# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:01:57 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-(2-chlorobenzyl)-1H-pyrazole-3,5-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(n(Cc2ccccc2Cl)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
 M81  M81  '1-(2-chlorobenzyl)-1H-pyrazole-3,5-dicarboxylic acid'  ligand  28  19  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M81
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
 M81  CL    CL  CL    0  -0.120   7.8504  34.4856  -3.1577
 M81  C3    C   CR6   0  -0.097   9.3420  35.1696  -2.5896
 M81  C2    C   CR16  0  -0.198   9.4697  36.5492  -2.5777
 M81  C1    C   CR16  0  -0.274  10.6579  37.1179  -2.1452
 M81  C4    C   CR6   0   0.163  10.3702  34.3277  -2.1739
 M81  C5    C   CR16  0  -0.302  11.5552  34.9228  -1.7537
 M81  C     C   CR16  0  -0.229  11.7012  36.3022  -1.7356
 M81  C6    C   CH2   0  -0.335  10.1903  32.8325  -2.2254
 M81  N     N   NR5   0  -0.330  11.2376  32.1142  -1.5286
 M81  N1    N   N     0  -0.237  12.2070  31.5752  -2.2231
 M81  C9    C   CR5   0   0.157  13.0299  31.0222  -1.3407
 M81  C10   C   C     0   0.503  14.2324  30.3189  -1.8148
 M81  O1    O   O     0  -0.433  14.5331  30.2049  -2.9757
 M81  O     O   OH1   0  -0.591  14.9351  29.8317  -0.8041
 M81  C8    C   CR15  0  -0.456  12.5729  31.2207  -0.0340
 M81  C7    C   CR5   0   0.311  11.4084  31.9367  -0.1888
 M81  C11   C   C     0   0.509  10.4861  32.4553   0.8304
 M81  O2    O   O     0  -0.420   9.5051  33.1144   0.5926
 M81  O3    O   OH1   0  -0.585  10.8799  32.1042   2.0422
 M81  H2    H   HCR6  0   0.282   8.6479  37.1726  -2.9033
 M81  H1    H   HCR6  0   0.270  10.7630  38.1944  -2.1335
 M81  H     H   HCR6  0   0.267  12.6337  36.7353  -1.4002
 M81  H5    H   HCR6  0   0.259  12.3889  34.3115  -1.4335
 M81  H61C  H   HCH2  0   0.293   9.2286  32.5391  -1.8120
 M81  H62C  H   HCH2  0   0.309  10.2175  32.4827  -3.2575
 M81  H8    H   HCR5  0   0.295  13.0227  30.8954   0.8885
 M81  HA    H   HOH1  0   0.492  15.7282  29.3821  -1.1326
 M81  H3    H   HOH1  0   0.496  10.2644  32.4479   2.7075

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
 M81  CL   C3    single    1.736  0.020  1.736
 M81  C3   C2    aromatic  1.386  0.020  1.386
 M81  C3   C4    aromatic  1.392  0.020  1.392
 M81  C2   C1    aromatic  1.387  0.020  1.387
 M81  C1   C     aromatic  1.386  0.020  1.386
 M81  C4   C5    aromatic  1.391  0.020  1.391
 M81  C4   C6    single    1.507  0.020  1.507
 M81  C5   C     aromatic  1.387  0.020  1.387
 M81  C6   N     single    1.449  0.020  1.449
 M81  N    N1    aromatic  1.309  0.020  1.309
 M81  N    C7    aromatic  1.362  0.020  1.362
 M81  N1   C9    aromatic  1.327  0.020  1.327
 M81  C9   C10   single    1.472  0.020  1.472
 M81  C9   C8    aromatic  1.398  0.020  1.398
 M81  C10  O1    double    1.205  0.020  1.205
 M81  C10  O     single    1.324  0.020  1.324
 M81  C8   C7    aromatic  1.376  0.020  1.376
 M81  C7   C11   single    1.469  0.020  1.469
 M81  C11  O2    double    1.205  0.020  1.205
 M81  C11  O3    single    1.322  0.020  1.322
 M81  C2   H2    single    0.930  0.020  1.080
 M81  C1   H1    single    0.930  0.020  1.080
 M81  C    H     single    0.930  0.020  1.080
 M81  C5   H5    single    0.930  0.020  1.080
 M81  C6   H61C  single    0.970  0.020  1.090
 M81  C6   H62C  single    0.970  0.020  1.090
 M81  C8   H8    single    0.930  0.020  1.080
 M81  O    HA    single    0.850  0.020  0.980
 M81  O3   H3    single    0.850  0.020  0.980

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
 M81  C4    C3   C2    122.10  3.000
 M81  C4    C3   CL    119.59  3.000
 M81  C2    C3   CL    118.30  3.000
 M81  H2    C2   C1    120.57  3.000
 M81  H2    C2   C3    120.09  3.000
 M81  C1    C2   C3    119.35  3.000
 M81  H1    C1   C     120.61  3.000
 M81  H1    C1   C2    119.66  3.000
 M81  C     C1   C2    119.72  3.000
 M81  C6    C4   C5    122.45  3.000
 M81  C6    C4   C3    120.10  3.000
 M81  C5    C4   C3    117.43  3.000
 M81  H5    C5   C     118.47  3.000
 M81  H5    C5   C4    120.27  3.000
 M81  C     C5   C4    121.26  3.000
 M81  H     C    C5    119.54  3.000
 M81  H     C    C1    120.32  3.000
 M81  C5    C    C1    120.13  3.000
 M81  H62C  C6   H61C  107.19  3.000
 M81  H62C  C6   N     106.15  3.000
 M81  H61C  C6   N     108.83  3.000
 M81  H62C  C6   C4    110.36  3.000
 M81  H61C  C6   C4    111.13  3.000
 M81  N     C6   C4    112.91  3.000
 M81  C7    N    N1    112.05  3.000
 M81  C7    N    C6    128.93  3.000
 M81  N1    N    C6    118.98  3.000
 M81  C9    N1   N     106.15  3.000
 M81  C8    C9   C10   129.49  3.000
 M81  C8    C9   N1    111.07  3.000
 M81  C10   C9   N1    119.45  3.000
 M81  O     C10  O1    124.64  3.000
 M81  O     C10  C9    111.33  3.000
 M81  O1    C10  C9    124.03  3.000
 M81  HA    O    C10   110.26  3.000
 M81  H8    C8   C7    127.40  3.000
 M81  H8    C8   C9    128.40  3.000
 M81  C7    C8   C9    104.20  3.000
 M81  C11   C7   C8    129.57  3.000
 M81  C11   C7   N     123.89  3.000
 M81  C8    C7   N     106.54  3.000
 M81  O3    C11  O2    124.65  3.000
 M81  O3    C11  C7    110.81  3.000
 M81  O2    C11  C7    124.54  3.000
 M81  H3    O3   C11   110.23  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
 M81  CONST_01  C    C1   C2   C3      0.00   0.0  0
 M81  CONST_02  C    C5   C4   C3      0.00   0.0  0
 M81  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 M81  CONST_04  C5   C    C1   C2      0.00   0.0  0
 M81  CONST_05  C4   C3   C2   C1      0.00   0.0  0
 M81  CONST_06  C4   C5   C    C1      0.00   0.0  0
 M81  CONST_07  C8   C9   N1   N       0.00   0.0  0
 M81  CONST_08  C9   C8   C7   N       0.00   0.0  0
 M81  CONST_09  C8   C7   N    N1      0.00   0.0  0
 M81  CONST_10  C7   C8   C9   N1      0.00   0.0  0
 M81  CONST_11  C7   N    N1   C9      0.00   0.0  0
 M81  CONST_12  C1   C2   C3   CL    180.00   0.0  0
 M81  CONST_13  C5   C4   C3   CL    180.00   0.0  0
 M81  CONST_14  C6   C4   C3   C2    180.00   0.0  0
 M81  CONST_15  C6   C4   C5   C     180.00   0.0  0
 M81  CONST_16  C9   N1   N    C6    180.00   0.0  0
 M81  CONST_17  C8   C7   N    C6    180.00   0.0  0
 M81  CONST_18  C10  C9   N1   N     180.00   0.0  0
 M81  CONST_19  C11  C7   N    N1    180.00   0.0  0
 M81  CONST_20  C11  C7   C8   C9    180.00   0.0  0
 M81  CONST_21  C7   C8   C9   C10   180.00   0.0  0
 M81  CONST_22  H1   C1   C2   C3    180.00   0.0  0
 M81  CONST_23  H5   C5   C4   C3    180.00   0.0  0
 M81  CONST_24  H    C    C1   C2    180.00   0.0  0
 M81  CONST_25  H2   C2   C3   C4    180.00   0.0  0
 M81  CONST_26  H8   C8   C7   N     180.00   0.0  0
 M81  CONST_27  HA   O    C10  C9    180.00   0.0  0
 M81  CONST_28  H3   O3   C11  C7    180.00   0.0  0
 M81  Var_01    N    C6   C4   C3   -168.94  30.0  2
 M81  Var_02    N1   N    C6   C4   -100.71  30.0  2
 M81  Var_03    O2   C11  C7   N      -1.81  30.0  2
 M81  Var_04    O1   C10  C9   N1      0.00  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
 M81  plan-1  C6   0.020
 M81  plan-1  N    0.020
 M81  plan-1  N1   0.020
 M81  plan-1  C9   0.020
 M81  plan-1  C10  0.020
 M81  plan-1  C8   0.020
 M81  plan-1  C7   0.020
 M81  plan-1  C11  0.020
 M81  plan-1  H8   0.020
 M81  plan-2  CL   0.020
 M81  plan-2  C3   0.020
 M81  plan-2  C2   0.020
 M81  plan-2  C1   0.020
 M81  plan-2  C4   0.020
 M81  plan-2  C5   0.020
 M81  plan-2  C    0.020
 M81  plan-2  C6   0.020
 M81  plan-2  H2   0.020
 M81  plan-2  H1   0.020
 M81  plan-2  H    0.020
 M81  plan-2  H5   0.020
 M81  plan-3  C9   0.020
 M81  plan-3  C10  0.020
 M81  plan-3  O1   0.020
 M81  plan-3  O    0.020
 M81  plan-3  HA   0.020
 M81  plan-4  C7   0.020
 M81  plan-4  C11  0.020
 M81  plan-4  O2   0.020
 M81  plan-4  O3   0.020
 M81  plan-4  H3   0.020

