# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 00:31:58 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: (4S,4aS,5aR,12aS)-4-(dimethylamino)-3,10,12,12a-tetrahydroxy-9-nitro-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]2C[C@@H]3Cc4ccc(c(O)c4C(=O)C3=C(O)[C@]2(O)C(=O)C(=C1O)C(N)=O)[N+]([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
 XTC  XTC  (4S,4aS,5aR,12aS)-4-(dimethylamino)-3,10,12,12a-tetrahydroxy-9-nitro-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide  ligand  54  33  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XTC
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
 XTC  O92   O  O     -1  -0.388   7.7140   0.4304   0.7936
 XTC  N9    N  N      1   0.336   6.8904   0.0665  -0.0172
 XTC  O91   O  O      0  -0.376   7.1633  -0.2798  -1.1417
 XTC  C9    C  CR6    0   0.153   5.5092   0.0283   0.4037
 XTC  C8    C  CR16   0  -0.256   5.2488  -0.1221   1.7591
 XTC  C7    C  CR16   0  -0.351   3.9527  -0.1794   2.2267
 XTC  C10   C  CR6    0   0.394   4.4607   0.1583  -0.5226
 XTC  O10   O  OH1    0  -0.588   4.7067   0.3819  -1.7946
 XTC  C1A   C  CR66   0  -0.150   3.1363   0.0757  -0.0274
 XTC  C61   C  CR66   0   0.102   2.8878  -0.0820   1.3412
 XTC  C6    C  C      0  -0.505   1.4759  -0.1002   1.8405
 XTC  C11   C  CR6    0   0.467   2.0126   0.1839  -0.9629
 XTC  O11   O  O      0  -0.568   2.2209   0.5657  -2.1412
 XTC  C1B   C  CR6    0  -0.170   0.6959  -0.1592  -0.5054
 XTC  C51   C  CR16   0  -0.302   0.5442  -0.7861   0.8540
 XTC  C5    C  CH2    0  -0.448  -0.9000  -0.7661   1.3244
 XTC  C12   C  C      0   0.393  -0.3636   0.0154  -1.3471
 XTC  O12   O  OH1    0  -0.588  -0.2566   0.4594  -2.5755
 XTC  C1C   C  CT     0   0.057  -1.7966  -0.2777  -0.9409
 XTC  O1C   O  OH1    0  -0.633  -2.5110  -0.8266  -2.0141
 XTC  C1    C  C      0   0.381  -2.4734   1.0476  -0.5365
 XTC  O1    O  O      0  -0.388  -2.0242   2.1106  -0.9133
 XTC  C41   C  CH1    0  -0.316  -1.8421  -1.2546   0.2262
 XTC  C4    C  CH1    0  -0.133  -3.2657  -1.4792   0.7588
 XTC  N4    N  NT     0  -0.403  -4.0006  -2.5193   0.0452
 XTC  C43   C  CH3    0  -0.527  -4.3180  -3.6654   0.8676
 XTC  C42   C  CH3    0  -0.535  -5.1116  -2.1428  -0.8025
 XTC  C3    C  C      0   0.445  -4.0370  -0.1969   0.8901
 XTC  O3    O  OH1    0  -0.572  -5.1055  -0.3414   1.6519
 XTC  C2    C  C      0  -0.344  -3.6811   0.9603   0.2686
 XTC  C21   C  C      0   0.480  -4.5432   2.1786   0.3292
 XTC  O21   O  O      0  -0.441  -4.8841   2.7750  -0.6729
 XTC  N21   N  NH2    0  -0.823  -4.9910   2.4962   1.5725
 XTC  H8    H  HCR6   0   0.304   6.0702  -0.2072   2.4562
 XTC  H7    H  HCR6   0   0.274   3.7703  -0.3038   3.2852
 XTC  H10   H  HOH1   0   0.497   3.8352   0.5483  -2.2388
 XTC  H61C  H  H      0   0.276   1.4369  -0.5967   2.8112
 XTC  H62C  H  H      0   0.275   1.1480   0.9338   2.0009
 XTC  H51   H  HCR6   0   0.271   0.8568  -1.8363   0.7788
 XTC  H51C  H  HCH2   0   0.268  -0.9936  -1.4161   2.1971
 XTC  H52C  H  HCH2   0   0.244  -1.1685   0.2421   1.6604
 XTC  H41   H  HCH1   0   0.281  -1.4860  -2.2288  -0.1244
 XTC  H12   H  HOH1   0   0.497   0.7082   0.6012  -2.7624
 XTC  H1C   H  HOH1   0   0.462  -2.4845  -0.2279  -2.7703
 XTC  H4    H  HCH1   0   0.286  -3.1370  -1.8257   1.7915
 XTC  H431  H  HCH3   0   0.202  -5.0918  -3.4699   1.6241
 XTC  H432  H  HCH3   0   0.234  -4.6764  -4.4788   0.2345
 XTC  H433  H  HCH3   0   0.237  -3.4261  -4.0254   1.3824
 XTC  H421  H  HCH3   0   0.245  -4.8805  -1.2544  -1.3839
 XTC  H422  H  HCH3   0   0.237  -5.3018  -2.9495  -1.5133
 XTC  H423  H  HCH3   0   0.199  -6.0478  -1.9632  -0.2573
 XTC  H3    H  HOH1   0   0.481  -5.5972   0.4940   1.7454
 XTC  H211  H  HNH2   0   0.419  -4.4106   2.2862   2.3715
 XTC  H212  H  HNH2   0   0.410  -5.5491   3.3330   1.6685

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
 XTC  O92  N9    single    1.212  0.020  1.212
 XTC  N9   O91   double    1.208  0.020  1.208
 XTC  N9   C9    single    1.444  0.020  1.444
 XTC  C9   C8    aromatic  1.388  0.020  1.388
 XTC  C9   C10   aromatic  1.405  0.020  1.405
 XTC  C8   C7    aromatic  1.379  0.020  1.379
 XTC  C7   C61   aromatic  1.388  0.020  1.388
 XTC  C10  O10   single    1.315  0.020  1.315
 XTC  C10  C1A   aromatic  1.416  0.020  1.416
 XTC  C1A  C61   aromatic  1.400  0.020  1.400
 XTC  C1A  C11   single    1.466  0.020  1.466
 XTC  C61  C6    single    1.498  0.020  1.498
 XTC  C6   C51   single    1.520  0.020  1.520
 XTC  C11  O11   double    1.256  0.020  1.256
 XTC  C11  C1B   single    1.436  0.020  1.436
 XTC  C1B  C51   single    1.505  0.020  1.505
 XTC  C1B  C12   double    1.364  0.020  1.364
 XTC  C51  C5    single    1.519  0.020  1.519
 XTC  C5   C41   single    1.527  0.020  1.527
 XTC  C12  O12   single    1.311  0.020  1.311
 XTC  C12  C1C   single    1.518  0.020  1.518
 XTC  C1C  O1C   single    1.401  0.020  1.401
 XTC  C1C  C1    single    1.542  0.020  1.542
 XTC  C1C  C41   single    1.523  0.020  1.523
 XTC  C1   O1    double    1.214  0.020  1.214
 XTC  C1   C2    single    1.454  0.020  1.454
 XTC  C41  C4    single    1.536  0.020  1.536
 XTC  C4   N4    single    1.460  0.020  1.460
 XTC  C4   C3    single    1.502  0.020  1.502
 XTC  N4   C43   single    1.446  0.020  1.446
 XTC  N4   C42   single    1.447  0.020  1.447
 XTC  C3   O3    single    1.320  0.020  1.320
 XTC  C3   C2    double    1.361  0.020  1.361
 XTC  C2   C21   single    1.494  0.020  1.494
 XTC  C21  O21   double    1.215  0.020  1.215
 XTC  C21  N21   single    1.359  0.020  1.359
 XTC  C8   H8    single    0.930  0.020  1.080
 XTC  C7   H7    single    0.930  0.020  1.080
 XTC  O10  H10   single    0.850  0.020  0.980
 XTC  C6   H61C  single    0.970  0.020  1.090
 XTC  C6   H62C  single    0.970  0.020  1.090
 XTC  C51  H51   single    0.970  0.020  1.090
 XTC  C5   H51C  single    0.970  0.020  1.090
 XTC  C5   H52C  single    0.970  0.020  1.090
 XTC  C41  H41   single    0.970  0.020  1.090
 XTC  O12  H12   single    0.850  0.020  0.980
 XTC  O1C  H1C   single    0.850  0.020  0.980
 XTC  C4   H4    single    0.970  0.020  1.090
 XTC  C43  H431  single    0.970  0.020  1.090
 XTC  C43  H432  single    0.970  0.020  1.090
 XTC  C43  H433  single    0.970  0.020  1.090
 XTC  C42  H421  single    0.970  0.020  1.090
 XTC  C42  H422  single    0.970  0.020  1.090
 XTC  C42  H423  single    0.970  0.020  1.090
 XTC  O3   H3    single    0.850  0.020  0.980
 XTC  N21  H211  single    0.890  0.020  1.040
 XTC  N21  H212  single    0.890  0.020  1.040

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
 XTC  C9    N9   O91   118.67  3.000
 XTC  C9    N9   O92   117.58  3.000
 XTC  O91   N9   O92   123.75  3.000
 XTC  C10   C9   C8    120.91  3.000
 XTC  C10   C9   N9    121.27  3.000
 XTC  C8    C9   N9    117.82  3.000
 XTC  H8    C8   C7    119.49  3.000
 XTC  H8    C8   C9    119.72  3.000
 XTC  C7    C8   C9    120.78  3.000
 XTC  H7    C7   C61   120.21  3.000
 XTC  H7    C7   C8    119.68  3.000
 XTC  C61   C7   C8    120.11  3.000
 XTC  C1A   C10  O10   121.54  3.000
 XTC  C1A   C10  C9    117.51  3.000
 XTC  O10   C10  C9    120.93  3.000
 XTC  H10   O10  C10   107.30  3.000
 XTC  C11   C1A  C61   119.74  3.000
 XTC  C11   C1A  C10   119.29  3.000
 XTC  C61   C1A  C10   120.96  3.000
 XTC  C6    C61  C1A   119.65  3.000
 XTC  C6    C61  C7    120.63  3.000
 XTC  C1A   C61  C7    119.69  3.000
 XTC  H62C  C6   H61C  106.76  3.000
 XTC  H62C  C6   C51   109.70  3.000
 XTC  H61C  C6   C51   110.50  3.000
 XTC  H62C  C6   C61   108.61  3.000
 XTC  H61C  C6   C61   109.62  3.000
 XTC  C51   C6   C61   111.52  3.000
 XTC  C1B   C11  O11   121.58  3.000
 XTC  C1B   C11  C1A   118.81  3.000
 XTC  O11   C11  C1A   119.60  3.000
 XTC  C12   C1B  C51   122.17  3.000
 XTC  C12   C1B  C11   119.02  3.000
 XTC  C51   C1B  C11   118.68  3.000
 XTC  H51   C51  C5    107.72  3.000
 XTC  H51   C51  C1B   107.93  3.000
 XTC  C5    C51  C1B   111.73  3.000
 XTC  H51   C51  C6    107.54  3.000
 XTC  C5    C51  C6    112.07  3.000
 XTC  C1B   C51  C6    109.66  3.000
 XTC  H52C  C5   H51C  106.35  3.000
 XTC  H52C  C5   C41   111.31  3.000
 XTC  H51C  C5   C41   109.35  3.000
 XTC  H52C  C5   C51   109.87  3.000
 XTC  H51C  C5   C51   108.73  3.000
 XTC  C41   C5   C51   111.08  3.000
 XTC  C1C   C12  O12   113.16  3.000
 XTC  C1C   C12  C1B   122.90  3.000
 XTC  O12   C12  C1B   123.93  3.000
 XTC  H12   O12  C12   107.71  3.000
 XTC  C41   C1C  C1    109.71  3.000
 XTC  C41   C1C  O1C   108.69  3.000
 XTC  C1    C1C  O1C   108.29  3.000
 XTC  C41   C1C  C12   110.93  3.000
 XTC  C1    C1C  C12   108.57  3.000
 XTC  O1C   C1C  C12   110.61  3.000
 XTC  H1C   O1C  C1C   110.07  3.000
 XTC  C2    C1   O1    122.12  3.000
 XTC  C2    C1   C1C   117.27  3.000
 XTC  O1    C1   C1C   120.58  3.000
 XTC  H41   C41  C4    106.40  3.000
 XTC  H41   C41  C1C   108.40  3.000
 XTC  C4    C41  C1C   112.77  3.000
 XTC  H41   C41  C5    108.31  3.000
 XTC  C4    C41  C5    111.66  3.000
 XTC  C1C   C41  C5    109.12  3.000
 XTC  H4    C4   C3    104.33  3.000
 XTC  H4    C4   N4    107.11  3.000
 XTC  C3    C4   N4    113.11  3.000
 XTC  H4    C4   C41   105.30  3.000
 XTC  C3    C4   C41   112.42  3.000
 XTC  N4    C4   C41   113.65  3.000
 XTC  C42   N4   C43   111.77  3.000
 XTC  C42   N4   C4    119.17  3.000
 XTC  C43   N4   C4    113.41  3.000
 XTC  H433  C43  H432  107.24  3.000
 XTC  H433  C43  H431  108.02  3.000
 XTC  H432  C43  H431  107.49  3.000
 XTC  H433  C43  N4    110.52  3.000
 XTC  H432  C43  N4    109.44  3.000
 XTC  H431  C43  N4    113.88  3.000
 XTC  H423  C42  H422  107.19  3.000
 XTC  H423  C42  H421  108.26  3.000
 XTC  H422  C42  H421  107.02  3.000
 XTC  H423  C42  N4    113.97  3.000
 XTC  H422  C42  N4    108.83  3.000
 XTC  H421  C42  N4    111.28  3.000
 XTC  C2    C3   O3    124.63  3.000
 XTC  C2    C3   C4    123.48  3.000
 XTC  O3    C3   C4    111.88  3.000
 XTC  H3    O3   C3    111.73  3.000
 XTC  C21   C2   C3    121.61  3.000
 XTC  C21   C2   C1    116.93  3.000
 XTC  C3    C2   C1    121.41  3.000
 XTC  N21   C21  O21   123.18  3.000
 XTC  N21   C21  C2    114.70  3.000
 XTC  O21   C21  C2    121.93  3.000
 XTC  H212  N21  H211  114.50  3.000
 XTC  H212  N21  C21   117.54  3.000
 XTC  H211  N21  C21   119.07  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
 XTC  CONST_01  C61   C7   C8   C9      0.00   0.0  0
 XTC  CONST_02  C61   C1A  C10  C9      0.00   0.0  0
 XTC  CONST_03  C1A   C10  C9   C8      0.00   0.0  0
 XTC  CONST_04  C1A   C61  C7   C8      0.00   0.0  0
 XTC  CONST_05  C10   C9   C8   C7      0.00   0.0  0
 XTC  CONST_06  C10   C1A  C61  C7      0.00   0.0  0
 XTC  CONST_07  C7    C8   C9   N9    180.00   0.0  0
 XTC  CONST_08  C1A   C10  C9   N9    180.00   0.0  0
 XTC  CONST_09  O10   C10  C9   C8    180.00   0.0  0
 XTC  CONST_10  C61   C1A  C10  O10   180.00   0.0  0
 XTC  CONST_11  C11   C1A  C10  O10     0.00   0.0  0
 XTC  CONST_12  H7    C7   C8   C9    180.00   0.0  0
 XTC  CONST_13  H8    C8   C9   C10   180.00   0.0  0
 XTC  CONST_19  H212  N21  C21  C2    180.00   0.0  0
 XTC  Var_01    C51   C6   C61  C7   -146.22  30.0  1
 XTC  Var_02    C1B   C11  C1A  C10   167.92  30.0  1
 XTC  Var_03    C51   C1B  C11  C1A    -7.93  30.0  1
 XTC  Var_04    C1C   C12  C1B  C11  -178.07  30.0  1
 XTC  Var_05    C3    C2   C1   C1C    14.35  30.0  1
 XTC  Var_06    C4    C3   C2   C1     -2.65  30.0  1
 XTC  Var_07    O21   C21  C2   C1     49.38  30.0  2
 XTC  Var_08    H431  C43  N4   C4     71.26  30.0  3
 XTC  Var_09    H421  C42  N4   C4     41.98  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
 XTC  chir_01  C51  C6   C1B  C5   positiv
 XTC  chir_02  C1C  C12  C1   C41  positiv
 XTC  chir_03  C41  C5   C1C  C4   positiv
 XTC  chir_04  C4   N4   C3   C41  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
 XTC  plan-1  C2    0.020
 XTC  plan-1  C21   0.020
 XTC  plan-1  O21   0.020
 XTC  plan-1  N21   0.020
 XTC  plan-1  H211  0.020
 XTC  plan-1  H212  0.020
 XTC  plan-2  N9    0.020
 XTC  plan-2  C9    0.020
 XTC  plan-2  C8    0.020
 XTC  plan-2  C7    0.020
 XTC  plan-2  C10   0.020
 XTC  plan-2  O10   0.020
 XTC  plan-2  C1A   0.020
 XTC  plan-2  C61   0.020
 XTC  plan-2  C6    0.020
 XTC  plan-2  C11   0.020
 XTC  plan-2  H8    0.020
 XTC  plan-2  H7    0.020
 XTC  plan-3  O92   0.020
 XTC  plan-3  N9    0.020
 XTC  plan-3  O91   0.020
 XTC  plan-3  C9    0.020
 XTC  plan-4  C1A   0.020
 XTC  plan-4  C11   0.020
 XTC  plan-4  O11   0.020
 XTC  plan-4  C1B   0.020
 XTC  plan-5  C1C   0.020
 XTC  plan-5  C1    0.020
 XTC  plan-5  O1    0.020
 XTC  plan-5  C2    0.020

