# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 01:10:15 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: N-[(cyclopropylamino)(oxo)acetyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)C(=O)NC2CC2)[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
 8GP  8GP  N-[(cyclopropylamino)(oxo)acetyl]-beta-D-glucopyranosylamine  D-saccharide  38  20  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8GP
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
 8GP  C1    C  CH1   0   0.218  -0.8312  -0.3578  -0.3001
 8GP  C2    C  CH1   0  -0.039  -1.6824  -1.4920   0.2747
 8GP  O2    O  OH1   0  -0.662  -1.2956  -2.7371  -0.2481
 8GP  C3    C  CH1   0  -0.002  -3.1386  -1.2665  -0.1066
 8GP  O3    O  OH1   0  -0.671  -3.9887  -2.2003   0.5114
 8GP  C4    C  CH1   0   0.035  -3.5921   0.1271   0.3088
 8GP  O4    O  OH1   0  -0.671  -4.8832   0.4100  -0.1696
 8GP  C5    C  CH1   0  -0.018  -2.6310   1.1646  -0.2754
 8GP  O5    O  O2    0  -0.486  -1.3114   0.8846   0.1492
 8GP  C6    C  CH2   0  -0.157  -2.9724   2.5695   0.1729
 8GP  O6    O  OH1   0  -0.670  -2.1098   3.4736  -0.4745
 8GP  N1    N  NH1   0  -0.679   0.5241  -0.4926   0.1257
 8GP  C7    C  C     0   0.460   1.5844  -0.2150  -0.6435
 8GP  O7    O  O     0  -0.455   1.5497   0.1452  -1.8048
 8GP  C8    C  C     0   0.450   2.9177  -0.4229   0.0974
 8GP  O8    O  O     0  -0.465   2.9394  -0.7904   1.2602
 8GP  N2    N  NH1   0  -0.629   3.9825  -0.1625  -0.6568
 8GP  C9    C  CH1   0  -0.082   5.3186  -0.3301  -0.1872
 8GP  C10   C  CH2   0  -0.509   6.3253   0.7067  -0.5632
 8GP  C11   C  CH2   0  -0.484   5.8498   0.6030   0.8531
 8GP  H1    H  HCH1  0   0.237  -0.8592  -0.4081  -1.3962
 8GP  H2    H  HCH1  0   0.235  -1.5964  -1.4712   1.3718
 8GP  HO2   H  HOH1  0   0.459  -0.5219  -3.0546   0.2270
 8GP  H3    H  HCH1  0   0.217  -3.2164  -1.3307  -1.2050
 8GP  HO3   H  HOH1  0   0.456  -3.7561  -3.0793   0.1938
 8GP  H4    H  HCH1  0   0.214  -3.5521   0.1973   1.4077
 8GP  HO4   H  HOH1  0   0.456  -5.4891  -0.2460   0.1902
 8GP  H5    H  HCH1  0   0.226  -2.6905   1.1128  -1.3751
 8GP  H61   H  HCH2  0   0.197  -2.8793   2.6261   1.2666
 8GP  H62   H  HCH2  0   0.215  -4.0213   2.7635  -0.0722
 8GP  HO6   H  HOH1  0   0.457  -2.3763   4.3642  -0.2303
 8GP  HN1   H  HNH1  0   0.414   0.7077  -0.7278   1.0924
 8GP  HN2   H  HNH1  0   0.412   3.8285   0.0802  -1.6244
 8GP  H9    H  HCH1  0   0.278   5.6575  -1.3605  -0.1463
 8GP  H101  H  HCH2  0   0.263   7.3240   0.3702  -0.8063
 8GP  H102  H  HCH2  0   0.262   5.9819   1.5527  -1.1456
 8GP  H111  H  HCH2  0   0.260   5.1895   1.3777   1.2204
 8GP  H112  H  HCH2  0   0.260   6.5170   0.1894   1.5977

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
 8GP  C1   C2    single  1.530  0.020  1.530
 8GP  C1   O5    single  1.406  0.020  1.406
 8GP  C1   N1    single  1.427  0.020  1.427
 8GP  C1   H1    single  0.970  0.020  1.090
 8GP  C2   O2    single  1.405  0.020  1.405
 8GP  C2   C3    single  1.522  0.020  1.522
 8GP  C2   H2    single  0.970  0.020  1.090
 8GP  O2   HO2   single  0.850  0.020  0.980
 8GP  C3   O3    single  1.406  0.020  1.406
 8GP  C3   C4    single  1.523  0.020  1.523
 8GP  C3   H3    single  0.970  0.020  1.090
 8GP  O3   HO3   single  0.850  0.020  0.980
 8GP  C4   O4    single  1.406  0.020  1.406
 8GP  C4   C5    single  1.530  0.020  1.530
 8GP  C4   H4    single  0.970  0.020  1.090
 8GP  O4   HO4   single  0.850  0.020  0.980
 8GP  C5   O5    single  1.414  0.020  1.414
 8GP  C5   C6    single  1.514  0.020  1.514
 8GP  C5   H5    single  0.970  0.020  1.090
 8GP  C6   O6    single  1.407  0.020  1.407
 8GP  C6   H61   single  0.970  0.020  1.090
 8GP  C6   H62   single  0.970  0.020  1.090
 8GP  O6   HO6   single  0.850  0.020  0.980
 8GP  N1   C7    single  1.339  0.020  1.339
 8GP  N1   HN1   single  0.860  0.020  1.020
 8GP  C7   O7    double  1.216  0.020  1.216
 8GP  C7   C8    single  1.539  0.020  1.539
 8GP  C8   O8    double  1.220  0.020  1.220
 8GP  C8   N2    single  1.331  0.020  1.331
 8GP  N2   C9    single  1.426  0.020  1.426
 8GP  N2   HN2   single  0.860  0.020  1.020
 8GP  C9   C10   single  1.493  0.020  1.493
 8GP  C9   C11   single  1.495  0.020  1.495
 8GP  C9   H9    single  0.970  0.020  1.090
 8GP  C10  C11   single  1.498  0.020  1.498
 8GP  C10  H101  single  0.970  0.020  1.090
 8GP  C10  H102  single  0.970  0.020  1.090
 8GP  C11  H111  single  0.970  0.020  1.090
 8GP  C11  H112  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
 8GP  H1    C1   N1    108.53  3.000
 8GP  H1    C1   O5    110.55  3.000
 8GP  N1    C1   O5    108.22  3.000
 8GP  H1    C1   C2    109.08  3.000
 8GP  N1    C1   C2    110.25  3.000
 8GP  O5    C1   C2    110.19  3.000
 8GP  H2    C2   C3    108.76  3.000
 8GP  H2    C2   O2    111.48  3.000
 8GP  C3    C2   O2    107.55  3.000
 8GP  H2    C2   C1    108.48  3.000
 8GP  C3    C2   C1    109.16  3.000
 8GP  O2    C2   C1    111.35  3.000
 8GP  HO2   O2   C2    109.29  3.000
 8GP  H3    C3   C4    107.69  3.000
 8GP  H3    C3   O3    110.88  3.000
 8GP  C4    C3   O3    107.92  3.000
 8GP  H3    C3   C2    107.96  3.000
 8GP  C4    C3   C2    110.61  3.000
 8GP  O3    C3   C2    111.71  3.000
 8GP  HO3   O3   C3    108.37  3.000
 8GP  H4    C4   C5    108.35  3.000
 8GP  H4    C4   O4    111.10  3.000
 8GP  C5    C4   O4    108.09  3.000
 8GP  H4    C4   C3    108.63  3.000
 8GP  C5    C4   C3    109.22  3.000
 8GP  O4    C4   C3    111.39  3.000
 8GP  HO4   O4   C4    108.28  3.000
 8GP  H5    C5   C6    109.07  3.000
 8GP  H5    C5   O5    109.91  3.000
 8GP  C6    C5   O5    107.78  3.000
 8GP  H5    C5   C4    108.37  3.000
 8GP  C6    C5   C4    112.00  3.000
 8GP  O5    C5   C4    109.71  3.000
 8GP  C5    O5   C1    113.44  3.000
 8GP  H62   C6   H61   107.14  3.000
 8GP  H62   C6   O6    111.75  3.000
 8GP  H61   C6   O6    111.89  3.000
 8GP  H62   C6   C5    108.32  3.000
 8GP  H61   C6   C5    108.86  3.000
 8GP  O6    C6   C5    108.77  3.000
 8GP  HO6   O6   C6    107.96  3.000
 8GP  HN1   N1   C7    116.96  3.000
 8GP  HN1   N1   C1    118.65  3.000
 8GP  C7    N1   C1    124.13  3.000
 8GP  C8    C7   O7    121.62  3.000
 8GP  C8    C7   N1    112.42  3.000
 8GP  O7    C7   N1    125.96  3.000
 8GP  N2    C8   O8    125.81  3.000
 8GP  N2    C8   C7    113.19  3.000
 8GP  O8    C8   C7    120.99  3.000
 8GP  HN2   N2   C9    119.13  3.000
 8GP  HN2   N2   C8    117.93  3.000
 8GP  C9    N2   C8    122.69  3.000
 8GP  H9    C9   C11   117.08  3.000
 8GP  H9    C9   C10   117.27  3.000
 8GP  C11   C9   C10    60.15  3.000
 8GP  H9    C9   N2    114.62  3.000
 8GP  C11   C9   N2    119.25  3.000
 8GP  C10   C9   N2    117.84  3.000
 8GP  H102  C10  H101  114.52  3.000
 8GP  H102  C10  C11   117.52  3.000
 8GP  H101  C10  C11   118.96  3.000
 8GP  H102  C10  C9    117.65  3.000
 8GP  H101  C10  C9    117.58  3.000
 8GP  C11   C10  C9     59.98  3.000
 8GP  H112  C11  H111  114.60  3.000
 8GP  H112  C11  C10   118.78  3.000
 8GP  H111  C11  C10   117.72  3.000
 8GP  H112  C11  C9    117.35  3.000
 8GP  H111  C11  C9    117.79  3.000
 8GP  C10   C11  C9     59.87  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
 8GP  CONST_01  O7    C7   N1   C1     0.00   0.0  0
 8GP  CONST_02  C8    C7   N1   C1   180.00   0.0  0
 8GP  CONST_03  C9    N2   C8   C7   180.00   0.0  0
 8GP  CONST_04  C9    N2   C8   O8     0.00   0.0  0
 8GP  CONST_05  N2    C8   C7   N1   180.00   0.0  0
 8GP  CONST_06  N2    C8   C7   O7     0.00   0.0  0
 8GP  CONST_07  HN2   N2   C8   C7     0.00   0.0  0
 8GP  CONST_08  HN1   N1   C7   O7   180.00   0.0  0
 8GP  Var_01    C11   C10  C9   N2   109.51  30.0  1
 8GP  Var_02    H111  C11  C10  C9  -107.70  30.0  1
 8GP  Var_03    C10   C9   N2   C8  -139.50  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
 8GP  chir_01  C1  C2  O5   N1   negativ
 8GP  chir_02  C2  O2  C1   C3   negativ
 8GP  chir_03  C3  O3  C2   C4   positiv
 8GP  chir_04  C4  O4  C5   C3   positiv
 8GP  chir_05  C5  O5  C4   C6   negativ
 8GP  chir_06  C9  N2  C10  C11  both

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
 8GP  plan-1  C1   0.020
 8GP  plan-1  N1   0.020
 8GP  plan-1  C7   0.020
 8GP  plan-1  O7   0.020
 8GP  plan-1  C8   0.020
 8GP  plan-1  O8   0.020
 8GP  plan-1  N2   0.020
 8GP  plan-1  C9   0.020
 8GP  plan-1  HN1  0.020
 8GP  plan-1  HN2  0.020

