# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:43:46 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (4aS,12aS)-3,10,11,12a-tetrahydroxy-6-methyl-1,12-dioxo-1,4,4a,5,12,12a-hexahydrotetracene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c2C[C@H]3CC(=C(C(N)=O)C(=O)[C@@]3(O)C(=O)c2c(O)c4c(O)cccc14)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
 4DM  4DM  (4aS,12aS)-3,10,11,12a-tetrahydroxy-6-methyl-1,12-dioxo-1,4,4a,5,12,12a-hexahydrotetracene-2-carboxamide  ligand  45  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4DM
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
 4DM  C4    C  CH2   0  -0.555  -1.6533   1.2113  -1.2739
 4DM  C3    C  C     0   0.454  -2.8965   0.3932  -1.3703
 4DM  O3    O  OH1   0  -0.569  -3.3563   0.3162  -2.6011
 4DM  C2    C  C     0  -0.360  -3.4930  -0.1856  -0.2851
 4DM  C1    C  C     0   0.400  -2.8912  -0.0722   1.0258
 4DM  C5    C  CH2   0  -0.515   0.0351   2.3065   0.2452
 4DM  C6    C  CR6   0  -0.030   2.4318   1.6990  -0.1388
 4DM  C12   C  C     0   0.428  -0.4486  -0.5239   0.7882
 4DM  C1B   C  CR6   0  -0.232   0.8741  -0.0831   0.3993
 4DM  C11   C  CR6   0   0.370   1.8819  -1.0512   0.2744
 4DM  O11   O  OH1   0  -0.592   1.6237  -2.3247   0.4850
 4DM  C1A   C  CR66  0  -0.144   3.2079  -0.6659  -0.0806
 4DM  C10   C  CR6   0   0.373   4.2723  -1.6016  -0.2472
 4DM  O10   O  OH1   0  -0.600   4.0326  -2.9050  -0.0601
 4DM  C9    C  CR16  0  -0.416   5.5326  -1.1640  -0.5994
 4DM  C8    C  CR16  0  -0.215   5.7743   0.1946  -0.7939
 4DM  C7    C  CR16  0  -0.369   4.7743   1.1204  -0.6372
 4DM  C61   C  CR66  0   0.117   3.4717   0.7200  -0.2789
 4DM  C62   C  CH3   0  -0.770   2.7873   3.1469  -0.3369
 4DM  C51   C  CR6   0   0.078   1.1577   1.3003   0.1611
 4DM  C1C   C  CT    0   0.029  -1.4937   0.5444   1.1105
 4DM  O1    O  O     0  -0.406  -3.4132  -0.4664   2.0508
 4DM  O1C   O  OH1   0  -0.653  -1.2330   0.9781   2.4137
 4DM  C41   C  CH1   0  -0.334  -1.3536   1.6971   0.1395
 4DM  C21   C  C     0   0.491  -4.8286  -0.8383  -0.3981
 4DM  O21   O  O     0  -0.434  -5.7615  -0.5494   0.3223
 4DM  N21   N  NH2   0  -0.829  -4.9352  -1.7089  -1.4436
 4DM  H4    H  HCH2  0   0.296  -0.8280   0.6125  -1.6776
 4DM  H4A   H  HCH2  0   0.309  -1.7490   2.0677  -1.9450
 4DM  HO3   H  HOH1  0   0.484  -4.1254  -0.2823  -2.6582
 4DM  H5    H  HCH2  0   0.286   0.1093   2.8632   1.1832
 4DM  H5A   H  HCH2  0   0.270   0.1428   3.0466  -0.5491
 4DM  HO11  H  HOH1  0   0.485   0.6565  -2.4005   0.7019
 4DM  HO10  H  HOH1  0   0.479   4.8414  -3.4060  -0.2197
 4DM  H9    H  HCR6  0   0.275   6.3355  -1.8809  -0.7256
 4DM  H8    H  HCR6  0   0.268   6.7682   0.5185  -1.0734
 4DM  H7    H  HCR6  0   0.259   4.9977   2.1635  -0.8007
 4DM  H62   H  HCH3  0   0.248   3.0592   3.3600  -1.3731
 4DM  H62A  H  HCH3  0   0.267   1.9765   3.8170  -0.0693
 4DM  H62B  H  HCH3  0   0.249   3.6393   3.4326   0.2816
 4DM  HO1C  H  HOH1  0   0.456  -1.7542   0.4248   3.0140
 4DM  H41   H  HCH1  0   0.290  -2.0912   2.4620   0.4009
 4DM  HN21  H  HNH2  0   0.419  -4.1277  -2.2651  -1.6876
 4DM  HN2A  H  HNH2  0   0.410  -5.8143  -2.1975  -1.5453
 4DM  O12   O  O     0  -0.467  -0.7455  -1.7112   0.9444

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
 4DM  C4   C3    single    1.491  0.020  1.491
 4DM  C4   C41   single    1.524  0.020  1.524
 4DM  C3   O3    single    1.316  0.020  1.316
 4DM  C3   C2    double    1.367  0.020  1.367
 4DM  C2   C1    single    1.447  0.020  1.447
 4DM  C2   C21   single    1.491  0.020  1.491
 4DM  C1   C1C   single    1.530  0.020  1.530
 4DM  C1   O1    double    1.216  0.020  1.216
 4DM  C5   C51   single    1.510  0.020  1.510
 4DM  C5   C41   single    1.520  0.020  1.520
 4DM  C6   C61   aromatic  1.435  0.020  1.435
 4DM  C6   C62   single    1.504  0.020  1.504
 4DM  C6   C51   aromatic  1.368  0.020  1.368
 4DM  O12  C12   double    1.234  0.020  1.234
 4DM  C12  C1B   single    1.447  0.020  1.447
 4DM  C12  C1C   single    1.529  0.020  1.529
 4DM  C1B  C11   aromatic  1.403  0.020  1.403
 4DM  C1B  C51   aromatic  1.432  0.020  1.432
 4DM  C11  O11   single    1.316  0.020  1.316
 4DM  C11  C1A   aromatic  1.426  0.020  1.426
 4DM  C1A  C10   aromatic  1.427  0.020  1.427
 4DM  C1A  C61   aromatic  1.425  0.020  1.425
 4DM  C10  O10   single    1.338  0.020  1.338
 4DM  C10  C9    aromatic  1.380  0.020  1.380
 4DM  C9   C8    aromatic  1.393  0.020  1.393
 4DM  C8   C7    aromatic  1.372  0.020  1.372
 4DM  C7   C61   aromatic  1.409  0.020  1.409
 4DM  C1C  O1C   single    1.398  0.020  1.398
 4DM  C1C  C41   single    1.514  0.020  1.514
 4DM  C21  O21   double    1.214  0.020  1.214
 4DM  C21  N21   single    1.365  0.020  1.365
 4DM  C4   H4    single    0.970  0.020  1.090
 4DM  C4   H4A   single    0.970  0.020  1.090
 4DM  O3   HO3   single    0.850  0.020  0.980
 4DM  C5   H5    single    0.970  0.020  1.090
 4DM  C5   H5A   single    0.970  0.020  1.090
 4DM  O11  HO11  single    0.850  0.020  0.980
 4DM  O10  HO10  single    0.850  0.020  0.980
 4DM  C9   H9    single    0.930  0.020  1.080
 4DM  C8   H8    single    0.930  0.020  1.080
 4DM  C7   H7    single    0.930  0.020  1.080
 4DM  C62  H62   single    0.970  0.020  1.090
 4DM  C62  H62A  single    0.970  0.020  1.090
 4DM  C62  H62B  single    0.970  0.020  1.090
 4DM  O1C  HO1C  single    0.850  0.020  0.980
 4DM  C41  H41   single    0.970  0.020  1.090
 4DM  N21  HN21  single    0.890  0.020  1.040
 4DM  N21  HN2A  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
 4DM  H4A   C4   H4    105.54  3.000
 4DM  H4A   C4   C41   109.70  3.000
 4DM  H4    C4   C41   111.55  3.000
 4DM  H4A   C4   C3    108.50  3.000
 4DM  H4    C4   C3    107.70  3.000
 4DM  C41   C4   C3    113.49  3.000
 4DM  C2    C3   O3    124.42  3.000
 4DM  C2    C3   C4    123.01  3.000
 4DM  O3    C3   C4    112.56  3.000
 4DM  HO3   O3   C3    111.45  3.000
 4DM  C21   C2   C1    118.40  3.000
 4DM  C21   C2   C3    121.07  3.000
 4DM  C1    C2   C3    120.31  3.000
 4DM  O1    C1   C1C   118.43  3.000
 4DM  O1    C1   C2    124.04  3.000
 4DM  C1C   C1   C2    117.49  3.000
 4DM  H5A   C5   H5    105.81  3.000
 4DM  H5A   C5   C41   108.15  3.000
 4DM  H5    C5   C41   109.01  3.000
 4DM  H5A   C5   C51   109.77  3.000
 4DM  H5    C5   C51   109.67  3.000
 4DM  C41   C5   C51   114.09  3.000
 4DM  C51   C6   C62   121.97  3.000
 4DM  C51   C6   C61   119.83  3.000
 4DM  C62   C6   C61   118.20  3.000
 4DM  C1C   C12  C1B   117.94  3.000
 4DM  C1C   C12  O12   118.77  3.000
 4DM  C1B   C12  O12   123.16  3.000
 4DM  C51   C1B  C11   120.63  3.000
 4DM  C51   C1B  C12   121.32  3.000
 4DM  C11   C1B  C12   118.04  3.000
 4DM  C1A   C11  O11   118.93  3.000
 4DM  C1A   C11  C1B   120.24  3.000
 4DM  O11   C11  C1B   120.82  3.000
 4DM  HO11  O11  C11   107.43  3.000
 4DM  C61   C1A  C10   118.91  3.000
 4DM  C61   C1A  C11   118.02  3.000
 4DM  C10   C1A  C11   123.06  3.000
 4DM  C9    C10  O10   120.54  3.000
 4DM  C9    C10  C1A   120.21  3.000
 4DM  O10   C10  C1A   119.26  3.000
 4DM  HO10  O10  C10   109.42  3.000
 4DM  H9    C9   C8    120.01  3.000
 4DM  H9    C9   C10   119.77  3.000
 4DM  C8    C9   C10   120.22  3.000
 4DM  H8    C8   C7    119.81  3.000
 4DM  H8    C8   C9    119.16  3.000
 4DM  C7    C8   C9    121.04  3.000
 4DM  H7    C7   C61   120.30  3.000
 4DM  H7    C7   C8    118.96  3.000
 4DM  C61   C7   C8    120.74  3.000
 4DM  C7    C61  C1A   118.88  3.000
 4DM  C7    C61  C6    120.06  3.000
 4DM  C1A   C61  C6    121.05  3.000
 4DM  H62B  C62  H62A  106.38  3.000
 4DM  H62B  C62  H62   107.00  3.000
 4DM  H62A  C62  H62   107.42  3.000
 4DM  H62B  C62  C6    111.23  3.000
 4DM  H62A  C62  C6    112.66  3.000
 4DM  H62   C62  C6    111.81  3.000
 4DM  C1B   C51  C6    120.16  3.000
 4DM  C1B   C51  C5    119.16  3.000
 4DM  C6    C51  C5    120.69  3.000
 4DM  C41   C1C  O1C   110.15  3.000
 4DM  C41   C1C  C12   109.49  3.000
 4DM  O1C   C1C  C12   106.61  3.000
 4DM  C41   C1C  C1    110.85  3.000
 4DM  O1C   C1C  C1    110.30  3.000
 4DM  C12   C1C  C1    109.34  3.000
 4DM  HO1C  O1C  C1C   107.46  3.000
 4DM  H41   C41  C1C   108.46  3.000
 4DM  H41   C41  C5    108.60  3.000
 4DM  C1C   C41  C5    110.19  3.000
 4DM  H41   C41  C4    108.17  3.000
 4DM  C1C   C41  C4    109.51  3.000
 4DM  C5    C41  C4    111.83  3.000
 4DM  N21   C21  O21   123.14  3.000
 4DM  N21   C21  C2    114.04  3.000
 4DM  O21   C21  C2    122.64  3.000
 4DM  HN2A  N21  HN21  113.87  3.000
 4DM  HN2A  N21  C21   116.96  3.000
 4DM  HN21  N21  C21   118.28  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
 4DM  CONST_01  C11   C1A  C61  C6      0.00   0.0  0
 4DM  CONST_02  C10   C1A  C61  C6    180.00   0.0  0
 4DM  CONST_03  C8    C7   C61  C6    180.00   0.0  0
 4DM  CONST_04  C11   C1B  C51  C6      0.00   0.0  0
 4DM  CONST_05  C10   C1A  C11  C1B   180.00   0.0  0
 4DM  CONST_06  C61   C1A  C11  C1B     0.00   0.0  0
 4DM  CONST_07  C61   C6   C51  C1B     0.00   0.0  0
 4DM  CONST_08  C9    C10  C1A  C11   180.00   0.0  0
 4DM  CONST_09  C7    C61  C1A  C11   180.00   0.0  0
 4DM  CONST_10  C51   C1B  C11  C1A     0.00   0.0  0
 4DM  CONST_11  C8    C9   C10  C1A     0.00   0.0  0
 4DM  CONST_12  C51   C6   C61  C1A     0.00   0.0  0
 4DM  CONST_13  C8    C7   C61  C1A     0.00   0.0  0
 4DM  CONST_14  C7    C61  C1A  C10     0.00   0.0  0
 4DM  CONST_15  C7    C8   C9   C10     0.00   0.0  0
 4DM  CONST_16  C61   C1A  C10  C9      0.00   0.0  0
 4DM  CONST_17  C61   C7   C8   C9      0.00   0.0  0
 4DM  CONST_18  C51   C6   C61  C7    180.00   0.0  0
 4DM  CONST_19  C62   C6   C51  C5      0.00   0.0  0
 4DM  CONST_20  O11   C11  C1B  C12     0.00   0.0  0
 4DM  CONST_21  C62   C6   C51  C1B   180.00   0.0  0
 4DM  CONST_22  O10   C10  C1A  C11     0.00   0.0  0
 4DM  CONST_23  C51   C1B  C11  O11   180.00   0.0  0
 4DM  CONST_24  C10   C1A  C11  O11     0.00   0.0  0
 4DM  CONST_25  C61   C1A  C11  O11   180.00   0.0  0
 4DM  CONST_26  C62   C6   C61  C1A   180.00   0.0  0
 4DM  CONST_27  C61   C1A  C10  O10   180.00   0.0  0
 4DM  CONST_28  C8    C9   C10  O10   180.00   0.0  0
 4DM  CONST_29  C62   C6   C61  C7      0.00   0.0  0
 4DM  CONST_30  H7    C7   C61  C6      0.00   0.0  0
 4DM  CONST_31  H9    C9   C10  C1A   180.00   0.0  0
 4DM  CONST_32  H8    C8   C9   C10   180.00   0.0  0
 4DM  CONST_34  HN2A  N21  C21  C2    180.00   0.0  0
 4DM  Var_01    C1    C2   C3   C4     -2.80  30.0  1
 4DM  Var_02    C1C   C1   C2   C3     -8.04  30.0  1
 4DM  Var_03    C41   C4   C3   C2    -17.74  30.0  1
 4DM  Var_04    C41   C5   C51  C6    161.35  30.0  1
 4DM  Var_05    C1C   C12  C1B  C11   171.76  30.0  1
 4DM  Var_06    O21   C21  C2   C3   -126.35  30.0  2
 4DM  Var_07    H62   C62  C6   C61    67.32  30.0  2

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
 4DM  chir_01  C1C  C12  C1  C41  positiv
 4DM  chir_02  C41  C4   C5  C1C  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
 4DM  plan-1  C2    0.020
 4DM  plan-1  C21   0.020
 4DM  plan-1  O21   0.020
 4DM  plan-1  N21   0.020
 4DM  plan-1  HN21  0.020
 4DM  plan-1  HN2A  0.020
 4DM  plan-2  C5    0.020
 4DM  plan-2  C6    0.020
 4DM  plan-2  C12   0.020
 4DM  plan-2  C1B   0.020
 4DM  plan-2  C11   0.020
 4DM  plan-2  O11   0.020
 4DM  plan-2  C1A   0.020
 4DM  plan-2  C10   0.020
 4DM  plan-2  O10   0.020
 4DM  plan-2  C9    0.020
 4DM  plan-2  C8    0.020
 4DM  plan-2  C7    0.020
 4DM  plan-2  C61   0.020
 4DM  plan-2  C62   0.020
 4DM  plan-2  C51   0.020
 4DM  plan-2  H9    0.020
 4DM  plan-2  H8    0.020
 4DM  plan-2  H7    0.020
 4DM  plan-3  C2    0.020
 4DM  plan-3  C1    0.020
 4DM  plan-3  C1C   0.020
 4DM  plan-3  O1    0.020
 4DM  plan-4  C12   0.020
 4DM  plan-4  C1B   0.020
 4DM  plan-4  C1C   0.020
 4DM  plan-4  O12   0.020

