# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 21:16:36 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 6-{[(1-{2-[(3-methylbenzoyl)amino]ethyl}cyclohexyl)methyl]amino}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)C(=O)NCCC2(CCCCC2)CNc3ccc(cn3)C(N)=O
#
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
 4GZ  4GZ  6-{[(1-{2-[(3-methylbenzoyl)amino]ethyl}cyclohexyl)methyl]amino}pyridine-3-carboxamide  ligand  59  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4GZ
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
 4GZ  C4   C  CR16  0  -0.228   5.4136  -3.0077   1.2306
 4GZ  C5   C  CR16  0  -0.314   4.6432  -1.8670   1.0604
 4GZ  C18  C  CR16  0  -0.151  -5.2259  -0.9697   0.9264
 4GZ  C3   C  CR16  0  -0.296   6.6427  -3.1226   0.5979
 4GZ  C17  C  CR16  0  -0.401  -4.1025  -0.1827   0.8838
 4GZ  C7   C  CR16  0  -0.325   6.3572  -0.9483  -0.3548
 4GZ  C20  C  CR16  0  -0.074  -4.6288  -1.8466  -1.1924
 4GZ  C6   C  CR6   0  -0.015   5.1121  -0.8301   0.2572
 4GZ  C19  C  CR6   0  -0.166  -5.5178  -1.8493  -0.1218
 4GZ  C2   C  CR6   0   0.114   7.1305  -2.0947  -0.2074
 4GZ  C16  C  CR6   0   0.516  -3.2615  -0.2734  -0.2461
 4GZ  C8   C  C     0   0.530   4.3387   0.4332   0.0474
 4GZ  C27  C  CH2   0  -0.427  -1.1561   4.9715  -0.3212
 4GZ  C26  C  CH2   0  -0.436  -1.4442   3.8725  -1.3399
 4GZ  C28  C  CH2   0  -0.445  -1.0887   4.4248   1.1013
 4GZ  C25  C  CH2   0  -0.439  -0.4303   2.7402  -1.2144
 4GZ  C29  C  CH2   0  -0.417  -0.1133   3.2531   1.2065
 4GZ  C13  C  CT    0  -0.151  -0.3856   2.1254   0.1945
 4GZ  C1   C  CH3   0  -0.720   8.4456  -2.2299  -0.9176
 4GZ  C12  C  CH2   0  -0.450   0.6957   1.0344   0.3006
 4GZ  C14  C  CH2   0  -0.239  -1.7276   1.4746   0.5713
 4GZ  C11  C  CH2   0  -0.245   2.1118   1.4477  -0.0753
 4GZ  N21  N  N     0  -0.465  -3.5452  -1.0962  -1.2646
 4GZ  N23  N  NH2   0  -0.823  -6.8444  -3.6956  -0.9253
 4GZ  N15  N  NH1   0  -0.661  -2.1367   0.4543  -0.3637
 4GZ  N10  N  NH1   0  -0.655   3.0041   0.3235   0.1275
 4GZ  O9   O  O     0  -0.495   4.9018   1.4955  -0.1867
 4GZ  O24  O  O     0  -0.492  -7.6401  -2.4143   0.7446
 4GZ  H1   H  HCR6  0   0.261   5.0567  -3.8071   1.8665
 4GZ  H2   H  HCR6  0   0.257   3.6982  -1.7863   1.5829
 4GZ  H3   H  HCR6  0   0.268  -5.8868  -0.9105   1.7812
 4GZ  H4   H  HCR6  0   0.254   7.2346  -4.0199   0.7363
 4GZ  H5   H  HCR6  0   0.277  -3.8757   0.4921   1.6970
 4GZ  H6   H  HCR6  0   0.250   6.7276  -0.1339  -0.9657
 4GZ  H7   H  HCR6  0   0.254  -4.8051  -2.4707  -2.0630
 4GZ  H8   H  HCH2  0   0.210  -0.1960   5.4368  -0.5695
 4GZ  H9   H  HCH2  0   0.229  -1.9092   5.7602  -0.3878
 4GZ  H10  H  HCH2  0   0.219  -2.4629   3.4940  -1.2120
 4GZ  H11  H  HCH2  0   0.234  -1.4018   4.2834  -2.3514
 4GZ  H12  H  HCH2  0   0.234  -0.7733   5.2141   1.7882
 4GZ  H13  H  HCH2  0   0.219  -2.0877   4.1255   1.4308
 4GZ  H14  H  HCH2  0   0.229  -0.6089   1.9768  -1.9789
 4GZ  H15  H  HCH2  0   0.235   0.5577   3.1477  -1.4485
 4GZ  H16  H  HCH2  0   0.231   0.8974   3.6360   1.0361
 4GZ  H17  H  HCH2  0   0.231  -0.1175   2.8439   2.2220
 4GZ  H18  H  HCH3  0   0.251   8.3113  -2.6925  -1.8977
 4GZ  H19  H  HCH3  0   0.245   8.9142  -1.2598  -1.0803
 4GZ  H20  H  HCH3  0   0.245   9.1412  -2.8541  -0.3578
 4GZ  H21  H  HCH2  0   0.240   0.7057   0.6613   1.3305
 4GZ  H22  H  HCH2  0   0.240   0.4104   0.1848  -0.3289
 4GZ  H23  H  HCH2  0   0.243  -1.6198   1.0380   1.5709
 4GZ  H24  H  HCH2  0   0.248  -2.5112   2.2332   0.6529
 4GZ  H25  H  HCH2  0   0.237   2.1601   1.7764  -1.1169
 4GZ  H26  H  HCH2  0   0.240   2.4526   2.2832   0.5381
 4GZ  H27  H  HNH2  0   0.410  -6.0789  -3.9998  -1.4996
 4GZ  H28  H  HNH2  0   0.403  -7.6682  -4.2739  -0.9221
 4GZ  H29  H  HNH1  0   0.387  -1.6518   0.3684  -1.2422
 4GZ  H30  H  HNH1  0   0.405   2.5932  -0.5954   0.1651
 4GZ  C22  C  C     0   0.486  -6.7507  -2.6717  -0.0595

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
 4GZ  C27  C26  single    1.526  0.020  1.526
 4GZ  C27  C28  single    1.525  0.020  1.525
 4GZ  C26  C25  single    1.525  0.020  1.525
 4GZ  C25  C13  single    1.538  0.020  1.538
 4GZ  C28  C29  single    1.528  0.020  1.528
 4GZ  C11  N10  single    1.450  0.020  1.450
 4GZ  C11  C12  single    1.522  0.020  1.522
 4GZ  O9   C8   double    1.225  0.020  1.225
 4GZ  N10  C8   single    1.341  0.020  1.341
 4GZ  C5   C4   aromatic  1.387  0.020  1.387
 4GZ  C5   C6   aromatic  1.393  0.020  1.393
 4GZ  C8   C6   single    1.496  0.020  1.496
 4GZ  C29  C13  single    1.540  0.020  1.540
 4GZ  C4   C3   aromatic  1.387  0.020  1.387
 4GZ  C6   C7   aromatic  1.392  0.020  1.392
 4GZ  C13  C12  single    1.540  0.020  1.540
 4GZ  C13  C14  single    1.538  0.020  1.538
 4GZ  C3   C2   aromatic  1.394  0.020  1.394
 4GZ  C7   C2   aromatic  1.391  0.020  1.391
 4GZ  C2   C1   single    1.501  0.020  1.501
 4GZ  C14  N15  single    1.443  0.020  1.443
 4GZ  N15  C16  single    1.345  0.020  1.345
 4GZ  C17  C16  aromatic  1.411  0.020  1.411
 4GZ  C17  C18  aromatic  1.372  0.020  1.372
 4GZ  C16  N21  aromatic  1.340  0.020  1.340
 4GZ  C18  C19  aromatic  1.399  0.020  1.399
 4GZ  N21  C20  aromatic  1.320  0.020  1.320
 4GZ  C19  C20  aromatic  1.392  0.020  1.392
 4GZ  C19  C22  single    1.483  0.020  1.483
 4GZ  O24  C22  double    1.226  0.020  1.226
 4GZ  C22  N23  single    1.344  0.020  1.344
 4GZ  C4   H1   single    0.930  0.020  1.080
 4GZ  C5   H2   single    0.930  0.020  1.080
 4GZ  C18  H3   single    0.930  0.020  1.080
 4GZ  C3   H4   single    0.930  0.020  1.080
 4GZ  C17  H5   single    0.930  0.020  1.080
 4GZ  C7   H6   single    0.930  0.020  1.080
 4GZ  C20  H7   single    0.930  0.020  1.080
 4GZ  C27  H8   single    0.970  0.020  1.090
 4GZ  C27  H9   single    0.970  0.020  1.090
 4GZ  C26  H10  single    0.970  0.020  1.090
 4GZ  C26  H11  single    0.970  0.020  1.090
 4GZ  C28  H12  single    0.970  0.020  1.090
 4GZ  C28  H13  single    0.970  0.020  1.090
 4GZ  C25  H14  single    0.970  0.020  1.090
 4GZ  C25  H15  single    0.970  0.020  1.090
 4GZ  C29  H16  single    0.970  0.020  1.090
 4GZ  C29  H17  single    0.970  0.020  1.090
 4GZ  C1   H18  single    0.970  0.020  1.090
 4GZ  C1   H19  single    0.970  0.020  1.090
 4GZ  C1   H20  single    0.970  0.020  1.090
 4GZ  C12  H21  single    0.970  0.020  1.090
 4GZ  C12  H22  single    0.970  0.020  1.090
 4GZ  C14  H23  single    0.970  0.020  1.090
 4GZ  C14  H24  single    0.970  0.020  1.090
 4GZ  C11  H25  single    0.970  0.020  1.090
 4GZ  C11  H26  single    0.970  0.020  1.090
 4GZ  N23  H27  single    0.860  0.020  1.020
 4GZ  N23  H28  single    0.860  0.020  1.020
 4GZ  N15  H29  single    0.860  0.020  1.020
 4GZ  N10  H30  single    0.860  0.020  1.020

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
 4GZ  H1   C4   C3   119.94  3.000
 4GZ  H1   C4   C5   119.77  3.000
 4GZ  C3   C4   C5   120.29  3.000
 4GZ  H2   C5   C6   121.10  3.000
 4GZ  H2   C5   C4   119.13  3.000
 4GZ  C6   C5   C4   119.73  3.000
 4GZ  H3   C18  C19  119.92  3.000
 4GZ  H3   C18  C17  119.54  3.000
 4GZ  C19  C18  C17  120.54  3.000
 4GZ  H4   C3   C2   119.55  3.000
 4GZ  H4   C3   C4   119.62  3.000
 4GZ  C2   C3   C4   120.83  3.000
 4GZ  H5   C17  C16  121.15  3.000
 4GZ  H5   C17  C18  120.43  3.000
 4GZ  C16  C17  C18  118.41  3.000
 4GZ  H6   C7   C2   119.30  3.000
 4GZ  H6   C7   C6   119.33  3.000
 4GZ  C2   C7   C6   121.37  3.000
 4GZ  H7   C20  N21  114.59  3.000
 4GZ  H7   C20  C19  120.81  3.000
 4GZ  N21  C20  C19  124.59  3.000
 4GZ  C8   C6   C7   118.19  3.000
 4GZ  C7   C6   C5   119.43  3.000
 4GZ  C8   C6   C5   122.37  3.000
 4GZ  C22  C19  C20  124.36  3.000
 4GZ  C22  C19  C18  119.38  3.000
 4GZ  C20  C19  C18  116.22  3.000
 4GZ  C1   C2   C7   120.76  3.000
 4GZ  C1   C2   C3   120.90  3.000
 4GZ  C7   C2   C3   118.33  3.000
 4GZ  N15  C16  N21  116.29  3.000
 4GZ  N21  C16  C17  121.45  3.000
 4GZ  N15  C16  C17  122.25  3.000
 4GZ  O9   C8   N10  122.66  3.000
 4GZ  N10  C8   C6   115.91  3.000
 4GZ  O9   C8   C6   121.43  3.000
 4GZ  H9   C27  H8   106.48  3.000
 4GZ  H9   C27  C28  110.24  3.000
 4GZ  H8   C27  C28  108.96  3.000
 4GZ  H9   C27  C26  110.43  3.000
 4GZ  H8   C27  C26  108.67  3.000
 4GZ  C28  C27  C26  111.88  3.000
 4GZ  H11  C26  H10  105.92  3.000
 4GZ  H11  C26  C25  109.24  3.000
 4GZ  H10  C26  C25  110.64  3.000
 4GZ  H11  C26  C27  109.87  3.000
 4GZ  H10  C26  C27  110.30  3.000
 4GZ  C25  C26  C27  110.75  3.000
 4GZ  H13  C28  H12  105.78  3.000
 4GZ  H13  C28  C29  110.64  3.000
 4GZ  H12  C28  C29  109.04  3.000
 4GZ  H13  C28  C27  109.79  3.000
 4GZ  H12  C28  C27  109.88  3.000
 4GZ  C29  C28  C27  111.54  3.000
 4GZ  H15  C25  H14  104.93  3.000
 4GZ  H15  C25  C13  108.58  3.000
 4GZ  H14  C25  C13  111.45  3.000
 4GZ  H15  C25  C26  107.83  3.000
 4GZ  H14  C25  C26  110.59  3.000
 4GZ  C13  C25  C26  113.05  3.000
 4GZ  H17  C29  H16  106.19  3.000
 4GZ  H17  C29  C13  109.59  3.000
 4GZ  H16  C29  C13  108.50  3.000
 4GZ  H17  C29  C28  110.36  3.000
 4GZ  H16  C29  C28  108.09  3.000
 4GZ  C13  C29  C28  113.80  3.000
 4GZ  C14  C13  C12  107.22  3.000
 4GZ  C14  C13  C29  107.65  3.000
 4GZ  C12  C13  C29  110.46  3.000
 4GZ  C14  C13  C25  111.60  3.000
 4GZ  C12  C13  C25  111.52  3.000
 4GZ  C29  C13  C25  108.33  3.000
 4GZ  H20  C1   H19  108.19  3.000
 4GZ  H20  C1   H18  107.27  3.000
 4GZ  H19  C1   H18  107.22  3.000
 4GZ  H20  C1   C2   111.59  3.000
 4GZ  H19  C1   C2   111.55  3.000
 4GZ  H18  C1   C2   110.80  3.000
 4GZ  H22  C12  H21  106.18  3.000
 4GZ  H22  C12  C11  108.12  3.000
 4GZ  H21  C12  C11  108.43  3.000
 4GZ  H22  C12  C13  109.09  3.000
 4GZ  H21  C12  C13  108.22  3.000
 4GZ  C11  C12  C13  116.35  3.000
 4GZ  H24  C14  H23  106.17  3.000
 4GZ  H24  C14  N15  109.61  3.000
 4GZ  H23  C14  N15  109.70  3.000
 4GZ  H24  C14  C13  110.48  3.000
 4GZ  H23  C14  C13  107.83  3.000
 4GZ  N15  C14  C13  112.81  3.000
 4GZ  H26  C11  H25  106.95  3.000
 4GZ  H26  C11  N10  108.84  3.000
 4GZ  H25  C11  N10  109.83  3.000
 4GZ  H26  C11  C12  111.08  3.000
 4GZ  H25  C11  C12  110.98  3.000
 4GZ  N10  C11  C12  109.12  3.000
 4GZ  C16  N21  C20  118.78  3.000
 4GZ  H28  N23  H27  116.85  3.000
 4GZ  H28  N23  C22  119.51  3.000
 4GZ  H27  N23  C22  123.10  3.000
 4GZ  H29  N15  C14  119.27  3.000
 4GZ  H29  N15  C16  115.65  3.000
 4GZ  C14  N15  C16  124.27  3.000
 4GZ  H30  N10  C11  117.48  3.000
 4GZ  H30  N10  C8   118.86  3.000
 4GZ  C11  N10  C8   122.73  3.000
 4GZ  O24  C22  N23  122.12  3.000
 4GZ  N23  C22  C19  116.95  3.000
 4GZ  O24  C22  C19  120.93  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
 4GZ  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 4GZ  CONST_02  C7   C2   C3   C4      0.00   0.0  0
 4GZ  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 4GZ  CONST_04  C2   C7   C6   C5      0.00   0.0  0
 4GZ  CONST_05  N21  C16  C17  C18     0.00   0.0  0
 4GZ  CONST_06  N21  C20  C19  C18     0.00   0.0  0
 4GZ  CONST_07  C6   C5   C4   C3      0.00   0.0  0
 4GZ  CONST_08  C6   C7   C2   C3      0.00   0.0  0
 4GZ  CONST_09  C20  N21  C16  C17     0.00   0.0  0
 4GZ  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 4GZ  CONST_11  C16  C17  C18  C19     0.00   0.0  0
 4GZ  CONST_12  C16  N21  C20  C19     0.00   0.0  0
 4GZ  CONST_13  C8   C6   C5   C4    180.00   0.0  0
 4GZ  CONST_14  C1   C2   C3   C4    180.00   0.0  0
 4GZ  CONST_15  N15  C16  C17  C18   180.00   0.0  0
 4GZ  CONST_16  C22  C19  C18  C17   180.00   0.0  0
 4GZ  CONST_17  N15  C16  N21  C20   180.00   0.0  0
 4GZ  CONST_18  C1   C2   C7   C6    180.00   0.0  0
 4GZ  CONST_19  C8   C6   C7   C2    180.00   0.0  0
 4GZ  CONST_20  N21  C20  C19  C22   180.00   0.0  0
 4GZ  CONST_21  H4   C3   C4   C5    180.00   0.0  0
 4GZ  CONST_22  H6   C7   C6   C5    180.00   0.0  0
 4GZ  CONST_23  H7   C20  C19  C18   180.00   0.0  0
 4GZ  CONST_24  H2   C5   C4   C3    180.00   0.0  0
 4GZ  CONST_25  H3   C18  C19  C20   180.00   0.0  0
 4GZ  CONST_26  H1   C4   C5   C6    180.00   0.0  0
 4GZ  CONST_27  H5   C17  C18  C19   180.00   0.0  0
 4GZ  CONST_28  C14  N15  C16  C17     0.00   0.0  0
 4GZ  CONST_29  N21  C16  N15  C14   180.00   0.0  0
 4GZ  CONST_30  H29  N15  C16  C17   180.00   0.0  0
 4GZ  CONST_31  C11  N10  C8   C6    180.00   0.0  0
 4GZ  CONST_32  H30  N10  C8   C6      0.00   0.0  0
 4GZ  CONST_33  H27  N23  C22  C19     0.00   0.0  0
 4GZ  CONST_34  H28  N23  C22  C19   180.00   0.0  0
 4GZ  CONST_35  O9   C8   N10  C11     0.00   0.0  0
 4GZ  Var_01    C13  C25  C26  C27    57.06  30.0  1
 4GZ  Var_02    C13  C29  C28  C27   -53.48  30.0  1
 4GZ  Var_03    C29  C28  C27  C26    52.74  30.0  1
 4GZ  Var_04    C25  C26  C27  C28   -54.47  30.0  1
 4GZ  Var_05    O9   C8   C6   C5    151.17  30.0  2
 4GZ  Var_06    O24  C22  C19  C18    14.42  30.0  2
 4GZ  Var_07    C13  C14  N15  C16   179.04  30.0  1
 4GZ  Var_08    H18  C1   C2   C3     88.61  30.0  2
 4GZ  Var_09    N10  C11  C12  C13   177.91  30.0  1
 4GZ  Var_10    C12  C11  N10  C8   -171.12  30.0  1

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
 4GZ  chir_01  C13  C29  C25  C14  positiv

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
 4GZ  plan-1  C4   0.020
 4GZ  plan-1  C5   0.020
 4GZ  plan-1  C3   0.020
 4GZ  plan-1  C7   0.020
 4GZ  plan-1  C6   0.020
 4GZ  plan-1  C2   0.020
 4GZ  plan-1  C8   0.020
 4GZ  plan-1  C1   0.020
 4GZ  plan-1  H1   0.020
 4GZ  plan-1  H2   0.020
 4GZ  plan-1  H4   0.020
 4GZ  plan-1  H6   0.020
 4GZ  plan-2  C18  0.020
 4GZ  plan-2  C17  0.020
 4GZ  plan-2  C20  0.020
 4GZ  plan-2  C19  0.020
 4GZ  plan-2  C16  0.020
 4GZ  plan-2  N21  0.020
 4GZ  plan-2  N15  0.020
 4GZ  plan-2  H3   0.020
 4GZ  plan-2  H5   0.020
 4GZ  plan-2  H7   0.020
 4GZ  plan-2  C22  0.020
 4GZ  plan-3  C6   0.020
 4GZ  plan-3  C8   0.020
 4GZ  plan-3  C11  0.020
 4GZ  plan-3  N10  0.020
 4GZ  plan-3  O9   0.020
 4GZ  plan-3  H30  0.020
 4GZ  plan-4  C19  0.020
 4GZ  plan-4  N23  0.020
 4GZ  plan-4  O24  0.020
 4GZ  plan-4  H27  0.020
 4GZ  plan-4  H28  0.020
 4GZ  plan-4  C22  0.020
 4GZ  plan-5  C16  0.020
 4GZ  plan-5  C14  0.020
 4GZ  plan-5  N15  0.020
 4GZ  plan-5  H29  0.020

