# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 12:18:38 2022
#   Inital geometry file: a 160 line input string
#   Ligand name: (1S,3S)-3-acetyl-3,12-dihydroxy-10-methoxy-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: COc1cccc2C(=O)c3cc4C[C@](O)(C[C@H](O[C@H]5C[C@H](N)[C@H](O)[C@H](C)O5)c4c(O)c3C(=O)c12)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
 DM3  DM3  '(1S,3S)-3-acetyl-3,12-dihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside'  ligand  66  37  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DM3
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
 DM3  C1    C  CR16  0  -0.302   8.7017  21.2182  33.9327
 DM3  C2    C  CR16  0  -0.217   7.4098  20.7708  33.7293
 DM3  C3    C  CR16  0  -0.381   7.1630  19.4362  33.4698
 DM3  C4    C  CR6   0   0.398   8.2101  18.5122  33.4027
 DM3  O4    O  O2    0  -0.431   7.9908  17.2215  33.1593
 DM3  C5    C  CR66  0  -0.147   9.5410  18.9528  33.6014
 DM3  C6    C  CR6   0   0.354  10.6912  18.0073  33.5284
 DM3  O6    O  O     0  -0.355  10.5209  16.8368  33.2613
 DM3  C7    C  CR66  0  -0.160  12.0494  18.5337  33.8184
 DM3  C8    C  CR6   0   0.342  13.1822  17.7011  33.7959
 DM3  O8    O  OH1   0  -0.597  13.0687  16.4320  33.3995
 DM3  C9    C  CR6   0  -0.045  14.4426  18.1805  34.2124
 DM3  C10   C  CH1   0  -0.043  15.5782  17.1886  34.3658
 DM3  O10   O  O2    0  -0.528  15.7913  16.5781  33.0927
 DM3  C11   C  CH2   0  -0.494  16.8187  17.8175  34.9935
 DM3  C12   C  CT    0   0.089  17.0858  19.2412  34.5085
 DM3  O12   O  OH1   0  -0.653  17.1908  19.2072  33.1079
 DM3  C13   C  C     0   0.391  18.3984  19.6932  35.1629
 DM3  O13   O  O     0  -0.385  18.4035  20.1351  36.2881
 DM3  C14   C  CH3   0  -0.775  19.6570  19.5179  34.3625
 DM3  C15   C  CH2   0  -0.517  15.9139  20.1044  34.9531
 DM3  C16   C  CR6   0   0.125  14.5970  19.5246  34.5245
 DM3  C17   C  CR16  0  -0.384  13.4945  20.3710  34.4633
 DM3  C18   C  CR66  0  -0.017  12.2436  19.8837  34.1442
 DM3  C19   C  CR6   0   0.316  11.1149  20.8389  34.1202
 DM3  O19   O  O     0  -0.372  11.2985  22.0250  34.3039
 DM3  C20   C  CR66  0  -0.028   9.7521  20.3128  33.8728
 DM3  C21   C  CH3   0  -0.445   6.6659  16.7594  32.9704
 DM3  C1'   C  CH1   0   0.265  16.3167  15.2604  33.0881
 DM3  C2'   C  CH2   0  -0.494  16.1216  14.6917  31.6907
 DM3  C3'   C  CH1   0  -0.087  17.1080  15.2861  30.6915
 DM3  N3'   N  NH2   0  -0.800  16.9450  14.6440  29.3977
 DM3  C4'   C  CH1   0   0.029  18.5313  15.1220  31.2215
 DM3  O4'   O  OH1   0  -0.668  18.8602  13.7550  31.2454
 DM3  C5'   C  CH1   0   0.001  18.6087  15.7690  32.6060
 DM3  O5'   O  O2    0  -0.495  17.6449  15.2046  33.4925
 DM3  C6'   C  CH3   0  -0.712  19.9596  15.6071  33.2727
 DM3  H1    H  HCR6  0   0.266   8.8938  22.2606  34.1412
 DM3  H2    H  HCR6  0   0.275   6.5800  21.4634  33.7750
 DM3  H3    H  HCR6  0   0.297   6.1409  19.1196  33.3191
 DM3  HO8   H  HOH1  0   0.494  13.9465  16.1263  33.1215
 DM3  H10   H  HCH1  0   0.263  15.2423  16.4067  35.0647
 DM3  H111  H  HCH2  0   0.274  16.6610  17.8556  36.0741
 DM3  H112  H  HCH2  0   0.297  17.6777  17.1677  34.8353
 DM3  HO12  H  HOH1  0   0.453  17.2191  20.1098  32.7699
 DM3  H141  H  HCH3  0   0.259  20.5314  19.6471  34.9963
 DM3  H142  H  HCH3  0   0.272  19.6951  18.5410  33.8813
 DM3  H143  H  HCH3  0   0.270  19.6967  20.2595  33.5615
 DM3  H151  H  HCH2  0   0.280  15.9213  20.2051  36.0408
 DM3  H152  H  HCH2  0   0.279  16.0089  21.1201  34.5566
 DM3  H17   H  HCR6  0   0.258  13.6202  21.4216  34.6898
 DM3  H211  H  HCH3  0   0.265   6.7444  15.6892  32.7985
 DM3  H212  H  HCH3  0   0.235   6.0415  16.9295  33.8508
 DM3  H213  H  HCH3  0   0.235   6.1908  17.2215  32.1017
 DM3  H1'   H  HCH1  0   0.240  15.7721  14.6566  33.8264
 DM3  H2'1  H  HCH2  0   0.246  16.2614  13.6099  31.7404
 DM3  H2'2  H  HCH2  0   0.251  15.0931  14.8581  31.3585
 DM3  H3'   H  HCH1  0   0.216  16.9340  16.3715  30.6394
 DM3  HN'1  H  HNH2  0   0.341  17.5856  15.0618  28.7324
 DM3  HN'2  H  HNH2  0   0.343  16.0182  14.8510  29.0441
 DM3  H4'   H  HCH1  0   0.221  19.2153  15.6811  30.5640
 DM3  HO4'  H  HOH1  0   0.452  19.8040  13.6673  31.4072
 DM3  H5'   H  HCH1  0   0.224  18.4148  16.8414  32.4753
 DM3  H6'1  H  HCH3  0   0.248  19.9878  16.1418  34.2224
 DM3  H6'2  H  HCH3  0   0.233  20.1937  14.5610  33.4751
 DM3  H6'3  H  HCH3  0   0.235  20.7449  16.0197  32.6384

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
 DM3  C1   C2    aromatic  1.382  0.020  1.382
 DM3  C1   C20   aromatic  1.388  0.020  1.388
 DM3  C1   H1    single    0.930  0.020  1.080
 DM3  C2   C3    aromatic  1.382  0.020  1.382
 DM3  C2   H2    single    0.930  0.020  1.080
 DM3  C3   C4    aromatic  1.398  0.020  1.398
 DM3  C3   H3    single    0.930  0.020  1.080
 DM3  C4   O4    single    1.332  0.020  1.332
 DM3  C4   C5    aromatic  1.416  0.020  1.416
 DM3  O4   C21   single    1.416  0.020  1.416
 DM3  C5   C6    single    1.491  0.020  1.491
 DM3  C5   C20   aromatic  1.403  0.020  1.403
 DM3  C6   O6    double    1.213  0.020  1.213
 DM3  C6   C7    single    1.485  0.020  1.485
 DM3  C7   C8    aromatic  1.406  0.020  1.406
 DM3  C7   C18   aromatic  1.402  0.020  1.402
 DM3  C8   O8    single    1.334  0.020  1.334
 DM3  C8   C9    aromatic  1.411  0.020  1.411
 DM3  O8   HO8   single    0.850  0.020  0.980
 DM3  C9   C10   single    1.516  0.020  1.516
 DM3  C9   C16   aromatic  1.388  0.020  1.388
 DM3  C10  O10   single    1.428  0.020  1.428
 DM3  C10  C11   single    1.526  0.020  1.526
 DM3  C10  H10   single    0.970  0.020  1.090
 DM3  O10  C1'   single    1.419  0.020  1.419
 DM3  C11  C12   single    1.528  0.020  1.528
 DM3  C11  H111  single    0.970  0.020  1.090
 DM3  C11  H112  single    0.970  0.020  1.090
 DM3  C12  O12   single    1.405  0.020  1.405
 DM3  C12  C13   single    1.535  0.020  1.535
 DM3  C12  C15   single    1.522  0.020  1.522
 DM3  O12  HO12  single    0.850  0.020  0.980
 DM3  C13  O13   double    1.209  0.020  1.209
 DM3  C13  C14   single    1.502  0.020  1.502
 DM3  C14  H141  single    0.970  0.020  1.090
 DM3  C14  H142  single    0.970  0.020  1.090
 DM3  C14  H143  single    0.970  0.020  1.090
 DM3  C15  C16   single    1.501  0.020  1.501
 DM3  C15  H151  single    0.970  0.020  1.090
 DM3  C15  H152  single    0.970  0.020  1.090
 DM3  C16  C17   aromatic  1.391  0.020  1.391
 DM3  C17  C18   aromatic  1.380  0.020  1.380
 DM3  C17  H17   single    0.930  0.020  1.080
 DM3  C18  C19   single    1.479  0.020  1.479
 DM3  C19  O19   double    1.214  0.020  1.214
 DM3  C19  C20   single    1.482  0.020  1.482
 DM3  C21  H211  single    0.970  0.020  1.090
 DM3  C21  H212  single    0.970  0.020  1.090
 DM3  C21  H213  single    0.970  0.020  1.090
 DM3  C1'  C2'   single    1.521  0.020  1.521
 DM3  C1'  O5'   single    1.390  0.020  1.390
 DM3  C1'  H1'   single    0.970  0.020  1.090
 DM3  C2'  C3'   single    1.525  0.020  1.525
 DM3  C2'  H2'1  single    0.970  0.020  1.090
 DM3  C2'  H2'2  single    0.970  0.020  1.090
 DM3  C3'  N3'   single    1.454  0.020  1.454
 DM3  C3'  C4'   single    1.528  0.020  1.528
 DM3  C3'  H3'   single    0.970  0.020  1.090
 DM3  N3'  HN'1  single    0.890  0.020  1.040
 DM3  N3'  HN'2  single    0.890  0.020  1.040
 DM3  C4'  O4'   single    1.406  0.020  1.406
 DM3  C4'  C5'   single    1.530  0.020  1.530
 DM3  C4'  H4'   single    0.970  0.020  1.090
 DM3  O4'  HO4'  single    0.850  0.020  0.980
 DM3  C5'  O5'   single    1.426  0.020  1.426
 DM3  C5'  C6'   single    1.515  0.020  1.515
 DM3  C5'  H5'   single    0.970  0.020  1.090
 DM3  C6'  H6'1  single    0.970  0.020  1.090
 DM3  C6'  H6'2  single    0.970  0.020  1.090
 DM3  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
 DM3  H1    C1   C20   120.21  3.000
 DM3  H1    C1   C2    120.46  3.000
 DM3  C20   C1   C2    119.33  3.000
 DM3  H2    C2   C3    119.29  3.000
 DM3  H2    C2   C1    120.23  3.000
 DM3  C3    C2   C1    120.47  3.000
 DM3  H3    C3   C4    120.54  3.000
 DM3  H3    C3   C2    118.56  3.000
 DM3  C4    C3   C2    120.90  3.000
 DM3  C5    C4   O4    118.82  3.000
 DM3  C5    C4   C3    119.44  3.000
 DM3  O4    C4   C3    121.73  3.000
 DM3  C21   O4   C4    119.66  3.000
 DM3  C20   C5   C6    120.55  3.000
 DM3  C20   C5   C4    118.05  3.000
 DM3  C6    C5   C4    121.40  3.000
 DM3  C7    C6   O6    120.90  3.000
 DM3  C7    C6   C5    118.11  3.000
 DM3  O6    C6   C5    120.98  3.000
 DM3  C18   C7   C8    117.53  3.000
 DM3  C18   C7   C6    120.88  3.000
 DM3  C8    C7   C6    121.59  3.000
 DM3  C9    C8   O8    119.12  3.000
 DM3  C9    C8   C7    120.90  3.000
 DM3  O8    C8   C7    119.96  3.000
 DM3  HO8   O8   C8    107.94  3.000
 DM3  C16   C9   C10   121.83  3.000
 DM3  C16   C9   C8    119.64  3.000
 DM3  C10   C9   C8    118.47  3.000
 DM3  H10   C10  C11   106.23  3.000
 DM3  H10   C10  O10   107.93  3.000
 DM3  C11   C10  O10   114.93  3.000
 DM3  H10   C10  C9    107.49  3.000
 DM3  C11   C10  C9    112.40  3.000
 DM3  O10   C10  C9    107.54  3.000
 DM3  C1'   O10  C10   117.08  3.000
 DM3  H112  C11  H111  106.16  3.000
 DM3  H112  C11  C12   111.85  3.000
 DM3  H111  C11  C12   107.86  3.000
 DM3  H112  C11  C10   109.62  3.000
 DM3  H111  C11  C10   107.69  3.000
 DM3  C12   C11  C10   113.31  3.000
 DM3  C15   C12  C13   111.53  3.000
 DM3  C15   C12  O12   111.25  3.000
 DM3  C13   C12  O12   111.61  3.000
 DM3  C15   C12  C11   107.53  3.000
 DM3  C13   C12  C11   106.78  3.000
 DM3  O12   C12  C11   107.89  3.000
 DM3  HO12  O12  C12   109.22  3.000
 DM3  C14   C13  O13   122.36  3.000
 DM3  C14   C13  C12   117.07  3.000
 DM3  O13   C13  C12   120.54  3.000
 DM3  H143  C14  H142  106.47  3.000
 DM3  H143  C14  H141  108.51  3.000
 DM3  H142  C14  H141  109.62  3.000
 DM3  H143  C14  C13   110.00  3.000
 DM3  H142  C14  C13   111.67  3.000
 DM3  H141  C14  C13   110.44  3.000
 DM3  H152  C15  H151  105.93  3.000
 DM3  H152  C15  C16   109.33  3.000
 DM3  H151  C15  C16   109.01  3.000
 DM3  H152  C15  C12   110.72  3.000
 DM3  H151  C15  C12   109.75  3.000
 DM3  C16   C15  C12   111.90  3.000
 DM3  C17   C16  C15   118.21  3.000
 DM3  C17   C16  C9    119.40  3.000
 DM3  C15   C16  C9    122.38  3.000
 DM3  H17   C17  C18   119.77  3.000
 DM3  H17   C17  C16   119.30  3.000
 DM3  C18   C17  C16   120.91  3.000
 DM3  C19   C18  C17   117.88  3.000
 DM3  C19   C18  C7    120.82  3.000
 DM3  C17   C18  C7    121.28  3.000
 DM3  C20   C19  O19   120.75  3.000
 DM3  C20   C19  C18   118.38  3.000
 DM3  O19   C19  C18   120.87  3.000
 DM3  C19   C20  C5    120.99  3.000
 DM3  C19   C20  C1    117.21  3.000
 DM3  C5    C20  C1    121.79  3.000
 DM3  H213  C21  H212  109.04  3.000
 DM3  H213  C21  H211  108.79  3.000
 DM3  H212  C21  H211  108.79  3.000
 DM3  H213  C21  O4    112.02  3.000
 DM3  H212  C21  O4    112.11  3.000
 DM3  H211  C21  O4    105.96  3.000
 DM3  H1'   C1'  O5'   104.84  3.000
 DM3  H1'   C1'  C2'   110.38  3.000
 DM3  O5'   C1'  C2'   112.02  3.000
 DM3  H1'   C1'  O10   108.96  3.000
 DM3  O5'   C1'  O10   112.98  3.000
 DM3  C2'   C1'  O10   107.63  3.000
 DM3  H2'2  C2'  H2'1  106.57  3.000
 DM3  H2'2  C2'  C3'   110.49  3.000
 DM3  H2'1  C2'  C3'   109.46  3.000
 DM3  H2'2  C2'  C1'   110.05  3.000
 DM3  H2'1  C2'  C1'   108.19  3.000
 DM3  C3'   C2'  C1'   111.91  3.000
 DM3  H3'   C3'  C4'   105.65  3.000
 DM3  H3'   C3'  N3'   112.08  3.000
 DM3  C4'   C3'  N3'   111.46  3.000
 DM3  H3'   C3'  C2'   108.25  3.000
 DM3  C4'   C3'  C2'   109.48  3.000
 DM3  N3'   C3'  C2'   109.79  3.000
 DM3  HN'2  N3'  HN'1  105.35  3.000
 DM3  HN'2  N3'  C3'   108.84  3.000
 DM3  HN'1  N3'  C3'   109.34  3.000
 DM3  H4'   C4'  C5'   107.11  3.000
 DM3  H4'   C4'  O4'   111.00  3.000
 DM3  C5'   C4'  O4'   112.57  3.000
 DM3  H4'   C4'  C3'   108.48  3.000
 DM3  C5'   C4'  C3'   108.40  3.000
 DM3  O4'   C4'  C3'   109.16  3.000
 DM3  HO4'  O4'  C4'   108.73  3.000
 DM3  H5'   C5'  C6'   108.32  3.000
 DM3  H5'   C5'  O5'   109.96  3.000
 DM3  C6'   C5'  O5'   106.67  3.000
 DM3  H5'   C5'  C4'   107.24  3.000
 DM3  C6'   C5'  C4'   113.46  3.000
 DM3  O5'   C5'  C4'   111.16  3.000
 DM3  C5'   O5'  C1'   116.69  3.000
 DM3  H6'3  C6'  H6'2  108.43  3.000
 DM3  H6'3  C6'  H6'1  107.60  3.000
 DM3  H6'2  C6'  H6'1  107.65  3.000
 DM3  H6'3  C6'  C5'   110.22  3.000
 DM3  H6'2  C6'  C5'   112.05  3.000
 DM3  H6'1  C6'  C5'   110.73  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
 DM3  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 DM3  CONST_02  C4    C5   C20  C1      0.00   0.0  0
 DM3  CONST_03  C5    C20  C1   C2      0.00   0.0  0
 DM3  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 DM3  CONST_05  C20   C1   C2   C3      0.00   0.0  0
 DM3  CONST_06  C20   C5   C4   C3      0.00   0.0  0
 DM3  CONST_07  C16   C9   C8   C7      0.00   0.0  0
 DM3  CONST_08  C16   C17  C18  C7      0.00   0.0  0
 DM3  CONST_09  C17   C18  C7   C8      0.00   0.0  0
 DM3  CONST_10  C17   C16  C9   C8      0.00   0.0  0
 DM3  CONST_11  C18   C7   C8   C9      0.00   0.0  0
 DM3  CONST_12  C18   C17  C16  C9      0.00   0.0  0
 DM3  CONST_13  O4    C4   C3   C2    180.00   0.0  0
 DM3  CONST_14  C6    C5   C4   O4      0.00   0.0  0
 DM3  CONST_15  C20   C5   C4   O4    180.00   0.0  0
 DM3  CONST_16  O8    C8   C7   C6      0.00   0.0  0
 DM3  CONST_17  C18   C7   C8   O8    180.00   0.0  0
 DM3  CONST_18  C10   C9   C8   O8      0.00   0.0  0
 DM3  CONST_19  C16   C9   C8   O8    180.00   0.0  0
 DM3  CONST_20  H3    C3   C2   C1    180.00   0.0  0
 DM3  CONST_21  H1    C1   C2   C3    180.00   0.0  0
 DM3  CONST_22  H2    C2   C3   C4    180.00   0.0  0
 DM3  CONST_23  H17   C17  C18  C7    180.00   0.0  0
 DM3  Var_01    C12   C15  C16  C9     21.54  30.0  1
 DM3  Var_02    H211  C21  O4   C4   -179.54  30.0  3
 DM3  Var_03    H141  C14  C13  C12  -166.72  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
 DM3  chir_01  C10  C9   O10  C11  negativ
 DM3  chir_02  C12  C11  C13  C15  positiv
 DM3  chir_03  C1'  O10  O5'  C2'  positiv
 DM3  chir_04  C3'  N3'  C4'  C2'  positiv
 DM3  chir_05  C4'  O4'  C5'  C3'  positiv
 DM3  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
 DM3  plan-1  C12  0.020
 DM3  plan-1  C13  0.020
 DM3  plan-1  O13  0.020
 DM3  plan-1  C14  0.020
 DM3  plan-2  C1   0.020
 DM3  plan-2  C2   0.020
 DM3  plan-2  C3   0.020
 DM3  plan-2  C4   0.020
 DM3  plan-2  O4   0.020
 DM3  plan-2  C5   0.020
 DM3  plan-2  C6   0.020
 DM3  plan-2  O6   0.020
 DM3  plan-2  C7   0.020
 DM3  plan-2  C8   0.020
 DM3  plan-2  O8   0.020
 DM3  plan-2  C9   0.020
 DM3  plan-2  C10  0.020
 DM3  plan-2  C15  0.020
 DM3  plan-2  C16  0.020
 DM3  plan-2  C17  0.020
 DM3  plan-2  C18  0.020
 DM3  plan-2  C19  0.020
 DM3  plan-2  O19  0.020
 DM3  plan-2  C20  0.020
 DM3  plan-2  H1   0.020
 DM3  plan-2  H2   0.020
 DM3  plan-2  H3   0.020
 DM3  plan-2  H17  0.020

