# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 21:38:05 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-deoxy-2-{[(2-methylphenyl)carbonyl]amino}-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1C(=O)N[C@H]2[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]2O
#
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
 OTG  OTG  2-deoxy-2-{[(2-methylphenyl)carbonyl]amino}-alpha-D-glucopyranose  D-saccharide  40  21  .  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_OTG
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
 OTG  C1    C  CH1   0   0.294   0.7458  -1.3222  -1.5867
 OTG  O1    O  OH1   0  -0.676  -0.3184  -2.1939  -1.3737
 OTG  C2    C  CH1   0  -0.162   0.5003  -0.0661  -0.7509
 OTG  N2    N  NH1   0  -0.687   0.3090  -0.4046   0.6356
 OTG  C3    C  CH1   0   0.015  -0.6803   0.7258  -1.3064
 OTG  O3    O  OH1   0  -0.649  -0.8039   1.9047  -0.5545
 OTG  C4    C  CH1   0   0.007  -0.4415   1.0139  -2.7849
 OTG  O4    O  OH1   0  -0.702  -1.5914   1.6653  -3.2808
 OTG  C5    C  CH1   0  -0.050  -0.1716  -0.2942  -3.5365
 OTG  O5    O  O2    0  -0.505   0.9120  -0.9853  -2.9338
 OTG  C6    C  CH2   0  -0.182   0.2042  -0.0454  -4.9811
 OTG  O6    O  OH1   0  -0.661   0.3431  -1.2815  -5.6392
 OTG  C1'   C  CR6   0   0.056  -0.0793   0.7190   3.9132
 OTG  C2'   C  CR6   0  -0.163   0.4635  -0.2025   3.0100
 OTG  C3'   C  CR16  0  -0.209   0.6378  -1.5341   3.3742
 OTG  C4'   C  CR16  0  -0.265   0.2961  -1.9675   4.6473
 OTG  C5'   C  CR16  0  -0.196  -0.2410  -1.0638   5.5515
 OTG  C6'   C  CR16  0  -0.242  -0.4314   0.2604   5.1796
 OTG  C8'   C  C     0   0.539   0.9005   0.2488   1.6517
 OTG  O8'   O  O     0  -0.432   1.7391   1.1250   1.5092
 OTG  H1    H  HCH1  0   0.262   1.6968  -1.7756  -1.2873
 OTG  HO1   H  HOH1  0   0.469  -0.0757  -3.0747  -1.6787
 OTG  H2    H  HCH1  0   0.309   1.3982   0.5521  -0.8179
 OTG  HN2   H  HNH1  0   0.418  -0.4313  -1.0539   0.8546
 OTG  H3    H  HCH1  0   0.211  -1.5929   0.1142  -1.2242
 OTG  HO3   H  HOH1  0   0.437  -1.5640   2.3897  -0.8926
 OTG  H4    H  HCH1  0   0.262   0.4442   1.6599  -2.8698
 OTG  HO4   H  HOH1  0   0.439  -1.3282   2.3151  -3.9377
 OTG  H5    H  HCH1  0   0.240  -1.0842  -0.9062  -3.5098
 OTG  H61   H  HCH2  0   0.174  -0.5813   0.5656  -5.4404
 OTG  H62   H  HCH2  0   0.245   1.1323   0.5428  -5.0135
 OTG  HO6   H  HOH1  0   0.449   0.5296  -1.1052  -6.5655
 OTG  H3'   H  HCR6  0   0.263   1.0573  -2.2364   2.6637
 OTG  H4'   H  HCR6  0   0.202   0.4450  -3.0024   4.9256
 OTG  H5'   H  HCR6  0   0.246  -0.5204  -1.3873   6.5457
 OTG  H6'   H  HCR6  0   0.261  -0.8680   0.9554   5.8871
 OTG  H7'1  H  HCH3  0   0.254   0.6193   2.7300   3.5706
 OTG  H7'2  H  HCH3  0   0.245  -0.7216   2.2618   2.5406
 OTG  H7'3  H  HCH3  0   0.186  -1.0032   2.6236   4.2410
 OTG  C7'   C  CH3   0  -0.701  -0.3083   2.1572   3.5443

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
 OTG  C1   O1    single    1.392  0.020  1.392
 OTG  C1   C2    single    1.529  0.020  1.529
 OTG  C1   O5    single    1.399  0.020  1.399
 OTG  C1   H1    single    0.970  0.020  1.090
 OTG  O1   HO1   single    0.850  0.020  0.980
 OTG  C2   N2    single    1.440  0.020  1.440
 OTG  C2   C3    single    1.526  0.020  1.526
 OTG  C2   H2    single    0.970  0.020  1.090
 OTG  N2   C8'   single    1.345  0.020  1.345
 OTG  N2   HN2   single    0.860  0.020  1.020
 OTG  C3   O3    single    1.404  0.020  1.404
 OTG  C3   C4    single    1.525  0.020  1.525
 OTG  C3   H3    single    0.970  0.020  1.090
 OTG  O3   HO3   single    0.850  0.020  0.980
 OTG  C4   O4    single    1.412  0.020  1.412
 OTG  C4   C5    single    1.533  0.020  1.533
 OTG  C4   H4    single    0.970  0.020  1.090
 OTG  O4   HO4   single    0.850  0.020  0.980
 OTG  C5   O5    single    1.419  0.020  1.419
 OTG  C5   C6    single    1.513  0.020  1.513
 OTG  C5   H5    single    0.970  0.020  1.090
 OTG  C6   O6    single    1.407  0.020  1.407
 OTG  C6   H61   single    0.970  0.020  1.090
 OTG  C6   H62   single    0.970  0.020  1.090
 OTG  O6   HO6   single    0.850  0.020  0.980
 OTG  C1'  C2'   aromatic  1.400  0.020  1.400
 OTG  C1'  C6'   aromatic  1.392  0.020  1.392
 OTG  C1'  C7'   single    1.502  0.020  1.502
 OTG  C2'  C3'   aromatic  1.391  0.020  1.391
 OTG  C2'  C8'   single    1.497  0.020  1.497
 OTG  C3'  C4'   aromatic  1.388  0.020  1.388
 OTG  C3'  H3'   single    0.930  0.020  1.080
 OTG  C4'  C5'   aromatic  1.387  0.020  1.387
 OTG  C4'  H4'   single    0.930  0.020  1.080
 OTG  C5'  C6'   aromatic  1.389  0.020  1.389
 OTG  C5'  H5'   single    0.930  0.020  1.080
 OTG  C6'  H6'   single    0.930  0.020  1.080
 OTG  C7'  H7'1  single    0.970  0.020  1.090
 OTG  C7'  H7'2  single    0.970  0.020  1.090
 OTG  C7'  H7'3  single    0.970  0.020  1.090
 OTG  C8'  O8'   double    1.221  0.020  1.221

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
 OTG  H1    C1   O5    105.06  3.000
 OTG  H1    C1   C2    109.28  3.000
 OTG  O5    C1   C2    110.36  3.000
 OTG  H1    C1   O1    111.27  3.000
 OTG  O5    C1   O1    112.90  3.000
 OTG  C2    C1   O1    107.95  3.000
 OTG  HO1   O1   C1    109.36  3.000
 OTG  H2    C2   C3    108.65  3.000
 OTG  H2    C2   N2    107.54  3.000
 OTG  C3    C2   N2    111.69  3.000
 OTG  H2    C2   C1    107.43  3.000
 OTG  C3    C2   C1    110.58  3.000
 OTG  N2    C2   C1    110.77  3.000
 OTG  HN2   N2   C8'   118.13  3.000
 OTG  HN2   N2   C2    117.25  3.000
 OTG  C8'   N2   C2    123.69  3.000
 OTG  H3    C3   C4    107.87  3.000
 OTG  H3    C3   O3    110.69  3.000
 OTG  C4    C3   O3    111.99  3.000
 OTG  H3    C3   C2    109.00  3.000
 OTG  C4    C3   C2    109.25  3.000
 OTG  O3    C3   C2    108.00  3.000
 OTG  HO3   O3   C3    107.73  3.000
 OTG  H4    C4   C5    108.77  3.000
 OTG  H4    C4   O4    110.97  3.000
 OTG  C5    C4   O4    111.41  3.000
 OTG  H4    C4   C3    108.18  3.000
 OTG  C5    C4   C3    109.98  3.000
 OTG  O4    C4   C3    107.47  3.000
 OTG  HO4   O4   C4    109.22  3.000
 OTG  H5    C5   C6    108.72  3.000
 OTG  H5    C5   O5    110.63  3.000
 OTG  C6    C5   O5    107.20  3.000
 OTG  H5    C5   C4    108.49  3.000
 OTG  C6    C5   C4    111.81  3.000
 OTG  O5    C5   C4    109.98  3.000
 OTG  C5    O5   C1    115.82  3.000
 OTG  H62   C6   H61   107.12  3.000
 OTG  H62   C6   O6    111.90  3.000
 OTG  H61   C6   O6    111.38  3.000
 OTG  H62   C6   C5    109.01  3.000
 OTG  H61   C6   C5    108.28  3.000
 OTG  O6    C6   C5    109.05  3.000
 OTG  HO6   O6   C6    107.98  3.000
 OTG  C7'   C1'  C6'   120.01  3.000
 OTG  C7'   C1'  C2'   122.07  3.000
 OTG  C6'   C1'  C2'   117.92  3.000
 OTG  C8'   C2'  C3'   119.31  3.000
 OTG  C8'   C2'  C1'   120.02  3.000
 OTG  C3'   C2'  C1'   120.64  3.000
 OTG  H3'   C3'  C4'   119.64  3.000
 OTG  H3'   C3'  C2'   119.81  3.000
 OTG  C4'   C3'  C2'   120.54  3.000
 OTG  H4'   C4'  C5'   120.60  3.000
 OTG  H4'   C4'  C3'   120.06  3.000
 OTG  C5'   C4'  C3'   119.35  3.000
 OTG  H5'   C5'  C6'   119.71  3.000
 OTG  H5'   C5'  C4'   120.28  3.000
 OTG  C6'   C5'  C4'   120.00  3.000
 OTG  H6'   C6'  C5'   119.48  3.000
 OTG  H6'   C6'  C1'   118.99  3.000
 OTG  C5'   C6'  C1'   121.54  3.000
 OTG  O8'   C8'  C2'   121.52  3.000
 OTG  O8'   C8'  N2    124.22  3.000
 OTG  C2'   C8'  N2    114.25  3.000
 OTG  H7'3  C7'  H7'2  107.81  3.000
 OTG  H7'3  C7'  H7'1  107.60  3.000
 OTG  H7'2  C7'  H7'1  107.11  3.000
 OTG  H7'3  C7'  C1'   110.50  3.000
 OTG  H7'2  C7'  C1'   112.06  3.000
 OTG  H7'1  C7'  C1'   111.55  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
 OTG  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 OTG  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 OTG  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 OTG  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 OTG  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 OTG  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 OTG  CONST_07  C7'   C1'  C2'  C3'   180.00   0.0  0
 OTG  CONST_08  C8'   C2'  C3'  C4'   180.00   0.0  0
 OTG  CONST_09  C7'   C1'  C6'  C5'   180.00   0.0  0
 OTG  CONST_10  C8'   C2'  C1'  C6'   180.00   0.0  0
 OTG  CONST_11  H3'   C3'  C2'  C1'   180.00   0.0  0
 OTG  CONST_12  H5'   C5'  C6'  C1'   180.00   0.0  0
 OTG  CONST_13  H6'   C6'  C1'  C2'   180.00   0.0  0
 OTG  CONST_14  H4'   C4'  C3'  C2'   180.00   0.0  0
 OTG  CONST_15  C2'   C8'  N2   C2    180.00   0.0  0
 OTG  CONST_16  O8'   C8'  N2   C2      0.00   0.0  0
 OTG  CONST_17  HN2   N2   C8'  C2'     0.00   0.0  0
 OTG  Var_01    C1'   C2'  C8'  N2   -123.10  30.0  2
 OTG  Var_02    H7'1  C7'  C1'  C2'   -78.03  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
 OTG  chir_01  C1  O1  C2  O5  positiv
 OTG  chir_02  C2  N2  C3  C1  positiv
 OTG  chir_03  C3  O3  C2  C4  positiv
 OTG  chir_04  C4  O4  C5  C3  positiv
 OTG  chir_05  C5  O5  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
 OTG  plan-1  C1'  0.020
 OTG  plan-1  C2'  0.020
 OTG  plan-1  C3'  0.020
 OTG  plan-1  C4'  0.020
 OTG  plan-1  C5'  0.020
 OTG  plan-1  C6'  0.020
 OTG  plan-1  C8'  0.020
 OTG  plan-1  H3'  0.020
 OTG  plan-1  H4'  0.020
 OTG  plan-1  H5'  0.020
 OTG  plan-1  H6'  0.020
 OTG  plan-1  C7'  0.020
 OTG  plan-2  C2   0.020
 OTG  plan-2  N2   0.020
 OTG  plan-2  C2'  0.020
 OTG  plan-2  C8'  0.020
 OTG  plan-2  O8'  0.020
 OTG  plan-2  HN2  0.020

