# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 01:44:52 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 4-[(1S,2R)-2-(carboxymethyl)cyclopentane-1-carbonyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H]1CCC[C@@H]1C(=O)c2ccc(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
 L1Y  L1Y  '4-[(1S,2R)-2-(carboxymethyl)cyclopentane-1-carbonyl]benzoic acid'  ligand  36  20  .  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_L1Y
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
 L1Y  C10  C  CR15  0  -0.409  -1.3515   0.4359   0.4006
 L1Y  C12  C  CH2   0  -0.436  -1.1481   1.8475   1.0288
 L1Y  C14  C  CH2   0  -0.433  -3.5011   1.2743   1.0377
 L1Y  O17  O  O     0  -0.444  -5.3835  -0.3969  -1.0710
 L1Y  C01  C  CR16  0  -0.237   2.8821  -0.1588   1.1562
 L1Y  C02  C  CR6   0  -0.084   3.8016  -0.1257   0.1126
 L1Y  C03  C  CR16  0  -0.246   3.3474   0.0117  -1.1985
 L1Y  C04  C  CR16  0  -0.251   1.9921   0.1094  -1.4554
 L1Y  C05  C  CR6   0  -0.005   1.0661   0.0850  -0.4127
 L1Y  C06  C  CR16  0  -0.277   1.5273  -0.0483   0.8956
 L1Y  C07  C  C     0   0.407  -0.3919   0.1951  -0.7370
 L1Y  C08  C  CH2   0  -0.584  -3.3423  -1.0795   0.0160
 L1Y  C09  C  C     0   0.554  -4.7615  -1.2287  -0.4580
 L1Y  C11  C  CR15  0  -0.216  -2.8346   0.3531   0.0170
 L1Y  C13  C  CH2   0  -0.439  -2.5528   2.4655   1.0948
 L1Y  O15  O  OH1   0  -0.597  -5.2624  -2.4207  -0.1464
 L1Y  O16  O  O     0  -0.383  -0.7573   0.1203  -1.8900
 L1Y  O19  O  OH1   0  -0.590   6.0290  -0.1572  -0.6198
 L1Y  O20  O  O     0  -0.431   5.6630  -0.3884   1.5677
 L1Y  H1   H  HCR5  0   0.280  -1.1542  -0.3182   1.1706
 L1Y  H2   H  HCH2  0   0.244  -0.7117   1.7536   2.0236
 L1Y  H3   H  HCH2  0   0.246  -0.4654   2.4688   0.4467
 L1Y  H4   H  HCH2  0   0.242  -4.5183   1.5512   0.7610
 L1Y  H5   H  HCH2  0   0.217  -3.5465   0.7763   2.0121
 L1Y  H6   H  HCR6  0   0.274   3.2214  -0.2696   2.1768
 L1Y  H7   H  HCR6  0   0.274   4.0412   0.0413  -2.0266
 L1Y  H8   H  HCR6  0   0.269   1.6521   0.2140  -2.4767
 L1Y  H9   H  HCR6  0   0.271   0.8378  -0.0770   1.7278
 L1Y  H10  H  HCH2  0   0.271  -3.2456  -1.5186   1.0132
 L1Y  H11  H  HCH2  0   0.294  -2.7269  -1.7042  -0.6417
 L1Y  H12  H  HCR5  0   0.243  -2.9733   0.7825  -0.9790
 L1Y  H13  H  HCH2  0   0.240  -2.6884   3.0834   1.9830
 L1Y  H14  H  HCH2  0   0.228  -2.7195   3.1083   0.2273
 L1Y  H15  H  HOH1  0   0.478  -6.1638  -2.5014  -0.4929
 L1Y  H16  H  HOH1  0   0.491   6.9586  -0.2321  -0.3569
 L1Y  C18  C  C     0   0.540   5.2469  -0.2393   0.4447

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
 L1Y  O17  C09  double    1.206  0.020  1.206
 L1Y  O16  C07  double    1.212  0.020  1.212
 L1Y  C08  C09  single    1.504  0.020  1.504
 L1Y  C08  C11  single    1.520  0.020  1.520
 L1Y  C09  O15  single    1.330  0.020  1.330
 L1Y  C07  C10  single    1.508  0.020  1.508
 L1Y  C07  C05  single    1.498  0.020  1.498
 L1Y  C10  C11  single    1.534  0.020  1.534
 L1Y  C10  C12  single    1.558  0.020  1.558
 L1Y  C06  C05  aromatic  1.394  0.020  1.394
 L1Y  C06  C01  aromatic  1.384  0.020  1.384
 L1Y  C11  C14  single    1.528  0.020  1.528
 L1Y  C12  C13  single    1.536  0.020  1.536
 L1Y  C05  C04  aromatic  1.395  0.020  1.395
 L1Y  C13  C14  single    1.524  0.020  1.524
 L1Y  C01  C02  aromatic  1.391  0.020  1.391
 L1Y  C04  C03  aromatic  1.383  0.020  1.383
 L1Y  C02  C03  aromatic  1.394  0.020  1.394
 L1Y  C02  C18  single    1.487  0.020  1.487
 L1Y  O20  C18  double    1.207  0.020  1.207
 L1Y  C18  O19  single    1.324  0.020  1.324
 L1Y  C10  H1   single    0.970  0.020  1.090
 L1Y  C12  H2   single    0.970  0.020  1.090
 L1Y  C12  H3   single    0.970  0.020  1.090
 L1Y  C14  H4   single    0.970  0.020  1.090
 L1Y  C14  H5   single    0.970  0.020  1.090
 L1Y  C01  H6   single    0.930  0.020  1.080
 L1Y  C03  H7   single    0.930  0.020  1.080
 L1Y  C04  H8   single    0.930  0.020  1.080
 L1Y  C06  H9   single    0.930  0.020  1.080
 L1Y  C08  H10  single    0.970  0.020  1.090
 L1Y  C08  H11  single    0.970  0.020  1.090
 L1Y  C11  H12  single    0.970  0.020  1.090
 L1Y  C13  H13  single    0.970  0.020  1.090
 L1Y  C13  H14  single    0.970  0.020  1.090
 L1Y  O15  H15  single    0.850  0.020  0.980
 L1Y  O19  H16  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
 L1Y  H1   C10  C11  108.22  3.000
 L1Y  H1   C10  C07  107.81  3.000
 L1Y  C11  C10  C07  114.71  3.000
 L1Y  H1   C10  C12  108.46  3.000
 L1Y  C11  C10  C12  106.01  3.000
 L1Y  C07  C10  C12  111.45  3.000
 L1Y  H3   C12  H2   106.58  3.000
 L1Y  H3   C12  C13  111.47  3.000
 L1Y  H2   C12  C13  111.19  3.000
 L1Y  H3   C12  C10  112.48  3.000
 L1Y  H2   C12  C10  110.00  3.000
 L1Y  C13  C12  C10  105.21  3.000
 L1Y  H5   C14  H4   107.62  3.000
 L1Y  H5   C14  C13  110.36  3.000
 L1Y  H4   C14  C13  113.06  3.000
 L1Y  H5   C14  C11  109.77  3.000
 L1Y  H4   C14  C11  113.00  3.000
 L1Y  C13  C14  C11  103.00  3.000
 L1Y  H6   C01  C06  119.54  3.000
 L1Y  H6   C01  C02  120.20  3.000
 L1Y  C06  C01  C02  120.26  3.000
 L1Y  C18  C02  C03  122.28  3.000
 L1Y  C18  C02  C01  118.23  3.000
 L1Y  C03  C02  C01  119.49  3.000
 L1Y  H7   C03  C04  119.01  3.000
 L1Y  H7   C03  C02  120.93  3.000
 L1Y  C04  C03  C02  120.06  3.000
 L1Y  H8   C04  C05  119.94  3.000
 L1Y  H8   C04  C03  119.36  3.000
 L1Y  C05  C04  C03  120.70  3.000
 L1Y  C07  C05  C06  122.17  3.000
 L1Y  C06  C05  C04  118.94  3.000
 L1Y  C07  C05  C04  118.89  3.000
 L1Y  H9   C06  C05  120.94  3.000
 L1Y  H9   C06  C01  118.51  3.000
 L1Y  C05  C06  C01  120.55  3.000
 L1Y  O16  C07  C05  119.67  3.000
 L1Y  C05  C07  C10  117.90  3.000
 L1Y  O16  C07  C10  122.40  3.000
 L1Y  H11  C08  H10  105.59  3.000
 L1Y  H11  C08  C11  110.49  3.000
 L1Y  H10  C08  C11  110.38  3.000
 L1Y  H11  C08  C09  106.51  3.000
 L1Y  H10  C08  C09  109.33  3.000
 L1Y  C11  C08  C09  114.14  3.000
 L1Y  O15  C09  C08  111.75  3.000
 L1Y  O15  C09  O17  122.89  3.000
 L1Y  C08  C09  O17  125.35  3.000
 L1Y  H12  C11  C08  109.09  3.000
 L1Y  H12  C11  C14  108.44  3.000
 L1Y  C08  C11  C14  115.02  3.000
 L1Y  H12  C11  C10  109.22  3.000
 L1Y  C14  C11  C10  102.84  3.000
 L1Y  C08  C11  C10  111.96  3.000
 L1Y  H14  C13  H13  107.12  3.000
 L1Y  H14  C13  C14  109.59  3.000
 L1Y  H13  C13  C14  113.34  3.000
 L1Y  H14  C13  C12  110.01  3.000
 L1Y  H13  C13  C12  112.13  3.000
 L1Y  C14  C13  C12  104.66  3.000
 L1Y  H15  O15  C09  109.95  3.000
 L1Y  H16  O19  C18  110.11  3.000
 L1Y  O20  C18  O19  123.53  3.000
 L1Y  O19  C18  C02  112.95  3.000
 L1Y  O20  C18  C02  123.52  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
 L1Y  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 L1Y  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 L1Y  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 L1Y  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 L1Y  CONST_05  C06  C05  C04  C03    0.00   0.0  0
 L1Y  CONST_06  C06  C01  C02  C03    0.00   0.0  0
 L1Y  CONST_07  C07  C05  C06  C01  180.00   0.0  0
 L1Y  CONST_08  C07  C05  C04  C03  180.00   0.0  0
 L1Y  CONST_09  C18  C02  C03  C04  180.00   0.0  0
 L1Y  CONST_10  C18  C02  C01  C06  180.00   0.0  0
 L1Y  CONST_11  H7   C03  C02  C01  180.00   0.0  0
 L1Y  CONST_12  H9   C06  C01  C02  180.00   0.0  0
 L1Y  CONST_13  H8   C04  C03  C02  180.00   0.0  0
 L1Y  CONST_14  H6   C01  C02  C03  180.00   0.0  0
 L1Y  CONST_15  H16  O19  C18  C02  180.00   0.0  0
 L1Y  CONST_16  H15  O15  C09  O17    0.00   0.0  0
 L1Y  Var_01    C14  C13  C12  C10   21.11  30.0  1
 L1Y  Var_02    C11  C14  C13  C12  -39.53  30.0  1
 L1Y  Var_03    C06  C05  C07  C10   12.01  30.0  2
 L1Y  Var_04    O20  C18  C02  C01    1.71  30.0  2
 L1Y  Var_05    C11  C08  C09  O17   16.38  30.0  2

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
 L1Y  chir_01  C10  C07  C11  C12  positiv
 L1Y  chir_02  C11  C08  C10  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
 L1Y  plan-1  C01  0.020
 L1Y  plan-1  C02  0.020
 L1Y  plan-1  C03  0.020
 L1Y  plan-1  C04  0.020
 L1Y  plan-1  C05  0.020
 L1Y  plan-1  C06  0.020
 L1Y  plan-1  C07  0.020
 L1Y  plan-1  H6   0.020
 L1Y  plan-1  H7   0.020
 L1Y  plan-1  H8   0.020
 L1Y  plan-1  H9   0.020
 L1Y  plan-1  C18  0.020
 L1Y  plan-2  O17  0.020
 L1Y  plan-2  C08  0.020
 L1Y  plan-2  C09  0.020
 L1Y  plan-2  O15  0.020
 L1Y  plan-2  H15  0.020
 L1Y  plan-3  C02  0.020
 L1Y  plan-3  O19  0.020
 L1Y  plan-3  O20  0.020
 L1Y  plan-3  H16  0.020
 L1Y  plan-3  C18  0.020
 L1Y  plan-4  C10  0.020
 L1Y  plan-4  C05  0.020
 L1Y  plan-4  C07  0.020
 L1Y  plan-4  O16  0.020

