# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:13:58 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-(2-carboxyethyl)-4,6-dichloro-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1c([nH]c2cc(Cl)cc(Cl)c12)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
 CLI  CLI  '3-(2-carboxyethyl)-4,6-dichloro-1H-indole-2-carboxylic acid'  ligand  26  19  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CLI
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
 CLI  O19   O   OC    -1  -0.635   2.2676  -1.5289   4.2116
 CLI  C16   C   C      0   0.408   1.7553  -0.4841   3.7544
 CLI  O18   O   O      0  -0.609   1.9074   0.6673   4.2082
 CLI  C12   C   CH2    0  -0.577   0.8527  -0.6633   2.5230
 CLI  C6    C   CH2    0  -0.509   0.2838   0.6192   1.9254
 CLI  C2    C   CR5    0   0.022  -0.5369   0.3544   0.7015
 CLI  C1    C   CR56   0   0.195  -0.0663   0.2137  -0.6476
 CLI  C5    C   CR5    0   0.095  -1.8970   0.1465   0.6482
 CLI  C11   C   C      0   0.369  -2.9690   0.1330   1.7085
 CLI  O14   O   OC    -1  -0.604  -4.1260  -0.0670   1.2849
 CLI  O15   O   O      0  -0.570  -2.6168   0.3121   2.8868
 CLI  N7    N   NR15   0  -0.718  -2.2726  -0.0951  -0.6484
 CLI  C3    C   CR56   0   0.342  -1.1965  -0.0633  -1.4613
 CLI  C8    C   CR16   0  -0.265  -1.1307  -0.2575  -2.8402
 CLI  C13   C   CR6    0  -0.085   0.1168  -0.1728  -3.4120
 CLI  CL17  CL  CL     0  -0.133   0.2848  -0.4009  -5.1246
 CLI  C9    C   CR16   0  -0.196   1.2721   0.0903  -2.6649
 CLI  C4    C   CR6    0  -0.243   1.1703   0.2786  -1.3028
 CLI  CL10  CL  CL     0  -0.132   2.6322   0.5888  -0.4234
 CLI  H121  H   HCH2   0   0.215   1.4140  -1.2160   1.7625
 CLI  H122  H   HCH2   0   0.224   0.0206  -1.3200   2.7991
 CLI  H61   H   HCH2   0   0.231  -0.3407   1.1131   2.6654
 CLI  H62   H   HCH2   0   0.210   1.0949   1.3076   1.6902
 CLI  HN7   H   HNR5   0   0.397  -3.2266  -0.2699  -0.9198
 CLI  HC8   H   HCR6   0   0.282  -2.0158  -0.4637  -3.4265
 CLI  HC9   H   HCR6   0   0.287   2.2346   0.1427  -3.1538

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
 CLI  O19  C16   deloc     1.250  0.020  1.250
 CLI  C16  O18   deloc     1.247  0.020  1.247
 CLI  C16  C12   single    1.537  0.020  1.537
 CLI  C12  C6    single    1.525  0.020  1.525
 CLI  C12  H121  single    0.970  0.020  1.090
 CLI  C12  H122  single    0.970  0.020  1.090
 CLI  C6   C2    single    1.497  0.020  1.497
 CLI  C6   H61   single    0.970  0.020  1.090
 CLI  C6   H62   single    0.970  0.020  1.090
 CLI  C2   C1    aromatic  1.436  0.020  1.436
 CLI  C2   C5    aromatic  1.377  0.020  1.377
 CLI  C1   C3    aromatic  1.420  0.020  1.420
 CLI  C1   C4    aromatic  1.401  0.020  1.401
 CLI  C5   C11   single    1.508  0.020  1.508
 CLI  C5   N7    aromatic  1.371  0.020  1.371
 CLI  C11  O14   deloc     1.248  0.020  1.248
 CLI  C11  O15   deloc     1.243  0.020  1.243
 CLI  N7   C3    aromatic  1.349  0.020  1.349
 CLI  N7   HN7   single    0.860  0.020  1.020
 CLI  C3   C8    aromatic  1.394  0.020  1.394
 CLI  C8   C13   aromatic  1.375  0.020  1.375
 CLI  C8   HC8   single    0.930  0.020  1.080
 CLI  C13  CL17  single    1.736  0.020  1.736
 CLI  C13  C9    aromatic  1.401  0.020  1.401
 CLI  C9   C4    aromatic  1.379  0.020  1.379
 CLI  C9   HC9   single    0.930  0.020  1.080
 CLI  C4   CL10  single    1.734  0.020  1.734

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
 CLI  C12   C16  O18   118.09  3.000
 CLI  C12   C16  O19   115.85  3.000
 CLI  O18   C16  O19   126.06  3.000
 CLI  H122  C12  H121  105.18  3.000
 CLI  H122  C12  C6    108.64  3.000
 CLI  H121  C12  C6    110.09  3.000
 CLI  H122  C12  C16   108.30  3.000
 CLI  H121  C12  C16   108.31  3.000
 CLI  C6    C12  C16   115.78  3.000
 CLI  H62   C6   H61   106.71  3.000
 CLI  H62   C6   C2    110.08  3.000
 CLI  H61   C6   C2    108.78  3.000
 CLI  H62   C6   C12   109.77  3.000
 CLI  H61   C6   C12   109.25  3.000
 CLI  C2    C6   C12   112.09  3.000
 CLI  C5    C2   C1    105.82  3.000
 CLI  C5    C2   C6    126.86  3.000
 CLI  C1    C2   C6    127.28  3.000
 CLI  C4    C1   C3    116.33  3.000
 CLI  C4    C1   C2    136.41  3.000
 CLI  C3    C1   C2    107.26  3.000
 CLI  N7    C5   C11   117.94  3.000
 CLI  N7    C5   C2    109.49  3.000
 CLI  C11   C5   C2    132.56  3.000
 CLI  O15   C11  O14   127.41  3.000
 CLI  O15   C11  C5    117.64  3.000
 CLI  O14   C11  C5    114.95  3.000
 CLI  HN7   N7   C3    126.67  3.000
 CLI  HN7   N7   C5    123.02  3.000
 CLI  C3    N7   C5    110.31  3.000
 CLI  C8    C3   N7    129.08  3.000
 CLI  C8    C3   C1    123.81  3.000
 CLI  N7    C3   C1    107.11  3.000
 CLI  HC8   C8   C13   121.92  3.000
 CLI  HC8   C8   C3    121.61  3.000
 CLI  C13   C8   C3    116.46  3.000
 CLI  C9    C13  CL17  118.10  3.000
 CLI  C9    C13  C8    122.55  3.000
 CLI  CL17  C13  C8    119.35  3.000
 CLI  HC9   C9   C4    120.40  3.000
 CLI  HC9   C9   C13   120.15  3.000
 CLI  C4    C9   C13   119.45  3.000
 CLI  CL10  C4   C9    117.59  3.000
 CLI  CL10  C4   C1    121.02  3.000
 CLI  C9    C4   C1    121.39  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
 CLI  CONST_01  N7    C3   C1   C2       0.00   0.0  0
 CLI  CONST_02  C8    C3   C1   C2     180.00   0.0  0
 CLI  CONST_03  C9    C4   C1   C2     180.00   0.0  0
 CLI  CONST_04  C3    N7   C5   C2       0.00   0.0  0
 CLI  CONST_05  N7    C5   C2   C1       0.00   0.0  0
 CLI  CONST_06  C5    N7   C3   C1       0.00   0.0  0
 CLI  CONST_07  C13   C8   C3   C1       0.00   0.0  0
 CLI  CONST_08  C13   C9   C4   C1       0.00   0.0  0
 CLI  CONST_09  C3    C1   C2   C5       0.00   0.0  0
 CLI  CONST_10  C4    C1   C2   C5     180.00   0.0  0
 CLI  CONST_11  C8    C3   N7   C5     180.00   0.0  0
 CLI  CONST_12  C4    C1   C3   N7     180.00   0.0  0
 CLI  CONST_13  C13   C8   C3   N7     180.00   0.0  0
 CLI  CONST_14  C9    C4   C1   C3       0.00   0.0  0
 CLI  CONST_15  C9    C13  C8   C3       0.00   0.0  0
 CLI  CONST_16  C4    C1   C3   C8       0.00   0.0  0
 CLI  CONST_17  C4    C9   C13  C8       0.00   0.0  0
 CLI  CONST_18  C3    C1   C2   C6     180.00   0.0  0
 CLI  CONST_19  C4    C1   C2   C6       0.00   0.0  0
 CLI  CONST_20  N7    C5   C2   C6     180.00   0.0  0
 CLI  CONST_21  CL10  C4   C1   C2       0.00   0.0  0
 CLI  CONST_22  C11   C5   C2   C1     180.00   0.0  0
 CLI  CONST_23  C3    N7   C5   C11    180.00   0.0  0
 CLI  CONST_24  CL10  C4   C1   C3     180.00   0.0  0
 CLI  CONST_25  CL17  C13  C8   C3     180.00   0.0  0
 CLI  CONST_26  CL10  C4   C9   C13    180.00   0.0  0
 CLI  CONST_27  C4    C9   C13  CL17   180.00   0.0  0
 CLI  CONST_28  HN7   N7   C5   C2     180.00   0.0  0
 CLI  CONST_29  HC8   C8   C3   C1     180.00   0.0  0
 CLI  CONST_30  HC9   C9   C4   C1     180.00   0.0  0
 CLI  Var_01    C1    C2   C6   C12    -85.00  30.0  2
 CLI  Var_02    O14   C11  C5   C2     178.59  30.0  2
 CLI  Var_03    C2    C6   C12  C16    177.75  30.0  3
 CLI  Var_04    C6    C12  C16  O19   -177.11  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
 CLI  plan-1  C6    0.020
 CLI  plan-1  C2    0.020
 CLI  plan-1  C1    0.020
 CLI  plan-1  C5    0.020
 CLI  plan-1  C11   0.020
 CLI  plan-1  N7    0.020
 CLI  plan-1  C3    0.020
 CLI  plan-1  C8    0.020
 CLI  plan-1  C13   0.020
 CLI  plan-1  CL17  0.020
 CLI  plan-1  C9    0.020
 CLI  plan-1  C4    0.020
 CLI  plan-1  CL10  0.020
 CLI  plan-1  HN7   0.020
 CLI  plan-1  HC8   0.020
 CLI  plan-1  HC9   0.020
 CLI  plan-2  O19   0.020
 CLI  plan-2  C16   0.020
 CLI  plan-2  O18   0.020
 CLI  plan-2  C12   0.020
 CLI  plan-3  C5    0.020
 CLI  plan-3  C11   0.020
 CLI  plan-3  O14   0.020
 CLI  plan-3  O15   0.020

