# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:25:11 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: 5,6-diethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOc1ccc(cc1C2=NC(=C(CC)C(=O)N2)CC)[S](=O)(=O)N3CCN(C)CC3
#
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
 NI0  NI0  5,6-diethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one  ligand  63  31  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NI0
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
 NI0  CAQ  C  CH2   0  -0.314  -4.6622   0.8195   0.1303
 NI0  CAO  C  CH2   0  -0.279  -5.7869   0.2432  -0.7088
 NI0  NBC  N  NT    0  -0.415  -5.2799  -0.7321  -1.6504
 NI0  CAD  C  CH3   0  -0.520  -6.3148  -1.2163  -2.5358
 NI0  CAP  C  CH2   0  -0.275  -4.6291  -1.8146  -0.9446
 NI0  CAR  C  CH2   0  -0.318  -3.4809  -1.2923  -0.1027
 NI0  NBD  N  N     0  -0.566  -3.9864  -0.2776   0.8250
 NI0  SBE  S  S     0   1.378  -2.9775   0.1338   2.0724
 NI0  OAF  O  OS    0  -0.651  -3.6450   1.1775   2.8324
 NI0  OAG  O  OS    0  -0.650  -2.5958  -1.1043   2.7314
 NI0  CAV  C  CR6   0  -0.218  -1.5306   0.8255   1.3367
 NI0  CAJ  C  CR16  0  -0.242  -0.4603  -0.0011   1.0183
 NI0  CAH  C  CR16  0  -0.214  -1.4839   2.1780   1.0291
 NI0  CAI  C  CR16  0  -0.377  -0.3750   2.7064   0.3923
 NI0  CAX  C  CR6   0   0.421   0.7064   1.8872   0.0643
 NI0  OAU  O  O2    0  -0.445   1.7946   2.3048  -0.5695
 NI0  CAN  C  CH2   0  -0.180   1.9069   3.6664  -0.9784
 NI0  CAK  C  CH2   0  -0.461   3.2531   3.8380  -1.6487
 NI0  CAA  C  CH3   0  -0.673   3.4476   5.2688  -2.1309
 NI0  CAY  C  CR6   0  -0.118   0.6593   0.5206   0.3950
 NI0  CAZ  C  CR6   0   0.462   1.8017  -0.3653   0.0863
 NI0  NAS  N  N     0  -0.429   2.9751  -0.1148   0.5563
 NI0  NAT  N  NR16  0  -0.674   1.5398  -1.4508  -0.6717
 NI0  CBB  C  CR6   0   0.534   2.4920  -2.3983  -1.0133
 NI0  OAE  O  O     0  -0.479   2.1769  -3.3683  -1.6889
 NI0  CBA  C  CR6   0  -0.128   3.8135  -2.0988  -0.5150
 NI0  CAM  C  CH2   0  -0.514   4.9091  -3.0659  -0.8521
 NI0  CAC  C  CH3   0  -0.655   4.9926  -4.2191   0.1474
 NI0  CAW  C  CR6   0   0.236   3.9874  -0.9829   0.2558
 NI0  CAL  C  CH2   0  -0.516   5.3178  -0.5749   0.8155
 NI0  CAB  C  CH3   0  -0.667   6.0054   0.4500  -0.0872
 NI0  H1   H  HCH2  0   0.237  -3.9642   1.3681  -0.5148
 NI0  H2   H  HCH2  0   0.275  -5.0853   1.5121   0.8541
 NI0  H3   H  HCH2  0   0.205  -6.5504  -0.1888  -0.0398
 NI0  H4   H  HCH2  0   0.252  -6.2595   1.0616  -1.2556
 NI0  H6   H  HCH3  0   0.236  -6.7691  -0.3802  -3.0688
 NI0  H7   H  HCH3  0   0.236  -5.8841  -1.8924  -3.2758
 NI0  H8   H  HCH3  0   0.196  -7.1170  -1.7583  -2.0122
 NI0  H9   H  HCH2  0   0.206  -5.3312  -2.3673  -0.2981
 NI0  H10  H  HCH2  0   0.252  -4.2220  -2.5253  -1.6669
 NI0  H11  H  HCH2  0   0.276  -3.0435  -2.1195   0.4530
 NI0  H12  H  HCH2  0   0.237  -2.7120  -0.8668  -0.7602
 NI0  H13  H  HCR6  0   0.301  -0.4820  -1.0515   1.2803
 NI0  H14  H  HCR6  0   0.295  -2.3035   2.8363   1.2843
 NI0  H15  H  HCR6  0   0.303  -0.3655   3.7609   0.1574
 NI0  H16  H  HCH2  0   0.233   1.0953   3.9145  -1.6712
 NI0  H17  H  HCH2  0   0.237   4.0430   3.5735  -0.9411
 NI0  H18  H  HCH3  0   0.241   4.4279   5.3908  -2.5899
 NI0  H19  H  HCH3  0   0.226   2.6985   5.5458  -2.8742
 NI0  H20  H  HCH3  0   0.226   3.3769   5.9800  -1.3067
 NI0  H21  H  HNR6  0   0.425   0.6059  -1.5864  -1.0395
 NI0  H22  H  HCH2  0   0.249   4.7367  -3.4672  -1.8519
 NI0  H23  H  HCH2  0   0.245   5.8676  -2.5487  -0.8984
 NI0  H24  H  HCH3  0   0.229   4.0546  -4.7731   0.1865
 NI0  H25  H  HCH3  0   0.233   5.7817  -4.9186  -0.1304
 NI0  H26  H  HCH3  0   0.224   5.2078  -3.8530   1.1521
 NI0  H27  H  HCH2  0   0.255   5.1515  -0.1350   1.8005
 NI0  H28  H  HCH2  0   0.247   5.9679  -1.4369   0.9622
 NI0  H29  H  HCH3  0   0.230   6.2165   0.0311  -1.0719
 NI0  H30  H  HCH3  0   0.233   5.3803   1.3330  -0.2245
 NI0  H31  H  HCH3  0   0.240   6.9499   0.7718   0.3507
 NI0  H5   H  HCH2  0   0.234   1.8245   4.3292  -0.1105
 NI0  H32  H  HCH2  0   0.236   3.3317   3.1459  -2.4901

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
 NI0  CAC  CAM  single    1.528  0.020  1.528
 NI0  CAM  CBA  single    1.500  0.020  1.500
 NI0  CAB  CAL  single    1.529  0.020  1.529
 NI0  CAL  CAW  single    1.500  0.020  1.500
 NI0  CBA  CAW  double    1.367  0.020  1.367
 NI0  CBA  CBB  single    1.444  0.020  1.444
 NI0  CAW  NAS  single    1.367  0.020  1.367
 NI0  OAE  CBB  double    1.223  0.020  1.223
 NI0  CBB  NAT  single    1.386  0.020  1.386
 NI0  NAS  CAZ  double    1.289  0.020  1.289
 NI0  NAT  CAZ  single    1.350  0.020  1.350
 NI0  CAZ  CAY  single    1.478  0.020  1.478
 NI0  CAA  CAK  single    1.522  0.020  1.522
 NI0  CAY  CAJ  aromatic  1.384  0.020  1.384
 NI0  CAY  CAX  aromatic  1.407  0.020  1.407
 NI0  CAK  CAN  single    1.514  0.020  1.514
 NI0  CAP  CAR  single    1.516  0.020  1.516
 NI0  CAP  NBC  single    1.447  0.020  1.447
 NI0  OAU  CAN  single    1.426  0.020  1.426
 NI0  OAU  CAX  single    1.327  0.020  1.327
 NI0  CAJ  CAV  aromatic  1.389  0.020  1.389
 NI0  CAX  CAI  aromatic  1.396  0.020  1.396
 NI0  CAR  NBD  single    1.465  0.020  1.465
 NI0  NBC  CAD  single    1.445  0.020  1.445
 NI0  NBC  CAO  single    1.447  0.020  1.447
 NI0  CAV  SBE  single    1.764  0.020  1.764
 NI0  CAV  CAH  aromatic  1.388  0.020  1.388
 NI0  OAG  SBE  double    1.454  0.020  1.454
 NI0  NBD  CAQ  single    1.464  0.020  1.464
 NI0  NBD  SBE  single    1.656  0.020  1.656
 NI0  CAI  CAH  aromatic  1.384  0.020  1.384
 NI0  CAO  CAQ  single    1.517  0.020  1.517
 NI0  SBE  OAF  double    1.453  0.020  1.453
 NI0  CAQ  H1   single    0.970  0.020  1.090
 NI0  CAQ  H2   single    0.970  0.020  1.090
 NI0  CAO  H3   single    0.970  0.020  1.090
 NI0  CAO  H4   single    0.970  0.020  1.090
 NI0  CAD  H6   single    0.970  0.020  1.090
 NI0  CAD  H7   single    0.970  0.020  1.090
 NI0  CAD  H8   single    0.970  0.020  1.090
 NI0  CAP  H9   single    0.970  0.020  1.090
 NI0  CAP  H10  single    0.970  0.020  1.090
 NI0  CAR  H11  single    0.970  0.020  1.090
 NI0  CAR  H12  single    0.970  0.020  1.090
 NI0  CAJ  H13  single    0.930  0.020  1.080
 NI0  CAH  H14  single    0.930  0.020  1.080
 NI0  CAI  H15  single    0.930  0.020  1.080
 NI0  CAN  H16  single    0.970  0.020  1.090
 NI0  CAK  H17  single    0.970  0.020  1.090
 NI0  CAA  H18  single    0.970  0.020  1.090
 NI0  CAA  H19  single    0.970  0.020  1.090
 NI0  CAA  H20  single    0.970  0.020  1.090
 NI0  NAT  H21  single    0.860  0.020  1.020
 NI0  CAM  H22  single    0.970  0.020  1.090
 NI0  CAM  H23  single    0.970  0.020  1.090
 NI0  CAC  H24  single    0.970  0.020  1.090
 NI0  CAC  H25  single    0.970  0.020  1.090
 NI0  CAC  H26  single    0.970  0.020  1.090
 NI0  CAL  H27  single    0.970  0.020  1.090
 NI0  CAL  H28  single    0.970  0.020  1.090
 NI0  CAB  H29  single    0.970  0.020  1.090
 NI0  CAB  H30  single    0.970  0.020  1.090
 NI0  CAB  H31  single    0.970  0.020  1.090
 NI0  CAN  H5   single    0.970  0.020  1.090
 NI0  CAK  H32  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
 NI0  H2   CAQ  H1   108.69  3.000
 NI0  H2   CAQ  NBD  109.94  3.000
 NI0  H1   CAQ  NBD  111.10  3.000
 NI0  H2   CAQ  CAO  108.77  3.000
 NI0  H1   CAQ  CAO  109.65  3.000
 NI0  NBD  CAQ  CAO  108.66  3.000
 NI0  H4   CAO  H3   107.31  3.000
 NI0  H4   CAO  NBC  109.32  3.000
 NI0  H3   CAO  NBC  111.91  3.000
 NI0  H4   CAO  CAQ  108.25  3.000
 NI0  H3   CAO  CAQ  109.05  3.000
 NI0  NBC  CAO  CAQ  110.87  3.000
 NI0  CAP  NBC  CAD  111.73  3.000
 NI0  CAD  NBC  CAO  111.93  3.000
 NI0  CAP  NBC  CAO  110.14  3.000
 NI0  H8   CAD  H7   107.77  3.000
 NI0  H8   CAD  H6   107.85  3.000
 NI0  H7   CAD  H6   107.94  3.000
 NI0  H8   CAD  NBC  113.28  3.000
 NI0  H7   CAD  NBC  109.90  3.000
 NI0  H6   CAD  NBC  109.92  3.000
 NI0  H10  CAP  H9   107.39  3.000
 NI0  H10  CAP  CAR  108.01  3.000
 NI0  H9   CAP  CAR  109.22  3.000
 NI0  H10  CAP  NBC  109.38  3.000
 NI0  H9   CAP  NBC  111.99  3.000
 NI0  CAR  CAP  NBC  110.71  3.000
 NI0  H12  CAR  H11  108.60  3.000
 NI0  H12  CAR  NBD  110.65  3.000
 NI0  H11  CAR  NBD  109.98  3.000
 NI0  H12  CAR  CAP  109.36  3.000
 NI0  H11  CAR  CAP  109.02  3.000
 NI0  NBD  CAR  CAP  109.20  3.000
 NI0  SBE  NBD  CAR  116.03  3.000
 NI0  SBE  NBD  CAQ  116.90  3.000
 NI0  CAR  NBD  CAQ  112.20  3.000
 NI0  CAV  SBE  OAG  107.91  3.000
 NI0  OAG  SBE  OAF  119.68  3.000
 NI0  CAV  SBE  OAF  108.25  3.000
 NI0  OAF  SBE  NBD  107.00  3.000
 NI0  OAG  SBE  NBD  106.85  3.000
 NI0  CAV  SBE  NBD  106.43  3.000
 NI0  CAH  CAV  CAJ  120.20  3.000
 NI0  CAH  CAV  SBE  120.14  3.000
 NI0  CAJ  CAV  SBE  119.61  3.000
 NI0  H13  CAJ  CAY  119.41  3.000
 NI0  H13  CAJ  CAV  120.42  3.000
 NI0  CAY  CAJ  CAV  120.16  3.000
 NI0  H14  CAH  CAI  118.91  3.000
 NI0  H14  CAH  CAV  121.02  3.000
 NI0  CAI  CAH  CAV  120.08  3.000
 NI0  H15  CAI  CAX  120.99  3.000
 NI0  H15  CAI  CAH  118.68  3.000
 NI0  CAX  CAI  CAH  120.33  3.000
 NI0  CAY  CAX  OAU  116.46  3.000
 NI0  OAU  CAX  CAI  124.26  3.000
 NI0  CAY  CAX  CAI  119.27  3.000
 NI0  CAN  OAU  CAX  120.14  3.000
 NI0  H5   CAN  H16  107.96  3.000
 NI0  H5   CAN  CAK  110.45  3.000
 NI0  H16  CAN  CAK  110.68  3.000
 NI0  H5   CAN  OAU  110.16  3.000
 NI0  H16  CAN  OAU  109.83  3.000
 NI0  CAK  CAN  OAU  107.78  3.000
 NI0  H32  CAK  H17  107.06  3.000
 NI0  H32  CAK  CAA  110.02  3.000
 NI0  H17  CAK  CAA  109.89  3.000
 NI0  H32  CAK  CAN  109.47  3.000
 NI0  H17  CAK  CAN  109.18  3.000
 NI0  CAA  CAK  CAN  111.13  3.000
 NI0  H20  CAA  H19  107.74  3.000
 NI0  H20  CAA  H18  107.68  3.000
 NI0  H19  CAA  H18  107.60  3.000
 NI0  H20  CAA  CAK  111.41  3.000
 NI0  H19  CAA  CAK  111.51  3.000
 NI0  H18  CAA  CAK  110.71  3.000
 NI0  CAZ  CAY  CAX  120.48  3.000
 NI0  CAX  CAY  CAJ  119.95  3.000
 NI0  CAZ  CAY  CAJ  119.57  3.000
 NI0  NAT  CAZ  NAS  122.54  3.000
 NI0  NAT  CAZ  CAY  116.70  3.000
 NI0  NAS  CAZ  CAY  120.73  3.000
 NI0  CAW  NAS  CAZ  118.08  3.000
 NI0  H21  NAT  CBB  116.89  3.000
 NI0  H21  NAT  CAZ  119.38  3.000
 NI0  CBB  NAT  CAZ  123.71  3.000
 NI0  CBA  CBB  OAE  126.22  3.000
 NI0  OAE  CBB  NAT  120.08  3.000
 NI0  CBA  CBB  NAT  113.70  3.000
 NI0  CAW  CBA  CAM  124.06  3.000
 NI0  CAW  CBA  CBB  118.71  3.000
 NI0  CAM  CBA  CBB  117.21  3.000
 NI0  H23  CAM  H22  105.93  3.000
 NI0  H23  CAM  CAC  109.74  3.000
 NI0  H22  CAM  CAC  109.29  3.000
 NI0  H23  CAM  CBA  110.24  3.000
 NI0  H22  CAM  CBA  109.13  3.000
 NI0  CAC  CAM  CBA  112.30  3.000
 NI0  H26  CAC  H25  107.89  3.000
 NI0  H26  CAC  H24  107.90  3.000
 NI0  H25  CAC  H24  107.81  3.000
 NI0  H26  CAC  CAM  111.09  3.000
 NI0  H25  CAC  CAM  110.91  3.000
 NI0  H24  CAC  CAM  111.09  3.000
 NI0  CAL  CAW  CBA  123.04  3.000
 NI0  CBA  CAW  NAS  123.23  3.000
 NI0  CAL  CAW  NAS  113.70  3.000
 NI0  H28  CAL  H27  106.76  3.000
 NI0  H28  CAL  CAB  109.96  3.000
 NI0  H27  CAL  CAB  109.33  3.000
 NI0  H28  CAL  CAW  111.36  3.000
 NI0  H27  CAL  CAW  108.14  3.000
 NI0  CAB  CAL  CAW  111.16  3.000
 NI0  H31  CAB  H30  107.96  3.000
 NI0  H31  CAB  H29  107.96  3.000
 NI0  H30  CAB  H29  107.95  3.000
 NI0  H31  CAB  CAL  110.52  3.000
 NI0  H30  CAB  CAL  111.06  3.000
 NI0  H29  CAB  CAL  111.26  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
 NI0  CONST_01  CAX  CAY  CAJ  CAV     0.00   0.0  0
 NI0  CONST_02  CAX  CAI  CAH  CAV     0.00   0.0  0
 NI0  CONST_03  CAI  CAX  CAY  CAJ     0.00   0.0  0
 NI0  CONST_04  CAI  CAH  CAV  CAJ     0.00   0.0  0
 NI0  CONST_05  CAY  CAJ  CAV  CAH     0.00   0.0  0
 NI0  CONST_06  CAY  CAX  CAI  CAH     0.00   0.0  0
 NI0  CONST_07  CAZ  CAY  CAJ  CAV   180.00   0.0  0
 NI0  CONST_08  CAZ  CAY  CAX  CAI   180.00   0.0  0
 NI0  CONST_09  CAW  NAS  CAZ  CAY   180.00   0.0  0
 NI0  CONST_10  CBB  NAT  CAZ  CAY   180.00   0.0  0
 NI0  CONST_11  CBA  CBB  NAT  CAZ     0.00   0.0  0
 NI0  CONST_12  CBB  NAT  CAZ  NAS     0.00   0.0  0
 NI0  CONST_13  CAW  NAS  CAZ  NAT     0.00   0.0  0
 NI0  CONST_14  CAY  CAJ  CAV  SBE   180.00   0.0  0
 NI0  CONST_15  CAI  CAH  CAV  SBE   180.00   0.0  0
 NI0  CONST_16  OAU  CAX  CAY  CAJ   180.00   0.0  0
 NI0  CONST_17  OAU  CAX  CAI  CAH   180.00   0.0  0
 NI0  CONST_18  CAZ  CAY  CAX  OAU     0.00   0.0  0
 NI0  CONST_19  OAE  CBB  NAT  CAZ   180.00   0.0  0
 NI0  CONST_20  H15  CAI  CAH  CAV   180.00   0.0  0
 NI0  CONST_21  H14  CAH  CAV  CAJ   180.00   0.0  0
 NI0  CONST_22  H13  CAJ  CAV  CAH   180.00   0.0  0
 NI0  CONST_23  H21  NAT  CAZ  CAY     0.00   0.0  0
 NI0  Var_01    CAP  CAR  NBD  CAQ   -56.78  30.0  1
 NI0  Var_02    CAP  NBC  CAO  CAQ    59.76  30.0  1
 NI0  Var_03    CAR  CAP  NBC  CAO   -59.18  30.0  1
 NI0  Var_04    CAR  NBD  CAQ  CAO    56.93  30.0  1
 NI0  Var_05    NBD  CAR  CAP  NBC    57.02  30.0  1
 NI0  Var_06    NBD  CAQ  CAO  NBC   -57.78  30.0  1
 NI0  Var_07    NAS  CAZ  CAY  CAJ  -121.78  30.0  2
 NI0  Var_08    CAV  SBE  NBD  CAQ   -73.63  30.0  3
 NI0  Var_09    CAJ  CAV  SBE  NBD   -90.63  30.0  3
 NI0  Var_10    CAY  CAX  OAU  CAN   178.08  30.0  2
 NI0  Var_11    CAB  CAL  CAW  NAS   -82.74  30.0  2
 NI0  Var_12    CAC  CAM  CBA  CBB   -86.21  30.0  2
 NI0  Var_13    H6   CAD  NBC  CAO    57.25  30.0  3
 NI0  Var_14    CAK  CAN  OAU  CAX   179.17  30.0  3
 NI0  Var_15    H24  CAC  CAM  CBA    58.93  30.0  3
 NI0  Var_16    H29  CAB  CAL  CAW   -62.56  30.0  3
 NI0  Var_17    CAA  CAK  CAN  OAU   179.40  30.0  2
 NI0  Var_18    H18  CAA  CAK  CAN   178.60  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
 NI0  plan-1  SBE  0.020
 NI0  plan-1  CAV  0.020
 NI0  plan-1  CAJ  0.020
 NI0  plan-1  CAH  0.020
 NI0  plan-1  CAI  0.020
 NI0  plan-1  CAX  0.020
 NI0  plan-1  OAU  0.020
 NI0  plan-1  CAY  0.020
 NI0  plan-1  CAZ  0.020
 NI0  plan-1  H13  0.020
 NI0  plan-1  H14  0.020
 NI0  plan-1  H15  0.020
 NI0  plan-2  CAY  0.020
 NI0  plan-2  CAZ  0.020
 NI0  plan-2  NAS  0.020
 NI0  plan-2  NAT  0.020
 NI0  plan-2  CBB  0.020
 NI0  plan-2  OAE  0.020
 NI0  plan-2  CBA  0.020
 NI0  plan-2  CAM  0.020
 NI0  plan-2  CAW  0.020
 NI0  plan-2  CAL  0.020
 NI0  plan-2  H21  0.020

