# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 01:18:21 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 6-[(4-methoxyphenyl)sulfanyl]-5,7-dimethyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Sc2n(C)c3nc(N)nc(N)c3c2C)cc1
#
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
 65H  65H  6-[(4-methoxyphenyl)sulfanyl]-5,7-dimethyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine  ligand  39  22  .  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_65H
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
 65H  C4   C  CR56  0   0.519   2.1345  -0.3827   0.7903
 65H  C5   C  CR56  0  -0.130   2.4436   0.4274  -0.3095
 65H  C6   C  CR6   0   0.434   3.6497   0.1025  -0.9686
 65H  N1   N  N     0  -0.525   4.3912  -0.9098  -0.5307
 65H  N3   N  N     0  -0.523   2.8653  -1.4008   1.2452
 65H  CAR  C  CR5   0   0.013   1.4003   1.3901  -0.4524
 65H  NAE  N  NH2   0  -0.834   4.1032   0.7910  -2.0262
 65H  C2   C  CR6   0   0.523   3.9712  -1.6031   0.5400
 65H  NAD  N  NH2   0  -0.825   4.7568  -2.6486   0.9070
 65H  NAV  N  NR5   0  -0.524   0.9691   0.0467   1.3194
 65H  CAC  C  CH3   0  -0.533   0.2977  -0.5253   2.4600
 65H  CAS  C  CR5   0   0.050   0.5171   1.1260   0.5614
 65H  SAM  S  S2    0   0.072  -0.9343   1.9861   0.9653
 65H  CAP  C  CR6   0  -0.154  -2.2148   0.8851   0.4028
 65H  CAH  C  CR16  0  -0.246  -3.4505   0.9380   1.0442
 65H  CAF  C  CR16  0  -0.330  -4.4962   0.1416   0.6170
 65H  CAO  C  CR6   0   0.376  -4.3217  -0.7415  -0.4505
 65H  OAL  O  O2    0  -0.470  -5.3891  -1.4885  -0.7898
 65H  CAA  C  CH3   0  -0.438  -5.2619  -2.3974  -1.8655
 65H  CAG  C  CR16  0  -0.372  -3.0833  -0.8030  -1.0851
 65H  CAI  C  CR16  0  -0.207  -2.0432   0.0159  -0.6627
 65H  H1   H  HCH3  0   0.248   2.1237   3.1498  -1.4443
 65H  H2   H  HCH3  0   0.246   1.2641   2.0272  -2.4943
 65H  H3   H  HCH3  0   0.258   0.3707   3.0303  -1.3610
 65H  H4   H  HNH2  0   0.414   3.5434   1.4883  -2.4822
 65H  H5   H  HNH2  0   0.397   4.9148   0.4577  -2.5178
 65H  H6   H  HNH2  0   0.385   5.7044  -2.6513   0.5709
 65H  H7   H  HNH2  0   0.385   4.6250  -3.0204   1.8323
 65H  H8   H  HCH3  0   0.253   0.1364   0.2257   3.2317
 65H  H9   H  HCH3  0   0.251  -0.6653  -0.9505   2.1777
 65H  H10  H  HCH3  0   0.265   0.9233  -1.3156   2.8644
 65H  H11  H  HCR6  0   0.267  -3.6004   1.6007   1.8878
 65H  H12  H  HCR6  0   0.267  -5.4541   0.1905   1.1196
 65H  H13  H  HCH3  0   0.261  -6.2255  -2.8896  -1.9700
 65H  H14  H  HCH3  0   0.229  -5.0228  -1.8897  -2.8037
 65H  H15  H  HCH3  0   0.229  -4.4991  -3.1560  -1.6712
 65H  H16  H  HCR6  0   0.283  -2.9080  -1.4760  -1.9132
 65H  H17  H  HCR6  0   0.269  -1.0902  -0.0388  -1.1746
 65H  CAB  C  CH3   0  -0.780   1.2849   2.4526  -1.4887

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
 65H  CAI  CAG  aromatic  1.390  0.020  1.390
 65H  CAI  CAP  aromatic  1.386  0.020  1.386
 65H  CAG  CAO  aromatic  1.393  0.020  1.393
 65H  SAM  CAP  single    1.780  0.020  1.780
 65H  SAM  CAS  single    1.735  0.020  1.735
 65H  CAP  CAH  aromatic  1.393  0.020  1.393
 65H  CAB  CAR  single    1.489  0.020  1.489
 65H  CAO  OAL  single    1.346  0.020  1.346
 65H  CAO  CAF  aromatic  1.396  0.020  1.396
 65H  OAL  CAA  single    1.414  0.020  1.414
 65H  CAH  CAF  aromatic  1.382  0.020  1.382
 65H  CAR  CAS  aromatic  1.370  0.020  1.370
 65H  CAR  C5   aromatic  1.427  0.020  1.427
 65H  CAS  NAV  aromatic  1.394  0.020  1.394
 65H  NAE  C6   single    1.341  0.020  1.341
 65H  C5   C6   aromatic  1.412  0.020  1.412
 65H  C5   C4   aromatic  1.400  0.020  1.400
 65H  NAV  CAC  single    1.442  0.020  1.442
 65H  NAV  C4   aromatic  1.350  0.020  1.350
 65H  C6   N1   aromatic  1.329  0.020  1.329
 65H  C4   N3   aromatic  1.333  0.020  1.333
 65H  N1   C2   aromatic  1.343  0.020  1.343
 65H  N3   C2   aromatic  1.327  0.020  1.327
 65H  C2   NAD  single    1.358  0.020  1.358
 65H  CAB  H1   single    0.970  0.020  1.090
 65H  CAB  H2   single    0.970  0.020  1.090
 65H  CAB  H3   single    0.970  0.020  1.090
 65H  NAE  H4   single    0.860  0.020  1.020
 65H  NAE  H5   single    0.860  0.020  1.020
 65H  NAD  H6   single    0.890  0.020  1.040
 65H  NAD  H7   single    0.890  0.020  1.040
 65H  CAC  H8   single    0.970  0.020  1.090
 65H  CAC  H9   single    0.970  0.020  1.090
 65H  CAC  H10  single    0.970  0.020  1.090
 65H  CAH  H11  single    0.930  0.020  1.080
 65H  CAF  H12  single    0.930  0.020  1.080
 65H  CAA  H13  single    0.970  0.020  1.090
 65H  CAA  H14  single    0.970  0.020  1.090
 65H  CAA  H15  single    0.970  0.020  1.090
 65H  CAG  H16  single    0.930  0.020  1.080
 65H  CAI  H17  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
 65H  NAV  C4   N3   125.61  3.000
 65H  N3   C4   C5   126.06  3.000
 65H  NAV  C4   C5   108.32  3.000
 65H  CAR  C5   C6   137.13  3.000
 65H  C6   C5   C4   114.96  3.000
 65H  CAR  C5   C4   107.91  3.000
 65H  NAE  C6   N1   117.53  3.000
 65H  N1   C6   C5   119.86  3.000
 65H  NAE  C6   C5   122.60  3.000
 65H  C2   N1   C6   118.78  3.000
 65H  C2   N3   C4   113.07  3.000
 65H  CAS  CAR  CAB  127.07  3.000
 65H  CAS  CAR  C5   105.49  3.000
 65H  CAB  CAR  C5   127.44  3.000
 65H  H5   NAE  H4   117.28  3.000
 65H  H5   NAE  C6   119.23  3.000
 65H  H4   NAE  C6   121.76  3.000
 65H  NAD  C2   N3   117.11  3.000
 65H  NAD  C2   N1   115.59  3.000
 65H  N3   C2   N1   127.27  3.000
 65H  H7   NAD  H6   115.46  3.000
 65H  H7   NAD  C2   117.22  3.000
 65H  H6   NAD  C2   117.18  3.000
 65H  CAS  NAV  CAC  125.89  3.000
 65H  CAC  NAV  C4   125.86  3.000
 65H  CAS  NAV  C4   108.24  3.000
 65H  H10  CAC  H9   108.75  3.000
 65H  H10  CAC  H8   108.87  3.000
 65H  H9   CAC  H8   108.77  3.000
 65H  H10  CAC  NAV  108.36  3.000
 65H  H9   CAC  NAV  111.18  3.000
 65H  H8   CAC  NAV  110.86  3.000
 65H  SAM  CAS  NAV  121.90  3.000
 65H  NAV  CAS  CAR  110.04  3.000
 65H  SAM  CAS  CAR  128.02  3.000
 65H  CAP  SAM  CAS  102.80  3.000
 65H  CAI  CAP  CAH  119.18  3.000
 65H  CAH  CAP  SAM  117.97  3.000
 65H  CAI  CAP  SAM  122.82  3.000
 65H  H11  CAH  CAF  119.24  3.000
 65H  H11  CAH  CAP  120.30  3.000
 65H  CAF  CAH  CAP  120.46  3.000
 65H  H12  CAF  CAO  119.60  3.000
 65H  H12  CAF  CAH  119.99  3.000
 65H  CAO  CAF  CAH  120.41  3.000
 65H  CAG  CAO  OAL  124.45  3.000
 65H  OAL  CAO  CAF  116.39  3.000
 65H  CAG  CAO  CAF  119.16  3.000
 65H  CAA  OAL  CAO  118.49  3.000
 65H  H15  CAA  H14  108.79  3.000
 65H  H15  CAA  H13  108.75  3.000
 65H  H14  CAA  H13  108.76  3.000
 65H  H15  CAA  OAL  111.94  3.000
 65H  H14  CAA  OAL  111.97  3.000
 65H  H13  CAA  OAL  106.53  3.000
 65H  H16  CAG  CAI  118.57  3.000
 65H  H16  CAG  CAO  121.36  3.000
 65H  CAI  CAG  CAO  120.07  3.000
 65H  H17  CAI  CAG  119.02  3.000
 65H  H17  CAI  CAP  120.26  3.000
 65H  CAG  CAI  CAP  120.71  3.000
 65H  H3   CAB  H2   107.38  3.000
 65H  H3   CAB  H1   107.54  3.000
 65H  H2   CAB  H1   107.51  3.000
 65H  H3   CAB  CAR  111.23  3.000
 65H  H2   CAB  CAR  111.38  3.000
 65H  H1   CAB  CAR  111.59  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
 65H  CONST_01  CAS  CAR  C5   C4      0.00   0.0  0
 65H  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 65H  CONST_03  CAR  CAS  NAV  C4      0.00   0.0  0
 65H  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 65H  CONST_05  NAV  CAS  CAR  C5      0.00   0.0  0
 65H  CONST_06  C2   N1   C6   C5      0.00   0.0  0
 65H  CONST_07  CAS  NAV  C4   C5      0.00   0.0  0
 65H  CONST_08  C2   N3   C4   C5      0.00   0.0  0
 65H  CONST_09  CAS  CAR  C5   C6    180.00   0.0  0
 65H  CONST_10  NAV  C4   C5   C6    180.00   0.0  0
 65H  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 65H  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 65H  CONST_13  CAR  C5   C6   N1    180.00   0.0  0
 65H  CONST_14  CAR  C5   C4   N3    180.00   0.0  0
 65H  CONST_15  CAS  NAV  C4   N3    180.00   0.0  0
 65H  CONST_16  NAV  C4   C5   CAR     0.00   0.0  0
 65H  CONST_17  NAV  C4   N3   C2    180.00   0.0  0
 65H  CONST_18  CAO  CAG  CAI  CAP     0.00   0.0  0
 65H  CONST_19  CAO  CAF  CAH  CAP     0.00   0.0  0
 65H  CONST_20  CAG  CAI  CAP  CAH     0.00   0.0  0
 65H  CONST_21  CAG  CAO  CAF  CAH     0.00   0.0  0
 65H  CONST_22  CAI  CAG  CAO  CAF     0.00   0.0  0
 65H  CONST_23  CAI  CAP  CAH  CAF     0.00   0.0  0
 65H  CONST_24  CAB  CAR  C5   C4    180.00   0.0  0
 65H  CONST_25  NAE  C6   C5   C4    180.00   0.0  0
 65H  CONST_26  SAM  CAS  NAV  C4    180.00   0.0  0
 65H  CONST_27  NAD  C2   N3   C4    180.00   0.0  0
 65H  CONST_28  SAM  CAS  CAR  C5    180.00   0.0  0
 65H  CONST_29  CAC  NAV  C4   C5    180.00   0.0  0
 65H  CONST_30  CAB  CAR  C5   C6      0.00   0.0  0
 65H  CONST_31  NAD  C2   N1   C6    180.00   0.0  0
 65H  CONST_32  CAC  NAV  C4   N3      0.00   0.0  0
 65H  CONST_33  NAV  CAS  CAR  CAB   180.00   0.0  0
 65H  CONST_34  CAC  NAV  CAS  CAR   180.00   0.0  0
 65H  CONST_35  NAE  C6   C5   CAR     0.00   0.0  0
 65H  CONST_36  C2   N1   C6   NAE   180.00   0.0  0
 65H  CONST_37  CAG  CAI  CAP  SAM   180.00   0.0  0
 65H  CONST_38  CAF  CAH  CAP  SAM   180.00   0.0  0
 65H  CONST_39  OAL  CAO  CAF  CAH   180.00   0.0  0
 65H  CONST_40  CAI  CAG  CAO  OAL   180.00   0.0  0
 65H  CONST_41  H16  CAG  CAI  CAP   180.00   0.0  0
 65H  CONST_42  H12  CAF  CAH  CAP   180.00   0.0  0
 65H  CONST_43  H17  CAI  CAP  CAH   180.00   0.0  0
 65H  CONST_44  H11  CAH  CAF  CAO   180.00   0.0  0
 65H  CONST_45  H4   NAE  C6   C5      0.00   0.0  0
 65H  CONST_46  H5   NAE  C6   C5    180.00   0.0  0
 65H  Var_01    CAI  CAP  SAM  CAS   -29.44  30.0  2
 65H  Var_02    CAG  CAO  OAL  CAA    -0.31  30.0  2
 65H  Var_03    H8   CAC  NAV  C4    123.36  30.0  2
 65H  Var_04    H1   CAB  CAR  C5    -60.94  30.0  2
 65H  Var_05    H13  CAA  OAL  CAO  -179.94  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
 65H  plan-1  SAM  0.020
 65H  plan-1  CAP  0.020
 65H  plan-1  CAH  0.020
 65H  plan-1  CAF  0.020
 65H  plan-1  CAO  0.020
 65H  plan-1  OAL  0.020
 65H  plan-1  CAG  0.020
 65H  plan-1  CAI  0.020
 65H  plan-1  H11  0.020
 65H  plan-1  H12  0.020
 65H  plan-1  H16  0.020
 65H  plan-1  H17  0.020
 65H  plan-2  C4   0.020
 65H  plan-2  C5   0.020
 65H  plan-2  C6   0.020
 65H  plan-2  N1   0.020
 65H  plan-2  N3   0.020
 65H  plan-2  CAR  0.020
 65H  plan-2  NAE  0.020
 65H  plan-2  C2   0.020
 65H  plan-2  NAD  0.020
 65H  plan-2  NAV  0.020
 65H  plan-2  CAC  0.020
 65H  plan-2  CAS  0.020
 65H  plan-2  SAM  0.020
 65H  plan-2  CAB  0.020
 65H  plan-3  C6   0.020
 65H  plan-3  NAE  0.020
 65H  plan-3  H4   0.020
 65H  plan-3  H5   0.020
 65H  plan-4  C2   0.020
 65H  plan-4  NAD  0.020
 65H  plan-4  H6   0.020
 65H  plan-4  H7   0.020

