# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 15 22:56:13 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (4S,4aR,5S,5aR,6S,12aS)-4-(dimethylamino)-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[C@H]1[C@@H]2[C@@H](O)[C@H]3C(=C(O)[C@]2(O)C(=O)C(=C1O)C(N)=O)C(=O)c4c(O)cccc4[C@@]3(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
 OTC  OTC  (4S,4aR,5S,5aR,6S,12aS)-4-(dimethylamino)-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide  ligand  57  33  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OTC
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
 OTC  C1    C  C     0   0.429  -1.6876  -0.9841  -0.7850
 OTC  O1    O  O     0  -0.387  -1.2441  -1.7092  -1.6492
 OTC  C2    C  C     0  -0.344  -2.8113  -0.0849  -1.0189
 OTC  O21   O  O     0  -0.438  -3.9687  -1.2685  -2.7164
 OTC  C21   C  C     0   0.483  -3.5305  -0.2066  -2.3231
 OTC  N21   N  NH2   0  -0.821  -3.7347   0.9723  -2.9659
 OTC  C3    C  C     0   0.421  -3.2052   0.8120  -0.0757
 OTC  O3    O  OH1   0  -0.567  -4.1485   1.7189  -0.2434
 OTC  C4    C  CH1   0  -0.118  -2.6148   0.8547   1.3110
 OTC  N4    N  NT    0  -0.485  -3.3744  -0.0012   2.2545
 OTC  C41   C  CH3   0  -0.532  -3.1555   0.4386   3.6275
 OTC  C42   C  CH3   0  -0.529  -4.8042  -0.1404   2.0030
 OTC  C4A   C  CH1   0  -0.426  -1.1596   0.3679   1.2726
 OTC  C5    C  CH1   0   0.072  -0.2327   1.3277   0.5225
 OTC  O5    O  OH1   0  -0.651  -0.3167   2.6151   1.0852
 OTC  C5A   C  CH1   0  -0.326   1.2168   0.8188   0.4890
 OTC  C6    C  CT    0   0.096   2.0344   1.3811  -0.6934
 OTC  O6    O  OH1   0  -0.646   1.5788   0.6777  -1.8350
 OTC  C61   C  CH3   0  -0.701   1.8486   2.8795  -0.9012
 OTC  C6A   C  CR6   0   0.165   3.4979   1.0206  -0.4336
 OTC  C7    C  CR16  0  -0.388   4.5360   1.8882  -0.7184
 OTC  C8    C  CR16  0  -0.216   5.8589   1.4908  -0.5228
 OTC  C9    C  CR16  0  -0.359   6.1657   0.2280  -0.0677
 OTC  C10   C  CR6   0   0.371   5.1342  -0.6706   0.2128
 OTC  O10   O  OH1   0  -0.631   5.4630  -1.8902   0.6285
 OTC  C6B   C  CR6   0  -0.188   3.7910  -0.2664   0.0554
 OTC  C11   C  C     0   0.443   2.7202  -1.2075   0.4143
 OTC  O11   O  O     0  -0.488   3.0021  -2.3898   0.6552
 OTC  C5B   C  C     0  -0.115   1.3630  -0.6899   0.4958
 OTC  C12   C  C     0   0.371   0.3066  -1.5248   0.6126
 OTC  O12   O  OH1   0  -0.578   0.4150  -2.8394   0.6895
 OTC  C4B   C  CT    0   0.021  -1.1130  -1.0124   0.6401
 OTC  O13   O  OH1   0  -0.702  -1.8951  -1.9578   1.3273
 OTC  H211  H  HNH2  0   0.418  -3.0642   1.7182  -2.8532
 OTC  H212  H  HNH2  0   0.413  -4.1881   0.9453  -3.8684
 OTC  H3    H  HOH1  0   0.483  -4.5217   1.6927  -1.1430
 OTC  H4    H  HCH1  0   0.292  -2.6500   1.9006   1.6390
 OTC  H4A   H  HCH1  0   0.292  -0.7880   0.2779   2.2993
 OTC  H411  H  HCH3  0   0.231  -3.5997   1.4223   3.8179
 OTC  H412  H  HCH3  0   0.258  -3.6026  -0.2820   4.3103
 OTC  H413  H  HCH3  0   0.251  -2.0930   0.4963   3.8577
 OTC  H421  H  HCH3  0   0.250  -4.9932  -0.5841   1.0268
 OTC  H422  H  HCH3  0   0.260  -5.2087  -0.8252   2.7467
 OTC  H423  H  HCH3  0   0.232  -5.3533   0.8037   2.0769
 OTC  H5    H  HCH1  0   0.250  -0.5898   1.4408  -0.5056
 OTC  HA    H  HOH1  0   0.448   0.0899   2.5982   1.9589
 OTC  H5A   H  HCH1  0   0.273   1.6968   1.1889   1.4065
 OTC  H6    H  HOH1  0   0.449   1.9969   1.0603  -2.6144
 OTC  H611  H  HCH3  0   0.238   2.1564   3.4588  -0.0323
 OTC  H612  H  HCH3  0   0.238   2.4356   3.2207  -1.7555
 OTC  H613  H  HCH3  0   0.260   0.8107   3.1169  -1.1207
 OTC  H7    H  HCR6  0   0.258   4.3463   2.8851  -1.0875
 OTC  H8    H  HCR6  0   0.266   6.6599   2.1854  -0.7414
 OTC  H9    H  HCR6  0   0.268   7.1935  -0.0828   0.0688
 OTC  H10   H  HOH1  0   0.477   4.6127  -2.3929   0.7185
 OTC  H12   H  HOH1  0   0.482  -0.4599  -3.1989   0.9124
 OTC  H13   H  HOH1  0   0.476  -2.5715  -1.4339   1.8481

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
 OTC  C1   O1    double    1.212  0.020  1.212
 OTC  C1   C2    single    1.458  0.020  1.458
 OTC  C1   C4B   single    1.537  0.020  1.537
 OTC  C2   C21   single    1.494  0.020  1.494
 OTC  C2   C3    double    1.360  0.020  1.360
 OTC  O21  C21   double    1.214  0.020  1.214
 OTC  C21  N21   single    1.358  0.020  1.358
 OTC  C3   O3    single    1.319  0.020  1.319
 OTC  C3   C4    single    1.508  0.020  1.508
 OTC  C4   N4    single    1.483  0.020  1.483
 OTC  C4   C4A   single    1.535  0.020  1.535
 OTC  N4   C41   single    1.458  0.020  1.458
 OTC  N4   C42   single    1.458  0.020  1.458
 OTC  C4A  C5    single    1.531  0.020  1.531
 OTC  C4A  C4B   single    1.519  0.020  1.519
 OTC  C5   O5    single    1.407  0.020  1.407
 OTC  C5   C5A   single    1.537  0.020  1.537
 OTC  C5A  C6    single    1.544  0.020  1.544
 OTC  C5A  C5B   single    1.516  0.020  1.516
 OTC  C6   O6    single    1.416  0.020  1.416
 OTC  C6   C61   single    1.524  0.020  1.524
 OTC  C6   C6A   single    1.529  0.020  1.529
 OTC  C6A  C7    aromatic  1.383  0.020  1.383
 OTC  C6A  C6B   aromatic  1.408  0.020  1.408
 OTC  C7   C8    aromatic  1.395  0.020  1.395
 OTC  C8   C9    aromatic  1.377  0.020  1.377
 OTC  C9   C10   aromatic  1.396  0.020  1.396
 OTC  C10  O10   single    1.330  0.020  1.330
 OTC  C10  C6B   aromatic  1.411  0.020  1.411
 OTC  C6B  C11   single    1.470  0.020  1.470
 OTC  C11  O11   double    1.239  0.020  1.239
 OTC  C11  C5B   single    1.455  0.020  1.455
 OTC  C5B  C12   double    1.352  0.020  1.352
 OTC  C12  O12   single    1.321  0.020  1.321
 OTC  C12  C4B   single    1.509  0.020  1.509
 OTC  C4B  O13   single    1.406  0.020  1.406
 OTC  N21  H211  single    0.890  0.020  1.040
 OTC  N21  H212  single    0.890  0.020  1.040
 OTC  O3   H3    single    0.850  0.020  0.980
 OTC  C4   H4    single    0.970  0.020  1.090
 OTC  C4A  H4A   single    0.970  0.020  1.090
 OTC  C41  H411  single    0.970  0.020  1.090
 OTC  C41  H412  single    0.970  0.020  1.090
 OTC  C41  H413  single    0.970  0.020  1.090
 OTC  C42  H421  single    0.970  0.020  1.090
 OTC  C42  H422  single    0.970  0.020  1.090
 OTC  C42  H423  single    0.970  0.020  1.090
 OTC  C5   H5    single    0.970  0.020  1.090
 OTC  O5   HA    single    0.850  0.020  0.980
 OTC  C5A  H5A   single    0.970  0.020  1.090
 OTC  O6   H6    single    0.850  0.020  0.980
 OTC  C61  H611  single    0.970  0.020  1.090
 OTC  C61  H612  single    0.970  0.020  1.090
 OTC  C61  H613  single    0.970  0.020  1.090
 OTC  C7   H7    single    0.930  0.020  1.080
 OTC  C8   H8    single    0.930  0.020  1.080
 OTC  C9   H9    single    0.930  0.020  1.080
 OTC  O10  H10   single    0.850  0.020  0.980
 OTC  O12  H12   single    0.850  0.020  0.980
 OTC  O13  H13   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
 OTC  C4B   C1   C2    116.63  3.000
 OTC  C4B   C1   O1    120.89  3.000
 OTC  C2    C1   O1    122.44  3.000
 OTC  C3    C2   C21   121.31  3.000
 OTC  C3    C2   C1    121.25  3.000
 OTC  C21   C2   C1    117.43  3.000
 OTC  N21   C21  O21   123.47  3.000
 OTC  N21   C21  C2    114.50  3.000
 OTC  O21   C21  C2    121.85  3.000
 OTC  H212  N21  H211  114.68  3.000
 OTC  H212  N21  C21   117.84  3.000
 OTC  H211  N21  C21   119.26  3.000
 OTC  C4    C3   O3    112.17  3.000
 OTC  C4    C3   C2    122.90  3.000
 OTC  O3    C3   C2    124.92  3.000
 OTC  H3    O3   C3    111.89  3.000
 OTC  H4    C4   C4A   109.90  3.000
 OTC  H4    C4   N4    110.10  3.000
 OTC  C4A   C4   N4    108.57  3.000
 OTC  H4    C4   C3    106.83  3.000
 OTC  C4A   C4   C3    109.83  3.000
 OTC  N4    C4   C3    111.60  3.000
 OTC  C42   N4   C41   109.78  3.000
 OTC  C42   N4   C4    116.58  3.000
 OTC  C41   N4   C4    110.37  3.000
 OTC  H413  C41  H412  107.65  3.000
 OTC  H413  C41  H411  108.13  3.000
 OTC  H412  C41  H411  108.59  3.000
 OTC  H413  C41  N4    111.20  3.000
 OTC  H412  C41  N4    109.22  3.000
 OTC  H411  C41  N4    111.93  3.000
 OTC  H423  C42  H422  108.06  3.000
 OTC  H423  C42  H421  108.96  3.000
 OTC  H422  C42  H421  106.95  3.000
 OTC  H423  C42  N4    113.44  3.000
 OTC  H422  C42  N4    107.85  3.000
 OTC  H421  C42  N4    111.33  3.000
 OTC  H4A   C4A  C4B   107.77  3.000
 OTC  H4A   C4A  C5    107.78  3.000
 OTC  C4B   C4A  C5    110.31  3.000
 OTC  H4A   C4A  C4    108.92  3.000
 OTC  C4B   C4A  C4    109.13  3.000
 OTC  C5    C4A  C4    112.80  3.000
 OTC  H5    C5   C5A   108.76  3.000
 OTC  H5    C5   O5    105.16  3.000
 OTC  C5A   C5   O5    111.59  3.000
 OTC  H5    C5   C4A   109.13  3.000
 OTC  C5A   C5   C4A   111.98  3.000
 OTC  O5    C5   C4A   109.97  3.000
 OTC  HA    O5   C5    108.74  3.000
 OTC  H5A   C5A  C5B   106.80  3.000
 OTC  H5A   C5A  C6    106.58  3.000
 OTC  C5B   C5A  C6    108.36  3.000
 OTC  H5A   C5A  C5    106.39  3.000
 OTC  C5B   C5A  C5    114.87  3.000
 OTC  C6    C5A  C5    113.31  3.000
 OTC  C6A   C6   C61   111.81  3.000
 OTC  C6A   C6   O6    109.13  3.000
 OTC  C61   C6   O6    109.83  3.000
 OTC  C6A   C6   C5A   106.91  3.000
 OTC  C61   C6   C5A   113.45  3.000
 OTC  O6    C6   C5A   105.44  3.000
 OTC  H6    O6   C6    108.37  3.000
 OTC  H613  C61  H612  106.69  3.000
 OTC  H613  C61  H611  108.35  3.000
 OTC  H612  C61  H611  107.84  3.000
 OTC  H613  C61  C6    111.02  3.000
 OTC  H612  C61  C6    110.40  3.000
 OTC  H611  C61  C6    112.33  3.000
 OTC  C6B   C6A  C7    119.27  3.000
 OTC  C6B   C6A  C6    118.28  3.000
 OTC  C7    C6A  C6    122.38  3.000
 OTC  H7    C7   C8    118.53  3.000
 OTC  H7    C7   C6A   121.19  3.000
 OTC  C8    C7   C6A   120.29  3.000
 OTC  H8    C8   C9    119.36  3.000
 OTC  H8    C8   C7    119.38  3.000
 OTC  C9    C8   C7    121.26  3.000
 OTC  H9    C9   C10   119.42  3.000
 OTC  H9    C9   C8    121.11  3.000
 OTC  C10   C9   C8    119.47  3.000
 OTC  C6B   C10  O10   122.19  3.000
 OTC  C6B   C10  C9    119.76  3.000
 OTC  O10   C10  C9    118.05  3.000
 OTC  H10   O10  C10   106.33  3.000
 OTC  C11   C6B  C10   118.86  3.000
 OTC  C11   C6B  C6A   121.23  3.000
 OTC  C10   C6B  C6A   119.91  3.000
 OTC  C5B   C11  O11   122.74  3.000
 OTC  C5B   C11  C6B   117.74  3.000
 OTC  O11   C11  C6B   119.51  3.000
 OTC  C12   C5B  C11   120.95  3.000
 OTC  C12   C5B  C5A   122.67  3.000
 OTC  C11   C5B  C5A   116.35  3.000
 OTC  C4B   C12  O12   114.45  3.000
 OTC  C4B   C12  C5B   121.80  3.000
 OTC  O12   C12  C5B   123.74  3.000
 OTC  H12   O12  C12   107.91  3.000
 OTC  O13   C4B  C12   107.68  3.000
 OTC  O13   C4B  C4A   112.97  3.000
 OTC  C12   C4B  C4A   110.17  3.000
 OTC  O13   C4B  C1    104.93  3.000
 OTC  C12   C4B  C1    109.94  3.000
 OTC  C4A   C4B  C1    110.98  3.000
 OTC  H13   O13  C4B   106.14  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
 OTC  CONST_01  C9    C8   C7   C6A    0.00   0.0  0
 OTC  CONST_02  C9    C10  C6B  C6A    0.00   0.0  0
 OTC  CONST_03  C10   C6B  C6A  C7     0.00   0.0  0
 OTC  CONST_04  C10   C9   C8   C7     0.00   0.0  0
 OTC  CONST_05  C6B   C6A  C7   C8     0.00   0.0  0
 OTC  CONST_06  C6B   C10  C9   C8     0.00   0.0  0
 OTC  CONST_07  O10   C10  C6B  C6A  180.00   0.0  0
 OTC  CONST_08  O10   C10  C9   C8   180.00   0.0  0
 OTC  CONST_09  C11   C6B  C10  O10    0.00   0.0  0
 OTC  CONST_10  H7    C7   C6A  C6     0.00   0.0  0
 OTC  CONST_11  H8    C8   C7   C6A  180.00   0.0  0
 OTC  CONST_12  H9    C9   C8   C7   180.00   0.0  0
 OTC  CONST_14  H212  N21  C21  C2   180.00   0.0  0
 OTC  Var_01    C4    C3   C2   C1    -6.22  30.0  1
 OTC  Var_02    C4B   C1   C2   C3     8.80  30.0  1
 OTC  Var_03    C6B   C11  C5B  C5A  -12.40  30.0  1
 OTC  Var_04    C4B   C12  C5B  C5A    4.73  30.0  1
 OTC  Var_05    C5B   C11  C6B  C6A  -11.60  30.0  1
 OTC  Var_06    O21   C21  C2   C1    53.14  30.0  2
 OTC  Var_07    H411  C41  N4   C4    67.71  30.0  3
 OTC  Var_08    H421  C42  N4   C4    60.59  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
 OTC  chir_01  C4   C3   N4   C4A  negativ
 OTC  chir_02  C4A  C4   C5   C4B  positiv
 OTC  chir_03  C5   O5   C4A  C5A  positiv
 OTC  chir_04  C5A  C5   C6   C5B  positiv
 OTC  chir_05  C6   C6A  C61  C5A  positiv
 OTC  chir_06  C4B  C1   C4A  C12  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
 OTC  plan-1  C2    0.020
 OTC  plan-1  O21   0.020
 OTC  plan-1  C21   0.020
 OTC  plan-1  N21   0.020
 OTC  plan-1  H211  0.020
 OTC  plan-1  H212  0.020
 OTC  plan-2  C6    0.020
 OTC  plan-2  C6A   0.020
 OTC  plan-2  C7    0.020
 OTC  plan-2  C8    0.020
 OTC  plan-2  C9    0.020
 OTC  plan-2  C10   0.020
 OTC  plan-2  O10   0.020
 OTC  plan-2  C6B   0.020
 OTC  plan-2  C11   0.020
 OTC  plan-2  H7    0.020
 OTC  plan-2  H8    0.020
 OTC  plan-2  H9    0.020
 OTC  plan-3  C1    0.020
 OTC  plan-3  O1    0.020
 OTC  plan-3  C2    0.020
 OTC  plan-3  C4B   0.020
 OTC  plan-4  C6B   0.020
 OTC  plan-4  C11   0.020
 OTC  plan-4  O11   0.020
 OTC  plan-4  C5B   0.020

