# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 08:55:53 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: [2,6-bis(3-methoxyphenyl)-1-benzofuran-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2ccc3c(CC(O)=O)c(oc3c2)c4cccc(OC)c4
#
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
 VCY  VCY  '[2,6-bis(3-methoxyphenyl)-1-benzofuran-3-yl]acetic acid'  ligand  48  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VCY
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
 VCY  C10   C  CR6    0   0.401  20.8336   -5.1891   0.2496
 VCY  C13   C  CR16   0  -0.482  20.2506   -6.4416   0.4130
 VCY  C15   C  CR56   0   0.390  19.7061  -10.4460   2.6061
 VCY  C17   C  CR6    0   0.057  18.8515  -12.5078   3.3963
 VCY  C20   C  CR6    0   0.403  17.2391  -15.0856   5.6286
 VCY  C22   C  CH3    0  -0.437  14.9736  -15.4569   5.0189
 VCY  C24   C  CR16   0  -0.224  19.5006  -14.7376   6.3596
 VCY  C26   C  CR16   0  -0.306  18.3385  -12.7485   2.1071
 VCY  C28   C  CR56   0   0.045  19.2116  -10.6713   1.3226
 VCY  C02   C  C      0   0.411  17.8173   -9.0464  -1.1812
 VCY  C04   C  CR5    0   0.015  19.5818   -9.5212   0.5426
 VCY  C05   C  CR5    0   0.310  20.2332   -8.6975   1.4066
 VCY  C06   C  CR6    0   0.020  20.8514   -7.3874   1.2501
 VCY  C07   C  CR16   0  -0.330  22.0216   -7.0690   1.9376
 VCY  C08   C  CR16   0  -0.228  22.5907   -5.8145   1.7672
 VCY  C09   C  CR16   0  -0.342  22.0119   -4.8764   0.9311
 VCY  C16   C  CR16   0  -0.412  19.5514  -11.3310   3.6549
 VCY  C18   C  CR6    0   0.112  18.6588  -13.4998   4.4745
 VCY  C19   C  CR16   0  -0.451  17.4283  -14.1485   4.6176
 VCY  C23   C  CR16   0  -0.351  18.2866  -15.3826   6.5035
 VCY  C25   C  CR16   0  -0.338  19.6954  -13.7986   5.3542
 VCY  C27   C  CR16   0  -0.346  18.5104  -11.8506   1.0703
 VCY  O01   O  O      0  -0.591  17.1394   -9.9477  -1.7051
 VCY  O11   O  O2     0  -0.469  20.3200   -4.2190  -0.5298
 VCY  O14   O  O      0  -0.472  20.3251   -9.2509   2.6571
 VCY  O29   O  OC    -1  -0.584  17.4258   -7.9153  -0.8272
 VCY  H131  H  HCR6   0   0.302  19.3141   -6.6988  -0.0676
 VCY  H222  H  HCH3   0   0.259  14.1578  -16.0835   5.3711
 VCY  H221  H  HCH3   0   0.227  14.6682  -14.4096   5.0942
 VCY  H223  H  HCH3   0   0.227  15.1675  -15.6912   3.9688
 VCY  H241  H  HCR6   0   0.255  20.3110  -14.9749   7.0368
 VCY  H261  H  HCR6   0   0.251  17.8073  -13.6728   1.9179
 VCY  H032  H  HCH2   0   0.231  19.6022  -10.2793  -1.4242
 VCY  H031  H  HCH2   0   0.240  19.9344   -8.5546  -1.3159
 VCY  H071  H  HCR6   0   0.249  22.4972   -7.7918   2.5868
 VCY  H081  H  HCR6   0   0.257  23.5032   -5.5643   2.2929
 VCY  H091  H  HCR6   0   0.261  22.4600   -3.8987   0.8053
 VCY  H123  H  HCH3   0   0.258  18.8972   -3.5852  -1.8046
 VCY  H122  H  HCH3   0   0.226  19.2185   -5.3260  -1.9136
 VCY  H121  H  HCH3   0   0.227  18.2865   -4.6781  -0.5488
 VCY  H161  H  HCR6   0   0.265  19.9372  -11.1087   4.6418
 VCY  H191  H  HCR6   0   0.275  16.6218  -13.8911   3.9437
 VCY  H231  H  HCR6   0   0.260  18.1368  -16.1137   7.2881
 VCY  H251  H  HCR6   0   0.249  20.6602  -13.3205   5.2440
 VCY  H271  H  HCR6   0   0.248  18.1046  -12.0565   0.0884
 VCY  C03   C  CH2    0  -0.660  19.3138   -9.3580  -0.9130
 VCY  C12   C  CH3    0  -0.439  19.1196   -4.4799  -1.2284
 VCY  O21   O  O2     0  -0.469  16.0850  -15.7452   5.8420

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
 VCY  O01  C02   deloc     1.244  0.020  1.244
 VCY  C12  O11   single    1.413  0.020  1.413
 VCY  C02  O29   deloc     1.248  0.020  1.248
 VCY  C02  C03   single    1.552  0.020  1.552
 VCY  C03  C04   single    1.489  0.020  1.489
 VCY  O11  C10   single    1.346  0.020  1.346
 VCY  C09  C10   aromatic  1.397  0.020  1.397
 VCY  C09  C08   aromatic  1.384  0.020  1.384
 VCY  C10  C13   aromatic  1.391  0.020  1.391
 VCY  C08  C07   aromatic  1.388  0.020  1.388
 VCY  C04  C05   aromatic  1.360  0.020  1.360
 VCY  C04  C28   aromatic  1.438  0.020  1.438
 VCY  C13  C06   aromatic  1.399  0.020  1.399
 VCY  C07  C06   aromatic  1.394  0.020  1.394
 VCY  C06  C05   single    1.457  0.020  1.457
 VCY  C05  O14   aromatic  1.371  0.020  1.371
 VCY  C28  C27   aromatic  1.395  0.020  1.395
 VCY  C28  C15   aromatic  1.394  0.020  1.394
 VCY  C27  C26   aromatic  1.382  0.020  1.382
 VCY  O14  C15   aromatic  1.347  0.020  1.347
 VCY  C15  C16   aromatic  1.381  0.020  1.381
 VCY  C26  C17   aromatic  1.408  0.020  1.408
 VCY  C16  C17   aromatic  1.393  0.020  1.393
 VCY  C17  C18   single    1.478  0.020  1.478
 VCY  C22  O21   single    1.413  0.020  1.413
 VCY  C19  C18   aromatic  1.398  0.020  1.398
 VCY  C19  C20   aromatic  1.391  0.020  1.391
 VCY  C18  C25   aromatic  1.392  0.020  1.392
 VCY  O21  C20   single    1.346  0.020  1.346
 VCY  C20  C23   aromatic  1.397  0.020  1.397
 VCY  C25  C24   aromatic  1.389  0.020  1.389
 VCY  C23  C24   aromatic  1.382  0.020  1.382
 VCY  C13  H131  single    0.930  0.020  1.080
 VCY  C22  H222  single    0.970  0.020  1.090
 VCY  C22  H221  single    0.970  0.020  1.090
 VCY  C22  H223  single    0.970  0.020  1.090
 VCY  C24  H241  single    0.930  0.020  1.080
 VCY  C26  H261  single    0.930  0.020  1.080
 VCY  C03  H032  single    0.970  0.020  1.090
 VCY  C03  H031  single    0.970  0.020  1.090
 VCY  C07  H071  single    0.930  0.020  1.080
 VCY  C08  H081  single    0.930  0.020  1.080
 VCY  C09  H091  single    0.930  0.020  1.080
 VCY  C12  H123  single    0.970  0.020  1.090
 VCY  C12  H122  single    0.970  0.020  1.090
 VCY  C12  H121  single    0.970  0.020  1.090
 VCY  C16  H161  single    0.930  0.020  1.080
 VCY  C19  H191  single    0.930  0.020  1.080
 VCY  C23  H231  single    0.930  0.020  1.080
 VCY  C25  H251  single    0.930  0.020  1.080
 VCY  C27  H271  single    0.930  0.020  1.080

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
 VCY  O11   C10  C09   116.29  3.000
 VCY  C09   C10  C13   119.86  3.000
 VCY  O11   C10  C13   123.84  3.000
 VCY  H131  C13  C06   118.44  3.000
 VCY  H131  C13  C10   121.59  3.000
 VCY  C06   C13  C10   119.94  3.000
 VCY  O14   C15  C16   126.25  3.000
 VCY  C16   C15  C28   123.78  3.000
 VCY  O14   C15  C28   109.96  3.000
 VCY  C18   C17  C16   119.80  3.000
 VCY  C18   C17  C26   120.38  3.000
 VCY  C16   C17  C26   119.82  3.000
 VCY  O21   C20  C23   116.07  3.000
 VCY  C23   C20  C19   119.76  3.000
 VCY  O21   C20  C19   124.18  3.000
 VCY  H223  C22  H221  108.72  3.000
 VCY  H223  C22  H222  108.71  3.000
 VCY  H221  C22  H222  108.67  3.000
 VCY  H223  C22  O21   112.11  3.000
 VCY  H221  C22  O21   112.02  3.000
 VCY  H222  C22  O21   106.49  3.000
 VCY  H241  C24  C25   119.73  3.000
 VCY  H241  C24  C23   119.35  3.000
 VCY  C25   C24  C23   120.92  3.000
 VCY  H261  C26  C27   118.98  3.000
 VCY  H261  C26  C17   118.99  3.000
 VCY  C27   C26  C17   122.03  3.000
 VCY  C27   C28  C04   135.02  3.000
 VCY  C27   C28  C15   118.78  3.000
 VCY  C04   C28  C15   106.19  3.000
 VCY  O29   C02  O01   127.25  3.000
 VCY  O29   C02  C03   115.81  3.000
 VCY  O01   C02  C03   116.93  3.000
 VCY  C05   C04  C03   129.86  3.000
 VCY  C05   C04  C28   105.25  3.000
 VCY  C03   C04  C28   124.85  3.000
 VCY  O14   C05  C06   115.63  3.000
 VCY  O14   C05  C04   111.55  3.000
 VCY  C06   C05  C04   132.81  3.000
 VCY  C07   C06  C05   120.57  3.000
 VCY  C05   C06  C13   119.34  3.000
 VCY  C07   C06  C13   120.08  3.000
 VCY  H071  C07  C08   119.82  3.000
 VCY  H071  C07  C06   120.82  3.000
 VCY  C08   C07  C06   119.34  3.000
 VCY  H081  C08  C09   119.31  3.000
 VCY  H081  C08  C07   119.66  3.000
 VCY  C09   C08  C07   121.03  3.000
 VCY  H091  C09  C08   120.61  3.000
 VCY  H091  C09  C10   119.65  3.000
 VCY  C08   C09  C10   119.74  3.000
 VCY  H161  C16  C17   121.43  3.000
 VCY  H161  C16  C15   121.38  3.000
 VCY  C17   C16  C15   117.17  3.000
 VCY  C25   C18  C19   119.41  3.000
 VCY  C25   C18  C17   120.54  3.000
 VCY  C19   C18  C17   120.05  3.000
 VCY  H191  C19  C18   118.80  3.000
 VCY  H191  C19  C20   120.75  3.000
 VCY  C18   C19  C20   120.43  3.000
 VCY  H231  C23  C24   120.79  3.000
 VCY  H231  C23  C20   119.58  3.000
 VCY  C24   C23  C20   119.62  3.000
 VCY  H251  C25  C18   120.30  3.000
 VCY  H251  C25  C24   119.82  3.000
 VCY  C18   C25  C24   119.86  3.000
 VCY  H271  C27  C28   120.89  3.000
 VCY  H271  C27  C26   120.69  3.000
 VCY  C28   C27  C26   118.42  3.000
 VCY  C12   O11  C10   118.50  3.000
 VCY  C05   O14  C15   107.03  3.000
 VCY  H031  C03  H032  107.32  3.000
 VCY  H031  C03  C04   109.81  3.000
 VCY  H032  C03  C04   108.51  3.000
 VCY  H031  C03  C02   109.66  3.000
 VCY  H032  C03  C02   110.06  3.000
 VCY  C04   C03  C02   111.38  3.000
 VCY  H121  C12  H122  108.56  3.000
 VCY  H121  C12  H123  108.83  3.000
 VCY  H122  C12  H123  108.86  3.000
 VCY  H121  C12  O11   111.93  3.000
 VCY  H122  C12  O11   112.07  3.000
 VCY  H123  C12  O11   106.49  3.000
 VCY  C22   O21  C20   118.82  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
 VCY  CONST_01  C07   C08  C09  C10     0.00   0.0  0
 VCY  CONST_02  C07   C06  C13  C10     0.00   0.0  0
 VCY  CONST_03  C05   C06  C13  C10   180.00   0.0  0
 VCY  CONST_04  C08   C09  C10  C13     0.00   0.0  0
 VCY  CONST_05  C08   C07  C06  C13     0.00   0.0  0
 VCY  CONST_08  C05   C04  C28  C15     0.00   0.0  0
 VCY  CONST_09  C26   C27  C28  C15     0.00   0.0  0
 VCY  CONST_10  C04   C05  O14  C15     0.00   0.0  0
 VCY  CONST_11  C06   C05  O14  C15   180.00   0.0  0
 VCY  CONST_12  C26   C17  C16  C15     0.00   0.0  0
 VCY  CONST_13  C18   C17  C16  C15   180.00   0.0  0
 VCY  CONST_14  C28   C27  C26  C17     0.00   0.0  0
 VCY  CONST_15  C28   C15  C16  C17     0.00   0.0  0
 VCY  CONST_16  O14   C15  C16  C17   180.00   0.0  0
 VCY  CONST_17  C20   C19  C18  C17   180.00   0.0  0
 VCY  CONST_18  C24   C25  C18  C17   180.00   0.0  0
 VCY  CONST_19  C25   C18  C19  C20     0.00   0.0  0
 VCY  CONST_20  C25   C24  C23  C20     0.00   0.0  0
 VCY  CONST_21  C19   C18  C25  C24     0.00   0.0  0
 VCY  CONST_22  C19   C20  C23  C24     0.00   0.0  0
 VCY  CONST_23  C04   C28  C27  C26   180.00   0.0  0
 VCY  CONST_26  C06   C05  C04  C28   180.00   0.0  0
 VCY  CONST_27  O14   C05  C04  C28     0.00   0.0  0
 VCY  CONST_28  C05   O14  C15  C28     0.00   0.0  0
 VCY  CONST_30  O14   C15  C28  C04     0.00   0.0  0
 VCY  CONST_31  C16   C15  C28  C04   180.00   0.0  0
 VCY  CONST_32  C27   C28  C04  C05   180.00   0.0  0
 VCY  CONST_33  C08   C07  C06  C05   180.00   0.0  0
 VCY  CONST_34  C16   C15  O14  C05   180.00   0.0  0
 VCY  CONST_35  C09   C10  C13  C06     0.00   0.0  0
 VCY  CONST_36  C09   C08  C07  C06     0.00   0.0  0
 VCY  CONST_38  C27   C28  C15  C16     0.00   0.0  0
 VCY  CONST_39  C27   C26  C17  C16     0.00   0.0  0
 VCY  CONST_42  C27   C26  C17  C18   180.00   0.0  0
 VCY  CONST_43  C23   C20  C19  C18     0.00   0.0  0
 VCY  CONST_44  C23   C24  C25  C18     0.00   0.0  0
 VCY  CONST_45  O14   C15  C28  C27   180.00   0.0  0
 VCY  CONST_46  C03   C04  C28  C15   180.00   0.0  0
 VCY  CONST_47  O21   C20  C23  C24   180.00   0.0  0
 VCY  CONST_48  C06   C05  C04  C03     0.00   0.0  0
 VCY  CONST_49  O14   C05  C04  C03   180.00   0.0  0
 VCY  CONST_50  C27   C28  C04  C03     0.00   0.0  0
 VCY  CONST_51  O11   C10  C13  C06   180.00   0.0  0
 VCY  CONST_52  O11   C10  C09  C08   180.00   0.0  0
 VCY  CONST_53  O21   C20  C19  C18   180.00   0.0  0
 VCY  CONST_54  H081  C08  C09  C10   180.00   0.0  0
 VCY  CONST_55  H091  C09  C10  C13   180.00   0.0  0
 VCY  CONST_56  H071  C07  C06  C13   180.00   0.0  0
 VCY  CONST_57  H271  C27  C28  C15   180.00   0.0  0
 VCY  CONST_58  H191  C19  C18  C17     0.00   0.0  0
 VCY  CONST_59  H251  C25  C18  C17     0.00   0.0  0
 VCY  CONST_60  H241  C24  C23  C20   180.00   0.0  0
 VCY  CONST_61  H161  C16  C17  C26   180.00   0.0  0
 VCY  CONST_62  H261  C26  C27  C28   180.00   0.0  0
 VCY  CONST_63  H131  C13  C06  C05     0.00   0.0  0
 VCY  CONST_64  H231  C23  C20  C19   180.00   0.0  0
 VCY  Var_01    C19   C20  O21  C22    -1.68  30.0  2
 VCY  Var_02    C02   C03  C04  C28    74.65  30.0  2
 VCY  Var_03    O01   C02  C03  C04  -108.65  30.0  2
 VCY  Var_04    H123  C12  O11  C10  -178.81  30.0  3
 VCY  Var_05    H222  C22  O21  C20  -179.20  30.0  3

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
 VCY  plan-1  C10   0.020
 VCY  plan-1  C13   0.020
 VCY  plan-1  C05   0.020
 VCY  plan-1  C06   0.020
 VCY  plan-1  C07   0.020
 VCY  plan-1  C08   0.020
 VCY  plan-1  C09   0.020
 VCY  plan-1  O11   0.020
 VCY  plan-1  H131  0.020
 VCY  plan-1  H071  0.020
 VCY  plan-1  H081  0.020
 VCY  plan-1  H091  0.020
 VCY  plan-2  C17   0.020
 VCY  plan-2  C20   0.020
 VCY  plan-2  C24   0.020
 VCY  plan-2  C18   0.020
 VCY  plan-2  C19   0.020
 VCY  plan-2  C23   0.020
 VCY  plan-2  C25   0.020
 VCY  plan-2  H241  0.020
 VCY  plan-2  H191  0.020
 VCY  plan-2  H231  0.020
 VCY  plan-2  H251  0.020
 VCY  plan-2  O21   0.020
 VCY  plan-3  C15   0.020
 VCY  plan-3  C17   0.020
 VCY  plan-3  C26   0.020
 VCY  plan-3  C28   0.020
 VCY  plan-3  C04   0.020
 VCY  plan-3  C05   0.020
 VCY  plan-3  C06   0.020
 VCY  plan-3  C16   0.020
 VCY  plan-3  C18   0.020
 VCY  plan-3  C27   0.020
 VCY  plan-3  O14   0.020
 VCY  plan-3  H261  0.020
 VCY  plan-3  H161  0.020
 VCY  plan-3  H271  0.020
 VCY  plan-3  C03   0.020
 VCY  plan-4  C02   0.020
 VCY  plan-4  O01   0.020
 VCY  plan-4  O29   0.020
 VCY  plan-4  C03   0.020

