# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 12:13:33 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: (3S,4S)-4-(3-methoxyphenyl)oxane-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)[C@H]2CCOC[C@H]2C(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
 W2V  W2V  '(3S,4S)-4-(3-methoxyphenyl)oxane-3-carboxylic acid'  ligand  32  17  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W2V
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
 W2V  C4   C  CR16   0  -0.348  -2.4992  13.0982  -3.0730
 W2V  C5   C  CR16   0  -0.226  -3.6812  13.0109  -2.3615
 W2V  C6   C  CR16   0  -0.408  -3.9202  13.8206  -1.2547
 W2V  C7   C  CH1    0  -0.292  -0.2501  14.1134  -3.5244
 W2V  C8   C  CH2    0  -0.457   0.7198  15.2184  -3.1143
 W2V  C10  C  CH2    0  -0.174   1.6580  13.0269  -4.6700
 W2V  C12  C  C      0   0.429   1.0343  12.1217  -2.3942
 W2V  O2   O  O      0  -0.616   1.6984  11.0788  -2.5679
 W2V  C11  C  CH1    0  -0.402   0.5111  12.7871  -3.6942
 W2V  O1   O  O2     0  -0.480   2.5438  14.0198  -4.2003
 W2V  C9   C  CH2    0  -0.174   1.8954  15.2657  -4.0786
 W2V  C3   C  CR6    0   0.224  -1.5047  14.0045  -2.6890
 W2V  C2   C  CR16   0  -0.443  -1.7457  14.8137  -1.5900
 W2V  C1   C  CR6    0   0.410  -2.9410  14.7308  -0.8720
 W2V  O    O  O2     0  -0.473  -3.0522  15.5714   0.1790
 W2V  C    C  CH3    0  -0.432  -4.2399  15.5427   0.9405
 W2V  H1   H  HCR6   0   0.237  -2.3504  12.4625  -3.9377
 W2V  H2   H  HCR6   0   0.247  -4.4429  12.3051  -2.6689
 W2V  H3   H  HCR6   0   0.268  -4.8561  13.7304  -0.7204
 W2V  H4   H  HCH1   0   0.229  -0.6051  14.3758  -4.5325
 W2V  H5   H  HCH2   0   0.229   1.0801  15.0525  -2.0983
 W2V  H6   H  HCH2   0   0.225   0.2260  16.1943  -3.1300
 W2V  H7   H  HCH2   0   0.190   1.2533  13.3202  -5.6520
 W2V  H8   H  HCH2   0   0.225   2.2358  12.1143  -4.8110
 W2V  H10  H  HCH1   0   0.236  -0.1509  12.0577  -4.1771
 W2V  H11  H  HCH2   0   0.227   2.6432  15.9854  -3.7398
 W2V  H12  H  HCH2   0   0.185   1.5394  15.6017  -5.0654
 W2V  H13  H  HCR6   0   0.244  -1.0010  15.5268  -1.2595
 W2V  H14  H  HCH3   0   0.254  -4.1252  16.2900   1.7224
 W2V  H15  H  HCH3   0   0.223  -5.1195  15.7959   0.3418
 W2V  H16  H  HCH3   0   0.223  -4.4050  14.5687   1.4095
 W2V  O3   O  OC    -1  -0.581   0.7531  12.6434  -1.2998

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
 W2V  C10  O1   single    1.411  0.020  1.411
 W2V  C10  C11  single    1.525  0.020  1.525
 W2V  C9   O1   single    1.410  0.020  1.410
 W2V  C9   C8   single    1.521  0.020  1.521
 W2V  C11  C7   single    1.539  0.020  1.539
 W2V  C11  C12  single    1.551  0.020  1.551
 W2V  C7   C8   single    1.526  0.020  1.526
 W2V  C7   C3   single    1.511  0.020  1.511
 W2V  C4   C3   aromatic  1.399  0.020  1.399
 W2V  C4   C5   aromatic  1.382  0.020  1.382
 W2V  C3   C2   aromatic  1.386  0.020  1.386
 W2V  C12  O2   deloc     1.249  0.020  1.249
 W2V  C12  O3   deloc     1.245  0.020  1.245
 W2V  C5   C6   aromatic  1.392  0.020  1.392
 W2V  C2   C1   aromatic  1.397  0.020  1.397
 W2V  C6   C1   aromatic  1.391  0.020  1.391
 W2V  C1   O    single    1.350  0.020  1.350
 W2V  O    C    single    1.411  0.020  1.411
 W2V  C4   H1   single    0.930  0.020  1.080
 W2V  C5   H2   single    0.930  0.020  1.080
 W2V  C6   H3   single    0.930  0.020  1.080
 W2V  C7   H4   single    0.970  0.020  1.090
 W2V  C8   H5   single    0.970  0.020  1.090
 W2V  C8   H6   single    0.970  0.020  1.090
 W2V  C10  H7   single    0.970  0.020  1.090
 W2V  C10  H8   single    0.970  0.020  1.090
 W2V  C11  H10  single    0.970  0.020  1.090
 W2V  C9   H11  single    0.970  0.020  1.090
 W2V  C9   H12  single    0.970  0.020  1.090
 W2V  C2   H13  single    0.930  0.020  1.080
 W2V  C    H14  single    0.970  0.020  1.090
 W2V  C    H15  single    0.970  0.020  1.090
 W2V  C    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
 W2V  H1   C4   C3   120.09  3.000
 W2V  H1   C4   C5   119.41  3.000
 W2V  C3   C4   C5   120.49  3.000
 W2V  H2   C5   C6   118.95  3.000
 W2V  H2   C5   C4   119.77  3.000
 W2V  C6   C5   C4   121.29  3.000
 W2V  H3   C6   C1   121.87  3.000
 W2V  H3   C6   C5   119.53  3.000
 W2V  C1   C6   C5   118.60  3.000
 W2V  H4   C7   C3   104.82  3.000
 W2V  H4   C7   C11  105.31  3.000
 W2V  C3   C7   C11  114.18  3.000
 W2V  H4   C7   C8   106.16  3.000
 W2V  C3   C7   C8   115.55  3.000
 W2V  C11  C7   C8   109.83  3.000
 W2V  H6   C8   H5   107.35  3.000
 W2V  H6   C8   C9   108.19  3.000
 W2V  H5   C8   C9   109.87  3.000
 W2V  H6   C8   C7   110.80  3.000
 W2V  H5   C8   C7   110.49  3.000
 W2V  C9   C8   C7   110.08  3.000
 W2V  H8   C10  H7   107.60  3.000
 W2V  H8   C10  O1   107.44  3.000
 W2V  H7   C10  O1   109.87  3.000
 W2V  H8   C10  C11  110.49  3.000
 W2V  H7   C10  C11  109.63  3.000
 W2V  O1   C10  C11  111.70  3.000
 W2V  C11  C12  O2   114.90  3.000
 W2V  O2   C12  O3   126.34  3.000
 W2V  C11  C12  O3   118.75  3.000
 W2V  H10  C11  C12  106.69  3.000
 W2V  H10  C11  C10  106.06  3.000
 W2V  C12  C11  C10  110.49  3.000
 W2V  H10  C11  C7   108.85  3.000
 W2V  C12  C11  C7   116.37  3.000
 W2V  C10  C11  C7   107.89  3.000
 W2V  C9   O1   C10  111.22  3.000
 W2V  H12  C9   H11  107.35  3.000
 W2V  H12  C9   O1   109.93  3.000
 W2V  H11  C9   O1   107.12  3.000
 W2V  H12  C9   C8   109.12  3.000
 W2V  H11  C9   C8   110.68  3.000
 W2V  O1   C9   C8   112.50  3.000
 W2V  C2   C3   C7   122.73  3.000
 W2V  C2   C3   C4   118.18  3.000
 W2V  C7   C3   C4   119.02  3.000
 W2V  H13  C2   C1   118.08  3.000
 W2V  H13  C2   C3   120.47  3.000
 W2V  C1   C2   C3   121.45  3.000
 W2V  O    C1   C2   115.69  3.000
 W2V  O    C1   C6   124.31  3.000
 W2V  C2   C1   C6   119.99  3.000
 W2V  C    O    C1   118.46  3.000
 W2V  H16  C    H15  108.63  3.000
 W2V  H16  C    H14  108.64  3.000
 W2V  H15  C    H14  108.62  3.000
 W2V  H16  C    O    112.12  3.000
 W2V  H15  C    O    112.13  3.000
 W2V  H14  C    O    106.57  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
 W2V  CONST_01  C1   C2   C3  C4     0.00   0.0  0
 W2V  CONST_02  C1   C6   C5  C4     0.00   0.0  0
 W2V  CONST_03  C2   C3   C4  C5     0.00   0.0  0
 W2V  CONST_04  C2   C1   C6  C5     0.00   0.0  0
 W2V  CONST_05  C3   C4   C5  C6     0.00   0.0  0
 W2V  CONST_06  C3   C2   C1  C6     0.00   0.0  0
 W2V  CONST_07  C7   C3   C4  C5   180.00   0.0  0
 W2V  CONST_08  C1   C2   C3  C7   180.00   0.0  0
 W2V  CONST_09  O    C1   C6  C5   180.00   0.0  0
 W2V  CONST_10  O    C1   C2  C3   180.00   0.0  0
 W2V  CONST_11  H13  C2   C3  C4   180.00   0.0  0
 W2V  CONST_12  H3   C6   C5  C4   180.00   0.0  0
 W2V  CONST_13  H1   C4   C5  C6   180.00   0.0  0
 W2V  CONST_14  H2   C5   C4  C3   180.00   0.0  0
 W2V  Var_01    O1   C9   C8  C7   -54.64  30.0  1
 W2V  Var_02    H7   C10  O1  C9    59.10  30.0  1
 W2V  Var_03    H14  C    O   C1  -179.69  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
 W2V  chir_01  C7   C11  C8  C3   positiv
 W2V  chir_02  C11  C10  C7  C12  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
 W2V  plan-1  C4   0.020
 W2V  plan-1  C5   0.020
 W2V  plan-1  C6   0.020
 W2V  plan-1  C7   0.020
 W2V  plan-1  C3   0.020
 W2V  plan-1  C2   0.020
 W2V  plan-1  C1   0.020
 W2V  plan-1  O    0.020
 W2V  plan-1  H1   0.020
 W2V  plan-1  H2   0.020
 W2V  plan-1  H3   0.020
 W2V  plan-1  H13  0.020
 W2V  plan-2  C12  0.020
 W2V  plan-2  O2   0.020
 W2V  plan-2  C11  0.020
 W2V  plan-2  O3   0.020

