# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 03:08:50 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 7-ethyl-6-[(3-methoxyphenyl)sulfanyl]-5-methyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1c(Sc2cccc(OC)c2)c(C)c3c(N)nc(N)nc13
#
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
 65J  65J  7-ethyl-6-[(3-methoxyphenyl)sulfanyl]-5-methyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine  ligand  42  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_65J
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
 65J  C4   C  CR56  0   0.527   2.3385  -0.3780  -0.0638
 65J  C5   C  CR56  0  -0.117   2.4588   0.9131  -0.5926
 65J  C6   C  CR6   0   0.425   3.6923   1.5491  -0.3307
 65J  N1   N  N     0  -0.524   4.6227   0.9215   0.3799
 65J  N3   N  N     0  -0.524   3.2587  -1.0251   0.6513
 65J  CAA  C  CH3   0  -0.664   0.0543  -2.1533   1.4206
 65J  NAW  N  NR5   0  -0.526   1.1290  -0.8708  -0.4017
 65J  C2   C  CR6   0   0.518   4.3656  -0.3162   0.8347
 65J  NAD  N  NH2   0  -0.825   5.3421  -0.8778   1.5923
 65J  NAE  N  NH2   0  -0.830   3.9673   2.7948  -0.7515
 65J  CAS  C  CR5   0   0.009   1.2432   1.2190  -1.2739
 65J  CAC  C  CH3   0  -0.778   0.8905   2.4799  -1.9829
 65J  CAT  C  CR5   0   0.053   0.4513   0.1088  -1.1312
 65J  SAN  S  S2    0   0.069  -1.1139  -0.1650  -1.8261
 65J  CAQ  C  CR6   0  -0.107  -2.2335   0.1401  -0.4774
 65J  CAI  C  CR16  0  -0.349  -3.4634  -0.4948  -0.5314
 65J  CAH  C  CR16  0  -0.252  -1.9264   1.0084   0.5664
 65J  CAF  C  CR16  0  -0.230  -2.8711   1.2174   1.5557
 65J  CAG  C  CR16  0  -0.390  -4.1151   0.5971   1.5190
 65J  CAO  C  CR6   0   0.394  -4.4145  -0.2622   0.4646
 65J  OAM  O  O2    0  -0.471  -5.5796  -0.9200   0.3270
 65J  CAB  C  CH3   0  -0.438  -6.5707  -0.7568   1.3228
 65J  H1   H  HCH3  0   0.237  -0.7700  -1.4461   1.5076
 65J  H2   H  HCH3  0   0.235  -0.3212  -3.1445   1.6755
 65J  H3   H  HCH3  0   0.233   0.8187  -1.8847   2.1496
 65J  H4   H  HCH2  0   0.256   1.4457  -2.8774  -0.0591
 65J  H5   H  HCH2  0   0.258  -0.1334  -2.4722  -0.7071
 65J  H6   H  HNH2  0   0.386   5.2987  -1.8719   1.7388
 65J  H7   H  HNH2  0   0.386   6.2663  -0.4881   1.5205
 65J  H8   H  HNH2  0   0.410   3.3943   3.2430  -1.4439
 65J  H9   H  HNH2  0   0.396   4.9100   3.1348  -0.6611
 65J  H10  H  HCH3  0   0.246   1.5596   2.6733  -2.8239
 65J  H11  H  HCH3  0   0.258  -0.1233   2.4349  -2.3784
 65J  H12  H  HCH3  0   0.248   0.9459   3.3408  -1.3139
 65J  H13  H  HCR6  0   0.269  -3.6976  -1.1828  -1.3357
 65J  H14  H  HCR6  0   0.263  -0.9655   1.5045   0.6081
 65J  H15  H  HCR6  0   0.263  -2.6436   1.8860   2.3761
 65J  H16  H  HCR6  0   0.280  -4.8255   0.7905   2.3103
 65J  H17  H  HCH3  0   0.261  -7.4075  -1.3865   1.0314
 65J  H18  H  HCH3  0   0.230  -6.2164  -1.0735   2.3070
 65J  H19  H  HCH3  0   0.230  -6.9173   0.2778   1.3889
 65J  CAJ  C  CH2   0  -0.316   0.6249  -2.1641   0.0119

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
 65J  NAD  C2   single    1.358  0.020  1.358
 65J  C2   N3   aromatic  1.327  0.020  1.327
 65J  C2   N1   aromatic  1.343  0.020  1.343
 65J  N3   C4   aromatic  1.333  0.020  1.333
 65J  CAA  CAJ  single    1.520  0.020  1.520
 65J  N1   C6   aromatic  1.328  0.020  1.328
 65J  CAJ  NAW  single    1.448  0.020  1.448
 65J  C4   NAW  aromatic  1.349  0.020  1.349
 65J  C4   C5   aromatic  1.400  0.020  1.400
 65J  NAW  CAT  aromatic  1.397  0.020  1.397
 65J  C6   C5   aromatic  1.412  0.020  1.412
 65J  C6   NAE  single    1.343  0.020  1.343
 65J  C5   CAS  aromatic  1.427  0.020  1.427
 65J  CAT  CAS  aromatic  1.371  0.020  1.371
 65J  CAT  SAN  single    1.734  0.020  1.734
 65J  CAS  CAC  single    1.489  0.020  1.489
 65J  CAB  OAM  single    1.414  0.020  1.414
 65J  OAM  CAO  single    1.345  0.020  1.345
 65J  CAG  CAF  aromatic  1.391  0.020  1.391
 65J  CAG  CAO  aromatic  1.393  0.020  1.393
 65J  CAF  CAH  aromatic  1.384  0.020  1.384
 65J  CAO  CAI  aromatic  1.397  0.020  1.397
 65J  CAH  CAQ  aromatic  1.392  0.020  1.392
 65J  CAI  CAQ  aromatic  1.385  0.020  1.385
 65J  CAQ  SAN  single    1.779  0.020  1.779
 65J  CAA  H1   single    0.970  0.020  1.090
 65J  CAA  H2   single    0.970  0.020  1.090
 65J  CAA  H3   single    0.970  0.020  1.090
 65J  CAJ  H4   single    0.970  0.020  1.090
 65J  CAJ  H5   single    0.970  0.020  1.090
 65J  NAD  H6   single    0.890  0.020  1.040
 65J  NAD  H7   single    0.890  0.020  1.040
 65J  NAE  H8   single    0.890  0.020  1.040
 65J  NAE  H9   single    0.890  0.020  1.040
 65J  CAC  H10  single    0.970  0.020  1.090
 65J  CAC  H11  single    0.970  0.020  1.090
 65J  CAC  H12  single    0.970  0.020  1.090
 65J  CAI  H13  single    0.930  0.020  1.080
 65J  CAH  H14  single    0.930  0.020  1.080
 65J  CAF  H15  single    0.930  0.020  1.080
 65J  CAG  H16  single    0.930  0.020  1.080
 65J  CAB  H17  single    0.970  0.020  1.090
 65J  CAB  H18  single    0.970  0.020  1.090
 65J  CAB  H19  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
 65J  NAW  C4   N3   125.17  3.000
 65J  NAW  C4   C5   108.62  3.000
 65J  N3   C4   C5   126.22  3.000
 65J  CAS  C5   C6   137.41  3.000
 65J  CAS  C5   C4   107.74  3.000
 65J  C6   C5   C4   114.85  3.000
 65J  NAE  C6   N1   117.53  3.000
 65J  NAE  C6   C5   122.57  3.000
 65J  N1   C6   C5   119.88  3.000
 65J  C2   N1   C6   118.84  3.000
 65J  C2   N3   C4   112.99  3.000
 65J  H3   CAA  H2   108.01  3.000
 65J  H3   CAA  H1   108.50  3.000
 65J  H2   CAA  H1   108.12  3.000
 65J  H3   CAA  CAJ  111.00  3.000
 65J  H2   CAA  CAJ  109.85  3.000
 65J  H1   CAA  CAJ  111.26  3.000
 65J  CAT  NAW  CAJ  127.34  3.000
 65J  CAT  NAW  C4   108.04  3.000
 65J  CAJ  NAW  C4   124.52  3.000
 65J  NAD  C2   N3   117.14  3.000
 65J  N3   C2   N1   127.22  3.000
 65J  NAD  C2   N1   115.62  3.000
 65J  H7   NAD  H6   115.66  3.000
 65J  H7   NAD  C2   117.45  3.000
 65J  H6   NAD  C2   117.33  3.000
 65J  H9   NAE  H8   116.47  3.000
 65J  H9   NAE  C6   118.49  3.000
 65J  H8   NAE  C6   120.87  3.000
 65J  CAT  CAS  CAC  126.75  3.000
 65J  CAC  CAS  C5   127.65  3.000
 65J  CAT  CAS  C5   105.60  3.000
 65J  H12  CAC  H11  107.60  3.000
 65J  H12  CAC  H10  107.53  3.000
 65J  H11  CAC  H10  107.34  3.000
 65J  H12  CAC  CAS  111.34  3.000
 65J  H11  CAC  CAS  111.01  3.000
 65J  H10  CAC  CAS  111.81  3.000
 65J  SAN  CAT  CAS  127.40  3.000
 65J  SAN  CAT  NAW  122.44  3.000
 65J  CAS  CAT  NAW  110.00  3.000
 65J  CAQ  SAN  CAT  103.72  3.000
 65J  CAH  CAQ  CAI  120.74  3.000
 65J  CAI  CAQ  SAN  116.78  3.000
 65J  CAH  CAQ  SAN  122.44  3.000
 65J  H13  CAI  CAO  119.19  3.000
 65J  H13  CAI  CAQ  120.78  3.000
 65J  CAO  CAI  CAQ  120.03  3.000
 65J  H14  CAH  CAF  120.62  3.000
 65J  H14  CAH  CAQ  120.72  3.000
 65J  CAF  CAH  CAQ  118.66  3.000
 65J  H15  CAF  CAG  118.92  3.000
 65J  H15  CAF  CAH  119.45  3.000
 65J  CAG  CAF  CAH  121.63  3.000
 65J  H16  CAG  CAO  121.56  3.000
 65J  H16  CAG  CAF  119.26  3.000
 65J  CAO  CAG  CAF  119.18  3.000
 65J  OAM  CAO  CAG  124.43  3.000
 65J  CAG  CAO  CAI  119.75  3.000
 65J  OAM  CAO  CAI  115.81  3.000
 65J  CAB  OAM  CAO  118.59  3.000
 65J  H19  CAB  H18  108.82  3.000
 65J  H19  CAB  H17  108.69  3.000
 65J  H18  CAB  H17  108.84  3.000
 65J  H19  CAB  OAM  111.96  3.000
 65J  H18  CAB  OAM  111.93  3.000
 65J  H17  CAB  OAM  106.49  3.000
 65J  H5   CAJ  H4   107.23  3.000
 65J  H5   CAJ  NAW  107.84  3.000
 65J  H4   CAJ  NAW  107.69  3.000
 65J  H5   CAJ  CAA  110.63  3.000
 65J  H4   CAJ  CAA  110.35  3.000
 65J  NAW  CAJ  CAA  112.89  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
 65J  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 65J  CONST_02  CAS  CAT  NAW  C4      0.00   0.0  0
 65J  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 65J  CONST_04  CAT  CAS  C5   C4      0.00   0.0  0
 65J  CONST_05  C2   N3   C4   C5      0.00   0.0  0
 65J  CONST_06  CAT  NAW  C4   C5      0.00   0.0  0
 65J  CONST_07  C2   N1   C6   C5      0.00   0.0  0
 65J  CONST_08  NAW  CAT  CAS  C5      0.00   0.0  0
 65J  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 65J  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 65J  CONST_11  NAW  C4   C5   C6    180.00   0.0  0
 65J  CONST_12  CAT  CAS  C5   C6    180.00   0.0  0
 65J  CONST_13  CAS  C5   C6   N1    180.00   0.0  0
 65J  CONST_14  CAT  NAW  C4   N3    180.00   0.0  0
 65J  CONST_15  CAS  C5   C4   N3    180.00   0.0  0
 65J  CONST_16  C2   N3   C4   NAW   180.00   0.0  0
 65J  CONST_17  CAS  C5   C4   NAW     0.00   0.0  0
 65J  CONST_18  CAG  CAF  CAH  CAQ     0.00   0.0  0
 65J  CONST_19  CAG  CAO  CAI  CAQ     0.00   0.0  0
 65J  CONST_20  CAF  CAG  CAO  CAI     0.00   0.0  0
 65J  CONST_21  CAF  CAH  CAQ  CAI     0.00   0.0  0
 65J  CONST_22  CAO  CAG  CAF  CAH     0.00   0.0  0
 65J  CONST_23  CAO  CAI  CAQ  CAH     0.00   0.0  0
 65J  CONST_24  NAD  C2   N3   C4    180.00   0.0  0
 65J  CONST_25  SAN  CAT  NAW  C4    180.00   0.0  0
 65J  CONST_26  NAE  C6   C5   C4    180.00   0.0  0
 65J  CONST_27  CAC  CAS  C5   C4    180.00   0.0  0
 65J  CONST_28  CAJ  NAW  C4   C5    180.00   0.0  0
 65J  CONST_29  SAN  CAT  CAS  C5    180.00   0.0  0
 65J  CONST_30  NAD  C2   N1   C6    180.00   0.0  0
 65J  CONST_31  CAC  CAS  C5   C6      0.00   0.0  0
 65J  CONST_32  CAJ  NAW  C4   N3      0.00   0.0  0
 65J  CONST_33  CAS  CAT  NAW  CAJ   180.00   0.0  0
 65J  CONST_34  CAC  CAS  CAT  NAW   180.00   0.0  0
 65J  CONST_35  NAE  C6   N1   C2    180.00   0.0  0
 65J  CONST_36  CAS  C5   C6   NAE     0.00   0.0  0
 65J  CONST_37  CAF  CAH  CAQ  SAN   180.00   0.0  0
 65J  CONST_38  CAO  CAI  CAQ  SAN   180.00   0.0  0
 65J  CONST_39  OAM  CAO  CAI  CAQ   180.00   0.0  0
 65J  CONST_40  OAM  CAO  CAG  CAF   180.00   0.0  0
 65J  CONST_41  H15  CAF  CAH  CAQ   180.00   0.0  0
 65J  CONST_42  H16  CAG  CAO  CAI   180.00   0.0  0
 65J  CONST_43  H14  CAH  CAQ  CAI   180.00   0.0  0
 65J  CONST_44  H13  CAI  CAQ  CAH   180.00   0.0  0
 65J  CONST_45  H8   NAE  C6   C5      0.00   0.0  0
 65J  CONST_46  H9   NAE  C6   C5    180.00   0.0  0
 65J  Var_01    CAH  CAQ  SAN  CAT    27.79  30.0  2
 65J  Var_02    CAA  CAJ  NAW  C4     81.01  30.0  2
 65J  Var_03    H10  CAC  CAS  C5     62.16  30.0  2
 65J  Var_04    H1   CAA  CAJ  NAW    59.59  30.0  3
 65J  Var_05    H17  CAB  OAM  CAO  -178.63  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
 65J  plan-1  SAN  0.020
 65J  plan-1  CAQ  0.020
 65J  plan-1  CAI  0.020
 65J  plan-1  CAH  0.020
 65J  plan-1  CAF  0.020
 65J  plan-1  CAG  0.020
 65J  plan-1  CAO  0.020
 65J  plan-1  OAM  0.020
 65J  plan-1  H13  0.020
 65J  plan-1  H14  0.020
 65J  plan-1  H15  0.020
 65J  plan-1  H16  0.020
 65J  plan-2  C4   0.020
 65J  plan-2  C5   0.020
 65J  plan-2  C6   0.020
 65J  plan-2  N1   0.020
 65J  plan-2  N3   0.020
 65J  plan-2  NAW  0.020
 65J  plan-2  C2   0.020
 65J  plan-2  NAD  0.020
 65J  plan-2  NAE  0.020
 65J  plan-2  CAS  0.020
 65J  plan-2  CAC  0.020
 65J  plan-2  CAT  0.020
 65J  plan-2  SAN  0.020
 65J  plan-2  CAJ  0.020
 65J  plan-3  C2   0.020
 65J  plan-3  NAD  0.020
 65J  plan-3  H6   0.020
 65J  plan-3  H7   0.020
 65J  plan-4  C6   0.020
 65J  plan-4  NAE  0.020
 65J  plan-4  H8   0.020
 65J  plan-4  H9   0.020

