# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 16:40:02 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 6-ethyl-4-methoxy-2-(pyridin-3-ylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1[nH]c2nc(Sc3cccnc3)nc(OC)c2c1C=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
 19Y  19Y  6-ethyl-4-methoxy-2-(pyridin-3-ylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbaldehyde  ligand  36  22  .  2021-08-03  2022-07-21
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_19Y
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
 19Y  O20  O  O     0  -0.402  -3.1574  -3.0330  -0.0933
 19Y  C19  C  C1    0   0.035  -3.7140  -1.9569  -0.1706
 19Y  C5   C  CR5   0  -0.202  -3.0724  -0.6657  -0.1671
 19Y  C1   C  CR5   0   0.411  -3.7783   0.5258  -0.2230
 19Y  C21  C  CH2   0  -0.536  -5.2456   0.7823  -0.2371
 19Y  C22  C  CH3   0  -0.655  -5.8330   0.8419   1.1742
 19Y  C4   C  CR56  0  -0.043  -1.6791  -0.3105  -0.1033
 19Y  C6   C  CR6   0   0.490  -0.4204  -0.9259  -0.0338
 19Y  O17  O  O2    0  -0.435  -0.3241  -2.2370  -0.0019
 19Y  C18  C  CH3   0  -0.417   0.9787  -2.8131   0.0826
 19Y  N7   N  N     0  -0.444   0.6794  -0.1965   0.0025
 19Y  C8   C  CR6   0   0.215   0.5748   1.1224  -0.0266
 19Y  N9   N  N     0  -0.449  -0.5270   1.8384  -0.0894
 19Y  C3   C  CR56  0   0.482  -1.6220   1.0868  -0.1249
 19Y  N2   N  NR15  0  -0.705  -2.8966   1.5571  -0.1940
 19Y  S10  S  S2    0   0.082   2.0528   2.0928   0.0342
 19Y  C11  C  CR6   0  -0.210   3.2972   0.8406   0.0529
 19Y  C16  C  CR16  0  -0.119   3.9644   0.4810  -1.1078
 19Y  C15  C  CR16  0  -0.324   4.9455  -0.4953  -1.0275
 19Y  C14  C  CR16  0  -0.054   5.2078  -1.0694   0.2067
 19Y  N13  N  N     0  -0.403   4.5744  -0.7247   1.3237
 19Y  C12  C  CR16  0  -0.017   3.6441   0.2138   1.2450
 19Y  H1   H  H     0   0.176  -4.8144  -1.9078  -0.2524
 19Y  H2   H  HCH2  0   0.274  -5.4365   1.7249  -0.7534
 19Y  H3   H  HCH2  0   0.270  -5.7504   0.0089  -0.8152
 19Y  H4   H  HCH3  0   0.234  -5.7053  -0.1068   1.6946
 19Y  H5   H  HCH3  0   0.236  -5.3575   1.6209   1.7700
 19Y  H6   H  HCH3  0   0.246  -6.8991   1.0604   1.1257
 19Y  H7   H  HCH3  0   0.251   0.8211  -3.8876   0.1071
 19Y  H8   H  HCH3  0   0.237   1.5898  -2.5509  -0.7808
 19Y  H9   H  HCH3  0   0.238   1.4974  -2.4971   0.9875
 19Y  H10  H  HNR5  0   0.426  -3.1437   2.5354  -0.2307
 19Y  H11  H  HCR6  0   0.288   3.7217   0.9500  -2.0524
 19Y  H12  H  HCR6  0   0.279   5.4953  -0.8083  -1.9042
 19Y  H13  H  HCR6  0   0.272   5.9661  -1.8385   0.2982
 19Y  H14  H  HCR6  0   0.273   3.1416   0.4874   2.1664

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
 19Y  C22  C21  single    1.530  0.020  1.530
 19Y  O20  C19  double    1.214  0.020  1.214
 19Y  C21  C1   single    1.490  0.020  1.490
 19Y  C19  C5   single    1.442  0.020  1.442
 19Y  C1   C5   aromatic  1.386  0.020  1.386
 19Y  C1   N2   aromatic  1.357  0.020  1.357
 19Y  C5   C4   aromatic  1.439  0.020  1.439
 19Y  N2   C3   aromatic  1.360  0.020  1.360
 19Y  C4   C3   aromatic  1.399  0.020  1.399
 19Y  C4   C6   aromatic  1.403  0.020  1.403
 19Y  O17  C6   single    1.315  0.020  1.315
 19Y  O17  C18  single    1.427  0.020  1.427
 19Y  C3   N9   aromatic  1.329  0.020  1.329
 19Y  C6   N7   aromatic  1.320  0.020  1.320
 19Y  N9   C8   aromatic  1.316  0.020  1.316
 19Y  N7   C8   aromatic  1.323  0.020  1.323
 19Y  C8   S10  single    1.769  0.020  1.769
 19Y  C12  N13  aromatic  1.324  0.020  1.324
 19Y  C12  C11  aromatic  1.391  0.020  1.391
 19Y  S10  C11  single    1.766  0.020  1.766
 19Y  N13  C14  aromatic  1.330  0.020  1.330
 19Y  C11  C16  aromatic  1.386  0.020  1.386
 19Y  C14  C15  aromatic  1.386  0.020  1.386
 19Y  C16  C15  aromatic  1.386  0.020  1.386
 19Y  C19  H1   single    0.930  0.020  1.080
 19Y  C21  H2   single    0.970  0.020  1.090
 19Y  C21  H3   single    0.970  0.020  1.090
 19Y  C22  H4   single    0.970  0.020  1.090
 19Y  C22  H5   single    0.970  0.020  1.090
 19Y  C22  H6   single    0.970  0.020  1.090
 19Y  C18  H7   single    0.970  0.020  1.090
 19Y  C18  H8   single    0.970  0.020  1.090
 19Y  C18  H9   single    0.970  0.020  1.090
 19Y  N2   H10  single    0.860  0.020  1.020
 19Y  C16  H11  single    0.930  0.020  1.080
 19Y  C15  H12  single    0.930  0.020  1.080
 19Y  C14  H13  single    0.930  0.020  1.080
 19Y  C12  H14  single    0.930  0.020  1.080

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
 19Y  H1   C19  C5   113.81  3.000
 19Y  H1   C19  O20  120.05  3.000
 19Y  C5   C19  O20  126.13  3.000
 19Y  C4   C5   C1   106.42  3.000
 19Y  C4   C5   C19  130.68  3.000
 19Y  C1   C5   C19  122.89  3.000
 19Y  N2   C1   C21  120.62  3.000
 19Y  N2   C1   C5   108.75  3.000
 19Y  C21  C1   C5   130.55  3.000
 19Y  H3   C21  H2   106.32  3.000
 19Y  H3   C21  C22  109.83  3.000
 19Y  H2   C21  C22  109.61  3.000
 19Y  H3   C21  C1   109.82  3.000
 19Y  H2   C21  C1   109.00  3.000
 19Y  C22  C21  C1   112.09  3.000
 19Y  H6   C22  H5   107.93  3.000
 19Y  H6   C22  H4   108.09  3.000
 19Y  H5   C22  H4   108.07  3.000
 19Y  H6   C22  C21  110.03  3.000
 19Y  H5   C22  C21  111.39  3.000
 19Y  H4   C22  C21  111.21  3.000
 19Y  C3   C4   C6   113.72  3.000
 19Y  C6   C4   C5   139.69  3.000
 19Y  C3   C4   C5   106.58  3.000
 19Y  N7   C6   O17  119.29  3.000
 19Y  N7   C6   C4   120.43  3.000
 19Y  O17  C6   C4   120.28  3.000
 19Y  C18  O17  C6   118.08  3.000
 19Y  H9   C18  H8   108.74  3.000
 19Y  H9   C18  H7   109.70  3.000
 19Y  H8   C18  H7   109.71  3.000
 19Y  H9   C18  O17  111.51  3.000
 19Y  H8   C18  O17  111.59  3.000
 19Y  H7   C18  O17  105.55  3.000
 19Y  C8   N7   C6   118.96  3.000
 19Y  S10  C8   N9   113.75  3.000
 19Y  S10  C8   N7   118.68  3.000
 19Y  N9   C8   N7   127.57  3.000
 19Y  C3   N9   C8   112.56  3.000
 19Y  N2   C3   N9   125.31  3.000
 19Y  N9   C3   C4   126.76  3.000
 19Y  N2   C3   C4   107.93  3.000
 19Y  H10  N2   C3   124.48  3.000
 19Y  H10  N2   C1   125.20  3.000
 19Y  C3   N2   C1   110.31  3.000
 19Y  C11  S10  C8   101.55  3.000
 19Y  C12  C11  C16  118.74  3.000
 19Y  C16  C11  S10  120.95  3.000
 19Y  C12  C11  S10  120.30  3.000
 19Y  H11  C16  C15  120.96  3.000
 19Y  H11  C16  C11  120.70  3.000
 19Y  C15  C16  C11  118.34  3.000
 19Y  H12  C15  C14  120.39  3.000
 19Y  H12  C15  C16  121.11  3.000
 19Y  C14  C15  C16  118.50  3.000
 19Y  H13  C14  N13  116.50  3.000
 19Y  H13  C14  C15  120.09  3.000
 19Y  N13  C14  C15  123.41  3.000
 19Y  C12  N13  C14  117.94  3.000
 19Y  H14  C12  N13  116.99  3.000
 19Y  H14  C12  C11  119.93  3.000
 19Y  N13  C12  C11  123.08  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
 19Y  CONST_01  C3   N2   C1   C5      0.00   0.0  0
 19Y  CONST_02  N2   C3   C4   C5      0.00   0.0  0
 19Y  CONST_03  N9   C3   C4   C5    180.00   0.0  0
 19Y  CONST_04  N7   C6   C4   C5    180.00   0.0  0
 19Y  CONST_05  C3   C4   C5   C1      0.00   0.0  0
 19Y  CONST_06  C6   C4   C5   C1    180.00   0.0  0
 19Y  CONST_07  C4   C3   N2   C1      0.00   0.0  0
 19Y  CONST_08  N9   C3   N2   C1    180.00   0.0  0
 19Y  CONST_09  N2   C1   C5   C4      0.00   0.0  0
 19Y  CONST_10  C8   N9   C3   C4      0.00   0.0  0
 19Y  CONST_11  C8   N7   C6   C4      0.00   0.0  0
 19Y  CONST_12  N2   C3   C4   C6    180.00   0.0  0
 19Y  CONST_13  N9   C3   C4   C6      0.00   0.0  0
 19Y  CONST_14  N9   C8   N7   C6      0.00   0.0  0
 19Y  CONST_15  C3   C4   C6   N7      0.00   0.0  0
 19Y  CONST_16  C3   N9   C8   N7      0.00   0.0  0
 19Y  CONST_17  N2   C3   N9   C8    180.00   0.0  0
 19Y  CONST_18  C14  N13  C12  C11     0.00   0.0  0
 19Y  CONST_19  C14  C15  C16  C11     0.00   0.0  0
 19Y  CONST_20  N13  C12  C11  C16     0.00   0.0  0
 19Y  CONST_21  N13  C14  C15  C16     0.00   0.0  0
 19Y  CONST_22  C12  N13  C14  C15     0.00   0.0  0
 19Y  CONST_23  C12  C11  C16  C15     0.00   0.0  0
 19Y  CONST_24  N2   C1   C5   C19   180.00   0.0  0
 19Y  CONST_25  C3   C4   C5   C19   180.00   0.0  0
 19Y  CONST_26  C6   C4   C5   C19     0.00   0.0  0
 19Y  CONST_27  O17  C6   C4   C5      0.00   0.0  0
 19Y  CONST_28  C4   C5   C1   C21   180.00   0.0  0
 19Y  CONST_29  C3   N2   C1   C21   180.00   0.0  0
 19Y  CONST_30  S10  C8   N7   C6    180.00   0.0  0
 19Y  CONST_31  C3   C4   C6   O17   180.00   0.0  0
 19Y  CONST_32  C8   N7   C6   O17   180.00   0.0  0
 19Y  CONST_33  S10  C8   N9   C3    180.00   0.0  0
 19Y  CONST_34  N13  C12  C11  S10   180.00   0.0  0
 19Y  CONST_35  C15  C16  C11  S10   180.00   0.0  0
 19Y  CONST_36  H10  N2   C1   C5    180.00   0.0  0
 19Y  CONST_37  H12  C15  C16  C11   180.00   0.0  0
 19Y  CONST_38  H14  C12  C11  C16   180.00   0.0  0
 19Y  CONST_39  H13  C14  C15  C16   180.00   0.0  0
 19Y  CONST_40  H11  C16  C15  C14   180.00   0.0  0
 19Y  Var_01    C12  C11  S10  C8    -82.50  30.0  2
 19Y  Var_02    C1   C5   C19  O20  -178.22  30.0  2
 19Y  Var_03    C22  C21  C1   C5     85.71  30.0  3
 19Y  Var_04    N7   C6   O17  C18     0.52  30.0  2
 19Y  Var_05    H4   C22  C21  C1    -61.97  30.0  3
 19Y  Var_06    H7   C18  O17  C6    179.36  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
 19Y  plan-1  S10  0.020
 19Y  plan-1  C11  0.020
 19Y  plan-1  C16  0.020
 19Y  plan-1  C15  0.020
 19Y  plan-1  C14  0.020
 19Y  plan-1  N13  0.020
 19Y  plan-1  C12  0.020
 19Y  plan-1  H11  0.020
 19Y  plan-1  H12  0.020
 19Y  plan-1  H13  0.020
 19Y  plan-1  H14  0.020
 19Y  plan-2  C19  0.020
 19Y  plan-2  C5   0.020
 19Y  plan-2  C1   0.020
 19Y  plan-2  C21  0.020
 19Y  plan-2  C4   0.020
 19Y  plan-2  C6   0.020
 19Y  plan-2  O17  0.020
 19Y  plan-2  N7   0.020
 19Y  plan-2  C8   0.020
 19Y  plan-2  N9   0.020
 19Y  plan-2  C3   0.020
 19Y  plan-2  N2   0.020
 19Y  plan-2  S10  0.020
 19Y  plan-2  H10  0.020
 19Y  plan-3  O20  0.020
 19Y  plan-3  C19  0.020
 19Y  plan-3  C5   0.020
 19Y  plan-3  H1   0.020

