# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:34:36 2021
#   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  33  17  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.337  -2.6919  13.4507  -3.4269
 W2V  C5   C  CR16  0  -0.226  -3.8655  13.3639  -2.7005
 W2V  C6   C  CR16  0  -0.401  -3.9591  13.8977  -1.4193
 W2V  C7   C  CH1   0  -0.338  -0.2900  14.1175  -3.6767
 W2V  C8   C  CH2   0  -0.443   0.5697  15.3624  -3.4677
 W2V  C10  C  CH2   0  -0.185   1.8528  12.9190  -4.2401
 W2V  C12  C  C     0   0.551   0.7016  12.4279  -2.0348
 W2V  O2   O  O     0  -0.445   0.2024  11.4498  -1.5333
 W2V  C11  C  CH1   0  -0.367   0.5241  12.8132  -3.4815
 W2V  O1   O  O2    0  -0.470   2.5782  14.0794  -3.9394
 W2V  C9   C  CH2   0  -0.186   1.8603  15.2503  -4.2625
 W2V  C3   C  CR6   0   0.175  -1.5727  14.0828  -2.8802
 W2V  C2   C  CR16  0  -0.417  -1.6621  14.6161  -1.6034
 W2V  C1   C  CR6   0   0.407  -2.8471  14.5265  -0.8687
 W2V  O    O  O2    0  -0.474  -2.8173  15.0777   0.3611
 W2V  C    C  CH3   0  -0.436  -3.9784  15.0016   1.1628
 W2V  H1   H  HCR6  0   0.245  -2.6383  13.0302  -4.4242
 W2V  H2   H  HCR6  0   0.257  -4.7314  12.8773  -3.1309
 W2V  H3   H  HCR6  0   0.277  -4.8920  13.8178  -0.8775
 W2V  H4   H  HCH1  0   0.264  -0.5745  14.1063  -4.7353
 W2V  H5   H  HCH2  0   0.241   0.8064  15.5250  -2.4161
 W2V  H6   H  HCH2  0   0.247   0.0212  16.2426  -3.8107
 W2V  H7   H  HCH2  0   0.221   1.6176  12.8776  -5.3140
 W2V  H8   H  HCH2  0   0.251   2.4966  12.0650  -4.0210
 W2V  H9   H  HOH1  0   0.478   1.5396  12.9724  -0.4332
 W2V  H10  H  HCH1  0   0.286  -0.0407  11.9964  -3.9360
 W2V  H11  H  HCH2  0   0.241   2.5172  16.0949  -4.0501
 W2V  H12  H  HCH2  0   0.199   1.6361  15.2709  -5.3398
 W2V  H13  H  HCR6  0   0.255  -0.8152  15.1111  -1.1446
 W2V  H14  H  HCH3  0   0.258  -3.7325  15.4773   2.1089
 W2V  H15  H  HCH3  0   0.227  -4.8225  15.5314   0.7133
 W2V  H16  H  HCH3  0   0.228  -4.2759  13.9677   1.3558
 W2V  O3   O  OH1   0  -0.582   1.4761  13.2646  -1.3554

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    1.401  0.020  1.401
 W2V  C10  C11  single    1.534  0.020  1.534
 W2V  C9   O1   single    1.411  0.020  1.411
 W2V  C9   C8   single    1.520  0.020  1.520
 W2V  C11  C7   single    1.550  0.020  1.550
 W2V  C11  C12  single    1.508  0.020  1.508
 W2V  C7   C8   single    1.527  0.020  1.527
 W2V  C7   C3   single    1.510  0.020  1.510
 W2V  C4   C3   aromatic  1.397  0.020  1.397
 W2V  C4   C5   aromatic  1.383  0.020  1.383
 W2V  C3   C2   aromatic  1.387  0.020  1.387
 W2V  C12  O2   double    1.207  0.020  1.207
 W2V  C12  O3   single    1.327  0.020  1.327
 W2V  C5   C6   aromatic  1.391  0.020  1.391
 W2V  C2   C1   aromatic  1.397  0.020  1.397
 W2V  C6   C1   aromatic  1.391  0.020  1.391
 W2V  C1   O    single    1.348  0.020  1.348
 W2V  O    C    single    1.413  0.020  1.413
 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  O3   H9   single    0.850  0.020  0.980
 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   119.75  3.000
 W2V  H1   C4   C5   120.07  3.000
 W2V  C3   C4   C5   120.19  3.000
 W2V  H2   C5   C6   119.00  3.000
 W2V  H2   C5   C4   119.88  3.000
 W2V  C6   C5   C4   121.12  3.000
 W2V  H3   C6   C1   121.64  3.000
 W2V  H3   C6   C5   119.41  3.000
 W2V  C1   C6   C5   118.96  3.000
 W2V  H4   C7   C3   106.78  3.000
 W2V  H4   C7   C11  104.44  3.000
 W2V  C3   C7   C11  111.12  3.000
 W2V  H4   C7   C8   106.65  3.000
 W2V  C3   C7   C8   115.13  3.000
 W2V  C11  C7   C8   111.90  3.000
 W2V  H6   C8   H5   106.96  3.000
 W2V  H6   C8   C9   108.76  3.000
 W2V  H5   C8   C9   109.33  3.000
 W2V  H6   C8   C7   109.34  3.000
 W2V  H5   C8   C7   112.07  3.000
 W2V  C9   C8   C7   110.26  3.000
 W2V  H8   C10  H7   107.01  3.000
 W2V  H8   C10  O1   107.43  3.000
 W2V  H7   C10  O1   110.57  3.000
 W2V  H8   C10  C11  110.96  3.000
 W2V  H7   C10  C11  107.16  3.000
 W2V  O1   C10  C11  113.55  3.000
 W2V  C11  C12  O2   123.85  3.000
 W2V  O2   C12  O3   122.64  3.000
 W2V  C11  C12  O3   113.50  3.000
 W2V  H10  C11  C12  105.61  3.000
 W2V  H10  C11  C10  107.08  3.000
 W2V  C12  C11  C10  112.97  3.000
 W2V  H10  C11  C7   107.78  3.000
 W2V  C12  C11  C7   113.44  3.000
 W2V  C10  C11  C7   109.56  3.000
 W2V  C9   O1   C10  112.01  3.000
 W2V  H12  C9   H11  107.38  3.000
 W2V  H12  C9   O1   110.08  3.000
 W2V  H11  C9   O1   106.95  3.000
 W2V  H12  C9   C8   109.72  3.000
 W2V  H11  C9   C8   110.64  3.000
 W2V  O1   C9   C8   111.94  3.000
 W2V  C2   C3   C7   122.11  3.000
 W2V  C2   C3   C4   118.87  3.000
 W2V  C7   C3   C4   118.98  3.000
 W2V  H13  C2   C1   118.02  3.000
 W2V  H13  C2   C3   121.03  3.000
 W2V  C1   C2   C3   120.95  3.000
 W2V  O    C1   C2   115.77  3.000
 W2V  O    C1   C6   124.30  3.000
 W2V  C2   C1   C6   119.93  3.000
 W2V  C    O    C1   118.52  3.000
 W2V  H16  C    H15  108.72  3.000
 W2V  H16  C    H14  108.77  3.000
 W2V  H15  C    H14  108.68  3.000
 W2V  H16  C    O    112.01  3.000
 W2V  H15  C    O    112.03  3.000
 W2V  H14  C    O    106.52  3.000
 W2V  H9   O3   C12  109.58  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  CONST_15  H9   O3   C12  C11  180.00   0.0  0
 W2V  Var_01    O1   C9   C8   C7   -55.88  30.0  1
 W2V  Var_02    H7   C10  O1   C9    60.11  30.0  1
 W2V  Var_03    H14  C    O    C1   178.54  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  H9   0.020
 W2V  plan-2  O3   0.020

