# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:13:58 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-methyl-1H-indene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(Cc2ccccc12)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
 38U  38U  '3-methyl-1H-indene-2-carboxylic acid'  ligand  22  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_38U
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
 38U  C59  C  CH3    0  -0.762  -0.8165   2.3460  -0.0224
 38U  C58  C  CR5    0   0.092  -0.4132   0.9116  -0.0050
 38U  C57  C  CR56   0   0.113   1.0002   0.5270  -0.0272
 38U  C56  C  CR16   0  -0.342   2.1472   1.3116  -0.0599
 38U  C55  C  CR16   0  -0.259   3.3864   0.6798  -0.0712
 38U  C54  C  CR16   0  -0.268   3.4764  -0.7093  -0.0503
 38U  C53  C  CR16   0  -0.330   2.3251  -1.4941  -0.0188
 38U  C52  C  CR56   0   0.063   1.0920  -0.8689  -0.0077
 38U  C51  C  CH2    0  -0.527  -0.2916  -1.4334   0.0232
 38U  C50  C  CR5    0  -0.187  -1.1695  -0.2106   0.0250
 38U  C2   C  C      0   0.365  -2.6684  -0.3555   0.0565
 38U  O3   O  O      0  -0.589  -3.3689   0.6766   0.1153
 38U  H4   H  HCH3   0   0.232  -0.4397   2.8395  -0.9222
 38U  H5   H  HCH3   0   0.263  -1.8945   2.4569   0.0122
 38U  H6   H  HCH3   0   0.232  -0.3806   2.8783   0.8271
 38U  H7   H  HCR6   0   0.242   2.0872   2.3931  -0.0759
 38U  H8   H  HCR6   0   0.249   4.2907   1.2746  -0.0965
 38U  H9   H  HCR6   0   0.249   4.4499  -1.1832  -0.0591
 38U  H10  H  HCR6   0   0.245   2.4025  -2.5749  -0.0034
 38U  H11  H  HCH2   0   0.259  -0.4883  -2.0792  -0.8383
 38U  H12  H  HCH2   0   0.259  -0.4576  -2.0601   0.9052
 38U  OXT  O  OC    -1  -0.599  -3.0927  -1.5301   0.0232

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
 38U  O3   C2   deloc     1.249  0.020  1.249
 38U  C2   C50  single    1.506  0.020  1.506
 38U  C50  C51  single    1.505  0.020  1.505
 38U  C50  C58  double    1.354  0.020  1.354
 38U  C51  C52  single    1.495  0.020  1.495
 38U  C59  C58  single    1.490  0.020  1.490
 38U  C58  C57  single    1.465  0.020  1.465
 38U  C52  C57  aromatic  1.399  0.020  1.399
 38U  C52  C53  aromatic  1.383  0.020  1.383
 38U  C57  C56  aromatic  1.390  0.020  1.390
 38U  C53  C54  aromatic  1.394  0.020  1.394
 38U  C56  C55  aromatic  1.391  0.020  1.391
 38U  C54  C55  aromatic  1.392  0.020  1.392
 38U  C59  H4   single    0.970  0.020  1.090
 38U  C59  H5   single    0.970  0.020  1.090
 38U  C59  H6   single    0.970  0.020  1.090
 38U  C56  H7   single    0.930  0.020  1.080
 38U  C55  H8   single    0.930  0.020  1.080
 38U  C54  H9   single    0.930  0.020  1.080
 38U  C53  H10  single    0.930  0.020  1.080
 38U  C51  H11  single    0.970  0.020  1.090
 38U  C51  H12  single    0.970  0.020  1.090
 38U  C2   OXT  deloc     1.249  0.020  1.249

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
 38U  H6   C59  H5   108.78  3.000
 38U  H6   C59  H4   106.40  3.000
 38U  H5   C59  H4   108.82  3.000
 38U  H6   C59  C58  110.60  3.000
 38U  H5   C59  C58  111.54  3.000
 38U  H4   C59  C58  110.54  3.000
 38U  C50  C58  C57  108.77  3.000
 38U  C57  C58  C59  120.91  3.000
 38U  C50  C58  C59  130.32  3.000
 38U  C52  C57  C56  120.62  3.000
 38U  C56  C57  C58  130.41  3.000
 38U  C52  C57  C58  108.97  3.000
 38U  H7   C56  C55  120.17  3.000
 38U  H7   C56  C57  121.21  3.000
 38U  C55  C56  C57  118.61  3.000
 38U  H8   C55  C54  119.63  3.000
 38U  H8   C55  C56  119.66  3.000
 38U  C54  C55  C56  120.71  3.000
 38U  H9   C54  C53  119.76  3.000
 38U  H9   C54  C55  119.66  3.000
 38U  C53  C54  C55  120.59  3.000
 38U  H10  C53  C52  120.98  3.000
 38U  H10  C53  C54  120.19  3.000
 38U  C52  C53  C54  118.83  3.000
 38U  C51  C52  C53  130.92  3.000
 38U  C53  C52  C57  120.64  3.000
 38U  C51  C52  C57  108.45  3.000
 38U  H12  C51  H11  105.61  3.000
 38U  H12  C51  C50  112.07  3.000
 38U  H11  C51  C50  112.05  3.000
 38U  H12  C51  C52  111.92  3.000
 38U  H11  C51  C52  111.90  3.000
 38U  C50  C51  C52  103.48  3.000
 38U  C2   C50  C51  120.15  3.000
 38U  C51  C50  C58  110.34  3.000
 38U  C2   C50  C58  129.51  3.000
 38U  OXT  C2   O3   126.00  3.000
 38U  OXT  C2   C50  115.33  3.000
 38U  O3   C2   C50  118.67  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
 38U  CONST_01  C54  C53  C52  C57    0.00   0.0  0
 38U  CONST_02  C54  C55  C56  C57    0.00   0.0  0
 38U  CONST_03  C53  C52  C57  C56    0.00   0.0  0
 38U  CONST_04  C53  C54  C55  C56    0.00   0.0  0
 38U  CONST_05  C52  C57  C56  C55    0.00   0.0  0
 38U  CONST_06  C52  C53  C54  C55    0.00   0.0  0
 38U  CONST_07  H7   C56  C57  C58    0.00   0.0  0
 38U  CONST_08  H10  C53  C52  C57  180.00   0.0  0
 38U  CONST_09  H8   C55  C56  C57  180.00   0.0  0
 38U  CONST_10  H9   C54  C55  C56  180.00   0.0  0
 38U  Var_01    O3   C2   C50  C58   -3.07  30.0  3
 38U  Var_02    H4   C59  C58  C57   59.59  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
 38U  plan-1  C50  0.020
 38U  plan-1  C2   0.020
 38U  plan-1  O3   0.020
 38U  plan-1  OXT  0.020
 38U  plan-2  C59  0.020
 38U  plan-2  C58  0.020
 38U  plan-2  C57  0.020
 38U  plan-2  C56  0.020
 38U  plan-2  C55  0.020
 38U  plan-2  C54  0.020
 38U  plan-2  C53  0.020
 38U  plan-2  C52  0.020
 38U  plan-2  C51  0.020
 38U  plan-2  C50  0.020
 38U  plan-2  C2   0.020
 38U  plan-2  H7   0.020
 38U  plan-2  H8   0.020
 38U  plan-2  H9   0.020
 38U  plan-2  H10  0.020
 38U  plan-2  H11  0.020
 38U  plan-2  H12  0.020

