# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:45:27 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 4-chloro-N-cyclopentyl-1-methyl-1H-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(Cl)c(n1)C(=O)NC2CCCC2
#
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
 JHP  JHP  4-chloro-N-cyclopentyl-1-methyl-1H-pyrazole-3-carboxamide  ligand  29  15  .  2022-07-25  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_JHP
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
 JHP  C10   C   CH1   0  -0.056  -2.5816  -0.0289   0.2347
 JHP  C13   C   CH2   0  -0.457  -4.7236  -0.3284  -0.7803
 JHP  C01   C   CH3   0  -0.506   3.1851   2.8956  -0.1386
 JHP  N02   N   NR5   0  -0.254   2.6511   1.5543  -0.0572
 JHP  C03   C   CR15  0   0.101   3.3458   0.4035  -0.0504
 JHP  C04   C   CR5   0  -0.302   2.4131  -0.6023   0.0387
 JHP  C05   C   CR5   0   0.230   1.1701   0.0506   0.0808
 JHP  N06   N   N     0  -0.302   1.3515   1.3620   0.0203
 JHP  C07   C   C     0   0.532  -0.1836  -0.5431   0.1836
 JHP  O08   O   O     0  -0.483  -0.3336  -1.7531   0.2783
 JHP  N09   N   NH1   0  -0.660  -1.1886   0.3439   0.1762
 JHP  C11   C   CH2   0  -0.461  -3.4589   1.0936   0.7879
 JHP  C12   C   CH2   0  -0.447  -4.8845   0.7286   0.3396
 JHP  C14   C   CH2   0  -0.437  -3.2322  -0.3421  -1.1130
 JHP  H101  H   HCH1  0   0.244  -2.6701  -0.9063   0.8810
 JHP  H132  H   HCH2  0   0.229  -5.0284  -1.3111  -0.4153
 JHP  H131  H   HCH2  0   0.235  -5.3411  -0.1099  -1.6515
 JHP  H013  H   HCH3  0   0.271   2.8674   3.4739   0.7257
 JHP  H011  H   HCH3  0   0.266   4.2690   2.8413  -0.1529
 JHP  H012  H   HCH3  0   0.270   2.8392   3.3815  -1.0482
 JHP  H031  H   HCR5  0   0.318   4.4212   0.3711  -0.1072
 JHP  H091  H   HNH1  0   0.400  -0.9636   1.3164   0.0287
 JHP  H112  H   HCH2  0   0.245  -3.3631   1.2028   1.8686
 JHP  H111  H   HCH2  0   0.229  -3.1519   2.0429   0.3389
 JHP  H121  H   HCH2  0   0.233  -5.4176   1.6113  -0.0141
 JHP  H122  H   HCH2  0   0.233  -5.4657   0.3255   1.1694
 JHP  H141  H   HCH2  0   0.220  -2.9849   0.4520  -1.8242
 JHP  H142  H   HCH2  0   0.239  -2.8915  -1.2873  -1.5380
 JHP  CL15  CL  CL    0  -0.130   2.7581  -2.2731   0.0813

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
 JHP  CL15  C04   single    1.707  0.020  1.707
 JHP  C03   C04   aromatic  1.375  0.020  1.375
 JHP  C03   N02   aromatic  1.344  0.020  1.344
 JHP  C04   C05   aromatic  1.405  0.020  1.405
 JHP  N02   C01   single    1.446  0.020  1.446
 JHP  N02   N06   aromatic  1.316  0.020  1.316
 JHP  C05   N06   aromatic  1.325  0.020  1.325
 JHP  C05   C07   single    1.482  0.020  1.482
 JHP  N09   C07   single    1.340  0.020  1.340
 JHP  N09   C10   single    1.443  0.020  1.443
 JHP  C11   C10   single    1.528  0.020  1.528
 JHP  C11   C12   single    1.538  0.020  1.538
 JHP  C14   C10   single    1.529  0.020  1.529
 JHP  C14   C13   single    1.528  0.020  1.528
 JHP  C07   O08   double    1.223  0.020  1.223
 JHP  C12   C13   single    1.548  0.020  1.548
 JHP  C10   H101  single    0.970  0.020  1.090
 JHP  C13   H132  single    0.970  0.020  1.090
 JHP  C13   H131  single    0.970  0.020  1.090
 JHP  C01   H013  single    0.970  0.020  1.090
 JHP  C01   H011  single    0.970  0.020  1.090
 JHP  C01   H012  single    0.970  0.020  1.090
 JHP  C03   H031  single    0.930  0.020  1.080
 JHP  N09   H091  single    0.860  0.020  1.020
 JHP  C11   H112  single    0.970  0.020  1.090
 JHP  C11   H111  single    0.970  0.020  1.090
 JHP  C12   H121  single    0.970  0.020  1.090
 JHP  C12   H122  single    0.970  0.020  1.090
 JHP  C14   H141  single    0.970  0.020  1.090
 JHP  C14   H142  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
 JHP  H101  C10  C14   108.80  3.000
 JHP  H101  C10  C11   109.21  3.000
 JHP  C14   C10  C11   103.02  3.000
 JHP  H101  C10  N09   108.02  3.000
 JHP  C14   C10  N09   115.33  3.000
 JHP  C11   C10  N09   112.27  3.000
 JHP  H131  C13  H132  106.83  3.000
 JHP  H131  C13  C14   112.38  3.000
 JHP  H132  C13  C14   109.71  3.000
 JHP  H131  C13  C12   112.48  3.000
 JHP  H132  C13  C12   110.10  3.000
 JHP  C14   C13  C12   105.37  3.000
 JHP  H012  C01  H011  109.21  3.000
 JHP  H012  C01  H013  109.52  3.000
 JHP  H011  C01  H013  109.20  3.000
 JHP  H012  C01  N02   110.12  3.000
 JHP  H011  C01  N02   108.85  3.000
 JHP  H013  C01  N02   109.92  3.000
 JHP  N06   N02  C03   112.64  3.000
 JHP  N06   N02  C01   120.24  3.000
 JHP  C03   N02  C01   127.13  3.000
 JHP  H031  C03  C04   131.20  3.000
 JHP  H031  C03  N02   122.77  3.000
 JHP  C04   C03  N02   106.03  3.000
 JHP  CL15  C04  C05   129.29  3.000
 JHP  C05   C04  C03   105.21  3.000
 JHP  CL15  C04  C03   125.51  3.000
 JHP  C07   C05  N06   121.65  3.000
 JHP  C07   C05  C04   128.63  3.000
 JHP  N06   C05  C04   109.72  3.000
 JHP  C05   N06  N02   106.41  3.000
 JHP  N09   C07  O08   124.27  3.000
 JHP  O08   C07  C05   120.92  3.000
 JHP  N09   C07  C05   114.80  3.000
 JHP  H091  N09  C07   118.13  3.000
 JHP  H091  N09  C10   118.04  3.000
 JHP  C07   N09  C10   123.54  3.000
 JHP  H111  C11  H112  107.17  3.000
 JHP  H111  C11  C12   110.26  3.000
 JHP  H112  C11  C12   113.20  3.000
 JHP  H111  C11  C10   109.12  3.000
 JHP  H112  C11  C10   112.44  3.000
 JHP  C12   C11  C10   104.61  3.000
 JHP  H122  C12  H121  106.59  3.000
 JHP  H122  C12  C11   111.10  3.000
 JHP  H121  C12  C11   110.83  3.000
 JHP  H122  C12  C13   110.70  3.000
 JHP  H121  C12  C13   111.65  3.000
 JHP  C11   C12  C13   106.05  3.000
 JHP  H142  C14  H141  107.76  3.000
 JHP  H142  C14  C13   113.42  3.000
 JHP  H141  C14  C13   110.83  3.000
 JHP  H142  C14  C10   112.83  3.000
 JHP  H141  C14  C10   109.15  3.000
 JHP  C13   C14  C10   102.80  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
 JHP  CONST_01  C05   C04  C03  N02     0.00   0.0  0
 JHP  CONST_02  C04   C05  N06  N02     0.00   0.0  0
 JHP  CONST_03  N06   C05  C04  C03     0.00   0.0  0
 JHP  CONST_04  C05   N06  N02  C03     0.00   0.0  0
 JHP  CONST_05  N06   N02  C03  C04     0.00   0.0  0
 JHP  CONST_06  C04   C03  N02  C01   180.00   0.0  0
 JHP  CONST_07  C05   N06  N02  C01   180.00   0.0  0
 JHP  CONST_08  CL15  C04  C03  N02   180.00   0.0  0
 JHP  CONST_09  C07   C05  N06  N02   180.00   0.0  0
 JHP  CONST_10  C07   C05  C04  C03   180.00   0.0  0
 JHP  CONST_11  CL15  C04  C05  N06   180.00   0.0  0
 JHP  CONST_12  H031  C03  C04  C05   180.00   0.0  0
 JHP  CONST_13  C05   C07  N09  C10   180.00   0.0  0
 JHP  CONST_14  O08   C07  N09  C10     0.00   0.0  0
 JHP  CONST_15  H091  N09  C07  C05     0.00   0.0  0
 JHP  Var_01    C13   C12  C11  C10   -16.30  30.0  1
 JHP  Var_02    C12   C13  C14  C10    32.63  30.0  1
 JHP  Var_03    C14   C13  C12  C11   -10.16  30.0  1
 JHP  Var_04    N09   C07  C05  C04  -178.79  30.0  2
 JHP  Var_05    H013  C01  N02  C03  -121.95  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
 JHP  chir_01  C10  N09  C11  C14  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
 JHP  plan-1  C01   0.020
 JHP  plan-1  N02   0.020
 JHP  plan-1  C03   0.020
 JHP  plan-1  C04   0.020
 JHP  plan-1  C05   0.020
 JHP  plan-1  N06   0.020
 JHP  plan-1  C07   0.020
 JHP  plan-1  H031  0.020
 JHP  plan-1  CL15  0.020
 JHP  plan-2  C10   0.020
 JHP  plan-2  C05   0.020
 JHP  plan-2  C07   0.020
 JHP  plan-2  O08   0.020
 JHP  plan-2  N09   0.020
 JHP  plan-2  H091  0.020

