# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 10:20:39 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (4-{[(1R,2R)-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
 L5J  L5J  '(4-{[(1R,2R)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid'  ligand  40  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 PERFECT
;

data_comp_L5J
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
 L5J  C10  C  CR15  0  -0.213  -1.5209  -0.3756  -0.1691
 L5J  C13  C  CH2   0  -0.442  -2.4467  -2.4718  -1.0179
 L5J  C11  C  CR15  0  -0.225  -3.0622  -0.3944  -0.0079
 L5J  C12  C  CH2   0  -0.441  -1.1742  -1.6245  -1.0094
 L5J  C14  C  CH2   0  -0.429  -3.5534  -1.4249  -1.0264
 L5J  C01  C  CR16  0  -0.290   2.9210  -1.0200   1.1107
 L5J  C02  C  CR6   0   0.129   3.4447   0.2278   0.7975
 L5J  C03  C  CR16  0  -0.276   2.5620   1.2940   0.6420
 L5J  C04  C  CR16  0  -0.298   1.1964   1.1115   0.7851
 L5J  C05  C  CR6   0   0.140   0.6647  -0.1419   1.0890
 L5J  C06  C  CR16  0  -0.307   1.5510  -1.2013   1.2554
 L5J  C07  C  CH2   0  -0.525  -0.8211  -0.3360   1.1949
 L5J  C08  C  CH2   0  -0.589  -3.6694   0.9903  -0.1573
 L5J  C09  C  C     0   0.552  -5.1396   1.0606   0.1510
 L5J  C18  C  C     0   0.556   5.3387   0.4306  -0.8286
 L5J  O15  O  O     0  -0.444  -5.7688   0.2233   0.7492
 L5J  O16  O  OH1   0  -0.598  -5.6840   2.1910  -0.2920
 L5J  O19  O  OH1   0  -0.594   6.6507   0.6017  -0.9515
 L5J  O20  O  O     0  -0.435   4.5969   0.3013  -1.7680
 L5J  H1   H  HCR5  0   0.236  -1.2257   0.5229  -0.7199
 L5J  H2   H  HCH2  0   0.230  -2.4932  -3.1605  -1.8628
 L5J  H3   H  HCH2  0   0.217  -2.5100  -3.0727  -0.1059
 L5J  H4   H  HCR5  0   0.234  -3.2961  -0.7735   0.9935
 L5J  H5   H  HCH2  0   0.227  -0.9288  -1.3274  -2.0315
 L5J  H6   H  HCH2  0   0.234  -0.3070  -2.1649  -0.6256
 L5J  H7   H  HCH2  0   0.212  -3.6227  -0.9677  -2.0198
 L5J  H8   H  HCH2  0   0.235  -4.5372  -1.8277  -0.7828
 L5J  H9   H  HCR6  0   0.248   3.5881  -1.8634   1.2459
 L5J  H10  H  HCR6  0   0.248   2.9459   2.2808   0.4101
 L5J  H11  H  HCR6  0   0.243   0.5310   1.9589   0.6636
 L5J  H12  H  HCR6  0   0.245   1.1681  -2.1839   1.5061
 L5J  H13  H  HCH2  0   0.246  -1.2546   0.4730   1.7913
 L5J  H14  H  HCH2  0   0.240  -1.0365  -1.2633   1.7336
 L5J  H15  H  HCH2  0   0.287  -3.1748   1.6993   0.5177
 L5J  H16  H  HCH2  0   0.270  -3.4922   1.3775  -1.1647
 L5J  H17  H  HCH2  0   0.302   5.2488   1.3652   1.0715
 L5J  H18  H  HCH2  0   0.303   5.4831  -0.3624   1.1332
 L5J  H19  H  HOH1  0   0.477  -6.6201   2.2260  -0.0445
 L5J  H20  H  HOH1  0   0.481   6.8976   0.6078  -1.8884
 L5J  C17  C  CH2   0  -0.688   4.9202   0.4234   0.6216

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
 L5J  O20  C18  double    1.204  0.020  1.204
 L5J  O19  C18  single    1.329  0.020  1.329
 L5J  C18  C17  single    1.509  0.020  1.509
 L5J  C17  C02  single    1.499  0.020  1.499
 L5J  C02  C01  aromatic  1.389  0.020  1.389
 L5J  C02  C03  aromatic  1.393  0.020  1.393
 L5J  C01  C06  aromatic  1.390  0.020  1.390
 L5J  C03  C04  aromatic  1.385  0.020  1.385
 L5J  C06  C05  aromatic  1.391  0.020  1.391
 L5J  C04  C05  aromatic  1.395  0.020  1.395
 L5J  C05  C07  single    1.502  0.020  1.502
 L5J  O15  C09  double    1.206  0.020  1.206
 L5J  C07  C10  single    1.534  0.020  1.534
 L5J  C09  O16  single    1.331  0.020  1.331
 L5J  C09  C08  single    1.504  0.020  1.504
 L5J  C12  C10  single    1.545  0.020  1.545
 L5J  C12  C13  single    1.529  0.020  1.529
 L5J  C10  C11  single    1.550  0.020  1.550
 L5J  C11  C08  single    1.519  0.020  1.519
 L5J  C11  C14  single    1.530  0.020  1.530
 L5J  C14  C13  single    1.523  0.020  1.523
 L5J  C10  H1   single    0.970  0.020  1.090
 L5J  C13  H2   single    0.970  0.020  1.090
 L5J  C13  H3   single    0.970  0.020  1.090
 L5J  C11  H4   single    0.970  0.020  1.090
 L5J  C12  H5   single    0.970  0.020  1.090
 L5J  C12  H6   single    0.970  0.020  1.090
 L5J  C14  H7   single    0.970  0.020  1.090
 L5J  C14  H8   single    0.970  0.020  1.090
 L5J  C01  H9   single    0.930  0.020  1.080
 L5J  C03  H10  single    0.930  0.020  1.080
 L5J  C04  H11  single    0.930  0.020  1.080
 L5J  C06  H12  single    0.930  0.020  1.080
 L5J  C07  H13  single    0.970  0.020  1.090
 L5J  C07  H14  single    0.970  0.020  1.090
 L5J  C08  H15  single    0.970  0.020  1.090
 L5J  C08  H16  single    0.970  0.020  1.090
 L5J  C17  H17  single    0.970  0.020  1.090
 L5J  C17  H18  single    0.970  0.020  1.090
 L5J  O16  H19  single    0.850  0.020  0.980
 L5J  O19  H20  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
 L5J  H1   C10  C07  107.66  3.000
 L5J  H1   C10  C12  109.23  3.000
 L5J  C07  C10  C12  113.72  3.000
 L5J  H1   C10  C11  109.30  3.000
 L5J  C12  C10  C11  105.66  3.000
 L5J  C07  C10  C11  111.20  3.000
 L5J  H3   C13  H2   107.25  3.000
 L5J  H3   C13  C14  109.88  3.000
 L5J  H2   C13  C14  113.48  3.000
 L5J  H3   C13  C12  110.36  3.000
 L5J  H2   C13  C12  112.93  3.000
 L5J  C14  C13  C12  102.93  3.000
 L5J  H4   C11  C08  108.65  3.000
 L5J  H4   C11  C14  107.87  3.000
 L5J  C08  C11  C14  114.84  3.000
 L5J  H4   C11  C10  108.14  3.000
 L5J  C14  C11  C10  104.97  3.000
 L5J  C08  C11  C10  112.09  3.000
 L5J  H6   C12  H5   106.56  3.000
 L5J  H6   C12  C13  112.88  3.000
 L5J  H5   C12  C13  109.42  3.000
 L5J  H6   C12  C10  112.79  3.000
 L5J  H5   C12  C10  109.85  3.000
 L5J  C13  C12  C10  105.33  3.000
 L5J  H8   C14  H7   107.43  3.000
 L5J  H8   C14  C11  112.94  3.000
 L5J  H7   C14  C11  110.05  3.000
 L5J  H8   C14  C13  113.59  3.000
 L5J  H7   C14  C13  109.74  3.000
 L5J  C11  C14  C13  103.06  3.000
 L5J  H9   C01  C06  119.49  3.000
 L5J  H9   C01  C02  119.69  3.000
 L5J  C06  C01  C02  120.82  3.000
 L5J  C17  C02  C03  120.72  3.000
 L5J  C03  C02  C01  118.29  3.000
 L5J  C17  C02  C01  120.99  3.000
 L5J  H10  C03  C04  119.42  3.000
 L5J  H10  C03  C02  119.76  3.000
 L5J  C04  C03  C02  120.82  3.000
 L5J  H11  C04  C05  119.52  3.000
 L5J  H11  C04  C03  119.37  3.000
 L5J  C05  C04  C03  121.11  3.000
 L5J  C07  C05  C06  121.55  3.000
 L5J  C07  C05  C04  120.56  3.000
 L5J  C06  C05  C04  117.87  3.000
 L5J  H12  C06  C05  119.53  3.000
 L5J  H12  C06  C01  119.38  3.000
 L5J  C05  C06  C01  121.09  3.000
 L5J  H14  C07  H13  106.27  3.000
 L5J  H14  C07  C05  109.82  3.000
 L5J  H13  C07  C05  109.55  3.000
 L5J  H14  C07  C10  109.04  3.000
 L5J  H13  C07  C10  108.84  3.000
 L5J  C05  C07  C10  113.08  3.000
 L5J  H16  C08  H15  105.37  3.000
 L5J  H16  C08  C09  109.31  3.000
 L5J  H15  C08  C09  106.53  3.000
 L5J  H16  C08  C11  110.39  3.000
 L5J  H15  C08  C11  110.39  3.000
 L5J  C09  C08  C11  114.40  3.000
 L5J  O16  C09  O15  122.78  3.000
 L5J  O16  C09  C08  111.80  3.000
 L5J  O15  C09  C08  125.40  3.000
 L5J  O20  C18  O19  123.37  3.000
 L5J  O19  C18  C17  111.30  3.000
 L5J  O20  C18  C17  125.33  3.000
 L5J  H19  O16  C09  109.93  3.000
 L5J  H20  O19  C18  109.98  3.000
 L5J  H18  C17  H17  105.75  3.000
 L5J  H18  C17  C18  108.07  3.000
 L5J  H17  C17  C18  107.92  3.000
 L5J  H18  C17  C02  110.98  3.000
 L5J  H17  C17  C02  111.08  3.000
 L5J  C18  C17  C02  112.73  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
 L5J  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 L5J  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 L5J  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 L5J  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 L5J  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 L5J  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 L5J  CONST_07  C07  C05  C06  C01   180.00   0.0  0
 L5J  CONST_08  C07  C05  C04  C03   180.00   0.0  0
 L5J  CONST_09  C17  C02  C03  C04   180.00   0.0  0
 L5J  CONST_10  C17  C02  C01  C06   180.00   0.0  0
 L5J  CONST_11  H10  C03  C02  C01   180.00   0.0  0
 L5J  CONST_12  H12  C06  C01  C02   180.00   0.0  0
 L5J  CONST_13  H11  C04  C03  C02   180.00   0.0  0
 L5J  CONST_14  H9   C01  C02  C03   180.00   0.0  0
 L5J  CONST_15  H19  O16  C09  C08   180.00   0.0  0
 L5J  CONST_16  H20  O19  C18  C17   180.00   0.0  0
 L5J  Var_01    C14  C13  C12  C10    34.49  30.0  1
 L5J  Var_02    C12  C13  C14  C11   -42.96  30.0  1
 L5J  Var_03    C06  C05  C07  C10  -102.69  30.0  2
 L5J  Var_04    C18  C17  C02  C01    99.21  30.0  2
 L5J  Var_05    O15  C09  C08  C11    16.36  30.0  2
 L5J  Var_06    O20  C18  C17  C02     0.26  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
 L5J  chir_01  C10  C07  C12  C11  negativ
 L5J  chir_02  C11  C14  C08  C10  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
 L5J  plan-1  C01  0.020
 L5J  plan-1  C02  0.020
 L5J  plan-1  C03  0.020
 L5J  plan-1  C04  0.020
 L5J  plan-1  C05  0.020
 L5J  plan-1  C06  0.020
 L5J  plan-1  C07  0.020
 L5J  plan-1  H9   0.020
 L5J  plan-1  H10  0.020
 L5J  plan-1  H11  0.020
 L5J  plan-1  H12  0.020
 L5J  plan-1  C17  0.020
 L5J  plan-2  C18  0.020
 L5J  plan-2  O19  0.020
 L5J  plan-2  O20  0.020
 L5J  plan-2  H20  0.020
 L5J  plan-2  C17  0.020
 L5J  plan-3  C08  0.020
 L5J  plan-3  C09  0.020
 L5J  plan-3  O15  0.020
 L5J  plan-3  O16  0.020
 L5J  plan-3  H19  0.020

