# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:46:29 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (4S,4aR,5S,5aR,6R,12aS)-4-(dimethylamino)-3,5,10,12,12a-pentahydroxy-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: C[C@@H]1[C@H]2[C@H](O)[C@H]3[C@H](N(C)C)C(=C(C(N)=O)C(=O)[C@@]3(O)C(=C2C(=O)c4c(O)cccc14)O)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
 DXT  DXT  (4S,4aR,5S,5aR,6R,12aS)-4-(dimethylamino)-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide  ligand  56  32  .  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_DXT
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
 DXT  C1    C  CR6   0   0.377   6.3851  -3.9192   4.6566
 DXT  O1    O  O     0  -0.387   5.3546  -4.4035   5.0782
 DXT  C2    C  CR6   0  -0.343   7.3507  -3.2610   5.5206
 DXT  O21   O  O     0  -0.443   7.0838  -4.5920   7.4669
 DXT  C21   C  C     0   0.478   7.2083  -3.4808   6.9908
 DXT  N21   N  NH2   0  -0.821   7.3253  -2.3573   7.7444
 DXT  C3    C  CR6   0   0.444   8.3695  -2.5225   5.0004
 DXT  O3    O  OH1   0  -0.573   9.2799  -1.8922   5.7197
 DXT  C4    C  CR16  0  -0.126   8.5923  -2.3271   3.5288
 DXT  N4    N  NT    0  -0.402   9.8213  -2.9419   3.0350
 DXT  C41   C  CH3   0  -0.532  10.5106  -3.9113   3.8571
 DXT  C42   C  CH3   0  -0.527  10.7358  -1.9938   2.4421
 DXT  C4A   C  C     0  -0.360   7.3584  -2.7099   2.6919
 DXT  C5    C  CR16  0   0.068   6.2989  -1.5925   2.6892
 DXT  O5    O  OH1   0  -0.650   6.8968  -0.3640   2.3489
 DXT  C5A   C  CR16  0  -0.316   5.1290  -1.9135   1.7508
 DXT  C6    C  CH1   0  -0.298   3.8494  -1.1030   2.0405
 DXT  C61   C  CH3   0  -0.680   4.0509   0.3892   2.2688
 DXT  C6A   C  CR6   0   0.136   2.8438  -1.4071   0.9461
 DXT  C7    C  CR16  0  -0.385   2.0397  -0.4356   0.3794
 DXT  C8    C  CR16  0  -0.212   1.0960  -0.7808  -0.5885
 DXT  C9    C  CR16  0  -0.360   0.9167  -2.0870  -0.9895
 DXT  C10   C  CR6   0   0.375   1.7031  -3.0897  -0.4222
 DXT  O10   O  OH1   0  -0.625   1.4906  -4.3455  -0.8089
 DXT  C6B   C  CR6   0  -0.160   2.6926  -2.7447   0.5225
 DXT  C11   C  C     0   0.456   3.5612  -3.7770   1.0691
 DXT  O11   O  O     0  -0.570   3.2743  -4.9910   0.9133
 DXT  C5B   C  CR6   0  -0.171   4.7554  -3.3754   1.7667
 DXT  C12   C  CR6   0   0.385   5.5039  -4.3375   2.3718
 DXT  O12   O  OH1   0  -0.596   5.2170  -5.6175   2.3415
 DXT  C4B   C  C     0   0.046   6.7484  -4.0194   3.1636
 DXT  O13   O  OH1   0  -0.632   7.7067  -5.0320   3.0170
 DXT  H10   H  HOH1  0   0.485   2.0683  -4.9288  -0.2685
 DXT  H12   H  HOH1  0   0.495   4.4041  -5.7216   1.7729
 DXT  H13   H  HOH1  0   0.462   7.3353  -5.8761   3.3012
 DXT  H211  H  HNH2  0   0.410   7.2034  -2.4439   8.7432
 DXT  H212  H  HNH2  0   0.418   7.0369  -1.4708   7.3580
 DXT  HO3   H  HOH1  0   0.481   9.1255  -1.9990   6.6745
 DXT  H4    H  HCR6  0   0.293   8.7038  -1.2433   3.4218
 DXT  H411  H  HCH3  0   0.241   9.8094  -4.5820   4.3473
 DXT  H412  H  HCH3  0   0.199  11.1538  -3.4632   4.6266
 DXT  H413  H  HCH3  0   0.237  11.1494  -4.5262   3.2201
 DXT  H421  H  HCH3  0   0.234  11.4977  -2.5266   1.8701
 DXT  H422  H  HCH3  0   0.201  11.2547  -1.3598   3.1761
 DXT  H423  H  HCH3  0   0.235  10.2096  -1.3375   1.7469
 DXT  H4A   H  H     0   0.282   7.7075  -2.8486   1.6620
 DXT  H5    H  HCR6  0   0.249   5.9087  -1.4529   3.7052
 DXT  HO5   H  HOH1  0   0.447   7.1550  -0.3935   1.4207
 DXT  H5A   H  HCR6  0   0.259   5.4629  -1.6655   0.7311
 DXT  H6    H  HCH1  0   0.260   3.4327  -1.5124   2.9716
 DXT  H7    H  HCR6  0   0.258   2.1248   0.5996   0.6739
 DXT  H8    H  HCR6  0   0.268   0.4798  -0.0059  -1.0261
 DXT  H9    H  HCR6  0   0.270   0.1683  -2.3464  -1.7271
 DXT  H611  H  HCH3  0   0.255   4.7211   0.5689   3.1047
 DXT  H612  H  HCH3  0   0.227   4.4612   0.8930   1.3929
 DXT  H613  H  HCH3  0   0.235   3.1030   0.8643   2.5212

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
 DXT  C1   C4B   single    1.540  0.020  1.540
 DXT  C1   O1    double    1.214  0.020  1.214
 DXT  C1   C2    single    1.453  0.020  1.453
 DXT  C2   C21   single    1.493  0.020  1.493
 DXT  C2   C3    double    1.362  0.020  1.362
 DXT  O21  C21   double    1.215  0.020  1.215
 DXT  C21  N21   single    1.358  0.020  1.358
 DXT  N21  H211  single    0.890  0.020  1.040
 DXT  N21  H212  single    0.890  0.020  1.040
 DXT  C3   O3    single    1.320  0.020  1.320
 DXT  C3   C4    single    1.501  0.020  1.501
 DXT  O3   HO3   single    0.850  0.020  0.980
 DXT  C4   H4    single    0.970  0.020  1.090
 DXT  C4   N4    single    1.460  0.020  1.460
 DXT  C4   C4A   single    1.539  0.020  1.539
 DXT  N4   C41   single    1.446  0.020  1.446
 DXT  N4   C42   single    1.445  0.020  1.445
 DXT  C41  H411  single    0.970  0.020  1.090
 DXT  C41  H412  single    0.970  0.020  1.090
 DXT  C41  H413  single    0.970  0.020  1.090
 DXT  C42  H421  single    0.970  0.020  1.090
 DXT  C42  H422  single    0.970  0.020  1.090
 DXT  C42  H423  single    0.970  0.020  1.090
 DXT  C4A  C4B   single    1.520  0.020  1.520
 DXT  C4A  H4A   single    0.970  0.020  1.090
 DXT  C4A  C5    single    1.540  0.020  1.540
 DXT  C5   H5    single    0.970  0.020  1.090
 DXT  C5   O5    single    1.408  0.020  1.408
 DXT  C5   C5A   single    1.534  0.020  1.534
 DXT  O5   HO5   single    0.850  0.020  0.980
 DXT  C5A  C5B   single    1.509  0.020  1.509
 DXT  C5A  H5A   single    0.970  0.020  1.090
 DXT  C5A  C6    single    1.542  0.020  1.542
 DXT  C6   H6    single    0.970  0.020  1.090
 DXT  C6   C6A   single    1.517  0.020  1.517
 DXT  C6   C61   single    1.523  0.020  1.523
 DXT  C61  H611  single    0.970  0.020  1.090
 DXT  C61  H612  single    0.970  0.020  1.090
 DXT  C61  H613  single    0.970  0.020  1.090
 DXT  C6A  C6B   aromatic  1.411  0.020  1.411
 DXT  C6A  C7    aromatic  1.383  0.020  1.383
 DXT  C7   H7    single    0.930  0.020  1.080
 DXT  C7   C8    aromatic  1.395  0.020  1.395
 DXT  C8   H8    single    0.930  0.020  1.080
 DXT  C8   C9    aromatic  1.378  0.020  1.378
 DXT  C9   C10   aromatic  1.395  0.020  1.395
 DXT  C9   H9    single    0.930  0.020  1.080
 DXT  C10  O10   single    1.331  0.020  1.331
 DXT  C10  C6B   aromatic  1.411  0.020  1.411
 DXT  O10  H10   single    0.850  0.020  0.980
 DXT  C6B  C11   single    1.456  0.020  1.456
 DXT  C11  O11   double    1.257  0.020  1.257
 DXT  C11  C5B   single    1.440  0.020  1.440
 DXT  C5B  C12   double    1.361  0.020  1.361
 DXT  C12  O12   single    1.312  0.020  1.312
 DXT  C12  C4B   single    1.509  0.020  1.509
 DXT  O12  H12   single    0.850  0.020  0.980
 DXT  C4B  O13   single    1.402  0.020  1.402
 DXT  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
 DXT  C4B   C1   C2    116.69  3.000
 DXT  C2    C1   O1    122.56  3.000
 DXT  C4B   C1   O1    120.73  3.000
 DXT  C3    C2   C21   121.82  3.000
 DXT  C3    C2   C1    121.04  3.000
 DXT  C21   C2   C1    117.08  3.000
 DXT  N21   C21  O21   123.23  3.000
 DXT  N21   C21  C2    114.60  3.000
 DXT  O21   C21  C2    122.01  3.000
 DXT  H212  N21  H211  114.81  3.000
 DXT  H212  N21  C21   119.32  3.000
 DXT  H211  N21  C21   117.87  3.000
 DXT  C4    C3   O3    111.69  3.000
 DXT  C4    C3   C2    123.79  3.000
 DXT  O3    C3   C2    124.52  3.000
 DXT  HO3   O3   C3    111.89  3.000
 DXT  H4    C4   C4A   105.94  3.000
 DXT  C4A   C4   N4    112.71  3.000
 DXT  H4    C4   N4    107.34  3.000
 DXT  C4A   C4   C3    112.43  3.000
 DXT  N4    C4   C3    113.68  3.000
 DXT  H4    C4   C3    103.87  3.000
 DXT  C42   N4   C41   111.81  3.000
 DXT  C42   N4   C4    113.28  3.000
 DXT  C41   N4   C4    119.42  3.000
 DXT  H413  C41  H412  107.21  3.000
 DXT  H413  C41  H411  107.04  3.000
 DXT  H412  C41  H411  108.26  3.000
 DXT  H413  C41  N4    108.96  3.000
 DXT  H412  C41  N4    113.83  3.000
 DXT  H411  C41  N4    111.25  3.000
 DXT  H423  C42  H422  107.81  3.000
 DXT  H423  C42  H421  107.23  3.000
 DXT  H422  C42  H421  107.56  3.000
 DXT  H423  C42  N4    110.54  3.000
 DXT  H422  C42  N4    113.77  3.000
 DXT  H421  C42  N4    109.67  3.000
 DXT  H4A   C4A  C4B   108.08  3.000
 DXT  H4A   C4A  C5    108.02  3.000
 DXT  C4B   C4A  C5    110.46  3.000
 DXT  C5    C4A  C4    111.84  3.000
 DXT  H4A   C4A  C4    106.68  3.000
 DXT  C4B   C4A  C4    111.55  3.000
 DXT  H5    C5   C5A   108.77  3.000
 DXT  C5A   C5   O5    111.01  3.000
 DXT  H5    C5   O5    105.29  3.000
 DXT  C5A   C5   C4A   111.97  3.000
 DXT  O5    C5   C4A   109.96  3.000
 DXT  H5    C5   C4A   109.60  3.000
 DXT  HO5   O5   C5    108.64  3.000
 DXT  H5A   C5A  C5B   107.64  3.000
 DXT  H5A   C5A  C6    107.89  3.000
 DXT  C5B   C5A  C6    107.56  3.000
 DXT  C6    C5A  C5    114.08  3.000
 DXT  H5A   C5A  C5    106.75  3.000
 DXT  C5B   C5A  C5    112.65  3.000
 DXT  H6    C6   C6A   106.57  3.000
 DXT  C6A   C6   C61   113.10  3.000
 DXT  H6    C6   C61   106.74  3.000
 DXT  C61   C6   C5A   115.68  3.000
 DXT  C6A   C6   C5A   108.01  3.000
 DXT  H6    C6   C5A   106.13  3.000
 DXT  H613  C61  H612  108.16  3.000
 DXT  H613  C61  H611  106.63  3.000
 DXT  H612  C61  H611  108.03  3.000
 DXT  H613  C61  C6    110.29  3.000
 DXT  H612  C61  C6    112.46  3.000
 DXT  H611  C61  C6    111.04  3.000
 DXT  C6B   C6A  C7    118.73  3.000
 DXT  C7    C6A  C6    122.71  3.000
 DXT  C6B   C6A  C6    118.53  3.000
 DXT  H7    C7   C8    118.67  3.000
 DXT  C8    C7   C6A   120.26  3.000
 DXT  H7    C7   C6A   121.07  3.000
 DXT  H8    C8   C9    119.13  3.000
 DXT  C9    C8   C7    121.63  3.000
 DXT  H8    C8   C7    119.24  3.000
 DXT  H9    C9   C10   119.65  3.000
 DXT  H9    C9   C8    121.03  3.000
 DXT  C10   C9   C8    119.31  3.000
 DXT  C6B   C10  O10   122.49  3.000
 DXT  C6B   C10  C9    119.47  3.000
 DXT  O10   C10  C9    118.04  3.000
 DXT  H10   O10  C10   107.84  3.000
 DXT  C11   C6B  C10   119.77  3.000
 DXT  C11   C6B  C6A   119.70  3.000
 DXT  C10   C6B  C6A   120.52  3.000
 DXT  C5B   C11  O11   121.23  3.000
 DXT  C5B   C11  C6B   118.62  3.000
 DXT  O11   C11  C6B   120.14  3.000
 DXT  C12   C5B  C11   118.32  3.000
 DXT  C12   C5B  C5A   123.60  3.000
 DXT  C11   C5B  C5A   118.05  3.000
 DXT  C4B   C12  O12   113.46  3.000
 DXT  C4B   C12  C5B   122.54  3.000
 DXT  O12   C12  C5B   123.99  3.000
 DXT  H12   O12  C12   107.05  3.000
 DXT  O13   C4B  C12   110.90  3.000
 DXT  O13   C4B  C4A   108.39  3.000
 DXT  C12   C4B  C4A   110.48  3.000
 DXT  O13   C4B  C1    108.04  3.000
 DXT  C12   C4B  C1    109.14  3.000
 DXT  C4A   C4B  C1    109.85  3.000
 DXT  H13   O13  C4B   109.75  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
 DXT  CONST_01  C9    C10  C6B  C6A     0.00   0.0  0
 DXT  CONST_02  C9    C8   C7   C6A     0.00   0.0  0
 DXT  CONST_03  C10   C6B  C6A  C7      0.00   0.0  0
 DXT  CONST_04  C10   C9   C8   C7      0.00   0.0  0
 DXT  CONST_05  C6B   C6A  C7   C8      0.00   0.0  0
 DXT  CONST_06  C6B   C10  C9   C8      0.00   0.0  0
 DXT  CONST_07  O10   C10  C6B  C6A   180.00   0.0  0
 DXT  CONST_08  O10   C10  C9   C8    180.00   0.0  0
 DXT  CONST_09  C11   C6B  C10  O10     0.00   0.0  0
 DXT  CONST_10  H7    C7   C6A  C6      0.00   0.0  0
 DXT  CONST_11  H8    C8   C7   C6A   180.00   0.0  0
 DXT  CONST_12  H9    C9   C8   C7    180.00   0.0  0
 DXT  CONST_13  H211  N21  C21  C2    180.00   0.0  0
 DXT  Var_01    C4    C3   C2   C1     -0.30  30.0  1
 DXT  Var_02    C4B   C1   C2   C3     13.85  30.0  1
 DXT  Var_03    C6B   C11  C5B  C5A    -7.21  30.0  1
 DXT  Var_04    C4B   C12  C5B  C5A     3.81  30.0  1
 DXT  Var_05    C5B   C11  C6B  C6A   -15.18  30.0  1
 DXT  Var_06    O21   C21  C2   C1     49.48  30.0  2
 DXT  Var_07    H411  C41  N4   C4     40.88  30.0  3
 DXT  Var_08    H421  C42  N4   C4   -165.42  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
 DXT  chir_01  C4   C3   N4   C4A  negativ
 DXT  chir_02  C4A  C4   C4B  C5   negativ
 DXT  chir_03  C5   O5   C4A  C5A  positiv
 DXT  chir_04  C5A  C5   C5B  C6   negativ
 DXT  chir_05  C6   C5A  C6A  C61  positiv
 DXT  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
 DXT  plan-1  C2    0.020
 DXT  plan-1  O21   0.020
 DXT  plan-1  C21   0.020
 DXT  plan-1  N21   0.020
 DXT  plan-1  H211  0.020
 DXT  plan-1  H212  0.020
 DXT  plan-2  C6    0.020
 DXT  plan-2  C6A   0.020
 DXT  plan-2  C7    0.020
 DXT  plan-2  C8    0.020
 DXT  plan-2  C9    0.020
 DXT  plan-2  C10   0.020
 DXT  plan-2  O10   0.020
 DXT  plan-2  C6B   0.020
 DXT  plan-2  C11   0.020
 DXT  plan-2  H7    0.020
 DXT  plan-2  H8    0.020
 DXT  plan-2  H9    0.020
 DXT  plan-3  C1    0.020
 DXT  plan-3  O1    0.020
 DXT  plan-3  C2    0.020
 DXT  plan-3  C4B   0.020
 DXT  plan-4  C6B   0.020
 DXT  plan-4  C11   0.020
 DXT  plan-4  O11   0.020
 DXT  plan-4  C5B   0.020

