# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 17:22:52 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[(naphthalen-2-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)NC(=O)c2ccc3ccccc3c2)[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
 VMP  VMP  N-[(naphthalen-2-ylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine  ligand  47  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VMP
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
 VMP  C10   C  CR16  0  -0.331  -4.3407  -0.7802  -0.7341
 VMP  C11   C  CR66  0   0.141  -5.5839  -0.4378  -0.1630
 VMP  C24   C  CR16  0  -0.306  -6.7490  -1.2043  -0.4052
 VMP  C26   C  CR16  0  -0.255  -7.9423  -0.8496   0.1605
 VMP  C27   C  CR16  0  -0.249  -8.0261   0.2870   0.9935
 VMP  C25   C  CR16  0  -0.307  -6.9168   1.0477   1.2440
 VMP  C12   C  CR66  0   0.115  -5.6697   0.7050   0.6732
 VMP  C13   C  CR16  0  -0.297  -4.5014   1.4670   0.9040
 VMP  C14   C  CR16  0  -0.295  -3.3069   1.1077   0.3479
 VMP  C9    C  CR6   0  -0.058  -3.2135  -0.0378  -0.4804
 VMP  C8    C  C     0   0.558  -1.9388  -0.4709  -1.1269
 VMP  O8    O  O     0  -0.420  -1.9303  -1.1656  -2.1177
 VMP  N2    N  NH1   0  -0.766  -0.7996  -0.0352  -0.4899
 VMP  C7    C  C     0   0.767   0.5079  -0.1843  -0.9466
 VMP  O7    O  O     0  -0.471   0.7954  -0.6561  -2.0229
 VMP  N1    N  NH1   0  -0.737   1.4175   0.2969  -0.0564
 VMP  C1    C  CH1   0   0.207   2.8226   0.2286  -0.2824
 VMP  O5    O  O2    0  -0.488   3.3328  -0.9015   0.3843
 VMP  C5    C  CH1   0  -0.015   4.7108  -1.1155   0.1571
 VMP  C6    C  CH2   0  -0.157   5.0970  -2.4089   0.8431
 VMP  O6    O  OH1   0  -0.670   4.3971  -3.4700   0.2394
 VMP  C4    C  CH1   0   0.035   5.5136   0.0726   0.6907
 VMP  O4    O  OH1   0  -0.672   6.8701  -0.1467   0.3944
 VMP  C3    C  CH1   0  -0.007   5.0095   1.3610   0.0512
 VMP  O3    O  OH1   0  -0.671   5.7123   2.4290   0.6393
 VMP  C2    C  CH1   0  -0.026   3.5050   1.4979   0.2344
 VMP  O2    O  OH1   0  -0.663   3.0893   2.6313  -0.4824
 VMP  H10   H  HCR6  0   0.265  -4.2854  -1.6520  -1.3743
 VMP  H24   H  HCR6  0   0.261  -6.6829  -2.0759  -1.0449
 VMP  H26   H  HCR6  0   0.264  -8.8293  -1.4399  -0.0275
 VMP  H27   H  HCR6  0   0.265  -8.9772   0.5547   1.4349
 VMP  H25   H  HCR6  0   0.261  -6.9821   1.9194   1.8833
 VMP  H13   H  HCR6  0   0.266  -4.5611   2.3510   1.5267
 VMP  H14   H  HCR6  0   0.262  -2.4454   1.7376   0.5305
 VMP  H2    H  HNH1  0   0.427  -0.9217   0.4254   0.3988
 VMP  H1    H  HNH1  0   0.410   1.1136   0.5639   0.8694
 VMP  HA    H  HCH1  0   0.237   2.9942   0.1460  -1.3625
 VMP  HB    H  HCH1  0   0.227   3.2878   1.5982   1.3097
 VMP  H5    H  HCH1  0   0.224   4.9040  -1.2112  -0.9242
 VMP  H61C  H  HCH2  0   0.213   6.1809  -2.5355   0.7553
 VMP  H62C  H  HCH2  0   0.197   4.8677  -2.3232   1.9144
 VMP  H4    H  HCH1  0   0.213   5.3515   0.1387   1.7788
 VMP  H6    H  HOH1  0   0.457   4.6843  -4.2884   0.6538
 VMP  HC    H  HOH1  0   0.455   7.3732   0.6074   0.7192
 VMP  H3    H  HCH1  0   0.219   5.2183   1.3043  -1.0295
 VMP  HD    H  HOH1  0   0.458   5.5529   3.2238   0.1208
 VMP  H2A   H  HOH1  0   0.457   2.1766   2.8297  -0.2501

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
 VMP  C10  C11   aromatic  1.410  0.020  1.410
 VMP  C10  C9    aromatic  1.373  0.020  1.373
 VMP  C11  C24   aromatic  1.416  0.020  1.416
 VMP  C11  C12   aromatic  1.419  0.020  1.419
 VMP  C24  C26   aromatic  1.367  0.020  1.367
 VMP  C26  C27   aromatic  1.412  0.020  1.412
 VMP  C27  C25   aromatic  1.368  0.020  1.368
 VMP  C25  C12   aromatic  1.414  0.020  1.414
 VMP  C12  C13   aromatic  1.414  0.020  1.414
 VMP  C13  C14   aromatic  1.366  0.020  1.366
 VMP  C14  C9    aromatic  1.417  0.020  1.417
 VMP  C9   C8    single    1.493  0.020  1.493
 VMP  C8   O8    double    1.210  0.020  1.210
 VMP  C8   N2    single    1.376  0.020  1.376
 VMP  N2   C7    single    1.393  0.020  1.393
 VMP  C7   O7    double    1.210  0.020  1.210
 VMP  C7   N1    single    1.361  0.020  1.361
 VMP  N1   C1    single    1.425  0.020  1.425
 VMP  C1   O5    single    1.408  0.020  1.408
 VMP  C1   C2    single    1.531  0.020  1.531
 VMP  O5   C5    single    1.413  0.020  1.413
 VMP  C5   C6    single    1.514  0.020  1.514
 VMP  C5   C4    single    1.530  0.020  1.530
 VMP  C6   O6    single    1.407  0.020  1.407
 VMP  C4   O4    single    1.406  0.020  1.406
 VMP  C4   C3    single    1.524  0.020  1.524
 VMP  C3   O3    single    1.407  0.020  1.407
 VMP  C3   C2    single    1.522  0.020  1.522
 VMP  C2   O2    single    1.404  0.020  1.404
 VMP  C10  H10   single    0.930  0.020  1.080
 VMP  C24  H24   single    0.930  0.020  1.080
 VMP  C26  H26   single    0.930  0.020  1.080
 VMP  C27  H27   single    0.930  0.020  1.080
 VMP  C25  H25   single    0.930  0.020  1.080
 VMP  C13  H13   single    0.930  0.020  1.080
 VMP  C14  H14   single    0.930  0.020  1.080
 VMP  N2   H2    single    0.860  0.020  1.020
 VMP  N1   H1    single    0.860  0.020  1.020
 VMP  C1   HA    single    0.970  0.020  1.090
 VMP  C2   HB    single    0.970  0.020  1.090
 VMP  C5   H5    single    0.970  0.020  1.090
 VMP  C6   H61C  single    0.970  0.020  1.090
 VMP  C6   H62C  single    0.970  0.020  1.090
 VMP  C4   H4    single    0.970  0.020  1.090
 VMP  O6   H6    single    0.850  0.020  0.980
 VMP  O4   HC    single    0.850  0.020  0.980
 VMP  C3   H3    single    0.970  0.020  1.090
 VMP  O3   HD    single    0.850  0.020  0.980
 VMP  O2   H2A   single    0.850  0.020  0.980

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
 VMP  H10   C10  C9    120.16  3.000
 VMP  H10   C10  C11   118.68  3.000
 VMP  C9    C10  C11   121.16  3.000
 VMP  C12   C11  C24   119.16  3.000
 VMP  C12   C11  C10   119.18  3.000
 VMP  C24   C11  C10   121.65  3.000
 VMP  H24   C24  C26   120.42  3.000
 VMP  H24   C24  C11   119.12  3.000
 VMP  C26   C24  C11   120.46  3.000
 VMP  H26   C26  C27   119.55  3.000
 VMP  H26   C26  C24   120.13  3.000
 VMP  C27   C26  C24   120.32  3.000
 VMP  H27   C27  C25   120.02  3.000
 VMP  H27   C27  C26   119.48  3.000
 VMP  C25   C27  C26   120.50  3.000
 VMP  H25   C25  C12   119.12  3.000
 VMP  H25   C25  C27   120.45  3.000
 VMP  C12   C25  C27   120.43  3.000
 VMP  C13   C12  C25   122.17  3.000
 VMP  C13   C12  C11   118.71  3.000
 VMP  C25   C12  C11   119.12  3.000
 VMP  H13   C13  C14   119.81  3.000
 VMP  H13   C13  C12   119.23  3.000
 VMP  C14   C13  C12   120.96  3.000
 VMP  H14   C14  C9    121.10  3.000
 VMP  H14   C14  C13   118.31  3.000
 VMP  C9    C14  C13   120.56  3.000
 VMP  C8    C9   C14   122.95  3.000
 VMP  C8    C9   C10   117.63  3.000
 VMP  C14   C9   C10   119.41  3.000
 VMP  N2    C8   O8    123.71  3.000
 VMP  N2    C8   C9    114.48  3.000
 VMP  O8    C8   C9    121.80  3.000
 VMP  H2    N2   C7    116.84  3.000
 VMP  H2    N2   C8    116.90  3.000
 VMP  C7    N2   C8    126.26  3.000
 VMP  N1    C7   O7    124.13  3.000
 VMP  N1    C7   N2    112.03  3.000
 VMP  O7    C7   N2    123.81  3.000
 VMP  H1    N1   C1    117.05  3.000
 VMP  H1    N1   C7    119.46  3.000
 VMP  C1    N1   C7    122.58  3.000
 VMP  HA    C1   C2    108.98  3.000
 VMP  HA    C1   O5    110.44  3.000
 VMP  C2    C1   O5    110.13  3.000
 VMP  HA    C1   N1    108.31  3.000
 VMP  C2    C1   N1    110.26  3.000
 VMP  O5    C1   N1    108.70  3.000
 VMP  C5    O5   C1    113.51  3.000
 VMP  H5    C5   C4    108.51  3.000
 VMP  H5    C5   C6    109.00  3.000
 VMP  C4    C5   C6    111.81  3.000
 VMP  H5    C5   O5    109.98  3.000
 VMP  C4    C5   O5    109.76  3.000
 VMP  C6    C5   O5    107.78  3.000
 VMP  H62C  C6   H61C  107.08  3.000
 VMP  H62C  C6   O6    111.92  3.000
 VMP  H61C  C6   O6    111.76  3.000
 VMP  H62C  C6   C5    108.78  3.000
 VMP  H61C  C6   C5    108.36  3.000
 VMP  O6    C6   C5    108.84  3.000
 VMP  H6    O6   C6    107.96  3.000
 VMP  H4    C4   C3    108.35  3.000
 VMP  H4    C4   O4    111.06  3.000
 VMP  C3    C4   O4    111.26  3.000
 VMP  H4    C4   C5    108.28  3.000
 VMP  C3    C4   C5    109.67  3.000
 VMP  O4    C4   C5    108.16  3.000
 VMP  HC    O4   C4    108.12  3.000
 VMP  H3    C3   C2    108.05  3.000
 VMP  H3    C3   O3    110.74  3.000
 VMP  C2    C3   O3    112.04  3.000
 VMP  H3    C3   C4    107.77  3.000
 VMP  C2    C3   C4    110.64  3.000
 VMP  O3    C3   C4    107.52  3.000
 VMP  HD    O3   C3    108.60  3.000
 VMP  HB    C2   O2    111.50  3.000
 VMP  HB    C2   C3    108.70  3.000
 VMP  O2    C2   C3    107.69  3.000
 VMP  HB    C2   C1    108.49  3.000
 VMP  O2    C2   C1    111.41  3.000
 VMP  C3    C2   C1    108.99  3.000
 VMP  H2A   O2   C2    108.90  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
 VMP  CONST_01  C26  C24  C11  C10  180.00   0.0  0
 VMP  CONST_02  C25  C12  C11  C10  180.00   0.0  0
 VMP  CONST_03  C13  C12  C11  C10    0.00   0.0  0
 VMP  CONST_04  C13  C14  C9   C10    0.00   0.0  0
 VMP  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 VMP  CONST_06  C27  C26  C24  C11    0.00   0.0  0
 VMP  CONST_07  C27  C25  C12  C11    0.00   0.0  0
 VMP  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 VMP  CONST_09  C9   C10  C11  C24  180.00   0.0  0
 VMP  CONST_10  C25  C12  C11  C24    0.00   0.0  0
 VMP  CONST_11  C13  C12  C11  C24  180.00   0.0  0
 VMP  CONST_12  C25  C27  C26  C24    0.00   0.0  0
 VMP  CONST_13  C12  C11  C24  C26    0.00   0.0  0
 VMP  CONST_14  C12  C25  C27  C26    0.00   0.0  0
 VMP  CONST_15  C13  C12  C25  C27  180.00   0.0  0
 VMP  CONST_16  C14  C13  C12  C25  180.00   0.0  0
 VMP  CONST_17  C9   C10  C11  C12    0.00   0.0  0
 VMP  CONST_18  C9   C14  C13  C12    0.00   0.0  0
 VMP  CONST_19  C8   C9   C10  C11  180.00   0.0  0
 VMP  CONST_20  C8   C9   C14  C13  180.00   0.0  0
 VMP  CONST_21  H24  C24  C11  C10    0.00   0.0  0
 VMP  CONST_22  H14  C14  C9   C10  180.00   0.0  0
 VMP  CONST_23  H26  C26  C24  C11  180.00   0.0  0
 VMP  CONST_24  H25  C25  C12  C11  180.00   0.0  0
 VMP  CONST_25  H13  C13  C12  C11  180.00   0.0  0
 VMP  CONST_26  H10  C10  C11  C24    0.00   0.0  0
 VMP  CONST_27  H27  C27  C26  C24  180.00   0.0  0
 VMP  CONST_28  C7   N2   C8   C9   180.00   0.0  0
 VMP  CONST_29  C1   N1   C7   O7     0.00   0.0  0
 VMP  CONST_30  C1   N1   C7   N2   180.00   0.0  0
 VMP  CONST_31  H2   N2   C8   C9     0.00   0.0  0
 VMP  CONST_32  O7   C7   N2   C8     0.00   0.0  0
 VMP  CONST_33  C7   N2   C8   O8     0.00   0.0  0
 VMP  CONST_34  N1   C7   N2   C8   180.00   0.0  0
 VMP  CONST_35  H1   N1   C7   O7   180.00   0.0  0
 VMP  Var_01    O8   C8   C9   C10   21.58  30.0  2

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
 VMP  chir_01  C1  N1  O5  C2  positiv
 VMP  chir_02  C5  O5  C6  C4  positiv
 VMP  chir_03  C4  O4  C5  C3  positiv
 VMP  chir_04  C3  O3  C2  C4  positiv
 VMP  chir_05  C2  O2  C3  C1  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
 VMP  plan-1  C10  0.020
 VMP  plan-1  C11  0.020
 VMP  plan-1  C24  0.020
 VMP  plan-1  C26  0.020
 VMP  plan-1  C27  0.020
 VMP  plan-1  C25  0.020
 VMP  plan-1  C12  0.020
 VMP  plan-1  C13  0.020
 VMP  plan-1  C14  0.020
 VMP  plan-1  C9   0.020
 VMP  plan-1  C8   0.020
 VMP  plan-1  H10  0.020
 VMP  plan-1  H24  0.020
 VMP  plan-1  H26  0.020
 VMP  plan-1  H27  0.020
 VMP  plan-1  H25  0.020
 VMP  plan-1  H13  0.020
 VMP  plan-1  H14  0.020
 VMP  plan-2  C9   0.020
 VMP  plan-2  C8   0.020
 VMP  plan-2  O8   0.020
 VMP  plan-2  N2   0.020
 VMP  plan-2  C7   0.020
 VMP  plan-2  O7   0.020
 VMP  plan-2  N1   0.020
 VMP  plan-2  C1   0.020
 VMP  plan-2  H2   0.020
 VMP  plan-2  H1   0.020

