# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 02:21:01 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-{[4-(2-chloro-4,5-dimethoxyphenyl)-5-cyano-7H-pyrrolo[2,3-d]pyrimidin-2-yl]sulfanyl}-N,N-dimethylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cl)c(cc1OC)c2nc(SCC(=O)N(C)C)nc3[nH]cc(C#N)c23
#
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
 0TM  0TM  2-{[4-(2-chloro-4,5-dimethoxyphenyl)-5-cyano-7H-pyrrolo[2,3-d]pyrimidin-2-yl]sulfanyl}-N,N-dimethylacetamide  ligand  47  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0TM
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
 0TM  C14  C   CH3   0  -0.445  -4.7851  -1.4533  -2.5551
 0TM  O1   O   O2    0  -0.460  -5.0616  -0.2734  -1.8251
 0TM  C5   C   CR6   0   0.342  -4.1030   0.2126  -1.0228
 0TM  C4   C   CR16  0  -0.437  -2.8308  -0.3082  -0.8991
 0TM  C6   C   CR6   0   0.318  -4.4581   1.3482  -0.2631
 0TM  O2   O   O2    0  -0.455  -5.7072   1.7950  -0.4338
 0TM  C17  C   CH3   0  -0.444  -6.1239   2.9298   0.3037
 0TM  C1   C   CR16  0  -0.332  -3.5294   1.9137   0.5941
 0TM  C2   C   CR6   0  -0.123  -2.2529   1.3704   0.6998
 0TM  CL   CL  CL    0  -0.125  -1.1646   2.0906   1.8382
 0TM  C3   C   CR6   0   0.101  -1.8849   0.2595  -0.0372
 0TM  C7   C   CR6   0   0.212  -0.5478  -0.3548   0.0511
 0TM  N1   N   N     0  -0.427   0.5073   0.4003  -0.2045
 0TM  C9   C   CR56  0   0.068  -0.3709  -1.6985   0.3857
 0TM  C12  C   CR5   0  -0.182  -1.1719  -2.8306   0.7558
 0TM  C13  C   CSP   0  -0.046  -2.5707  -2.9180   0.9098
 0TM  N4   N   NS    0  -0.252  -3.7139  -3.0058   1.0384
 0TM  C11  C   CR15  0   0.064  -0.3019  -3.8715   0.9716
 0TM  N3   N   NR15  0  -0.660   0.9681  -3.4511   0.7639
 0TM  C10  C   CR56  0   0.545   0.9627  -2.1391   0.4139
 0TM  N2   N   N     0  -0.424   2.0238  -1.3922   0.1608
 0TM  C8   C   CR6   0   0.223   1.7262  -0.1415  -0.1348
 0TM  S    S   S2    0   0.084   2.9905   1.0153  -0.4998
 0TM  C15  C   CH2   0  -0.721   4.4655   0.0009  -0.2450
 0TM  C16  C   C     0   0.587   5.6613   0.8959  -0.5138
 0TM  O3   O   O     0  -0.496   5.4831   2.0579  -0.8576
 0TM  N5   N   NT    0  -0.448   6.8783   0.3472  -0.3671
 0TM  C18  C   CH3   0  -0.523   8.0658   1.1596  -0.5407
 0TM  C19  C   CH3   0  -0.526   7.1155  -0.9789   0.1642
 0TM  H1   H   HCH3  0   0.265  -5.6900  -1.6925  -3.1074
 0TM  H2   H   HCH3  0   0.232  -3.9662  -1.3109  -3.2650
 0TM  H3   H   HCH3  0   0.231  -4.5407  -2.2890  -1.8938
 0TM  H4   H   HCR6  0   0.296  -2.5356  -1.1700  -1.4830
 0TM  H5   H   HCH3  0   0.235  -6.0755   2.7534   1.3811
 0TM  H6   H   HCH3  0   0.235  -5.5261   3.8116   0.0603
 0TM  H7   H   HCH3  0   0.266  -7.1571   3.1150   0.0231
 0TM  H8   H   HCR6  0   0.306  -3.7827   2.7773   1.1928
 0TM  H9   H   HCR5  0   0.330  -0.5159  -4.8863   1.2636
 0TM  H10  H   HNR5  0   0.436   1.7919  -4.0243   0.8692
 0TM  H11  H   HCH2  0   0.316   4.4758  -0.3836   0.7756
 0TM  H12  H   HCH2  0   0.317   4.4514  -0.8576  -0.9183
 0TM  H13  H   HCH3  0   0.243   8.4756   1.4675   0.4241
 0TM  H14  H   HCH3  0   0.245   8.8255   0.5806  -1.0648
 0TM  H15  H   HCH3  0   0.260   7.8416   2.0469  -1.1232
 0TM  H16  H   HCH3  0   0.268   6.2452  -1.6199   0.0678
 0TM  H17  H   HCH3  0   0.254   7.9292  -1.4466  -0.3890
 0TM  H18  H   HCH3  0   0.247   7.3987  -0.9377   1.2183

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
 0TM  N4   C13  triple    1.154  0.020  1.154
 0TM  C13  C12  single    1.410  0.020  1.410
 0TM  C11  C12  aromatic  1.374  0.020  1.374
 0TM  C11  N3   aromatic  1.354  0.020  1.354
 0TM  C12  C9   aromatic  1.435  0.020  1.435
 0TM  O2   C17  single    1.416  0.020  1.416
 0TM  O2   C6   single    1.338  0.020  1.338
 0TM  C14  O1   single    1.415  0.020  1.415
 0TM  O1   C5   single    1.341  0.020  1.341
 0TM  C6   C5   aromatic  1.412  0.020  1.412
 0TM  C6   C1   aromatic  1.385  0.020  1.385
 0TM  C5   C4   aromatic  1.380  0.020  1.380
 0TM  C1   C2   aromatic  1.391  0.020  1.391
 0TM  N3   C10  aromatic  1.358  0.020  1.358
 0TM  C4   C3   aromatic  1.400  0.020  1.400
 0TM  C9   C10  aromatic  1.405  0.020  1.405
 0TM  C9   C7   aromatic  1.396  0.020  1.396
 0TM  C2   C3   aromatic  1.383  0.020  1.383
 0TM  C2   CL   single    1.732  0.020  1.732
 0TM  C3   C7   single    1.474  0.020  1.474
 0TM  C10  N2   aromatic  1.322  0.020  1.322
 0TM  C7   N1   aromatic  1.322  0.020  1.322
 0TM  N2   C8   aromatic  1.319  0.020  1.319
 0TM  N1   C8   aromatic  1.336  0.020  1.336
 0TM  C8   S    single    1.752  0.020  1.752
 0TM  O3   C16  double    1.225  0.020  1.225
 0TM  C19  N5   single    1.448  0.020  1.448
 0TM  C16  N5   single    1.343  0.020  1.343
 0TM  C16  C15  single    1.518  0.020  1.518
 0TM  N5   C18  single    1.449  0.020  1.449
 0TM  S    C15  single    1.808  0.020  1.808
 0TM  C14  H1   single    0.970  0.020  1.090
 0TM  C14  H2   single    0.970  0.020  1.090
 0TM  C14  H3   single    0.970  0.020  1.090
 0TM  C4   H4   single    0.930  0.020  1.080
 0TM  C17  H5   single    0.970  0.020  1.090
 0TM  C17  H6   single    0.970  0.020  1.090
 0TM  C17  H7   single    0.970  0.020  1.090
 0TM  C1   H8   single    0.930  0.020  1.080
 0TM  C11  H9   single    0.930  0.020  1.080
 0TM  N3   H10  single    0.860  0.020  1.020
 0TM  C15  H11  single    0.970  0.020  1.090
 0TM  C15  H12  single    0.970  0.020  1.090
 0TM  C18  H13  single    0.970  0.020  1.090
 0TM  C18  H14  single    0.970  0.020  1.090
 0TM  C18  H15  single    0.970  0.020  1.090
 0TM  C19  H16  single    0.970  0.020  1.090
 0TM  C19  H17  single    0.970  0.020  1.090
 0TM  C19  H18  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
 0TM  H3   C14  H2   108.96  3.000
 0TM  H3   C14  H1   108.98  3.000
 0TM  H2   C14  H1   108.81  3.000
 0TM  H3   C14  O1   111.66  3.000
 0TM  H2   C14  O1   111.90  3.000
 0TM  H1   C14  O1   106.44  3.000
 0TM  C5   O1   C14  118.11  3.000
 0TM  C6   C5   C4   119.15  3.000
 0TM  C4   C5   O1   125.15  3.000
 0TM  C6   C5   O1   115.70  3.000
 0TM  H4   C4   C3   118.09  3.000
 0TM  H4   C4   C5   120.24  3.000
 0TM  C3   C4   C5   121.67  3.000
 0TM  C1   C6   O2   124.68  3.000
 0TM  C1   C6   C5   119.54  3.000
 0TM  O2   C6   C5   115.78  3.000
 0TM  C17  O2   C6   118.43  3.000
 0TM  H7   C17  H6   108.98  3.000
 0TM  H7   C17  H5   108.92  3.000
 0TM  H6   C17  H5   109.00  3.000
 0TM  H7   C17  O2   106.38  3.000
 0TM  H6   C17  O2   111.69  3.000
 0TM  H5   C17  O2   111.78  3.000
 0TM  H8   C1   C2   119.00  3.000
 0TM  H8   C1   C6   120.80  3.000
 0TM  C2   C1   C6   120.20  3.000
 0TM  C3   C2   CL   121.14  3.000
 0TM  CL   C2   C1   117.65  3.000
 0TM  C3   C2   C1   121.15  3.000
 0TM  C7   C3   C2   122.96  3.000
 0TM  C7   C3   C4   118.74  3.000
 0TM  C2   C3   C4   118.30  3.000
 0TM  C9   C7   N1   119.66  3.000
 0TM  N1   C7   C3   118.31  3.000
 0TM  C9   C7   C3   122.03  3.000
 0TM  C8   N1   C7   119.11  3.000
 0TM  C10  C9   C12  106.10  3.000
 0TM  C10  C9   C7   115.28  3.000
 0TM  C12  C9   C7   138.61  3.000
 0TM  C11  C12  C13  124.35  3.000
 0TM  C11  C12  C9   106.54  3.000
 0TM  C13  C12  C9   129.10  3.000
 0TM  N4   C13  C12  180.00  3.000
 0TM  H9   C11  N3   121.36  3.000
 0TM  H9   C11  C12  129.09  3.000
 0TM  N3   C11  C12  109.55  3.000
 0TM  H10  N3   C10  125.37  3.000
 0TM  H10  N3   C11  124.99  3.000
 0TM  C10  N3   C11  109.63  3.000
 0TM  N2   C10  N3   126.30  3.000
 0TM  N2   C10  C9   125.52  3.000
 0TM  N3   C10  C9   108.18  3.000
 0TM  C8   N2   C10  113.42  3.000
 0TM  S    C8   N2   120.65  3.000
 0TM  S    C8   N1   112.32  3.000
 0TM  N2   C8   N1   127.02  3.000
 0TM  C15  S    C8   100.89  3.000
 0TM  H12  C15  H11  107.47  3.000
 0TM  H12  C15  C16  111.40  3.000
 0TM  H11  C15  C16  111.48  3.000
 0TM  H12  C15  S    110.12  3.000
 0TM  H11  C15  S    109.72  3.000
 0TM  C16  C15  S    106.67  3.000
 0TM  N5   C16  O3   123.37  3.000
 0TM  N5   C16  C15  116.98  3.000
 0TM  O3   C16  C15  119.64  3.000
 0TM  C19  N5   C18  115.03  3.000
 0TM  C18  N5   C16  120.03  3.000
 0TM  C19  N5   C16  124.24  3.000
 0TM  H15  C18  H14  108.69  3.000
 0TM  H15  C18  H13  108.73  3.000
 0TM  H14  C18  H13  108.24  3.000
 0TM  H15  C18  N5   110.70  3.000
 0TM  H14  C18  N5   109.33  3.000
 0TM  H13  C18  N5   111.08  3.000
 0TM  H18  C19  H17  108.22  3.000
 0TM  H18  C19  H16  108.42  3.000
 0TM  H17  C19  H16  107.47  3.000
 0TM  H18  C19  N5   111.22  3.000
 0TM  H17  C19  N5   109.22  3.000
 0TM  H16  C19  N5   112.14  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
 0TM  CONST_01  C2   C1   C6   C5      0.00   0.0  0
 0TM  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 0TM  CONST_03  C7   C3   C4   C5    180.00   0.0  0
 0TM  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 0TM  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 0TM  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 0TM  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 0TM  CONST_10  C7   C3   C2   C1    180.00   0.0  0
 0TM  CONST_13  C12  C9   C7   C3      0.00   0.0  0
 0TM  CONST_14  C10  C9   C7   C3    180.00   0.0  0
 0TM  CONST_15  C8   N1   C7   C3    180.00   0.0  0
 0TM  CONST_16  C11  C12  C9   C7    180.00   0.0  0
 0TM  CONST_17  N3   C10  C9   C7    180.00   0.0  0
 0TM  CONST_18  N2   C10  C9   C7      0.00   0.0  0
 0TM  CONST_19  N2   C8   N1   C7      0.00   0.0  0
 0TM  CONST_20  C12  C9   C7   N1    180.00   0.0  0
 0TM  CONST_21  C10  C9   C7   N1      0.00   0.0  0
 0TM  CONST_22  C10  N2   C8   N1      0.00   0.0  0
 0TM  CONST_23  N3   C11  C12  C9      0.00   0.0  0
 0TM  CONST_24  C11  N3   C10  C9      0.00   0.0  0
 0TM  CONST_25  C8   N2   C10  C9      0.00   0.0  0
 0TM  CONST_26  C8   N1   C7   C9      0.00   0.0  0
 0TM  CONST_27  C10  N3   C11  C12     0.00   0.0  0
 0TM  CONST_28  N3   C10  C9   C12     0.00   0.0  0
 0TM  CONST_29  N2   C10  C9   C12   180.00   0.0  0
 0TM  CONST_30  C10  C9   C12  C11     0.00   0.0  0
 0TM  CONST_31  N2   C10  N3   C11   180.00   0.0  0
 0TM  CONST_32  C8   N2   C10  N3    180.00   0.0  0
 0TM  CONST_33  C1   C6   C5   O1    180.00   0.0  0
 0TM  CONST_34  C3   C4   C5   O1    180.00   0.0  0
 0TM  CONST_35  O2   C6   C5   C4    180.00   0.0  0
 0TM  CONST_36  CL   C2   C3   C4    180.00   0.0  0
 0TM  CONST_37  CL   C2   C1   C6    180.00   0.0  0
 0TM  CONST_38  C2   C1   C6   O2    180.00   0.0  0
 0TM  CONST_39  C7   C3   C2   CL      0.00   0.0  0
 0TM  CONST_40  C13  C12  C9   C7      0.00   0.0  0
 0TM  CONST_41  S    C8   N1   C7    180.00   0.0  0
 0TM  CONST_42  N3   C11  C12  C13   180.00   0.0  0
 0TM  CONST_43  C10  C9   C12  C13   180.00   0.0  0
 0TM  CONST_44  S    C8   N2   C10   180.00   0.0  0
 0TM  CONST_45  H8   C1   C6   C5    180.00   0.0  0
 0TM  CONST_46  H4   C4   C5   C6    180.00   0.0  0
 0TM  CONST_47  H9   C11  C12  C9    180.00   0.0  0
 0TM  CONST_48  H10  N3   C10  C9    180.00   0.0  0
 0TM  CONST_49  C19  N5   C16  C15     0.00   0.0  0
 0TM  CONST_50  C18  N5   C16  C15   180.00   0.0  0
 0TM  CONST_51  C19  N5   C16  O3    180.00   0.0  0
 0TM  CONST_52  C18  N5   C16  O3      0.00   0.0  0
 0TM  Var_01    C6   C5   O1   C14  -176.64  30.0  2
 0TM  Var_02    C1   C6   O2   C17     0.25  30.0  2
 0TM  Var_03    C16  C15  S    C8   -179.28  30.0  3
 0TM  Var_04    H1   C14  O1   C5    178.13  30.0  3
 0TM  Var_05    H5   C17  O2   C6    -60.85  30.0  3
 0TM  Var_06    O3   C16  C15  S      -1.31  30.0  2
 0TM  Var_07    H16  C19  N5   C16    22.55  30.0  3
 0TM  Var_08    H13  C18  N5   C16   100.07  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
 0TM  plan-1  O1   0.020
 0TM  plan-1  C5   0.020
 0TM  plan-1  C4   0.020
 0TM  plan-1  C6   0.020
 0TM  plan-1  O2   0.020
 0TM  plan-1  C1   0.020
 0TM  plan-1  C2   0.020
 0TM  plan-1  CL   0.020
 0TM  plan-1  C3   0.020
 0TM  plan-1  C7   0.020
 0TM  plan-1  H4   0.020
 0TM  plan-1  H8   0.020
 0TM  plan-2  C3   0.020
 0TM  plan-2  C7   0.020
 0TM  plan-2  N1   0.020
 0TM  plan-2  C9   0.020
 0TM  plan-2  C12  0.020
 0TM  plan-2  C13  0.020
 0TM  plan-2  N4   0.020
 0TM  plan-2  C11  0.020
 0TM  plan-2  N3   0.020
 0TM  plan-2  C10  0.020
 0TM  plan-2  N2   0.020
 0TM  plan-2  C8   0.020
 0TM  plan-2  S    0.020
 0TM  plan-2  H9   0.020
 0TM  plan-2  H10  0.020
 0TM  plan-3  C15  0.020
 0TM  plan-3  C16  0.020
 0TM  plan-3  O3   0.020
 0TM  plan-3  N5   0.020
 0TM  plan-3  C18  0.020
 0TM  plan-3  C19  0.020

