# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 21:52:47 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  34  20  .  2021-08-12  2021-08-12  
;
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  -0.397  -1.3661   0.5250   0.3999
 L1Y  C12  C  CH2    0  -0.435  -1.2337   1.9363   1.0481
 L1Y  C14  C  CH2    0  -0.432  -3.5496   1.2177   1.0689
 L1Y  O17  O  O      0  -0.613  -5.2625  -0.4602  -1.2479
 L1Y  C01  C  CR16   0  -0.272   2.8611  -0.1052   1.1878
 L1Y  C02  C  CR6    0  -0.099   3.7949  -0.1683   0.1582
 L1Y  C03  C  CR16   0  -0.277   3.3407  -0.0566  -1.1551
 L1Y  C04  C  CR16   0  -0.256   1.9958   0.1113  -1.4316
 L1Y  C05  C  CR6    0  -0.020   1.0584   0.1741  -0.3977
 L1Y  C06  C  CR16   0  -0.282   1.5123   0.0635   0.9165
 L1Y  C07  C  C      0   0.393  -0.3850   0.3531  -0.7333
 L1Y  C08  C  CH2    0  -0.570  -3.2946  -1.0772  -0.0536
 L1Y  C09  C  C      0   0.409  -4.7640  -1.2872  -0.4573
 L1Y  C11  C  CR15   0  -0.193  -2.8419   0.3725   0.0121
 L1Y  C13  C  CH2    0  -0.437  -2.6741   2.4616   1.1709
 L1Y  O15  O  OC    -1  -0.626  -5.3355  -2.2929   0.0134
 L1Y  O16  O  O      0  -0.399  -0.7364   0.3876  -1.8956
 L1Y  O19  O  OC    -1  -0.588   6.0433  -0.4035  -0.5219
 L1Y  O20  O  O      0  -0.588   5.5941  -0.4399   1.6615
 L1Y  H1   H  HCR5   0   0.262  -1.1420  -0.2256   1.1651
 L1Y  H2   H  HCH2   0   0.238  -0.7558   1.8557   2.0252
 L1Y  H3   H  HCH2   0   0.238  -0.6123   2.6102   0.4556
 L1Y  H4   H  HCH2   0   0.230  -4.5838   1.4394   0.8033
 L1Y  H5   H  HCH2   0   0.205  -3.5626   0.6812   2.0245
 L1Y  H6   H  HCR6   0   0.249   3.1919  -0.1926   2.2139
 L1Y  H7   H  HCR6   0   0.248   4.0531  -0.1016  -1.9677
 L1Y  H8   H  HCR6   0   0.252   1.6676   0.1978  -2.4591
 L1Y  H9   H  HCR6   0   0.256   0.8182   0.1039   1.7450
 L1Y  H10  H  HCH2   0   0.200  -3.1006  -1.5644   0.9076
 L1Y  H11  H  HCH2   0   0.231  -2.6767  -1.6136  -0.7855
 L1Y  H12  H  HCR5   0   0.214  -3.0120   0.8381  -0.9621
 L1Y  H13  H  HCH2   0   0.232  -2.8286   3.0261   2.0915
 L1Y  H14  H  HCH2   0   0.222  -2.8979   3.1361   0.3408
 L1Y  C18  C  C      0   0.402   5.2793  -0.3542   0.4600

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  deloc     1.248  0.020  1.248
 L1Y  O16  C07  double    1.215  0.020  1.215
 L1Y  C08  C09  single    1.538  0.020  1.538
 L1Y  C08  C11  single    1.520  0.020  1.520
 L1Y  C09  O15  deloc     1.249  0.020  1.249
 L1Y  C07  C10  single    1.509  0.020  1.509
 L1Y  C07  C05  single    1.493  0.020  1.493
 L1Y  C10  C11  single    1.534  0.020  1.534
 L1Y  C10  C12  single    1.559  0.020  1.559
 L1Y  C06  C05  aromatic  1.395  0.020  1.395
 L1Y  C06  C01  aromatic  1.386  0.020  1.386
 L1Y  C11  C14  single    1.527  0.020  1.527
 L1Y  C12  C13  single    1.538  0.020  1.538
 L1Y  C05  C04  aromatic  1.397  0.020  1.397
 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    1.526  0.020  1.526
 L1Y  O20  C18  deloc     1.245  0.020  1.245
 L1Y  C18  O19  deloc     1.245  0.020  1.245
 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

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  107.79  3.000
 L1Y  H1   C10  C07  108.29  3.000
 L1Y  C11  C10  C07  115.12  3.000
 L1Y  H1   C10  C12  108.22  3.000
 L1Y  C11  C10  C12  106.08  3.000
 L1Y  C07  C10  C12  111.12  3.000
 L1Y  H3   C12  H2   106.41  3.000
 L1Y  H3   C12  C13  111.45  3.000
 L1Y  H2   C12  C13  111.35  3.000
 L1Y  H3   C12  C10  112.43  3.000
 L1Y  H2   C12  C10  110.05  3.000
 L1Y  C13  C12  C10  105.24  3.000
 L1Y  H5   C14  H4   107.49  3.000
 L1Y  H5   C14  C13  110.36  3.000
 L1Y  H4   C14  C13  113.27  3.000
 L1Y  H5   C14  C11  109.75  3.000
 L1Y  H4   C14  C11  112.55  3.000
 L1Y  C13  C14  C11  103.40  3.000
 L1Y  H6   C01  C06  119.55  3.000
 L1Y  H6   C01  C02  119.54  3.000
 L1Y  C06  C01  C02  120.91  3.000
 L1Y  C18  C02  C03  120.86  3.000
 L1Y  C18  C02  C01  120.80  3.000
 L1Y  C03  C02  C01  118.35  3.000
 L1Y  H7   C03  C04  119.69  3.000
 L1Y  H7   C03  C02  119.33  3.000
 L1Y  C04  C03  C02  120.98  3.000
 L1Y  H8   C04  C05  119.71  3.000
 L1Y  H8   C04  C03  119.63  3.000
 L1Y  C05  C04  C03  120.66  3.000
 L1Y  C07  C05  C06  122.41  3.000
 L1Y  C06  C05  C04  118.38  3.000
 L1Y  C07  C05  C04  119.20  3.000
 L1Y  H9   C06  C05  120.66  3.000
 L1Y  H9   C06  C01  118.63  3.000
 L1Y  C05  C06  C01  120.72  3.000
 L1Y  O16  C07  C05  119.88  3.000
 L1Y  C05  C07  C10  118.27  3.000
 L1Y  O16  C07  C10  121.83  3.000
 L1Y  H11  C08  H10  105.55  3.000
 L1Y  H11  C08  C11  109.10  3.000
 L1Y  H10  C08  C11  109.49  3.000
 L1Y  H11  C08  C09  107.22  3.000
 L1Y  H10  C08  C09  109.80  3.000
 L1Y  C11  C08  C09  115.22  3.000
 L1Y  O15  C09  C08  116.63  3.000
 L1Y  O15  C09  O17  126.13  3.000
 L1Y  C08  C09  O17  117.21  3.000
 L1Y  H12  C11  C08  108.74  3.000
 L1Y  H12  C11  C14  107.99  3.000
 L1Y  C08  C11  C14  114.82  3.000
 L1Y  H12  C11  C10  109.44  3.000
 L1Y  C14  C11  C10  102.47  3.000
 L1Y  C08  C11  C10  113.10  3.000
 L1Y  H14  C13  H13  107.01  3.000
 L1Y  H14  C13  C14  109.59  3.000
 L1Y  H13  C13  C14  113.41  3.000
 L1Y  H14  C13  C12  110.00  3.000
 L1Y  H13  C13  C12  112.13  3.000
 L1Y  C14  C13  C12  104.70  3.000
 L1Y  O20  C18  O19  127.10  3.000
 L1Y  O19  C18  C02  116.47  3.000
 L1Y  O20  C18  C02  116.43  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  Var_01    C14  C13  C12  C10   19.05  30.0  1
 L1Y  Var_02    C11  C14  C13  C12  -38.43  30.0  1
 L1Y  Var_03    C06  C05  C07  C10    4.77  30.0  2
 L1Y  Var_04    O20  C18  C02  C01   -0.21  30.0  2
 L1Y  Var_05    C11  C08  C09  O17   32.25  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-3  C02  0.020
 L1Y  plan-3  O19  0.020
 L1Y  plan-3  O20  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

