# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:25:36 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 9-chloro-2-({5-[3-(dimethylamino)propyl]-2-methylpyridin-3-yl}amino)-5,7-dihydro-6H-pyrimido[5,4-d][1]benzazepine-6-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCc1cnc(C)c(Nc2ncc3CC(=S)Nc4cc(Cl)ccc4c3n2)c1
#
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
 3TA  3TA  9-chloro-2-({5-[3-(dimethylamino)propyl]-2-methylpyridin-3-yl}amino)-5,7-dihydro-6H-pyrimido[5,4-d][1]benzazepine-6-thione  ligand  56  31  .  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_3TA
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
 3TA  C1    C   CR6   0  -0.023   1.8441   0.6670   1.4961
 3TA  CL1   CL  CL    0  -0.105   7.6392  -0.9207  -1.7994
 3TA  C2    C   CR16  0  -0.022   0.5157   0.6860   1.8908
 3TA  N3    N   N     0  -0.447  -0.4016  -0.1259   1.3969
 3TA  C4    C   CR6   0   0.589   0.0134  -0.9925   0.4762
 3TA  N5    N   N     0  -0.480   1.2564  -1.0881   0.0070
 3TA  C6    C   CR6   0   0.296   2.1617  -0.2587   0.5037
 3TA  C7    C   CR6   0   0.308   4.3671   0.7249  -0.2296
 3TA  C8    C   CR6   0   0.049   3.5322  -0.3805  -0.0166
 3TA  N9    N   NH1   0  -0.659   3.9761   2.0539   0.0015
 3TA  C10   C   C     0   0.168   3.3110   2.5642   1.0445
 3TA  C11   C   CH2   0  -0.624   2.8788   1.5719   2.0841
 3TA  C12   C   CR16  0  -0.203   5.2657  -1.8335  -0.9000
 3TA  C13   C   CR6   0  -0.042   6.0658  -0.7201  -1.1176
 3TA  C14   C   CR16  0  -0.262   5.6305   0.5483  -0.7921
 3TA  C15   C   CR16  0  -0.301   4.0086  -1.6461  -0.3629
 3TA  S16   S   S1    0  -0.315   2.9805   4.1787   1.1552
 3TA  N18   N   NH1   0  -0.774  -0.8701  -1.8828  -0.0503
 3TA  C19   C   CR6   0   0.264  -2.2324  -2.0163   0.2169
 3TA  C20   C   CR16  0  -0.221  -3.0701  -0.9317   0.4443
 3TA  C21   C   CR6   0   0.046  -4.4224  -1.1418   0.6822
 3TA  C22   C   CR16  0  -0.138  -4.8720  -2.4541   0.6646
 3TA  N23   N   N     0  -0.411  -4.0851  -3.4959   0.4281
 3TA  C24   C   CR6   0   0.185  -2.7920  -3.3057   0.2102
 3TA  C25   C   CH2   0  -0.514  -5.3657   0.0076   0.8816
 3TA  C26   C   CH2   0  -0.438  -5.8390   0.5897  -0.4514
 3TA  C27   C   CH2   0  -0.256  -6.7656   1.7801  -0.2450
 3TA  N28   N   NT    0  -0.407  -7.1526   2.4348  -1.4810
 3TA  C29   C   CH3   0  -0.527  -8.0159   1.6092  -2.2985
 3TA  C30   C   CH3   0  -0.518  -7.7755   3.7140  -1.2171
 3TA  C31   C   CH3   0  -0.758  -1.9441  -4.5147  -0.0473
 3TA  H2    H   HCR6  0   0.277   0.1848   1.3838   2.6540
 3TA  HN9   H   HNH1  0   0.422   4.3270   2.7314  -0.6636
 3TA  H11   H   HCH2  0   0.301   2.4794   2.1048   2.9429
 3TA  H11A  H   HCH2  0   0.308   3.7474   0.9957   2.4223
 3TA  H12   H   HCR6  0   0.290   5.6144  -2.8254  -1.1498
 3TA  H14   H   HCR6  0   0.305   6.2630   1.4088  -0.9676
 3TA  H15   H   HCR6  0   0.276   3.3692  -2.5039  -0.2056
 3TA  HN18  H   HNH1  0   0.410  -0.4472  -2.5672  -0.6582
 3TA  H20   H   HCR6  0   0.269  -2.6777   0.0757   0.4351
 3TA  H22   H   HCR6  0   0.250  -5.9192  -2.6717   0.8528
 3TA  H25   H   HCH2  0   0.244  -6.2308  -0.3249   1.4622
 3TA  H25A  H   HCH2  0   0.244  -4.8761   0.7893   1.4683
 3TA  H26   H   HCH2  0   0.228  -4.9748   0.9084  -1.0415
 3TA  H26A  H   HCH2  0   0.233  -6.3361  -0.1993  -1.0212
 3TA  H27   H   HCH2  0   0.185  -7.6486   1.4601   0.3385
 3TA  H27A  H   HCH2  0   0.226  -6.2417   2.5155   0.3730
 3TA  H29   H   HCH3  0   0.189  -8.9612   1.3463  -1.7969
 3TA  H29A  H   HCH3  0   0.233  -8.2653   2.1358  -3.2207
 3TA  H29B  H   HCH3  0   0.235  -7.5207   0.6801  -2.5792
 3TA  H30   H   HCH3  0   0.231  -7.0888   4.3637  -0.6722
 3TA  H30A  H   HCH3  0   0.230  -8.0256   4.2078  -2.1575
 3TA  H30B  H   HCH3  0   0.188  -8.7033   3.6362  -0.6275
 3TA  H31   H   HCH3  0   0.251  -1.5430  -4.5254  -1.0643
 3TA  H31A  H   HCH3  0   0.254  -1.0923  -4.5627   0.6337
 3TA  H31B  H   HCH3  0   0.263  -2.5368  -5.4175   0.0806

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
 3TA  C2   C1    aromatic  1.386  0.020  1.386
 3TA  C1   C6    aromatic  1.394  0.020  1.394
 3TA  C1   C11   single    1.495  0.020  1.495
 3TA  C13  CL1   single    1.726  0.020  1.726
 3TA  N3   C2    aromatic  1.321  0.020  1.321
 3TA  C2   H2    single    0.930  0.020  1.080
 3TA  N3   C4    aromatic  1.331  0.020  1.331
 3TA  N18  C4    single    1.360  0.020  1.360
 3TA  C4   N5    aromatic  1.332  0.020  1.332
 3TA  N5   C6    aromatic  1.324  0.020  1.324
 3TA  C6   C8    aromatic  1.471  0.020  1.471
 3TA  C8   C7    aromatic  1.402  0.020  1.402
 3TA  C7   N9    single    1.404  0.020  1.404
 3TA  C7   C14   aromatic  1.394  0.020  1.394
 3TA  C8   C15   aromatic  1.396  0.020  1.396
 3TA  C10  N9    single    1.338  0.020  1.338
 3TA  N9   HN9   single    0.860  0.020  1.020
 3TA  C11  C10   single    1.501  0.020  1.501
 3TA  C10  S16   double    1.652  0.020  1.652
 3TA  C11  H11   single    0.970  0.020  1.090
 3TA  C11  H11A  single    0.970  0.020  1.090
 3TA  C15  C12   aromatic  1.380  0.020  1.380
 3TA  C12  C13   aromatic  1.388  0.020  1.388
 3TA  C12  H12   single    0.930  0.020  1.080
 3TA  C14  C13   aromatic  1.380  0.020  1.380
 3TA  C14  H14   single    0.930  0.020  1.080
 3TA  C15  H15   single    0.930  0.020  1.080
 3TA  N18  C19   single    1.395  0.020  1.395
 3TA  N18  HN18  single    0.860  0.020  1.020
 3TA  C24  C19   aromatic  1.406  0.020  1.406
 3TA  C19  C20   aromatic  1.389  0.020  1.389
 3TA  C21  C20   aromatic  1.389  0.020  1.389
 3TA  C20  H20   single    0.930  0.020  1.080
 3TA  C22  C21   aromatic  1.387  0.020  1.387
 3TA  C21  C25   single    1.500  0.020  1.500
 3TA  N23  C22   aromatic  1.327  0.020  1.327
 3TA  C22  H22   single    0.930  0.020  1.080
 3TA  N23  C24   aromatic  1.325  0.020  1.325
 3TA  C31  C24   single    1.499  0.020  1.499
 3TA  C25  C26   single    1.530  0.020  1.530
 3TA  C25  H25   single    0.970  0.020  1.090
 3TA  C25  H25A  single    0.970  0.020  1.090
 3TA  C26  C27   single    1.523  0.020  1.523
 3TA  C26  H26   single    0.970  0.020  1.090
 3TA  C26  H26A  single    0.970  0.020  1.090
 3TA  N28  C27   single    1.451  0.020  1.451
 3TA  C27  H27   single    0.970  0.020  1.090
 3TA  C27  H27A  single    0.970  0.020  1.090
 3TA  N28  C29   single    1.447  0.020  1.447
 3TA  N28  C30   single    1.447  0.020  1.447
 3TA  C29  H29   single    0.970  0.020  1.090
 3TA  C29  H29A  single    0.970  0.020  1.090
 3TA  C29  H29B  single    0.970  0.020  1.090
 3TA  C30  H30   single    0.970  0.020  1.090
 3TA  C30  H30A  single    0.970  0.020  1.090
 3TA  C30  H30B  single    0.970  0.020  1.090
 3TA  C31  H31   single    0.970  0.020  1.090
 3TA  C31  H31A  single    0.970  0.020  1.090
 3TA  C31  H31B  single    0.970  0.020  1.090

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
 3TA  C11   C1   C6    121.62  3.000
 3TA  C11   C1   C2    122.89  3.000
 3TA  C6    C1   C2    115.49  3.000
 3TA  H2    C2   N3    116.51  3.000
 3TA  H2    C2   C1    120.07  3.000
 3TA  N3    C2   C1    123.41  3.000
 3TA  C4    N3   C2    116.26  3.000
 3TA  N18   C4   N5    115.01  3.000
 3TA  N5    C4   N3    125.55  3.000
 3TA  N18   C4   N3    119.44  3.000
 3TA  C6    N5   C4    117.44  3.000
 3TA  C8    C6   N5    116.89  3.000
 3TA  C8    C6   C1    121.27  3.000
 3TA  N5    C6   C1    121.82  3.000
 3TA  C14   C7   N9    116.01  3.000
 3TA  C14   C7   C8    120.08  3.000
 3TA  N9    C7   C8    123.74  3.000
 3TA  C15   C8   C7    118.30  3.000
 3TA  C15   C8   C6    118.73  3.000
 3TA  C7    C8   C6    122.92  3.000
 3TA  HN9   N9   C10   115.42  3.000
 3TA  HN9   N9   C7    115.39  3.000
 3TA  C10   N9   C7    128.87  3.000
 3TA  S16   C10  C11   122.84  3.000
 3TA  S16   C10  N9    121.63  3.000
 3TA  C11   C10  N9    115.52  3.000
 3TA  H11A  C11  H11   107.78  3.000
 3TA  H11A  C11  C10   109.46  3.000
 3TA  H11   C11  C10   109.21  3.000
 3TA  H11A  C11  C1    110.59  3.000
 3TA  H11   C11  C1    110.68  3.000
 3TA  C10   C11  C1    109.09  3.000
 3TA  H12   C12  C15   120.57  3.000
 3TA  H12   C12  C13   120.92  3.000
 3TA  C15   C12  C13   118.50  3.000
 3TA  C14   C13  C12   121.22  3.000
 3TA  C14   C13  CL1   119.17  3.000
 3TA  C12   C13  CL1   119.60  3.000
 3TA  H14   C14  C13   120.54  3.000
 3TA  H14   C14  C7    119.63  3.000
 3TA  C13   C14  C7    119.83  3.000
 3TA  H15   C15  C12   119.18  3.000
 3TA  H15   C15  C8    118.77  3.000
 3TA  C12   C15  C8    122.05  3.000
 3TA  HN18  N18  C19   117.40  3.000
 3TA  HN18  N18  C4    113.90  3.000
 3TA  C19   N18  C4    128.53  3.000
 3TA  C24   C19  C20   118.48  3.000
 3TA  C20   C19  N18   123.07  3.000
 3TA  C24   C19  N18   118.41  3.000
 3TA  H20   C20  C21   119.71  3.000
 3TA  H20   C20  C19   120.48  3.000
 3TA  C21   C20  C19   119.81  3.000
 3TA  C25   C21  C22   121.51  3.000
 3TA  C25   C21  C20   121.27  3.000
 3TA  C22   C21  C20   117.16  3.000
 3TA  H22   C22  N23   116.45  3.000
 3TA  H22   C22  C21   120.00  3.000
 3TA  N23   C22  C21   123.55  3.000
 3TA  C24   N23  C22   119.69  3.000
 3TA  C31   C24  N23   117.68  3.000
 3TA  C31   C24  C19   121.03  3.000
 3TA  N23   C24  C19   121.30  3.000
 3TA  H25A  C25  H25   106.66  3.000
 3TA  H25A  C25  C26   109.52  3.000
 3TA  H25   C25  C26   109.49  3.000
 3TA  H25A  C25  C21   109.73  3.000
 3TA  H25   C25  C21   109.57  3.000
 3TA  C26   C25  C21   111.73  3.000
 3TA  H26A  C26  H26   106.77  3.000
 3TA  H26A  C26  C27   111.00  3.000
 3TA  H26   C26  C27   109.03  3.000
 3TA  H26A  C26  C25   108.69  3.000
 3TA  H26   C26  C25   109.67  3.000
 3TA  C27   C26  C25   111.57  3.000
 3TA  H27A  C27  H27   106.19  3.000
 3TA  H27A  C27  N28   107.79  3.000
 3TA  H27   C27  N28   111.53  3.000
 3TA  H27A  C27  C26   108.10  3.000
 3TA  H27   C27  C26   109.35  3.000
 3TA  N28   C27  C26   113.55  3.000
 3TA  C30   N28  C29   110.52  3.000
 3TA  C30   N28  C27   111.00  3.000
 3TA  C29   N28  C27   112.50  3.000
 3TA  H29B  C29  H29A  107.33  3.000
 3TA  H29B  C29  H29   107.68  3.000
 3TA  H29A  C29  H29   107.70  3.000
 3TA  H29B  C29  N28   111.15  3.000
 3TA  H29A  C29  N28   109.78  3.000
 3TA  H29   C29  N28   112.99  3.000
 3TA  H30B  C30  H30A  107.46  3.000
 3TA  H30B  C30  H30   107.74  3.000
 3TA  H30A  C30  H30   107.77  3.000
 3TA  H30B  C30  N28   113.42  3.000
 3TA  H30A  C30  N28   109.97  3.000
 3TA  H30   C30  N28   110.28  3.000
 3TA  H31B  C31  H31A  108.38  3.000
 3TA  H31B  C31  H31   107.53  3.000
 3TA  H31A  C31  H31   107.07  3.000
 3TA  H31B  C31  C24   109.94  3.000
 3TA  H31A  C31  C24   111.70  3.000
 3TA  H31   C31  C24   112.04  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
 3TA  CONST_01  C4   N3   C2   C1      0.00   0.0  0
 3TA  CONST_02  C4   N5   C6   C1      0.00   0.0  0
 3TA  CONST_05  N5   C6   C1   C2      0.00   0.0  0
 3TA  CONST_06  C8   C6   C1   C2    180.00   0.0  0
 3TA  CONST_07  N5   C4   N3   C2      0.00   0.0  0
 3TA  CONST_08  C6   C1   C2   N3      0.00   0.0  0
 3TA  CONST_09  C6   N5   C4   N3      0.00   0.0  0
 3TA  CONST_10  C8   C6   N5   C4    180.00   0.0  0
 3TA  CONST_13  C14  C7   C8   C6    180.00   0.0  0
 3TA  CONST_14  C12  C15  C8   C6    180.00   0.0  0
 3TA  CONST_15  C12  C15  C8   C7      0.00   0.0  0
 3TA  CONST_16  C12  C13  C14  C7      0.00   0.0  0
 3TA  CONST_17  C13  C14  C7   C8      0.00   0.0  0
 3TA  CONST_18  C13  C12  C15  C8      0.00   0.0  0
 3TA  CONST_19  C15  C8   C7   C14     0.00   0.0  0
 3TA  CONST_20  C15  C12  C13  C14     0.00   0.0  0
 3TA  CONST_21  C22  N23  C24  C19     0.00   0.0  0
 3TA  CONST_22  C22  C21  C20  C19     0.00   0.0  0
 3TA  CONST_23  N23  C24  C19  C20     0.00   0.0  0
 3TA  CONST_24  N23  C22  C21  C20     0.00   0.0  0
 3TA  CONST_25  C24  C19  C20  C21     0.00   0.0  0
 3TA  CONST_26  C24  N23  C22  C21     0.00   0.0  0
 3TA  CONST_27  C15  C12  C13  CL1   180.00   0.0  0
 3TA  CONST_28  C7   C14  C13  CL1   180.00   0.0  0
 3TA  CONST_29  N18  C4   N3   C2    180.00   0.0  0
 3TA  CONST_30  N18  C4   N5   C6    180.00   0.0  0
 3TA  CONST_31  N23  C24  C19  N18   180.00   0.0  0
 3TA  CONST_32  C21  C20  C19  N18   180.00   0.0  0
 3TA  CONST_33  C25  C21  C20  C19   180.00   0.0  0
 3TA  CONST_34  C31  C24  C19  C20   180.00   0.0  0
 3TA  CONST_35  C31  C24  N23  C22   180.00   0.0  0
 3TA  CONST_36  C25  C21  C22  N23   180.00   0.0  0
 3TA  CONST_37  H2   C2   N3   C4    180.00   0.0  0
 3TA  CONST_38  H15  C15  C8   C6      0.00   0.0  0
 3TA  CONST_39  H14  C14  C7   C8    180.00   0.0  0
 3TA  CONST_40  H12  C12  C15  C8    180.00   0.0  0
 3TA  CONST_41  H22  C22  C21  C20   180.00   0.0  0
 3TA  CONST_42  H20  C20  C21  C22   180.00   0.0  0
 3TA  Var_01    N9   C10  C11  C1    -66.92  30.0  1
 3TA  Var_02    C10  C11  C1   C2   -111.17  30.0  1
 3TA  Var_03    C11  C10  N9   C7     -2.56  30.0  1
 3TA  Var_04    C10  N9   C7   C8     44.43  30.0  1
 3TA  Var_05    C19  N18  C4   N3      1.80  30.0  2
 3TA  Var_06    C24  C19  N18  C4   -145.12  30.0  2
 3TA  Var_07    C26  C25  C21  C20    82.93  30.0  2
 3TA  Var_08    H31  C31  C24  C19   -65.77  30.0  2
 3TA  Var_09    C27  C26  C25  C21  -178.42  30.0  3
 3TA  Var_10    N28  C27  C26  C25   175.19  30.0  3
 3TA  Var_11    C29  N28  C27  C26    68.35  30.0  2
 3TA  Var_12    H29  C29  N28  C27    60.71  30.0  3
 3TA  Var_13    H30  C30  N28  C27    59.18  30.0  3

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
 3TA  plan-1  N18  0.020
 3TA  plan-1  C19  0.020
 3TA  plan-1  C20  0.020
 3TA  plan-1  C21  0.020
 3TA  plan-1  C22  0.020
 3TA  plan-1  N23  0.020
 3TA  plan-1  C24  0.020
 3TA  plan-1  C25  0.020
 3TA  plan-1  C31  0.020
 3TA  plan-1  H20  0.020
 3TA  plan-1  H22  0.020
 3TA  plan-2  C1   0.020
 3TA  plan-2  C2   0.020
 3TA  plan-2  N3   0.020
 3TA  plan-2  C4   0.020
 3TA  plan-2  N5   0.020
 3TA  plan-2  C6   0.020
 3TA  plan-2  C8   0.020
 3TA  plan-2  C11  0.020
 3TA  plan-2  N18  0.020
 3TA  plan-2  H2   0.020
 3TA  plan-3  CL1  0.020
 3TA  plan-3  C6   0.020
 3TA  plan-3  C7   0.020
 3TA  plan-3  C8   0.020
 3TA  plan-3  N9   0.020
 3TA  plan-3  C12  0.020
 3TA  plan-3  C13  0.020
 3TA  plan-3  C14  0.020
 3TA  plan-3  C15  0.020
 3TA  plan-3  H12  0.020
 3TA  plan-3  H14  0.020
 3TA  plan-3  H15  0.020
 3TA  plan-4  C7   0.020
 3TA  plan-4  N9   0.020
 3TA  plan-4  C10  0.020
 3TA  plan-4  HN9  0.020

