# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:57:44 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-(2,4-dichlorobenzyl)-1H-pyrazole-3,5-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(n(Cc2ccc(Cl)cc2Cl)n1)C(O)=O
#
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
 ZKW  ZKW  '1-(2,4-dichlorobenzyl)-1H-pyrazole-3,5-dicarboxylic acid'  ligand  28  20  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZKW
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
 ZKW  O3    O   OH1   0  -0.584  10.5879  32.0806   1.9010
 ZKW  C11   C   C     0   0.509  10.2576  32.4375   0.6724
 ZKW  O2    O   O     0  -0.420   9.3024  33.1156   0.3881
 ZKW  C7    C   CR5   0   0.309  11.2167  31.9014  -0.3030
 ZKW  C8    C   CR15  0  -0.452  12.3628  31.1704  -0.0968
 ZKW  C9    C   CR5   0   0.146  12.8739  30.9645  -1.3815
 ZKW  C10   C   C     0   0.516  14.0984  30.2255  -1.7221
 ZKW  O1    O   OH1   0  -0.587  14.3318  30.1895  -3.0221
 ZKW  O     O   O     0  -0.432  14.7999  29.7138  -0.8845
 ZKW  N1    N   N     0  -0.238  12.0999  31.5262  -2.3011
 ZKW  N     N   NR5   0  -0.333  11.1074  32.0802  -1.6498
 ZKW  C6    C   CH2   0  -0.334  10.0975  32.8036  -2.3938
 ZKW  C2    C   CR6   0   0.172  10.2823  34.2971  -2.3341
 ZKW  C1    C   CR16  0  -0.310  11.4487  34.8877  -1.8631
 ZKW  C3    C   CR6   0  -0.103   9.2783  35.1453  -2.7928
 ZKW  CL1   CL  CL    0  -0.103   7.8116  34.4760  -3.4255
 ZKW  C4    C   CR16  0  -0.150   9.4075  36.5242  -2.7753
 ZKW  C5    C   CR6   0  -0.064  10.5823  37.0718  -2.2883
 ZKW  CL    CL  CL    0  -0.113  10.7613  38.7911  -2.2563
 ZKW  C     C   CR16  0  -0.183  11.6094  36.2639  -1.8325
 ZKW  H3    H   HOH1  0   0.496   9.9501  32.4384   2.5372
 ZKW  H8    H   HCR5  0   0.296  12.7727  30.8373   0.8411
 ZKW  H1    H   HOH1  0   0.491  15.1488  29.6987  -3.1979
 ZKW  H61C  H   HCH2  0   0.312  10.1703  32.4552  -3.4241
 ZKW  H62C  H   HCH2  0   0.296   9.1156  32.5163  -2.0263
 ZKW  HA    H   HCR6  0   0.270  12.2674  34.2769  -1.5064
 ZKW  H     H   HCR6  0   0.289  12.5275  36.6936  -1.4576
 ZKW  H4    H   HCR6  0   0.304   8.6066  37.1545  -3.1356

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
 ZKW  O3   C11   single    1.321  0.020  1.321
 ZKW  C11  O2    double    1.205  0.020  1.205
 ZKW  C11  C7    single    1.469  0.020  1.469
 ZKW  C7   C8    aromatic  1.375  0.020  1.375
 ZKW  C7   N     aromatic  1.363  0.020  1.363
 ZKW  C8   C9    aromatic  1.398  0.020  1.398
 ZKW  C9   C10   single    1.470  0.020  1.470
 ZKW  C9   N1    aromatic  1.327  0.020  1.327
 ZKW  C10  O1    single    1.321  0.020  1.321
 ZKW  C10  O     double    1.206  0.020  1.206
 ZKW  N1   N     aromatic  1.310  0.020  1.310
 ZKW  N    C6    single    1.448  0.020  1.448
 ZKW  C6   C2    single    1.506  0.020  1.506
 ZKW  C2   C1    aromatic  1.390  0.020  1.390
 ZKW  C2   C3    aromatic  1.392  0.020  1.392
 ZKW  C1   C     aromatic  1.386  0.020  1.386
 ZKW  C3   CL1   single    1.732  0.020  1.732
 ZKW  C3   C4    aromatic  1.385  0.020  1.385
 ZKW  C4   C5    aromatic  1.385  0.020  1.385
 ZKW  C5   CL    single    1.729  0.020  1.729
 ZKW  C5   C     aromatic  1.384  0.020  1.384
 ZKW  O3   H3    single    0.850  0.020  0.980
 ZKW  C8   H8    single    0.930  0.020  1.080
 ZKW  O1   H1    single    0.850  0.020  0.980
 ZKW  C6   H61C  single    0.970  0.020  1.090
 ZKW  C6   H62C  single    0.970  0.020  1.090
 ZKW  C1   HA    single    0.930  0.020  1.080
 ZKW  C    H     single    0.930  0.020  1.080
 ZKW  C4   H4    single    0.930  0.020  1.080

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
 ZKW  H3    O3   C11   110.25  3.000
 ZKW  C7    C11  O2    124.47  3.000
 ZKW  C7    C11  O3    110.83  3.000
 ZKW  O2    C11  O3    124.70  3.000
 ZKW  N     C7   C8    106.54  3.000
 ZKW  N     C7   C11   123.77  3.000
 ZKW  C8    C7   C11   129.68  3.000
 ZKW  H8    C8   C9    128.02  3.000
 ZKW  H8    C8   C7    127.78  3.000
 ZKW  C9    C8   C7    104.20  3.000
 ZKW  N1    C9   C10   122.56  3.000
 ZKW  N1    C9   C8    111.18  3.000
 ZKW  C10   C9   C8    126.26  3.000
 ZKW  O     C10  O1    124.66  3.000
 ZKW  O     C10  C9    122.46  3.000
 ZKW  O1    C10  C9    112.88  3.000
 ZKW  H1    O1   C10   109.95  3.000
 ZKW  N     N1   C9    106.05  3.000
 ZKW  C6    N    N1    118.96  3.000
 ZKW  C6    N    C7    128.98  3.000
 ZKW  N1    N    C7    112.03  3.000
 ZKW  H62C  C6   H61C  107.18  3.000
 ZKW  H62C  C6   C2    111.07  3.000
 ZKW  H61C  C6   C2    110.26  3.000
 ZKW  H62C  C6   N     108.92  3.000
 ZKW  H61C  C6   N     106.22  3.000
 ZKW  C2    C6   N     112.92  3.000
 ZKW  C3    C2   C1    117.26  3.000
 ZKW  C3    C2   C6    120.18  3.000
 ZKW  C1    C2   C6    122.54  3.000
 ZKW  HA    C1   C     117.75  3.000
 ZKW  HA    C1   C2    120.45  3.000
 ZKW  C     C1   C2    121.79  3.000
 ZKW  C4    C3   CL1   117.93  3.000
 ZKW  C4    C3   C2    122.36  3.000
 ZKW  CL1   C3   C2    119.71  3.000
 ZKW  H4    C4   C5    121.02  3.000
 ZKW  H4    C4   C3    120.47  3.000
 ZKW  C5    C4   C3    118.51  3.000
 ZKW  C     C5   CL    119.84  3.000
 ZKW  C     C5   C4    120.97  3.000
 ZKW  CL    C5   C4    119.18  3.000
 ZKW  H     C    C5    120.84  3.000
 ZKW  H     C    C1    120.06  3.000
 ZKW  C5    C    C1    119.10  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
 ZKW  CONST_01  N1   C9   C8   C7     0.00   0.0  0
 ZKW  CONST_02  C9   N1   N    C7     0.00   0.0  0
 ZKW  CONST_03  N1   N    C7   C8     0.00   0.0  0
 ZKW  CONST_04  N    N1   C9   C8     0.00   0.0  0
 ZKW  CONST_05  N    C7   C8   C9     0.00   0.0  0
 ZKW  CONST_06  C5   C    C1   C2     0.00   0.0  0
 ZKW  CONST_07  C5   C4   C3   C2     0.00   0.0  0
 ZKW  CONST_08  C4   C3   C2   C1     0.00   0.0  0
 ZKW  CONST_09  C4   C5   C    C1     0.00   0.0  0
 ZKW  CONST_10  C    C1   C2   C3     0.00   0.0  0
 ZKW  CONST_11  C    C5   C4   C3     0.00   0.0  0
 ZKW  CONST_12  C9   C8   C7   C11  180.00   0.0  0
 ZKW  CONST_13  N1   N    C7   C11  180.00   0.0  0
 ZKW  CONST_14  C10  C9   C8   C7   180.00   0.0  0
 ZKW  CONST_15  C6   N    C7   C8   180.00   0.0  0
 ZKW  CONST_16  C6   N    N1   C9   180.00   0.0  0
 ZKW  CONST_17  N    N1   C9   C10  180.00   0.0  0
 ZKW  CONST_18  C    C1   C2   C6   180.00   0.0  0
 ZKW  CONST_19  C4   C3   C2   C6   180.00   0.0  0
 ZKW  CONST_20  CL1  C3   C2   C1   180.00   0.0  0
 ZKW  CONST_21  CL   C5   C    C1   180.00   0.0  0
 ZKW  CONST_22  CL   C5   C4   C3   180.00   0.0  0
 ZKW  CONST_23  C5   C4   C3   CL1  180.00   0.0  0
 ZKW  CONST_24  H8   C8   C9   N1   180.00   0.0  0
 ZKW  CONST_25  H    C    C1   C2   180.00   0.0  0
 ZKW  CONST_26  H4   C4   C3   C2   180.00   0.0  0
 ZKW  CONST_27  HA   C1   C2   C3   180.00   0.0  0
 ZKW  CONST_28  H3   O3   C11  C7   180.00   0.0  0
 ZKW  CONST_29  H1   O1   C10  C9   180.00   0.0  0
 ZKW  Var_01    C2   C6   N    C7    76.76  30.0  2
 ZKW  Var_02    C1   C2   C6   N     12.95  30.0  2
 ZKW  Var_03    C8   C7   C11  O3    -2.72  30.0  2
 ZKW  Var_04    O1   C10  C9   C8   179.76  30.0  2

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
 ZKW  plan-1  C11  0.020
 ZKW  plan-1  C7   0.020
 ZKW  plan-1  C8   0.020
 ZKW  plan-1  C9   0.020
 ZKW  plan-1  C10  0.020
 ZKW  plan-1  N1   0.020
 ZKW  plan-1  N    0.020
 ZKW  plan-1  C6   0.020
 ZKW  plan-1  H8   0.020
 ZKW  plan-2  C6   0.020
 ZKW  plan-2  C2   0.020
 ZKW  plan-2  C1   0.020
 ZKW  plan-2  C3   0.020
 ZKW  plan-2  CL1  0.020
 ZKW  plan-2  C4   0.020
 ZKW  plan-2  C5   0.020
 ZKW  plan-2  CL   0.020
 ZKW  plan-2  C    0.020
 ZKW  plan-2  HA   0.020
 ZKW  plan-2  H    0.020
 ZKW  plan-2  H4   0.020
 ZKW  plan-3  O3   0.020
 ZKW  plan-3  C11  0.020
 ZKW  plan-3  O2   0.020
 ZKW  plan-3  C7   0.020
 ZKW  plan-3  H3   0.020
 ZKW  plan-4  C9   0.020
 ZKW  plan-4  C10  0.020
 ZKW  plan-4  O1   0.020
 ZKW  plan-4  O    0.020
 ZKW  plan-4  H1   0.020

