# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 05:58:30 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H]1CCC[C@H]1Cc2ccc(cc2)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
 L4M  L4M  '4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}benzoic acid'  ligand  37  19  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_L4M
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
 L4M  C10  C  CH1   0  -0.212   1.2688  -0.4613  -0.1286
 L4M  C13  C  CH2   0  -0.441   2.2024  -2.6009  -0.8957
 L4M  C01  C  CR16  0  -0.239  -2.8717   1.2230  -0.5225
 L4M  C02  C  CR6   0  -0.100  -3.7374   0.2737   0.0196
 L4M  C03  C  CR16  0  -0.245  -3.2276  -0.6884   0.8901
 L4M  C04  C  CR16  0  -0.297  -1.8788  -0.6950   1.2078
 L4M  C05  C  CR6   0   0.157  -1.0073   0.2479   0.6681
 L4M  C06  C  CR16  0  -0.296  -1.5269   1.2067  -0.2018
 L4M  C07  C  CH2   0  -0.523   0.4617   0.2202   0.9765
 L4M  C08  C  CH2   0  -0.588   3.4190   0.9076  -0.0551
 L4M  C11  C  CH1   0  -0.225   2.7841  -0.4628   0.1048
 L4M  C14  C  CH2   0  -0.436   3.2720  -1.4982  -0.9093
 L4M  C09  C  C     0   0.555   4.8863   0.9477   0.2714
 L4M  C12  C  CH2   0  -0.435   0.9311  -1.9461  -0.3150
 L4M  O15  O  OH1   0  -0.597   5.4698   2.0435  -0.2066
 L4M  O16  O  O     0  -0.444   5.4814   0.1168   0.9118
 L4M  O18  O  O     0  -0.443  -5.6396   1.1607  -1.0958
 L4M  O19  O  OH1   0  -0.595  -5.8948  -0.6239   0.2149
 L4M  H1   H  HCH1  0   0.229   1.0748   0.0642  -1.0731
 L4M  H2   H  HCH2  0   0.229   2.0353  -3.0041  -1.8951
 L4M  H3   H  HCH2  0   0.228   2.5201  -3.4384  -0.2728
 L4M  H4   H  HCR6  0   0.262  -3.2525   1.9803  -1.1948
 L4M  H5   H  HCR6  0   0.264  -3.8724  -1.4366   1.3299
 L4M  H6   H  HCR6  0   0.254  -1.4981  -1.4469   1.8883
 L4M  H7   H  HCR6  0   0.253  -0.8698   1.9536  -0.6316
 L4M  H8   H  HCH2  0   0.244   0.6355  -0.3046   1.9202
 L4M  H9   H  HCH2  0   0.253   0.8142   1.2461   1.1156
 L4M  H10  H  HCH2  0   0.267   3.2620   1.2832  -1.0704
 L4M  H11  H  HCH2  0   0.291   2.9372   1.6396   0.6039
 L4M  H12  H  HCH1  0   0.228   2.9742  -0.8355   1.1188
 L4M  H13  H  HCH2  0   0.237   4.2694  -1.8773  -0.6854
 L4M  H14  H  HCH2  0   0.217   3.3208  -1.0300  -1.8977
 L4M  H15  H  HCH2  0   0.222   0.6840  -2.3888   0.6540
 L4M  H16  H  HCH2  0   0.234   0.0583  -2.0875  -0.9530
 L4M  H17  H  HOH1  0   0.478   6.4043   2.0580   0.0490
 L4M  H18  H  HOH1  0   0.487  -6.8203  -0.5408  -0.0584
 L4M  C17  C  C     0   0.529  -5.1696   0.3318  -0.3520

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
 L4M  O16  C09  double    1.206  0.020  1.206
 L4M  C11  C14  single    1.529  0.020  1.529
 L4M  C11  C08  single    1.519  0.020  1.519
 L4M  C11  C10  single    1.533  0.020  1.533
 L4M  C09  C08  single    1.504  0.020  1.504
 L4M  C09  O15  single    1.330  0.020  1.330
 L4M  C07  C10  single    1.529  0.020  1.529
 L4M  C07  C05  single    1.501  0.020  1.501
 L4M  C14  C13  single    1.536  0.020  1.536
 L4M  C06  C05  aromatic  1.395  0.020  1.395
 L4M  C06  C01  aromatic  1.383  0.020  1.383
 L4M  C13  C12  single    1.543  0.020  1.543
 L4M  C10  C12  single    1.534  0.020  1.534
 L4M  C05  C04  aromatic  1.393  0.020  1.393
 L4M  C01  C02  aromatic  1.394  0.020  1.394
 L4M  C04  C03  aromatic  1.386  0.020  1.386
 L4M  C02  C03  aromatic  1.394  0.020  1.394
 L4M  C02  C17  single    1.481  0.020  1.481
 L4M  O18  C17  double    1.209  0.020  1.209
 L4M  C17  O19  single    1.327  0.020  1.327
 L4M  C10  H1   single    0.970  0.020  1.090
 L4M  C13  H2   single    0.970  0.020  1.090
 L4M  C13  H3   single    0.970  0.020  1.090
 L4M  C01  H4   single    0.930  0.020  1.080
 L4M  C03  H5   single    0.930  0.020  1.080
 L4M  C04  H6   single    0.930  0.020  1.080
 L4M  C06  H7   single    0.930  0.020  1.080
 L4M  C07  H8   single    0.970  0.020  1.090
 L4M  C07  H9   single    0.970  0.020  1.090
 L4M  C08  H10  single    0.970  0.020  1.090
 L4M  C08  H11  single    0.970  0.020  1.090
 L4M  C11  H12  single    0.970  0.020  1.090
 L4M  C14  H13  single    0.970  0.020  1.090
 L4M  C14  H14  single    0.970  0.020  1.090
 L4M  C12  H15  single    0.970  0.020  1.090
 L4M  C12  H16  single    0.970  0.020  1.090
 L4M  O15  H17  single    0.850  0.020  0.980
 L4M  O19  H18  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
 L4M  H1   C10  C12  108.65  3.000
 L4M  H1   C10  C11  107.82  3.000
 L4M  C12  C10  C11  103.60  3.000
 L4M  H1   C10  C07  108.37  3.000
 L4M  C12  C10  C07  113.77  3.000
 L4M  C11  C10  C07  114.34  3.000
 L4M  H3   C13  H2   106.50  3.000
 L4M  H3   C13  C12  110.53  3.000
 L4M  H2   C13  C12  112.05  3.000
 L4M  H3   C13  C14  110.69  3.000
 L4M  H2   C13  C14  111.34  3.000
 L4M  C12  C13  C14  105.80  3.000
 L4M  H4   C01  C06  119.65  3.000
 L4M  H4   C01  C02  119.98  3.000
 L4M  C06  C01  C02  120.37  3.000
 L4M  C17  C02  C03  122.51  3.000
 L4M  C17  C02  C01  118.44  3.000
 L4M  C03  C02  C01  119.05  3.000
 L4M  H5   C03  C04  118.94  3.000
 L4M  H5   C03  C02  120.90  3.000
 L4M  C04  C03  C02  120.16  3.000
 L4M  H6   C04  C05  119.56  3.000
 L4M  H6   C04  C03  119.31  3.000
 L4M  C05  C04  C03  121.13  3.000
 L4M  C07  C05  C06  120.35  3.000
 L4M  C06  C05  C04  118.28  3.000
 L4M  C07  C05  C04  121.35  3.000
 L4M  H7   C06  C05  119.68  3.000
 L4M  H7   C06  C01  119.32  3.000
 L4M  C05  C06  C01  121.00  3.000
 L4M  H9   C07  H8   106.81  3.000
 L4M  H9   C07  C05  108.92  3.000
 L4M  H8   C07  C05  109.97  3.000
 L4M  H9   C07  C10  109.88  3.000
 L4M  H8   C07  C10  109.02  3.000
 L4M  C05  C07  C10  112.10  3.000
 L4M  H11  C08  H10  105.40  3.000
 L4M  H11  C08  C09  106.29  3.000
 L4M  H10  C08  C09  109.41  3.000
 L4M  H11  C08  C11  110.82  3.000
 L4M  H10  C08  C11  110.34  3.000
 L4M  C09  C08  C11  114.15  3.000
 L4M  H12  C11  C14  109.13  3.000
 L4M  H12  C11  C08  109.35  3.000
 L4M  C14  C11  C08  114.06  3.000
 L4M  H12  C11  C10  108.20  3.000
 L4M  C08  C11  C10  113.34  3.000
 L4M  C14  C11  C10  102.42  3.000
 L4M  H14  C14  H13  107.06  3.000
 L4M  H14  C14  C11  108.86  3.000
 L4M  H13  C14  C11  113.02  3.000
 L4M  H14  C14  C13  110.24  3.000
 L4M  H13  C14  C13  112.68  3.000
 L4M  C11  C14  C13  104.95  3.000
 L4M  O16  C09  O15  122.81  3.000
 L4M  O15  C09  C08  111.84  3.000
 L4M  O16  C09  C08  125.33  3.000
 L4M  H16  C12  H15  106.56  3.000
 L4M  H16  C12  C13  112.59  3.000
 L4M  H15  C12  C13  110.35  3.000
 L4M  H16  C12  C10  111.89  3.000
 L4M  H15  C12  C10  109.51  3.000
 L4M  C13  C12  C10  105.96  3.000
 L4M  H17  O15  C09  109.91  3.000
 L4M  H18  O19  C17  109.87  3.000
 L4M  O19  C17  O18  122.98  3.000
 L4M  O19  C17  C02  113.15  3.000
 L4M  O18  C17  C02  123.87  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
 L4M  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 L4M  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 L4M  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 L4M  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 L4M  CONST_05  C06  C05  C04  C03    0.00   0.0  0
 L4M  CONST_06  C06  C01  C02  C03    0.00   0.0  0
 L4M  CONST_07  C07  C05  C06  C01  180.00   0.0  0
 L4M  CONST_08  C07  C05  C04  C03  180.00   0.0  0
 L4M  CONST_09  C17  C02  C03  C04  180.00   0.0  0
 L4M  CONST_10  C17  C02  C01  C06  180.00   0.0  0
 L4M  CONST_11  H5   C03  C02  C01  180.00   0.0  0
 L4M  CONST_12  H7   C06  C01  C02  180.00   0.0  0
 L4M  CONST_13  H6   C04  C03  C02  180.00   0.0  0
 L4M  CONST_14  H4   C01  C02  C03  180.00   0.0  0
 L4M  CONST_15  H18  O19  C17  C02  180.00   0.0  0
 L4M  CONST_16  H17  O15  C09  C08  180.00   0.0  0
 L4M  Var_01    C14  C13  C12  C10    4.87  30.0  1
 L4M  Var_02    C12  C13  C14  C11   20.67  30.0  1
 L4M  Var_03    C06  C05  C07  C10  -80.07  30.0  2
 L4M  Var_04    O18  C17  C02  C01   -0.39  30.0  2
 L4M  Var_05    O16  C09  C08  C11  -18.02  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 L4M  chir_01  C10  C11  C07  C12  positiv
 L4M  chir_02  C11  C10  C08  C14  positiv

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
 L4M  plan-1  C01  0.020
 L4M  plan-1  C02  0.020
 L4M  plan-1  C03  0.020
 L4M  plan-1  C04  0.020
 L4M  plan-1  C05  0.020
 L4M  plan-1  C06  0.020
 L4M  plan-1  C07  0.020
 L4M  plan-1  H4   0.020
 L4M  plan-1  H5   0.020
 L4M  plan-1  H6   0.020
 L4M  plan-1  H7   0.020
 L4M  plan-1  C17  0.020
 L4M  plan-2  C02  0.020
 L4M  plan-2  O18  0.020
 L4M  plan-2  O19  0.020
 L4M  plan-2  H18  0.020
 L4M  plan-2  C17  0.020
 L4M  plan-3  C08  0.020
 L4M  plan-3  C09  0.020
 L4M  plan-3  O15  0.020
 L4M  plan-3  O16  0.020
 L4M  plan-3  H17  0.020

