# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 07:42:59 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 5-[3-(2,5-dimethoxyphenyl)prop-1-yn-1-yl]-6-propylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1nc(N)nc(N)c1C#CCc2cc(OC)ccc2OC
#
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
 QLZ  QLZ  5-[3-(2,5-dimethoxyphenyl)prop-1-yn-1-yl]-6-propylpyrimidine-2,4-diamine  ligand  46  24  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QLZ
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
 QLZ  N1    N  N     0  -0.505   3.6428  -1.8083   1.5448
 QLZ  C2    C  CR6   0   0.534   4.6211  -1.2157   0.8618
 QLZ  N3    N  N     0  -0.500   4.5462  -0.0430   0.2224
 QLZ  C4    C  CR6   0   0.278   3.3866   0.6006   0.2880
 QLZ  C5    C  CR6   0  -0.321   2.2942   0.0939   0.9863
 QLZ  C6    C  CR6   0   0.463   2.4808  -1.1691   1.6108
 QLZ  CAA   C  CH3   0  -0.665   2.6428   2.9173  -2.7029
 QLZ  CAB   C  CH3   0  -0.434  -5.5311   0.7001  -3.0303
 QLZ  CAC   C  CH3   0  -0.444  -2.3812  -2.1258   2.5569
 QLZ  NAD   N  NH2   0  -0.820   5.8108  -1.8461   0.8331
 QLZ  NAE   N  NH2   0  -0.836   1.4818  -1.7499   2.2842
 QLZ  CAF   C  CSP   0   0.044  -0.0592   1.2208   1.2263
 QLZ  CAG   C  CSP   0   0.131   1.0427   0.7485   1.0842
 QLZ  CAH   C  CR16  0  -0.381  -4.3138  -0.5274  -0.8136
 QLZ  CAI   C  CR16  0  -0.367  -3.6742  -1.0841   0.2940
 QLZ  CAJ   C  CR16  0  -0.388  -3.0664   1.4921  -0.4849
 QLZ  CAK   C  CH2   0  -0.427   2.7396   1.6342  -1.8912
 QLZ  CAL   C  CH2   0  -0.675  -1.4059   1.7587   1.3753
 QLZ  CAM   C  CH2   0  -0.517   3.2777   1.8821  -0.4784
 QLZ  CAT   C  CR6   0   0.374  -4.0142   0.7658  -1.2111
 QLZ  CAU   C  CR6   0   0.038  -2.4287   0.9502   0.6137
 QLZ  CAW   C  CR6   0   0.339  -2.7355  -0.3601   1.0116
 QLZ  HAA   H  HCH3  0   0.220   1.9758   3.6370  -2.2253
 QLZ  HAAA  H  HCH3  0   0.220   3.6194   3.3925  -2.8098
 QLZ  HAAB  H  HCH3  0   0.231   2.2573   2.7223  -3.7041
 QLZ  HAB   H  HCH3  0   0.225  -6.4011   0.4102  -2.4342
 QLZ  HABA  H  HCH3  0   0.258  -5.8573   1.3768  -3.8167
 QLZ  HABB  H  HCH3  0   0.225  -5.1099  -0.1968  -3.4936
 QLZ  HAC   H  HCH3  0   0.235  -3.4303  -2.2161   2.8512
 QLZ  HACA  H  HCH3  0   0.229  -2.1591  -2.8896   1.8071
 QLZ  HACB  H  HCH3  0   0.258  -1.7586  -2.3024   3.4310
 QLZ  HNAD  H  HNH2  0   0.394   5.8649  -2.8015   1.1400
 QLZ  HNAA  H  HNH2  0   0.394   6.5128  -1.5280   0.1883
 QLZ  HNAE  H  HNH2  0   0.399   1.6216  -2.6424   2.7240
 QLZ  HNAB  H  HNH2  0   0.408   0.5759  -1.3169   2.3415
 QLZ  HAH   H  HCR6  0   0.280  -5.0388  -1.1325  -1.3404
 QLZ  HAI   H  HCR6  0   0.282  -3.9344  -2.0963   0.5722
 QLZ  HAJ   H  HCR6  0   0.261  -2.8292   2.5047  -0.7914
 QLZ  HAK   H  HCH2  0   0.229   1.7542   1.1664  -1.8231
 QLZ  HAKA  H  HCH2  0   0.227   3.3898   0.9187  -2.4011
 QLZ  HAL   H  HCH2  0   0.287  -1.6648   1.8027   2.4372
 QLZ  HALA  H  HCH2  0   0.288  -1.4210   2.7904   1.0174
 QLZ  HAM   H  HCH2  0   0.241   2.6179   2.5809   0.0409
 QLZ  HAMA  H  HCH2  0   0.245   4.2661   2.3427  -0.5403
 QLZ  OAP   O  O2    0  -0.478  -4.5745   1.4004  -2.2647
 QLZ  OAQ   O  O2    0  -0.475  -2.0732  -0.8268   2.0953

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
 QLZ  C2   N1    aromatic  1.332  0.020  1.332
 QLZ  N1   C6    aromatic  1.328  0.020  1.328
 QLZ  N3   C2    aromatic  1.338  0.020  1.338
 QLZ  NAD  C2    single    1.347  0.020  1.347
 QLZ  N3   C4    aromatic  1.328  0.020  1.328
 QLZ  CAM  C4    single    1.497  0.020  1.497
 QLZ  C4   C5    aromatic  1.392  0.020  1.392
 QLZ  C5   CAG   single    1.416  0.020  1.416
 QLZ  C5   C6    aromatic  1.421  0.020  1.421
 QLZ  C6   NAE   single    1.337  0.020  1.337
 QLZ  CAA  CAK   single    1.521  0.020  1.521
 QLZ  CAA  HAA   single    0.970  0.020  1.090
 QLZ  CAA  HAAA  single    0.970  0.020  1.090
 QLZ  CAA  HAAB  single    0.970  0.020  1.090
 QLZ  OAP  CAB   single    1.411  0.020  1.411
 QLZ  CAB  HAB   single    0.970  0.020  1.090
 QLZ  CAB  HABA  single    0.970  0.020  1.090
 QLZ  CAB  HABB  single    0.970  0.020  1.090
 QLZ  CAC  OAQ   single    1.413  0.020  1.413
 QLZ  CAC  HAC   single    0.970  0.020  1.090
 QLZ  CAC  HACA  single    0.970  0.020  1.090
 QLZ  CAC  HACB  single    0.970  0.020  1.090
 QLZ  NAD  HNAD  single    0.890  0.020  1.040
 QLZ  NAD  HNAA  single    0.890  0.020  1.040
 QLZ  NAE  HNAE  single    0.860  0.020  1.020
 QLZ  NAE  HNAB  single    0.860  0.020  1.020
 QLZ  CAG  CAF   triple    1.207  0.020  1.207
 QLZ  CAF  CAL   single    1.458  0.020  1.458
 QLZ  CAH  CAI   aromatic  1.395  0.020  1.395
 QLZ  CAH  CAT   aromatic  1.386  0.020  1.386
 QLZ  CAH  HAH   single    0.930  0.020  1.080
 QLZ  CAI  CAW   aromatic  1.386  0.020  1.386
 QLZ  CAI  HAI   single    0.930  0.020  1.080
 QLZ  CAT  CAJ   aromatic  1.398  0.020  1.398
 QLZ  CAJ  CAU   aromatic  1.381  0.020  1.381
 QLZ  CAJ  HAJ   single    0.930  0.020  1.080
 QLZ  CAK  CAM   single    1.532  0.020  1.532
 QLZ  CAK  HAK   single    0.970  0.020  1.090
 QLZ  CAK  HAKA  single    0.970  0.020  1.090
 QLZ  CAU  CAL   single    1.510  0.020  1.510
 QLZ  CAL  HAL   single    0.970  0.020  1.090
 QLZ  CAL  HALA  single    0.970  0.020  1.090
 QLZ  CAM  HAM   single    0.970  0.020  1.090
 QLZ  CAM  HAMA  single    0.970  0.020  1.090
 QLZ  OAP  CAT   single    1.352  0.020  1.352
 QLZ  CAW  OAQ   single    1.353  0.020  1.353
 QLZ  CAW  CAU   aromatic  1.403  0.020  1.403

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
 QLZ  C6    N1   C2    117.00  3.000
 QLZ  NAD   C2   N3    116.72  3.000
 QLZ  NAD   C2   N1    116.83  3.000
 QLZ  N3    C2   N1    126.44  3.000
 QLZ  C4    N3   C2    116.75  3.000
 QLZ  CAM   C4   C5    120.75  3.000
 QLZ  C5    C4   N3    122.25  3.000
 QLZ  CAM   C4   N3    116.94  3.000
 QLZ  CAG   C5   C6    119.77  3.000
 QLZ  C6    C5   C4    116.16  3.000
 QLZ  CAG   C5   C4    124.06  3.000
 QLZ  NAE   C6   C5    120.60  3.000
 QLZ  NAE   C6   N1    118.01  3.000
 QLZ  C5    C6   N1    121.39  3.000
 QLZ  HAAB  CAA  HAAA  107.71  3.000
 QLZ  HAAB  CAA  HAA   107.68  3.000
 QLZ  HAAA  CAA  HAA   107.61  3.000
 QLZ  HAAB  CAA  CAK   111.20  3.000
 QLZ  HAAA  CAA  CAK   111.26  3.000
 QLZ  HAA   CAA  CAK   111.20  3.000
 QLZ  HABB  CAB  HABA  108.63  3.000
 QLZ  HABB  CAB  HAB   108.65  3.000
 QLZ  HABA  CAB  HAB   108.69  3.000
 QLZ  HABB  CAB  OAP   112.06  3.000
 QLZ  HABA  CAB  OAP   106.67  3.000
 QLZ  HAB   CAB  OAP   112.03  3.000
 QLZ  HACB  CAC  HACA  108.76  3.000
 QLZ  HACB  CAC  HAC   108.64  3.000
 QLZ  HACA  CAC  HAC   108.78  3.000
 QLZ  HACB  CAC  OAQ   106.68  3.000
 QLZ  HACA  CAC  OAQ   111.97  3.000
 QLZ  HAC   CAC  OAQ   111.91  3.000
 QLZ  HNAA  NAD  HNAD  117.34  3.000
 QLZ  HNAA  NAD  C2    118.85  3.000
 QLZ  HNAD  NAD  C2    119.09  3.000
 QLZ  HNAB  NAE  HNAE  118.87  3.000
 QLZ  HNAB  NAE  C6    120.96  3.000
 QLZ  HNAE  NAE  C6    120.15  3.000
 QLZ  CAL   CAF  CAG   180.00  3.000
 QLZ  CAF   CAG  C5    180.00  3.000
 QLZ  HAH   CAH  CAT   121.84  3.000
 QLZ  HAH   CAH  CAI   118.09  3.000
 QLZ  CAT   CAH  CAI   120.07  3.000
 QLZ  HAI   CAI  CAW   121.25  3.000
 QLZ  HAI   CAI  CAH   117.87  3.000
 QLZ  CAW   CAI  CAH   120.88  3.000
 QLZ  HAJ   CAJ  CAU   119.36  3.000
 QLZ  HAJ   CAJ  CAT   119.13  3.000
 QLZ  CAU   CAJ  CAT   121.51  3.000
 QLZ  HAKA  CAK  HAK   106.57  3.000
 QLZ  HAKA  CAK  CAM   109.10  3.000
 QLZ  HAK   CAK  CAM   109.18  3.000
 QLZ  HAKA  CAK  CAA   109.94  3.000
 QLZ  HAK   CAK  CAA   109.68  3.000
 QLZ  CAM   CAK  CAA   112.20  3.000
 QLZ  HALA  CAL  HAL   106.07  3.000
 QLZ  HALA  CAL  CAU   109.34  3.000
 QLZ  HAL   CAL  CAU   110.54  3.000
 QLZ  HALA  CAL  CAF   109.14  3.000
 QLZ  HAL   CAL  CAF   109.43  3.000
 QLZ  CAU   CAL  CAF   112.13  3.000
 QLZ  HAMA  CAM  HAM   107.68  3.000
 QLZ  HAMA  CAM  CAK   109.50  3.000
 QLZ  HAM   CAM  CAK   109.26  3.000
 QLZ  HAMA  CAM  C4    108.92  3.000
 QLZ  HAM   CAM  C4    110.37  3.000
 QLZ  CAK   CAM  C4    111.05  3.000
 QLZ  OAP   CAT  CAJ   116.24  3.000
 QLZ  OAP   CAT  CAH   124.90  3.000
 QLZ  CAJ   CAT  CAH   118.85  3.000
 QLZ  CAW   CAU  CAL   120.34  3.000
 QLZ  CAW   CAU  CAJ   119.40  3.000
 QLZ  CAL   CAU  CAJ   120.26  3.000
 QLZ  CAU   CAW  OAQ   116.23  3.000
 QLZ  CAU   CAW  CAI   119.29  3.000
 QLZ  OAQ   CAW  CAI   124.48  3.000
 QLZ  CAT   OAP  CAB   118.09  3.000
 QLZ  CAW   OAQ  CAC   118.17  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
 QLZ  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 QLZ  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 QLZ  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 QLZ  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 QLZ  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 QLZ  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 QLZ  CONST_07  CAU   CAW  CAI  CAH     0.00   0.0  0
 QLZ  CONST_08  CAU   CAJ  CAT  CAH     0.00   0.0  0
 QLZ  CONST_09  CAJ   CAT  CAH  CAI     0.00   0.0  0
 QLZ  CONST_10  CAJ   CAU  CAW  CAI     0.00   0.0  0
 QLZ  CONST_11  CAW   CAI  CAH  CAT     0.00   0.0  0
 QLZ  CONST_12  CAW   CAU  CAJ  CAT     0.00   0.0  0
 QLZ  CONST_13  CAG   C5   C6   N1    180.00   0.0  0
 QLZ  CONST_14  NAE   C6   N1   C2    180.00   0.0  0
 QLZ  CONST_15  CAM   C4   N3   C2    180.00   0.0  0
 QLZ  CONST_16  CAG   C5   C4   N3    180.00   0.0  0
 QLZ  CONST_17  NAD   C2   N3   C4    180.00   0.0  0
 QLZ  CONST_18  NAE   C6   C5   C4    180.00   0.0  0
 QLZ  CONST_19  NAD   C2   N1   C6    180.00   0.0  0
 QLZ  CONST_20  CAM   C4   C5   C6    180.00   0.0  0
 QLZ  CONST_21  OAQ   CAW  CAI  CAH   180.00   0.0  0
 QLZ  CONST_22  OAP   CAT  CAH  CAI   180.00   0.0  0
 QLZ  CONST_23  CAL   CAU  CAW  CAI   180.00   0.0  0
 QLZ  CONST_24  OAQ   CAW  CAU  CAJ   180.00   0.0  0
 QLZ  CONST_25  CAT   CAJ  CAU  CAL   180.00   0.0  0
 QLZ  CONST_26  CAU   CAJ  CAT  OAP   180.00   0.0  0
 QLZ  CONST_27  HAJ   CAJ  CAT  CAH   180.00   0.0  0
 QLZ  CONST_28  HAH   CAH  CAT  CAJ   180.00   0.0  0
 QLZ  CONST_29  HAI   CAI  CAH  CAT   180.00   0.0  0
 QLZ  CONST_30  HNAD  NAD  C2   N1      0.00   0.0  0
 QLZ  CONST_31  HNAA  NAD  C2   N1    180.00   0.0  0
 QLZ  CONST_32  HNAE  NAE  C6   N1      0.00   0.0  0
 QLZ  CONST_33  HNAB  NAE  C6   N1    180.00   0.0  0
 QLZ  Var_01    CAK   CAM  C4   N3     91.38  30.0  1
 QLZ  Var_02    CAH   CAT  OAP  CAB    -0.46  30.0  2
 QLZ  Var_03    CAI   CAW  OAQ  CAC    -1.91  30.0  2
 QLZ  Var_04    CAJ   CAU  CAL  CAF  -112.04  30.0  1
 QLZ  Var_05    CAA   CAK  CAM  C4   -178.93  30.0  2
 QLZ  Var_06    CAU   CAL  CAF  CAG    -3.74  30.0  3
 QLZ  Var_07    HAB   CAB  OAP  CAT    61.03  30.0  3
 QLZ  Var_08    HAC   CAC  OAQ  CAW   -60.58  30.0  3
 QLZ  Var_09    HAA   CAA  CAK  CAM   -59.95  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
 QLZ  plan-1  N1    0.020
 QLZ  plan-1  C2    0.020
 QLZ  plan-1  N3    0.020
 QLZ  plan-1  C4    0.020
 QLZ  plan-1  C5    0.020
 QLZ  plan-1  C6    0.020
 QLZ  plan-1  NAD   0.020
 QLZ  plan-1  NAE   0.020
 QLZ  plan-1  CAF   0.020
 QLZ  plan-1  CAG   0.020
 QLZ  plan-1  CAM   0.020
 QLZ  plan-2  CAH   0.020
 QLZ  plan-2  CAI   0.020
 QLZ  plan-2  CAJ   0.020
 QLZ  plan-2  CAL   0.020
 QLZ  plan-2  CAT   0.020
 QLZ  plan-2  CAU   0.020
 QLZ  plan-2  CAW   0.020
 QLZ  plan-2  HAH   0.020
 QLZ  plan-2  HAI   0.020
 QLZ  plan-2  HAJ   0.020
 QLZ  plan-2  OAP   0.020
 QLZ  plan-2  OAQ   0.020
 QLZ  plan-3  C2    0.020
 QLZ  plan-3  NAD   0.020
 QLZ  plan-3  HNAD  0.020
 QLZ  plan-3  HNAA  0.020
 QLZ  plan-4  C6    0.020
 QLZ  plan-4  NAE   0.020
 QLZ  plan-4  HNAE  0.020
 QLZ  plan-4  HNAB  0.020

