# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:08:42 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)N=C(CCn2cc(nn2)c3ccc4OCCOc4c3)N1
#
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
 JPH  JPH  2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one  ligand  42  25  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JPH
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
 JPH  N1   N  N     0  -0.497   4.8930   0.9281  -0.4783
 JPH  N3   N  NR16  0  -0.672   5.1968  -1.0210   0.7463
 JPH  C4   C  CR6   0   0.401   6.5435  -0.8307   0.8728
 JPH  C5   C  CR16  0  -0.526   7.0832   0.2695   0.3041
 JPH  C6   C  CR6   0   0.455   6.2501   1.2070  -0.4173
 JPH  CAU  C  CR16  0  -0.418  -3.6917  -0.6515  -0.4843
 JPH  CAT  C  CR6   0   0.347  -5.0087  -0.4676  -0.0933
 JPH  OAV  O  O2    0  -0.481  -5.9282  -1.3841  -0.4773
 JPH  CAW  C  CH2   0  -0.228  -7.1468  -1.3238   0.2490
 JPH  CAX  C  CH2   0  -0.225  -7.6063   0.1079   0.3789
 JPH  OAY  O  O2    0  -0.478  -6.6324   0.8754   1.0711
 JPH  CAS  C  CR6   0   0.308  -5.3581   0.6442   0.6811
 JPH  CAR  C  CR16  0  -0.344  -4.3692   1.5423   1.0615
 JPH  CAQ  C  CR16  0  -0.343  -3.0554   1.3499   0.6746
 JPH  CAP  C  CR6   0   0.059  -2.7013   0.2544  -0.1133
 JPH  CAM  C  CR5   0   0.162  -1.3197   0.0471  -0.5377
 JPH  CAL  C  CR15  0  -0.082  -0.1903   0.7817  -0.2571
 JPH  NAN  N  N     0  -0.324  -0.9433  -0.9799  -1.3345
 JPH  NAO  N  N     0  -0.092   0.3233  -0.9145  -1.5508
 JPH  NAK  N  NR5   0  -0.269   0.7904   0.1428  -0.9135
 JPH  CAJ  C  CH2   0  -0.284   2.2072   0.4483  -0.9327
 JPH  C2   C  CR6   0   0.515   4.4241  -0.1323   0.0847
 JPH  CAA  C  CH3   0  -0.731   7.3001  -1.8642   1.6297
 JPH  O6   O  O     0  -0.492   6.6904   2.2137  -0.9602
 JPH  H1   H  HCR6  0   0.272   8.1453   0.4544   0.3846
 JPH  H4   H  HCH2  0   0.262  -7.8802  -1.9105  -0.3020
 JPH  H5   H  HCH2  0   0.244  -7.0160  -1.7737   1.2390
 JPH  H6   H  HCH2  0   0.245  -7.7926   0.5409  -0.6095
 JPH  H7   H  HCH2  0   0.261  -8.5278   0.1601   0.9569
 JPH  H8   H  HCR6  0   0.270  -4.6415   2.4003   1.6634
 JPH  H9   H  HCR6  0   0.247  -2.3093   2.0699   0.9847
 JPH  H10  H  HCR5  0   0.309  -0.0142   1.6688   0.3272
 JPH  H11  H  HCH2  0   0.291   2.5682   0.2987  -1.9483
 JPH  H12  H  HCH2  0   0.286   2.3224   1.5011  -0.6895
 JPH  H15  H  HCH3  0   0.273   7.2134  -2.8380   1.1450
 JPH  H16  H  HCH3  0   0.270   8.3527  -1.6011   1.6891
 JPH  H17  H  HCH3  0   0.272   6.9100  -1.9649   2.6437
 JPH  H18  H  HNR6  0   0.436   4.7703  -1.8388   1.1588
 JPH  CAI  C  CH2   0  -0.556   2.9572  -0.4325   0.0547
 JPH  H3   H  HCR6  0   0.263  -3.4439  -1.5178  -1.0851
 JPH  H13  H  HCH2  0   0.303   2.5583  -0.2876   1.0634
 JPH  H14  H  HCH2  0   0.293   2.8058  -1.4862  -0.1916

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
 JPH  CAR  CAQ  aromatic  1.383  0.020  1.383
 JPH  CAR  CAS  aromatic  1.389  0.020  1.389
 JPH  CAX  OAY  single    1.420  0.020  1.420
 JPH  CAX  CAW  single    1.509  0.020  1.509
 JPH  OAY  CAS  single    1.353  0.020  1.353
 JPH  CAQ  CAP  aromatic  1.395  0.020  1.395
 JPH  CAS  CAT  aromatic  1.399  0.020  1.399
 JPH  CAP  CAM  single    1.460  0.020  1.460
 JPH  CAP  CAU  aromatic  1.393  0.020  1.393
 JPH  CAT  CAU  aromatic  1.386  0.020  1.386
 JPH  CAT  OAV  single    1.354  0.020  1.354
 JPH  CAW  OAV  single    1.420  0.020  1.420
 JPH  CAM  CAL  aromatic  1.376  0.020  1.376
 JPH  CAM  NAN  aromatic  1.353  0.020  1.353
 JPH  CAL  NAK  aromatic  1.342  0.020  1.342
 JPH  NAN  NAO  aromatic  1.287  0.020  1.287
 JPH  NAK  NAO  aromatic  1.320  0.020  1.320
 JPH  NAK  CAJ  single    1.450  0.020  1.450
 JPH  CAJ  CAI  single    1.521  0.020  1.521
 JPH  CAI  C2   single    1.498  0.020  1.498
 JPH  N1   C2   double    1.289  0.020  1.289
 JPH  N1   C6   single    1.387  0.020  1.387
 JPH  C2   N3   single    1.351  0.020  1.351
 JPH  O6   C6   double    1.226  0.020  1.226
 JPH  C6   C5   single    1.447  0.020  1.447
 JPH  N3   C4   single    1.366  0.020  1.366
 JPH  C5   C4   double    1.351  0.020  1.351
 JPH  C4   CAA  single    1.488  0.020  1.488
 JPH  C5   H1   single    0.930  0.020  1.080
 JPH  CAU  H3   single    0.930  0.020  1.080
 JPH  CAW  H4   single    0.970  0.020  1.090
 JPH  CAW  H5   single    0.970  0.020  1.090
 JPH  CAX  H6   single    0.970  0.020  1.090
 JPH  CAX  H7   single    0.970  0.020  1.090
 JPH  CAR  H8   single    0.930  0.020  1.080
 JPH  CAQ  H9   single    0.930  0.020  1.080
 JPH  CAL  H10  single    0.930  0.020  1.080
 JPH  CAJ  H11  single    0.970  0.020  1.090
 JPH  CAJ  H12  single    0.970  0.020  1.090
 JPH  CAI  H13  single    0.970  0.020  1.090
 JPH  CAI  H14  single    0.970  0.020  1.090
 JPH  CAA  H15  single    0.970  0.020  1.090
 JPH  CAA  H16  single    0.970  0.020  1.090
 JPH  CAA  H17  single    0.970  0.020  1.090
 JPH  N3   H18  single    0.860  0.020  1.020

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
 JPH  C2   N1   C6   120.15  3.000
 JPH  H18  N3   C2   119.41  3.000
 JPH  H18  N3   C4   119.42  3.000
 JPH  C2   N3   C4   121.17  3.000
 JPH  CAA  C4   C5   125.22  3.000
 JPH  CAA  C4   N3   116.85  3.000
 JPH  C5   C4   N3   117.92  3.000
 JPH  H1   C5   C6   119.47  3.000
 JPH  H1   C5   C4   120.03  3.000
 JPH  C6   C5   C4   120.50  3.000
 JPH  O6   C6   C5   123.11  3.000
 JPH  C5   C6   N1   117.07  3.000
 JPH  O6   C6   N1   119.83  3.000
 JPH  H3   CAU  CAP  120.37  3.000
 JPH  H3   CAU  CAT  118.68  3.000
 JPH  CAP  CAU  CAT  120.95  3.000
 JPH  CAS  CAT  OAV  121.69  3.000
 JPH  OAV  CAT  CAU  118.39  3.000
 JPH  CAS  CAT  CAU  119.92  3.000
 JPH  CAW  OAV  CAT  114.14  3.000
 JPH  H5   CAW  H4   108.45  3.000
 JPH  H5   CAW  CAX  110.39  3.000
 JPH  H4   CAW  CAX  110.46  3.000
 JPH  H5   CAW  OAV  110.02  3.000
 JPH  H4   CAW  OAV  107.24  3.000
 JPH  CAX  CAW  OAV  110.22  3.000
 JPH  H7   CAX  H6   108.43  3.000
 JPH  H7   CAX  OAY  107.20  3.000
 JPH  H6   CAX  OAY  110.06  3.000
 JPH  H7   CAX  CAW  110.41  3.000
 JPH  H6   CAX  CAW  110.44  3.000
 JPH  OAY  CAX  CAW  110.23  3.000
 JPH  CAS  OAY  CAX  114.40  3.000
 JPH  CAR  CAS  OAY  118.77  3.000
 JPH  OAY  CAS  CAT  122.05  3.000
 JPH  CAR  CAS  CAT  119.18  3.000
 JPH  H8   CAR  CAQ  120.30  3.000
 JPH  H8   CAR  CAS  119.05  3.000
 JPH  CAQ  CAR  CAS  120.65  3.000
 JPH  H9   CAQ  CAP  120.62  3.000
 JPH  H9   CAQ  CAR  118.83  3.000
 JPH  CAP  CAQ  CAR  120.55  3.000
 JPH  CAM  CAP  CAQ  121.05  3.000
 JPH  CAM  CAP  CAU  120.21  3.000
 JPH  CAQ  CAP  CAU  118.74  3.000
 JPH  NAN  CAM  CAL  107.27  3.000
 JPH  NAN  CAM  CAP  122.83  3.000
 JPH  CAL  CAM  CAP  129.90  3.000
 JPH  H10  CAL  NAK  122.56  3.000
 JPH  H10  CAL  CAM  133.21  3.000
 JPH  NAK  CAL  CAM  104.24  3.000
 JPH  NAO  NAN  CAM  109.53  3.000
 JPH  NAK  NAO  NAN  107.93  3.000
 JPH  CAJ  NAK  NAO  120.55  3.000
 JPH  CAJ  NAK  CAL  128.35  3.000
 JPH  NAO  NAK  CAL  111.03  3.000
 JPH  H12  CAJ  H11  107.87  3.000
 JPH  H12  CAJ  CAI  111.32  3.000
 JPH  H11  CAJ  CAI  111.26  3.000
 JPH  H12  CAJ  NAK  107.75  3.000
 JPH  H11  CAJ  NAK  107.92  3.000
 JPH  CAI  CAJ  NAK  110.57  3.000
 JPH  CAI  C2   N3   115.99  3.000
 JPH  N3   C2   N1   123.17  3.000
 JPH  CAI  C2   N1   120.83  3.000
 JPH  H17  CAA  H16  108.54  3.000
 JPH  H17  CAA  H15  107.58  3.000
 JPH  H16  CAA  H15  108.51  3.000
 JPH  H17  CAA  C4   110.80  3.000
 JPH  H16  CAA  C4   110.62  3.000
 JPH  H15  CAA  C4   110.70  3.000
 JPH  H14  CAI  H13  106.55  3.000
 JPH  H14  CAI  C2   109.49  3.000
 JPH  H13  CAI  C2   108.18  3.000
 JPH  H14  CAI  CAJ  110.11  3.000
 JPH  H13  CAI  CAJ  109.99  3.000
 JPH  C2   CAI  CAJ  112.33  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
 JPH  CONST_01  CAR  CAQ  CAP  CAU     0.00   0.0  0
 JPH  CONST_02  CAL  CAM  CAP  CAU   180.00   0.0  0
 JPH  CONST_03  NAN  CAM  CAP  CAU     0.00   0.0  0
 JPH  CONST_04  CAR  CAS  CAT  CAU     0.00   0.0  0
 JPH  CONST_05  CAQ  CAR  CAS  CAT     0.00   0.0  0
 JPH  CONST_06  CAQ  CAP  CAU  CAT     0.00   0.0  0
 JPH  CONST_07  CAM  CAP  CAU  CAT   180.00   0.0  0
 JPH  CONST_08  CAP  CAQ  CAR  CAS     0.00   0.0  0
 JPH  CONST_09  CAP  CAU  CAT  CAS     0.00   0.0  0
 JPH  CONST_10  CAM  CAP  CAQ  CAR   180.00   0.0  0
 JPH  CONST_11  CAL  CAM  CAP  CAQ     0.00   0.0  0
 JPH  CONST_12  NAN  CAM  CAP  CAQ   180.00   0.0  0
 JPH  CONST_13  NAK  CAL  CAM  CAP   180.00   0.0  0
 JPH  CONST_14  NAO  NAN  CAM  CAP   180.00   0.0  0
 JPH  CONST_15  NAO  NAK  CAL  CAM     0.00   0.0  0
 JPH  CONST_16  NAK  NAO  NAN  CAM     0.00   0.0  0
 JPH  CONST_17  NAO  NAN  CAM  CAL     0.00   0.0  0
 JPH  CONST_18  NAN  NAO  NAK  CAL     0.00   0.0  0
 JPH  CONST_19  NAK  CAL  CAM  NAN     0.00   0.0  0
 JPH  CONST_20  C4   N3   C2   N1      0.00   0.0  0
 JPH  CONST_21  C6   N1   C2   N3      0.00   0.0  0
 JPH  CONST_22  CAJ  NAK  CAL  CAM   180.00   0.0  0
 JPH  CONST_23  CAJ  NAK  NAO  NAN   180.00   0.0  0
 JPH  CONST_24  CAI  C2   N3   C4    180.00   0.0  0
 JPH  CONST_25  CAI  C2   N1   C6    180.00   0.0  0
 JPH  CONST_26  H9   CAQ  CAP  CAU   180.00   0.0  0
 JPH  CONST_27  H8   CAR  CAS  CAT   180.00   0.0  0
 JPH  CONST_28  H3   CAU  CAT  OAV     0.00   0.0  0
 JPH  CONST_29  H10  CAL  CAM  CAP     0.00   0.0  0
 JPH  CONST_30  H18  N3   C2   N1    180.00   0.0  0
 JPH  Var_01    CAX  CAW  OAV  CAT    45.40  30.0  1
 JPH  Var_02    OAY  CAX  CAW  OAV   -60.33  30.0  1
 JPH  Var_03    CAS  CAT  OAV  CAW   -16.10  30.0  1
 JPH  Var_04    CAR  CAS  OAY  CAX   165.37  30.0  1
 JPH  Var_05    CAJ  CAI  C2   N1     12.53  30.0  1
 JPH  Var_06    CAI  CAJ  NAK  CAL    97.87  30.0  2
 JPH  Var_07    C2   CAI  CAJ  NAK  -178.97  30.0  3
 JPH  Var_08    H15  CAA  C4   N3     61.08  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
 JPH  plan-1  CAP  0.020
 JPH  plan-1  CAM  0.020
 JPH  plan-1  CAL  0.020
 JPH  plan-1  NAN  0.020
 JPH  plan-1  NAO  0.020
 JPH  plan-1  NAK  0.020
 JPH  plan-1  CAJ  0.020
 JPH  plan-1  H10  0.020
 JPH  plan-2  N1   0.020
 JPH  plan-2  N3   0.020
 JPH  plan-2  C4   0.020
 JPH  plan-2  C5   0.020
 JPH  plan-2  C6   0.020
 JPH  plan-2  C2   0.020
 JPH  plan-2  CAA  0.020
 JPH  plan-2  O6   0.020
 JPH  plan-2  H1   0.020
 JPH  plan-2  H18  0.020
 JPH  plan-2  CAI  0.020
 JPH  plan-3  CAU  0.020
 JPH  plan-3  CAT  0.020
 JPH  plan-3  OAV  0.020
 JPH  plan-3  OAY  0.020
 JPH  plan-3  CAS  0.020
 JPH  plan-3  CAR  0.020
 JPH  plan-3  CAQ  0.020
 JPH  plan-3  CAP  0.020
 JPH  plan-3  CAM  0.020
 JPH  plan-3  H8   0.020
 JPH  plan-3  H9   0.020
 JPH  plan-3  H3   0.020

