# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:19:26 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (4S,4aS,5aR,12aS)-4-(dimethylamino)-3,10,12,12a-tetrahydroxy-7-iodo-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]3Cc4c(I)ccc(O)c4C(=O)C3=C(O)[C@]2(O)C(=O)C(=C1O)C(N)=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
 I7T  I7T  (4S,4aS,5aR,12aS)-4-(dimethylamino)-3,10,12,12a-tetrahydroxy-7-iodo-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide  ligand  52  31  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_I7T
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
 I7T  O12   O  OH1   0  -0.574  -1.6964   3.2895   0.1299
 I7T  C12   C  C     0   0.390  -1.3709   2.0436  -0.1641
 I7T  C1B   C  C     0  -0.146  -0.0889   1.6150  -0.2587
 I7T  C11   C  C     0   0.434   1.0383   2.5122  -0.0607
 I7T  O11   O  O     0  -0.485   0.9103   3.7424  -0.0076
 I7T  C1A   C  CR6   0  -0.182   2.3882   1.9232   0.0763
 I7T  C10   C  CR6   0   0.378   3.4998   2.7943   0.1274
 I7T  O10   O  OH1   0  -0.624   3.3750   4.1110   0.0343
 I7T  C9    C  CR16  0  -0.359   4.7823   2.2671   0.2819
 I7T  C8    C  CR16  0  -0.202   4.9537   0.9100   0.4292
 I7T  C7    C  CR6   0  -0.352   3.8567   0.0498   0.4087
 I7T  C61   C  CR6   0   0.174   2.5702   0.5310   0.2162
 I7T  C6    C  CH2   0  -0.508   1.3625  -0.3563   0.1809
 I7T  C5    C  CH2   0  -0.430  -0.9340  -0.7337  -0.7239
 I7T  C1C   C  CT    0   0.023  -2.5494   1.1117  -0.3716
 I7T  C1    C  C     0   0.419  -3.0356   0.5854   0.9922
 I7T  O1    O  O     0  -0.392  -2.8405   1.2220   2.0069
 I7T  O1C   O  OH1   0  -0.698  -3.6118   1.8873  -0.8712
 I7T  C41   C  CH1   0  -0.374  -2.1669  -0.0430  -1.2868
 I7T  C4    C  CH1   0  -0.136  -3.3643  -0.9806  -1.4624
 I7T  N4    N  NT    0  -0.477  -4.4359  -0.2651  -2.1928
 I7T  C42   C  CH3   0  -0.534  -4.1696  -0.2773  -3.6271
 I7T  C43   C  CH3   0  -0.530  -5.8013  -0.7135  -1.9451
 I7T  C3    C  C     0   0.423  -3.8435  -1.4521  -0.1150
 I7T  O3    O  OH1   0  -0.566  -4.3718  -2.6597  -0.1599
 I7T  C2    C  C     0  -0.340  -3.7597  -0.6784   0.9993
 I7T  C21   C  C     0   0.483  -4.4120  -1.0909   2.2789
 I7T  C5A   C  CH1   0  -0.302   0.2574   0.2132  -0.6942
 I7T  O21   O  O     0  -0.438  -5.2024  -0.3719   2.8557
 I7T  I7    I  I     0   0.050   4.2540  -1.9997   0.7222
 I7T  N21   N  NH2   0  -0.820  -4.1267  -2.3589   2.6724
 I7T  H12   H  HOH1  0   0.484  -2.6555   3.3950   0.0277
 I7T  H5A   H  HCH1  0   0.268   0.6540   0.2806  -1.7162
 I7T  H10   H  HOH1  0   0.481   2.3990   4.2977   0.0026
 I7T  H9    H  HCR6  0   0.278   5.6350   2.9328   0.3051
 I7T  H8    H  HCR6  0   0.285   5.9541   0.5223   0.5669
 I7T  H61C  H  HCH2  0   0.268   1.6253  -1.3454  -0.1954
 I7T  H62C  H  HCH2  0   0.271   0.9902  -0.5002   1.2024
 I7T  H51C  H  HCH2  0   0.242  -1.1257  -1.1122   0.2847
 I7T  H52C  H  HCH2  0   0.272  -0.6822  -1.6048  -1.3327
 I7T  H41   H  HCH1  0   0.293  -1.9012   0.3692  -2.2649
 I7T  H1C   H  HOH1  0   0.473  -4.1395   1.2832  -1.4626
 I7T  H4    H  HCH1  0   0.290  -3.0461  -1.8720  -2.0215
 I7T  H431  H  HCH3  0   0.249  -6.0774  -0.5863  -0.8992
 I7T  H432  H  HCH3  0   0.259  -6.4714  -0.0848  -2.5291
 I7T  H433  H  HCH3  0   0.230  -5.9737  -1.7546  -2.2369
 I7T  H421  H  HCH3  0   0.230  -4.2924  -1.2784  -4.0567
 I7T  H422  H  HCH3  0   0.257  -4.8606   0.3999  -4.1268
 I7T  H423  H  HCH3  0   0.253  -3.1590   0.0635  -3.8421
 I7T  H3    H  HOH1  0   0.483  -4.6507  -2.9666   0.7218
 I7T  H211  H  HNH2  0   0.420  -3.2275  -2.7558   2.4423
 I7T  H212  H  HNH2  0   0.412  -4.5184  -2.6814   3.5462

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
 I7T  O12  C12   single    1.321  0.020  1.321
 I7T  C12  C1B   double    1.355  0.020  1.355
 I7T  C12  C1C   single    1.517  0.020  1.517
 I7T  C1B  C11   single    1.454  0.020  1.454
 I7T  C1B  C5A   single    1.508  0.020  1.508
 I7T  C11  O11   double    1.238  0.020  1.238
 I7T  C11  C1A   single    1.479  0.020  1.479
 I7T  C1A  C10   aromatic  1.413  0.020  1.413
 I7T  C1A  C61   aromatic  1.411  0.020  1.411
 I7T  C10  O10   single    1.326  0.020  1.326
 I7T  C10  C9    aromatic  1.395  0.020  1.395
 I7T  C9   C8    aromatic  1.376  0.020  1.376
 I7T  C8   C7    aromatic  1.394  0.020  1.394
 I7T  C7   C61   aromatic  1.387  0.020  1.387
 I7T  C7   I7    single    2.111  0.020  2.111
 I7T  C61  C6    single    1.499  0.020  1.499
 I7T  C6   C5A   single    1.520  0.020  1.520
 I7T  C5   C41   single    1.521  0.020  1.521
 I7T  C5   C5A   single    1.522  0.020  1.522
 I7T  C1C  C1    single    1.541  0.020  1.541
 I7T  C1C  O1C   single    1.407  0.020  1.407
 I7T  C1C  C41   single    1.522  0.020  1.522
 I7T  C1   O1    double    1.214  0.020  1.214
 I7T  C1   C2    single    1.457  0.020  1.457
 I7T  C41  C4    single    1.531  0.020  1.531
 I7T  C4   N4    single    1.481  0.020  1.481
 I7T  C4   C3    single    1.506  0.020  1.506
 I7T  N4   C43   single    1.458  0.020  1.458
 I7T  N4   C42   single    1.459  0.020  1.459
 I7T  C3   O3    single    1.319  0.020  1.319
 I7T  C3   C2    double    1.359  0.020  1.359
 I7T  C2   C21   single    1.494  0.020  1.494
 I7T  C21  O21   double    1.214  0.020  1.214
 I7T  C21  N21   single    1.358  0.020  1.358
 I7T  O12  H12   single    0.850  0.020  0.980
 I7T  C5A  H5A   single    0.970  0.020  1.090
 I7T  O10  H10   single    0.850  0.020  0.980
 I7T  C9   H9    single    0.930  0.020  1.080
 I7T  C8   H8    single    0.930  0.020  1.080
 I7T  C6   H61C  single    0.970  0.020  1.090
 I7T  C6   H62C  single    0.970  0.020  1.090
 I7T  C5   H51C  single    0.970  0.020  1.090
 I7T  C5   H52C  single    0.970  0.020  1.090
 I7T  C41  H41   single    0.970  0.020  1.090
 I7T  O1C  H1C   single    0.850  0.020  0.980
 I7T  C4   H4    single    0.970  0.020  1.090
 I7T  C43  H431  single    0.970  0.020  1.090
 I7T  C43  H432  single    0.970  0.020  1.090
 I7T  C43  H433  single    0.970  0.020  1.090
 I7T  C42  H421  single    0.970  0.020  1.090
 I7T  C42  H422  single    0.970  0.020  1.090
 I7T  C42  H423  single    0.970  0.020  1.090
 I7T  O3   H3    single    0.850  0.020  0.980
 I7T  N21  H211  single    0.890  0.020  1.040
 I7T  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
 I7T  H12   O12  C12   108.82  3.000
 I7T  C1C   C12  C1B   122.09  3.000
 I7T  C1C   C12  O12   114.74  3.000
 I7T  C1B   C12  O12   123.16  3.000
 I7T  C5A   C1B  C11   115.77  3.000
 I7T  C5A   C1B  C12   122.10  3.000
 I7T  C11   C1B  C12   121.92  3.000
 I7T  C1A   C11  O11   119.08  3.000
 I7T  C1A   C11  C1B   118.31  3.000
 I7T  O11   C11  C1B   122.60  3.000
 I7T  C61   C1A  C10   120.21  3.000
 I7T  C61   C1A  C11   121.32  3.000
 I7T  C10   C1A  C11   118.41  3.000
 I7T  C9    C10  O10   118.00  3.000
 I7T  C9    C10  C1A   119.62  3.000
 I7T  O10   C10  C1A   122.38  3.000
 I7T  H10   O10  C10   106.32  3.000
 I7T  H9    C9   C8    120.43  3.000
 I7T  H9    C9   C10   119.62  3.000
 I7T  C8    C9   C10   119.94  3.000
 I7T  H8    C8   C7    120.56  3.000
 I7T  H8    C8   C9    118.84  3.000
 I7T  C7    C8   C9    120.60  3.000
 I7T  I7    C7   C61   122.14  3.000
 I7T  I7    C7   C8    116.66  3.000
 I7T  C61   C7   C8    121.19  3.000
 I7T  C6    C61  C7    123.04  3.000
 I7T  C6    C61  C1A   118.54  3.000
 I7T  C7    C61  C1A   118.40  3.000
 I7T  H62C  C6   H61C  106.51  3.000
 I7T  H62C  C6   C5A   109.79  3.000
 I7T  H61C  C6   C5A   108.44  3.000
 I7T  H62C  C6   C61   109.22  3.000
 I7T  H61C  C6   C61   110.54  3.000
 I7T  C5A   C6   C61   112.17  3.000
 I7T  H52C  C5   H51C  106.16  3.000
 I7T  H52C  C5   C5A   109.06  3.000
 I7T  H51C  C5   C5A   109.53  3.000
 I7T  H52C  C5   C41   110.04  3.000
 I7T  H51C  C5   C41   110.87  3.000
 I7T  C5A   C5   C41   111.05  3.000
 I7T  C41   C1C  O1C   113.22  3.000
 I7T  C41   C1C  C1    110.63  3.000
 I7T  O1C   C1C  C1    105.33  3.000
 I7T  C41   C1C  C12   110.67  3.000
 I7T  O1C   C1C  C12   107.26  3.000
 I7T  C1    C1C  C12   109.51  3.000
 I7T  C2    C1   O1    122.07  3.000
 I7T  C2    C1   C1C   117.24  3.000
 I7T  O1    C1   C1C   120.68  3.000
 I7T  H1C   O1C  C1C   106.05  3.000
 I7T  H41   C41  C4    108.55  3.000
 I7T  H41   C41  C1C   108.22  3.000
 I7T  C4    C41  C1C   109.69  3.000
 I7T  H41   C41  C5    107.77  3.000
 I7T  C4    C41  C5    113.47  3.000
 I7T  C1C   C41  C5    109.00  3.000
 I7T  H4    C4   C3    107.06  3.000
 I7T  H4    C4   N4    110.50  3.000
 I7T  C3    C4   N4    111.24  3.000
 I7T  H4    C4   C41   109.17  3.000
 I7T  C3    C4   C41   109.76  3.000
 I7T  N4    C4   C41   109.07  3.000
 I7T  C43   N4   C42   109.59  3.000
 I7T  C42   N4   C4    110.42  3.000
 I7T  C43   N4   C4    116.43  3.000
 I7T  H423  C42  H422  107.70  3.000
 I7T  H423  C42  H421  108.21  3.000
 I7T  H422  C42  H421  108.48  3.000
 I7T  H423  C42  N4    111.18  3.000
 I7T  H422  C42  N4    109.28  3.000
 I7T  H421  C42  N4    111.86  3.000
 I7T  H433  C43  H432  108.01  3.000
 I7T  H433  C43  H431  109.09  3.000
 I7T  H432  C43  H431  106.96  3.000
 I7T  H433  C43  N4    113.24  3.000
 I7T  H432  C43  N4    107.91  3.000
 I7T  H431  C43  N4    111.38  3.000
 I7T  C2    C3   O3    125.02  3.000
 I7T  C2    C3   C4    122.39  3.000
 I7T  O3    C3   C4    112.56  3.000
 I7T  H3    O3   C3    111.86  3.000
 I7T  C21   C2   C3    121.20  3.000
 I7T  C21   C2   C1    117.43  3.000
 I7T  C3    C2   C1    121.37  3.000
 I7T  N21   C21  O21   123.51  3.000
 I7T  N21   C21  C2    114.47  3.000
 I7T  O21   C21  C2    121.83  3.000
 I7T  H5A   C5A  C5    107.61  3.000
 I7T  H5A   C5A  C6    107.23  3.000
 I7T  C5    C5A  C6    110.31  3.000
 I7T  H5A   C5A  C1B   107.13  3.000
 I7T  C5    C5A  C1B   113.83  3.000
 I7T  C6    C5A  C1B   110.42  3.000
 I7T  H212  N21  H211  114.64  3.000
 I7T  H212  N21  C21   117.85  3.000
 I7T  H211  N21  C21   119.23  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
 I7T  CONST_01  C8    C9   C10  C1A    0.00   0.0  0
 I7T  CONST_02  C8    C7   C61  C1A    0.00   0.0  0
 I7T  CONST_03  C7    C61  C1A  C10    0.00   0.0  0
 I7T  CONST_04  C7    C8   C9   C10    0.00   0.0  0
 I7T  CONST_05  C61   C1A  C10  C9     0.00   0.0  0
 I7T  CONST_06  C61   C7   C8   C9     0.00   0.0  0
 I7T  CONST_07  O10   C10  C1A  C11    0.00   0.0  0
 I7T  CONST_08  I7    C7   C61  C1A  180.00   0.0  0
 I7T  CONST_09  C61   C1A  C10  O10  180.00   0.0  0
 I7T  CONST_10  C8    C9   C10  O10  180.00   0.0  0
 I7T  CONST_11  I7    C7   C8   C9   180.00   0.0  0
 I7T  CONST_12  I7    C7   C61  C6     0.00   0.0  0
 I7T  CONST_13  H9    C9   C10  C1A  180.00   0.0  0
 I7T  CONST_14  H8    C8   C9   C10  180.00   0.0  0
 I7T  CONST_16  H212  N21  C21  C2   180.00   0.0  0
 I7T  Var_01    C1A   C11  C1B  C12  168.45  30.0  1
 I7T  Var_02    C10   C1A  C11  C1B  173.44  30.0  1
 I7T  Var_03    C1C   C12  C1B  C11  179.92  30.0  1
 I7T  Var_04    C5A   C6   C61  C1A   30.53  30.0  1
 I7T  Var_05    C3    C2   C1   C1C    8.88  30.0  1
 I7T  Var_06    C4    C3   C2   C1    -8.44  30.0  1
 I7T  Var_07    O21   C21  C2   C1    55.15  30.0  2
 I7T  Var_08    H431  C43  N4   C4    61.64  30.0  3
 I7T  Var_09    H421  C42  N4   C4    70.05  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
 I7T  chir_01  C1C  C1  C12  C41  negativ
 I7T  chir_02  C41  C5  C1C  C4   positiv
 I7T  chir_03  C4   N4  C41  C3   negativ
 I7T  chir_04  C5A  C5  C6   C1B  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
 I7T  plan-1  C2    0.020
 I7T  plan-1  C21   0.020
 I7T  plan-1  O21   0.020
 I7T  plan-1  N21   0.020
 I7T  plan-1  H211  0.020
 I7T  plan-1  H212  0.020
 I7T  plan-2  C11   0.020
 I7T  plan-2  C1A   0.020
 I7T  plan-2  C10   0.020
 I7T  plan-2  O10   0.020
 I7T  plan-2  C9    0.020
 I7T  plan-2  C8    0.020
 I7T  plan-2  C7    0.020
 I7T  plan-2  C61   0.020
 I7T  plan-2  C6    0.020
 I7T  plan-2  I7    0.020
 I7T  plan-2  H9    0.020
 I7T  plan-2  H8    0.020
 I7T  plan-3  C1B   0.020
 I7T  plan-3  C11   0.020
 I7T  plan-3  O11   0.020
 I7T  plan-3  C1A   0.020
 I7T  plan-4  C1C   0.020
 I7T  plan-4  C1    0.020
 I7T  plan-4  O1    0.020
 I7T  plan-4  C2    0.020

