# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 04:27:11 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H]1CCC[C@H]1Cc2ccc(CC(O)=O)cc2
#
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
 L5A  L5A  '(4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid'  ligand  38  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 PERFECT
;

data_comp_L5A
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
 L5A  C10  C  CH1    0  -0.205   1.5453   0.4271  -0.0835
 L5A  C11  C  CH1    0  -0.192   3.0786   0.4334  -0.2336
 L5A  C12  C  CH2    0  -0.422   1.1958   1.8821   0.2155
 L5A  C01  C  CR16   0  -0.289  -2.6006  -1.3791  -0.1752
 L5A  C02  C  CR6    0   0.155  -3.4603  -0.4058  -0.6830
 L5A  C03  C  CR16   0  -0.305  -2.8919   0.6398  -1.4042
 L5A  C04  C  CR16   0  -0.302  -1.5190   0.7140  -1.6097
 L5A  C05  C  CR6    0   0.133  -0.6633  -0.2586  -1.1040
 L5A  C06  C  CR16   0  -0.306  -1.2323  -1.3093  -0.3843
 L5A  C07  C  CH2    0  -0.514   0.8250  -0.1706  -1.2915
 L5A  C08  C  CH2    0  -0.579   3.7231  -0.8830   0.1690
 L5A  C09  C  C      0   0.407   5.2358  -0.9735  -0.0939
 L5A  C13  C  CH2    0  -0.443   2.3058   2.3093   1.1704
 L5A  C14  C  CH2    0  -0.436   3.5678   1.6425   0.6012
 L5A  C18  C  C      0   0.418  -5.3955  -0.0369   0.9608
 L5A  O15  O  OC    -1  -0.628   5.9000  -1.6918   0.6836
 L5A  O16  O  O      0  -0.613   5.6828  -0.3528  -1.0799
 L5A  O19  O  O      0  -0.598  -4.5477  -0.0468   1.8705
 L5A  O20  O  OC    -1  -0.623  -6.6021   0.2610   1.0632
 L5A  H1   H  HCH1   0   0.212   1.2816  -0.1689   0.8013
 L5A  H2   H  HCH1   0   0.207   3.3128   0.6189  -1.2865
 L5A  H3   H  HCH2   0   0.204   1.2422   2.4735  -0.7066
 L5A  H4   H  HCH2   0   0.226   0.1935   2.0092   0.6290
 L5A  H5   H  HCR6   0   0.233  -3.0102  -2.2168   0.3769
 L5A  H6   H  HCR6   0   0.236  -3.5306   1.4110  -1.8207
 L5A  H7   H  HCR6   0   0.234  -1.1090   1.5427  -2.1766
 L5A  H8   H  HCR6   0   0.234  -0.5938  -2.0891   0.0175
 L5A  H9   H  HCH2   0   0.228   1.0538   0.4361  -2.1737
 L5A  H10  H  HCH2   0   0.237   1.2254  -1.1700  -1.4898
 L5A  H11  H  HCH2   0   0.202   3.5208  -1.0834   1.2265
 L5A  H12  H  HCH2   0   0.225   3.2459  -1.7042  -0.3831
 L5A  H13  H  HCH2   0   0.223   2.4015   3.3925   1.2639
 L5A  H14  H  HCH2   0   0.213   2.0916   1.9214   2.1701
 L5A  H15  H  HCH2   0   0.217   4.2536   1.3390   1.3960
 L5A  H16  H  HCH2   0   0.219   4.1185   2.3408  -0.0312
 L5A  H17  H  HCH2   0   0.233  -5.4674   0.1138  -1.2024
 L5A  H18  H  HCH2   0   0.246  -5.2813  -1.5092  -0.5889
 L5A  C17  C  CH2    0  -0.686  -4.9366  -0.4775  -0.4526

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
 L5A  O16  C09  deloc     1.248  0.020  1.248
 L5A  C06  C01  aromatic  1.386  0.020  1.386
 L5A  C06  C05  aromatic  1.395  0.020  1.395
 L5A  C11  C08  single    1.520  0.020  1.520
 L5A  C11  C14  single    1.549  0.020  1.549
 L5A  C11  C10  single    1.541  0.020  1.541
 L5A  C07  C05  single    1.503  0.020  1.503
 L5A  C07  C10  single    1.528  0.020  1.528
 L5A  C09  C08  single    1.538  0.020  1.538
 L5A  C09  O15  deloc     1.250  0.020  1.250
 L5A  C14  C13  single    1.537  0.020  1.537
 L5A  C01  C02  aromatic  1.394  0.020  1.394
 L5A  C13  C12  single    1.525  0.020  1.525
 L5A  C12  C10  single    1.526  0.020  1.526
 L5A  C05  C04  aromatic  1.391  0.020  1.391
 L5A  C02  C17  single    1.496  0.020  1.496
 L5A  C02  C03  aromatic  1.392  0.020  1.392
 L5A  C04  C03  aromatic  1.390  0.020  1.390
 L5A  C17  C18  single    1.550  0.020  1.550
 L5A  O19  C18  deloc     1.243  0.020  1.243
 L5A  C18  O20  deloc     1.247  0.020  1.247
 L5A  C10  H1   single    0.970  0.020  1.090
 L5A  C11  H2   single    0.970  0.020  1.090
 L5A  C12  H3   single    0.970  0.020  1.090
 L5A  C12  H4   single    0.970  0.020  1.090
 L5A  C01  H5   single    0.930  0.020  1.080
 L5A  C03  H6   single    0.930  0.020  1.080
 L5A  C04  H7   single    0.930  0.020  1.080
 L5A  C06  H8   single    0.930  0.020  1.080
 L5A  C07  H9   single    0.970  0.020  1.090
 L5A  C07  H10  single    0.970  0.020  1.090
 L5A  C08  H11  single    0.970  0.020  1.090
 L5A  C08  H12  single    0.970  0.020  1.090
 L5A  C13  H13  single    0.970  0.020  1.090
 L5A  C13  H14  single    0.970  0.020  1.090
 L5A  C14  H15  single    0.970  0.020  1.090
 L5A  C14  H16  single    0.970  0.020  1.090
 L5A  C17  H17  single    0.970  0.020  1.090
 L5A  C17  H18  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
 L5A  H1   C10  C07  108.14  3.000
 L5A  H1   C10  C12  107.72  3.000
 L5A  C07  C10  C12  114.83  3.000
 L5A  H1   C10  C11  108.63  3.000
 L5A  C12  C10  C11  104.07  3.000
 L5A  C07  C10  C11  113.18  3.000
 L5A  H2   C11  C14  108.58  3.000
 L5A  H2   C11  C08  108.11  3.000
 L5A  C14  C11  C08  113.55  3.000
 L5A  H2   C11  C10  107.90  3.000
 L5A  C14  C11  C10  105.37  3.000
 L5A  C08  C11  C10  113.12  3.000
 L5A  H4   C12  H3   107.13  3.000
 L5A  H4   C12  C13  113.48  3.000
 L5A  H3   C12  C13  110.17  3.000
 L5A  H4   C12  C10  113.29  3.000
 L5A  H3   C12  C10  109.87  3.000
 L5A  C13  C12  C10  102.89  3.000
 L5A  H5   C01  C06  119.27  3.000
 L5A  H5   C01  C02  119.47  3.000
 L5A  C06  C01  C02  121.24  3.000
 L5A  C17  C02  C03  121.26  3.000
 L5A  C03  C02  C01  117.47  3.000
 L5A  C17  C02  C01  121.26  3.000
 L5A  H6   C03  C04  119.13  3.000
 L5A  H6   C03  C02  119.52  3.000
 L5A  C04  C03  C02  121.34  3.000
 L5A  H7   C04  C05  119.46  3.000
 L5A  H7   C04  C03  119.44  3.000
 L5A  C05  C04  C03  121.10  3.000
 L5A  C07  C05  C06  120.83  3.000
 L5A  C07  C05  C04  121.54  3.000
 L5A  C06  C05  C04  117.61  3.000
 L5A  H8   C06  C05  119.50  3.000
 L5A  H8   C06  C01  119.27  3.000
 L5A  C05  C06  C01  121.23  3.000
 L5A  H10  C07  H9   106.47  3.000
 L5A  H10  C07  C05  109.35  3.000
 L5A  H9   C07  C05  109.88  3.000
 L5A  H10  C07  C10  109.14  3.000
 L5A  H9   C07  C10  108.77  3.000
 L5A  C05  C07  C10  113.02  3.000
 L5A  H12  C08  H11  105.56  3.000
 L5A  H12  C08  C09  107.30  3.000
 L5A  H11  C08  C09  109.63  3.000
 L5A  H12  C08  C11  109.27  3.000
 L5A  H11  C08  C11  109.63  3.000
 L5A  C09  C08  C11  115.00  3.000
 L5A  O16  C09  O15  125.96  3.000
 L5A  O15  C09  C08  116.76  3.000
 L5A  O16  C09  C08  117.26  3.000
 L5A  H14  C13  H13  106.91  3.000
 L5A  H14  C13  C14  110.22  3.000
 L5A  H13  C13  C14  112.98  3.000
 L5A  H14  C13  C12  109.30  3.000
 L5A  H13  C13  C12  113.29  3.000
 L5A  C14  C13  C12  104.14  3.000
 L5A  H16  C14  H15  106.41  3.000
 L5A  H16  C14  C13  110.58  3.000
 L5A  H15  C14  C13  111.50  3.000
 L5A  H16  C14  C11  110.28  3.000
 L5A  H15  C14  C11  111.93  3.000
 L5A  C13  C14  C11  106.21  3.000
 L5A  O20  C18  O19  126.98  3.000
 L5A  O20  C18  C17  115.42  3.000
 L5A  O19  C18  C17  117.58  3.000
 L5A  H18  C17  H17  105.74  3.000
 L5A  H18  C17  C18  106.73  3.000
 L5A  H17  C17  C18  109.15  3.000
 L5A  H18  C17  C02  109.65  3.000
 L5A  H17  C17  C02  110.36  3.000
 L5A  C18  C17  C02  114.77  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
 L5A  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 L5A  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 L5A  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 L5A  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 L5A  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 L5A  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 L5A  CONST_07  C07  C05  C06  C01  180.00   0.0  0
 L5A  CONST_08  C07  C05  C04  C03  180.00   0.0  0
 L5A  CONST_09  C17  C02  C03  C04  180.00   0.0  0
 L5A  CONST_10  C17  C02  C01  C06  180.00   0.0  0
 L5A  CONST_11  H6   C03  C02  C01  180.00   0.0  0
 L5A  CONST_12  H8   C06  C01  C02  180.00   0.0  0
 L5A  CONST_13  H7   C04  C03  C02  180.00   0.0  0
 L5A  CONST_14  H5   C01  C02  C03  180.00   0.0  0
 L5A  Var_01    C14  C13  C12  C10   39.55  30.0  1
 L5A  Var_02    C12  C13  C14  C11  -23.46  30.0  1
 L5A  Var_03    C06  C05  C07  C10  -81.17  30.0  2
 L5A  Var_04    C18  C17  C02  C01   77.46  30.0  2
 L5A  Var_05    O16  C09  C08  C11  -32.19  30.0  2
 L5A  Var_06    O19  C18  C17  C02  -20.52  30.0  3

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
 L5A  chir_01  C10  C11  C07  C12  positiv
 L5A  chir_02  C11  C10  C14  C08  negativ

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
 L5A  plan-1  C01  0.020
 L5A  plan-1  C02  0.020
 L5A  plan-1  C03  0.020
 L5A  plan-1  C04  0.020
 L5A  plan-1  C05  0.020
 L5A  plan-1  C06  0.020
 L5A  plan-1  C07  0.020
 L5A  plan-1  H5   0.020
 L5A  plan-1  H6   0.020
 L5A  plan-1  H7   0.020
 L5A  plan-1  H8   0.020
 L5A  plan-1  C17  0.020
 L5A  plan-2  C18  0.020
 L5A  plan-2  O19  0.020
 L5A  plan-2  O20  0.020
 L5A  plan-2  C17  0.020
 L5A  plan-3  C08  0.020
 L5A  plan-3  C09  0.020
 L5A  plan-3  O15  0.020
 L5A  plan-3  O16  0.020

