# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 23:56:34 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 4-[(1R,2S)-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
 L1V  L1V  '4-[(1R,2S)-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_L1V
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
 L1V  C14  C  CH2   0  -0.440   2.5636   2.7094   0.2700
 L1V  C11  C  CH1   0  -0.410   1.3164   0.5867   0.2338
 L1V  C12  C  CH1   0  -0.216   2.8025   0.3546  -0.0634
 L1V  C01  C  CR16  0  -0.251  -1.9885  -0.4606  -1.4273
 L1V  C02  C  CR16  0  -0.242  -3.3462  -0.4892  -1.1757
 L1V  C03  C  CR6   0  -0.084  -3.8370  -0.1216   0.0760
 L1V  C04  C  CR16  0  -0.239  -2.9481   0.2789   1.0693
 L1V  C05  C  CR16  0  -0.277  -1.5869   0.3123   0.8107
 L1V  C07  C  C     0   0.540  -5.3060  -0.1771   0.3009
 L1V  O08  O  OH1   0  -0.590  -5.6550   0.1758   1.5278
 L1V  C09  C  C     0   0.406   0.3721  -0.0453  -0.7561
 L1V  C16  C  CH2   0  -0.583   3.2783  -1.0123   0.3968
 L1V  O19  O  O     0  -0.444   5.3355  -0.7535  -0.8329
 L1V  O20  O  O     0  -0.432  -6.0970  -0.5125  -0.5467
 L1V  C06  C  CR6   0  -0.004  -1.0911  -0.0568  -0.4376
 L1V  C13  C  CH2   0  -0.433   1.1368   2.1332   0.2866
 L1V  C15  C  CH2   0  -0.434   3.4669   1.5372   0.6379
 L1V  C17  C  C     0   0.553   4.7037  -1.3179   0.0257
 L1V  O10  O  O     0  -0.384   0.7594  -0.5103  -1.8065
 L1V  O18  O  OH1   0  -0.596   5.1966  -2.3258   0.7392
 L1V  H1   H  HCH2  0   0.229   2.8134   3.0631  -0.7325
 L1V  H2   H  HCH2  0   0.240   2.6712   3.5584   0.9455
 L1V  H3   H  HCH1  0   0.278   1.0971   0.1802   1.2269
 L1V  H4   H  HCH1  0   0.243   2.9690   0.4533  -1.1397
 L1V  H5   H  HCR6  0   0.269  -1.6222  -0.7529  -2.4017
 L1V  H6   H  HCR6  0   0.272  -4.0275  -0.8005  -1.9559
 L1V  H7   H  HCR6  0   0.276  -3.3002   0.5696   2.0487
 L1V  H8   H  HCR6  0   0.270  -0.9232   0.6222   1.6061
 L1V  H9   H  HOH1  0   0.491  -6.6168   0.1167   1.6305
 L1V  H10  H  HCH2  0   0.269   3.1523  -1.1180   1.4781
 L1V  H11  H  HCH2  0   0.294   2.6685  -1.8046  -0.0523
 L1V  H12  H  HCH2  0   0.244   0.6044   2.4199   1.1932
 L1V  H13  H  HCH2  0   0.245   0.5485   2.5090  -0.5525
 L1V  H14  H  HCH2  0   0.242   4.5031   1.6879   0.3341
 L1V  H15  H  HCH2  0   0.217   3.4616   1.3761   1.7214
 L1V  H16  H  HOH1  0   0.478   6.0984  -2.5273   0.4475

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
 L1V  O19  C17  double    1.206  0.020  1.206
 L1V  O10  C09  double    1.212  0.020  1.212
 L1V  C17  C16  single    1.504  0.020  1.504
 L1V  C17  O18  single    1.330  0.020  1.330
 L1V  C12  C16  single    1.519  0.020  1.519
 L1V  C12  C15  single    1.527  0.020  1.527
 L1V  C12  C11  single    1.533  0.020  1.533
 L1V  C09  C11  single    1.507  0.020  1.507
 L1V  C09  C06  single    1.498  0.020  1.498
 L1V  C15  C14  single    1.525  0.020  1.525
 L1V  C01  C06  aromatic  1.396  0.020  1.396
 L1V  C01  C02  aromatic  1.381  0.020  1.381
 L1V  C11  C13  single    1.558  0.020  1.558
 L1V  C13  C14  single    1.539  0.020  1.539
 L1V  C06  C05  aromatic  1.393  0.020  1.393
 L1V  C02  C03  aromatic  1.394  0.020  1.394
 L1V  C05  C04  aromatic  1.386  0.020  1.386
 L1V  C03  C04  aromatic  1.392  0.020  1.392
 L1V  C03  C07  single    1.487  0.020  1.487
 L1V  O20  C07  double    1.207  0.020  1.207
 L1V  C07  O08  single    1.323  0.020  1.323
 L1V  C14  H1   single    0.970  0.020  1.090
 L1V  C14  H2   single    0.970  0.020  1.090
 L1V  C11  H3   single    0.970  0.020  1.090
 L1V  C12  H4   single    0.970  0.020  1.090
 L1V  C01  H5   single    0.930  0.020  1.080
 L1V  C02  H6   single    0.930  0.020  1.080
 L1V  C04  H7   single    0.930  0.020  1.080
 L1V  C05  H8   single    0.930  0.020  1.080
 L1V  O08  H9   single    0.850  0.020  0.980
 L1V  C16  H10  single    0.970  0.020  1.090
 L1V  C16  H11  single    0.970  0.020  1.090
 L1V  C13  H12  single    0.970  0.020  1.090
 L1V  C13  H13  single    0.970  0.020  1.090
 L1V  C15  H14  single    0.970  0.020  1.090
 L1V  C15  H15  single    0.970  0.020  1.090
 L1V  O18  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
 L1V  H2   C14  H1   107.09  3.000
 L1V  H2   C14  C15  113.00  3.000
 L1V  H1   C14  C15  109.57  3.000
 L1V  H2   C14  C13  112.11  3.000
 L1V  H1   C14  C13  110.08  3.000
 L1V  C15  C14  C13  105.00  3.000
 L1V  H3   C11  C13  108.34  3.000
 L1V  H3   C11  C09  108.33  3.000
 L1V  C13  C11  C09  111.49  3.000
 L1V  H3   C11  C12  108.28  3.000
 L1V  C13  C11  C12  105.58  3.000
 L1V  C09  C11  C12  114.61  3.000
 L1V  H4   C12  C15  108.41  3.000
 L1V  H4   C12  C16  109.38  3.000
 L1V  C15  C12  C16  114.94  3.000
 L1V  H4   C12  C11  108.94  3.000
 L1V  C15  C12  C11  102.44  3.000
 L1V  C16  C12  C11  112.41  3.000
 L1V  H5   C01  C06  119.96  3.000
 L1V  H5   C01  C02  119.45  3.000
 L1V  C06  C01  C02  120.59  3.000
 L1V  H6   C02  C03  120.13  3.000
 L1V  H6   C02  C01  119.59  3.000
 L1V  C03  C02  C01  120.28  3.000
 L1V  C07  C03  C04  122.25  3.000
 L1V  C07  C03  C02  118.28  3.000
 L1V  C04  C03  C02  119.47  3.000
 L1V  H7   C04  C05  118.86  3.000
 L1V  H7   C04  C03  121.07  3.000
 L1V  C05  C04  C03  120.07  3.000
 L1V  H8   C05  C06  121.11  3.000
 L1V  H8   C05  C04  118.20  3.000
 L1V  C06  C05  C04  120.69  3.000
 L1V  O20  C07  O08  123.52  3.000
 L1V  O08  C07  C03  113.00  3.000
 L1V  O20  C07  C03  123.47  3.000
 L1V  H9   O08  C07  110.11  3.000
 L1V  O10  C09  C06  119.57  3.000
 L1V  C06  C09  C11  118.41  3.000
 L1V  O10  C09  C11  122.00  3.000
 L1V  H11  C16  H10  105.74  3.000
 L1V  H11  C16  C17  106.21  3.000
 L1V  H10  C16  C17  109.47  3.000
 L1V  H11  C16  C12  110.62  3.000
 L1V  H10  C16  C12  110.51  3.000
 L1V  C17  C16  C12  113.88  3.000
 L1V  C09  C06  C05  122.44  3.000
 L1V  C05  C06  C01  118.90  3.000
 L1V  C09  C06  C01  118.67  3.000
 L1V  H13  C13  H12  106.60  3.000
 L1V  H13  C13  C11  112.20  3.000
 L1V  H12  C13  C11  110.22  3.000
 L1V  H13  C13  C14  111.26  3.000
 L1V  H12  C13  C14  111.31  3.000
 L1V  C11  C13  C14  105.33  3.000
 L1V  H15  C15  H14  107.49  3.000
 L1V  H15  C15  C12  109.77  3.000
 L1V  H14  C15  C12  113.11  3.000
 L1V  H15  C15  C14  110.42  3.000
 L1V  H14  C15  C14  112.93  3.000
 L1V  C12  C15  C14  103.11  3.000
 L1V  O18  C17  O19  122.86  3.000
 L1V  O18  C17  C16  111.89  3.000
 L1V  O19  C17  C16  125.23  3.000
 L1V  H16  O18  C17  109.94  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
 L1V  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 L1V  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 L1V  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 L1V  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 L1V  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 L1V  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 L1V  CONST_07  C07  C03  C02  C01  180.00   0.0  0
 L1V  CONST_08  C09  C06  C01  C02  180.00   0.0  0
 L1V  CONST_09  C09  C06  C05  C04  180.00   0.0  0
 L1V  CONST_10  C07  C03  C04  C05  180.00   0.0  0
 L1V  CONST_11  H8   C05  C06  C01  180.00   0.0  0
 L1V  CONST_12  H7   C04  C03  C02  180.00   0.0  0
 L1V  CONST_13  H5   C01  C02  C03  180.00   0.0  0
 L1V  CONST_14  H6   C02  C03  C04  180.00   0.0  0
 L1V  CONST_15  H9   O08  C07  C03  180.00   0.0  0
 L1V  CONST_16  H16  O18  C17  C16  180.00   0.0  0
 L1V  Var_01    C15  C14  C13  C11  -16.82  30.0  1
 L1V  Var_02    C13  C14  C15  C12   37.42  30.0  1
 L1V  Var_03    C01  C06  C09  C11  170.79  30.0  2
 L1V  Var_04    O20  C07  C03  C02   -0.67  30.0  2
 L1V  Var_05    O19  C17  C16  C12  -18.96  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
 L1V  chir_01  C11  C12  C09  C13  positiv
 L1V  chir_02  C12  C11  C15  C16  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
 L1V  plan-1  C01  0.020
 L1V  plan-1  C02  0.020
 L1V  plan-1  C03  0.020
 L1V  plan-1  C04  0.020
 L1V  plan-1  C05  0.020
 L1V  plan-1  C07  0.020
 L1V  plan-1  C09  0.020
 L1V  plan-1  C06  0.020
 L1V  plan-1  H5   0.020
 L1V  plan-1  H6   0.020
 L1V  plan-1  H7   0.020
 L1V  plan-1  H8   0.020
 L1V  plan-2  C03  0.020
 L1V  plan-2  C07  0.020
 L1V  plan-2  O08  0.020
 L1V  plan-2  O20  0.020
 L1V  plan-2  H9   0.020
 L1V  plan-3  C16  0.020
 L1V  plan-3  O19  0.020
 L1V  plan-3  C17  0.020
 L1V  plan-3  O18  0.020
 L1V  plan-3  H16  0.020
 L1V  plan-4  C11  0.020
 L1V  plan-4  C09  0.020
 L1V  plan-4  C06  0.020
 L1V  plan-4  O10  0.020

