# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:23:15 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 5-[(Z)-2-phenylethenyl]-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c2OCOc2ccc1\C=C/c3ccccc3
#
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
 JNS  JNS  '5-[(Z)-2-phenylethenyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  32  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JNS
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
 JNS  C1    C  CR16  0  -0.240  -3.0223  -1.0682   1.6658
 JNS  C2    C  CR16  0  -0.270  -4.3455  -1.3010   1.3089
 JNS  C3    C  CR16  0  -0.290  -2.2724  -0.1158   0.9937
 JNS  C4    C  CR16  0  -0.293  -0.1547  -0.6587  -1.4924
 JNS  C5    C  CR16  0  -0.242  -4.9165  -0.5602   0.2830
 JNS  C6    C  CR16  0  -0.319   0.6905  -1.7709  -1.4481
 JNS  C7    C  CR6   0   0.078  -2.8286   0.6240  -0.0535
 JNS  C8    C  CR6   0   0.001   0.1725   0.5525  -0.9003
 JNS  C9    C  CR6   0  -0.207   1.4211   0.6997  -0.2392
 JNS  C10   C  CR16  0  -0.308  -4.1671   0.3987  -0.3841
 JNS  C11   C  CR56  0   0.303   1.8854  -1.6139  -0.8003
 JNS  C12   C  CR56  0   0.337   2.2515  -0.4087  -0.2154
 JNS  C14   C  C1    0  -0.254  -2.0755   1.6579  -0.7757
 JNS  C15   C  C1    0  -0.222  -0.7719   1.6734  -1.0682
 JNS  C16   C  C     0   0.517   1.7725   1.9663   0.4372
 JNS  C17   C  CH2   0   0.069   3.9333  -1.8513   0.0262
 JNS  O19   O  OH1   0  -0.589   3.0553   2.0410   0.7639
 JNS  O20   O  O     0  -0.429   0.9831   2.8482   0.6742
 JNS  O21   O  O     0  -0.481   2.8577  -2.5313  -0.6001
 JNS  O22   O  O     0  -0.465   3.4577  -0.5525   0.3643
 JNS  H1    H  HCR6  0   0.255  -2.5737  -1.6256   2.4783
 JNS  H2    H  HCR6  0   0.255  -4.9298  -2.0455   1.8338
 JNS  H3    H  HCR6  0   0.252  -1.2500   0.0648   1.2979
 JNS  H5    H  HCR6  0   0.255  -5.9494  -0.7242   0.0038
 JNS  H6    H  HCR6  0   0.283   0.4099  -2.7076  -1.9101
 JNS  H10   H  HCR6  0   0.251  -4.6240   0.9774  -1.1784
 JNS  H14   H  H     0   0.252  -2.6581   2.5153  -1.0974
 JNS  H15   H  H     0   0.260  -0.3832   2.5634  -1.5502
 JNS  H19   H  HOH1  0   0.486   3.2220   2.8793   1.2205
 JNS  H171  H  HCH2  0   0.250   4.2324  -2.3790   0.9323
 JNS  H172  H  HCH2  0   0.242   4.7765  -1.7639  -0.6649
 JNS  H4    H  HCR6  0   0.264  -1.0970  -0.7443  -2.0158

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
 JNS  C1   C2    aromatic  1.390  0.020  1.390
 JNS  C1   C3    aromatic  1.386  0.020  1.386
 JNS  C2   C5    aromatic  1.388  0.020  1.388
 JNS  C3   C7    aromatic  1.398  0.020  1.398
 JNS  C4   C6    aromatic  1.398  0.020  1.398
 JNS  C4   C8    aromatic  1.387  0.020  1.387
 JNS  C5   C10   aromatic  1.388  0.020  1.388
 JNS  C6   C11   aromatic  1.368  0.020  1.368
 JNS  C7   C10   aromatic  1.397  0.020  1.397
 JNS  C7   C14   single    1.469  0.020  1.469
 JNS  C8   C9    aromatic  1.420  0.020  1.420
 JNS  C8   C15   single    1.475  0.020  1.475
 JNS  C9   C12   aromatic  1.385  0.020  1.385
 JNS  C9   C16   single    1.478  0.020  1.478
 JNS  C11  C12   aromatic  1.389  0.020  1.389
 JNS  C11  O21   single    1.352  0.020  1.352
 JNS  C12  O22   single    1.346  0.020  1.346
 JNS  C14  C15   double    1.336  0.020  1.336
 JNS  C16  O19   single    1.326  0.020  1.326
 JNS  C16  O20   double    1.207  0.020  1.207
 JNS  C17  O21   single    1.418  0.020  1.418
 JNS  C17  O22   single    1.424  0.020  1.424
 JNS  C1   H1    single    0.930  0.020  1.080
 JNS  C2   H2    single    0.930  0.020  1.080
 JNS  C3   H3    single    0.930  0.020  1.080
 JNS  C5   H5    single    0.930  0.020  1.080
 JNS  C4   H4    single    0.930  0.020  1.080
 JNS  C6   H6    single    0.930  0.020  1.080
 JNS  C10  H10   single    0.930  0.020  1.080
 JNS  C14  H14   single    0.930  0.020  1.080
 JNS  C15  H15   single    0.930  0.020  1.080
 JNS  O19  H19   single    0.850  0.020  0.980
 JNS  C17  H171  single    0.970  0.020  1.090
 JNS  C17  H172  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
 JNS  H1    C1   C3    119.57  3.000
 JNS  H1    C1   C2    120.06  3.000
 JNS  C3    C1   C2    120.37  3.000
 JNS  H2    C2   C5    120.23  3.000
 JNS  H2    C2   C1    120.30  3.000
 JNS  C5    C2   C1    119.46  3.000
 JNS  H3    C3   C7    119.89  3.000
 JNS  H3    C3   C1    119.32  3.000
 JNS  C7    C3   C1    120.78  3.000
 JNS  H4    C4   C8    118.77  3.000
 JNS  H4    C4   C6    118.64  3.000
 JNS  C8    C4   C6    122.59  3.000
 JNS  H5    C5   C10   119.74  3.000
 JNS  H5    C5   C2    120.15  3.000
 JNS  C10   C5   C2    120.11  3.000
 JNS  H6    C6   C11   121.89  3.000
 JNS  H6    C6   C4    121.25  3.000
 JNS  C11   C6   C4    116.86  3.000
 JNS  C14   C7   C10   119.24  3.000
 JNS  C14   C7   C3    122.47  3.000
 JNS  C10   C7   C3    118.24  3.000
 JNS  C15   C8   C9    122.48  3.000
 JNS  C15   C8   C4    117.63  3.000
 JNS  C9    C8   C4    119.76  3.000
 JNS  C16   C9   C12   122.36  3.000
 JNS  C16   C9   C8    120.71  3.000
 JNS  C12   C9   C8    116.88  3.000
 JNS  H10   C10  C7    119.42  3.000
 JNS  H10   C10  C5    119.57  3.000
 JNS  C7    C10  C5    121.01  3.000
 JNS  O21   C11  C12   109.69  3.000
 JNS  O21   C11  C6    128.35  3.000
 JNS  C12   C11  C6    121.96  3.000
 JNS  O22   C12  C11   108.96  3.000
 JNS  O22   C12  C9    129.07  3.000
 JNS  C11   C12  C9    121.94  3.000
 JNS  H14   C14  C15   116.72  3.000
 JNS  H14   C14  C7    115.25  3.000
 JNS  C15   C14  C7    128.03  3.000
 JNS  H15   C15  C14   117.17  3.000
 JNS  H15   C15  C8    116.41  3.000
 JNS  C14   C15  C8    126.21  3.000
 JNS  O20   C16  O19   122.90  3.000
 JNS  O20   C16  C9    124.08  3.000
 JNS  O19   C16  C9    113.02  3.000
 JNS  H172  C17  H171  110.62  3.000
 JNS  H172  C17  O22   109.55  3.000
 JNS  H171  C17  O22   109.62  3.000
 JNS  H172  C17  O21   110.12  3.000
 JNS  H171  C17  O21   110.06  3.000
 JNS  O22   C17  O21   106.79  3.000
 JNS  H19   O19  C16   109.35  3.000
 JNS  C17   O21  C11   106.59  3.000
 JNS  C17   O22  C12   107.13  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
 JNS  CONST_01  C10  C5   C2   C1      0.00   0.0  0
 JNS  CONST_02  C10  C7   C3   C1      0.00   0.0  0
 JNS  CONST_03  C7   C3   C1   C2      0.00   0.0  0
 JNS  CONST_04  C7   C10  C5   C2      0.00   0.0  0
 JNS  CONST_05  C5   C2   C1   C3      0.00   0.0  0
 JNS  CONST_06  C5   C10  C7   C3      0.00   0.0  0
 JNS  CONST_07  C12  C11  C6   C4      0.00   0.0  0
 JNS  CONST_08  C12  C9   C8   C4      0.00   0.0  0
 JNS  CONST_09  C9   C8   C4   C6      0.00   0.0  0
 JNS  CONST_10  C9   C12  C11  C6      0.00   0.0  0
 JNS  CONST_11  C11  C6   C4   C8      0.00   0.0  0
 JNS  CONST_12  C11  C12  C9   C8      0.00   0.0  0
 JNS  CONST_13  C14  C7   C3   C1    180.00   0.0  0
 JNS  CONST_14  C16  C9   C8   C4    180.00   0.0  0
 JNS  CONST_15  C14  C7   C10  C5    180.00   0.0  0
 JNS  CONST_16  C15  C8   C4   C6    180.00   0.0  0
 JNS  CONST_17  C16  C9   C12  C11   180.00   0.0  0
 JNS  CONST_18  C15  C8   C9   C12   180.00   0.0  0
 JNS  CONST_19  O22  C12  C9   C16     0.00   0.0  0
 JNS  CONST_20  H5   C5   C2   C1    180.00   0.0  0
 JNS  CONST_21  H3   C3   C1   C2    180.00   0.0  0
 JNS  CONST_22  H10  C10  C5   C2    180.00   0.0  0
 JNS  CONST_23  H2   C2   C1   C3    180.00   0.0  0
 JNS  CONST_24  H1   C1   C2   C5    180.00   0.0  0
 JNS  CONST_25  H6   C6   C4   C8    180.00   0.0  0
 JNS  CONST_26  H4   C4   C8   C9    180.00   0.0  0
 JNS  CONST_27  H19  O19  C16  C9    180.00   0.0  0
 JNS  Var_01    O22  C17  O21  C11     8.81  30.0  1
 JNS  Var_02    O21  C17  O22  C12    -8.99  30.0  1
 JNS  Var_03    C8   C15  C14  C7      9.66   0.0  2
 JNS  Var_04    C15  C14  C7   C3     34.32  30.0  2
 JNS  Var_05    C14  C15  C8   C4     53.94  30.0  2
 JNS  Var_06    O19  C16  C9   C8   -167.09  30.0  2

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
 JNS  plan-1  C1   0.020
 JNS  plan-1  C2   0.020
 JNS  plan-1  C3   0.020
 JNS  plan-1  C5   0.020
 JNS  plan-1  C7   0.020
 JNS  plan-1  C10  0.020
 JNS  plan-1  C14  0.020
 JNS  plan-1  H1   0.020
 JNS  plan-1  H2   0.020
 JNS  plan-1  H3   0.020
 JNS  plan-1  H5   0.020
 JNS  plan-1  H10  0.020
 JNS  plan-2  C4   0.020
 JNS  plan-2  C6   0.020
 JNS  plan-2  C8   0.020
 JNS  plan-2  C9   0.020
 JNS  plan-2  C11  0.020
 JNS  plan-2  C12  0.020
 JNS  plan-2  C15  0.020
 JNS  plan-2  C16  0.020
 JNS  plan-2  O21  0.020
 JNS  plan-2  O22  0.020
 JNS  plan-2  H6   0.020
 JNS  plan-2  H4   0.020
 JNS  plan-3  C9   0.020
 JNS  plan-3  C16  0.020
 JNS  plan-3  O19  0.020
 JNS  plan-3  O20  0.020
 JNS  plan-3  H19  0.020
 JNS  plan-4  C7   0.020
 JNS  plan-4  C8   0.020
 JNS  plan-4  C14  0.020
 JNS  plan-4  C15  0.020
 JNS  plan-4  H14  0.020
 JNS  plan-4  H15  0.020

