# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 14:47:06 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl 2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS)C(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@H]2[C@H](O)[C@@H](O)[C@H](O)[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
 MA8  MA8  '(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl 2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranoside'  D-saccharide  57  29  .  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_MA8
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
 MA8  O1    O  O2    0  -0.506  -0.5582  -1.7493  -1.3339
 MA8  C1    C  CH1   0   0.291  -0.8467  -0.3839  -1.3422
 MA8  C2    C  CH1   0   0.029   1.6498  -1.4773  -0.4277
 MA8  C3    C  CH1   0  -0.037   0.8084  -2.0771  -1.5493
 MA8  O2    O  OH1   0  -0.670   2.9950  -1.7934  -0.6786
 MA8  O3    O  OH1   0  -0.653   2.1951   0.6362   0.6454
 MA8  O4    O  O2    0  -0.500  -0.5291   0.2126  -2.5537
 MA8  N1    N  NH1   0  -0.629  -0.2845   1.7686  -0.2957
 MA8  C4    C  CH2   0  -0.172   0.8795  -3.5925  -1.6102
 MA8  C5    C  CH1   0  -0.158  -0.0565   0.3453  -0.2482
 MA8  C6    C  CH1   0  -0.022   1.4350   0.0368  -0.3755
 MA8  O5    O  OH1   0  -0.664   0.1341  -4.1164  -2.6837
 MA8  C7    C  CH1   0   0.030  -1.6602   2.5584  -3.9128
 MA8  C8    C  CH1   0  -0.018  -0.8917   2.4607  -5.2303
 MA8  C9    C  CH1   0  -0.071  -1.4862   0.0702  -3.5851
 MA8  C10   C  CH1   0  -0.017  -2.4237   1.2839  -3.5481
 MA8  O6    O  OH1   0  -0.671   0.1669  -1.0994  -4.9454
 MA8  O7    O  OH1   0  -0.682   0.6772   1.1853  -6.4587
 MA8  O8    O  OH1   0  -0.663  -3.5150   1.1264  -4.4230
 MA8  O9    O  OH1   0  -0.666  -1.8040   2.4174  -6.2990
 MA8  C11   C  CH1   0   0.015   0.0301   1.2429  -5.2079
 MA8  C12   C  CH1   0   0.042  -0.7543  -0.0333  -4.9200
 MA8  O10   O  OH1   0  -0.670  -2.4987   3.6871  -3.8755
 MA8  C13   C  C     0   0.537  -1.3790   2.3587   0.2028
 MA8  O11   O  O     0  -0.496  -2.2863   1.7406   0.7454
 MA8  C14   C  CH1   0  -0.200  -1.4448   3.8796   0.0663
 MA8  N2    N  NH2   0  -0.794  -2.6642   4.3322  -0.5731
 MA8  C15   C  CH2   0  -0.561  -1.3544   4.5125   1.4534
 MA8  S1    S  S2    0  -0.240   0.1784   4.1186   2.3491
 MA8  H1    H  HCH1  0   0.246  -1.9204  -0.3152  -1.1298
 MA8  H2    H  HCH1  0   0.208   1.3133  -1.9083   0.5313
 MA8  H3    H  HCH1  0   0.238   1.1473  -1.6719  -2.5106
 MA8  HA    H  HOH1  0   0.454   3.5323  -1.3928   0.0131
 MA8  HB    H  HOH1  0   0.449   1.8520   0.3549   1.5016
 MA8  HC    H  HNH1  0   0.404   0.4109   2.3444  -0.7430
 MA8  H4C1  H  HCH2  0   0.199   0.5581  -4.0132  -0.6470
 MA8  H4C2  H  HCH2  0   0.234   1.9154  -3.8940  -1.7652
 MA8  H5    H  HCH1  0   0.274  -0.4166  -0.0353   0.7142
 MA8  H6    H  HCH1  0   0.250   1.8155   0.4645  -1.3105
 MA8  HD    H  HOH1  0   0.447  -0.7890  -3.8816  -2.5477
 MA8  H7    H  HCH1  0   0.244  -0.9097   2.7094  -3.1314
 MA8  H8    H  HCH1  0   0.231  -0.2571   3.3574  -5.3034
 MA8  H9    H  HCH1  0   0.254  -2.0795  -0.8442  -3.4390
 MA8  H10   H  HCH1  0   0.232  -2.7824   1.4017  -2.5147
 MA8  HH    H  HOH1  0   0.452  -0.3090  -1.9344  -4.8924
 MA8  HI    H  HOH1  0   0.452   1.1654   0.3564  -6.5074
 MA8  HG    H  HOH1  0   0.459  -4.1762   0.5833  -3.9838
 MA8  HF    H  HOH1  0   0.450  -1.2974   2.3756  -7.1166
 MA8  H11   H  HCH1  0   0.214   0.7624   1.3951  -4.4017
 MA8  H12   H  HCH1  0   0.223  -1.5169  -0.1567  -5.6998
 MA8  HE    H  HOH1  0   0.447  -3.2528   3.5147  -4.4510
 MA8  H14   H  HCH1  0   0.259  -0.5974   4.2430  -0.5215
 MA8  H2N1  H  HNH2  0   0.346  -3.4630   3.8557  -0.1724
 MA8  H2N2  H  HNH2  0   0.360  -2.6580   4.1180  -1.5635
 MA8  H151  H  HCH2  0   0.293  -1.3641   5.5965   1.3441
 MA8  H152  H  HCH2  0   0.278  -2.2133   4.2355   2.0653
 MA8  HS1   H  HSH1  0   0.219  -0.1428   2.8790   2.7353

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
 MA8  O1   C1    single  1.396  0.020  1.396
 MA8  O1   C3    single  1.422  0.020  1.422
 MA8  C1   O4    single  1.387  0.020  1.387
 MA8  C1   C5    single  1.534  0.020  1.534
 MA8  C1   H1    single  0.970  0.020  1.090
 MA8  C2   C3    single  1.525  0.020  1.525
 MA8  C2   O2    single  1.404  0.020  1.404
 MA8  C2   C6    single  1.530  0.020  1.530
 MA8  C2   H2    single  0.970  0.020  1.090
 MA8  C3   C4    single  1.518  0.020  1.518
 MA8  C3   H3    single  0.970  0.020  1.090
 MA8  O2   HA    single  0.850  0.020  0.980
 MA8  O3   C6    single  1.407  0.020  1.407
 MA8  O3   HB    single  0.850  0.020  0.980
 MA8  O4   C9    single  1.414  0.020  1.414
 MA8  N1   C5    single  1.442  0.020  1.442
 MA8  N1   C13   single  1.340  0.020  1.340
 MA8  N1   HC    single  0.860  0.020  1.020
 MA8  C4   O5    single  1.408  0.020  1.408
 MA8  C4   H4C1  single  0.970  0.020  1.090
 MA8  C4   H4C2  single  0.970  0.020  1.090
 MA8  C5   C6    single  1.528  0.020  1.528
 MA8  C5   H5    single  0.970  0.020  1.090
 MA8  C6   H6    single  0.970  0.020  1.090
 MA8  O5   HD    single  0.850  0.020  0.980
 MA8  C7   C8    single  1.528  0.020  1.528
 MA8  C7   C10   single  1.530  0.020  1.530
 MA8  C7   O10   single  1.407  0.020  1.407
 MA8  C7   H7    single  0.970  0.020  1.090
 MA8  C8   O9    single  1.406  0.020  1.406
 MA8  C8   C11   single  1.528  0.020  1.528
 MA8  C8   H8    single  0.970  0.020  1.090
 MA8  C9   C10   single  1.534  0.020  1.534
 MA8  C9   C12   single  1.526  0.020  1.526
 MA8  C9   H9    single  0.970  0.020  1.090
 MA8  C10  O8    single  1.407  0.020  1.407
 MA8  C10  H10   single  0.970  0.020  1.090
 MA8  O6   C12   single  1.409  0.020  1.409
 MA8  O6   HH    single  0.850  0.020  0.980
 MA8  O7   C11   single  1.409  0.020  1.409
 MA8  O7   HI    single  0.850  0.020  0.980
 MA8  O8   HG    single  0.850  0.020  0.980
 MA8  O9   HF    single  0.850  0.020  0.980
 MA8  C11  C12   single  1.525  0.020  1.525
 MA8  C11  H11   single  0.970  0.020  1.090
 MA8  C12  H12   single  0.970  0.020  1.090
 MA8  O10  HE    single  0.850  0.020  0.980
 MA8  C13  O11   double  1.225  0.020  1.225
 MA8  C13  C14   single  1.528  0.020  1.528
 MA8  C14  N2    single  1.449  0.020  1.449
 MA8  C14  C15   single  1.527  0.020  1.527
 MA8  C14  H14   single  0.970  0.020  1.090
 MA8  N2   H2N1  single  0.890  0.020  1.040
 MA8  N2   H2N2  single  0.890  0.020  1.040
 MA8  C15  S1    single  1.819  0.020  1.819
 MA8  C15  H151  single  0.970  0.020  1.090
 MA8  C15  H152  single  0.970  0.020  1.090
 MA8  HS1  S1    single  1.200  0.020  1.300

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
 MA8  C3    O1   C1    115.05  3.000
 MA8  H1    C1   C5    109.66  3.000
 MA8  H1    C1   O4    111.49  3.000
 MA8  C5    C1   O4    107.48  3.000
 MA8  H1    C1   O1    105.22  3.000
 MA8  C5    C1   O1    110.75  3.000
 MA8  O4    C1   O1    112.24  3.000
 MA8  H2    C2   C6    108.29  3.000
 MA8  H2    C2   O2    111.06  3.000
 MA8  C6    C2   O2    111.30  3.000
 MA8  H2    C2   C3    108.50  3.000
 MA8  C6    C2   C3    109.68  3.000
 MA8  O2    C2   C3    107.97  3.000
 MA8  H3    C3   C4    108.61  3.000
 MA8  H3    C3   C2    109.20  3.000
 MA8  C4    C3   C2    113.34  3.000
 MA8  H3    C3   O1    110.16  3.000
 MA8  C4    C3   O1    106.33  3.000
 MA8  C2    C3   O1    109.16  3.000
 MA8  HA    O2   C2    108.20  3.000
 MA8  HB    O3   C6    109.14  3.000
 MA8  C9    O4   C1    116.02  3.000
 MA8  HC    N1   C13   118.52  3.000
 MA8  HC    N1   C5    118.00  3.000
 MA8  C13   N1   C5    123.48  3.000
 MA8  H4C2  C4   H4C1  107.26  3.000
 MA8  H4C2  C4   O5    106.96  3.000
 MA8  H4C1  C4   O5    111.77  3.000
 MA8  H4C2  C4   C3    109.04  3.000
 MA8  H4C1  C4   C3    109.46  3.000
 MA8  O5    C4   C3    112.16  3.000
 MA8  H5    C5   C6    108.89  3.000
 MA8  H5    C5   N1    108.64  3.000
 MA8  C6    C5   N1    110.53  3.000
 MA8  H5    C5   C1    106.98  3.000
 MA8  C6    C5   C1    110.33  3.000
 MA8  N1    C5   C1    111.36  3.000
 MA8  H6    C6   C5    109.33  3.000
 MA8  H6    C6   O3    105.38  3.000
 MA8  C5    C6   O3    112.38  3.000
 MA8  H6    C6   C2    107.95  3.000
 MA8  C5    C6   C2    109.85  3.000
 MA8  O3    C6   C2    111.74  3.000
 MA8  HD    O5   C4    108.02  3.000
 MA8  H7    C7   O10   106.22  3.000
 MA8  H7    C7   C10   106.69  3.000
 MA8  O10   C7   C10   111.39  3.000
 MA8  H7    C7   C8    106.24  3.000
 MA8  O10   C7   C8    111.96  3.000
 MA8  C10   C7   C8    113.78  3.000
 MA8  H8    C8   C11   107.60  3.000
 MA8  H8    C8   O9    110.40  3.000
 MA8  C11   C8   O9    112.22  3.000
 MA8  H8    C8   C7    107.16  3.000
 MA8  C11   C8   C7    109.99  3.000
 MA8  O9    C8   C7    109.33  3.000
 MA8  H9    C9   C12   108.58  3.000
 MA8  H9    C9   C10   108.96  3.000
 MA8  C12   C9   C10   111.58  3.000
 MA8  H9    C9   O4    110.60  3.000
 MA8  C12   C9   O4    108.68  3.000
 MA8  C10   C9   O4    108.44  3.000
 MA8  H10   C10  O8    110.06  3.000
 MA8  H10   C10  C9    107.85  3.000
 MA8  O8    C10  C9    111.73  3.000
 MA8  H10   C10  C7    107.31  3.000
 MA8  O8    C10  C7    109.39  3.000
 MA8  C9    C10  C7    110.39  3.000
 MA8  HH    O6   C12   109.40  3.000
 MA8  HI    O7   C11   108.22  3.000
 MA8  HG    O8   C10   108.20  3.000
 MA8  HF    O9   C8    107.78  3.000
 MA8  H11   C11  C12   108.66  3.000
 MA8  H11   C11  O7    110.52  3.000
 MA8  C12   C11  O7    111.68  3.000
 MA8  H11   C11  C8    107.59  3.000
 MA8  C12   C11  C8    111.06  3.000
 MA8  O7    C11  C8    107.26  3.000
 MA8  H12   C12  C11   108.50  3.000
 MA8  H12   C12  O6    110.87  3.000
 MA8  C11   C12  O6    107.06  3.000
 MA8  H12   C12  C9    107.21  3.000
 MA8  C11   C12  C9    110.80  3.000
 MA8  O6    C12  C9    112.37  3.000
 MA8  HE    O10  C7    107.87  3.000
 MA8  C14   C13  O11   120.66  3.000
 MA8  C14   C13  N1    116.12  3.000
 MA8  O11   C13  N1    123.22  3.000
 MA8  H14   C14  C15   107.74  3.000
 MA8  H14   C14  N2    108.12  3.000
 MA8  C15   C14  N2    108.72  3.000
 MA8  H14   C14  C13   110.21  3.000
 MA8  C15   C14  C13   109.19  3.000
 MA8  N2    C14  C13   112.73  3.000
 MA8  H2N2  N2   H2N1  106.98  3.000
 MA8  H2N2  N2   C14   111.10  3.000
 MA8  H2N1  N2   C14   110.00  3.000
 MA8  H152  C15  H151  107.58  3.000
 MA8  H152  C15  S1    109.43  3.000
 MA8  H151  C15  S1    105.81  3.000
 MA8  H152  C15  C14   110.96  3.000
 MA8  H151  C15  C14   108.70  3.000
 MA8  S1    C15  C14   114.04  3.000
 MA8  HS1   S1   C15    98.08  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
 MA8  CONST_01  O11  C13  N1   C5     0.00  0.0  0
 MA8  CONST_02  C14  C13  N1   C5   180.00  0.0  0
 MA8  CONST_03  HC   N1   C13  O11  180.00  0.0  0

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
 MA8  chir_01  C1   O1   O4   C5   positiv
 MA8  chir_02  C2   O2   C6   C3   negativ
 MA8  chir_03  C3   O1   C2   C4   negativ
 MA8  chir_04  C5   N1   C1   C6   negativ
 MA8  chir_05  C6   O3   C5   C2   positiv
 MA8  chir_06  C7   O10  C8   C10  positiv
 MA8  chir_07  C8   O9   C7   C11  negativ
 MA8  chir_08  C9   O4   C12  C10  positiv
 MA8  chir_09  C10  O8   C9   C7   negativ
 MA8  chir_10  C11  O7   C12  C8   positiv
 MA8  chir_11  C12  O6   C11  C9   positiv
 MA8  chir_12  C14  C13  N2   C15  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
 MA8  plan-1  N1   0.020
 MA8  plan-1  C5   0.020
 MA8  plan-1  C13  0.020
 MA8  plan-1  O11  0.020
 MA8  plan-1  C14  0.020
 MA8  plan-1  HC   0.020

