# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:43:05 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-methyl-2-oxo-2H-chromen-7-yl alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)Oc2cc(O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)ccc12
#
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
 MUG  MUG  '4-methyl-2-oxo-2H-chromen-7-yl alpha-D-glucopyranoside'  D-saccharide  42  24  .  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_MUG
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
 MUG  O1    O  O     0  -0.470   1.5260   0.8807   3.5657
 MUG  C2    C  CR6   0   0.549   1.3414   0.8067   4.9111
 MUG  O2    O  OC    0  -0.439   2.0689   1.4781   5.6017
 MUG  C3    C  CR16  0  -0.554   0.2931  -0.0676   5.3786
 MUG  C4    C  CR6   0   0.273  -0.4777  -0.7873   4.5339
 MUG  CM4   C  CH3   0  -0.749  -1.5530  -1.6881   5.0402
 MUG  C4A   C  CR66  0  -0.052  -0.2389  -0.6732   3.1149
 MUG  C5    C  CR16  0  -0.316  -0.9631  -1.3577   2.1354
 MUG  C6    C  CR16  0  -0.346  -0.6910  -1.2078   0.7916
 MUG  C7    C  CR6   0   0.398   0.3481  -0.3583   0.3929
 MUG  C8    C  CR16  0  -0.434   1.0821   0.3413   1.3429
 MUG  C8A   C  CR66  0   0.398   0.7798   0.1795   2.6825
 MUG  C1'   C  CH1   0   0.201   0.3287  -1.0664  -1.8892
 MUG  O1'   O  O2    0  -0.490   0.7021  -0.1457  -0.8876
 MUG  C2'   C  CH1   0  -0.011   1.2604  -0.8337  -3.0804
 MUG  O2'   O  OH1   0  -0.663   2.6125  -0.8685  -2.7128
 MUG  C3'   C  CH1   0  -0.009   0.9641   0.5180  -3.7178
 MUG  O3'   O  OH1   0  -0.673   1.6854   0.6979  -4.9133
 MUG  C4'   C  CH1   0   0.030  -0.5175   0.6101  -4.0651
 MUG  O4'   O  OH1   0  -0.671  -0.8611   1.8930  -4.5254
 MUG  C5'   C  CH1   0  -0.018  -1.3689   0.3182  -2.8297
 MUG  O5'   O  O2    0  -0.491  -0.9988  -0.9333  -2.2649
 MUG  C6'   C  CH2   0  -0.160  -2.8413   0.2283  -3.1697
 MUG  O6'   O  OH1   0  -0.666  -3.5692   0.0228  -1.9831
 MUG  H3    H  HCR6  0   0.280   0.1510  -0.1190   6.4497
 MUG  HM41  H  HCH3  0   0.269  -1.6139  -1.6556   6.1255
 MUG  HM42  H  HCH3  0   0.265  -2.5244  -1.4027   4.6337
 MUG  HM43  H  HCH3  0   0.266  -1.3692  -2.7204   4.7384
 MUG  H5    H  HCR6  0   0.275  -1.7711  -2.0142   2.4290
 MUG  H6    H  HCR6  0   0.294  -1.3015  -1.7310   0.0708
 MUG  H8    H  HCR6  0   0.289   1.8882   0.9965   1.0378
 MUG  H1'   H  HCH1  0   0.270   0.4363  -2.0897  -1.5107
 MUG  H2'   H  HCH1  0   0.240   1.0271  -1.6168  -3.8149
 MUG  HO2'  H  HOH1  0   0.461   2.8922  -1.7858  -2.6376
 MUG  H3'   H  HCH1  0   0.223   1.2002   1.3161  -2.9985
 MUG  HO3'  H  HOH1  0   0.457   2.6194   0.7807  -4.6969
 MUG  H4'   H  HCH1  0   0.214  -0.7377  -0.1558  -4.8266
 MUG  HO4'  H  HOH1  0   0.455  -0.3227   2.0889  -5.2993
 MUG  H5'   H  HCH1  0   0.236  -1.2213   1.1248  -2.0985
 MUG  H6'1  H  HCH2  0   0.214  -3.1354   1.1562  -3.6707
 MUG  H6'2  H  HCH2  0   0.197  -2.9906  -0.5888  -3.8897
 MUG  HO6'  H  HOH1  0   0.456  -4.5044   0.0384  -2.2049

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
 MUG  O1   C2    aromatic  1.360  0.020  1.360
 MUG  O1   C8A   aromatic  1.352  0.020  1.352
 MUG  C2   O2    double    1.207  0.020  1.207
 MUG  C2   C3    aromatic  1.443  0.020  1.443
 MUG  C3   C4    aromatic  1.351  0.020  1.351
 MUG  C3   H3    single    0.930  0.020  1.080
 MUG  C4   CM4   single    1.491  0.020  1.491
 MUG  C4   C4A   aromatic  1.444  0.020  1.444
 MUG  CM4  HM41  single    0.970  0.020  1.090
 MUG  CM4  HM42  single    0.970  0.020  1.090
 MUG  CM4  HM43  single    0.970  0.020  1.090
 MUG  C4A  C5    aromatic  1.397  0.020  1.397
 MUG  C4A  C8A   aromatic  1.397  0.020  1.397
 MUG  C5   C6    aromatic  1.379  0.020  1.379
 MUG  C5   H5    single    0.930  0.020  1.080
 MUG  C6   C7    aromatic  1.400  0.020  1.400
 MUG  C6   H6    single    0.930  0.020  1.080
 MUG  C7   C8    aromatic  1.390  0.020  1.390
 MUG  C7   O1'   single    1.345  0.020  1.345
 MUG  C8   C8A   aromatic  1.383  0.020  1.383
 MUG  C8   H8    single    0.930  0.020  1.080
 MUG  C1'  O1'   single    1.411  0.020  1.411
 MUG  C1'  C2'   single    1.530  0.020  1.530
 MUG  C1'  O5'   single    1.386  0.020  1.386
 MUG  C1'  H1'   single    0.970  0.020  1.090
 MUG  C2'  O2'   single    1.402  0.020  1.402
 MUG  C2'  C3'   single    1.523  0.020  1.523
 MUG  C2'  H2'   single    0.970  0.020  1.090
 MUG  O2'  HO2'  single    0.850  0.020  0.980
 MUG  C3'  O3'   single    1.408  0.020  1.408
 MUG  C3'  C4'   single    1.524  0.020  1.524
 MUG  C3'  H3'   single    0.970  0.020  1.090
 MUG  O3'  HO3'  single    0.850  0.020  0.980
 MUG  C4'  O4'   single    1.406  0.020  1.406
 MUG  C4'  C5'   single    1.528  0.020  1.528
 MUG  C4'  H4'   single    0.970  0.020  1.090
 MUG  O4'  HO4'  single    0.850  0.020  0.980
 MUG  C5'  O5'   single    1.422  0.020  1.422
 MUG  C5'  C6'   single    1.514  0.020  1.514
 MUG  C5'  H5'   single    0.970  0.020  1.090
 MUG  C6'  O6'   single    1.407  0.020  1.407
 MUG  C6'  H6'1  single    0.970  0.020  1.090
 MUG  C6'  H6'2  single    0.970  0.020  1.090
 MUG  O6'  HO6'  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
 MUG  C8A   O1   C2    122.89  3.000
 MUG  C3    C2   O2    126.12  3.000
 MUG  C3    C2   O1    116.88  3.000
 MUG  O2    C2   O1    117.00  3.000
 MUG  H3    C3   C4    121.25  3.000
 MUG  H3    C3   C2    116.43  3.000
 MUG  C4    C3   C2    122.32  3.000
 MUG  C4A   C4   CM4   120.05  3.000
 MUG  C4A   C4   C3    118.56  3.000
 MUG  CM4   C4   C3    121.39  3.000
 MUG  HM43  CM4  HM42  107.13  3.000
 MUG  HM43  CM4  HM41  108.29  3.000
 MUG  HM42  CM4  HM41  108.31  3.000
 MUG  HM43  CM4  C4    110.86  3.000
 MUG  HM42  CM4  C4    110.95  3.000
 MUG  HM41  CM4  C4    111.16  3.000
 MUG  C8A   C4A  C5    117.38  3.000
 MUG  C8A   C4A  C4    118.24  3.000
 MUG  C5    C4A  C4    124.38  3.000
 MUG  H5    C5   C6    118.54  3.000
 MUG  H5    C5   C4A   119.62  3.000
 MUG  C6    C5   C4A   121.84  3.000
 MUG  H6    C6   C7    121.57  3.000
 MUG  H6    C6   C5    119.09  3.000
 MUG  C7    C6   C5    119.33  3.000
 MUG  O1'   C7   C8    115.60  3.000
 MUG  O1'   C7   C6    124.21  3.000
 MUG  C8    C7   C6    120.19  3.000
 MUG  H8    C8   C8A   120.44  3.000
 MUG  H8    C8   C7    120.35  3.000
 MUG  C8A   C8   C7    119.20  3.000
 MUG  C8    C8A  C4A   122.05  3.000
 MUG  C8    C8A  O1    116.83  3.000
 MUG  C4A   C8A  O1    121.11  3.000
 MUG  H1'   C1'  O5'   106.10  3.000
 MUG  H1'   C1'  C2'   110.55  3.000
 MUG  O5'   C1'  C2'   110.95  3.000
 MUG  H1'   C1'  O1'   109.76  3.000
 MUG  O5'   C1'  O1'   112.53  3.000
 MUG  C2'   C1'  O1'   106.99  3.000
 MUG  C1'   O1'  C7    120.19  3.000
 MUG  H2'   C2'  C3'   108.14  3.000
 MUG  H2'   C2'  O2'   111.25  3.000
 MUG  C3'   C2'  O2'   108.63  3.000
 MUG  H2'   C2'  C1'   106.42  3.000
 MUG  C3'   C2'  C1'   110.01  3.000
 MUG  O2'   C2'  C1'   112.30  3.000
 MUG  HO2'  O2'  C2'   108.95  3.000
 MUG  H3'   C3'  C4'   108.28  3.000
 MUG  H3'   C3'  O3'   110.64  3.000
 MUG  C4'   C3'  O3'   107.26  3.000
 MUG  H3'   C3'  C2'   109.17  3.000
 MUG  C4'   C3'  C2'   109.75  3.000
 MUG  O3'   C3'  C2'   111.66  3.000
 MUG  HO3'  O3'  C3'   108.50  3.000
 MUG  H4'   C4'  C5'   108.32  3.000
 MUG  H4'   C4'  O4'   111.04  3.000
 MUG  C5'   C4'  O4'   107.63  3.000
 MUG  H4'   C4'  C3'   108.03  3.000
 MUG  C5'   C4'  C3'   110.23  3.000
 MUG  O4'   C4'  C3'   111.55  3.000
 MUG  HO4'  O4'  C4'   108.19  3.000
 MUG  H5'   C5'  C6'   108.89  3.000
 MUG  H5'   C5'  O5'   110.29  3.000
 MUG  C6'   C5'  O5'   106.86  3.000
 MUG  H5'   C5'  C4'   108.84  3.000
 MUG  C6'   C5'  C4'   111.82  3.000
 MUG  O5'   C5'  C4'   110.13  3.000
 MUG  C5'   O5'  C1'   116.20  3.000
 MUG  H6'2  C6'  H6'1  107.08  3.000
 MUG  H6'2  C6'  O6'   111.94  3.000
 MUG  H6'1  C6'  O6'   111.76  3.000
 MUG  H6'2  C6'  C5'   108.87  3.000
 MUG  H6'1  C6'  C5'   108.28  3.000
 MUG  O6'   C6'  C5'   108.81  3.000
 MUG  HO6'  O6'  C6'   107.84  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
 MUG  CONST_01  C4    C3   C2   O1     0.00   0.0  0
 MUG  CONST_02  C4    C4A  C8A  O1     0.00   0.0  0
 MUG  CONST_03  C5    C4A  C8A  O1   180.00   0.0  0
 MUG  CONST_04  C7    C8   C8A  O1   180.00   0.0  0
 MUG  CONST_05  C4A   C8A  O1   C2     0.00   0.0  0
 MUG  CONST_06  C8    C8A  O1   C2   180.00   0.0  0
 MUG  CONST_07  C4A   C4   C3   C2     0.00   0.0  0
 MUG  CONST_08  C8A   O1   C2   C3     0.00   0.0  0
 MUG  CONST_09  C5    C4A  C4   C3   180.00   0.0  0
 MUG  CONST_10  C8A   C4A  C4   C3     0.00   0.0  0
 MUG  CONST_11  C6    C5   C4A  C4   180.00   0.0  0
 MUG  CONST_12  C8    C8A  C4A  C4   180.00   0.0  0
 MUG  CONST_13  C7    C6   C5   C4A    0.00   0.0  0
 MUG  CONST_14  C7    C8   C8A  C4A    0.00   0.0  0
 MUG  CONST_15  C8    C8A  C4A  C5     0.00   0.0  0
 MUG  CONST_16  C8    C7   C6   C5     0.00   0.0  0
 MUG  CONST_17  C8A   C4A  C5   C6     0.00   0.0  0
 MUG  CONST_18  C8A   C8   C7   C6     0.00   0.0  0
 MUG  CONST_19  CM4   C4   C3   C2   180.00   0.0  0
 MUG  CONST_20  C8A   O1   C2   O2   180.00   0.0  0
 MUG  CONST_21  C4    C3   C2   O2   180.00   0.0  0
 MUG  CONST_22  C5    C4A  C4   CM4    0.00   0.0  0
 MUG  CONST_23  C8A   C4A  C4   CM4  180.00   0.0  0
 MUG  CONST_24  O1'   C7   C6   C5   180.00   0.0  0
 MUG  CONST_25  O1'   C7   C8   C8A  180.00   0.0  0
 MUG  CONST_26  H3    C3   C2   O1   180.00   0.0  0
 MUG  CONST_27  H8    C8   C8A  O1     0.00   0.0  0
 MUG  CONST_28  H5    C5   C4A  C4     0.00   0.0  0
 MUG  CONST_29  H6    C6   C5   C4A  180.00   0.0  0
 MUG  Var_01    HM41  CM4  C4   C3     0.80  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
 MUG  chir_01  C1'  O1'  C2'  O5'  positiv
 MUG  chir_02  C2'  O2'  C1'  C3'  negativ
 MUG  chir_03  C3'  O3'  C2'  C4'  positiv
 MUG  chir_04  C4'  O4'  C5'  C3'  positiv
 MUG  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
 MUG  plan-1  O1   0.020
 MUG  plan-1  C2   0.020
 MUG  plan-1  O2   0.020
 MUG  plan-1  C3   0.020
 MUG  plan-2  O1   0.020
 MUG  plan-2  C4   0.020
 MUG  plan-2  C4A  0.020
 MUG  plan-2  C5   0.020
 MUG  plan-2  C6   0.020
 MUG  plan-2  C7   0.020
 MUG  plan-2  C8   0.020
 MUG  plan-2  C8A  0.020
 MUG  plan-2  O1'  0.020
 MUG  plan-2  H5   0.020
 MUG  plan-2  H6   0.020
 MUG  plan-2  H8   0.020

