# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 10:50:40 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: {(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H]1CCC[C@H]1C(=O)c2ccc(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
 L67  L67  '{(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetic acid'  ligand  39  21  .  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_L67
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
 L67  C13  C  CH2   0  -0.436   1.6480   2.0760   0.8297
 L67  C15  C  CH2   0  -0.432   3.9080   1.2322   0.9890
 L67  C17  C  C     0   0.553   4.8863  -1.5488  -0.2108
 L67  C01  C  CR16  0  -0.251  -1.6233   0.2925  -1.5645
 L67  C02  C  CR16  0  -0.281  -2.9884   0.3646  -1.3552
 L67  C03  C  CR6   0   0.145  -3.5041   0.5371  -0.0732
 L67  C04  C  CR16  0  -0.277  -2.6193   0.6375   0.9943
 L67  C05  C  CR16  0  -0.277  -1.2507   0.5685   0.7886
 L67  C06  C  CR6   0  -0.023  -0.7328   0.3946  -0.4941
 L67  C08  C  C     0   0.559  -5.5776  -0.7639   0.4177
 L67  C09  C  C     0   0.401   0.7324   0.3136  -0.7629
 L67  C11  C  CH1   0  -0.406   1.6855   0.5843   0.3775
 L67  C12  C  CH1   0  -0.216   3.1562   0.2838   0.0569
 L67  C14  C  CH2   0  -0.439   3.1155   2.5269   0.8547
 L67  C16  C  CH2   0  -0.585   3.4910  -1.1882   0.2198
 L67  O10  O  O     0  -0.395   1.1293   0.0561  -1.8807
 L67  O18  O  O     0  -0.433  -4.9546  -1.7925   0.4691
 L67  O19  O  OH1   0  -0.591  -6.8909  -0.6901   0.5950
 L67  O20  O  O     0  -0.444   5.5956  -0.8713  -0.9130
 L67  O21  O  OH1   0  -0.597   5.2548  -2.7413   0.2488
 L67  H1   H  HCH2  0   0.244   1.0437   2.6988   0.1685
 L67  H2   H  HCH2  0   0.244   1.2011   2.1510   1.8211
 L67  H3   H  HCH2  0   0.216   3.8633   0.8611   2.0185
 L67  H4   H  HCH2  0   0.241   4.9593   1.3467   0.7243
 L67  H5   H  HCR6  0   0.260  -1.2439   0.1609  -2.5690
 L67  H6   H  HCR6  0   0.260  -3.6633   0.2895  -2.1995
 L67  H7   H  HCR6  0   0.261  -2.9996   0.7747   1.9992
 L67  H8   H  HCR6  0   0.264  -0.5960   0.6465   1.6459
 L67  H9   H  HCH2  0   0.310  -5.2219   1.2438   1.0022
 L67  H10  H  HCH2  0   0.309  -5.4949   1.0350  -0.7095
 L67  H11  H  HCH1  0   0.276   1.3794  -0.0385   1.2254
 L67  H13  H  HCH1  0   0.241   3.3592   0.5898  -0.9733
 L67  H15  H  HCH2  0   0.227   3.3760   3.0128  -0.0883
 L67  H16  H  HCH2  0   0.239   3.3144   3.2430   1.6526
 L67  H17  H  HCH2  0   0.293   2.8125  -1.8033  -0.3826
 L67  H18  H  HCH2  0   0.270   3.3365  -1.5076   1.2548
 L67  H19  H  HOH1  0   0.483  -7.2517  -1.5707   0.7772
 L67  H20  H  HOH1  0   0.478   6.1404  -2.9615  -0.0772
 L67  C07  C  CH2   0  -0.691  -4.9835   0.5982   0.1525

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
 L67  C13  C11  single    1.559  0.020  1.559
 L67  C13  C14  single    1.535  0.020  1.535
 L67  C15  C12  single    1.528  0.020  1.528
 L67  C15  C14  single    1.524  0.020  1.524
 L67  C17  C16  single    1.504  0.020  1.504
 L67  C17  O20  double    1.206  0.020  1.206
 L67  C17  O21  single    1.330  0.020  1.330
 L67  C01  C02  aromatic  1.383  0.020  1.383
 L67  C01  C06  aromatic  1.396  0.020  1.396
 L67  C02  C03  aromatic  1.393  0.020  1.393
 L67  C03  C04  aromatic  1.390  0.020  1.390
 L67  C03  C07  single    1.498  0.020  1.498
 L67  C04  C05  aromatic  1.386  0.020  1.386
 L67  C05  C06  aromatic  1.394  0.020  1.394
 L67  C06  C09  single    1.492  0.020  1.492
 L67  C07  C08  single    1.510  0.020  1.510
 L67  C08  O18  double    1.204  0.020  1.204
 L67  C08  O19  single    1.327  0.020  1.327
 L67  C09  C11  single    1.511  0.020  1.511
 L67  C09  O10  double    1.214  0.020  1.214
 L67  C12  C16  single    1.518  0.020  1.518
 L67  C13  H1   single    0.970  0.020  1.090
 L67  C13  H2   single    0.970  0.020  1.090
 L67  C15  H3   single    0.970  0.020  1.090
 L67  C15  H4   single    0.970  0.020  1.090
 L67  C01  H5   single    0.930  0.020  1.080
 L67  C02  H6   single    0.930  0.020  1.080
 L67  C04  H7   single    0.930  0.020  1.080
 L67  C05  H8   single    0.930  0.020  1.080
 L67  C07  H9   single    0.970  0.020  1.090
 L67  C07  H10  single    0.970  0.020  1.090
 L67  C11  H11  single    0.970  0.020  1.090
 L67  C12  H13  single    0.970  0.020  1.090
 L67  C14  H15  single    0.970  0.020  1.090
 L67  C14  H16  single    0.970  0.020  1.090
 L67  C16  H17  single    0.970  0.020  1.090
 L67  C16  H18  single    0.970  0.020  1.090
 L67  O19  H19  single    0.850  0.020  0.980
 L67  O21  H20  single    0.850  0.020  0.980
 L67  C12  C11  single    1.535  0.020  1.535

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
 L67  H2   C13  H1   106.55  3.000
 L67  H2   C13  C14  110.91  3.000
 L67  H1   C13  C14  111.82  3.000
 L67  H2   C13  C11  109.84  3.000
 L67  H1   C13  C11  112.56  3.000
 L67  C14  C13  C11  105.23  3.000
 L67  H4   C15  H3   107.65  3.000
 L67  H4   C15  C14  113.01  3.000
 L67  H3   C15  C14  110.45  3.000
 L67  H4   C15  C12  113.06  3.000
 L67  H3   C15  C12  110.07  3.000
 L67  C14  C15  C12  102.57  3.000
 L67  O21  C17  O20  122.81  3.000
 L67  O21  C17  C16  111.90  3.000
 L67  O20  C17  C16  125.27  3.000
 L67  H5   C01  C06  119.81  3.000
 L67  H5   C01  C02  119.54  3.000
 L67  C06  C01  C02  120.65  3.000
 L67  H6   C02  C03  119.69  3.000
 L67  H6   C02  C01  119.56  3.000
 L67  C03  C02  C01  120.75  3.000
 L67  C07  C03  C04  120.67  3.000
 L67  C07  C03  C02  120.63  3.000
 L67  C04  C03  C02  118.70  3.000
 L67  H7   C04  C05  119.39  3.000
 L67  H7   C04  C03  119.87  3.000
 L67  C05  C04  C03  120.73  3.000
 L67  H8   C05  C06  120.90  3.000
 L67  H8   C05  C04  118.46  3.000
 L67  C06  C05  C04  120.64  3.000
 L67  C09  C06  C05  122.50  3.000
 L67  C09  C06  C01  118.97  3.000
 L67  C05  C06  C01  118.53  3.000
 L67  O19  C08  O18  123.64  3.000
 L67  O19  C08  C07  111.27  3.000
 L67  O18  C08  C07  125.09  3.000
 L67  O10  C09  C11  121.80  3.000
 L67  O10  C09  C06  119.90  3.000
 L67  C11  C09  C06  118.29  3.000
 L67  H11  C11  C12  108.54  3.000
 L67  C12  C11  C09  114.32  3.000
 L67  H11  C11  C09  107.82  3.000
 L67  C12  C11  C13  105.72  3.000
 L67  H11  C11  C13  108.22  3.000
 L67  C09  C11  C13  112.04  3.000
 L67  H13  C12  C16  109.35  3.000
 L67  H13  C12  C11  108.65  3.000
 L67  C16  C12  C11  112.25  3.000
 L67  C11  C12  C15  102.86  3.000
 L67  H13  C12  C15  108.04  3.000
 L67  C16  C12  C15  115.34  3.000
 L67  H16  C14  H15  107.22  3.000
 L67  H16  C14  C15  113.49  3.000
 L67  H15  C14  C15  109.27  3.000
 L67  H16  C14  C13  112.28  3.000
 L67  H15  C14  C13  110.15  3.000
 L67  C15  C14  C13  104.42  3.000
 L67  H18  C16  H17  105.59  3.000
 L67  H18  C16  C12  110.69  3.000
 L67  H17  C16  C12  110.40  3.000
 L67  H18  C16  C17  109.38  3.000
 L67  H17  C16  C17  106.40  3.000
 L67  C12  C16  C17  113.97  3.000
 L67  H19  O19  C08  110.06  3.000
 L67  H20  O21  C17  109.91  3.000
 L67  H10  C07  H9   105.95  3.000
 L67  H10  C07  C08  108.36  3.000
 L67  H9   C07  C08  108.08  3.000
 L67  H10  C07  C03  111.07  3.000
 L67  H9   C07  C03  110.89  3.000
 L67  C08  C07  C03  112.23  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
 L67  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 L67  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 L67  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 L67  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 L67  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 L67  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 L67  CONST_07  C07  C03  C02  C01  180.00   0.0  0
 L67  CONST_08  C09  C06  C01  C02  180.00   0.0  0
 L67  CONST_09  C09  C06  C05  C04  180.00   0.0  0
 L67  CONST_10  C07  C03  C04  C05  180.00   0.0  0
 L67  CONST_11  H8   C05  C06  C01  180.00   0.0  0
 L67  CONST_12  H7   C04  C03  C02  180.00   0.0  0
 L67  CONST_13  H5   C01  C02  C03  180.00   0.0  0
 L67  CONST_14  H6   C02  C03  C04  180.00   0.0  0
 L67  CONST_15  H19  O19  C08  C07  180.00   0.0  0
 L67  CONST_16  H20  O21  C17  C16  180.00   0.0  0
 L67  Var_01    C12  C15  C14  C13   40.68  30.0  1
 L67  Var_02    C11  C13  C14  C15  -22.21  30.0  1
 L67  Var_03    C11  C09  C06  C01  173.05  30.0  2
 L67  Var_04    C08  C07  C03  C02   90.21  30.0  2
 L67  Var_05    O18  C08  C07  C03    1.14  30.0  3
 L67  Var_06    O20  C17  C16  C12  -17.40  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
 L67  chir_01  C11  C13  C09  C12  negativ
 L67  chir_02  C12  C15  C16  C11  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
 L67  plan-1  C01  0.020
 L67  plan-1  C02  0.020
 L67  plan-1  C03  0.020
 L67  plan-1  C04  0.020
 L67  plan-1  C05  0.020
 L67  plan-1  C06  0.020
 L67  plan-1  C09  0.020
 L67  plan-1  H5   0.020
 L67  plan-1  H6   0.020
 L67  plan-1  H7   0.020
 L67  plan-1  H8   0.020
 L67  plan-1  C07  0.020
 L67  plan-2  C17  0.020
 L67  plan-2  C16  0.020
 L67  plan-2  O20  0.020
 L67  plan-2  O21  0.020
 L67  plan-2  H20  0.020
 L67  plan-3  C08  0.020
 L67  plan-3  O18  0.020
 L67  plan-3  O19  0.020
 L67  plan-3  H19  0.020
 L67  plan-3  C07  0.020
 L67  plan-4  C06  0.020
 L67  plan-4  C09  0.020
 L67  plan-4  C11  0.020
 L67  plan-4  O10  0.020

