# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 20:34:00 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-(3-aminophenyl)-~{N}-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]furan-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@H](NC(=O)c2oc(cc2)c3cccc(N)c3)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 VJW  VJW  "5-(3-aminophenyl)furan-2-carboxamido-(beta-L-fucopyranose)"
  ligand  45  25  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VJW
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
 VJW  N1   N  NH1   0  -0.699  6.0408  11.6284   8.5537
 VJW  C4   C  CH1   0   0.015  5.8571  14.7564  11.3325
 VJW  C5   C  CH1   0   0.012  7.1410  13.9976  11.0182
 VJW  C6   C  CH3   0  -0.679  8.3662  14.8846  10.9353
 VJW  C7   C  C     0   0.492  6.8752  10.5853   8.3418
 VJW  C8   C  CR5   0   0.225  6.8415   9.9864   7.0034
 VJW  C10  C  CR15  0  -0.371  7.1172   8.7869   5.1565
 VJW  C13  C  CR16  0  -0.411  5.5352   9.3793   2.5968
 VJW  C15  C  CR16  0  -0.328  3.9124  10.7713   1.5002
 VJW  C17  C  CR16  0  -0.334  4.5099  11.2046   3.8011
 VJW  C1   C  CH1   0   0.232  6.0051  12.3308   9.7946
 VJW  O5   O  O2    0  -0.486  7.0191  13.3055   9.7872
 VJW  C3   C  CH1   0  -0.037  4.6828  13.7756  11.3107
 VJW  O3   O  OH1   0  -0.667  3.4457  14.4436  11.4342
 VJW  C2   C  CH1   0   0.006  4.6433  12.9896  10.0048
 VJW  O2   O  OH1   0  -0.664  3.6734  11.9760  10.0311
 VJW  O4   O  OH1   0  -0.667  5.6832  15.7917  10.3992
 VJW  O7   O  O     0  -0.468  7.6234  10.1297   9.1924
 VJW  O8   O  O     0  -0.446  6.0220  10.4876   6.0533
 VJW  C11  C  CR5   0   0.419  6.1871   9.7633   4.9314
 VJW  C9   C  CR15  0  -0.305  7.5395   8.9340   6.4988
 VJW  C12  C  CR6   0   0.009  5.3976  10.1272   3.7655
 VJW  C16  C  CR16  0  -0.233  3.7779  11.5092   2.6627
 VJW  C14  C  CR6   0   0.346  4.8005   9.6882   1.4504
 VJW  N2   N  NH2   0  -0.861  4.9821   8.9787   0.2849
 VJW  H1   H  HNH1  0   0.410  5.4935  11.9906   7.7869
 VJW  H2   H  HCH1  0   0.218  5.9506  15.1544  12.3557
 VJW  H3   H  HCH1  0   0.220  7.2843  13.2715  11.8341
 VJW  H5   H  HCH3  0   0.239  9.2646  14.2853  10.7893
 VJW  H6   H  HCH3  0   0.234  8.2910  15.5977  10.1155
 VJW  H7   H  HCR5  0   0.272  7.4618   8.0496   4.4503
 VJW  H8   H  HCR6  0   0.256  6.2194   8.5390   2.5648
 VJW  H9   H  HCR6  0   0.258  3.3297  11.0293   0.6239
 VJW  H10  H  HCR6  0   0.249  4.3840  11.7989   4.6952
 VJW  H11  H  HCH1  0   0.224  6.1808  11.6121  10.6074
 VJW  H12  H  HCH1  0   0.226  4.8286  13.0590  12.1319
 VJW  H13  H  HOH1  0   0.460  3.3066  14.6737  12.3588
 VJW  H14  H  HCH1  0   0.218  4.4687  13.6924   9.1750
 VJW  H15  H  HOH1  0   0.452  2.8226  12.3828  10.2265
 VJW  H16  H  HOH1  0   0.446  4.7928  16.1413  10.5161
 VJW  H17  H  HCR5  0   0.275  8.2673   8.3369   7.0235
 VJW  H18  H  HCR6  0   0.255  3.0855  12.3412   2.6830
 VJW  H19  H  HNH2  0   0.380  5.3512   8.0471   0.3877
 VJW  H20  H  HNH2  0   0.380  4.2195   9.0113  -0.3725
 VJW  H4   H  HCH3  0   0.231  8.4865  15.4429  11.8637

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
 VJW  N2   C14  single    1.376  0.020  1.376
 VJW  C15  C14  aromatic  1.402  0.020  1.402
 VJW  C15  C16  aromatic  1.384  0.020  1.384
 VJW  C14  C13  aromatic  1.396  0.020  1.396
 VJW  C16  C17  aromatic  1.387  0.020  1.387
 VJW  C13  C12  aromatic  1.394  0.020  1.394
 VJW  C17  C12  aromatic  1.397  0.020  1.397
 VJW  C12  C11  single    1.454  0.020  1.454
 VJW  C11  C10  aromatic  1.367  0.020  1.367
 VJW  C11  O8   aromatic  1.346  0.020  1.346
 VJW  C10  C9   aromatic  1.415  0.020  1.415
 VJW  O8   C8   aromatic  1.351  0.020  1.351
 VJW  C9   C8   aromatic  1.360  0.020  1.360
 VJW  C8   C7   single    1.467  0.020  1.467
 VJW  C7   N1   single    1.352  0.020  1.352
 VJW  C7   O7   double    1.221  0.020  1.221
 VJW  N1   C1   single    1.426  0.020  1.426
 VJW  C1   O5   single    1.407  0.020  1.407
 VJW  C1   C2   single    1.527  0.020  1.527
 VJW  O5   C5   single    1.417  0.020  1.417
 VJW  C2   O2   single    1.403  0.020  1.403
 VJW  C2   C3   single    1.525  0.020  1.525
 VJW  O4   C4   single    1.405  0.020  1.405
 VJW  C6   C5   single    1.515  0.020  1.515
 VJW  C5   C4   single    1.524  0.020  1.524
 VJW  C3   O3   single    1.411  0.020  1.411
 VJW  C3   C4   single    1.530  0.020  1.530
 VJW  N1   H1   single    0.860  0.020  1.020
 VJW  C4   H2   single    0.970  0.020  1.090
 VJW  C5   H3   single    0.970  0.020  1.090
 VJW  C6   H4   single    0.970  0.020  1.090
 VJW  C6   H5   single    0.970  0.020  1.090
 VJW  C6   H6   single    0.970  0.020  1.090
 VJW  C10  H7   single    0.930  0.020  1.080
 VJW  C13  H8   single    0.930  0.020  1.080
 VJW  C15  H9   single    0.930  0.020  1.080
 VJW  C17  H10  single    0.930  0.020  1.080
 VJW  C1   H11  single    0.970  0.020  1.090
 VJW  C3   H12  single    0.970  0.020  1.090
 VJW  O3   H13  single    0.850  0.020  0.980
 VJW  C2   H14  single    0.970  0.020  1.090
 VJW  O2   H15  single    0.850  0.020  0.980
 VJW  O4   H16  single    0.850  0.020  0.980
 VJW  C9   H17  single    0.930  0.020  1.080
 VJW  C16  H18  single    0.930  0.020  1.080
 VJW  N2   H19  single    0.890  0.020  1.040
 VJW  N2   H20  single    0.890  0.020  1.040

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
 VJW  H1   N1   C1   118.08  3.000
 VJW  H1   N1   C7   119.49  3.000
 VJW  C1   N1   C7   122.11  3.000
 VJW  H2   C4   O4   111.18  3.000
 VJW  H2   C4   C3   108.05  3.000
 VJW  O4   C4   C3   111.59  3.000
 VJW  H2   C4   C5   107.45  3.000
 VJW  C3   C4   C5   108.93  3.000
 VJW  O4   C4   C5   109.52  3.000
 VJW  H3   C5   O5   109.43  3.000
 VJW  H3   C5   C6   108.74  3.000
 VJW  O5   C5   C6   107.93  3.000
 VJW  H3   C5   C4   106.56  3.000
 VJW  C6   C5   C4   113.65  3.000
 VJW  O5   C5   C4   110.47  3.000
 VJW  H6   C6   H5   108.43  3.000
 VJW  H6   C6   H4   108.26  3.000
 VJW  H5   C6   H4   107.74  3.000
 VJW  H6   C6   C5   111.64  3.000
 VJW  H5   C6   C5   110.62  3.000
 VJW  H4   C6   C5   110.04  3.000
 VJW  O7   C7   C8   119.83  3.000
 VJW  O7   C7   N1   123.83  3.000
 VJW  C8   C7   N1   116.34  3.000
 VJW  C9   C8   O8   109.73  3.000
 VJW  C9   C8   C7   130.00  3.000
 VJW  O8   C8   C7   120.27  3.000
 VJW  H7   C10  C9   126.69  3.000
 VJW  H7   C10  C11  126.75  3.000
 VJW  C9   C10  C11  106.56  3.000
 VJW  H8   C13  C14  118.64  3.000
 VJW  H8   C13  C12  120.19  3.000
 VJW  C14  C13  C12  121.17  3.000
 VJW  H9   C15  C14  119.74  3.000
 VJW  H9   C15  C16  120.02  3.000
 VJW  C14  C15  C16  120.24  3.000
 VJW  H10  C17  C16  119.78  3.000
 VJW  H10  C17  C12  121.28  3.000
 VJW  C16  C17  C12  118.94  3.000
 VJW  H11  C1   C2   108.83  3.000
 VJW  H11  C1   O5   109.98  3.000
 VJW  C2   C1   O5   110.16  3.000
 VJW  H11  C1   N1   108.50  3.000
 VJW  C2   C1   N1   110.76  3.000
 VJW  O5   C1   N1   108.58  3.000
 VJW  C1   O5   C5   113.32  3.000
 VJW  H12  C3   C2   107.89  3.000
 VJW  H12  C3   O3   111.06  3.000
 VJW  C2   C3   O3   107.23  3.000
 VJW  H12  C3   C4   107.78  3.000
 VJW  O3   C3   C4   111.59  3.000
 VJW  C2   C3   C4   111.26  3.000
 VJW  H13  O3   C3   108.89  3.000
 VJW  H14  C2   O2   111.44  3.000
 VJW  H14  C2   C3   108.69  3.000
 VJW  O2   C2   C3   111.98  3.000
 VJW  H14  C2   C1   108.23  3.000
 VJW  C3   C2   C1   108.49  3.000
 VJW  O2   C2   C1   107.90  3.000
 VJW  H15  O2   C2   108.02  3.000
 VJW  H16  O4   C4   107.52  3.000
 VJW  C11  O8   C8   108.19  3.000
 VJW  C12  C11  O8   117.85  3.000
 VJW  O8   C11  C10  109.31  3.000
 VJW  C12  C11  C10  132.84  3.000
 VJW  H17  C9   C10  127.29  3.000
 VJW  H17  C9   C8   126.49  3.000
 VJW  C10  C9   C8   106.21  3.000
 VJW  C11  C12  C17  121.17  3.000
 VJW  C11  C12  C13  118.96  3.000
 VJW  C17  C12  C13  119.87  3.000
 VJW  H18  C16  C17  119.40  3.000
 VJW  H18  C16  C15  119.19  3.000
 VJW  C17  C16  C15  121.41  3.000
 VJW  N2   C14  C15  120.80  3.000
 VJW  C15  C14  C13  118.38  3.000
 VJW  N2   C14  C13  120.78  3.000
 VJW  H20  N2   H19  111.96  3.000
 VJW  H20  N2   C14  115.85  3.000
 VJW  H19  N2   C14  116.02  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
 VJW  CONST_01  C12  C11  O8   C8    180.00   0.0  0
 VJW  CONST_02  C10  C11  O8   C8      0.00   0.0  0
 VJW  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 VJW  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 VJW  CONST_05  C17  C12  C11  C10   180.00   0.0  0
 VJW  CONST_06  O8   C8   C9   C10     0.00   0.0  0
 VJW  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 VJW  CONST_08  C16  C17  C12  C13     0.00   0.0  0
 VJW  CONST_09  O8   C11  C12  C13   180.00   0.0  0
 VJW  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 VJW  CONST_11  C12  C17  C16  C15     0.00   0.0  0
 VJW  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 VJW  CONST_13  C14  C13  C12  C17     0.00   0.0  0
 VJW  CONST_14  O8   C11  C12  C17     0.00   0.0  0
 VJW  CONST_15  C9   C10  C11  O8      0.00   0.0  0
 VJW  CONST_16  C14  C13  C12  C11   180.00   0.0  0
 VJW  CONST_17  C16  C17  C12  C11   180.00   0.0  0
 VJW  CONST_18  C9   C8   O8   C11     0.00   0.0  0
 VJW  CONST_19  C12  C11  C10  C9    180.00   0.0  0
 VJW  CONST_20  C11  O8   C8   C7    180.00   0.0  0
 VJW  CONST_21  C10  C9   C8   C7    180.00   0.0  0
 VJW  CONST_22  N2   C14  C13  C12   180.00   0.0  0
 VJW  CONST_23  N2   C14  C15  C16   180.00   0.0  0
 VJW  CONST_24  H7   C10  C9   C8    180.00   0.0  0
 VJW  CONST_25  H9   C15  C14  C13   180.00   0.0  0
 VJW  CONST_26  H10  C17  C12  C13   180.00   0.0  0
 VJW  CONST_27  H8   C13  C14  C15   180.00   0.0  0
 VJW  CONST_28  H10  C17  C16  C15   180.00   0.0  0
 VJW  CONST_29  H9   C15  C16  C17   180.00   0.0  0
 VJW  CONST_30  H8   C13  C12  C17   180.00   0.0  0
 VJW  CONST_31  H7   C10  C11  O8    180.00   0.0  0
 VJW  CONST_32  H17  C9   C8   O8    180.00   0.0  0
 VJW  CONST_33  H8   C13  C12  C11     0.00   0.0  0
 VJW  CONST_34  H10  C17  C12  C11     0.00   0.0  0
 VJW  CONST_35  H17  C9   C10  C11   180.00   0.0  0
 VJW  CONST_36  H18  C16  C17  C12   180.00   0.0  0
 VJW  CONST_37  H7   C10  C11  C12     0.00   0.0  0
 VJW  CONST_38  H18  C16  C15  C14   180.00   0.0  0
 VJW  CONST_39  C1   N1   C7   C8    180.00   0.0  0
 VJW  CONST_44  O7   C7   N1   C1      0.00   0.0  0
 VJW  CONST_45  H1   N1   C7   C8      0.00   0.0  0
 VJW  CONST_46  H1   N1   C7   O7    180.00   0.0  0
 VJW  Var_01    O8   C8   C7   N1      0.87  30.0  3
 VJW  Var_02    C9   C8   C7   N1   -179.16  30.0  3
 VJW  Var_03    O8   C8   C7   O7   -179.67  30.0  3
 VJW  Var_04    C9   C8   C7   O7      0.30  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
 VJW  chir_01  C4  O4  C5  C3  positiv
 VJW  chir_02  C5  O5  C4  C6  positiv
 VJW  chir_03  C1  O5  N1  C2  positiv
 VJW  chir_04  C3  O3  C2  C4  negativ
 VJW  chir_05  C2  O2  C3  C1  negativ

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
 VJW  plan-1  C7   0.020
 VJW  plan-1  C8   0.020
 VJW  plan-1  C10  0.020
 VJW  plan-1  O8   0.020
 VJW  plan-1  C11  0.020
 VJW  plan-1  C9   0.020
 VJW  plan-1  C12  0.020
 VJW  plan-1  H7   0.020
 VJW  plan-1  H17  0.020
 VJW  plan-2  C13  0.020
 VJW  plan-2  C15  0.020
 VJW  plan-2  C17  0.020
 VJW  plan-2  C11  0.020
 VJW  plan-2  C12  0.020
 VJW  plan-2  C16  0.020
 VJW  plan-2  C14  0.020
 VJW  plan-2  N2   0.020
 VJW  plan-2  H8   0.020
 VJW  plan-2  H9   0.020
 VJW  plan-2  H10  0.020
 VJW  plan-2  H18  0.020
 VJW  plan-3  N1   0.020
 VJW  plan-3  C7   0.020
 VJW  plan-3  C8   0.020
 VJW  plan-3  C1   0.020
 VJW  plan-3  O7   0.020
 VJW  plan-3  H1   0.020
 VJW  plan-4  C14  0.020
 VJW  plan-4  N2   0.020
 VJW  plan-4  H19  0.020
 VJW  plan-4  H20  0.020

