# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 10:15:55 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (1R,2S,5R)-N-(4-methoxyphenyl)-5-methyl-2-(propan-2-yl)cyclohexane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)[C@@H]2C[C@H](C)CC[C@H]2C(C)C)cc1
#
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
 KXS  KXS  (1R,2S,5R)-N-(4-methoxyphenyl)-5-methyl-2-(propan-2-yl)cyclohexane-1-carboxamide  ligand  48  21  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KXS
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
 KXS  C12   C  CR16  0  -0.276  -2.5071  -0.7182   0.7217
 KXS  C14   C  CR6   0   0.373  -4.6660   0.0021  -0.0820
 KXS  C15   C  CR16  0  -0.336  -4.0396   0.5735  -1.1908
 KXS  C16   C  CR16  0  -0.305  -2.6662   0.5103  -1.3266
 KXS  C18   C  CH3   0  -0.436  -6.6835  -0.4668   1.0729
 KXS  C01   C  CH3   0  -0.654   4.3455  -3.2329   0.4655
 KXS  C02   C  CH1   0  -0.234   3.8493  -1.8919  -0.0574
 KXS  C03   C  CH2   0  -0.405   4.7370  -0.7404   0.3998
 KXS  C04   C  CH2   0  -0.439   4.2312   0.6015  -0.1144
 KXS  C05   C  CH1   0  -0.188   2.7896   0.8811   0.3161
 KXS  C06   C  CH1   0  -0.392   1.8884  -0.2781  -0.1359
 KXS  C07   C  CH2   0  -0.391   2.4104  -1.6290   0.3734
 KXS  C08   C  C     0   0.553   0.4693  -0.1084   0.3693
 KXS  C11   C  CR6   0   0.328  -1.8810  -0.1380  -0.3742
 KXS  C13   C  CR16  0  -0.380  -3.8864  -0.6438   0.8731
 KXS  N10   N  NH1   0  -0.742  -0.4909  -0.2146  -0.5809
 KXS  O09   O  O     0  -0.479   0.2197   0.0682   1.5511
 KXS  O17   O  O2    0  -0.472  -6.0073   0.1189  -0.0213
 KXS  H121  H  HCR6  0   0.269  -1.9338  -1.2459   1.4690
 KXS  H151  H  HCR6  0   0.265  -4.6346   1.0764  -1.9429
 KXS  H161  H  HCR6  0   0.268  -2.1970   0.9689  -2.1885
 KXS  H182  H  HCH3  0   0.260  -7.7415  -0.2614   0.9291
 KXS  H183  H  HCH3  0   0.228  -6.5385  -1.5496   1.1113
 KXS  H181  H  HCH3  0   0.228  -6.3701  -0.0356   2.0275
 KXS  H201  H  HCH3  0   0.217   1.5157   1.7000  -2.1190
 KXS  H203  H  HCH3  0   0.231   1.8287   3.4130  -1.9168
 KXS  H202  H  HCH3  0   0.220   3.1719   2.2986  -2.1328
 KXS  H011  H  HCH3  0   0.213   4.3257  -3.2616   1.5576
 KXS  H012  H  HCH3  0   0.224   3.7291  -4.0567   0.1009
 KXS  H013  H  HCH3  0   0.225   5.3724  -3.4221   0.1477
 KXS  H021  H  HCH1  0   0.211   3.8753  -1.9238  -1.1545
 KXS  H031  H  HCH2  0   0.206   4.7673  -0.7257   1.4960
 KXS  H032  H  HCH2  0   0.226   5.7654  -0.9039   0.0649
 KXS  H041  H  HCH2  0   0.234   4.8875   1.3975   0.2443
 KXS  H042  H  HCH2  0   0.213   4.3026   0.6125  -1.2074
 KXS  H051  H  HCH1  0   0.217   2.7726   0.8894   1.4136
 KXS  H061  H  HCH1  0   0.242   1.8885  -0.3172  -1.2318
 KXS  H071  H  HCH2  0   0.235   1.7616  -2.4320   0.0097
 KXS  H072  H  HCH2  0   0.218   2.3536  -1.6463   1.4673
 KXS  H131  H  HCR6  0   0.281  -4.3297  -1.1089   1.7428
 KXS  H213  H  HCH3  0   0.223   3.1429   3.2878   1.5641
 KXS  H212  H  HCH3  0   0.217   4.0998   3.4305   0.0910
 KXS  H211  H  HCH3  0   0.228   2.6170   4.3586   0.2661
 KXS  H101  H  HNH1  0   0.407  -0.1830  -0.2993  -1.5371
 KXS  C19   C  CH1   0  -0.235   2.2709   2.2579  -0.1422
 KXS  C21   C  CH3   0  -0.658   3.0804   3.3937   0.4790
 KXS  C20   C  CH3   0  -0.663   2.1961   2.4185  -1.6590
 KXS  H191  H  HCH1  0   0.225   1.2497   2.3625   0.2425

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
 KXS  C18  O17   single    1.413  0.020  1.413
 KXS  O17  C14   single    1.348  0.020  1.348
 KXS  C14  C15   aromatic  1.396  0.020  1.396
 KXS  C14  C13   aromatic  1.392  0.020  1.392
 KXS  C15  C16   aromatic  1.382  0.020  1.382
 KXS  C13  C12   aromatic  1.390  0.020  1.390
 KXS  C16  C11   aromatic  1.394  0.020  1.394
 KXS  C12  C11   aromatic  1.389  0.020  1.389
 KXS  C11  N10   single    1.407  0.020  1.407
 KXS  N10  C08   single    1.355  0.020  1.355
 KXS  C21  C19   single    1.527  0.020  1.527
 KXS  C08  O09   double    1.221  0.020  1.221
 KXS  C08  C06   single    1.516  0.020  1.516
 KXS  C19  C20   single    1.527  0.020  1.527
 KXS  C19  C05   single    1.541  0.020  1.541
 KXS  C06  C05   single    1.536  0.020  1.536
 KXS  C06  C07   single    1.535  0.020  1.535
 KXS  C05  C04   single    1.530  0.020  1.530
 KXS  C07  C02   single    1.525  0.020  1.525
 KXS  C04  C03   single    1.523  0.020  1.523
 KXS  C02  C03   single    1.524  0.020  1.524
 KXS  C02  C01   single    1.523  0.020  1.523
 KXS  C12  H121  single    0.930  0.020  1.080
 KXS  C15  H151  single    0.930  0.020  1.080
 KXS  C16  H161  single    0.930  0.020  1.080
 KXS  C18  H182  single    0.970  0.020  1.090
 KXS  C18  H183  single    0.970  0.020  1.090
 KXS  C18  H181  single    0.970  0.020  1.090
 KXS  C20  H201  single    0.970  0.020  1.090
 KXS  C20  H203  single    0.970  0.020  1.090
 KXS  C20  H202  single    0.970  0.020  1.090
 KXS  C01  H011  single    0.970  0.020  1.090
 KXS  C01  H012  single    0.970  0.020  1.090
 KXS  C01  H013  single    0.970  0.020  1.090
 KXS  C02  H021  single    0.970  0.020  1.090
 KXS  C03  H031  single    0.970  0.020  1.090
 KXS  C03  H032  single    0.970  0.020  1.090
 KXS  C04  H041  single    0.970  0.020  1.090
 KXS  C04  H042  single    0.970  0.020  1.090
 KXS  C05  H051  single    0.970  0.020  1.090
 KXS  C06  H061  single    0.970  0.020  1.090
 KXS  C07  H071  single    0.970  0.020  1.090
 KXS  C07  H072  single    0.970  0.020  1.090
 KXS  C13  H131  single    0.930  0.020  1.080
 KXS  C19  H191  single    0.970  0.020  1.090
 KXS  C21  H213  single    0.970  0.020  1.090
 KXS  C21  H212  single    0.970  0.020  1.090
 KXS  C21  H211  single    0.970  0.020  1.090
 KXS  N10  H101  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
 KXS  H121  C12  C13   118.55  3.000
 KXS  H121  C12  C11   120.72  3.000
 KXS  C13   C12  C11   120.73  3.000
 KXS  O17   C14  C13   124.52  3.000
 KXS  C13   C14  C15   118.93  3.000
 KXS  O17   C14  C15   116.55  3.000
 KXS  H151  C15  C16   119.95  3.000
 KXS  H151  C15  C14   119.69  3.000
 KXS  C16   C15  C14   120.36  3.000
 KXS  H161  C16  C11   119.77  3.000
 KXS  H161  C16  C15   119.30  3.000
 KXS  C11   C16  C15   120.93  3.000
 KXS  H181  C18  H183  108.78  3.000
 KXS  H181  C18  H182  108.66  3.000
 KXS  H183  C18  H182  108.71  3.000
 KXS  H181  C18  O17   112.05  3.000
 KXS  H183  C18  O17   111.97  3.000
 KXS  H182  C18  O17   106.55  3.000
 KXS  H013  C01  H012  107.65  3.000
 KXS  H013  C01  H011  107.67  3.000
 KXS  H012  C01  H011  107.68  3.000
 KXS  H013  C01  C02   111.06  3.000
 KXS  H012  C01  C02   111.47  3.000
 KXS  H011  C01  C02   111.13  3.000
 KXS  H021  C02  C07   108.04  3.000
 KXS  H021  C02  C03   107.94  3.000
 KXS  C07   C02  C03   109.55  3.000
 KXS  H021  C02  C01   108.05  3.000
 KXS  C03   C02  C01   111.87  3.000
 KXS  C07   C02  C01   111.25  3.000
 KXS  H032  C03  H031  106.38  3.000
 KXS  H032  C03  C04   109.90  3.000
 KXS  H031  C03  C04   109.56  3.000
 KXS  H032  C03  C02   110.05  3.000
 KXS  H031  C03  C02   109.03  3.000
 KXS  C04   C03  C02   111.77  3.000
 KXS  H042  C04  H041  106.33  3.000
 KXS  H042  C04  C05   109.90  3.000
 KXS  H041  C04  C05   109.91  3.000
 KXS  H042  C04  C03   108.90  3.000
 KXS  H041  C04  C03   109.37  3.000
 KXS  C05   C04  C03   112.25  3.000
 KXS  H051  C05  C19   106.58  3.000
 KXS  H051  C05  C06   106.91  3.000
 KXS  C19   C05  C06   112.90  3.000
 KXS  H051  C05  C04   107.30  3.000
 KXS  C06   C05  C04   109.39  3.000
 KXS  C19   C05  C04   113.37  3.000
 KXS  H061  C06  C08   109.70  3.000
 KXS  H061  C06  C07   107.46  3.000
 KXS  C08   C06  C07   107.83  3.000
 KXS  H061  C06  C05   108.72  3.000
 KXS  C07   C06  C05   111.52  3.000
 KXS  C08   C06  C05   111.51  3.000
 KXS  H072  C07  H071  106.83  3.000
 KXS  H072  C07  C06   109.12  3.000
 KXS  H071  C07  C06   109.50  3.000
 KXS  H072  C07  C02   109.17  3.000
 KXS  H071  C07  C02   109.81  3.000
 KXS  C06   C07  C02   112.26  3.000
 KXS  O09   C08  N10   123.05  3.000
 KXS  O09   C08  C06   122.02  3.000
 KXS  N10   C08  C06   114.89  3.000
 KXS  N10   C11  C16   118.76  3.000
 KXS  N10   C11  C12   122.57  3.000
 KXS  C16   C11  C12   118.64  3.000
 KXS  H131  C13  C14   121.46  3.000
 KXS  H131  C13  C12   118.13  3.000
 KXS  C14   C13  C12   120.40  3.000
 KXS  H101  N10  C11   116.46  3.000
 KXS  H101  N10  C08   117.08  3.000
 KXS  C11   N10  C08   126.34  3.000
 KXS  C18   O17  C14   118.37  3.000
 KXS  H191  C19  C21   106.27  3.000
 KXS  H191  C19  C05   107.12  3.000
 KXS  C21   C19  C05   111.42  3.000
 KXS  H191  C19  C20   107.03  3.000
 KXS  C05   C19  C20   113.94  3.000
 KXS  C21   C19  C20   110.60  3.000
 KXS  H211  C21  H212  107.31  3.000
 KXS  H211  C21  H213  107.69  3.000
 KXS  H212  C21  H213  107.64  3.000
 KXS  H211  C21  C19   110.68  3.000
 KXS  H212  C21  C19   112.07  3.000
 KXS  H213  C21  C19   111.25  3.000
 KXS  H202  C20  H203  107.38  3.000
 KXS  H202  C20  H201  107.59  3.000
 KXS  H203  C20  H201  106.90  3.000
 KXS  H202  C20  C19   112.08  3.000
 KXS  H203  C20  C19   110.30  3.000
 KXS  H201  C20  C19   112.33  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
 KXS  CONST_01  C15   C14  C13  C12     0.00   0.0  0
 KXS  CONST_02  C15   C16  C11  C12     0.00   0.0  0
 KXS  CONST_03  C11   C16  C15  C14     0.00   0.0  0
 KXS  CONST_04  C11   C12  C13  C14     0.00   0.0  0
 KXS  CONST_05  C13   C14  C15  C16     0.00   0.0  0
 KXS  CONST_06  C13   C12  C11  C16     0.00   0.0  0
 KXS  CONST_07  O17   C14  C13  C12   180.00   0.0  0
 KXS  CONST_08  N10   C11  C16  C15   180.00   0.0  0
 KXS  CONST_09  O17   C14  C15  C16   180.00   0.0  0
 KXS  CONST_10  N10   C11  C12  C13   180.00   0.0  0
 KXS  CONST_11  H161  C16  C11  C12   180.00   0.0  0
 KXS  CONST_12  H121  C12  C13  C14   180.00   0.0  0
 KXS  CONST_13  H131  C13  C14  C15   180.00   0.0  0
 KXS  CONST_14  H151  C15  C16  C11   180.00   0.0  0
 KXS  CONST_15  C11   N10  C08  C06   180.00   0.0  0
 KXS  CONST_19  O09   C08  N10  C11     0.00   0.0  0
 KXS  Var_01    C05   C04  C03  C02    57.11  30.0  1
 KXS  Var_02    C13   C14  O17  C18    -0.94  30.0  2
 KXS  Var_03    H182  C18  O17  C14  -179.86  30.0  3
 KXS  Var_04    H213  C21  C19  C05   -52.04  30.0  3
 KXS  Var_05    H201  C20  C19  C05    61.20  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
 KXS  chir_01  C02  C07  C03  C01  negativ
 KXS  chir_02  C05  C04  C06  C19  positiv
 KXS  chir_03  C06  C07  C05  C08  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
 KXS  plan-1  C12   0.020
 KXS  plan-1  C14   0.020
 KXS  plan-1  C15   0.020
 KXS  plan-1  C16   0.020
 KXS  plan-1  C11   0.020
 KXS  plan-1  C13   0.020
 KXS  plan-1  N10   0.020
 KXS  plan-1  O17   0.020
 KXS  plan-1  H121  0.020
 KXS  plan-1  H151  0.020
 KXS  plan-1  H161  0.020
 KXS  plan-1  H131  0.020
 KXS  plan-2  C06   0.020
 KXS  plan-2  C08   0.020
 KXS  plan-2  C11   0.020
 KXS  plan-2  N10   0.020
 KXS  plan-2  O09   0.020
 KXS  plan-2  H101  0.020

