# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:42:14 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (5S)-5-(3-aminopropyl)-3-(2,5-difluorophenyl)-N-ethyl-5-phenyl-4,5-dihydro-1H-pyrazole-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)N1N=C(C[C@@]1(CCCN)c2ccccc2)c3cc(F)ccc3F
#
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
 N9H  N9H  (5S)-5-(3-aminopropyl)-3-(2,5-difluorophenyl)-N-ethyl-5-phenyl-4,5-dihydro-1H-pyrazole-1-carboxamide  ligand  52  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N9H
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
 N9H  C1    C  CR6   0   0.562  -4.6804  -0.7781  -0.0602
 N9H  C2    C  CR16  0  -0.492  -3.3160  -0.8973   0.0951
 N9H  C3    C  CR6   0  -0.125  -2.4684   0.1403  -0.3048
 N9H  C4    C  CR6   0   0.533  -3.0688   1.2727  -0.8586
 N9H  C5    C  CR16  0  -0.391  -4.4352   1.3848  -1.0102
 N9H  C6    C  CR16  0  -0.403  -5.2628   0.3476  -0.6066
 N9H  C10   C  CR5   0   0.274  -1.0317  -0.0125  -0.1181
 N9H  N1    N  N     0  -0.233  -0.1761   0.8692  -0.4678
 N9H  N12   N  NR5   0  -0.410   1.0654   0.4431  -0.1649
 N9H  C13   C  CR5   0   0.074   1.1078  -0.8560   0.5285
 N9H  C14   C  CH2   0  -0.586  -0.3996  -1.2270   0.4969
 N9H  C17   C  CR6   0   0.199   1.9146  -1.8600  -0.2797
 N9H  C19   C  CR16  0  -0.302   1.8026  -1.8699  -1.6700
 N9H  C20   C  CR16  0  -0.244   2.4791  -2.8086  -2.4330
 N9H  C21   C  CR16  0  -0.271   3.2802  -3.7643  -1.8192
 N9H  C22   C  CR16  0  -0.238   3.3920  -3.7677  -0.4377
 N9H  C23   C  CR16  0  -0.335   2.7139  -2.8230   0.3251
 N9H  C29   C  C     0   0.763   2.1637   1.2217  -0.4580
 N9H  N30   N  NH1   0  -0.678   1.8959   2.3839  -1.0787
 N9H  C31   C  CH2   0  -0.250   2.9437   3.3118  -1.4503
 N9H  O39   O  O     0  -0.527   3.2908   0.8466  -0.1648
 N9H  F40   F  F     0  -0.295  -2.3104   2.2972  -1.2611
 N9H  F41   F  F     0  -0.313  -5.4651  -1.7913   0.3359
 N9H  C7    C  CH2   0  -0.455   1.5930  -0.7002   1.9758
 N9H  C8    C  CH2   0  -0.439   0.9416   0.4470   2.7375
 N9H  C9    C  CH3   0  -0.703   2.3438   4.5226  -2.1398
 N9H  C11   C  CH2   0  -0.268   1.3262   0.4295   4.2101
 N9H  N2    N  NH2   0  -0.801   0.7346   1.5600   4.9104
 N9H  H2    H  HCR6  0   0.297  -2.9105  -1.8023   0.5275
 N9H  H5    H  HCR6  0   0.295  -4.8541   2.2834  -1.4426
 N9H  H6    H  HCR6  0   0.296  -6.3360   0.4215  -0.7177
 N9H  H141  H  HCH2  0   0.291  -0.7859  -1.4347   1.4976
 N9H  H142  H  HCH2  0   0.300  -0.5952  -2.1189  -0.1026
 N9H  H19   H  HCR6  0   0.250   1.1870  -1.1340  -2.1741
 N9H  H20   H  HCR6  0   0.255   2.3800  -2.7932  -3.5108
 N9H  H21   H  HCR6  0   0.255   3.8091  -4.4978  -2.4135
 N9H  H22   H  HCR6  0   0.256   4.0089  -4.5072   0.0567
 N9H  H23   H  HCR6  0   0.255   2.8227  -2.8532   1.4007
 N9H  HN30  H  HNH1  0   0.402   0.9369   2.6253  -1.2689
 N9H  H311  H  HCH2  0   0.230   3.6604   2.8238  -2.1155
 N9H  H312  H  HCH2  0   0.229   3.4993   3.6299  -0.5643
 N9H  H71   H  HCH2  0   0.240   1.3784  -1.6382   2.4960
 N9H  H72   H  HCH2  0   0.250   2.6769  -0.5753   1.9953
 N9H  H81   H  HCH2  0   0.229   1.2393   1.4086   2.3125
 N9H  H82   H  HCH2  0   0.222  -0.1500   0.3953   2.6604
 N9H  H91   H  HCH3  0   0.234   1.8095   4.2399  -3.0478
 N9H  H92   H  HCH3  0   0.234   1.6498   5.0493  -1.4834
 N9H  H93   H  HCH3  0   0.245   3.1323   5.2195  -2.4199
 N9H  H111  H  HCH2  0   0.190   1.0503  -0.5450   4.6391
 N9H  H112  H  HCH2  0   0.215   2.4139   0.5051   4.2961
 N9H  HN21  H  HNH2  0   0.338  -0.2721   1.4492   4.9282
 N9H  HN22  H  HNH2  0   0.346   1.0243   1.5437   5.8799

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
 N9H  C1   C2    aromatic  1.378  0.020  1.378
 N9H  C1   C6    aromatic  1.380  0.020  1.380
 N9H  C1   F41   single    1.341  0.020  1.341
 N9H  C2   C3    aromatic  1.398  0.020  1.398
 N9H  C2   H2    single    0.930  0.020  1.080
 N9H  C3   C4    aromatic  1.396  0.020  1.396
 N9H  C3   C10   single    1.457  0.020  1.457
 N9H  C4   C5    aromatic  1.379  0.020  1.379
 N9H  C4   F40   single    1.337  0.020  1.337
 N9H  C5   C6    aromatic  1.387  0.020  1.387
 N9H  C5   H5    single    0.930  0.020  1.080
 N9H  C6   H6    single    0.930  0.020  1.080
 N9H  C10  N1    double    1.277  0.020  1.277
 N9H  C10  C14   single    1.501  0.020  1.501
 N9H  N1   N12   single    1.347  0.020  1.347
 N9H  N12  C13   single    1.473  0.020  1.473
 N9H  N12  C29   single    1.378  0.020  1.378
 N9H  C13  C14   single    1.553  0.020  1.553
 N9H  C13  C17   single    1.521  0.020  1.521
 N9H  C13  C7    single    1.534  0.020  1.534
 N9H  C14  H141  single    0.970  0.020  1.090
 N9H  C14  H142  single    0.970  0.020  1.090
 N9H  C17  C19   aromatic  1.395  0.020  1.395
 N9H  C17  C23   aromatic  1.390  0.020  1.390
 N9H  C19  C20   aromatic  1.386  0.020  1.386
 N9H  C19  H19   single    0.930  0.020  1.080
 N9H  C20  C21   aromatic  1.390  0.020  1.390
 N9H  C20  H20   single    0.930  0.020  1.080
 N9H  C21  C22   aromatic  1.386  0.020  1.386
 N9H  C21  H21   single    0.930  0.020  1.080
 N9H  C22  C23   aromatic  1.391  0.020  1.391
 N9H  C22  H22   single    0.930  0.020  1.080
 N9H  C23  H23   single    0.930  0.020  1.080
 N9H  C29  N30   single    1.345  0.020  1.345
 N9H  C29  O39   double    1.224  0.020  1.224
 N9H  N30  C31   single    1.448  0.020  1.448
 N9H  N30  HN30  single    0.860  0.020  1.020
 N9H  C31  C9    single    1.517  0.020  1.517
 N9H  C31  H311  single    0.970  0.020  1.090
 N9H  C31  H312  single    0.970  0.020  1.090
 N9H  C7   C8    single    1.523  0.020  1.523
 N9H  C7   H71   single    0.970  0.020  1.090
 N9H  C7   H72   single    0.970  0.020  1.090
 N9H  C8   C11   single    1.522  0.020  1.522
 N9H  C8   H81   single    0.970  0.020  1.090
 N9H  C8   H82   single    0.970  0.020  1.090
 N9H  C9   H91   single    0.970  0.020  1.090
 N9H  C9   H92   single    0.970  0.020  1.090
 N9H  C9   H93   single    0.970  0.020  1.090
 N9H  C11  N2    single    1.456  0.020  1.456
 N9H  C11  H111  single    0.970  0.020  1.090
 N9H  C11  H112  single    0.970  0.020  1.090
 N9H  N2   HN21  single    0.890  0.020  1.040
 N9H  N2   HN22  single    0.890  0.020  1.040

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
 N9H  F41   C1   C6    119.09  3.000
 N9H  F41   C1   C2    118.72  3.000
 N9H  C6    C1   C2    122.19  3.000
 N9H  H2    C2   C3    120.52  3.000
 N9H  H2    C2   C1    119.23  3.000
 N9H  C3    C2   C1    120.25  3.000
 N9H  C10   C3   C4    124.06  3.000
 N9H  C10   C3   C2    118.90  3.000
 N9H  C4    C3   C2    117.04  3.000
 N9H  F40   C4   C5    117.82  3.000
 N9H  F40   C4   C3    119.80  3.000
 N9H  C5    C4   C3    122.38  3.000
 N9H  H5    C5   C6    120.43  3.000
 N9H  H5    C5   C4    119.68  3.000
 N9H  C6    C5   C4    119.89  3.000
 N9H  H6    C6   C5    120.74  3.000
 N9H  H6    C6   C1    121.01  3.000
 N9H  C5    C6   C1    118.25  3.000
 N9H  C14   C10  N1    112.87  3.000
 N9H  C14   C10  C3    123.55  3.000
 N9H  N1    C10  C3    123.57  3.000
 N9H  N12   N1   C10   109.72  3.000
 N9H  C29   N12  C13   125.14  3.000
 N9H  C29   N12  N1    120.53  3.000
 N9H  C13   N12  N1    114.29  3.000
 N9H  C7    C13  C17   113.62  3.000
 N9H  C7    C13  C14   110.52  3.000
 N9H  C17   C13  C14   110.27  3.000
 N9H  C7    C13  N12   111.31  3.000
 N9H  C17   C13  N12   110.32  3.000
 N9H  C14   C13  N12    99.97  3.000
 N9H  H142  C14  H141  106.51  3.000
 N9H  H142  C14  C13   112.35  3.000
 N9H  H141  C14  C13   111.72  3.000
 N9H  H142  C14  C10   111.12  3.000
 N9H  H141  C14  C10   112.34  3.000
 N9H  C13   C14  C10   102.94  3.000
 N9H  C23   C17  C19   118.36  3.000
 N9H  C23   C17  C13   122.09  3.000
 N9H  C19   C17  C13   119.47  3.000
 N9H  H19   C19  C20   118.76  3.000
 N9H  H19   C19  C17   120.29  3.000
 N9H  C20   C19  C17   120.95  3.000
 N9H  H20   C20  C21   120.15  3.000
 N9H  H20   C20  C19   119.59  3.000
 N9H  C21   C20  C19   120.26  3.000
 N9H  H21   C21  C22   120.42  3.000
 N9H  H21   C21  C20   120.35  3.000
 N9H  C22   C21  C20   119.24  3.000
 N9H  H22   C22  C23   119.43  3.000
 N9H  H22   C22  C21   120.20  3.000
 N9H  C23   C22  C21   120.38  3.000
 N9H  H23   C23  C22   118.53  3.000
 N9H  H23   C23  C17   120.66  3.000
 N9H  C22   C23  C17   120.81  3.000
 N9H  O39   C29  N30   124.00  3.000
 N9H  O39   C29  N12   120.67  3.000
 N9H  N30   C29  N12   115.34  3.000
 N9H  HN30  N30  C31   119.15  3.000
 N9H  HN30  N30  C29   118.95  3.000
 N9H  C31   N30  C29   121.88  3.000
 N9H  H312  C31  H311  106.86  3.000
 N9H  H312  C31  C9    109.70  3.000
 N9H  H311  C31  C9    109.82  3.000
 N9H  H312  C31  N30   110.26  3.000
 N9H  H311  C31  N30   110.16  3.000
 N9H  C9    C31  N30   109.99  3.000
 N9H  H72   C7   H71   106.53  3.000
 N9H  H72   C7   C8    109.25  3.000
 N9H  H71   C7   C8    108.91  3.000
 N9H  H72   C7   C13   110.03  3.000
 N9H  H71   C7   C13   107.42  3.000
 N9H  C8    C7   C13   114.39  3.000
 N9H  H82   C8   H81   106.60  3.000
 N9H  H82   C8   C11   108.62  3.000
 N9H  H81   C8   C11   108.51  3.000
 N9H  H82   C8   C7    110.82  3.000
 N9H  H81   C8   C7    110.60  3.000
 N9H  C11   C8   C7    111.54  3.000
 N9H  H93   C9   H92   107.84  3.000
 N9H  H93   C9   H91   107.84  3.000
 N9H  H92   C9   H91   108.32  3.000
 N9H  H93   C9   C31   109.96  3.000
 N9H  H92   C9   C31   111.31  3.000
 N9H  H91   C9   C31   111.42  3.000
 N9H  H112  C11  H111  106.26  3.000
 N9H  H112  C11  N2    108.22  3.000
 N9H  H111  C11  N2    113.48  3.000
 N9H  H112  C11  C8    109.06  3.000
 N9H  H111  C11  C8    108.92  3.000
 N9H  N2    C11  C8    110.72  3.000
 N9H  HN22  N2   HN21  105.42  3.000
 N9H  HN22  N2   C11   109.40  3.000
 N9H  HN21  N2   C11   109.11  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
 N9H  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 N9H  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 N9H  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 N9H  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 N9H  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 N9H  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 N9H  CONST_07  C21   C20  C19  C17     0.00   0.0  0
 N9H  CONST_08  C21   C22  C23  C17     0.00   0.0  0
 N9H  CONST_09  C22   C23  C17  C19     0.00   0.0  0
 N9H  CONST_10  C22   C21  C20  C19     0.00   0.0  0
 N9H  CONST_11  C23   C17  C19  C20     0.00   0.0  0
 N9H  CONST_12  C23   C22  C21  C20     0.00   0.0  0
 N9H  CONST_13  C10   C3   C2   C1    180.00   0.0  0
 N9H  CONST_14  C10   C3   C4   C5    180.00   0.0  0
 N9H  CONST_15  C20   C19  C17  C13   180.00   0.0  0
 N9H  CONST_16  C22   C23  C17  C13   180.00   0.0  0
 N9H  CONST_17  F40   C4   C3   C2    180.00   0.0  0
 N9H  CONST_18  F41   C1   C2   C3    180.00   0.0  0
 N9H  CONST_19  F41   C1   C6   C5    180.00   0.0  0
 N9H  CONST_20  F40   C4   C5   C6    180.00   0.0  0
 N9H  CONST_21  F40   C4   C3   C10     0.00   0.0  0
 N9H  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 N9H  CONST_23  H6    C6   C1   C2    180.00   0.0  0
 N9H  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 N9H  CONST_25  H19   C19  C17  C13     0.00   0.0  0
 N9H  CONST_26  H23   C23  C17  C13     0.00   0.0  0
 N9H  CONST_27  H20   C20  C19  C17   180.00   0.0  0
 N9H  CONST_28  H22   C22  C23  C17   180.00   0.0  0
 N9H  CONST_29  H21   C21  C20  C19   180.00   0.0  0
 N9H  CONST_30  O39   C29  N12  N1    180.00   0.0  0
 N9H  CONST_31  O39   C29  N12  C13     0.00   0.0  0
 N9H  CONST_32  N30   C29  N12  N1      0.00   0.0  0
 N9H  CONST_33  N30   C29  N12  C13   180.00   0.0  0
 N9H  CONST_34  C31   N30  C29  N12   180.00   0.0  0
 N9H  CONST_35  HN30  N30  C29  N12     0.00   0.0  0
 N9H  CONST_36  O39   C29  N30  C31     0.00   0.0  0
 N9H  Var_01    N1    C10  C3   C2    178.97  30.0  2
 N9H  Var_02    C13   C14  C10  C3   -177.17  30.0  1
 N9H  Var_03    C13   N12  N1   C10    -2.80  30.0  1
 N9H  Var_04    C11   C8   C7   C13   172.39  30.0  3
 N9H  Var_05    C9    C31  N30  C29   179.60  30.0  3
 N9H  Var_06    N2    C11  C8   C7    177.90  30.0  3
 N9H  Var_07    H91   C9   C31  N30   -60.42  30.0  3
 N9H  Var_08    HN21  N2   C11  C8     66.76  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
 N9H  chir_01  C13  C14  C17  N12  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
 N9H  plan-1  C1    0.020
 N9H  plan-1  C2    0.020
 N9H  plan-1  C3    0.020
 N9H  plan-1  C4    0.020
 N9H  plan-1  C5    0.020
 N9H  plan-1  C6    0.020
 N9H  plan-1  C10   0.020
 N9H  plan-1  F40   0.020
 N9H  plan-1  F41   0.020
 N9H  plan-1  H2    0.020
 N9H  plan-1  H5    0.020
 N9H  plan-1  H6    0.020
 N9H  plan-2  C13   0.020
 N9H  plan-2  C17   0.020
 N9H  plan-2  C19   0.020
 N9H  plan-2  C20   0.020
 N9H  plan-2  C21   0.020
 N9H  plan-2  C22   0.020
 N9H  plan-2  C23   0.020
 N9H  plan-2  H19   0.020
 N9H  plan-2  H20   0.020
 N9H  plan-2  H21   0.020
 N9H  plan-2  H22   0.020
 N9H  plan-2  H23   0.020
 N9H  plan-3  N1    0.020
 N9H  plan-3  N12   0.020
 N9H  plan-3  C13   0.020
 N9H  plan-3  C29   0.020
 N9H  plan-3  N30   0.020
 N9H  plan-3  C31   0.020
 N9H  plan-3  O39   0.020
 N9H  plan-3  HN30  0.020

