# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:18:59 2022
#   Inital geometry file: a 160 line input string
#   Ligand name: (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-(acetylamino)-6-amino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)CC[C@H]3NC(C)=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
 8MM  8MM  '(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-(acetylamino)-6-amino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside'  ligand  75  34  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8MM
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
 8MM  C4   C  CH2   0  -0.460  -5.3073  -1.1108  -0.3873
 8MM  C14  C  CH1   0   0.025   4.3113   0.3551   0.8199
 8MM  C5   C  CH1   0  -0.129  -4.1658  -1.2571   0.6124
 8MM  C6   C  CH1   0   0.297  -3.4188   0.0709   0.8005
 8MM  C11  C  CH1   0   0.044   0.9810   1.0800  -0.0327
 8MM  C7   C  CH1   0   0.056  -1.5333   1.1205  -0.2506
 8MM  C8   C  CH1   0  -0.103  -1.3951   1.9576  -1.5205
 8MM  C9   C  CH2   0  -0.475  -0.1427   2.8196  -1.4210
 8MM  C10  C  CH1   0  -0.104   1.1200   1.9821  -1.2540
 8MM  C12  C  CH1   0   0.040  -0.2969   0.2414  -0.0746
 8MM  C13  C  CH1   0   0.217   2.8477   0.0708   1.1697
 8MM  N1   N  NH2   0  -0.806   2.3437   2.7664  -1.1417
 8MM  N2   N  NH2   0  -0.801  -2.5602   2.8085  -1.6964
 8MM  C3   C  CH2   0  -0.452  -6.1857   0.0743   0.0005
 8MM  N3   N  NH1   0  -0.624  -3.2537  -2.3042   0.2204
 8MM  N    N  NH1   0  -0.594   6.2416  -0.5576  -0.4991
 8MM  O    O  O2    0  -0.494  -4.2997   1.1114   1.1005
 8MM  C1   C  CH2   0  -0.280  -6.1289   2.5432   0.5826
 8MM  C15  C  CH1   0  -0.101   4.8508  -0.7254  -0.1334
 8MM  C16  C  CT    0   0.181   4.6156  -2.1146   0.4935
 8MM  C17  C  CH2   0  -0.192   3.1420  -2.2545   0.8756
 8MM  C18  C  CH3   0  -0.677   4.9725  -3.2271  -0.4838
 8MM  C19  C  CH3   0  -0.517   6.4986   0.2713  -1.6588
 8MM  C2   C  CH1   0   0.017  -5.3367   1.3248   0.1535
 8MM  CAC  C  CH3   0  -0.778  -1.4741  -3.9101   0.4791
 8MM  CAW  C  C     0   0.533  -2.5267  -3.0225   1.0959
 8MM  N4   N  NH2   0  -0.803  -5.2705   3.7103   0.7151
 8MM  O1   O  O2    0  -0.524  -2.6906   0.3160  -0.3676
 8MM  O2   O  OH1   0  -0.666  -0.4410  -0.5047   1.1106
 8MM  O3   O  O2    0  -0.522   2.0906   0.2091   0.0009
 8MM  O4   O  O2    0  -0.496   2.6781  -1.2064   1.7106
 8MM  O5   O  OH1   0  -0.681   5.4346  -2.1744   1.6487
 8MM  OAH  O  O     0  -0.510  -2.7079  -2.9869   2.3056
 8MM  H1   H  HCH2  0   0.231  -4.9087  -0.9626  -1.3960
 8MM  H2   H  HCH2  0   0.251  -5.8915  -2.0326  -0.4100
 8MM  H3   H  HCH1  0   0.217   4.8856   0.2986   1.7520
 8MM  H4   H  HCH1  0   0.261  -4.5887  -1.5247   1.5829
 8MM  H5   H  HCH1  0   0.237  -2.7570  -0.0023   1.6668
 8MM  H6   H  HCH1  0   0.227   0.9601   1.7071   0.8724
 8MM  H7   H  HCH1  0   0.223  -1.6278   1.8078   0.6023
 8MM  H8   H  HCH1  0   0.207  -1.2582   1.2591  -2.3632
 8MM  H9   H  HCH2  0   0.252  -0.0504   3.4380  -2.3184
 8MM  H10  H  HCH2  0   0.229  -0.2481   3.5064  -0.5726
 8MM  H11  H  HCH1  0   0.242   1.2303   1.3372  -2.1328
 8MM  H12  H  HCH1  0   0.205  -0.2323  -0.4266  -0.9485
 8MM  H13  H  HCH1  0   0.245   2.5011   0.7736   1.9377
 8MM  H14  H  HNH2  0   0.369   2.5864   3.1607  -2.0419
 8MM  H15  H  HNH2  0   0.358   2.1894   3.5550  -0.5219
 8MM  H17  H  HNH2  0   0.347  -2.4296   3.3767  -2.5250
 8MM  H18  H  HNH2  0   0.359  -3.3688   2.2331  -1.8894
 8MM  H20  H  HCH2  0   0.242  -6.9498   0.2411  -0.7616
 8MM  H21  H  HCH2  0   0.226  -6.7070  -0.1370   0.9400
 8MM  H22  H  HNH1  0   0.392  -2.9572  -2.3037  -0.7425
 8MM  H24  H  HNH1  0   0.339   6.7793  -0.2287   0.2918
 8MM  H26  H  HCH2  0   0.199  -6.9317   2.6644  -0.1577
 8MM  H27  H  HCH2  0   0.209  -6.6202   2.3445   1.5410
 8MM  H28  H  HCH1  0   0.231   4.2640  -0.6971  -1.0586
 8MM  H29  H  HCH2  0   0.211   2.5345  -2.3244  -0.0338
 8MM  H30  H  HCH2  0   0.242   2.9893  -3.1800   1.4371
 8MM  H31  H  HCH3  0   0.244   6.0124  -3.1382  -0.7928
 8MM  H32  H  HCH3  0   0.227   4.8293  -4.2101  -0.0271
 8MM  H33  H  HCH3  0   0.223   4.3487  -3.1889  -1.3783
 8MM  H34  H  HCH3  0   0.220   7.5682   0.2650  -1.8755
 8MM  H35  H  HCH3  0   0.216   5.9938  -0.1511  -2.5297
 8MM  H36  H  HCH3  0   0.199   6.1810   1.3148  -1.5672
 8MM  H37  H  HCH1  0   0.204  -4.9017   1.5567  -0.8273
 8MM  H38  H  HCH3  0   0.253  -0.4926  -3.6023   0.8399
 8MM  H39  H  HCH3  0   0.265  -1.6275  -4.9403   0.7984
 8MM  H40  H  HCH3  0   0.248  -1.4615  -3.8826  -0.6088
 8MM  H42  H  HNH2  0   0.334  -4.6598   3.7794  -0.0913
 8MM  H43  H  HNH2  0   0.344  -5.8358   4.5487   0.7161
 8MM  H45  H  HOH1  0   0.446   0.3319  -1.0692   1.2227
 8MM  H46  H  HOH1  0   0.446   5.3493  -3.0513   2.0374
 8MM  O6   O  OH1   0  -0.704   4.4626   1.6625   0.3453
 8MM  H47  H  HOH1  0   0.461   3.7520   1.8933  -0.3001

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
 8MM  OAH  CAW  double  1.224  0.020  1.224
 8MM  CAC  CAW  single  1.509  0.020  1.509
 8MM  CAW  N3   single  1.346  0.020  1.346
 8MM  C4   C3   single  1.525  0.020  1.525
 8MM  C4   C5   single  1.524  0.020  1.524
 8MM  C3   C2   single  1.519  0.020  1.519
 8MM  N3   C5   single  1.443  0.020  1.443
 8MM  C5   C6   single  1.535  0.020  1.535
 8MM  C2   C1   single  1.515  0.020  1.515
 8MM  C2   O    single  1.420  0.020  1.420
 8MM  C1   N4   single  1.455  0.020  1.455
 8MM  C6   O    single  1.396  0.020  1.396
 8MM  C6   O1   single  1.398  0.020  1.398
 8MM  N2   C8   single  1.453  0.020  1.453
 8MM  O1   C7   single  1.414  0.020  1.414
 8MM  C8   C7   single  1.527  0.020  1.527
 8MM  C8   C9   single  1.524  0.020  1.524
 8MM  C7   C12  single  1.527  0.020  1.527
 8MM  C9   C10  single  1.524  0.020  1.524
 8MM  C12  O2   single  1.408  0.020  1.408
 8MM  C12  C11  single  1.529  0.020  1.529
 8MM  C10  C11  single  1.525  0.020  1.525
 8MM  C10  N1   single  1.458  0.020  1.458
 8MM  C11  O3   single  1.411  0.020  1.411
 8MM  O3   C13  single  1.399  0.020  1.399
 8MM  O4   C13  single  1.397  0.020  1.397
 8MM  O4   C17  single  1.418  0.020  1.418
 8MM  C13  C14  single  1.531  0.020  1.531
 8MM  C17  C16  single  1.529  0.020  1.529
 8MM  C14  O6   single  1.399  0.020  1.399
 8MM  C14  C15  single  1.539  0.020  1.539
 8MM  C16  C18  single  1.523  0.020  1.523
 8MM  C16  C15  single  1.542  0.020  1.542
 8MM  C16  O5   single  1.417  0.020  1.417
 8MM  C15  N    single  1.448  0.020  1.448
 8MM  N    C19  single  1.448  0.020  1.448
 8MM  C4   H1   single  0.970  0.020  1.090
 8MM  C4   H2   single  0.970  0.020  1.090
 8MM  C14  H3   single  0.970  0.020  1.090
 8MM  C5   H4   single  0.970  0.020  1.090
 8MM  C6   H5   single  0.970  0.020  1.090
 8MM  C11  H6   single  0.970  0.020  1.090
 8MM  C7   H7   single  0.970  0.020  1.090
 8MM  C8   H8   single  0.970  0.020  1.090
 8MM  C9   H9   single  0.970  0.020  1.090
 8MM  C9   H10  single  0.970  0.020  1.090
 8MM  C10  H11  single  0.970  0.020  1.090
 8MM  C12  H12  single  0.970  0.020  1.090
 8MM  C13  H13  single  0.970  0.020  1.090
 8MM  N1   H14  single  0.890  0.020  1.040
 8MM  N1   H15  single  0.890  0.020  1.040
 8MM  N2   H17  single  0.890  0.020  1.040
 8MM  N2   H18  single  0.890  0.020  1.040
 8MM  C3   H20  single  0.970  0.020  1.090
 8MM  C3   H21  single  0.970  0.020  1.090
 8MM  N3   H22  single  0.860  0.020  1.020
 8MM  N    H24  single  0.890  0.020  1.040
 8MM  C1   H26  single  0.970  0.020  1.090
 8MM  C1   H27  single  0.970  0.020  1.090
 8MM  C15  H28  single  0.970  0.020  1.090
 8MM  C17  H29  single  0.970  0.020  1.090
 8MM  C17  H30  single  0.970  0.020  1.090
 8MM  C18  H31  single  0.970  0.020  1.090
 8MM  C18  H32  single  0.970  0.020  1.090
 8MM  C18  H33  single  0.970  0.020  1.090
 8MM  C19  H34  single  0.970  0.020  1.090
 8MM  C19  H35  single  0.970  0.020  1.090
 8MM  C19  H36  single  0.970  0.020  1.090
 8MM  C2   H37  single  0.970  0.020  1.090
 8MM  CAC  H38  single  0.970  0.020  1.090
 8MM  CAC  H39  single  0.970  0.020  1.090
 8MM  CAC  H40  single  0.970  0.020  1.090
 8MM  N4   H42  single  0.890  0.020  1.040
 8MM  N4   H43  single  0.890  0.020  1.040
 8MM  O2   H45  single  0.850  0.020  0.980
 8MM  O5   H46  single  0.850  0.020  0.980
 8MM  O6   H47  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
 8MM  H2   C4   H1   106.86  3.000
 8MM  H2   C4   C3   110.68  3.000
 8MM  H1   C4   C3   109.80  3.000
 8MM  H2   C4   C5   109.47  3.000
 8MM  H1   C4   C5   110.16  3.000
 8MM  C3   C4   C5   109.83  3.000
 8MM  H3   C14  O6   106.25  3.000
 8MM  H3   C14  C15  107.88  3.000
 8MM  O6   C14  C15  114.09  3.000
 8MM  H3   C14  C13  107.27  3.000
 8MM  C15  C14  C13  110.26  3.000
 8MM  O6   C14  C13  110.75  3.000
 8MM  H4   C5   N3   107.96  3.000
 8MM  H4   C5   C6   106.94  3.000
 8MM  N3   C5   C6   110.70  3.000
 8MM  H4   C5   C4   108.45  3.000
 8MM  C6   C5   C4   111.20  3.000
 8MM  N3   C5   C4   111.40  3.000
 8MM  H5   C6   O1   111.02  3.000
 8MM  H5   C6   O    105.18  3.000
 8MM  O1   C6   O    112.18  3.000
 8MM  H5   C6   C5   109.51  3.000
 8MM  O1   C6   C5   107.62  3.000
 8MM  O    C6   C5   111.35  3.000
 8MM  H6   C11  O3   110.29  3.000
 8MM  H6   C11  C12  108.60  3.000
 8MM  O3   C11  C12  108.63  3.000
 8MM  H6   C11  C10  108.85  3.000
 8MM  O3   C11  C10  108.21  3.000
 8MM  C12  C11  C10  112.25  3.000
 8MM  H7   C7   O1   110.45  3.000
 8MM  H7   C7   C12  109.88  3.000
 8MM  O1   C7   C12  110.16  3.000
 8MM  H7   C7   C8   108.07  3.000
 8MM  C12  C7   C8   109.76  3.000
 8MM  O1   C7   C8   108.48  3.000
 8MM  H8   C8   N2   112.20  3.000
 8MM  H8   C8   C9   107.82  3.000
 8MM  N2   C8   C9   109.61  3.000
 8MM  H8   C8   C7   107.42  3.000
 8MM  C9   C8   C7   109.28  3.000
 8MM  N2   C8   C7   110.43  3.000
 8MM  H10  C9   H9   106.79  3.000
 8MM  H10  C9   C10  109.81  3.000
 8MM  H9   C9   C10  109.30  3.000
 8MM  H10  C9   C8   109.02  3.000
 8MM  H9   C9   C8   109.61  3.000
 8MM  C10  C9   C8   112.16  3.000
 8MM  H11  C10  N1   107.10  3.000
 8MM  H11  C10  C9   108.60  3.000
 8MM  N1   C10  C9   114.09  3.000
 8MM  H11  C10  C11  107.66  3.000
 8MM  N1   C10  C11  109.46  3.000
 8MM  C9   C10  C11  109.71  3.000
 8MM  H12  C12  O2   110.63  3.000
 8MM  H12  C12  C7   107.76  3.000
 8MM  O2   C12  C7   108.61  3.000
 8MM  H12  C12  C11  107.77  3.000
 8MM  O2   C12  C11  110.67  3.000
 8MM  C7   C12  C11  111.35  3.000
 8MM  H13  C13  O4   106.03  3.000
 8MM  H13  C13  O3   110.51  3.000
 8MM  O4   C13  O3   110.37  3.000
 8MM  H13  C13  C14  110.05  3.000
 8MM  O4   C13  C14  111.97  3.000
 8MM  O3   C13  C14  107.93  3.000
 8MM  H15  N1   H14  106.07  3.000
 8MM  H15  N1   C10  109.72  3.000
 8MM  H14  N1   C10  110.01  3.000
 8MM  H18  N2   H17  105.44  3.000
 8MM  H18  N2   C8   109.33  3.000
 8MM  H17  N2   C8   108.90  3.000
 8MM  H21  C3   H20  107.17  3.000
 8MM  H21  C3   C2   109.78  3.000
 8MM  H20  C3   C2   109.61  3.000
 8MM  H21  C3   C4   110.02  3.000
 8MM  H20  C3   C4   110.14  3.000
 8MM  C2   C3   C4   110.07  3.000
 8MM  H22  N3   CAW  117.58  3.000
 8MM  H22  N3   C5   116.45  3.000
 8MM  CAW  N3   C5   123.51  3.000
 8MM  H24  N    C19  110.22  3.000
 8MM  H24  N    C15  110.54  3.000
 8MM  C19  N    C15  116.04  3.000
 8MM  C2   O    C6   115.43  3.000
 8MM  H27  C1   H26  106.37  3.000
 8MM  H27  C1   N4   109.31  3.000
 8MM  H26  C1   N4   113.83  3.000
 8MM  H27  C1   C2   109.66  3.000
 8MM  H26  C1   C2   106.25  3.000
 8MM  N4   C1   C2   111.24  3.000
 8MM  H28  C15  C16  106.54  3.000
 8MM  H28  C15  N    107.35  3.000
 8MM  C16  C15  N    110.71  3.000
 8MM  H28  C15  C14  108.49  3.000
 8MM  N    C15  C14  114.33  3.000
 8MM  C16  C15  C14  109.10  3.000
 8MM  O5   C16  C18  110.90  3.000
 8MM  O5   C16  C17  110.45  3.000
 8MM  C18  C16  C17  108.63  3.000
 8MM  O5   C16  C15  106.33  3.000
 8MM  C18  C16  C15  111.19  3.000
 8MM  C17  C16  C15  109.34  3.000
 8MM  H30  C17  H29  107.14  3.000
 8MM  H30  C17  O4   106.11  3.000
 8MM  H29  C17  O4   110.75  3.000
 8MM  H30  C17  C16  109.91  3.000
 8MM  H29  C17  C16  109.44  3.000
 8MM  O4   C17  C16  113.26  3.000
 8MM  H33  C18  H32  107.40  3.000
 8MM  H33  C18  H31  108.10  3.000
 8MM  H32  C18  H31  108.49  3.000
 8MM  H33  C18  C16  111.49  3.000
 8MM  H32  C18  C16  110.98  3.000
 8MM  H31  C18  C16  110.26  3.000
 8MM  H36  C19  H35  107.55  3.000
 8MM  H36  C19  H34  107.85  3.000
 8MM  H35  C19  H34  107.00  3.000
 8MM  H36  C19  N    115.28  3.000
 8MM  H35  C19  N    109.59  3.000
 8MM  H34  C19  N    109.24  3.000
 8MM  H37  C2   C1   106.87  3.000
 8MM  H37  C2   O    109.76  3.000
 8MM  C1   C2   O    108.28  3.000
 8MM  H37  C2   C3   107.78  3.000
 8MM  O    C2   C3   110.58  3.000
 8MM  C1   C2   C3   113.46  3.000
 8MM  H40  CAC  H39  108.58  3.000
 8MM  H40  CAC  H38  108.26  3.000
 8MM  H39  CAC  H38  107.26  3.000
 8MM  H40  CAC  CAW  113.70  3.000
 8MM  H39  CAC  CAW  109.77  3.000
 8MM  H38  CAC  CAW  109.07  3.000
 8MM  OAH  CAW  CAC  121.64  3.000
 8MM  CAC  CAW  N3   115.15  3.000
 8MM  OAH  CAW  N3   123.20  3.000
 8MM  H43  N4   H42  106.32  3.000
 8MM  H43  N4   C1   109.59  3.000
 8MM  H42  N4   C1   109.73  3.000
 8MM  C7   O1   C6   117.18  3.000
 8MM  H45  O2   C12  109.04  3.000
 8MM  C13  O3   C11  120.42  3.000
 8MM  C17  O4   C13  114.07  3.000
 8MM  H46  O5   C16  108.44  3.000
 8MM  H47  O6   C14  111.24  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
 8MM  CONST_01  OAH  CAW  N3   C5      0.00   0.0  0
 8MM  CONST_02  CAC  CAW  N3   C5    180.00   0.0  0
 8MM  CONST_03  H22  N3   CAW  CAC     0.00   0.0  0
 8MM  Var_01    C2   C3   C4   C5     53.79  30.0  1
 8MM  Var_02    C16  C17  O4   C13    56.87  30.0  1
 8MM  Var_03    H34  C19  N    C15  -176.04  30.0  3
 8MM  Var_04    H42  N4   C1   C2     46.16  30.0  3
 8MM  Var_05    H38  CAC  CAW  N3    118.80  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
 8MM  chir_01  C14  C13  O6   C15  positiv
 8MM  chir_02  C5   C4   N3   C6   negativ
 8MM  chir_03  C6   O    O1   C5   positiv
 8MM  chir_04  C11  O3   C12  C10  positiv
 8MM  chir_05  C7   O1   C12  C8   negativ
 8MM  chir_06  C8   N2   C9   C7   negativ
 8MM  chir_07  C10  N1   C11  C9   negativ
 8MM  chir_08  C12  O2   C7   C11  negativ
 8MM  chir_09  C13  O3   O4   C14  negativ
 8MM  chir_10  C15  N    C14  C16  positiv
 8MM  chir_11  C16  C17  C18  C15  negativ
 8MM  chir_12  C2   C3   C1   O    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
 8MM  plan-1  C5   0.020
 8MM  plan-1  N3   0.020
 8MM  plan-1  CAC  0.020
 8MM  plan-1  CAW  0.020
 8MM  plan-1  OAH  0.020
 8MM  plan-1  H22  0.020

