# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 22:50:52 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (1R,2S)-2-[(7-hydroxy-5-phenylpyrazolo[1,5-a]pyrimidine-3-carbonyl)amino]cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCCC[C@@H]1NC(=O)c2cnn3c(O)cc(nc23)c4ccccc4
#
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
 KHM  KHM  '(1R,2S)-2-[(7-hydroxy-5-phenylpyrazolo[1,5-a]pyrimidine-3-carbonyl)amino]cyclohexane-1-carboxylic acid'  ligand  48  28  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KHM
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
 KHM  C10   C  CR16  0  -0.280  -3.9420  -2.0883   0.4289
 KHM  C13   C  CR5   0  -0.394   0.2940   0.7968   0.0490
 KHM  C17   C  CH2   0  -0.421   3.6425  -1.8330  -1.7073
 KHM  C20   C  CH2   0  -0.442   5.4025   0.2521  -0.5911
 KHM  C21   C  CH1   0  -0.413   4.7170  -0.7802   0.3097
 KHM  C22   C  C     0   0.582   4.4938  -0.3401   1.7412
 KHM  C26   C  CR15  0  -0.024   0.6803   2.1476   0.0440
 KHM  C02   C  CR6   0   0.662  -2.6977   2.6085   0.1199
 KHM  C03   C  CR16  0  -0.513  -3.6757   1.6497   0.1371
 KHM  C04   C  CR6   0   0.266  -3.3004   0.2885   0.1071
 KHM  C05   C  CR6   0   0.052  -4.3207  -0.7803   0.1166
 KHM  C06   C  CR16  0  -0.320  -5.6581  -0.5235  -0.1870
 KHM  C07   C  CR16  0  -0.236  -6.5944  -1.5467  -0.1723
 KHM  C08   C  CR16  0  -0.256  -6.2095  -2.8411   0.1482
 KHM  C09   C  CR16  0  -0.238  -4.8791  -3.1079   0.4481
 KHM  N11   N  N     0  -0.462  -2.0419  -0.0978   0.0825
 KHM  C12   C  CR56  0   0.645  -1.1018   0.8404   0.0809
 KHM  N15   N  NH1   0  -0.668   2.4137  -0.2278  -0.2901
 KHM  C16   C  CH1   0  -0.087   3.4022  -1.2886  -0.2983
 KHM  C18   C  CH2   0  -0.449   4.3187  -0.8103  -2.6127
 KHM  C19   C  CH2   0  -0.432   5.6188  -0.3130  -1.9923
 KHM  O23   O  OH1   0  -0.587   5.3107   0.6331   2.1230
 KHM  O24   O  O     0  -0.440   3.6847  -0.8398   2.4831
 KHM  O25   O  O     0  -0.484   0.6700  -1.5030   0.3906
 KHM  N28   N  N     0  -0.426  -1.4126   2.1874   0.0851
 KHM  N27   N  N     0  -0.289  -0.3352   2.9851   0.0677
 KHM  H101  H  HCR6  0   0.265  -2.9069  -2.2998   0.6605
 KHM  H172  H  HCH2  0   0.228   4.2744  -2.7237  -1.6286
 KHM  H171  H  HCH2  0   0.243   2.6906  -2.1610  -2.1300
 KHM  H201  H  HCH2  0   0.221   4.8049   1.1688  -0.6508
 KHM  H202  H  HCH2  0   0.256   6.3620   0.5449  -0.1647
 KHM  H211  H  HCH1  0   0.298   5.3874  -1.6487   0.3787
 KHM  H261  H  HCR5  0   0.275   1.6832   2.5504   0.0412
 KHM  H011  H  HOH1  0   0.508  -3.7906   4.1463   0.1540
 KHM  H031  H  HCR6  0   0.303  -4.7094   1.9582   0.1907
 KHM  H061  H  HCR6  0   0.258  -5.9843   0.4718  -0.4575
 KHM  H071  H  HCR6  0   0.264  -7.6261  -1.3294  -0.4149
 KHM  H081  H  HCR6  0   0.264  -6.9414  -3.6379   0.1617
 KHM  H091  H  HCR6  0   0.262  -4.5701  -4.1141   0.6986
 KHM  H151  H  HNH1  0   0.395   2.6716   0.6556  -0.6990
 KHM  H161  H  HCH1  0   0.271   3.0106  -2.0906   0.3246
 KHM  H181  H  HCH2  0   0.241   4.5112  -1.2531  -3.5920
 KHM  H182  H  HCH2  0   0.215   3.6454   0.0358  -2.7903
 KHM  H192  H  HCH2  0   0.239   6.0786   0.4479  -2.6260
 KHM  H191  H  HCH2  0   0.218   6.3308  -1.1429  -1.9342
 KHM  H1    H  HOH1  0   0.481   5.1499   0.8504   3.0539
 KHM  C14   C  C     0   0.517   1.1231  -0.4143   0.0655
 KHM  O01   O  OH1   0  -0.564  -2.8529   3.9101   0.1403

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
 KHM  O24  C22   double    1.206  0.020  1.206
 KHM  C22  C21   single    1.514  0.020  1.514
 KHM  C22  O23   single    1.327  0.020  1.327
 KHM  C21  C16   single    1.535  0.020  1.535
 KHM  C21  C20   single    1.532  0.020  1.532
 KHM  C16  C17   single    1.530  0.020  1.530
 KHM  C16  N15   single    1.450  0.020  1.450
 KHM  C18  C17   single    1.524  0.020  1.524
 KHM  C18  C19   single    1.524  0.020  1.524
 KHM  C20  C19   single    1.526  0.020  1.526
 KHM  O25  C14   double    1.223  0.020  1.223
 KHM  N15  C14   single    1.352  0.020  1.352
 KHM  C14  C13   single    1.468  0.020  1.468
 KHM  C13  C26   aromatic  1.405  0.020  1.405
 KHM  C13  C12   aromatic  1.397  0.020  1.397
 KHM  C26  N27   aromatic  1.317  0.020  1.317
 KHM  C12  N11   aromatic  1.328  0.020  1.328
 KHM  C12  N28   aromatic  1.382  0.020  1.382
 KHM  N11  C04   aromatic  1.317  0.020  1.317
 KHM  C07  C06   aromatic  1.387  0.020  1.387
 KHM  C07  C08   aromatic  1.388  0.020  1.388
 KHM  C06  C05   aromatic  1.395  0.020  1.395
 KHM  N27  N28   aromatic  1.341  0.020  1.341
 KHM  N28  C02   aromatic  1.353  0.020  1.353
 KHM  C04  C05   single    1.478  0.020  1.478
 KHM  C04  C03   aromatic  1.412  0.020  1.412
 KHM  C05  C10   aromatic  1.397  0.020  1.397
 KHM  C08  C09   aromatic  1.390  0.020  1.390
 KHM  C02  C03   aromatic  1.370  0.020  1.370
 KHM  C02  O01   single    1.311  0.020  1.311
 KHM  C10  C09   aromatic  1.385  0.020  1.385
 KHM  C10  H101  single    0.930  0.020  1.080
 KHM  C17  H172  single    0.970  0.020  1.090
 KHM  C17  H171  single    0.970  0.020  1.090
 KHM  C20  H201  single    0.970  0.020  1.090
 KHM  C20  H202  single    0.970  0.020  1.090
 KHM  C21  H211  single    0.970  0.020  1.090
 KHM  C26  H261  single    0.930  0.020  1.080
 KHM  O01  H011  single    0.850  0.020  0.980
 KHM  C03  H031  single    0.930  0.020  1.080
 KHM  C06  H061  single    0.930  0.020  1.080
 KHM  C07  H071  single    0.930  0.020  1.080
 KHM  C08  H081  single    0.930  0.020  1.080
 KHM  C09  H091  single    0.930  0.020  1.080
 KHM  N15  H151  single    0.860  0.020  1.020
 KHM  C16  H161  single    0.970  0.020  1.090
 KHM  C18  H181  single    0.970  0.020  1.090
 KHM  C18  H182  single    0.970  0.020  1.090
 KHM  C19  H192  single    0.970  0.020  1.090
 KHM  C19  H191  single    0.970  0.020  1.090
 KHM  O23  H1    single    0.850  0.020  0.980

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
 KHM  H101  C10  C09   120.04  3.000
 KHM  H101  C10  C05   119.37  3.000
 KHM  C09   C10  C05   120.59  3.000
 KHM  C14   C13  C12   126.16  3.000
 KHM  C12   C13  C26   104.17  3.000
 KHM  C14   C13  C26   129.64  3.000
 KHM  H171  C17  H172  106.65  3.000
 KHM  H171  C17  C18   111.00  3.000
 KHM  H172  C17  C18   109.43  3.000
 KHM  H171  C17  C16   109.06  3.000
 KHM  H172  C17  C16   108.30  3.000
 KHM  C18   C17  C16   112.22  3.000
 KHM  H202  C20  H201  106.06  3.000
 KHM  H202  C20  C19   109.50  3.000
 KHM  H201  C20  C19   109.69  3.000
 KHM  H202  C20  C21   110.18  3.000
 KHM  H201  C20  C21   110.59  3.000
 KHM  C19   C20  C21   110.72  3.000
 KHM  H211  C21  C16   106.59  3.000
 KHM  H211  C21  C22   105.08  3.000
 KHM  C16   C21  C22   110.15  3.000
 KHM  H211  C21  C20   107.24  3.000
 KHM  C16   C21  C20   111.93  3.000
 KHM  C22   C21  C20   115.21  3.000
 KHM  O24   C22  O23   122.68  3.000
 KHM  O23   C22  C21   113.24  3.000
 KHM  O24   C22  C21   124.06  3.000
 KHM  H261  C26  N27   118.61  3.000
 KHM  H261  C26  C13   127.84  3.000
 KHM  N27   C26  C13   113.54  3.000
 KHM  N28   C02  C03   117.44  3.000
 KHM  C03   C02  O01   127.61  3.000
 KHM  N28   C02  O01   114.95  3.000
 KHM  H031  C03  C04   122.05  3.000
 KHM  H031  C03  C02   118.95  3.000
 KHM  C04   C03  C02   118.99  3.000
 KHM  N11   C04  C05   116.61  3.000
 KHM  C05   C04  C03   120.90  3.000
 KHM  N11   C04  C03   122.49  3.000
 KHM  C06   C05  C04   121.82  3.000
 KHM  C04   C05  C10   119.44  3.000
 KHM  C06   C05  C10   118.74  3.000
 KHM  H061  C06  C07   118.54  3.000
 KHM  H061  C06  C05   120.85  3.000
 KHM  C07   C06  C05   120.60  3.000
 KHM  H071  C07  C08   120.23  3.000
 KHM  H071  C07  C06   119.55  3.000
 KHM  C08   C07  C06   120.22  3.000
 KHM  H081  C08  C09   120.23  3.000
 KHM  H081  C08  C07   120.14  3.000
 KHM  C09   C08  C07   119.63  3.000
 KHM  H091  C09  C08   120.13  3.000
 KHM  H091  C09  C10   119.64  3.000
 KHM  C08   C09  C10   120.23  3.000
 KHM  C12   N11  C04   117.99  3.000
 KHM  N28   C12  N11   121.96  3.000
 KHM  N28   C12  C13   104.78  3.000
 KHM  N11   C12  C13   133.25  3.000
 KHM  H151  N15  C16   117.71  3.000
 KHM  H151  N15  C14   118.18  3.000
 KHM  C16   N15  C14   123.47  3.000
 KHM  H161  C16  N15   106.89  3.000
 KHM  H161  C16  C21   109.00  3.000
 KHM  N15   C16  C21   109.84  3.000
 KHM  H161  C16  C17   108.75  3.000
 KHM  N15   C16  C17   111.88  3.000
 KHM  C21   C16  C17   110.37  3.000
 KHM  H182  C18  H181  106.03  3.000
 KHM  H182  C18  C19   109.77  3.000
 KHM  H181  C18  C19   110.31  3.000
 KHM  H182  C18  C17   109.99  3.000
 KHM  H181  C18  C17   109.80  3.000
 KHM  C19   C18  C17   110.83  3.000
 KHM  H191  C19  H192  106.57  3.000
 KHM  H191  C19  C18   109.21  3.000
 KHM  H192  C19  C18   110.52  3.000
 KHM  H191  C19  C20   108.90  3.000
 KHM  H192  C19  C20   109.54  3.000
 KHM  C18   C19  C20   111.94  3.000
 KHM  H1    O23  C22   109.80  3.000
 KHM  N27   N28  C12   113.52  3.000
 KHM  N27   N28  C02   125.35  3.000
 KHM  C12   N28  C02   121.12  3.000
 KHM  N28   N27  C26   103.98  3.000
 KHM  O25   C14  N15   123.12  3.000
 KHM  N15   C14  C13   115.00  3.000
 KHM  O25   C14  C13   121.88  3.000
 KHM  H011  O01  C02   110.94  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
 KHM  CONST_01  C07   C06  C05  C10    0.00   0.0  0
 KHM  CONST_04  C07   C08  C09  C10    0.00   0.0  0
 KHM  CONST_05  N28   N27  C26  C13    0.00   0.0  0
 KHM  CONST_06  C04   N11  C12  C13  180.00   0.0  0
 KHM  CONST_07  N27   N28  C12  C13    0.00   0.0  0
 KHM  CONST_08  C02   N28  C12  C13  180.00   0.0  0
 KHM  CONST_09  N11   C12  C13  C26  180.00   0.0  0
 KHM  CONST_10  N28   C12  C13  C26    0.00   0.0  0
 KHM  CONST_11  C12   N28  N27  C26    0.00   0.0  0
 KHM  CONST_12  C02   N28  N27  C26  180.00   0.0  0
 KHM  CONST_13  N11   C12  N28  C02    0.00   0.0  0
 KHM  CONST_14  N11   C04  C03  C02    0.00   0.0  0
 KHM  CONST_15  C05   C04  C03  C02  180.00   0.0  0
 KHM  CONST_16  C12   N11  C04  C03    0.00   0.0  0
 KHM  CONST_18  C12   N28  C02  C03    0.00   0.0  0
 KHM  CONST_19  N27   N28  C02  C03  180.00   0.0  0
 KHM  CONST_20  N28   C12  N11  C04    0.00   0.0  0
 KHM  CONST_21  C07   C06  C05  C04  180.00   0.0  0
 KHM  CONST_22  C09   C10  C05  C04  180.00   0.0  0
 KHM  CONST_23  N28   C02  C03  C04    0.00   0.0  0
 KHM  CONST_24  C08   C07  C06  C05    0.00   0.0  0
 KHM  CONST_25  C12   N11  C04  C05  180.00   0.0  0
 KHM  CONST_26  C08   C09  C10  C05    0.00   0.0  0
 KHM  CONST_27  C09   C08  C07  C06    0.00   0.0  0
 KHM  CONST_29  C09   C10  C05  C06    0.00   0.0  0
 KHM  CONST_30  N27   N28  C12  N11  180.00   0.0  0
 KHM  CONST_31  N27   C26  C13  C12    0.00   0.0  0
 KHM  CONST_32  C12   N28  C02  O01  180.00   0.0  0
 KHM  CONST_33  N27   N28  C02  O01    0.00   0.0  0
 KHM  CONST_34  C04   C03  C02  O01  180.00   0.0  0
 KHM  CONST_35  C14   C13  C12  N11    0.00   0.0  0
 KHM  CONST_36  N27   C26  C13  C14  180.00   0.0  0
 KHM  CONST_37  N28   C12  C13  C14  180.00   0.0  0
 KHM  CONST_38  H061  C06  C05  C10  180.00   0.0  0
 KHM  CONST_39  H081  C08  C09  C10  180.00   0.0  0
 KHM  CONST_40  H101  C10  C05  C04    0.00   0.0  0
 KHM  CONST_41  H071  C07  C06  C05  180.00   0.0  0
 KHM  CONST_42  H031  C03  C04  C05    0.00   0.0  0
 KHM  CONST_43  H091  C09  C10  C05  180.00   0.0  0
 KHM  CONST_44  H261  C26  C13  C12  180.00   0.0  0
 KHM  CONST_45  C16   N15  C14  C13  180.00   0.0  0
 KHM  CONST_46  O25   C14  N15  C16    0.00   0.0  0
 KHM  CONST_47  H151  N15  C14  C13    0.00   0.0  0
 KHM  CONST_48  H1    O23  C22  C21  180.00   0.0  0
 KHM  Var_01    C20   C19  C18  C17  -55.37  30.0  1
 KHM  Var_02    C18   C19  C20  C21   55.26  30.0  1
 KHM  Var_03    C19   C18  C17  C16   55.38  30.0  1
 KHM  Var_04    O25   C14  C13  C26  161.91  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
 KHM  chir_01  C21  C22  C16  C20  negativ
 KHM  chir_02  C16  N15  C17  C21  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
 KHM  plan-1  C10   0.020
 KHM  plan-1  C04   0.020
 KHM  plan-1  C05   0.020
 KHM  plan-1  C06   0.020
 KHM  plan-1  C07   0.020
 KHM  plan-1  C08   0.020
 KHM  plan-1  C09   0.020
 KHM  plan-1  H101  0.020
 KHM  plan-1  H061  0.020
 KHM  plan-1  H071  0.020
 KHM  plan-1  H081  0.020
 KHM  plan-1  H091  0.020
 KHM  plan-2  C13   0.020
 KHM  plan-2  C26   0.020
 KHM  plan-2  C02   0.020
 KHM  plan-2  C03   0.020
 KHM  plan-2  C04   0.020
 KHM  plan-2  C05   0.020
 KHM  plan-2  N11   0.020
 KHM  plan-2  C12   0.020
 KHM  plan-2  N28   0.020
 KHM  plan-2  N27   0.020
 KHM  plan-2  H261  0.020
 KHM  plan-2  H031  0.020
 KHM  plan-2  C14   0.020
 KHM  plan-2  O01   0.020
 KHM  plan-3  C13   0.020
 KHM  plan-3  N15   0.020
 KHM  plan-3  C16   0.020
 KHM  plan-3  O25   0.020
 KHM  plan-3  H151  0.020
 KHM  plan-3  C14   0.020
 KHM  plan-4  C21   0.020
 KHM  plan-4  C22   0.020
 KHM  plan-4  O23   0.020
 KHM  plan-4  O24   0.020
 KHM  plan-4  H1    0.020

