# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 13:42:43 2022
#   Inital geometry file: a 162 line input string
#   Ligand name: (1S,3S)-3-acetyl-3,5,12-trihydroxy-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)c3c(O)c4C[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
 DM1  DM1  '(1S,3S)-3-acetyl-3,5,12-trihydroxy-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  67  38  .  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_DM1
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
 DM1  C1    C  CR16  0  -0.302  14.9530  18.4406   4.5452
 DM1  C2    C  CR16  0  -0.219  16.0845  19.1993   4.7815
 DM1  C3    C  CR16  0  -0.379  17.3143  18.5949   4.9768
 DM1  C4    C  CR6   0   0.401  17.4428  17.2055   4.9150
 DM1  O4    O  O2    0  -0.438  18.6025  16.5814   5.1160
 DM1  C5    C  CR66  0  -0.153  16.3005  16.4181   4.6595
 DM1  C6    C  CR6   0   0.333  16.3892  14.9451   4.4884
 DM1  O6    O  O     0  -0.353  17.4320  14.4036   4.1897
 DM1  C7    C  CR66  0  -0.174  15.1375  14.1722   4.6584
 DM1  C8    C  CR6   0   0.310  15.1607  12.8086   4.9137
 DM1  O8    O  OH1   0  -0.612  16.3292  12.1762   5.0940
 DM1  C9    C  CR6   0  -0.024  13.9507  12.0725   4.9858
 DM1  C10   C  CH1   0  -0.042  14.0487  10.5671   5.1366
 DM1  O10   O  O2    0  -0.527  14.7663  10.3110   6.3419
 DM1  C11   C  CH2   0  -0.487  12.6961   9.8691   5.0304
 DM1  C12   C  CT    0   0.087  11.5667  10.6547   5.6899
 DM1  O12   O  OH1   0  -0.653  11.9129  10.8442   7.0382
 DM1  C13   C  C     0   0.391  10.2915   9.8097   5.5452
 DM1  O13   O  O     0  -0.385   9.6480   9.8391   4.5222
 DM1  C14   C  CH3   0  -0.773   9.9209   8.9292   6.7042
 DM1  C15   C  CH2   0  -0.495  11.4234  11.9842   4.9617
 DM1  C16   C  CR6   0  -0.027  12.7331  12.7085   4.8518
 DM1  C17   C  CR6   0   0.329  12.7032  14.0933   4.5818
 DM1  O17   O  OH1   0  -0.613  11.5083  14.6522   4.4139
 DM1  C18   C  CR66  0  -0.185  13.8924  14.8197   4.5038
 DM1  C19   C  CR6   0   0.392  13.8310  16.2638   4.3163
 DM1  O19   O  O     0  -0.449  12.7665  16.8328   4.0772
 DM1  C20   C  CR66  0   0.001  15.0645  17.0567   4.5002
 DM1  C21   C  CH3   0  -0.444  19.7569  17.3411   5.4253
 DM1  C1'   C  CH1   0   0.263  15.5136   9.1067   6.4076
 DM1  C2'   C  CH2   0  -0.496  16.5109   9.2485   7.5479
 DM1  C3'   C  CH1   0  -0.087  15.8279   9.1451   8.9062
 DM1  N3'   N  NH2   0  -0.801  16.8183   9.2231   9.9667
 DM1  C4'   C  CH1   0   0.028  15.0374   7.8404   8.9679
 DM1  O4'   O  OH1   0  -0.668  15.9356   6.7583   8.9297
 DM1  C5'   C  CH1   0   0.006  14.0438   7.8277   7.8029
 DM1  O5'   O  O2    0  -0.494  14.7135   7.9794   6.5535
 DM1  C6'   C  CH3   0  -0.710  13.2356   6.5496   7.7146
 DM1  H1    H  HCR6  0   0.268  13.9929  18.9165   4.4084
 DM1  H2    H  HCR6  0   0.276  16.0136  20.2779   4.8256
 DM1  H3    H  HCR6  0   0.298  18.1729  19.2203   5.1763
 DM1  HO8   H  HOH1  0   0.492  16.1644  11.4205   5.6776
 DM1  H10   H  HCH1  0   0.266  14.6527  10.1993   4.2927
 DM1  H111  H  HCH2  0   0.274  12.4589   9.7600   3.9693
 DM1  H112  H  HCH2  0   0.294  12.7751   8.8595   5.4326
 DM1  HO12  H  HOH1  0   0.453  11.2897  11.4571   7.4448
 DM1  H141  H  HCH3  0   0.259   9.1379   8.2312   6.4167
 DM1  H142  H  HCH3  0   0.271  10.7831   8.3764   7.0776
 DM1  H143  H  HCH3  0   0.270   9.5569   9.5365   7.5358
 DM1  H151  H  HCH2  0   0.279  11.0126  11.8193   3.9627
 DM1  H152  H  HCH2  0   0.277  10.6950  12.6135   5.4817
 DM1  HO17  H  HOH1  0   0.484  11.6515  15.6081   4.2206
 DM1  H211  H  HCH3  0   0.265  20.5624  16.6237   5.5575
 DM1  H212  H  HCH3  0   0.236  20.0233  18.0253   4.6165
 DM1  H213  H  HCH3  0   0.235  19.6361  17.9102   6.3500
 DM1  H1'   H  HCH1  0   0.242  16.0381   8.9607   5.4540
 DM1  H2'1  H  HCH2  0   0.248  17.2559   8.4565   7.4496
 DM1  H2'2  H  HCH2  0   0.251  17.0529  10.1944   7.4615
 DM1  H3'   H  HCH1  0   0.217  15.0804   9.9495   8.9801
 DM1  HN'1  H  HNH2  0   0.342  16.3516   9.1777  10.8654
 DM1  HN'2  H  HNH2  0   0.344  17.2575  10.1356   9.9370
 DM1  H4'   H  HCH1  0   0.222  14.4469   7.8318   9.8974
 DM1  HO4'  H  HOH1  0   0.452  15.4544   5.9502   9.1293
 DM1  H5'   H  HCH1  0   0.222  13.3498   8.6638   7.9591
 DM1  H6'1  H  HCH3  0   0.249  12.4952   6.6147   6.9169
 DM1  H6'2  H  HCH3  0   0.231  13.8633   5.6801   7.5137
 DM1  H6'3  H  HCH3  0   0.235  12.7016   6.3784   8.6498

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
 DM1  C1   C2    aromatic  1.383  0.020  1.383
 DM1  C1   C20   aromatic  1.389  0.020  1.389
 DM1  C1   H1    single    0.930  0.020  1.080
 DM1  C2   C3    aromatic  1.384  0.020  1.384
 DM1  C2   H2    single    0.930  0.020  1.080
 DM1  C3   C4    aromatic  1.397  0.020  1.397
 DM1  C3   H3    single    0.930  0.020  1.080
 DM1  C4   O4    single    1.332  0.020  1.332
 DM1  C4   C5    aromatic  1.411  0.020  1.411
 DM1  O4   C21   single    1.416  0.020  1.416
 DM1  C5   C6    single    1.486  0.020  1.486
 DM1  C5   C20   aromatic  1.400  0.020  1.400
 DM1  C6   O6    double    1.212  0.020  1.212
 DM1  C6   C7    single    1.481  0.020  1.481
 DM1  C7   C8    aromatic  1.387  0.020  1.387
 DM1  C7   C18   aromatic  1.412  0.020  1.412
 DM1  C8   O8    single    1.341  0.020  1.341
 DM1  C8   C9    aromatic  1.418  0.020  1.418
 DM1  O8   HO8   single    0.850  0.020  0.980
 DM1  C9   C10   single    1.516  0.020  1.516
 DM1  C9   C16   aromatic  1.380  0.020  1.380
 DM1  C10  O10   single    1.426  0.020  1.426
 DM1  C10  C11   single    1.526  0.020  1.526
 DM1  C10  H10   single    0.970  0.020  1.090
 DM1  O10  C1'   single    1.419  0.020  1.419
 DM1  C11  C12   single    1.526  0.020  1.526
 DM1  C11  H111  single    0.970  0.020  1.090
 DM1  C11  H112  single    0.970  0.020  1.090
 DM1  C12  O12   single    1.405  0.020  1.405
 DM1  C12  C13   single    1.537  0.020  1.537
 DM1  C12  C15   single    1.523  0.020  1.523
 DM1  O12  HO12  single    0.850  0.020  0.980
 DM1  C13  O13   double    1.209  0.020  1.209
 DM1  C13  C14   single    1.502  0.020  1.502
 DM1  C14  H141  single    0.970  0.020  1.090
 DM1  C14  H142  single    0.970  0.020  1.090
 DM1  C14  H143  single    0.970  0.020  1.090
 DM1  C15  C16   single    1.501  0.020  1.501
 DM1  C15  H151  single    0.970  0.020  1.090
 DM1  C15  H152  single    0.970  0.020  1.090
 DM1  C16  C17   aromatic  1.411  0.020  1.411
 DM1  C17  O17   single    1.330  0.020  1.330
 DM1  C17  C18   aromatic  1.396  0.020  1.396
 DM1  O17  HO17  single    0.850  0.020  0.980
 DM1  C18  C19   single    1.457  0.020  1.457
 DM1  C19  O19   double    1.230  0.020  1.230
 DM1  C19  C20   single    1.478  0.020  1.478
 DM1  C21  H211  single    0.970  0.020  1.090
 DM1  C21  H212  single    0.970  0.020  1.090
 DM1  C21  H213  single    0.970  0.020  1.090
 DM1  C1'  C2'   single    1.522  0.020  1.522
 DM1  C1'  O5'   single    1.390  0.020  1.390
 DM1  C1'  H1'   single    0.970  0.020  1.090
 DM1  C2'  C3'   single    1.524  0.020  1.524
 DM1  C2'  H2'1  single    0.970  0.020  1.090
 DM1  C2'  H2'2  single    0.970  0.020  1.090
 DM1  C3'  N3'   single    1.453  0.020  1.453
 DM1  C3'  C4'   single    1.527  0.020  1.527
 DM1  C3'  H3'   single    0.970  0.020  1.090
 DM1  N3'  HN'1  single    0.890  0.020  1.040
 DM1  N3'  HN'2  single    0.890  0.020  1.040
 DM1  C4'  O4'   single    1.407  0.020  1.407
 DM1  C4'  C5'   single    1.531  0.020  1.531
 DM1  C4'  H4'   single    0.970  0.020  1.090
 DM1  O4'  HO4'  single    0.850  0.020  0.980
 DM1  C5'  O5'   single    1.426  0.020  1.426
 DM1  C5'  C6'   single    1.515  0.020  1.515
 DM1  C5'  H5'   single    0.970  0.020  1.090
 DM1  C6'  H6'1  single    0.970  0.020  1.090
 DM1  C6'  H6'2  single    0.970  0.020  1.090
 DM1  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
 DM1  H1    C1   C20   120.40  3.000
 DM1  H1    C1   C2    120.48  3.000
 DM1  C20   C1   C2    119.11  3.000
 DM1  H2    C2   C3    119.20  3.000
 DM1  H2    C2   C1    120.03  3.000
 DM1  C3    C2   C1    120.77  3.000
 DM1  H3    C3   C4    120.71  3.000
 DM1  H3    C3   C2    118.64  3.000
 DM1  C4    C3   C2    120.65  3.000
 DM1  C5    C4   O4    118.08  3.000
 DM1  C5    C4   C3    119.26  3.000
 DM1  O4    C4   C3    122.64  3.000
 DM1  C21   O4   C4    119.42  3.000
 DM1  C20   C5   C6    119.46  3.000
 DM1  C20   C5   C4    118.73  3.000
 DM1  C6    C5   C4    121.73  3.000
 DM1  C7    C6   O6    121.48  3.000
 DM1  C7    C6   C5    116.99  3.000
 DM1  O6    C6   C5    121.51  3.000
 DM1  C18   C7   C8    119.05  3.000
 DM1  C18   C7   C6    119.57  3.000
 DM1  C8    C7   C6    121.33  3.000
 DM1  C9    C8   O8    119.47  3.000
 DM1  C9    C8   C7    120.35  3.000
 DM1  O8    C8   C7    120.19  3.000
 DM1  HO8   O8   C8    107.49  3.000
 DM1  C16   C9   C10   121.61  3.000
 DM1  C16   C9   C8    120.57  3.000
 DM1  C10   C9   C8    117.73  3.000
 DM1  H10   C10  C11   106.27  3.000
 DM1  H10   C10  O10   108.17  3.000
 DM1  C11   C10  O10   115.02  3.000
 DM1  H10   C10  C9    106.91  3.000
 DM1  C11   C10  C9    112.96  3.000
 DM1  O10   C10  C9    107.15  3.000
 DM1  C1'   O10  C10   117.17  3.000
 DM1  H112  C11  H111  106.36  3.000
 DM1  H112  C11  C12   111.79  3.000
 DM1  H111  C11  C12   108.09  3.000
 DM1  H112  C11  C10   109.50  3.000
 DM1  H111  C11  C10   107.80  3.000
 DM1  C12   C11  C10   112.99  3.000
 DM1  C15   C12  C13   110.92  3.000
 DM1  C15   C12  O12   111.37  3.000
 DM1  C13   C12  O12   111.66  3.000
 DM1  C15   C12  C11   108.21  3.000
 DM1  C13   C12  C11   106.88  3.000
 DM1  O12   C12  C11   107.58  3.000
 DM1  HO12  O12  C12   109.35  3.000
 DM1  C14   C13  O13   122.40  3.000
 DM1  C14   C13  C12   117.03  3.000
 DM1  O13   C13  C12   120.54  3.000
 DM1  H143  C14  H142  106.55  3.000
 DM1  H143  C14  H141  108.55  3.000
 DM1  H142  C14  H141  109.54  3.000
 DM1  H143  C14  C13   110.11  3.000
 DM1  H142  C14  C13   111.49  3.000
 DM1  H141  C14  C13   110.48  3.000
 DM1  H152  C15  H151  105.72  3.000
 DM1  H152  C15  C16   109.77  3.000
 DM1  H151  C15  C16   109.51  3.000
 DM1  H152  C15  C12   109.73  3.000
 DM1  H151  C15  C12   109.93  3.000
 DM1  C16   C15  C12   111.98  3.000
 DM1  C17   C16  C15   117.98  3.000
 DM1  C17   C16  C9    119.30  3.000
 DM1  C15   C16  C9    122.71  3.000
 DM1  C18   C17  O17   122.67  3.000
 DM1  C18   C17  C16   120.23  3.000
 DM1  O17   C17  C16   117.11  3.000
 DM1  HO17  O17  C17   107.57  3.000
 DM1  C19   C18  C17   119.15  3.000
 DM1  C19   C18  C7    120.37  3.000
 DM1  C17   C18  C7    120.43  3.000
 DM1  C20   C19  O19   119.88  3.000
 DM1  C20   C19  C18   118.72  3.000
 DM1  O19   C19  C18   121.30  3.000
 DM1  C19   C20  C5    120.41  3.000
 DM1  C19   C20  C1    118.14  3.000
 DM1  C5    C20  C1    121.43  3.000
 DM1  H213  C21  H212  109.12  3.000
 DM1  H213  C21  H211  108.84  3.000
 DM1  H212  C21  H211  108.83  3.000
 DM1  H213  C21  O4    111.97  3.000
 DM1  H212  C21  O4    111.90  3.000
 DM1  H211  C21  O4    106.06  3.000
 DM1  H1'   C1'  O5'   104.97  3.000
 DM1  H1'   C1'  C2'   110.49  3.000
 DM1  O5'   C1'  C2'   111.98  3.000
 DM1  H1'   C1'  O10   108.92  3.000
 DM1  O5'   C1'  O10   112.96  3.000
 DM1  C2'   C1'  O10   107.50  3.000
 DM1  H2'2  C2'  H2'1  106.39  3.000
 DM1  H2'2  C2'  C3'   110.57  3.000
 DM1  H2'1  C2'  C3'   109.69  3.000
 DM1  H2'2  C2'  C1'   110.26  3.000
 DM1  H2'1  C2'  C1'   108.19  3.000
 DM1  C3'   C2'  C1'   111.59  3.000
 DM1  H3'   C3'  C4'   105.68  3.000
 DM1  H3'   C3'  N3'   112.00  3.000
 DM1  C4'   C3'  N3'   111.67  3.000
 DM1  H3'   C3'  C2'   108.34  3.000
 DM1  C4'   C3'  C2'   109.03  3.000
 DM1  N3'   C3'  C2'   109.97  3.000
 DM1  HN'2  N3'  HN'1  105.42  3.000
 DM1  HN'2  N3'  C3'   108.81  3.000
 DM1  HN'1  N3'  C3'   109.32  3.000
 DM1  H4'   C4'  C5'   107.11  3.000
 DM1  H4'   C4'  O4'   111.05  3.000
 DM1  C5'   C4'  O4'   112.78  3.000
 DM1  H4'   C4'  C3'   108.57  3.000
 DM1  C5'   C4'  C3'   108.20  3.000
 DM1  O4'   C4'  C3'   109.01  3.000
 DM1  HO4'  O4'  C4'   108.75  3.000
 DM1  H5'   C5'  C6'   108.28  3.000
 DM1  H5'   C5'  O5'   109.92  3.000
 DM1  C6'   C5'  O5'   106.82  3.000
 DM1  H5'   C5'  C4'   107.20  3.000
 DM1  C6'   C5'  C4'   113.42  3.000
 DM1  O5'   C5'  C4'   111.16  3.000
 DM1  C5'   O5'  C1'   116.66  3.000
 DM1  H6'3  C6'  H6'2  108.33  3.000
 DM1  H6'3  C6'  H6'1  107.72  3.000
 DM1  H6'2  C6'  H6'1  107.67  3.000
 DM1  H6'3  C6'  C5'   110.11  3.000
 DM1  H6'2  C6'  C5'   112.10  3.000
 DM1  H6'1  C6'  C5'   110.76  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
 DM1  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 DM1  CONST_02  C4    C5   C20  C1      0.00   0.0  0
 DM1  CONST_03  C5    C20  C1   C2      0.00   0.0  0
 DM1  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 DM1  CONST_05  C20   C1   C2   C3      0.00   0.0  0
 DM1  CONST_06  C20   C5   C4   C3      0.00   0.0  0
 DM1  CONST_07  C16   C9   C8   C7      0.00   0.0  0
 DM1  CONST_08  C16   C17  C18  C7      0.00   0.0  0
 DM1  CONST_09  C17   C18  C7   C8      0.00   0.0  0
 DM1  CONST_10  C17   C16  C9   C8      0.00   0.0  0
 DM1  CONST_11  C18   C7   C8   C9      0.00   0.0  0
 DM1  CONST_12  C18   C17  C16  C9      0.00   0.0  0
 DM1  CONST_13  O4    C4   C3   C2    180.00   0.0  0
 DM1  CONST_14  C6    C5   C4   O4      0.00   0.0  0
 DM1  CONST_15  C20   C5   C4   O4    180.00   0.0  0
 DM1  CONST_16  O8    C8   C7   C6      0.00   0.0  0
 DM1  CONST_17  O17   C17  C18  C7    180.00   0.0  0
 DM1  CONST_18  C18   C7   C8   O8    180.00   0.0  0
 DM1  CONST_19  C10   C9   C8   O8      0.00   0.0  0
 DM1  CONST_20  C16   C9   C8   O8    180.00   0.0  0
 DM1  CONST_21  O17   C17  C16  C9    180.00   0.0  0
 DM1  CONST_22  O17   C17  C16  C15     0.00   0.0  0
 DM1  CONST_23  C19   C18  C17  O17     0.00   0.0  0
 DM1  CONST_24  H3    C3   C2   C1    180.00   0.0  0
 DM1  CONST_25  H1    C1   C2   C3    180.00   0.0  0
 DM1  CONST_26  H2    C2   C3   C4    180.00   0.0  0
 DM1  Var_01    C12   C15  C16  C9     19.80  30.0  1
 DM1  Var_02    H211  C21  O4   C4    179.20  30.0  3
 DM1  Var_03    H141  C14  C13  C12  -168.01  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
 DM1  chir_01  C10  C9   O10  C11  negativ
 DM1  chir_02  C12  C11  C13  C15  positiv
 DM1  chir_03  C1'  O10  O5'  C2'  positiv
 DM1  chir_04  C3'  N3'  C4'  C2'  positiv
 DM1  chir_05  C4'  O4'  C5'  C3'  positiv
 DM1  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
 DM1  plan-1  C12  0.020
 DM1  plan-1  C13  0.020
 DM1  plan-1  O13  0.020
 DM1  plan-1  C14  0.020
 DM1  plan-2  C1   0.020
 DM1  plan-2  C2   0.020
 DM1  plan-2  C3   0.020
 DM1  plan-2  C4   0.020
 DM1  plan-2  O4   0.020
 DM1  plan-2  C5   0.020
 DM1  plan-2  C6   0.020
 DM1  plan-2  O6   0.020
 DM1  plan-2  C7   0.020
 DM1  plan-2  C8   0.020
 DM1  plan-2  O8   0.020
 DM1  plan-2  C9   0.020
 DM1  plan-2  C10  0.020
 DM1  plan-2  C15  0.020
 DM1  plan-2  C16  0.020
 DM1  plan-2  C17  0.020
 DM1  plan-2  O17  0.020
 DM1  plan-2  C18  0.020
 DM1  plan-2  C19  0.020
 DM1  plan-2  O19  0.020
 DM1  plan-2  C20  0.020
 DM1  plan-2  H1   0.020
 DM1  plan-2  H2   0.020
 DM1  plan-2  H3   0.020

