# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:42:56 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 3-(1H-indol-3-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1c[nH]c2ccccc12
#
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
 IOP  IOP  '3-(1H-indol-3-yl)propanoic acid'  ligand  25  14  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IOP
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
 IOP  C1'   C  C     0   0.552   0.3875  -0.0913   3.4745
 IOP  O1    O  O     0  -0.446   0.2071   0.9666   4.0253
 IOP  O2    O  OH1   0  -0.597   0.9454  -1.1360   4.0798
 IOP  C2'   C  CH2   0  -0.579   0.0219  -0.4012   2.0498
 IOP  C3'   C  CH2   0  -0.535  -0.5968   0.7800   1.3075
 IOP  N1    N  NR15  0  -0.687  -2.0198  -0.0907  -1.9858
 IOP  C2    C  CR15  0  -0.088  -2.1386   0.2460  -0.6656
 IOP  C3    C  CR5   0   0.013  -0.9044   0.4364  -0.1127
 IOP  C3A   C  CR56  0   0.033   0.0405   0.2015  -1.1653
 IOP  C4    C  CR16  0  -0.376   1.4380   0.2433  -1.2423
 IOP  C5    C  CR16  0  -0.269   2.0521  -0.0428  -2.4460
 IOP  C6    C  CR16  0  -0.285   1.2966  -0.3725  -3.5838
 IOP  C7    C  CR16  0  -0.306  -0.0838  -0.4174  -3.5407
 IOP  C7A   C  CR56  0   0.353  -0.6995  -0.1277  -2.3238
 IOP  HO2   H  HOH1  0   0.478   1.1743  -0.9056   4.9927
 IOP  H2'1  H  HCH2  0   0.281   0.9214  -0.7539   1.5369
 IOP  H2'2  H  HCH2  0   0.285  -0.6668  -1.2513   2.0489
 IOP  H3'1  H  HCH2  0   0.252  -1.5112   1.0937   1.8144
 IOP  H3'2  H  HCH2  0   0.242   0.0872   1.6324   1.3453
 IOP  H2    H  HCR5  0   0.280  -3.1117   0.3283  -0.2066
 IOP  H4    H  HCR6  0   0.239   2.0334   0.4974  -0.3732
 IOP  H5    H  HCR6  0   0.245   3.1318  -0.0147  -2.5180
 IOP  H6    H  HCR6  0   0.248   1.8060  -0.5965  -4.5124
 IOP  H7    H  HCR6  0   0.258  -0.6636  -0.6713  -4.4192
 IOP  HN1   H  HNR5  0   0.407  -2.7903  -0.2760  -2.6053

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
 IOP  C1'  O1    double    1.206  0.020  1.206
 IOP  C1'  O2    single    1.330  0.020  1.330
 IOP  C1'  C2'   single    1.503  0.020  1.503
 IOP  O2   HO2   single    0.850  0.020  0.980
 IOP  C2'  C3'   single    1.526  0.020  1.526
 IOP  C2'  H2'1  single    0.970  0.020  1.090
 IOP  C2'  H2'2  single    0.970  0.020  1.090
 IOP  C3'  C3    single    1.493  0.020  1.493
 IOP  C3'  H3'1  single    0.970  0.020  1.090
 IOP  C3'  H3'2  single    0.970  0.020  1.090
 IOP  N1   C2    aromatic  1.368  0.020  1.368
 IOP  N1   C7A   aromatic  1.363  0.020  1.363
 IOP  N1   HN1   single    0.860  0.020  1.020
 IOP  C2   C3    aromatic  1.366  0.020  1.366
 IOP  C2   H2    single    0.930  0.020  1.080
 IOP  C3   C3A   aromatic  1.434  0.020  1.434
 IOP  C3A  C4    aromatic  1.400  0.020  1.400
 IOP  C3A  C7A   aromatic  1.413  0.020  1.413
 IOP  C4   C5    aromatic  1.381  0.020  1.381
 IOP  C4   H4    single    0.930  0.020  1.080
 IOP  C5   C6    aromatic  1.405  0.020  1.405
 IOP  C5   H5    single    0.930  0.020  1.080
 IOP  C6   C7    aromatic  1.382  0.020  1.382
 IOP  C6   H6    single    0.930  0.020  1.080
 IOP  C7   C7A   aromatic  1.394  0.020  1.394
 IOP  C7   H7    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
 IOP  C2'   C1'  O2    111.80  3.000
 IOP  C2'   C1'  O1    125.26  3.000
 IOP  O2    C1'  O1    122.94  3.000
 IOP  HO2   O2   C1'   109.95  3.000
 IOP  H2'2  C2'  H2'1  105.47  3.000
 IOP  H2'2  C2'  C3'   110.23  3.000
 IOP  H2'1  C2'  C3'   110.79  3.000
 IOP  H2'2  C2'  C1'   108.31  3.000
 IOP  H2'1  C2'  C1'   108.11  3.000
 IOP  C3'   C2'  C1'   113.58  3.000
 IOP  H3'2  C3'  H3'1  106.50  3.000
 IOP  H3'2  C3'  C3    109.94  3.000
 IOP  H3'1  C3'  C3    109.59  3.000
 IOP  H3'2  C3'  C2'   109.45  3.000
 IOP  H3'1  C3'  C2'   109.65  3.000
 IOP  C3    C3'  C2'   111.59  3.000
 IOP  HN1   N1   C7A   125.74  3.000
 IOP  HN1   N1   C2    124.99  3.000
 IOP  C7A   N1   C2    109.27  3.000
 IOP  H2    C2   C3    129.21  3.000
 IOP  H2    C2   N1    120.51  3.000
 IOP  C3    C2   N1    110.28  3.000
 IOP  C3A   C3   C2    105.99  3.000
 IOP  C3A   C3   C3'   126.88  3.000
 IOP  C2    C3   C3'   127.11  3.000
 IOP  C7A   C3A  C4    118.97  3.000
 IOP  C7A   C3A  C3    107.15  3.000
 IOP  C4    C3A  C3    133.88  3.000
 IOP  H4    C4   C5    120.21  3.000
 IOP  H4    C4   C3A   120.75  3.000
 IOP  C5    C4   C3A   119.04  3.000
 IOP  H5    C5   C6    119.25  3.000
 IOP  H5    C5   C4    119.74  3.000
 IOP  C6    C5   C4    121.02  3.000
 IOP  H6    C6   C7    119.35  3.000
 IOP  H6    C6   C5    119.35  3.000
 IOP  C7    C6   C5    121.30  3.000
 IOP  H7    C7   C7A   121.36  3.000
 IOP  H7    C7   C6    121.15  3.000
 IOP  C7A   C7   C6    117.49  3.000
 IOP  C7    C7A  C3A   122.18  3.000
 IOP  C7    C7A  N1    130.52  3.000
 IOP  C3A   C7A  N1    107.31  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
 IOP  CONST_01  C3A  C3   C2   N1     0.00   0.0  0
 IOP  CONST_02  C3   C3A  C7A  N1     0.00   0.0  0
 IOP  CONST_03  C4   C3A  C7A  N1   180.00   0.0  0
 IOP  CONST_04  C6   C7   C7A  N1   180.00   0.0  0
 IOP  CONST_05  C3A  C7A  N1   C2     0.00   0.0  0
 IOP  CONST_06  C7   C7A  N1   C2   180.00   0.0  0
 IOP  CONST_07  C4   C3A  C3   C2   180.00   0.0  0
 IOP  CONST_08  C7A  C3A  C3   C2     0.00   0.0  0
 IOP  CONST_09  C7A  N1   C2   C3     0.00   0.0  0
 IOP  CONST_10  C5   C4   C3A  C3   180.00   0.0  0
 IOP  CONST_11  C7   C7A  C3A  C3   180.00   0.0  0
 IOP  CONST_12  C6   C5   C4   C3A    0.00   0.0  0
 IOP  CONST_13  C6   C7   C7A  C3A    0.00   0.0  0
 IOP  CONST_14  C7   C7A  C3A  C4     0.00   0.0  0
 IOP  CONST_15  C7   C6   C5   C4     0.00   0.0  0
 IOP  CONST_16  C7A  C3A  C4   C5     0.00   0.0  0
 IOP  CONST_17  C7A  C7   C6   C5     0.00   0.0  0
 IOP  CONST_18  N1   C2   C3   C3'  180.00   0.0  0
 IOP  CONST_19  C4   C3A  C3   C3'    0.00   0.0  0
 IOP  CONST_20  C7A  C3A  C3   C3'  180.00   0.0  0
 IOP  CONST_21  H7   C7   C7A  N1     0.00   0.0  0
 IOP  CONST_22  HN1  N1   C2   C3   180.00   0.0  0
 IOP  CONST_23  H4   C4   C3A  C3     0.00   0.0  0
 IOP  CONST_24  H2   C2   C3   C3A  180.00   0.0  0
 IOP  CONST_25  H5   C5   C4   C3A  180.00   0.0  0
 IOP  CONST_26  H6   C6   C5   C4   180.00   0.0  0
 IOP  CONST_27  HO2  O2   C1'  O1     0.00   0.0  0
 IOP  Var_01    C2   C3   C3'  C2'  108.34  30.0  2
 IOP  Var_02    C3   C3'  C2'  C1'  178.28  30.0  3
 IOP  Var_03    C3'  C2'  C1'  O1     1.19  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
 IOP  plan-1  C3'  0.020
 IOP  plan-1  N1   0.020
 IOP  plan-1  C2   0.020
 IOP  plan-1  C3   0.020
 IOP  plan-1  C3A  0.020
 IOP  plan-1  C4   0.020
 IOP  plan-1  C5   0.020
 IOP  plan-1  C6   0.020
 IOP  plan-1  C7   0.020
 IOP  plan-1  C7A  0.020
 IOP  plan-1  H2   0.020
 IOP  plan-1  H4   0.020
 IOP  plan-1  H5   0.020
 IOP  plan-1  H6   0.020
 IOP  plan-1  H7   0.020
 IOP  plan-1  HN1  0.020
 IOP  plan-2  C1'  0.020
 IOP  plan-2  O1   0.020
 IOP  plan-2  O2   0.020
 IOP  plan-2  C2'  0.020
 IOP  plan-2  HO2  0.020

