# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 01:21:54 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H]1CCC[C@H]1Cc2ccc(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
 L4M  L4M  '4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}benzoic acid'  ligand  35  19  .  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_L4M
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
 L4M  C10  C  CH1    0  -0.200   1.2477  -0.4446  -0.1446
 L4M  C13  C  CH2    0  -0.442   2.1917  -2.5725  -0.9327
 L4M  C01  C  CR16   0  -0.275  -2.9093   1.2387  -0.5149
 L4M  C02  C  CR6    0  -0.117  -3.7868   0.2976   0.0201
 L4M  C03  C  CR16   0  -0.277  -3.2659  -0.6620   0.8840
 L4M  C04  C  CR16   0  -0.304  -1.9143  -0.6822   1.2007
 L4M  C05  C  CR6    0   0.145  -1.0362   0.2560   0.6638
 L4M  C06  C  CR16   0  -0.303  -1.5594   1.2183  -0.1991
 L4M  C07  C  CH2    0  -0.516   0.4355   0.2196   0.9660
 L4M  C08  C  CH2    0  -0.575   3.4152   0.9298  -0.0585
 L4M  C11  C  CH1    0  -0.201   2.7632  -0.4341   0.0865
 L4M  C14  C  CH2    0  -0.432   3.2553  -1.4632  -0.9309
 L4M  C09  C  C      0   0.411   4.9265   0.9743   0.2287
 L4M  C12  C  CH2    0  -0.431   0.9161  -1.9293  -0.3462
 L4M  O15  O  OC    -1  -0.629   5.5810   1.8592  -0.3626
 L4M  O16  O  O      0  -0.611   5.3778   0.1537   1.0532
 L4M  O18  O  O      0  -0.597  -5.6429   1.2112  -1.1180
 L4M  O19  O  OC    -1  -0.597  -5.9823  -0.5533   0.1983
 L4M  H1   H  HCH1   0   0.212   1.0478   0.0897  -1.0833
 L4M  H2   H  HCH2   0   0.221   2.0265  -2.9676  -1.9362
 L4M  H3   H  HCH2   0   0.220   2.5115  -3.4164  -0.3187
 L4M  H4   H  HCR6   0   0.237  -3.2911   1.9990  -1.1839
 L4M  H5   H  HCR6   0   0.236  -3.9262  -1.4023   1.3168
 L4M  H6   H  HCR6   0   0.234  -1.5341  -1.4409   1.8759
 L4M  H7   H  HCR6   0   0.234  -0.8999   1.9647  -0.6290
 L4M  H8   H  HCH2   0   0.229   0.6103  -0.3202   1.9021
 L4M  H9   H  HCH2   0   0.241   0.7960   1.2409   1.1218
 L4M  H10  H  HCH2   0   0.199   3.2192   1.3206  -1.0627
 L4M  H11  H  HCH2   0   0.228   2.9388   1.6419   0.6283
 L4M  H12  H  HCH1   0   0.198   2.9587  -0.8167   1.0960
 L4M  H13  H  HCH2   0   0.226   4.2554  -1.8325  -0.7016
 L4M  H14  H  HCH2   0   0.204   3.3070  -0.9883  -1.9166
 L4M  H15  H  HCH2   0   0.214   0.6697  -2.3823   0.6186
 L4M  H16  H  HCH2   0   0.226   0.0433  -2.0712  -0.9849
 L4M  C17  C  C      0   0.390  -5.2674   0.3209  -0.3299

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
 L4M  O16  C09  deloc     1.248  0.020  1.248
 L4M  C11  C14  single    1.529  0.020  1.529
 L4M  C11  C08  single    1.519  0.020  1.519
 L4M  C11  C10  single    1.533  0.020  1.533
 L4M  C09  C08  single    1.539  0.020  1.539
 L4M  C09  O15  deloc     1.249  0.020  1.249
 L4M  C07  C10  single    1.528  0.020  1.528
 L4M  C07  C05  single    1.503  0.020  1.503
 L4M  C14  C13  single    1.537  0.020  1.537
 L4M  C06  C05  aromatic  1.394  0.020  1.394
 L4M  C06  C01  aromatic  1.386  0.020  1.386
 L4M  C13  C12  single    1.544  0.020  1.544
 L4M  C10  C12  single    1.535  0.020  1.535
 L4M  C05  C04  aromatic  1.393  0.020  1.393
 L4M  C01  C02  aromatic  1.393  0.020  1.393
 L4M  C04  C03  aromatic  1.388  0.020  1.388
 L4M  C02  C03  aromatic  1.392  0.020  1.392
 L4M  C02  C17  single    1.522  0.020  1.522
 L4M  O18  C17  deloc     1.247  0.020  1.247
 L4M  C17  O19  deloc     1.247  0.020  1.247
 L4M  C10  H1   single    0.970  0.020  1.090
 L4M  C13  H2   single    0.970  0.020  1.090
 L4M  C13  H3   single    0.970  0.020  1.090
 L4M  C01  H4   single    0.930  0.020  1.080
 L4M  C03  H5   single    0.930  0.020  1.080
 L4M  C04  H6   single    0.930  0.020  1.080
 L4M  C06  H7   single    0.930  0.020  1.080
 L4M  C07  H8   single    0.970  0.020  1.090
 L4M  C07  H9   single    0.970  0.020  1.090
 L4M  C08  H10  single    0.970  0.020  1.090
 L4M  C08  H11  single    0.970  0.020  1.090
 L4M  C11  H12  single    0.970  0.020  1.090
 L4M  C14  H13  single    0.970  0.020  1.090
 L4M  C14  H14  single    0.970  0.020  1.090
 L4M  C12  H15  single    0.970  0.020  1.090
 L4M  C12  H16  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
 L4M  H1   C10  C12  108.60  3.000
 L4M  H1   C10  C11  107.78  3.000
 L4M  C12  C10  C11  103.89  3.000
 L4M  H1   C10  C07  108.24  3.000
 L4M  C12  C10  C07  113.66  3.000
 L4M  C11  C10  C07  114.39  3.000
 L4M  H3   C13  H2   106.37  3.000
 L4M  H3   C13  C12  110.51  3.000
 L4M  H2   C13  C12  112.03  3.000
 L4M  H3   C13  C14  110.77  3.000
 L4M  H2   C13  C14  111.54  3.000
 L4M  C12  C13  C14  105.70  3.000
 L4M  H4   C01  C06  119.64  3.000
 L4M  H4   C01  C02  119.31  3.000
 L4M  C06  C01  C02  121.04  3.000
 L4M  C17  C02  C03  121.15  3.000
 L4M  C17  C02  C01  120.94  3.000
 L4M  C03  C02  C01  117.91  3.000
 L4M  H5   C03  C04  119.52  3.000
 L4M  H5   C03  C02  119.43  3.000
 L4M  C04  C03  C02  121.05  3.000
 L4M  H6   C04  C05  119.35  3.000
 L4M  H6   C04  C03  119.58  3.000
 L4M  C05  C04  C03  121.07  3.000
 L4M  C07  C05  C06  120.57  3.000
 L4M  C06  C05  C04  117.83  3.000
 L4M  C07  C05  C04  121.58  3.000
 L4M  H7   C06  C05  119.46  3.000
 L4M  H7   C06  C01  119.44  3.000
 L4M  C05  C06  C01  121.09  3.000
 L4M  H9   C07  H8   106.61  3.000
 L4M  H9   C07  C05  109.19  3.000
 L4M  H8   C07  C05  109.89  3.000
 L4M  H9   C07  C10  109.52  3.000
 L4M  H8   C07  C10  108.80  3.000
 L4M  C05  C07  C10  112.64  3.000
 L4M  H11  C08  H10  105.34  3.000
 L4M  H11  C08  C09  106.89  3.000
 L4M  H10  C08  C09  109.67  3.000
 L4M  H11  C08  C11  109.66  3.000
 L4M  H10  C08  C11  109.34  3.000
 L4M  C09  C08  C11  115.45  3.000
 L4M  H12  C11  C14  108.68  3.000
 L4M  H12  C11  C08  108.94  3.000
 L4M  C14  C11  C08  113.76  3.000
 L4M  H12  C11  C10  108.21  3.000
 L4M  C08  C11  C10  114.59  3.000
 L4M  C14  C11  C10  102.31  3.000
 L4M  H14  C14  H13  107.02  3.000
 L4M  H14  C14  C11  108.80  3.000
 L4M  H13  C14  C11  112.53  3.000
 L4M  H14  C14  C13  110.16  3.000
 L4M  H13  C14  C13  112.99  3.000
 L4M  C11  C14  C13  105.30  3.000
 L4M  O16  C09  O15  126.09  3.000
 L4M  O15  C09  C08  116.52  3.000
 L4M  O16  C09  C08  117.35  3.000
 L4M  H16  C12  H15  106.40  3.000
 L4M  H16  C12  C13  112.61  3.000
 L4M  H15  C12  C13  110.40  3.000
 L4M  H16  C12  C10  112.07  3.000
 L4M  H15  C12  C10  109.48  3.000
 L4M  C13  C12  C10  105.92  3.000
 L4M  O19  C17  O18  126.56  3.000
 L4M  O19  C17  C02  116.73  3.000
 L4M  O18  C17  C02  116.70  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
 L4M  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 L4M  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 L4M  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 L4M  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 L4M  CONST_05  C06  C05  C04  C03    0.00   0.0  0
 L4M  CONST_06  C06  C01  C02  C03    0.00   0.0  0
 L4M  CONST_07  C07  C05  C06  C01  180.00   0.0  0
 L4M  CONST_08  C07  C05  C04  C03  180.00   0.0  0
 L4M  CONST_09  C17  C02  C03  C04  180.00   0.0  0
 L4M  CONST_10  C17  C02  C01  C06  180.00   0.0  0
 L4M  CONST_11  H5   C03  C02  C01  180.00   0.0  0
 L4M  CONST_12  H7   C06  C01  C02  180.00   0.0  0
 L4M  CONST_13  H6   C04  C03  C02  180.00   0.0  0
 L4M  CONST_14  H4   C01  C02  C03  180.00   0.0  0
 L4M  Var_01    C14  C13  C12  C10    4.95  30.0  1
 L4M  Var_02    C12  C13  C14  C11   20.36  30.0  1
 L4M  Var_03    C06  C05  C07  C10  -79.41  30.0  2
 L4M  Var_04    O18  C17  C02  C01    0.47  30.0  2
 L4M  Var_05    O16  C09  C08  C11  -29.81  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
 L4M  chir_01  C10  C11  C07  C12  positiv
 L4M  chir_02  C11  C10  C08  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
 L4M  plan-1  C01  0.020
 L4M  plan-1  C02  0.020
 L4M  plan-1  C03  0.020
 L4M  plan-1  C04  0.020
 L4M  plan-1  C05  0.020
 L4M  plan-1  C06  0.020
 L4M  plan-1  C07  0.020
 L4M  plan-1  H4   0.020
 L4M  plan-1  H5   0.020
 L4M  plan-1  H6   0.020
 L4M  plan-1  H7   0.020
 L4M  plan-1  C17  0.020
 L4M  plan-2  C02  0.020
 L4M  plan-2  O18  0.020
 L4M  plan-2  O19  0.020
 L4M  plan-2  C17  0.020
 L4M  plan-3  C08  0.020
 L4M  plan-3  C09  0.020
 L4M  plan-3  O15  0.020
 L4M  plan-3  O16  0.020

