# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 00:07:18 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 5-{3-[3-(1,3-benzodioxol-5-yl)-5-methoxyphenyl]prop-1-yn-1-yl}-6-ethylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#CCc2cc(OC)cc(c2)c3ccc4OCOc4c3
#
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
 14Q  14Q  5-{3-[3-(1,3-benzodioxol-5-yl)-5-methoxyphenyl]prop-1-yn-1-yl}-6-ethylpyrimidine-2,4-diamine  ligand  52  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_14Q
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
 14Q  CAY  C  CH3   0  -0.665   1.3340   1.9976   0.6207
 14Q  CAH  C  CH2   0  -0.520   2.2822   1.0256   1.3228
 14Q  C4   C  CR6   0   0.263   3.6592   1.0743   0.7308
 14Q  N3   N  N     0  -0.499   4.5472   1.8558   1.3325
 14Q  C2   C  CR6   0   0.537   5.7656   1.9164   0.7822
 14Q  NAG  N  NH2   0  -0.820   6.6563   2.7339   1.3736
 14Q  N1   N  N     0  -0.504   6.1755   1.2634  -0.3036
 14Q  C6   C  CR6   0   0.469   5.2893   0.4832  -0.9111
 14Q  NAI  N  NH2   0  -0.825   5.6820  -0.1627  -2.0166
 14Q  C5   C  CR6   0  -0.315   3.9649   0.3483  -0.4195
 14Q  CAJ  C  CSP   0   0.162   3.0159  -0.4778  -1.0700
 14Q  CAK  C  CSP   0   0.019   2.1922  -1.1736  -1.6131
 14Q  CAL  C  CH2   0  -0.686   1.1248  -1.9759  -2.1989
 14Q  CAM  C  CR6   0   0.155  -0.0359  -2.0598  -1.2324
 14Q  CAR  C  CR16  0  -0.390  -0.9554  -1.0261  -1.1664
 14Q  CAN  C  CR16  0  -0.447  -0.1492  -3.1574  -0.3850
 14Q  CAO  C  CR6   0   0.422  -1.1931  -3.2105   0.5345
 14Q  OAZ  O  O2    0  -0.473  -1.3872  -4.2243   1.3988
 14Q  CBA  C  CH3   0  -0.438  -0.4618  -5.2928   1.4091
 14Q  CAP  C  CR16  0  -0.429  -2.1107  -2.1631   0.6050
 14Q  CAQ  C  CR6   0   0.133  -2.0005  -1.0656  -0.2407
 14Q  CAS  C  CR6   0   0.069  -2.9701   0.0460  -0.1543
 14Q  CAX  C  CR16  0  -0.402  -4.3234  -0.2188   0.1302
 14Q  CAW  C  CR56  0   0.320  -5.1755   0.8518   0.2088
 14Q  OBB  O  O     0  -0.487  -6.5031   0.8518   0.4756
 14Q  CBC  C  CH2   0   0.071  -6.9498   2.1910   0.3033
 14Q  OBD  O  O     0  -0.485  -5.7904   3.0023   0.1611
 14Q  CAV  C  CR56  0   0.290  -4.7450   2.1551   0.0159
 14Q  CAU  C  CR16  0  -0.327  -3.4329   2.4428  -0.2642
 14Q  CAT  C  CR16  0  -0.328  -2.5512   1.3599  -0.3447
 14Q  H1   H  HCH3  0   0.234   0.3502   1.9735   1.0900
 14Q  H2   H  HCH3  0   0.230   1.7058   3.0211   0.6757
 14Q  H3   H  HCH3  0   0.232   1.2083   1.7366  -0.4309
 14Q  H4   H  HCH2  0   0.248   2.3516   1.2789   2.3812
 14Q  H5   H  HCH2  0   0.246   1.8810   0.0132   1.2476
 14Q  H6   H  HNH2  0   0.394   6.4463   3.1101   2.2812
 14Q  H7   H  HNH2  0   0.394   7.6226   2.6878   1.1021
 14Q  H8   H  HNH2  0   0.404   5.0951  -0.8594  -2.4414
 14Q  H9   H  HNH2  0   0.397   6.6511  -0.1425  -2.2828
 14Q  H10  H  HCH2  0   0.286   0.7990  -1.5301  -3.1424
 14Q  H11  H  HCH2  0   0.285   1.4940  -2.9757  -2.4390
 14Q  H12  H  HCR6  0   0.244  -0.8687  -0.1912  -1.8512
 14Q  H13  H  HCR6  0   0.277   0.5833  -3.9509  -0.4555
 14Q  H14  H  HCH3  0   0.261  -0.7842  -5.9728   2.1938
 14Q  H15  H  HCH3  0   0.229  -0.4502  -5.8338   0.4594
 14Q  H16  H  HCH3  0   0.229   0.5526  -4.9527   1.6329
 14Q  H17  H  HCR6  0   0.258  -2.8964  -2.2095   1.3495
 14Q  H18  H  HCR6  0   0.272  -4.6856  -1.2296   0.2639
 14Q  H19  H  HCH2  0   0.236  -7.5664   2.2643  -0.5980
 14Q  H20  H  HCH2  0   0.245  -7.5164   2.5067   1.1798
 14Q  H21  H  HCR6  0   0.275  -3.0878   3.4574  -0.4082
 14Q  H22  H  HCR6  0   0.255  -1.5076   1.5630  -0.5452

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
 14Q  CAL  CAM  single    1.513  0.020  1.513
 14Q  CAL  CAK  single    1.458  0.020  1.458
 14Q  NAI  C6   single    1.339  0.020  1.339
 14Q  CAN  CAM  aromatic  1.391  0.020  1.391
 14Q  CAN  CAO  aromatic  1.392  0.020  1.392
 14Q  CAM  CAR  aromatic  1.385  0.020  1.385
 14Q  CAK  CAJ  triple    1.207  0.020  1.207
 14Q  OAZ  CAO  single    1.346  0.020  1.346
 14Q  OAZ  CBA  single    1.414  0.020  1.414
 14Q  CAO  CAP  aromatic  1.394  0.020  1.394
 14Q  CAJ  C5   single    1.416  0.020  1.416
 14Q  C6   C5   aromatic  1.419  0.020  1.419
 14Q  C6   N1   aromatic  1.328  0.020  1.328
 14Q  CAR  CAQ  aromatic  1.397  0.020  1.397
 14Q  CAP  CAQ  aromatic  1.390  0.020  1.390
 14Q  C5   C4   aromatic  1.394  0.020  1.394
 14Q  N1   C2   aromatic  1.332  0.020  1.332
 14Q  CAQ  CAS  single    1.478  0.020  1.478
 14Q  CAX  CAS  aromatic  1.408  0.020  1.408
 14Q  CAX  CAW  aromatic  1.371  0.020  1.371
 14Q  C4   N3   aromatic  1.327  0.020  1.327
 14Q  C4   CAH  single    1.500  0.020  1.500
 14Q  CAS  CAT  aromatic  1.392  0.020  1.392
 14Q  C2   N3   aromatic  1.338  0.020  1.338
 14Q  C2   NAG  single    1.346  0.020  1.346
 14Q  CAH  CAY  single    1.529  0.020  1.529
 14Q  CAW  OBB  single    1.354  0.020  1.354
 14Q  CAW  CAV  aromatic  1.386  0.020  1.386
 14Q  OBB  CBC  single    1.422  0.020  1.422
 14Q  CAT  CAU  aromatic  1.399  0.020  1.399
 14Q  CAV  CAU  aromatic  1.372  0.020  1.372
 14Q  CAV  OBD  single    1.353  0.020  1.353
 14Q  CBC  OBD  single    1.422  0.020  1.422
 14Q  CAY  H1   single    0.970  0.020  1.090
 14Q  CAY  H2   single    0.970  0.020  1.090
 14Q  CAY  H3   single    0.970  0.020  1.090
 14Q  CAH  H4   single    0.970  0.020  1.090
 14Q  CAH  H5   single    0.970  0.020  1.090
 14Q  NAG  H6   single    0.890  0.020  1.040
 14Q  NAG  H7   single    0.890  0.020  1.040
 14Q  NAI  H8   single    0.860  0.020  1.020
 14Q  NAI  H9   single    0.860  0.020  1.020
 14Q  CAL  H10  single    0.970  0.020  1.090
 14Q  CAL  H11  single    0.970  0.020  1.090
 14Q  CAR  H12  single    0.930  0.020  1.080
 14Q  CAN  H13  single    0.930  0.020  1.080
 14Q  CBA  H14  single    0.970  0.020  1.090
 14Q  CBA  H15  single    0.970  0.020  1.090
 14Q  CBA  H16  single    0.970  0.020  1.090
 14Q  CAP  H17  single    0.930  0.020  1.080
 14Q  CAX  H18  single    0.930  0.020  1.080
 14Q  CBC  H19  single    0.970  0.020  1.090
 14Q  CBC  H20  single    0.970  0.020  1.090
 14Q  CAU  H21  single    0.930  0.020  1.080
 14Q  CAT  H22  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
 14Q  H3   CAY  H2   108.22  3.000
 14Q  H3   CAY  H1   107.80  3.000
 14Q  H2   CAY  H1   107.87  3.000
 14Q  H3   CAY  CAH  111.23  3.000
 14Q  H2   CAY  CAH  111.24  3.000
 14Q  H1   CAY  CAH  110.36  3.000
 14Q  H5   CAH  H4   107.80  3.000
 14Q  H5   CAH  C4   109.90  3.000
 14Q  H4   CAH  C4   108.49  3.000
 14Q  H5   CAH  CAY  109.28  3.000
 14Q  H4   CAH  CAY  109.73  3.000
 14Q  C4   CAH  CAY  111.57  3.000
 14Q  C5   C4   N3   122.28  3.000
 14Q  N3   C4   CAH  117.04  3.000
 14Q  C5   C4   CAH  120.67  3.000
 14Q  C2   N3   C4   116.71  3.000
 14Q  N1   C2   NAG  116.89  3.000
 14Q  NAG  C2   N3   116.70  3.000
 14Q  N1   C2   N3   126.39  3.000
 14Q  H7   NAG  H6   117.53  3.000
 14Q  H7   NAG  C2   119.33  3.000
 14Q  H6   NAG  C2   119.08  3.000
 14Q  C6   N1   C2   117.11  3.000
 14Q  C5   C6   NAI  120.91  3.000
 14Q  C5   C6   N1   121.35  3.000
 14Q  NAI  C6   N1   117.74  3.000
 14Q  H9   NAI  H8   117.70  3.000
 14Q  H9   NAI  C6   119.45  3.000
 14Q  H8   NAI  C6   120.79  3.000
 14Q  CAJ  C5   C6   121.44  3.000
 14Q  C6   C5   C4   116.16  3.000
 14Q  CAJ  C5   C4   122.39  3.000
 14Q  CAK  CAJ  C5   180.00  3.000
 14Q  CAL  CAK  CAJ  180.00  3.000
 14Q  H11  CAL  H10  106.51  3.000
 14Q  H11  CAL  CAM  110.42  3.000
 14Q  H10  CAL  CAM  110.20  3.000
 14Q  H11  CAL  CAK  110.15  3.000
 14Q  H10  CAL  CAK  109.91  3.000
 14Q  CAM  CAL  CAK  109.60  3.000
 14Q  CAN  CAM  CAR  120.38  3.000
 14Q  CAR  CAM  CAL  119.90  3.000
 14Q  CAN  CAM  CAL  119.69  3.000
 14Q  H12  CAR  CAQ  120.04  3.000
 14Q  H12  CAR  CAM  119.47  3.000
 14Q  CAQ  CAR  CAM  120.48  3.000
 14Q  H13  CAN  CAO  121.51  3.000
 14Q  H13  CAN  CAM  118.93  3.000
 14Q  CAO  CAN  CAM  119.57  3.000
 14Q  CAP  CAO  OAZ  116.00  3.000
 14Q  CAP  CAO  CAN  119.88  3.000
 14Q  OAZ  CAO  CAN  124.12  3.000
 14Q  CBA  OAZ  CAO  118.65  3.000
 14Q  H16  CBA  H15  108.79  3.000
 14Q  H16  CBA  H14  108.78  3.000
 14Q  H15  CBA  H14  108.70  3.000
 14Q  H16  CBA  OAZ  111.96  3.000
 14Q  H15  CBA  OAZ  112.01  3.000
 14Q  H14  CBA  OAZ  106.49  3.000
 14Q  H17  CAP  CAQ  120.63  3.000
 14Q  H17  CAP  CAO  118.68  3.000
 14Q  CAQ  CAP  CAO  120.68  3.000
 14Q  CAS  CAQ  CAP  120.43  3.000
 14Q  CAS  CAQ  CAR  120.57  3.000
 14Q  CAP  CAQ  CAR  119.00  3.000
 14Q  CAT  CAS  CAX  119.63  3.000
 14Q  CAT  CAS  CAQ  120.30  3.000
 14Q  CAX  CAS  CAQ  120.06  3.000
 14Q  H18  CAX  CAW  120.96  3.000
 14Q  H18  CAX  CAS  121.50  3.000
 14Q  CAW  CAX  CAS  117.53  3.000
 14Q  CAV  CAW  OBB  109.39  3.000
 14Q  CAV  CAW  CAX  122.23  3.000
 14Q  OBB  CAW  CAX  128.38  3.000
 14Q  CBC  OBB  CAW  106.50  3.000
 14Q  H20  CBC  H19  110.48  3.000
 14Q  H20  CBC  OBD  109.81  3.000
 14Q  H19  CBC  OBD  109.80  3.000
 14Q  H20  CBC  OBB  109.78  3.000
 14Q  H19  CBC  OBB  109.86  3.000
 14Q  OBD  CBC  OBB  107.05  3.000
 14Q  CAV  OBD  CBC  106.46  3.000
 14Q  CAU  CAV  OBD  129.00  3.000
 14Q  OBD  CAV  CAW  109.49  3.000
 14Q  CAU  CAV  CAW  121.50  3.000
 14Q  H21  CAU  CAT  121.17  3.000
 14Q  H21  CAU  CAV  121.94  3.000
 14Q  CAT  CAU  CAV  116.88  3.000
 14Q  H22  CAT  CAU  118.26  3.000
 14Q  H22  CAT  CAS  119.52  3.000
 14Q  CAU  CAT  CAS  122.22  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
 14Q  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 14Q  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 14Q  CONST_03  C6   C5   C4   N3      0.00   0.0  0
 14Q  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 14Q  CONST_05  C5   C6   N1   C2      0.00   0.0  0
 14Q  CONST_06  C5   C4   N3   C2      0.00   0.0  0
 14Q  CONST_07  CAP  CAO  CAN  CAM     0.00   0.0  0
 14Q  CONST_08  CAP  CAQ  CAR  CAM     0.00   0.0  0
 14Q  CONST_09  CAS  CAQ  CAR  CAM   180.00   0.0  0
 14Q  CONST_10  CAO  CAN  CAM  CAR     0.00   0.0  0
 14Q  CONST_11  CAO  CAP  CAQ  CAR     0.00   0.0  0
 14Q  CONST_14  CAQ  CAR  CAM  CAN     0.00   0.0  0
 14Q  CONST_15  CAQ  CAP  CAO  CAN     0.00   0.0  0
 14Q  CONST_16  CAS  CAQ  CAP  CAO   180.00   0.0  0
 14Q  CONST_19  CAW  CAX  CAS  CAQ   180.00   0.0  0
 14Q  CONST_20  CAU  CAT  CAS  CAQ   180.00   0.0  0
 14Q  CONST_21  CAV  CAW  CAX  CAS     0.00   0.0  0
 14Q  CONST_22  CAV  CAU  CAT  CAS     0.00   0.0  0
 14Q  CONST_23  CAU  CAT  CAS  CAX     0.00   0.0  0
 14Q  CONST_24  CAU  CAV  CAW  CAX     0.00   0.0  0
 14Q  CONST_25  CAT  CAS  CAX  CAW     0.00   0.0  0
 14Q  CONST_26  CAT  CAU  CAV  CAW     0.00   0.0  0
 14Q  CONST_27  C6   C5   C4   CAH   180.00   0.0  0
 14Q  CONST_28  C2   N3   C4   CAH   180.00   0.0  0
 14Q  CONST_29  NAI  C6   C5   C4    180.00   0.0  0
 14Q  CONST_30  NAG  C2   N3   C4    180.00   0.0  0
 14Q  CONST_31  CAJ  C5   C4   N3    180.00   0.0  0
 14Q  CONST_32  NAI  C6   N1   C2    180.00   0.0  0
 14Q  CONST_33  C6   N1   C2   NAG   180.00   0.0  0
 14Q  CONST_34  CAJ  C5   C6   N1    180.00   0.0  0
 14Q  CONST_35  CAO  CAN  CAM  CAL   180.00   0.0  0
 14Q  CONST_36  CAQ  CAR  CAM  CAL   180.00   0.0  0
 14Q  CONST_37  OAZ  CAO  CAN  CAM   180.00   0.0  0
 14Q  CONST_38  CAQ  CAP  CAO  OAZ   180.00   0.0  0
 14Q  CONST_39  H13  CAN  CAM  CAR   180.00   0.0  0
 14Q  CONST_40  H17  CAP  CAQ  CAR   180.00   0.0  0
 14Q  CONST_41  H12  CAR  CAM  CAN   180.00   0.0  0
 14Q  CONST_42  H18  CAX  CAS  CAQ     0.00   0.0  0
 14Q  CONST_43  H22  CAT  CAS  CAQ     0.00   0.0  0
 14Q  CONST_44  H21  CAU  CAT  CAS   180.00   0.0  0
 14Q  CONST_45  H6   NAG  C2   N3      0.00   0.0  0
 14Q  CONST_46  H7   NAG  C2   N3    180.00   0.0  0
 14Q  CONST_47  H8   NAI  C6   N1    180.00   0.0  0
 14Q  CONST_48  H9   NAI  C6   N1      0.00   0.0  0
 14Q  Var_01    OBD  CBC  OBB  CAW   -10.18  30.0  1
 14Q  Var_02    CAV  CAW  OBB  CBC     6.28  30.0  1
 14Q  Var_03    CAU  CAV  OBD  CBC   174.01  30.0  1
 14Q  Var_04    C5   C4   CAH  CAY   -82.87  30.0  2
 14Q  Var_05    CAN  CAM  CAL  CAK   -95.81  30.0  2
 14Q  Var_06    CAP  CAO  OAZ  CBA  -177.73  30.0  2
 14Q  Var_07    CAM  CAL  CAK  CAJ   -17.08  30.0  1
 14Q  Var_08    H1   CAY  CAH  C4   -177.88  30.0  3
 14Q  Var_09    H14  CBA  OAZ  CAO   178.05  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
 14Q  plan-1  CAH  0.020
 14Q  plan-1  C4   0.020
 14Q  plan-1  N3   0.020
 14Q  plan-1  C2   0.020
 14Q  plan-1  NAG  0.020
 14Q  plan-1  N1   0.020
 14Q  plan-1  C6   0.020
 14Q  plan-1  NAI  0.020
 14Q  plan-1  C5   0.020
 14Q  plan-1  CAJ  0.020
 14Q  plan-1  CAK  0.020
 14Q  plan-2  CAL  0.020
 14Q  plan-2  CAM  0.020
 14Q  plan-2  CAR  0.020
 14Q  plan-2  CAN  0.020
 14Q  plan-2  CAO  0.020
 14Q  plan-2  OAZ  0.020
 14Q  plan-2  CAP  0.020
 14Q  plan-2  CAQ  0.020
 14Q  plan-2  CAS  0.020
 14Q  plan-2  H12  0.020
 14Q  plan-2  H13  0.020
 14Q  plan-2  H17  0.020
 14Q  plan-3  CAQ  0.020
 14Q  plan-3  CAS  0.020
 14Q  plan-3  CAX  0.020
 14Q  plan-3  CAW  0.020
 14Q  plan-3  OBB  0.020
 14Q  plan-3  OBD  0.020
 14Q  plan-3  CAV  0.020
 14Q  plan-3  CAU  0.020
 14Q  plan-3  CAT  0.020
 14Q  plan-3  H18  0.020
 14Q  plan-3  H21  0.020
 14Q  plan-3  H22  0.020
 14Q  plan-4  C2   0.020
 14Q  plan-4  NAG  0.020
 14Q  plan-4  H6   0.020
 14Q  plan-4  H7   0.020
 14Q  plan-5  C6   0.020
 14Q  plan-5  NAI  0.020
 14Q  plan-5  H8   0.020
 14Q  plan-5  H9   0.020

