# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 12:37:46 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: (1S,3S)-3-acetyl-3,5,12-trihydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@H](C[C@H](N)[C@@H]1O)O[C@H]2C[C@@](O)(Cc3c(O)c4C(=O)c5ccccc5C(=O)c4c(O)c23)C(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
 DM5  DM5  '(1S,3S)-3-acetyl-3,5,12-trihydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside'  ligand  63  36  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DM5
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
 DM5  C1    C  CR16  0  -0.258  -0.4933  -0.5912  -6.3636
 DM5  C2    C  CR16  0  -0.209  -1.5488  -0.1533  -7.1455
 DM5  C3    C  CR16  0  -0.209  -2.5910   0.5656  -6.5714
 DM5  C4    C  CR16  0  -0.255  -2.5804   0.8429  -5.2146
 DM5  C5    C  CR66  0  -0.002  -1.5246   0.4048  -4.4208
 DM5  C6    C  CR6   0   0.390  -1.5278   0.7065  -2.9759
 DM5  O6    O  O     0  -0.461  -2.4559   1.3532  -2.4835
 DM5  C7    C  CR66  0  -0.220  -0.4248   0.2229  -2.1642
 DM5  C8    C  CR6   0   0.368  -0.4168   0.4759  -0.7928
 DM5  O8    O  OH1   0  -0.606  -1.3724   1.1795  -0.2054
 DM5  C9    C  CR6   0  -0.022   0.6513   0.0026   0.0150
 DM5  C10   C  CH1   0   0.014   0.5861   0.2462   1.5093
 DM5  O10   O  O2    0  -0.501  -0.6374  -0.2773   1.9888
 DM5  C11   C  CH2   0  -0.475   1.7277  -0.4205   2.2691
 DM5  C12   C  CT    0   0.118   3.0691  -0.3267   1.5537
 DM5  O12   O  OH1   0  -0.639   4.0089  -0.9724   2.3796
 DM5  C13   C  C     0   0.381   3.4532   1.1510   1.3954
 DM5  O13   O  O     0  -0.367   3.3099   1.7248   0.3413
 DM5  C14   C  CH3   0  -0.727   4.0162   1.8342   2.6106
 DM5  C15   C  CH2   0  -0.510   2.9425  -1.0309   0.2096
 DM5  C16   C  CR6   0  -0.019   1.7305  -0.6162  -0.5717
 DM5  C17   C  CR6   0   0.351   1.7200  -0.8935  -1.9647
 DM5  O17   O  OH1   0  -0.603   2.7665  -1.5482  -2.4537
 DM5  C18   C  CR66  0  -0.211   0.6501  -0.4895  -2.7536
 DM5  C19   C  CR6   0   0.383   0.6625  -0.7775  -4.1806
 DM5  O19   O  O     0  -0.439   1.5965  -1.3864  -4.7047
 DM5  C20   C  CR66  0  -0.009  -0.4743  -0.3161  -4.9993
 DM5  C1'   C  CH1   0   0.279  -1.3919   0.5672   2.8144
 DM5  C2'   C  CH2   0  -0.479  -2.7835  -0.0276   2.9489
 DM5  C3'   C  CH1   0  -0.095  -2.7860  -1.2579   3.8482
 DM5  N3'   N  NH2   0  -0.741  -4.1428  -1.7469   4.0233
 DM5  C4'   C  CH1   0   0.036  -2.1462  -0.9050   5.1886
 DM5  O4'   O  OH1   0  -0.625  -2.9624   0.0235   5.8613
 DM5  C5'   C  CH1   0   0.035  -0.7399  -0.3631   4.9253
 DM5  O5'   O  O2    0  -0.484  -0.7770   0.7625   4.0572
 DM5  C6'   C  CH3   0  -0.688  -0.0205   0.0733   6.1853
 DM5  H1    H  HCR6  0   0.265   0.3169  -1.1479  -6.8135
 DM5  H2    H  HCR6  0   0.255  -1.5594  -0.3700  -8.2051
 DM5  H3    H  HCR6  0   0.254  -3.4131   0.9105  -7.1839
 DM5  H4    H  HCR6  0   0.257  -3.3942   1.3999  -4.7712
 DM5  HO8   H  HOH1  0   0.479  -2.0264   1.4305  -0.9029
 DM5  H10   H  HCH1  0   0.233   0.6217   1.3326   1.6748
 DM5  H111  H  HCH2  0   0.261   1.7944   0.0106   3.2703
 DM5  H112  H  HCH2  0   0.257   1.4983  -1.4838   2.3877
 DM5  HO12  H  HOH1  0   0.430   4.8502  -1.0354   1.9131
 DM5  H141  H  HCH3  0   0.257   3.9050   2.9129   2.5241
 DM5  H142  H  HCH3  0   0.245   3.5527   1.4926   3.5349
 DM5  H143  H  HCH3  0   0.257   5.0818   1.6077   2.6899
 DM5  H151  H  HCH2  0   0.262   3.8408  -0.8720  -0.3913
 DM5  H152  H  HCH2  0   0.281   2.8918  -2.1083   0.4017
 DM5  HO17  H  HOH1  0   0.479   2.6186  -1.6630  -3.4225
 DM5  H1'   H  HCH1  0   0.221  -1.4493   1.5680   2.3737
 DM5  H2'1  H  HCH2  0   0.261  -3.4459   0.7325   3.3687
 DM5  H2'2  H  HCH2  0   0.231  -3.1669  -0.2697   1.9548
 DM5  H3'   H  HCH1  0   0.198  -2.1256  -2.0144   3.3974
 DM5  HN'1  H  HNH2  0   0.319  -4.5167  -2.0104   3.1193
 DM5  HN'2  H  HNH2  0   0.315  -4.1240  -2.6037   4.5650
 DM5  H4'   H  HCH1  0   0.184  -2.0354  -1.8298   5.7765
 DM5  HO4'  H  HOH1  0   0.424  -2.6549   0.1005   6.7689
 DM5  H5'   H  HCH1  0   0.196  -0.1640  -1.1790   4.4674
 DM5  H6'1  H  HCH3  0   0.238   1.0091   0.3585   5.9674
 DM5  H6'2  H  HCH3  0   0.227  -0.5076   0.9274   6.6588
 DM5  H6'3  H  HCH3  0   0.212   0.0111  -0.7449   6.9057

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
 DM5  C1   C2    aromatic  1.385  0.020  1.385
 DM5  C1   C20   aromatic  1.392  0.020  1.392
 DM5  C1   H1    single    0.930  0.020  1.080
 DM5  C2   C3    aromatic  1.390  0.020  1.390
 DM5  C2   H2    single    0.930  0.020  1.080
 DM5  C3   C4    aromatic  1.385  0.020  1.385
 DM5  C3   H3    single    0.930  0.020  1.080
 DM5  C4   C5    aromatic  1.392  0.020  1.392
 DM5  C4   H4    single    0.930  0.020  1.080
 DM5  C5   C6    single    1.476  0.020  1.476
 DM5  C5   C20   aromatic  1.399  0.020  1.399
 DM5  C6   O6    double    1.234  0.020  1.234
 DM5  C6   C7    single    1.452  0.020  1.452
 DM5  C7   C8    aromatic  1.395  0.020  1.395
 DM5  C7   C18   aromatic  1.418  0.020  1.418
 DM5  C8   O8    single    1.324  0.020  1.324
 DM5  C8   C9    aromatic  1.420  0.020  1.420
 DM5  O8   HO8   single    0.850  0.020  0.980
 DM5  C9   C10   single    1.515  0.020  1.515
 DM5  C9   C16   aromatic  1.375  0.020  1.375
 DM5  C10  O10   single    1.415  0.020  1.415
 DM5  C10  C11   single    1.525  0.020  1.525
 DM5  C10  H10   single    0.970  0.020  1.090
 DM5  O10  C1'   single    1.401  0.020  1.401
 DM5  C11  C12   single    1.523  0.020  1.523
 DM5  C11  H111  single    0.970  0.020  1.090
 DM5  C11  H112  single    0.970  0.020  1.090
 DM5  C12  O12   single    1.408  0.020  1.408
 DM5  C12  C13   single    1.535  0.020  1.535
 DM5  C12  C15   single    1.523  0.020  1.523
 DM5  O12  HO12  single    0.850  0.020  0.980
 DM5  C13  O13   double    1.209  0.020  1.209
 DM5  C13  C14   single    1.504  0.020  1.504
 DM5  C14  H141  single    0.970  0.020  1.090
 DM5  C14  H142  single    0.970  0.020  1.090
 DM5  C14  H143  single    0.970  0.020  1.090
 DM5  C15  C16   single    1.500  0.020  1.500
 DM5  C15  H151  single    0.970  0.020  1.090
 DM5  C15  H152  single    0.970  0.020  1.090
 DM5  C16  C17   aromatic  1.420  0.020  1.420
 DM5  C17  O17   single    1.328  0.020  1.328
 DM5  C17  C18   aromatic  1.389  0.020  1.389
 DM5  O17  HO17  single    0.850  0.020  0.980
 DM5  C18  C19   single    1.456  0.020  1.456
 DM5  C19  O19   double    1.232  0.020  1.232
 DM5  C19  C20   single    1.475  0.020  1.475
 DM5  C1'  C2'   single    1.519  0.020  1.519
 DM5  C1'  O5'   single    1.400  0.020  1.400
 DM5  C1'  H1'   single    0.970  0.020  1.090
 DM5  C2'  C3'   single    1.524  0.020  1.524
 DM5  C2'  H2'1  single    0.970  0.020  1.090
 DM5  C2'  H2'2  single    0.970  0.020  1.090
 DM5  C3'  N3'   single    1.453  0.020  1.453
 DM5  C3'  C4'   single    1.527  0.020  1.527
 DM5  C3'  H3'   single    0.970  0.020  1.090
 DM5  N3'  HN'1  single    0.890  0.020  1.040
 DM5  N3'  HN'2  single    0.890  0.020  1.040
 DM5  C4'  O4'   single    1.407  0.020  1.407
 DM5  C4'  C5'   single    1.530  0.020  1.530
 DM5  C4'  H4'   single    0.970  0.020  1.090
 DM5  O4'  HO4'  single    0.850  0.020  0.980
 DM5  C5'  O5'   single    1.422  0.020  1.422
 DM5  C5'  C6'   single    1.515  0.020  1.515
 DM5  C5'  H5'   single    0.970  0.020  1.090
 DM5  C6'  H6'1  single    0.970  0.020  1.090
 DM5  C6'  H6'2  single    0.970  0.020  1.090
 DM5  C6'  H6'3  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
 DM5  H1    C1   C20   119.96  3.000
 DM5  H1    C1   C2    119.94  3.000
 DM5  C20   C1   C2    120.09  3.000
 DM5  H2    C2   C3    120.06  3.000
 DM5  H2    C2   C1    119.82  3.000
 DM5  C3    C2   C1    120.12  3.000
 DM5  H3    C3   C4    119.78  3.000
 DM5  H3    C3   C2    120.06  3.000
 DM5  C4    C3   C2    120.16  3.000
 DM5  H4    C4   C5    119.95  3.000
 DM5  H4    C4   C3    119.94  3.000
 DM5  C5    C4   C3    120.11  3.000
 DM5  C20   C5   C6    120.78  3.000
 DM5  C20   C5   C4    119.72  3.000
 DM5  C6    C5   C4    119.50  3.000
 DM5  C7    C6   O6    121.52  3.000
 DM5  C7    C6   C5    118.52  3.000
 DM5  O6    C6   C5    119.96  3.000
 DM5  C18   C7   C8    119.71  3.000
 DM5  C18   C7   C6    120.71  3.000
 DM5  C8    C7   C6    119.57  3.000
 DM5  C9    C8   O8    117.87  3.000
 DM5  C9    C8   C7    120.21  3.000
 DM5  O8    C8   C7    121.91  3.000
 DM5  HO8   O8   C8    107.42  3.000
 DM5  C16   C9   C10   121.78  3.000
 DM5  C16   C9   C8    119.82  3.000
 DM5  C10   C9   C8    118.36  3.000
 DM5  H10   C10  C11   109.44  3.000
 DM5  H10   C10  O10   110.04  3.000
 DM5  C11   C10  O10   108.47  3.000
 DM5  H10   C10  C9    107.81  3.000
 DM5  C11   C10  C9    112.88  3.000
 DM5  O10   C10  C9    108.17  3.000
 DM5  C1'   O10  C10   116.25  3.000
 DM5  H112  C11  H111  107.28  3.000
 DM5  H112  C11  C12   107.18  3.000
 DM5  H111  C11  C12   110.64  3.000
 DM5  H112  C11  C10   108.78  3.000
 DM5  H111  C11  C10   109.26  3.000
 DM5  C12   C11  C10   113.48  3.000
 DM5  C15   C12  C13   112.02  3.000
 DM5  C15   C12  O12   111.18  3.000
 DM5  C13   C12  O12   109.57  3.000
 DM5  C15   C12  C11   108.24  3.000
 DM5  C13   C12  C11   109.15  3.000
 DM5  O12   C12  C11   106.50  3.000
 DM5  HO12  O12  C12   109.18  3.000
 DM5  C14   C13  O13   122.24  3.000
 DM5  C14   C13  C12   116.61  3.000
 DM5  O13   C13  C12   121.15  3.000
 DM5  H143  C14  H142  106.78  3.000
 DM5  H143  C14  H141  108.13  3.000
 DM5  H142  C14  H141  109.57  3.000
 DM5  H143  C14  C13   109.25  3.000
 DM5  H142  C14  C13   112.59  3.000
 DM5  H141  C14  C13   110.36  3.000
 DM5  H152  C15  H151  106.12  3.000
 DM5  H152  C15  C16   109.01  3.000
 DM5  H151  C15  C16   109.73  3.000
 DM5  H152  C15  C12   107.69  3.000
 DM5  H151  C15  C12   110.49  3.000
 DM5  C16   C15  C12   113.51  3.000
 DM5  C17   C16  C15   117.56  3.000
 DM5  C17   C16  C9    120.02  3.000
 DM5  C15   C16  C9    122.42  3.000
 DM5  C18   C17  O17   122.77  3.000
 DM5  C18   C17  C16   120.38  3.000
 DM5  O17   C17  C16   116.85  3.000
 DM5  HO17  O17  C17   107.51  3.000
 DM5  C19   C18  C17   119.51  3.000
 DM5  C19   C18  C7    120.88  3.000
 DM5  C17   C18  C7    119.60  3.000
 DM5  C20   C19  O19   120.18  3.000
 DM5  C20   C19  C18   118.40  3.000
 DM5  O19   C19  C18   121.41  3.000
 DM5  C19   C20  C5    120.68  3.000
 DM5  C19   C20  C1    119.52  3.000
 DM5  C5    C20  C1    119.79  3.000
 DM5  H1'   C1'  O5'   104.64  3.000
 DM5  H1'   C1'  C2'   110.21  3.000
 DM5  O5'   C1'  C2'   112.23  3.000
 DM5  H1'   C1'  O10   109.99  3.000
 DM5  O5'   C1'  O10   111.74  3.000
 DM5  C2'   C1'  O10   108.02  3.000
 DM5  H2'2  C2'  H2'1  106.92  3.000
 DM5  H2'2  C2'  C3'   110.94  3.000
 DM5  H2'1  C2'  C3'   109.51  3.000
 DM5  H2'2  C2'  C1'   109.12  3.000
 DM5  H2'1  C2'  C1'   108.49  3.000
 DM5  C3'   C2'  C1'   111.70  3.000
 DM5  H3'   C3'  C4'   105.49  3.000
 DM5  H3'   C3'  N3'   112.23  3.000
 DM5  C4'   C3'  N3'   111.31  3.000
 DM5  H3'   C3'  C2'   108.18  3.000
 DM5  C4'   C3'  C2'   109.32  3.000
 DM5  N3'   C3'  C2'   110.15  3.000
 DM5  HN'2  N3'  HN'1  105.30  3.000
 DM5  HN'2  N3'  C3'   109.36  3.000
 DM5  HN'1  N3'  C3'   108.94  3.000
 DM5  H4'   C4'  C5'   107.27  3.000
 DM5  H4'   C4'  O4'   110.92  3.000
 DM5  C5'   C4'  O4'   112.44  3.000
 DM5  H4'   C4'  C3'   108.46  3.000
 DM5  C5'   C4'  C3'   108.42  3.000
 DM5  O4'   C4'  C3'   109.21  3.000
 DM5  HO4'  O4'  C4'   108.58  3.000
 DM5  H5'   C5'  C6'   108.16  3.000
 DM5  H5'   C5'  O5'   110.31  3.000
 DM5  C6'   C5'  O5'   106.98  3.000
 DM5  H5'   C5'  C4'   106.89  3.000
 DM5  C6'   C5'  C4'   113.29  3.000
 DM5  O5'   C5'  C4'   111.19  3.000
 DM5  C5'   O5'  C1'   116.29  3.000
 DM5  H6'3  C6'  H6'2  108.27  3.000
 DM5  H6'3  C6'  H6'1  107.51  3.000
 DM5  H6'2  C6'  H6'1  107.67  3.000
 DM5  H6'3  C6'  C5'   110.30  3.000
 DM5  H6'2  C6'  C5'   111.98  3.000
 DM5  H6'1  C6'  C5'   110.95  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
 DM5  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 DM5  CONST_02  C4    C5   C20  C1      0.00   0.0  0
 DM5  CONST_03  C5    C20  C1   C2      0.00   0.0  0
 DM5  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 DM5  CONST_05  C20   C1   C2   C3      0.00   0.0  0
 DM5  CONST_06  C20   C5   C4   C3      0.00   0.0  0
 DM5  CONST_07  C16   C9   C8   C7      0.00   0.0  0
 DM5  CONST_08  C16   C17  C18  C7      0.00   0.0  0
 DM5  CONST_09  C17   C18  C7   C8      0.00   0.0  0
 DM5  CONST_10  C17   C16  C9   C8      0.00   0.0  0
 DM5  CONST_11  C18   C7   C8   C9      0.00   0.0  0
 DM5  CONST_12  C18   C17  C16  C9      0.00   0.0  0
 DM5  CONST_13  O8    C8   C7   C6      0.00   0.0  0
 DM5  CONST_14  O17   C17  C18  C7    180.00   0.0  0
 DM5  CONST_15  C18   C7   C8   O8    180.00   0.0  0
 DM5  CONST_16  C10   C9   C8   O8      0.00   0.0  0
 DM5  CONST_17  C16   C9   C8   O8    180.00   0.0  0
 DM5  CONST_18  O17   C17  C16  C9    180.00   0.0  0
 DM5  CONST_19  O17   C17  C16  C15     0.00   0.0  0
 DM5  CONST_20  C19   C18  C17  O17     0.00   0.0  0
 DM5  CONST_21  H3    C3   C2   C1    180.00   0.0  0
 DM5  CONST_22  H4    C4   C3   C2    180.00   0.0  0
 DM5  CONST_23  H1    C1   C2   C3    180.00   0.0  0
 DM5  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 DM5  Var_01    C12   C15  C16  C9    -18.70  30.0  1
 DM5  Var_02    H141  C14  C13  C12  -158.76  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
 DM5  chir_01  C10  C9   O10  C11  negativ
 DM5  chir_02  C12  C11  C13  C15  positiv
 DM5  chir_03  C1'  O10  O5'  C2'  positiv
 DM5  chir_04  C3'  N3'  C4'  C2'  positiv
 DM5  chir_05  C4'  O4'  C5'  C3'  positiv
 DM5  chir_06  C5'  O5'  C4'  C6'  positiv

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
 DM5  plan-1  C12  0.020
 DM5  plan-1  C13  0.020
 DM5  plan-1  O13  0.020
 DM5  plan-1  C14  0.020
 DM5  plan-2  C1   0.020
 DM5  plan-2  C2   0.020
 DM5  plan-2  C3   0.020
 DM5  plan-2  C4   0.020
 DM5  plan-2  C5   0.020
 DM5  plan-2  C6   0.020
 DM5  plan-2  O6   0.020
 DM5  plan-2  C7   0.020
 DM5  plan-2  C8   0.020
 DM5  plan-2  O8   0.020
 DM5  plan-2  C9   0.020
 DM5  plan-2  C10  0.020
 DM5  plan-2  C15  0.020
 DM5  plan-2  C16  0.020
 DM5  plan-2  C17  0.020
 DM5  plan-2  O17  0.020
 DM5  plan-2  C18  0.020
 DM5  plan-2  C19  0.020
 DM5  plan-2  O19  0.020
 DM5  plan-2  C20  0.020
 DM5  plan-2  H1   0.020
 DM5  plan-2  H2   0.020
 DM5  plan-2  H3   0.020
 DM5  plan-2  H4   0.020

