# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:59:01 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 5-chloro-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]c2ccc(Cl)cc2c1
#
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
 3ZB  3ZB  '5-chloro-1H-indole-2-carboxylic acid'  ligand  19  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3ZB
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
 3ZB  C1   C   CR56  0   0.366  -0.0894   0.9070   0.0143
 3ZB  C2   C   CR56  0   0.059   0.1814  -0.4803   0.0044
 3ZB  N3   N   NR15  0  -0.723  -1.4365   1.0673   0.0088
 3ZB  C4   C   CR16  0  -0.304   0.9334   1.8579   0.0283
 3ZB  C5   C   CR15  0  -0.383  -1.0731  -1.1445  -0.0064
 3ZB  C6   C   CR16  0  -0.295   1.5101  -0.9289   0.0073
 3ZB  C7   C   CR5   0   0.220  -2.0333  -0.1665  -0.0033
 3ZB  C8   C   CR16  0  -0.233   2.2308   1.4003   0.0315
 3ZB  C9   C   CR6   0  -0.050   2.5032   0.0196   0.0209
 3ZB  C10  C   C     0   0.494  -3.4843  -0.3608  -0.0119
 3ZB  CL   CL  CL    0  -0.137   4.1661  -0.4869   0.0250
 3ZB  O12  O   OH1   0  -0.601  -4.1440   0.7893  -0.0125
 3ZB  O13  O   O     0  -0.431  -4.0084  -1.4480  -0.0178
 3ZB  H14  H   HNR5  0   0.420  -1.9177   1.9525   0.0155
 3ZB  H15  H   HCR6  0   0.277   0.7221   2.9190   0.0366
 3ZB  H16  H   HCR5  0   0.270  -1.2500  -2.2079  -0.0158
 3ZB  H17  H   HCR6  0   0.276   1.7400  -1.9862  -0.0010
 3ZB  H18  H   HCR6  0   0.280   3.0494   2.1064   0.0426
 3ZB  H19  H   HOH1  0   0.494  -5.0999   0.6307  -0.0183

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
 3ZB  O12  C10  single    1.326  0.020  1.326
 3ZB  C5   C2   aromatic  1.419  0.020  1.419
 3ZB  C5   C7   aromatic  1.371  0.020  1.371
 3ZB  C6   C2   aromatic  1.402  0.020  1.402
 3ZB  C6   C9   aromatic  1.373  0.020  1.373
 3ZB  C2   C1   aromatic  1.413  0.020  1.413
 3ZB  C10  C7   single    1.464  0.020  1.464
 3ZB  C10  O13  double    1.207  0.020  1.207
 3ZB  CL   C9   single    1.738  0.020  1.738
 3ZB  C7   N3   aromatic  1.371  0.020  1.371
 3ZB  C9   C8   aromatic  1.407  0.020  1.407
 3ZB  C1   N3   aromatic  1.357  0.020  1.357
 3ZB  C1   C4   aromatic  1.397  0.020  1.397
 3ZB  C8   C4   aromatic  1.376  0.020  1.376
 3ZB  N3   H14  single    0.860  0.020  1.020
 3ZB  C4   H15  single    0.930  0.020  1.080
 3ZB  C5   H16  single    0.930  0.020  1.080
 3ZB  C6   H17  single    0.930  0.020  1.080
 3ZB  C8   H18  single    0.930  0.020  1.080
 3ZB  O12  H19  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
 3ZB  C4   C1   N3   130.30  3.000
 3ZB  C4   C1   C2   121.88  3.000
 3ZB  N3   C1   C2   107.83  3.000
 3ZB  C6   C2   C5   133.45  3.000
 3ZB  C6   C2   C1   119.70  3.000
 3ZB  C5   C2   C1   106.86  3.000
 3ZB  H14  N3   C7   125.66  3.000
 3ZB  H14  N3   C1   125.31  3.000
 3ZB  C7   N3   C1   109.03  3.000
 3ZB  H15  C4   C8   120.69  3.000
 3ZB  H15  C4   C1   121.66  3.000
 3ZB  C8   C4   C1   117.65  3.000
 3ZB  H16  C5   C7   126.08  3.000
 3ZB  H16  C5   C2   127.34  3.000
 3ZB  C7   C5   C2   106.58  3.000
 3ZB  H17  C6   C9   121.42  3.000
 3ZB  H17  C6   C2   120.92  3.000
 3ZB  C9   C6   C2   117.66  3.000
 3ZB  C10  C7   C5   126.85  3.000
 3ZB  C10  C7   N3   123.44  3.000
 3ZB  C5   C7   N3   109.71  3.000
 3ZB  H18  C8   C9   119.62  3.000
 3ZB  H18  C8   C4   119.79  3.000
 3ZB  C9   C8   C4   120.59  3.000
 3ZB  CL   C9   C8   118.10  3.000
 3ZB  C8   C9   C6   122.53  3.000
 3ZB  CL   C9   C6   119.38  3.000
 3ZB  O13  C10  O12  124.42  3.000
 3ZB  O13  C10  C7   123.37  3.000
 3ZB  O12  C10  C7   112.21  3.000
 3ZB  H19  O12  C10  110.43  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
 3ZB  CONST_01  C7   C5   C2   C1    0.00   0.0  0
 3ZB  CONST_02  C9   C6   C2   C1    0.00   0.0  0
 3ZB  CONST_03  C5   C7   N3   C1    0.00   0.0  0
 3ZB  CONST_04  C9   C8   C4   C1    0.00   0.0  0
 3ZB  CONST_05  N3   C7   C5   C2    0.00   0.0  0
 3ZB  CONST_06  C8   C9   C6   C2    0.00   0.0  0
 3ZB  CONST_07  C7   N3   C1   C2    0.00   0.0  0
 3ZB  CONST_08  C8   C4   C1   C2    0.00   0.0  0
 3ZB  CONST_09  C5   C2   C1   N3    0.00   0.0  0
 3ZB  CONST_10  C6   C2   C1   N3  180.00   0.0  0
 3ZB  CONST_11  C8   C4   C1   N3  180.00   0.0  0
 3ZB  CONST_12  C5   C2   C1   C4  180.00   0.0  0
 3ZB  CONST_13  C6   C2   C1   C4    0.00   0.0  0
 3ZB  CONST_14  C7   N3   C1   C4  180.00   0.0  0
 3ZB  CONST_15  C6   C9   C8   C4    0.00   0.0  0
 3ZB  CONST_16  C9   C6   C2   C5  180.00   0.0  0
 3ZB  CONST_17  C7   C5   C2   C6  180.00   0.0  0
 3ZB  CONST_18  C10  C7   N3   C1  180.00   0.0  0
 3ZB  CONST_19  C10  C7   C5   C2  180.00   0.0  0
 3ZB  CONST_20  CL   C9   C6   C2  180.00   0.0  0
 3ZB  CONST_21  CL   C9   C8   C4  180.00   0.0  0
 3ZB  CONST_22  H16  C5   C2   C1  180.00   0.0  0
 3ZB  CONST_23  H17  C6   C2   C1  180.00   0.0  0
 3ZB  CONST_24  H18  C8   C4   C1  180.00   0.0  0
 3ZB  CONST_25  H14  N3   C1   C2  180.00   0.0  0
 3ZB  CONST_26  H15  C4   C1   C2  180.00   0.0  0
 3ZB  CONST_27  H19  O12  C10  C7  180.00   0.0  0
 3ZB  Var_01    O12  C10  C7   N3    0.28  30.0  3

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
 3ZB  plan-1  C1   0.020
 3ZB  plan-1  C2   0.020
 3ZB  plan-1  N3   0.020
 3ZB  plan-1  C4   0.020
 3ZB  plan-1  C5   0.020
 3ZB  plan-1  C6   0.020
 3ZB  plan-1  C7   0.020
 3ZB  plan-1  C8   0.020
 3ZB  plan-1  C9   0.020
 3ZB  plan-1  C10  0.020
 3ZB  plan-1  CL   0.020
 3ZB  plan-1  H14  0.020
 3ZB  plan-1  H15  0.020
 3ZB  plan-1  H16  0.020
 3ZB  plan-1  H17  0.020
 3ZB  plan-1  H18  0.020
 3ZB  plan-2  C7   0.020
 3ZB  plan-2  C10  0.020
 3ZB  plan-2  O12  0.020
 3ZB  plan-2  O13  0.020
 3ZB  plan-2  H19  0.020

