# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 01:57:42 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-(3-cyclopropyl-1H-pyrazol-5-yl)-2-[4-(trifluoromethoxy)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)Oc1ccc(CC(=O)Nc2[nH]nc(c2)C3CC3)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
 09K  09K  N-(3-cyclopropyl-1H-pyrazol-5-yl)-2-[4-(trifluoromethoxy)phenyl]acetamide  ligand  37  23  .  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_09K
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
 09K  C1    C  CT    0   1.072  -5.3529   0.8752   0.1380
 09K  F1    F  F     0  -0.300  -4.9193   1.5024  -0.9579
 09K  N1    N  NH1   0  -0.741   2.5280  -1.6336  -0.0255
 09K  O1    O  O2    0  -0.523  -5.1124  -0.4403   0.1123
 09K  C2    C  CR6   0   0.299  -3.7854  -0.8581   0.0646
 09K  F2    F  F     0  -0.300  -4.7837   1.4852   1.1794
 09K  N2    N  NR15  0  -0.513   4.8745  -1.3724  -0.0168
 09K  O2    O  O     0  -0.442   0.9393  -0.0208  -0.0086
 09K  C3    C  CR16  0  -0.285  -3.1766  -1.0469  -1.1636
 09K  F3    F  F     0  -0.277  -6.6634   1.0429   0.2214
 09K  N3    N  N     0  -0.318   5.8497  -0.4551  -0.0078
 09K  C4    C  CR16  0  -0.298  -1.8755  -1.5262  -1.1985
 09K  C5    C  CR6   0   0.157  -1.1856  -1.8173  -0.0267
 09K  C6    C  CR16  0  -0.297  -1.8264  -1.6223   1.1922
 09K  C7    C  CR16  0  -0.284  -3.1264  -1.1426   1.2478
 09K  C8    C  CH2   0  -0.704   0.2239  -2.3220  -0.0750
 09K  C9    C  C     0   0.560   1.2397  -1.1952  -0.0311
 09K  C10   C  CR5   0   0.639   3.6464  -0.8238  -0.0088
 09K  C11   C  CR5   0   0.332   5.2274   0.7071   0.0093
 09K  C12   C  CR15  0  -0.563   3.8245   0.5438   0.0101
 09K  C13   C  CH1   0  -0.352   5.9933   1.9644   0.0250
 09K  C14   C  CH2   0  -0.481   5.4322   3.2016  -0.6197
 09K  C15   C  CH2   0  -0.479   5.5339   3.1238   0.8670
 09K  HN1   H  HNH1  0   0.426   2.6816  -2.6312  -0.0464
 09K  H3    H  HCR6  0   0.280  -3.7090  -0.8431  -2.0831
 09K  H4    H  HCR6  0   0.264  -1.3985  -1.6820  -2.1580
 09K  H6    H  HCR6  0   0.264  -1.3116  -1.8521   2.1167
 09K  H7    H  HCR6  0   0.280  -3.6216  -1.0096   2.2005
 09K  H8    H  HCH2  0   0.306   0.4178  -3.0053   0.7565
 09K  H8A   H  HCH2  0   0.308   0.3933  -2.9032  -0.9862
 09K  H12   H  HCR5  0   0.270   3.0695   1.3076   0.0190
 09K  H13   H  HCH1  0   0.260   7.0654   1.8237  -0.0525
 09K  H14   H  HCH2  0   0.259   6.1194   3.8454  -1.1531
 09K  H14A  H  HCH2  0   0.252   4.4485   3.1318  -1.0679
 09K  H15   H  HCH2  0   0.252   4.6219   2.9996   1.4378
 09K  H15A  H  HCH2  0   0.258   6.2931   3.7130   1.3648
 09K  HN2   H  HNR5  0   0.419   5.1079  -2.3523  -0.0367

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
 09K  O1   C1    single    1.338  0.020  1.338
 09K  F3   C1    single    1.324  0.020  1.324
 09K  C1   F1    single    1.335  0.020  1.335
 09K  C1   F2    single    1.334  0.020  1.334
 09K  C9   N1    single    1.361  0.020  1.361
 09K  C10  N1    single    1.381  0.020  1.381
 09K  N1   HN1   single    0.860  0.020  1.020
 09K  C2   O1    single    1.392  0.020  1.392
 09K  C3   C2    aromatic  1.384  0.020  1.384
 09K  C2   C7    aromatic  1.384  0.020  1.384
 09K  C10  N2    aromatic  1.345  0.020  1.345
 09K  N3   N2    aromatic  1.339  0.020  1.339
 09K  O2   C9    double    1.212  0.020  1.212
 09K  C4   C3    aromatic  1.387  0.020  1.387
 09K  C3   H3    single    0.930  0.020  1.080
 09K  C11  N3    aromatic  1.318  0.020  1.318
 09K  C4   C5    aromatic  1.391  0.020  1.391
 09K  C4   H4    single    0.930  0.020  1.080
 09K  C8   C5    single    1.498  0.020  1.498
 09K  C5   C6    aromatic  1.391  0.020  1.391
 09K  C6   C7    aromatic  1.387  0.020  1.387
 09K  C6   H6    single    0.930  0.020  1.080
 09K  C7   H7    single    0.930  0.020  1.080
 09K  C9   C8    single    1.518  0.020  1.518
 09K  C8   H8    single    0.970  0.020  1.090
 09K  C8   H8A   single    0.970  0.020  1.090
 09K  C12  C10   aromatic  1.379  0.020  1.379
 09K  C13  C11   single    1.472  0.020  1.472
 09K  C12  C11   aromatic  1.412  0.020  1.412
 09K  C12  H12   single    0.930  0.020  1.080
 09K  C15  C13   single    1.505  0.020  1.505
 09K  C14  C13   single    1.504  0.020  1.504
 09K  C13  H13   single    0.970  0.020  1.090
 09K  C15  C14   single    1.492  0.020  1.492
 09K  C14  H14   single    0.970  0.020  1.090
 09K  C14  H14A  single    0.970  0.020  1.090
 09K  C15  H15   single    0.970  0.020  1.090
 09K  C15  H15A  single    0.970  0.020  1.090
 09K  N2   HN2   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
 09K  F3    C1   F2   108.37  3.000
 09K  F2    C1   O1   112.83  3.000
 09K  F3    C1   O1   107.69  3.000
 09K  F2    C1   F1   106.70  3.000
 09K  F3    C1   F1   108.29  3.000
 09K  O1    C1   F1   112.82  3.000
 09K  HN1   N1   C10  117.16  3.000
 09K  HN1   N1   C9   117.54  3.000
 09K  C10   N1   C9   125.30  3.000
 09K  C2    O1   C1   117.85  3.000
 09K  C7    C2   C3   121.42  3.000
 09K  C7    C2   O1   119.10  3.000
 09K  C3    C2   O1   119.39  3.000
 09K  HN2   N2   C10  127.47  3.000
 09K  HN2   N2   N3   119.85  3.000
 09K  C10   N2   N3   112.67  3.000
 09K  H3    C3   C4   120.35  3.000
 09K  H3    C3   C2   120.81  3.000
 09K  C4    C3   C2   118.83  3.000
 09K  C11   N3   N2   105.09  3.000
 09K  H4    C4   C5   119.87  3.000
 09K  H4    C4   C3   119.03  3.000
 09K  C5    C4   C3   121.10  3.000
 09K  C8    C5   C6   120.60  3.000
 09K  C6    C5   C4   118.72  3.000
 09K  C8    C5   C4   120.67  3.000
 09K  H6    C6   C7   119.00  3.000
 09K  H6    C6   C5   119.96  3.000
 09K  C7    C6   C5   121.03  3.000
 09K  H7    C7   C6   120.45  3.000
 09K  H7    C7   C2   120.64  3.000
 09K  C6    C7   C2   118.90  3.000
 09K  H8A   C8   H8   105.90  3.000
 09K  H8A   C8   C9   108.35  3.000
 09K  H8    C8   C9   108.86  3.000
 09K  H8A   C8   C5   110.59  3.000
 09K  H8    C8   C5   110.66  3.000
 09K  C9    C8   C5   112.25  3.000
 09K  C8    C9   O2   123.63  3.000
 09K  C8    C9   N1   113.24  3.000
 09K  O2    C9   N1   123.13  3.000
 09K  C12   C10  N2   106.65  3.000
 09K  C12   C10  N1   133.33  3.000
 09K  N2    C10  N1   120.01  3.000
 09K  C13   C11  C12  127.99  3.000
 09K  C12   C11  N3   111.53  3.000
 09K  C13   C11  N3   120.49  3.000
 09K  H12   C12  C11  128.03  3.000
 09K  H12   C12  C10  127.91  3.000
 09K  C11   C12  C10  104.06  3.000
 09K  H13   C13  C15  116.23  3.000
 09K  H13   C13  C14  116.44  3.000
 09K  C15   C13  C14   59.47  3.000
 09K  H13   C13  C11  113.76  3.000
 09K  C14   C13  C11  120.26  3.000
 09K  C15   C13  C11  120.33  3.000
 09K  H14A  C14  H14  114.27  3.000
 09K  H14A  C14  C15  118.08  3.000
 09K  H14   C14  C15  118.61  3.000
 09K  H14A  C14  C13  117.60  3.000
 09K  H14   C14  C13  117.63  3.000
 09K  C15   C14  C13   60.30  3.000
 09K  H15A  C15  H15  114.25  3.000
 09K  H15A  C15  C14  118.53  3.000
 09K  H15   C15  C14  118.28  3.000
 09K  H15A  C15  C13  117.56  3.000
 09K  H15   C15  C13  117.63  3.000
 09K  C14   C15  C13   60.23  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
 09K  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 09K  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 09K  CONST_03  C11  C12  C10  N2      0.00   0.0  0
 09K  CONST_04  C12  C11  N3   N2      0.00   0.0  0
 09K  CONST_05  C6   C7   C2   C3      0.00   0.0  0
 09K  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 09K  CONST_07  C12  C10  N2   N3      0.00   0.0  0
 09K  CONST_08  C10  C12  C11  N3      0.00   0.0  0
 09K  CONST_09  C7   C2   C3   C4      0.00   0.0  0
 09K  CONST_10  C7   C6   C5   C4      0.00   0.0  0
 09K  CONST_11  C11  N3   N2   C10     0.00   0.0  0
 09K  CONST_12  C13  C11  N3   N2    180.00   0.0  0
 09K  CONST_13  C13  C11  C12  C10   180.00   0.0  0
 09K  CONST_14  N3   N2   C10  N1    180.00   0.0  0
 09K  CONST_15  C11  C12  C10  N1    180.00   0.0  0
 09K  CONST_16  C4   C3   C2   O1    180.00   0.0  0
 09K  CONST_17  C6   C7   C2   O1    180.00   0.0  0
 09K  CONST_18  C8   C5   C4   C3    180.00   0.0  0
 09K  CONST_19  C8   C5   C6   C7    180.00   0.0  0
 09K  CONST_20  H4   C4   C3   C2    180.00   0.0  0
 09K  CONST_21  H6   C6   C7   C2    180.00   0.0  0
 09K  CONST_22  H12  C12  C10  N2    180.00   0.0  0
 09K  CONST_23  H7   C7   C2   C3    180.00   0.0  0
 09K  CONST_24  H3   C3   C4   C5    180.00   0.0  0
 09K  CONST_25  HN2  N2   N3   C11   180.00   0.0  0
 09K  CONST_26  C9   N1   C10  N2    180.00   0.0  0
 09K  CONST_27  C12  C10  N1   C9      0.00   0.0  0
 09K  CONST_28  HN1  N1   C10  N2      0.00   0.0  0
 09K  CONST_29  C10  N1   C9   O2      0.00   0.0  0
 09K  CONST_30  C10  N1   C9   C8    180.00   0.0  0
 09K  Var_01    C15  C13  C11  N3   -140.55  30.0  1
 09K  Var_02    C14  C15  C13  C11  -109.44  30.0  1
 09K  Var_03    C3   C2   O1   C1    -90.08  30.0  2
 09K  Var_04    C9   C8   C5   C4     90.56  30.0  2
 09K  Var_05    C5   C8   C9   N1    177.78  30.0  3
 09K  Var_06    F3   C1   O1   C2   -178.20  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
 09K  chir_01  C13  C11  C15  C14  both

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
 09K  plan-1  N1   0.020
 09K  plan-1  N2   0.020
 09K  plan-1  N3   0.020
 09K  plan-1  C10  0.020
 09K  plan-1  C11  0.020
 09K  plan-1  C12  0.020
 09K  plan-1  C13  0.020
 09K  plan-1  H12  0.020
 09K  plan-1  HN2  0.020
 09K  plan-2  O1   0.020
 09K  plan-2  C2   0.020
 09K  plan-2  C3   0.020
 09K  plan-2  C4   0.020
 09K  plan-2  C5   0.020
 09K  plan-2  C6   0.020
 09K  plan-2  C7   0.020
 09K  plan-2  C8   0.020
 09K  plan-2  H3   0.020
 09K  plan-2  H4   0.020
 09K  plan-2  H6   0.020
 09K  plan-2  H7   0.020
 09K  plan-3  N1   0.020
 09K  plan-3  O2   0.020
 09K  plan-3  C8   0.020
 09K  plan-3  C9   0.020
 09K  plan-3  C10  0.020
 09K  plan-3  HN1  0.020

