# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:33:10 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (5R,6R,7R,8S)-8-(acetylamino)-6,7-dihydroxy-5-(hydroxymethyl)-2-(phenylcarbamoyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)[n+]2cc([nH]c12)C(=O)Nc3ccccc3
#
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
 GDV  GDV  (5R,6R,7R,8S)-8-(acetylamino)-6,7-dihydroxy-5-(hydroxymethyl)-2-(phenylcarbamoyl)-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  47  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GDV
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
 GDV  O1    O  O     0  -0.474   4.2076  -5.7314   0.2677
 GDV  C10   C  C     0   0.540   4.2537  -5.0497   1.2754
 GDV  C12   C  CH3   0  -0.783   4.7688  -5.5731   2.5870
 GDV  N4    N  NH1   0  -0.645   3.8261  -3.7586   1.3008
 GDV  C2    C  CH1   0  -0.261   3.4286  -3.0587   0.1172
 GDV  C3    C  CH1   0   0.037   4.4017  -1.9515  -0.3070
 GDV  O3    O  OH1   0  -0.643   5.6602  -2.4725  -0.6098
 GDV  C4    C  CH1   0  -0.012   3.7969  -1.1864  -1.4911
 GDV  O4    O  OH1   0  -0.652   4.6561  -0.1855  -1.9519
 GDV  C5    C  CH1   0  -0.111   2.5039  -0.4569  -1.1133
 GDV  C6    C  CH2   0  -0.215   1.7082   0.0090  -2.3321
 GDV  O5    O  OH1   0  -0.656   1.1661  -1.0608  -3.0567
 GDV  C1    C  CR5   0   0.712   2.0791  -2.4553   0.2915
 GDV  N1    N  NR5   1  -0.485   1.6703  -1.3258  -0.2728
 GDV  C7    C  CR15  0  -0.033   0.3749  -1.0883   0.0957
 GDV  C8    C  CR5   0   0.147  -0.0051  -2.1026   0.9129
 GDV  N2    N  NR15  0  -0.668   1.0843  -2.9366   1.0152
 GDV  C9    C  C     0   0.552  -1.3418  -2.2356   1.5386
 GDV  O2    O  O     0  -0.441  -2.2164  -1.4657   1.1904
 GDV  N3    N  NH1   0  -0.762  -1.4722  -3.2100   2.4600
 GDV  C11   C  CR6   0   0.383  -2.6164  -3.5917   3.1786
 GDV  C17   C  CR16  0  -0.311  -3.8495  -2.9449   3.1001
 GDV  C16   C  CR16  0  -0.245  -4.9132  -3.4139   3.8607
 GDV  C15   C  CR16  0  -0.266  -4.7731  -4.5097   4.6984
 GDV  C14   C  CR16  0  -0.243  -3.5425  -5.1495   4.7731
 GDV  C13   C  CR16  0  -0.350  -2.4733  -4.6965   4.0206
 GDV  H121  H  HCH3  0   0.276   4.2176  -6.4728   2.8576
 GDV  H122  H  HCH3  0   0.277   5.8156  -5.8549   2.4725
 GDV  H123  H  HCH3  0   0.256   4.6898  -4.8577   3.4024
 GDV  H4    H  HNH1  0   0.419   3.9846  -3.2123   2.1345
 GDV  H2    H  HCH1  0   0.337   3.3497  -3.7964  -0.6909
 GDV  H3    H  HCH1  0   0.278   4.5467  -1.2591   0.5296
 GDV  HA    H  HOH1  0   0.457   5.5812  -3.1338  -1.3079
 GDV  HB    H  HCH1  0   0.237   3.5805  -1.9241  -2.2813
 GDV  HC    H  HOH1  0   0.463   5.4487  -0.5963  -2.3128
 GDV  H5    H  HCH1  0   0.320   2.7648   0.4161  -0.5091
 GDV  H6C1  H  HCH2  0   0.265   2.3643   0.6452  -2.9316
 GDV  H6C2  H  HCH2  0   0.259   0.8816   0.6414  -2.0024
 GDV  HD    H  HOH1  0   0.463   1.8119  -1.3717  -3.6973
 GDV  H7    H  HCR5  0   0.354  -0.1760  -0.2227  -0.2279
 GDV  HE    H  HNR5  0   0.457   1.1578  -3.8052   1.5288
 GDV  HF    H  HNH1  0   0.421  -0.6546  -3.7494   2.6974
 GDV  H17   H  HCR6  0   0.285  -3.9912  -2.0880   2.4632
 GDV  H16   H  HCR6  0   0.262  -5.8655  -2.9043   3.7914
 GDV  H15   H  HCR6  0   0.260  -5.6097  -4.8614   5.2870
 GDV  H14   H  HCR6  0   0.265  -3.4112  -6.0079   5.4186
 GDV  H13   H  HCR6  0   0.275  -1.5186  -5.2059   4.0850

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
 GDV  O1   C10   double    1.217  0.020  1.217
 GDV  C10  C12   single    1.503  0.020  1.503
 GDV  C10  N4    single    1.360  0.020  1.360
 GDV  C12  H121  single    0.970  0.020  1.090
 GDV  C12  H122  single    0.970  0.020  1.090
 GDV  C12  H123  single    0.970  0.020  1.090
 GDV  N4   C2    single    1.431  0.020  1.431
 GDV  N4   H4    single    0.860  0.020  1.020
 GDV  C2   C3    single    1.534  0.020  1.534
 GDV  C2   C1    single    1.489  0.020  1.489
 GDV  C2   H2    single    0.970  0.020  1.090
 GDV  C3   O3    single    1.395  0.020  1.395
 GDV  C3   C4    single    1.534  0.020  1.534
 GDV  C3   H3    single    0.970  0.020  1.090
 GDV  O3   HA    single    0.850  0.020  0.980
 GDV  C4   O4    single    1.397  0.020  1.397
 GDV  C4   C5    single    1.532  0.020  1.532
 GDV  C4   HB    single    0.970  0.020  1.090
 GDV  O4   HC    single    0.850  0.020  0.980
 GDV  C5   C6    single    1.528  0.020  1.528
 GDV  C5   N1    single    1.468  0.020  1.468
 GDV  C5   H5    single    0.970  0.020  1.090
 GDV  C6   O5    single    1.401  0.020  1.401
 GDV  C6   H6C1  single    0.970  0.020  1.090
 GDV  C6   H6C2  single    0.970  0.020  1.090
 GDV  O5   HD    single    0.850  0.020  0.980
 GDV  C1   N1    aromatic  1.327  0.020  1.327
 GDV  C1   N2    aromatic  1.321  0.020  1.321
 GDV  N1   C7    aromatic  1.368  0.020  1.368
 GDV  C7   C8    aromatic  1.357  0.020  1.357
 GDV  C7   H7    single    0.930  0.020  1.080
 GDV  C8   N2    aromatic  1.376  0.020  1.376
 GDV  C8   C9    single    1.482  0.020  1.482
 GDV  N2   HE    single    0.860  0.020  1.020
 GDV  C9   O2    double    1.216  0.020  1.216
 GDV  C9   N3    single    1.347  0.020  1.347
 GDV  N3   C11   single    1.404  0.020  1.404
 GDV  N3   HF    single    0.860  0.020  1.020
 GDV  C11  C17   aromatic  1.395  0.020  1.395
 GDV  C11  C13   aromatic  1.396  0.020  1.396
 GDV  C17  C16   aromatic  1.389  0.020  1.389
 GDV  C17  H17   single    0.930  0.020  1.080
 GDV  C16  C15   aromatic  1.386  0.020  1.386
 GDV  C16  H16   single    0.930  0.020  1.080
 GDV  C15  C14   aromatic  1.389  0.020  1.389
 GDV  C15  H15   single    0.930  0.020  1.080
 GDV  C14  C13   aromatic  1.384  0.020  1.384
 GDV  C14  H14   single    0.930  0.020  1.080
 GDV  C13  H13   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
 GDV  N4    C10  C12   114.95  3.000
 GDV  N4    C10  O1    122.35  3.000
 GDV  C12   C10  O1    122.70  3.000
 GDV  H123  C12  H122  108.58  3.000
 GDV  H123  C12  H121  108.68  3.000
 GDV  H122  C12  H121  107.36  3.000
 GDV  H123  C12  C10   113.59  3.000
 GDV  H122  C12  C10   109.11  3.000
 GDV  H121  C12  C10   109.32  3.000
 GDV  H4    N4   C2    117.52  3.000
 GDV  H4    N4   C10   118.68  3.000
 GDV  C2    N4   C10   122.40  3.000
 GDV  H2    C2   C1    107.08  3.000
 GDV  H2    C2   C3    109.11  3.000
 GDV  C1    C2   C3    108.35  3.000
 GDV  H2    C2   N4    107.48  3.000
 GDV  C1    C2   N4    110.68  3.000
 GDV  C3    C2   N4    113.92  3.000
 GDV  H3    C3   C4    109.05  3.000
 GDV  H3    C3   O3    106.40  3.000
 GDV  C4    C3   O3    111.98  3.000
 GDV  H3    C3   C2    109.21  3.000
 GDV  C4    C3   C2    108.87  3.000
 GDV  O3    C3   C2    111.26  3.000
 GDV  HA    O3   C3    109.82  3.000
 GDV  HB    C4   C5    109.26  3.000
 GDV  HB    C4   O4    111.32  3.000
 GDV  C5    C4   O4    105.02  3.000
 GDV  HB    C4   C3    107.27  3.000
 GDV  C5    C4   C3    112.33  3.000
 GDV  O4    C4   C3    111.68  3.000
 GDV  HC    O4   C4    108.91  3.000
 GDV  H5    C5   N1    106.95  3.000
 GDV  H5    C5   C6    108.76  3.000
 GDV  N1    C5   C6    109.96  3.000
 GDV  H5    C5   C4    108.37  3.000
 GDV  N1    C5   C4    109.78  3.000
 GDV  C6    C5   C4    112.83  3.000
 GDV  H6C2  C6   H6C1  106.44  3.000
 GDV  H6C2  C6   O5    107.79  3.000
 GDV  H6C1  C6   O5    113.14  3.000
 GDV  H6C2  C6   C5    109.27  3.000
 GDV  H6C1  C6   C5    107.59  3.000
 GDV  O5    C6   C5    112.40  3.000
 GDV  HD    O5   C6    109.37  3.000
 GDV  N2    C1   N1    108.13  3.000
 GDV  N2    C1   C2    126.81  3.000
 GDV  N1    C1   C2    125.06  3.000
 GDV  C7    N1   C1    108.96  3.000
 GDV  C7    N1   C5    126.10  3.000
 GDV  C1    N1   C5    124.90  3.000
 GDV  H7    C7   C8    129.73  3.000
 GDV  H7    C7   N1    122.94  3.000
 GDV  C8    C7   N1    107.32  3.000
 GDV  C9    C8   N2    128.94  3.000
 GDV  C9    C8   C7    125.03  3.000
 GDV  N2    C8   C7    106.03  3.000
 GDV  HE    N2   C8    128.00  3.000
 GDV  HE    N2   C1    122.42  3.000
 GDV  C8    N2   C1    109.56  3.000
 GDV  N3    C9   O2    125.73  3.000
 GDV  N3    C9   C8    116.16  3.000
 GDV  O2    C9   C8    118.10  3.000
 GDV  HF    N3   C11   113.27  3.000
 GDV  HF    N3   C9    118.01  3.000
 GDV  C11   N3   C9    128.72  3.000
 GDV  C13   C11  C17   119.43  3.000
 GDV  C13   C11  N3    116.12  3.000
 GDV  C17   C11  N3    124.45  3.000
 GDV  H17   C17  C16   119.45  3.000
 GDV  H17   C17  C11   121.24  3.000
 GDV  C16   C17  C11   119.32  3.000
 GDV  H16   C16  C15   119.99  3.000
 GDV  H16   C16  C17   118.67  3.000
 GDV  C15   C16  C17   121.35  3.000
 GDV  H15   C15  C14   120.42  3.000
 GDV  H15   C15  C16   120.50  3.000
 GDV  C14   C15  C16   119.09  3.000
 GDV  H14   C14  C13   119.37  3.000
 GDV  H14   C14  C15   120.33  3.000
 GDV  C13   C14  C15   120.30  3.000
 GDV  H13   C13  C14   119.63  3.000
 GDV  H13   C13  C11   119.86  3.000
 GDV  C14   C13  C11   120.51  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
 GDV  CONST_01  C8    C7   N1   C1     0.00   0.0  0
 GDV  CONST_02  C7    C8   N2   C1     0.00   0.0  0
 GDV  CONST_03  C8    N2   C1   N1     0.00   0.0  0
 GDV  CONST_04  N2    C8   C7   N1     0.00   0.0  0
 GDV  CONST_05  N2    C1   N1   C7     0.00   0.0  0
 GDV  CONST_06  C15   C16  C17  C11    0.00   0.0  0
 GDV  CONST_07  C15   C14  C13  C11    0.00   0.0  0
 GDV  CONST_08  C14   C13  C11  C17    0.00   0.0  0
 GDV  CONST_09  C14   C15  C16  C17    0.00   0.0  0
 GDV  CONST_10  C13   C11  C17  C16    0.00   0.0  0
 GDV  CONST_11  C13   C14  C15  C16    0.00   0.0  0
 GDV  CONST_12  C9    C8   N2   C1   180.00   0.0  0
 GDV  CONST_13  C9    C8   C7   N1   180.00   0.0  0
 GDV  CONST_14  C16   C17  C11  N3   180.00   0.0  0
 GDV  CONST_15  C14   C13  C11  N3   180.00   0.0  0
 GDV  CONST_16  HE    N2   C1   C2     0.00   0.0  0
 GDV  CONST_17  H7    C7   N1   C5     0.00   0.0  0
 GDV  CONST_18  H16   C16  C17  C11  180.00   0.0  0
 GDV  CONST_19  H14   C14  C13  C11  180.00   0.0  0
 GDV  CONST_20  H13   C13  C11  C17  180.00   0.0  0
 GDV  CONST_21  H15   C15  C16  C17  180.00   0.0  0
 GDV  CONST_22  H17   C17  C16  C15  180.00   0.0  0
 GDV  CONST_23  C11   N3   C9   C8   180.00   0.0  0
 GDV  CONST_24  C17   C11  N3   C9     0.00   0.0  0
 GDV  CONST_25  C13   C11  N3   C9   180.00   0.0  0
 GDV  CONST_26  HF    N3   C11  C17  180.00   0.0  0
 GDV  CONST_27  C2    N4   C10  O1     0.00   0.0  0
 GDV  CONST_28  C2    N4   C10  C12  180.00   0.0  0
 GDV  CONST_29  C11   N3   C9   O2     0.00   0.0  0
 GDV  CONST_30  H4    N4   C10  O1   180.00   0.0  0
 GDV  Var_01    O2    C9   C8   C7     8.35  30.0  2
 GDV  Var_02    H121  C12  C10  O1   -55.06  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
 GDV  chir_01  C2  N4  C3  C1  positiv
 GDV  chir_02  C3  O3  C2  C4  positiv
 GDV  chir_03  C4  O4  C5  C3  positiv
 GDV  chir_04  C5  N1  C4  C6  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
 GDV  plan-1  N3   0.020
 GDV  plan-1  C11  0.020
 GDV  plan-1  C17  0.020
 GDV  plan-1  C16  0.020
 GDV  plan-1  C15  0.020
 GDV  plan-1  C14  0.020
 GDV  plan-1  C13  0.020
 GDV  plan-1  H17  0.020
 GDV  plan-1  H16  0.020
 GDV  plan-1  H15  0.020
 GDV  plan-1  H14  0.020
 GDV  plan-1  H13  0.020
 GDV  plan-2  C2   0.020
 GDV  plan-2  C5   0.020
 GDV  plan-2  C1   0.020
 GDV  plan-2  N1   0.020
 GDV  plan-2  C7   0.020
 GDV  plan-2  C8   0.020
 GDV  plan-2  N2   0.020
 GDV  plan-2  C9   0.020
 GDV  plan-2  H7   0.020
 GDV  plan-2  HE   0.020
 GDV  plan-3  O1   0.020
 GDV  plan-3  C10  0.020
 GDV  plan-3  C12  0.020
 GDV  plan-3  N4   0.020
 GDV  plan-3  C2   0.020
 GDV  plan-3  H4   0.020
 GDV  plan-4  C8   0.020
 GDV  plan-4  C9   0.020
 GDV  plan-4  O2   0.020
 GDV  plan-4  N3   0.020
 GDV  plan-4  C11  0.020
 GDV  plan-4  HF   0.020

