# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 00:36:09 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  47  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  -3.9645  -2.1030   0.3514
 KHM  C13   C  CR5    0  -0.383   0.2568   0.7630  -0.3372
 KHM  C17   C  CH2    0  -0.440   3.6535  -1.8438  -1.6747
 KHM  C20   C  CH2    0  -0.419   5.3453   0.2571  -0.5309
 KHM  C21   C  CH1    0  -0.400   4.6808  -0.7905   0.3694
 KHM  C22   C  C      0   0.441   4.4441  -0.2391   1.7878
 KHM  C26   C  CR15   0  -0.027   0.6551   2.1092  -0.3003
 KHM  C02   C  CR6    0   0.658  -2.6993   2.5864   0.0806
 KHM  C03   C  CR16   0  -0.514  -3.6815   1.6340   0.1384
 KHM  C04   C  CR6    0   0.262  -3.3226   0.2729   0.0159
 KHM  C05   C  CR6    0   0.052  -4.3503  -0.7869   0.0864
 KHM  C06   C  CR16   0  -0.318  -5.7041  -0.5107  -0.1077
 KHM  C07   C  CR16   0  -0.237  -6.6493  -1.5227  -0.0299
 KHM  C08   C  CR16   0  -0.256  -6.2568  -2.8253   0.2455
 KHM  C09   C  CR16   0  -0.239  -4.9102  -3.1116   0.4347
 KHM  N11   N  N      0  -0.462  -2.0771  -0.1201  -0.1466
 KHM  C12   C  CR56   0   0.637  -1.1312   0.8131  -0.2004
 KHM  N15   N  NH1    0  -0.677   2.3908  -0.2571  -0.2453
 KHM  C16   C  CH1    0  -0.060   3.3785  -1.3231  -0.2620
 KHM  C18   C  CH2    0  -0.430   4.3148  -0.7984  -2.5639
 KHM  C19   C  CH2    0  -0.430   5.6021  -0.2815  -1.9334
 KHM  O23   O  OC    -1  -0.608   3.7954   0.8365   1.8621
 KHM  O24   O  O      0  -0.594   4.8975  -0.8802   2.7507
 KHM  O25   O  O      0  -0.498   0.6017  -1.5116  -0.8630
 KHM  N28   N  N      0  -0.424  -1.4272   2.1606  -0.0922
 KHM  N27   N  N      0  -0.292  -0.3478   2.9519  -0.1586
 KHM  H101  H  HCR6   0   0.263  -2.9174  -2.3295   0.4987
 KHM  H172  H  HCH2   0   0.217   4.3133  -2.7135  -1.5840
 KHM  H171  H  HCH2   0   0.238   2.7283  -2.2057  -2.1237
 KHM  H201  H  HCH2   0   0.211   4.7183   1.1510  -0.5934
 KHM  H202  H  HCH2   0   0.227   6.2867   0.5766  -0.0749
 KHM  H211  H  HCH1   0   0.220   5.3541  -1.6510   0.4405
 KHM  H261  H  HCR5   0   0.276   1.6574   2.5015  -0.3945
 KHM  H011  H  HOH1   0   0.507  -3.7663   4.1259   0.3087
 KHM  H031  H  HCR6   0   0.302  -4.7022   1.9438   0.3061
 KHM  H061  H  HCR6   0   0.258  -6.0366   0.4920  -0.3416
 KHM  H071  H  HCR6   0   0.263  -7.6942  -1.2910  -0.1882
 KHM  H081  H  HCR6   0   0.263  -6.9956  -3.6131   0.3102
 KHM  H091  H  HCR6   0   0.262  -4.5955  -4.1241   0.6502
 KHM  H151  H  HNH1   0   0.400   2.6633   0.5253   0.3481
 KHM  H161  H  HCH1   0   0.238   3.0167  -2.1613   0.3472
 KHM  H181  H  HCH2   0   0.225   4.5173  -1.2277  -3.5482
 KHM  H182  H  HCH2   0   0.212   3.6250   0.0361  -2.7256
 KHM  H192  H  HCH2   0   0.224   6.0496   0.4955  -2.5583
 KHM  H191  H  HCH2   0   0.206   6.3315  -1.0973  -1.8808
 KHM  O01   O  OH1    0  -0.565  -2.8379   3.8864   0.1845
 KHM  C14   C  C      0   0.493   1.0845  -0.4427  -0.5036

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   deloc     1.243  0.020  1.243
 KHM  C22  C21   single    1.540  0.020  1.540
 KHM  C22  O23   deloc     1.258  0.020  1.258
 KHM  C21  C16   single    1.542  0.020  1.542
 KHM  C21  C20   single    1.533  0.020  1.533
 KHM  C16  C17   single    1.531  0.020  1.531
 KHM  C16  N15   single    1.453  0.020  1.453
 KHM  C18  C17   single    1.523  0.020  1.523
 KHM  C18  C19   single    1.524  0.020  1.524
 KHM  C20  C19   single    1.524  0.020  1.524
 KHM  O25  C14   double    1.227  0.020  1.227
 KHM  N15  C14   single    1.344  0.020  1.344
 KHM  C14  C13   single    1.472  0.020  1.472
 KHM  C13  C26   aromatic  1.404  0.020  1.404
 KHM  C13  C12   aromatic  1.396  0.020  1.396
 KHM  C26  N27   aromatic  1.318  0.020  1.318
 KHM  C12  N11   aromatic  1.330  0.020  1.330
 KHM  C12  N28   aromatic  1.384  0.020  1.384
 KHM  N11  C04   aromatic  1.316  0.020  1.316
 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  1.340  0.020  1.340
 KHM  N28  C02   aromatic  1.353  0.020  1.353
 KHM  C04  C05   single    1.478  0.020  1.478
 KHM  C04  C03   aromatic  1.413  0.020  1.413
 KHM  C05  C10   aromatic  1.397  0.020  1.397
 KHM  C08  C09   aromatic  1.390  0.020  1.390
 KHM  C02  C03   aromatic  1.369  0.020  1.369
 KHM  C02  O01   single    1.312  0.020  1.312
 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    0.890  0.020  1.040
 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

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   120.03  3.000
 KHM  H101  C10  C05   119.38  3.000
 KHM  C09   C10  C05   120.60  3.000
 KHM  C14   C13  C12   126.85  3.000
 KHM  C12   C13  C26   104.18  3.000
 KHM  C14   C13  C26   128.96  3.000
 KHM  H171  C17  H172  106.37  3.000
 KHM  H171  C17  C18   110.84  3.000
 KHM  H172  C17  C18   109.37  3.000
 KHM  H171  C17  C16   109.92  3.000
 KHM  H172  C17  C16   107.57  3.000
 KHM  C18   C17  C16   112.54  3.000
 KHM  H202  C20  H201  106.17  3.000
 KHM  H202  C20  C19   109.99  3.000
 KHM  H201  C20  C19   109.44  3.000
 KHM  H202  C20  C21   109.14  3.000
 KHM  H201  C20  C21   110.10  3.000
 KHM  C19   C20  C21   111.84  3.000
 KHM  H211  C21  C16   105.93  3.000
 KHM  H211  C21  C22   108.42  3.000
 KHM  C16   C21  C22   111.77  3.000
 KHM  H211  C21  C20   107.98  3.000
 KHM  C16   C21  C20   111.20  3.000
 KHM  C22   C21  C20   111.27  3.000
 KHM  O24   C22  O23   125.70  3.000
 KHM  O23   C22  C21   116.08  3.000
 KHM  O24   C22  C21   118.22  3.000
 KHM  H261  C26  N27   118.90  3.000
 KHM  H261  C26  C13   127.50  3.000
 KHM  N27   C26  C13   113.58  3.000
 KHM  N28   C02  C03   117.45  3.000
 KHM  C03   C02  O01   127.62  3.000
 KHM  N28   C02  O01   114.93  3.000
 KHM  H031  C03  C04   122.00  3.000
 KHM  H031  C03  C02   119.01  3.000
 KHM  C04   C03  C02   118.96  3.000
 KHM  N11   C04  C05   116.74  3.000
 KHM  C05   C04  C03   120.66  3.000
 KHM  N11   C04  C03   122.60  3.000
 KHM  C06   C05  C04   121.74  3.000
 KHM  C04   C05  C10   119.52  3.000
 KHM  C06   C05  C10   118.74  3.000
 KHM  H061  C06  C07   118.61  3.000
 KHM  H061  C06  C05   120.78  3.000
 KHM  C07   C06  C05   120.60  3.000
 KHM  H071  C07  C08   120.21  3.000
 KHM  H071  C07  C06   119.59  3.000
 KHM  C08   C07  C06   120.21  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   120.12  3.000
 KHM  H091  C09  C10   119.66  3.000
 KHM  C08   C09  C10   120.22  3.000
 KHM  C12   N11  C04   117.94  3.000
 KHM  N28   C12  N11   121.87  3.000
 KHM  N28   C12  C13   104.79  3.000
 KHM  N11   C12  C13   133.33  3.000
 KHM  H151  N15  C16   112.84  3.000
 KHM  H151  N15  C14   118.53  3.000
 KHM  C16   N15  C14   123.83  3.000
 KHM  H161  C16  N15   109.26  3.000
 KHM  H161  C16  C21   108.36  3.000
 KHM  N15   C16  C21   108.41  3.000
 KHM  H161  C16  C17   108.16  3.000
 KHM  N15   C16  C17   112.47  3.000
 KHM  C21   C16  C17   110.10  3.000
 KHM  H182  C18  H181  106.45  3.000
 KHM  H182  C18  C19   109.57  3.000
 KHM  H181  C18  C19   110.45  3.000
 KHM  H182  C18  C17   109.62  3.000
 KHM  H181  C18  C17   109.67  3.000
 KHM  C19   C18  C17   110.97  3.000
 KHM  H191  C19  H192  106.51  3.000
 KHM  H191  C19  C18   109.26  3.000
 KHM  H192  C19  C18   110.52  3.000
 KHM  H191  C19  C20   109.34  3.000
 KHM  H192  C19  C20   110.11  3.000
 KHM  C18   C19  C20   111.00  3.000
 KHM  N27   N28  C12   113.51  3.000
 KHM  N27   N28  C02   125.31  3.000
 KHM  C12   N28  C02   121.17  3.000
 KHM  N28   N27  C26   103.93  3.000
 KHM  H011  O01  C02   110.93  3.000
 KHM  O25   C14  N15   123.99  3.000
 KHM  N15   C14  C13   114.30  3.000
 KHM  O25   C14  C13   121.70  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  Var_01    C20   C19  C18  C17   -55.32  30.0  1
 KHM  Var_02    C18   C19  C20  C21    55.70  30.0  1
 KHM  Var_03    C19   C18  C17  C16    55.96  30.0  1
 KHM  Var_04    O25   C14  C13  C26  -160.63  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  O01   0.020
 KHM  plan-2  C14   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

