.2168
 0LB  C16  C  CH2   0  -0.420   4.2111  -0.7722  -1.4290
 0LB  C20  C  CH1   0  -0.392   2.2319  -1.7012  -0.1897
 0LB  C21  C  CH2   0  -0.422   2.8983  -3.0839  -0.1583
 0LB  C19  C  CH2   0  -0.435   3.8470  -3.2590  -1.3392
 0LB  C17  C  CH2   0  -0.436   4.8805  -2.1412  -1.3938
 0LB  C14  C  C     0   0.600   1.3268  -1.5197   1.0182
 0LB  O15  O  O     0  -0.497   1.7569  -0.9684   2.0239
 0LB  N8   N  NT    0  -0.460   0.0752  -2.0320   0.9694
 0LB  C10  C  CH2   0  -0.337  -0.6047  -2.5009  -0.2225
 0LB  C12  C  CH2   0  -0.298  -1.5825  -1.4480  -0.7217
 0LB  N11  N  NT    0  -0.521  -2.5202  -1.0974   0.3273
 0LB  C9   C  CH2   0  -0.297  -1.8568  -0.6789   1.5572
 0LB  C7   C  CH2   0  -0.331  -0.8747  -1.7379   2.0264
 0LB  C2   C  CR6   0   0.357  -3.6619  -0.3790  -0.0412
 0LB  C4   C  CR16  0  -0.308  -4.7000  -0.2008   0.8845
 0LB  C6   C  CR16  0  -0.397  -5.8568   0.4806   0.5520
 0LB  C5   C  CR6   0   0.493  -5.9976   0.9827  -0.7284
 0LB  F13  F  F     0  -0.323  -7.1276   1.6391  -1.0563
 0LB  C3   C  CR16  0  -0.400  -5.0070   0.8221  -1.6711
 0LB  C1   C  CR16  0  -0.340  -3.8398   0.1513  -1.3224
 0LB  H3   H  HCH2  0   0.289   3.7370   5.1362   0.5377
 0LB  H4   H  HCH2  0   0.291   4.8834   3.9043  -0.1662
 0LB  H5   H  HCH2  0   0.288   3.1760   3.3139  -1.9240
 0LB  H6   H  HCH2  0   0.285   2.0268   4.5470  -1.2235
 0LB  H7   H  HNH1  0   0.412   4.1736   1.5692   0.8103
 0LB  H8   H  HCH1  0   0.260   3.9007  -0.6640   0.6863
 0LB  H9   H  HCH2  0   0.228   3.6306  -0.6697  -2.3520
 0LB  H10  H  HCH2  0   0.245   4.9660   0.0174  -1.4385
 0LB  H11  H  HCH1  0   0.259   1.6554  -1.6226  -1.1138
 0LB  H12  H  HCH2  0   0.230   3.4488  -3.1974   0.7812
 0LB  H13  H  HCH2  0   0.246   2.1364  -3.8674  -0.1722
 0LB  H14  H  HCH2  0   0.238   4.3410  -4.2310  -1.2754
 0LB  H15  H  HCH2  0   0.219   3.2679  -3.2632  -2.2688
 0LB  H16  H  HCH2  0   0.238   5.5252  -2.2601  -2.2672
 0LB  H17  H  HCH2  0   0.219   5.5292  -2.2000  -0.5138
 0LB  H18  H  HCH2  0   0.271   0.0959  -2.7513  -1.0133
 0LB  H19  H  HCH2  0   0.258  -1.1457  -3.4167   0.0295
 0LB  H20  H  HCH2  0   0.221  -1.0114  -0.5780  -1.0817
 0LB  H21  H  HCH2  0   0.258  -2.1291  -1.8615  -1.5705
 0LB  H22  H  HCH2  0   0.221  -1.3219   0.2716   1.4123
 0LB  H23  H  HCH2  0   0.261  -2.5919  -0.5210   2.3444
 0LB  H24  H  HCH2  0   0.251  -1.4104  -2.6557   2.2837
 0LB  H25  H  HCH2  0   0.270  -0.3543  -1.3926   2.9146
 0LB  H26  H  HCR6  0   0.272  -4.6177  -0.6178   1.8796
 0LB  H27  H  HCR6  0   0.277  -6.6459   0.6042   1.2822
 0LB  H28  H  HCR6  0   0.277  -5.1258   1.2243  -2.6689
 0LB  H29  H  HCR6  0   0.278  -3.0678   0.0585  -2.0731

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
 0LB  C3   C1   aromatic  1.391  0.020  1.391
 0LB  C3   C5   aromatic  1.377  0.020  1.377
 0LB  F13  C5   single    1.347  0.020  1.347
 0LB  C1   C2   aromatic  1.398  0.020  1.398
 0LB  C5   C6   aromatic  1.383  0.020  1.383
 0LB  C12  C10  single    1.521  0.020  1.521
 0LB  C12  N11  single    1.450  0.020  1.450
 0LB  C19  C17  single    1.523  0.020  1.523
 0LB  C19  C21  single    1.525  0.020  1.525
 0LB  C2   N11  single    1.398  0.020  1.398
 0LB  C2   C4   aromatic  1.402  0.020  1.402
 0LB  C6   C4   aromatic  1.383  0.020  1.383
 0LB  C10  N8   single    1.450  0.020  1.450
 0LB  C17  C16  single    1.524  0.020  1.524
 0LB  N11  C9   single    1.459  0.020  1.459
 0LB  C21  C20  single    1.535  0.020  1.535
 0LB  C16  C18  single    1.535  0.020  1.535
 0LB  C20  C18  single    1.526  0.020  1.526
 0LB  C20  C14  single    1.520  0.020  1.520
 0LB  N8   C14  single    1.353  0.020  1.353
 0LB  N8   C7   single    1.451  0.020  1.451
 0LB  O23  C22  double    1.218  0.020  1.218
 0LB  C18  C22  single    1.513  0.020  1.513
 0LB  C9   C7   single    1.519  0.020  1.519
 0LB  C14  O15  double    1.225  0.020  1.225
 0LB  C22  N24  single    1.355  0.020  1.355
 0LB  N24  C25  single    1.417  0.020  1.417
 0LB  C28  C25  single    1.444  0.020  1.444
 0LB  C28  N29  triple    1.151  0.020  1.151
 0LB  C25  C27  single    1.508  0.020  1.508
 0LB  C25  C26  single    1.508  0.020  1.508
 0LB  C27  C26  single    1.484  0.020  1.484
 0LB  C27  H3   single    0.970  0.020  1.090
 0LB  C27  H4   single    0.970  0.020  1.090
 0LB  C26  H5   single    0.970  0.020  1.090
 0LB  C26  H6   single    0.970  0.020  1.090
 0LB  N24  H7   single    0.860  0.020  1.020
 0LB  C18  H8   single    0.970  0.020  1.090
 0LB  C16  H9   single    0.970  0.020  1.090
 0LB  C16  H10  single    0.970  0.020  1.090
 0LB  C20  H11  single    0.970  0.020  1.090
 0LB  C21  H12  single    0.970  0.020  1.090
 0LB  C21  H13  single    0.970  0.020  1.090
 0LB  C19  H14  single    0.970  0.020  1.090
 0LB  C19  H15  single    0.970  0.020  1.090
 0LB  C17  H16  single    0.970  0.020  1.090
 0LB  C17  H17  single    0.970  0.020  1.090
 0LB  C10  H18  single    0.970  0.020  1.090
 0LB  C10  H19  single    0.970  0.020  1.090
 0LB  C12  H20  single    0.970  0.020  1.090
 0LB  C12  H21  single    0.970  0.020  1.090
 0LB  C9   H22  single    0.970  0.020  1.090
 0LB  C9   H23  single    0.970  0.020  1.090
 0LB  C7   H24  single    0.970  0.020  1.090
 0LB  C7   H25  single    0.970  0.020  1.090
 0LB  C4   H26  single    0.930  0.020  1.080
 0LB  C6   H27  single    0.930  0.020  1.080
 0LB  C3   H28  single    0.930  0.020  1.080
 0LB  C1   H29  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
 0LB  C25  C28  N29  180.00  3.000
 0LB  N24  C25  C26  119.29  3.000
 0LB  C26  C25  C27   58.95  3.000
 0LB  N24  C25  C27  118.25  3.000
 0LB  C26  C25  C28  116.84  3.000
 0LB  C27  C25  C28  117.50  3.000
 0LB  N24  C25  C28  114.80  3.000
 0LB  H4   C27  H3   114.94  3.000
 0LB  H4   C27  C26  118.65  3.000
 0LB  H3   C27  C26  118.87  3.000
 0LB  H4   C27  C25  115.51  3.000
 0LB  H3   C27  C25  117.42  3.000
 0LB  C26  C27  C25   60.55  3.000
 0LB  H6   C26  H5   115.10  3.000
 0LB  H6   C26  C27  118.65  3.000
 0LB  H5   C26  C27  118.61  3.000
 0LB  H6   C26  C25  117.45  3.000
 0LB  H5   C26  C25  115.55  3.000
 0LB  C27  C26  C25   60.50  3.000
 0LB  H7   N24  C22  119.76  3.000
 0LB  H7   N24  C25  118.32  3.000
 0LB  C22  N24  C25  121.17  3.000
 0LB  C18  C22  O23  123.21  3.000
 0LB  C18  C22  N24  115.11  3.000
 0LB  O23  C22  N24  121.62  3.000
 0LB  H8   C18  C20  109.25  3.000
 0LB  H8   C18  C16  107.82  3.000
 0LB  C20  C18  C16  110.38  3.000
 0LB  H8   C18  C22  109.02  3.000
 0LB  C20  C18  C22  110.33  3.000
 0LB  C16  C18  C22  109.99  3.000
 0LB  H10  C16  H9   106.93  3.000
 0LB  H10  C16  C17  110.23  3.000
 0LB  H9   C16  C17  109.66  3.000
 0LB  H10  C16  C18  109.96  3.000
 0LB  H9   C16  C18  109.60  3.000
 0LB  C17  C16  C18  110.40  3.000
 0LB  H11  C20  C14  110.46  3.000
 0LB  H11  C20  C21  108.14  3.000
 0LB  C14  C20  C21  110.47  3.000
 0LB  H11  C20  C18  107.31  3.000
 0LB  C14  C20  C18  109.81  3.000
 0LB  C21  C20  C18  110.60  3.000
 0LB  H13  C21  H12  106.69  3.000
 0LB  H13  C21  C19  109.97  3.000
 0LB  H12  C21  C19  109.86  3.000
 0LB  H13  C21  C20  110.05  3.000
 0LB  H12  C21  C20  109.22  3.000
 0LB  C19  C21  C20  110.95  3.000
 0LB  H15  C19  H14  106.58  3.000
 0LB  H15  C19  C17  109.34  3.000
 0LB  H14  C19  C17  110.38  3.000
 0LB  H15  C19  C21  109.20  3.000
 0LB  H14  C19  C21  109.78  3.000
 0LB  C17  C19  C21  111.44  3.000
 0LB  H17  C17  H16  106.69  3.000
 0LB  H17  C17  C19  109.50  3.000
 0LB  H16  C17  C19  110.44  3.000
 0LB  H17  C17  C16  109.09  3.000
 0LB  H16  C17  C16  109.79  3.000
 0LB  C19  C17  C16  111.21  3.000
 0LB  N8   C14  O15  121.65  3.000
 0LB  O15  C14  C20  119.81  3.000
 0LB  N8   C14  C20  118.47  3.000
 0LB  C7   N8   C10  110.93  3.000
 0LB  C7   N8   C14  120.15  3.000
 0LB  C10  N8   C14  125.85  3.000
 0LB  H19  C10  H18  107.10  3.000
 0LB  H19  C10  C12  109.73  3.000
 0LB  H18  C10  C12  109.60  3.000
 0LB  H19  C10  N8   108.27  3.000
 0LB  H18  C10  N8   111.75  3.000
 0LB  C12  C10  N8   110.32  3.000
 0LB  H21  C12  H20  107.75  3.000
 0LB  H21  C12  N11  109.30  3.000
 0LB  H20  C12  N11  112.39  3.000
 0LB  H21  C12  C10  108.36  3.000
 0LB  H20  C12  C10  108.71  3.000
 0LB  N11  C12  C10  110.22  3.000
 0LB  C2   N11  C9   116.49  3.000
 0LB  C9   N11  C12  112.66  3.000
 0LB  C2   N11  C12  117.49  3.000
 0LB  H23  C9   H22  107.35  3.000
 0LB  H23  C9   C7   108.33  3.000
 0LB  H22  C9   C7   109.19  3.000
 0LB  H23  C9   N11  110.13  3.000
 0LB  H22  C9   N11  110.97  3.000
 0LB  C7   C9   N11  110.76  3.000
 0LB  H25  C7   H24  108.01  3.000
 0LB  H25  C7   C9   109.94  3.000
 0LB  H24  C7   C9   109.95  3.000
 0LB  H25  C7   N8   110.27  3.000
 0LB  H24  C7   N8   108.78  3.000
 0LB  C9   C7   N8   109.86  3.000
 0LB  C1   C2   C4   117.56  3.000
 0LB  C4   C2   N11  119.72  3.000
 0LB  C1   C2   N11  122.70  3.000
 0LB  H26  C4   C6   118.33  3.000
 0LB  H26  C4   C2   120.12  3.000
 0LB  C6   C4   C2   121.54  3.000
 0LB  H27  C6   C5   120.60  3.000
 0LB  H27  C6   C4   120.26  3.000
 0LB  C5   C6   C4   119.13  3.000
 0LB  C3   C5   F13  119.58  3.000
 0LB  F13  C5   C6   119.19  3.000
 0LB  C3   C5   C6   121.23  3.000
 0LB  H28  C3   C1   120.17  3.000
 0LB  H28  C3   C5   120.59  3.000
 0LB  C1   C3   C5   119.24  3.000
 0LB  H29  C1   C3   117.82  3.000
 0LB  H29  C1   C2   120.87  3.000
 0LB  C3   C1   C2   121.30  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
 0LB  CONST_01  C5   C3   C1   C2      0.00   0.0  0
 0LB  CONST_02  C5   C6   C4   C2      0.00   0.0  0
 0LB  CONST_03  C3   C1   C2   C4      0.00   0.0  0
 0LB  CONST_04  C3   C5   C6   C4      0.00   0.0  0
 0LB  CONST_05  C1   C3   C5   C6      0.00   0.0  0
 0LB  CONST_06  C1   C2   C4   C6      0.00   0.0  0
 0LB  CONST_07  C3   C1   C2   N11   180.00   0.0  0
 0LB  CONST_08  C6   C4   C2   N11   180.00   0.0  0
 0LB  CONST_09  F13  C5   C6   C4    180.00   0.0  0
 0LB  CONST_10  C1   C3   C5   F13   180.00   0.0  0
 0LB  CONST_11  C10  N8   C14  C20     0.00   0.0  0
 0LB  CONST_12  C7   N8   C14  C20   180.00   0.0  0
 0LB  CONST_13  H29  C1   C2   N11     0.00   0.0  0
 0LB  CONST_14  H26  C4   C2   N11     0.00   0.0  0
 0LB  CONST_15  H28  C3   C1   C2    180.00   0.0  0
 0LB  CONST_16  H27  C6   C4   C2    180.00   0.0  0
 0LB  CONST_17  C18  C22  N24  C25   180.00   0.0  0
 0LB  CONST_18  C10  N8   C14  O15   180.00   0.0  0
 0LB  CONST_19  C7   N8   C14  O15     0.00   0.0  0
 0LB  CONST_20  O23  C22  N24  C25     0.00   0.0  0
 0LB  CONST_21  H7   N24  C22  C18     0.00   0.0  0
 0LB  Var_01    C19  C17  C16  C18    56.68  30.0  1
 0LB  Var_02    C21  C19  C17  C16   -55.56  30.0  1
 0LB  Var_03    C17  C19  C21  C20    55.06  30.0  1
 0LB  Var_04    N11  C12  C10  N8    -56.19  30.0  1
 0LB  Var_05    N11  C9   C7   N8     55.74  30.0  1
 0LB  Var_06    C2   N11  C12  C10  -165.90  30.0  1
 0LB  Var_07    C9   C7   N8   C10   -58.95  30.0  1
 0LB  Var_08    C7   N8   C10  C12    59.38  30.0  1
 0LB  Var_09    C1   C2   N11  C12    -8.45  30.0  2
 0LB  Var_10    C7   C9   N11  C12   -54.59  30.0  1
 0LB  Var_11    C26  C27  C25  C28  -106.31  30.0  1
 0LB  Var_12    H5   C26  C27  C25  -104.83  30.0  1
 0LB  Var_13    C27  C25  C28  N29  -159.48  30.0  3
 0LB  Var_14    C22  N24  C25  C27  -141.20  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
 0LB  chir_02  C18  C16  C20  C22  positiv
 0LB  chir_03  C20  C21  C18  C14  positiv
 0LB  chir_04  C25  C28  C27  C26  both

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
 0LB  plan-1  C25  0.020
 0LB  plan-1  N24  0.020
 0LB  plan-1  C22  0.020
 0LB  plan-1  O23  0.020
 0LB  plan-1  C18  0.020
 0LB  plan-1  H7   0.020
 0LB  plan-2  C20  0.020
 0LB  plan-2  C14  0.020
 0LB  plan-2  O15  0.020
 0LB  plan-2  N8   0.020
 0LB  plan-2  C10  0.020
 0LB  plan-2  C7   0.020
 0LB  plan-3  N11  0.020
 0LB  plan-3  C2   0.020
 0LB  plan-3  C4   0.020
 0LB  plan-3  C6   0.020
 0LB  plan-3  C5   0.020
 0LB  plan-3  F13  0.020
 0LB  plan-3  C3   0.020
 0LB  plan-3  C1   0.020
 0LB  plan-3  H26  0.020
 0LB  plan-3  H27  0.020
 0LB  plan-3  H28  0.020
 0LB  plan-3  H29  0.020

