# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:20:50 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: (4S,4aS,6S,8aS)-6-[(1S)-7-chloro-4-hydroxy-1-methyl-3-oxo-1,3-dihydro-2-benzofuran-1-yl]-4-(dimethylamino)-3,8a-dihydroxy-1,8-dioxo-1,4,4a,5,6,7,8,8a-octahydronaphthalene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[C@H]1[C@@H]2C[C@@H](CC(=O)[C@]2(O)C(=O)C(=C1O)C#N)[C@]3(C)OC(=O)c4c(O)ccc(Cl)c34
#
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
 2TC  2TC  (4S,4aS,6S,8aS)-6-[(1S)-7-chloro-4-hydroxy-1-methyl-3-oxo-1,3-dihydro-2-benzofuran-1-yl]-4-(dimethylamino)-3,8a-dihydroxy-1,8-dioxo-1,4,4a,5,6,7,8,8a-octahydronaphthalene-2-carbonitrile  ligand  53  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2TC
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
 2TC  C1    C   C     0   0.409  -2.4492   0.8564  -1.3830
 2TC  O1    O   O     0  -0.378  -2.2192   1.5475  -2.3528
 2TC  C2    C   C     0  -0.240  -3.1866   1.3675  -0.2378
 2TC  C21   C   CSP   0   0.048  -3.5097   2.7486  -0.2428
 2TC  N21   N   NS    0  -0.229  -3.7859   3.8681  -0.2257
 2TC  C3    C   C     0   0.413  -3.4806   0.5949   0.8505
 2TC  O3    O   OH1   0  -0.519  -3.9843   1.0510   1.9649
 2TC  C4    C   CH1   0  -0.107  -3.2382  -0.8935   0.8365
 2TC  N4    N   NT    0  -0.385  -4.3798  -1.5737   0.2412
 2TC  C43   C   CH3   0  -0.512  -4.2258  -3.0163   0.2996
 2TC  C42   C   CH3   0  -0.511  -5.6524  -1.1803   0.8212
 2TC  C41   C   CH1   0  -0.365  -1.9130  -1.1481   0.0970
 2TC  C5    C   CH2   0  -0.418  -0.7593  -0.5843   0.9378
 2TC  C51   C   CH1   0  -0.243   0.5954  -0.7298   0.2515
 2TC  C6    C   CR5   0   0.162   1.7581  -0.2222   1.1252
 2TC  C62   C   CH3   0  -0.621   1.8237  -0.8901   2.4914
 2TC  O6    O   O     0  -0.463   1.5801   1.1980   1.3329
 2TC  C61   C   CR56  0   0.278   3.0887  -0.2938   0.4125
 2TC  C7    C   CR6   0  -0.217   3.8341  -1.3498  -0.0604
 2TC  C8    C   CR16  0  -0.149   5.0550  -1.0770  -0.6780
 2TC  C9    C   CR16  0  -0.327   5.5257   0.2169  -0.8223
 2TC  C10   C   CR6   0   0.381   4.7811   1.2954  -0.3439
 2TC  O10   O   OH1   0  -0.587   5.2491   2.5333  -0.4879
 2TC  C1A   C   CR56  0  -0.250   3.5672   0.9969   0.2671
 2TC  C1B   C   CH2   0  -0.566   0.5624  -0.0280  -1.1128
 2TC  C12   C   C     0   0.402  -0.5423  -0.6064  -1.9383
 2TC  O12   O   O     0  -0.338  -0.3776  -1.1015  -3.0264
 2TC  C1C   C   CT    0   0.070  -1.9532  -0.5976  -1.3361
 2TC  CL7   CL  CL    0  -0.131   3.3079  -2.9910   0.0905
 2TC  C11   C   CR5   0   0.564   2.6016   1.9138   0.8556
 2TC  O1C   O   OH1   0  -0.627  -2.8047  -1.3425  -2.1508
 2TC  H3    H   HOH1  0   0.479  -4.1407   2.0086   1.9609
 2TC  H4    H   HCH1  0   0.245  -3.0938  -1.2023   1.8872
 2TC  H41   H   HCH1  0   0.285  -1.7509  -2.2257   0.0224
 2TC  H421  H   HCH3  0   0.233  -5.8823  -0.1362   0.6092
 2TC  H422  H   HCH3  0   0.236  -6.4427  -1.7694   0.3583
 2TC  H423  H   HCH3  0   0.199  -5.7134  -1.3338   1.9082
 2TC  H431  H   HCH3  0   0.194  -4.0674  -3.3933   1.3210
 2TC  H432  H   HCH3  0   0.232  -5.1288  -3.4844  -0.0906
 2TC  H433  H   HCH3  0   0.244  -3.4003  -3.3544  -0.3221
 2TC  H51C  H   HCH2  0   0.249  -0.9222   0.4670   1.1911
 2TC  H52C  H   HCH2  0   0.263  -0.7612  -1.1356   1.8783
 2TC  H51   H   HCH1  0   0.261   0.7819  -1.7958   0.0863
 2TC  H1B   H   HCH2  0   0.272   0.3752   1.0437  -0.9816
 2TC  H621  H   HCH3  0   0.238   1.8924  -1.9707   2.3807
 2TC  H622  H   HCH3  0   0.253   2.7016  -0.5482   3.0386
 2TC  H623  H   HCH3  0   0.243   0.9418  -0.6627   3.0875
 2TC  H8    H   HCR6  0   0.266   5.6535  -1.8952  -1.0560
 2TC  H9    H   HCR6  0   0.271   6.4766   0.3909  -1.3083
 2TC  H10   H   HOH1  0   0.463   4.6299   3.1811  -0.1214
 2TC  H2B   H   HCH2  0   0.300   1.4963  -0.1358  -1.6645
 2TC  H1C   H   HOH1  0   0.441  -2.3281  -1.5027  -2.9804
 2TC  O11   O   O     0  -0.406   2.6521   3.1159   0.9344

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
 2TC  C1   O1    double    1.213  0.020  1.213
 2TC  C1   C2    single    1.455  0.020  1.455
 2TC  C1   C1C   single    1.537  0.020  1.537
 2TC  C2   C21   single    1.418  0.020  1.418
 2TC  C2   C3    double    1.367  0.020  1.367
 2TC  C21  N21   triple    1.153  0.020  1.153
 2TC  C3   O3    single    1.305  0.020  1.305
 2TC  C3   C4    single    1.508  0.020  1.508
 2TC  C4   N4    single    1.456  0.020  1.456
 2TC  C4   C41   single    1.539  0.020  1.539
 2TC  N4   C42   single    1.453  0.020  1.453
 2TC  N4   C43   single    1.452  0.020  1.452
 2TC  C41  C5    single    1.535  0.020  1.535
 2TC  C41  C1C   single    1.536  0.020  1.536
 2TC  C5   C51   single    1.526  0.020  1.526
 2TC  C51  C6    single    1.540  0.020  1.540
 2TC  C51  C1B   single    1.535  0.020  1.535
 2TC  C6   C62   single    1.522  0.020  1.522
 2TC  C6   O6    single    1.446  0.020  1.446
 2TC  C6   C61   single    1.511  0.020  1.511
 2TC  O6   C11   single    1.336  0.020  1.336
 2TC  C61  C7    aromatic  1.376  0.020  1.376
 2TC  C61  C1A   aromatic  1.384  0.020  1.384
 2TC  C7   C8    aromatic  1.395  0.020  1.395
 2TC  C7   CL7   single    1.730  0.020  1.730
 2TC  C8   C9    aromatic  1.384  0.020  1.384
 2TC  C9   C10   aromatic  1.395  0.020  1.395
 2TC  C10  O10   single    1.331  0.020  1.331
 2TC  C10  C1A   aromatic  1.391  0.020  1.391
 2TC  C1A  C11   single    1.456  0.020  1.456
 2TC  O11  C11   double    1.206  0.020  1.206
 2TC  C1B  C12   single    1.495  0.020  1.495
 2TC  C12  O12   double    1.207  0.020  1.207
 2TC  C12  C1C   single    1.534  0.020  1.534
 2TC  C1C  O1C   single    1.394  0.020  1.394
 2TC  O3   H3    single    0.850  0.020  0.980
 2TC  C4   H4    single    0.970  0.020  1.090
 2TC  C41  H41   single    0.970  0.020  1.090
 2TC  C42  H421  single    0.970  0.020  1.090
 2TC  C42  H422  single    0.970  0.020  1.090
 2TC  C42  H423  single    0.970  0.020  1.090
 2TC  C43  H431  single    0.970  0.020  1.090
 2TC  C43  H432  single    0.970  0.020  1.090
 2TC  C43  H433  single    0.970  0.020  1.090
 2TC  C5   H51C  single    0.970  0.020  1.090
 2TC  C5   H52C  single    0.970  0.020  1.090
 2TC  C51  H51   single    0.970  0.020  1.090
 2TC  C1B  H1B   single    0.970  0.020  1.090
 2TC  C62  H621  single    0.970  0.020  1.090
 2TC  C62  H622  single    0.970  0.020  1.090
 2TC  C62  H623  single    0.970  0.020  1.090
 2TC  C8   H8    single    0.930  0.020  1.080
 2TC  C9   H9    single    0.930  0.020  1.080
 2TC  O10  H10   single    0.850  0.020  0.980
 2TC  C1B  H2B   single    0.970  0.020  1.090
 2TC  O1C  H1C   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
 2TC  C1C   C1   C2    118.16  3.000
 2TC  C1C   C1   O1    120.15  3.000
 2TC  C2    C1   O1    121.69  3.000
 2TC  C3    C2   C21   120.28  3.000
 2TC  C3    C2   C1    122.50  3.000
 2TC  C21   C2   C1    117.05  3.000
 2TC  N21   C21  C2    180.00  3.000
 2TC  C4    C3   O3    114.51  3.000
 2TC  C4    C3   C2    121.06  3.000
 2TC  O3    C3   C2    124.43  3.000
 2TC  H3    O3   C3    113.80  3.000
 2TC  H4    C4   C41   107.35  3.000
 2TC  H4    C4   N4    111.14  3.000
 2TC  C41   C4   N4    113.67  3.000
 2TC  H4    C4   C3    106.74  3.000
 2TC  C41   C4   C3    107.83  3.000
 2TC  N4    C4   C3    109.80  3.000
 2TC  C42   N4   C43   110.24  3.000
 2TC  C43   N4   C4    111.38  3.000
 2TC  C42   N4   C4    113.39  3.000
 2TC  H433  C43  H432  106.91  3.000
 2TC  H433  C43  H431  108.36  3.000
 2TC  H432  C43  H431  107.74  3.000
 2TC  H433  C43  N4    111.50  3.000
 2TC  H432  C43  N4    108.94  3.000
 2TC  H431  C43  N4    113.15  3.000
 2TC  H423  C42  H422  107.73  3.000
 2TC  H423  C42  H421  108.32  3.000
 2TC  H422  C42  H421  106.40  3.000
 2TC  H423  C42  N4    113.93  3.000
 2TC  H422  C42  N4    108.63  3.000
 2TC  H421  C42  N4    111.51  3.000
 2TC  H41   C41  C1C   107.09  3.000
 2TC  H41   C41  C5    106.75  3.000
 2TC  C1C   C41  C5    113.53  3.000
 2TC  H41   C41  C4    108.89  3.000
 2TC  C1C   C41  C4    111.51  3.000
 2TC  C5    C41  C4    108.86  3.000
 2TC  H52C  C5   H51C  106.63  3.000
 2TC  H52C  C5   C51   109.97  3.000
 2TC  H51C  C5   C51   109.15  3.000
 2TC  H52C  C5   C41   106.59  3.000
 2TC  H51C  C5   C41   111.59  3.000
 2TC  C51   C5   C41   112.70  3.000
 2TC  H51   C51  C1B   108.35  3.000
 2TC  H51   C51  C6    106.13  3.000
 2TC  C1B   C51  C6    111.70  3.000
 2TC  H51   C51  C5    108.18  3.000
 2TC  C1B   C51  C5    109.71  3.000
 2TC  C6    C51  C5    112.56  3.000
 2TC  C61   C6   O6    102.86  3.000
 2TC  C61   C6   C62   111.38  3.000
 2TC  O6    C6   C62   107.90  3.000
 2TC  C61   C6   C51   112.43  3.000
 2TC  O6    C6   C51   108.19  3.000
 2TC  C62   C6   C51   113.39  3.000
 2TC  H623  C62  H622  108.19  3.000
 2TC  H623  C62  H621  108.31  3.000
 2TC  H622  C62  H621  108.17  3.000
 2TC  H623  C62  C6    111.40  3.000
 2TC  H622  C62  C6    110.36  3.000
 2TC  H621  C62  C6    110.31  3.000
 2TC  C11   O6   C6    112.39  3.000
 2TC  C1A   C61  C7    119.48  3.000
 2TC  C1A   C61  C6    108.05  3.000
 2TC  C7    C61  C6    132.47  3.000
 2TC  CL7   C7   C8    119.36  3.000
 2TC  CL7   C7   C61   122.22  3.000
 2TC  C8    C7   C61   118.43  3.000
 2TC  H8    C8   C9    118.83  3.000
 2TC  H8    C8   C7    119.40  3.000
 2TC  C9    C8   C7    121.76  3.000
 2TC  H9    C9   C10   119.91  3.000
 2TC  H9    C9   C8    119.74  3.000
 2TC  C10   C9   C8    120.35  3.000
 2TC  C1A   C10  O10   123.63  3.000
 2TC  C1A   C10  C9    116.77  3.000
 2TC  O10   C10  C9    119.61  3.000
 2TC  H10   O10  C10   110.87  3.000
 2TC  C11   C1A  C10   128.39  3.000
 2TC  C11   C1A  C61   108.40  3.000
 2TC  C10   C1A  C61   123.21  3.000
 2TC  H2B   C1B  H1B   107.68  3.000
 2TC  H2B   C1B  C12   108.38  3.000
 2TC  H1B   C1B  C12   108.55  3.000
 2TC  H2B   C1B  C51   112.72  3.000
 2TC  H1B   C1B  C51   110.15  3.000
 2TC  C12   C1B  C51   109.25  3.000
 2TC  C1C   C12  O12   118.80  3.000
 2TC  C1C   C12  C1B   117.42  3.000
 2TC  O12   C12  C1B   123.75  3.000
 2TC  O1C   C1C  C12   109.23  3.000
 2TC  O1C   C1C  C41   111.70  3.000
 2TC  C12   C1C  C41   109.89  3.000
 2TC  O1C   C1C  C1    106.89  3.000
 2TC  C12   C1C  C1    106.87  3.000
 2TC  C41   C1C  C1    112.09  3.000
 2TC  O11   C11  C1A   128.80  3.000
 2TC  O11   C11  O6    122.89  3.000
 2TC  C1A   C11  O6    108.31  3.000
 2TC  H1C   O1C  C1C   106.73  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
 2TC  CONST_01  C9    C8   C7   C61    0.00   0.0  0
 2TC  CONST_02  C9    C10  C1A  C61    0.00   0.0  0
 2TC  CONST_03  C10   C1A  C61  C7     0.00   0.0  0
 2TC  CONST_04  C10   C9   C8   C7     0.00   0.0  0
 2TC  CONST_05  C1A   C61  C7   C8     0.00   0.0  0
 2TC  CONST_06  C1A   C10  C9   C8     0.00   0.0  0
 2TC  CONST_07  CL7   C7   C61  C6     0.00   0.0  0
 2TC  CONST_08  O10   C10  C1A  C61  180.00   0.0  0
 2TC  CONST_09  O10   C10  C9   C8   180.00   0.0  0
 2TC  CONST_10  CL7   C7   C8   C9   180.00   0.0  0
 2TC  CONST_11  C11   C1A  C10  O10    0.00   0.0  0
 2TC  CONST_12  CL7   C7   C61  C1A  180.00   0.0  0
 2TC  CONST_13  H8    C8   C7   C61  180.00   0.0  0
 2TC  CONST_14  H9    C9   C8   C7   180.00   0.0  0
 2TC  Var_01    C4    C3   C2   C1    -9.40  30.0  1
 2TC  Var_02    C1C   C1   C2   C3    -1.80  30.0  1
 2TC  Var_03    C1C   C12  C1B  C51   55.18  30.0  1
 2TC  Var_04    C1A   C11  O6   C6     0.32  30.0  1
 2TC  Var_05    C61   C1A  C11  O6    -0.16  30.0  1
 2TC  Var_06    H421  C42  N4   C4    65.94  30.0  3
 2TC  Var_07    H431  C43  N4   C4    56.26  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
 2TC  chir_01  C4   C3   N4   C41  negativ
 2TC  chir_02  C41  C4   C5   C1C  positiv
 2TC  chir_03  C51  C5   C6   C1B  positiv
 2TC  chir_04  C6   C61  O6   C51  negativ
 2TC  chir_05  C1C  C12  C41  C1   negativ

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
 2TC  plan-1  C1   0.020
 2TC  plan-1  O1   0.020
 2TC  plan-1  C2   0.020
 2TC  plan-1  C1C  0.020
 2TC  plan-2  C6   0.020
 2TC  plan-2  C61  0.020
 2TC  plan-2  C7   0.020
 2TC  plan-2  C8   0.020
 2TC  plan-2  C9   0.020
 2TC  plan-2  C10  0.020
 2TC  plan-2  O10  0.020
 2TC  plan-2  C1A  0.020
 2TC  plan-2  CL7  0.020
 2TC  plan-2  C11  0.020
 2TC  plan-2  H8   0.020
 2TC  plan-2  H9   0.020
 2TC  plan-3  C1B  0.020
 2TC  plan-3  C12  0.020
 2TC  plan-3  O12  0.020
 2TC  plan-3  C1C  0.020
 2TC  plan-4  O6   0.020
 2TC  plan-4  C1A  0.020
 2TC  plan-4  C11  0.020
 2TC  plan-4  O11  0.020

