# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:37:49 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: methyl 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@H](C)C(O)=O)[C@H]1NC(C)=O
#
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
 MMR  MMR  'methyl 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside'  ligand  41  21  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MMR
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
 MMR  C1    C  CH1    0   0.344  -1.7733  -1.0727   0.3352
 MMR  O1    O  O2     0  -0.485  -2.0747  -2.3497  -0.0721
 MMR  C2    C  CH1    0  -0.146  -0.3669  -0.7123  -0.1380
 MMR  N2    N  NH1    0  -0.628   0.6237  -1.5855   0.4301
 MMR  C3    C  CH1    0   0.040  -0.0567   0.7472   0.2200
 MMR  O3    O  O2     0  -0.495   1.1656   1.1260  -0.3367
 MMR  C4    C  CH1    0   0.012  -1.1584   1.6763  -0.2776
 MMR  O4    O  OH1    0  -0.664  -0.9132   2.9601   0.2438
 MMR  C5    C  CH1    0  -0.018  -2.5259   1.1516   0.1827
 MMR  O5    O  O2     0  -0.496  -2.6978  -0.1852  -0.2370
 MMR  C6    C  CH2    0  -0.162  -3.6658   1.9657  -0.3884
 MMR  O6    O  OH1    0  -0.668  -4.8772   1.5091   0.1636
 MMR  C7    C  CH3    0  -0.410  -3.2251  -2.9055   0.5345
 MMR  C8    C  C      0   0.524   1.4089  -2.4202  -0.2802
 MMR  O8    O  O      0  -0.500   1.2985  -2.5859  -1.4852
 MMR  C9    C  CH3    0  -0.797   2.4661  -3.1202   0.5380
 MMR  C10   C  CH1    0  -0.073   2.2862   1.1566   0.5306
 MMR  C11   C  C      0   0.402   3.4846   0.4176  -0.0952
 MMR  O11   O  O      0  -0.602   3.4726   0.2177  -1.3206
 MMR  C12   C  CH3    0  -0.667   2.6509   2.6034   0.8432
 MMR  O12   O  OC    -1  -0.630   4.3909   0.1166   0.7107
 MMR  H1    H  HCH1   0   0.177  -1.8277  -0.9911   1.4396
 MMR  H2    H  HCH1   0   0.265  -0.3331  -0.8248  -1.2245
 MMR  HN2   H  HNH1   0   0.397   0.7833  -1.5240   1.4239
 MMR  H3    H  HCH1   0   0.213  -0.0325   0.8337   1.3198
 MMR  H4    H  HCH1   0   0.223  -1.1381   1.6805  -1.3771
 MMR  HO4   H  HOH1   0   0.459  -1.1882   3.6184  -0.3999
 MMR  H5    H  HCH1   0   0.218  -2.5638   1.2139   1.2836
 MMR  H6    H  HCH2   0   0.205  -3.4906   3.0208  -0.1514
 MMR  H6A   H  HCH2   0   0.198  -3.6546   1.8756  -1.4840
 MMR  HO6   H  HOH1   0   0.456  -5.5769   2.1002  -0.1274
 MMR  H7    H  HCH3   0   0.212  -3.1887  -2.8102   1.6248
 MMR  H7A   H  HCH3   0   0.219  -4.1485  -2.4431   0.1784
 MMR  H7B   H  HCH3   0   0.238  -3.2468  -3.9639   0.2814
 MMR  H9    H  HCH3   0   0.250   2.1298  -3.3418   1.5504
 MMR  H9A   H  HCH3   0   0.257   2.7657  -4.0466   0.0541
 MMR  H9B   H  HCH3   0   0.274   3.3432  -2.4750   0.6158
 MMR  H10   H  HCH1   0   0.197   2.0400   0.6566   1.4750
 MMR  H12   H  HCH3   0   0.227   1.8042   3.1269   1.2885
 MMR  H12A  H  HCH3   0   0.218   3.4870   2.6481   1.5403
 MMR  H12B  H  HCH3   0   0.216   2.9384   3.1394  -0.0638

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
 MMR  C1   O1    single  1.374  0.020  1.374
 MMR  C1   C2    single  1.527  0.020  1.527
 MMR  C1   O5    single  1.404  0.020  1.404
 MMR  O1   C7    single  1.414  0.020  1.414
 MMR  C2   N2    single  1.438  0.020  1.438
 MMR  C2   C3    single  1.534  0.020  1.534
 MMR  N2   C8    single  1.348  0.020  1.348
 MMR  C3   O3    single  1.395  0.020  1.395
 MMR  C3   C4    single  1.525  0.020  1.525
 MMR  O3   C10   single  1.417  0.020  1.417
 MMR  C4   O4    single  1.407  0.020  1.407
 MMR  C4   C5    single  1.535  0.020  1.535
 MMR  C5   O5    single  1.412  0.020  1.412
 MMR  C5   C6    single  1.513  0.020  1.513
 MMR  C6   O6    single  1.407  0.020  1.407
 MMR  C8   O8    double  1.221  0.020  1.221
 MMR  C8   C9    single  1.509  0.020  1.509
 MMR  C10  C11   single  1.541  0.020  1.541
 MMR  C10  C12   single  1.524  0.020  1.524
 MMR  C11  O11   deloc   1.242  0.020  1.242
 MMR  C11  O12   deloc   1.250  0.020  1.250
 MMR  C1   H1    single  0.970  0.020  1.090
 MMR  C2   H2    single  0.970  0.020  1.090
 MMR  N2   HN2   single  0.860  0.020  1.020
 MMR  C3   H3    single  0.970  0.020  1.090
 MMR  C4   H4    single  0.970  0.020  1.090
 MMR  O4   HO4   single  0.850  0.020  0.980
 MMR  C5   H5    single  0.970  0.020  1.090
 MMR  C6   H6    single  0.970  0.020  1.090
 MMR  C6   H6A   single  0.970  0.020  1.090
 MMR  O6   HO6   single  0.850  0.020  0.980
 MMR  C7   H7    single  0.970  0.020  1.090
 MMR  C7   H7A   single  0.970  0.020  1.090
 MMR  C7   H7B   single  0.970  0.020  1.090
 MMR  C9   H9    single  0.970  0.020  1.090
 MMR  C9   H9A   single  0.970  0.020  1.090
 MMR  C9   H9B   single  0.970  0.020  1.090
 MMR  C10  H10   single  0.970  0.020  1.090
 MMR  C12  H12   single  0.970  0.020  1.090
 MMR  C12  H12A  single  0.970  0.020  1.090
 MMR  C12  H12B  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
 MMR  H1    C1   O5    109.10  3.000
 MMR  H1    C1   C2    109.67  3.000
 MMR  O5    C1   C2    109.33  3.000
 MMR  H1    C1   O1    110.67  3.000
 MMR  O5    C1   O1    108.81  3.000
 MMR  C2    C1   O1    109.24  3.000
 MMR  C7    O1   C1    114.62  3.000
 MMR  H2    C2   C3    108.89  3.000
 MMR  H2    C2   N2    108.01  3.000
 MMR  C3    C2   N2    110.26  3.000
 MMR  H2    C2   C1    108.20  3.000
 MMR  C3    C2   C1    109.78  3.000
 MMR  N2    C2   C1    111.64  3.000
 MMR  HN2   N2   C8    117.70  3.000
 MMR  HN2   N2   C2    117.49  3.000
 MMR  C8    N2   C2    124.69  3.000
 MMR  H3    C3   C4    107.06  3.000
 MMR  H3    C3   O3    110.92  3.000
 MMR  C4    C3   O3    109.71  3.000
 MMR  H3    C3   C2    108.16  3.000
 MMR  C4    C3   C2    110.94  3.000
 MMR  O3    C3   C2    110.01  3.000
 MMR  C10   O3   C3    117.01  3.000
 MMR  H4    C4   C5    108.51  3.000
 MMR  H4    C4   O4    111.33  3.000
 MMR  C5    C4   O4    110.85  3.000
 MMR  H4    C4   C3    108.38  3.000
 MMR  C5    C4   C3    109.72  3.000
 MMR  O4    C4   C3    108.00  3.000
 MMR  HO4   O4   C4    109.08  3.000
 MMR  H5    C5   C6    108.69  3.000
 MMR  H5    C5   O5    110.24  3.000
 MMR  C6    C5   O5    107.80  3.000
 MMR  H5    C5   C4    108.09  3.000
 MMR  C6    C5   C4    111.96  3.000
 MMR  O5    C5   C4    110.05  3.000
 MMR  C5    O5   C1    113.42  3.000
 MMR  H6A   C6   H6    107.03  3.000
 MMR  H6A   C6   O6    111.91  3.000
 MMR  H6    C6   O6    111.43  3.000
 MMR  H6A   C6   C5    108.93  3.000
 MMR  H6    C6   C5    108.43  3.000
 MMR  O6    C6   C5    109.02  3.000
 MMR  HO6   O6   C6    107.96  3.000
 MMR  H7B   C7   H7A   108.60  3.000
 MMR  H7B   C7   H7    108.47  3.000
 MMR  H7A   C7   H7    108.41  3.000
 MMR  H7B   C7   O1    107.37  3.000
 MMR  H7A   C7   O1    112.42  3.000
 MMR  H7    C7   O1    111.46  3.000
 MMR  C9    C8   O8    122.37  3.000
 MMR  C9    C8   N2    114.18  3.000
 MMR  O8    C8   N2    123.44  3.000
 MMR  H9B   C9   H9A   108.29  3.000
 MMR  H9B   C9   H9    107.57  3.000
 MMR  H9A   C9   H9    108.98  3.000
 MMR  H9B   C9   C8    109.11  3.000
 MMR  H9A   C9   C8    110.30  3.000
 MMR  H9    C9   C8    112.46  3.000
 MMR  H10   C10  C12   108.05  3.000
 MMR  H10   C10  C11   107.81  3.000
 MMR  C12   C10  C11   110.63  3.000
 MMR  H10   C10  O3    109.86  3.000
 MMR  C12   C10  O3    109.58  3.000
 MMR  C11   C10  O3    110.86  3.000
 MMR  O12   C11  O11   127.20  3.000
 MMR  O12   C11  C10   114.69  3.000
 MMR  O11   C11  C10   118.07  3.000
 MMR  H12B  C12  H12A  108.01  3.000
 MMR  H12B  C12  H12   107.93  3.000
 MMR  H12A  C12  H12   108.35  3.000
 MMR  H12B  C12  C10   111.01  3.000
 MMR  H12A  C12  C10   110.71  3.000
 MMR  H12   C12  C10   110.71  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
 MMR  CONST_01  O8   C8  N2  C2    0.00   0.0  0
 MMR  CONST_02  C9   C8  N2  C2  180.00   0.0  0
 MMR  CONST_03  HN2  N2  C8  O8  180.00   0.0  0
 MMR  Var_01    H7   C7  O1  C1  -50.71  30.0  3
 MMR  Var_02    H9   C9  C8  N2   33.90  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
 MMR  chir_01  C1   O1  C2   O5   negativ
 MMR  chir_02  C2   N2  C3   C1   positiv
 MMR  chir_03  C3   O3  C4   C2   negativ
 MMR  chir_04  C4   O4  C5   C3   positiv
 MMR  chir_05  C5   O5  C4   C6   negativ
 MMR  chir_06  C10  O3  C11  C12  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
 MMR  plan-1  C2   0.020
 MMR  plan-1  N2   0.020
 MMR  plan-1  C8   0.020
 MMR  plan-1  O8   0.020
 MMR  plan-1  C9   0.020
 MMR  plan-1  HN2  0.020
 MMR  plan-2  C10  0.020
 MMR  plan-2  C11  0.020
 MMR  plan-2  O11  0.020
 MMR  plan-2  O12  0.020

