# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:09:06 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOc1ccc(cc1C2=NC3=C(CCC3)C(=O)N2)[S](=O)(=O)N4CCN(C)CC4
#
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
 NI5  NI5  2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one  ligand  58  30  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NI5
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
 NI5  CAP  C  CH2   0  -0.328  -4.8181   0.1239   0.5334
 NI5  CAN  C  CH2   0  -0.282  -4.0481   0.6784   1.7197
 NI5  NBB  N  NT    0  -0.412  -3.5934  -0.3939   2.5827
 NI5  CAB  C  CH3   0  -0.517  -2.9346   0.1206   3.7623
 NI5  CAO  C  CH2   0  -0.280  -2.7314  -1.2977   1.8475
 NI5  CAQ  C  CH2   0  -0.332  -3.4723  -1.9031   0.6678
 NI5  NBC  N  N     0  -0.559  -4.0516  -0.8801  -0.2016
 NI5  SBD  S  S     0   1.377  -3.3170  -0.5016  -1.6185
 NI5  OAD  O  OS    0  -0.653  -2.9400  -1.7593  -2.2445
 NI5  OAE  O  OS    0  -0.653  -4.1986   0.4168  -2.3210
 NI5  CAU  C  CR6   0  -0.219  -1.8236   0.3673  -1.2505
 NI5  CAH  C  CR16  0  -0.239  -0.6437  -0.3412  -1.0701
 NI5  CAF  C  CR16  0  -0.217  -1.8458   1.7419  -1.0663
 NI5  CAG  C  CR16  0  -0.379  -0.6965   2.4100  -0.6849
 NI5  CAW  C  CR6   0   0.419   0.4924   1.7079  -0.4777
 NI5  OAT  O  O2    0  -0.445   1.6421   2.2757  -0.1337
 NI5  CAK  C  CH2   0  -0.179   1.7020   3.6853   0.0726
 NI5  CAI  C  CH2   0  -0.458   3.1215   4.0452   0.4528
 NI5  CAA  C  CH3   0  -0.674   3.2540   5.5405   0.7062
 NI5  CAX  C  CR6   0  -0.122   0.5087   0.3148  -0.6722
 NI5  CAY  C  CR6   0   0.471   1.7464  -0.4631  -0.4561
 NI5  NAR  N  N     0  -0.435   2.3489  -0.4338   0.6907
 NI5  CAV  C  CR6   0   0.226   3.4440  -1.2252   0.7928
 NI5  CAL  C  CH2   0  -0.506   4.2964  -1.3064   2.0216
 NI5  CAJ  C  CH2   0  -0.465   5.1540  -2.5572   1.7631
 NI5  CAM  C  CH2   0  -0.480   5.1655  -2.7532   0.2319
 NI5  CAZ  C  CR6   0  -0.132   3.9304  -2.0263  -0.1937
 NI5  CBA  C  CR6   0   0.512   3.2856  -2.0580  -1.4667
 NI5  OAC  O  O     0  -0.474   3.6075  -2.7033  -2.4534
 NI5  NAS  N  NR16  0  -0.680   2.1705  -1.2190  -1.4942
 NI5  H1   H  HCH2  0   0.260  -5.7270  -0.3694   0.8880
 NI5  H2   H  HCH2  0   0.277  -5.1298   0.9281  -0.1295
 NI5  H3   H  HCH2  0   0.200  -3.2062   1.2968   1.3652
 NI5  H4   H  HCH2  0   0.252  -4.7136   1.3371   2.2826
 NI5  H6   H  HCH3  0   0.236  -3.6174   0.7604   4.3226
 NI5  H7   H  HCH3  0   0.236  -2.6377  -0.7036   4.4127
 NI5  H8   H  HCH3  0   0.194  -2.0330   0.7088   3.5314
 NI5  H9   H  HCH2  0   0.199  -1.8144  -0.7905   1.5010
 NI5  H10  H  HCH2  0   0.253  -2.4163  -2.1111   2.5051
 NI5  H11  H  HCH2  0   0.276  -2.8169  -2.5611   0.1005
 NI5  H12  H  HCH2  0   0.263  -4.2997  -2.5146   1.0365
 NI5  H13  H  HCR6  0   0.298  -0.6190  -1.4138  -1.2179
 NI5  H14  H  HCR6  0   0.296  -2.7528   2.3109  -1.2211
 NI5  H15  H  HCR6  0   0.303  -0.7398   3.4827  -0.5609
 NI5  H16  H  HCH2  0   0.232   1.4053   4.2104  -0.8413
 NI5  H17  H  HCH2  0   0.233   1.0070   3.9764   0.8675
 NI5  H18  H  HCH2  0   0.235   3.4113   3.4882   1.3469
 NI5  H19  H  HCH2  0   0.235   3.8006   3.7426  -0.3477
 NI5  H20  H  HCH3  0   0.241   4.2777   5.7978   0.9746
 NI5  H21  H  HCH3  0   0.226   2.9880   6.1205  -0.1789
 NI5  H22  H  HCH3  0   0.226   2.6066   5.8664   1.5218
 NI5  H23  H  HCH2  0   0.261   4.9050  -0.3994   2.0972
 NI5  H24  H  HCH2  0   0.260   3.7052  -1.3676   2.9364
 NI5  H25  H  HCH2  0   0.243   6.1568  -2.4700   2.1782
 NI5  H26  H  HCH2  0   0.245   4.6803  -3.4210   2.2320
 NI5  H27  H  HCH2  0   0.250   6.0524  -2.3056  -0.2271
 NI5  H28  H  HCH2  0   0.251   5.1618  -3.8069  -0.0515
 NI5  H29  H  HNR6  0   0.432   1.6666  -1.1619  -2.3716

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
 NI5  OAE  SBD  double    1.454  0.020  1.454
 NI5  CAF  CAG  aromatic  1.383  0.020  1.383
 NI5  CAF  CAU  aromatic  1.387  0.020  1.387
 NI5  SBD  OAD  double    1.455  0.020  1.455
 NI5  SBD  CAU  single    1.767  0.020  1.767
 NI5  SBD  NBC  single    1.640  0.020  1.640
 NI5  CAP  CAN  single    1.519  0.020  1.519
 NI5  CAP  NBC  single    1.461  0.020  1.461
 NI5  CAG  CAW  aromatic  1.396  0.020  1.396
 NI5  CAN  NBB  single    1.450  0.020  1.450
 NI5  CAU  CAH  aromatic  1.388  0.020  1.388
 NI5  NBC  CAQ  single    1.462  0.020  1.462
 NI5  CAK  CAI  single    1.513  0.020  1.513
 NI5  CAK  OAT  single    1.426  0.020  1.426
 NI5  CAW  OAT  single    1.328  0.020  1.328
 NI5  CAW  CAX  aromatic  1.407  0.020  1.407
 NI5  NBB  CAB  single    1.446  0.020  1.446
 NI5  NBB  CAO  single    1.449  0.020  1.449
 NI5  CAI  CAA  single    1.522  0.020  1.522
 NI5  CAH  CAX  aromatic  1.384  0.020  1.384
 NI5  CAQ  CAO  single    1.519  0.020  1.519
 NI5  CAX  CAY  single    1.478  0.020  1.478
 NI5  CAY  NAS  single    1.352  0.020  1.352
 NI5  CAY  NAR  double    1.296  0.020  1.296
 NI5  NAS  CBA  single    1.396  0.020  1.396
 NI5  NAR  CAV  single    1.355  0.020  1.355
 NI5  CBA  OAC  double    1.222  0.020  1.222
 NI5  CBA  CAZ  single    1.427  0.020  1.427
 NI5  CAV  CAZ  double    1.361  0.020  1.361
 NI5  CAV  CAL  single    1.498  0.020  1.498
 NI5  CAZ  CAM  single    1.495  0.020  1.495
 NI5  CAL  CAJ  single    1.538  0.020  1.538
 NI5  CAM  CAJ  single    1.544  0.020  1.544
 NI5  CAP  H1   single    0.970  0.020  1.090
 NI5  CAP  H2   single    0.970  0.020  1.090
 NI5  CAN  H3   single    0.970  0.020  1.090
 NI5  CAN  H4   single    0.970  0.020  1.090
 NI5  CAB  H6   single    0.970  0.020  1.090
 NI5  CAB  H7   single    0.970  0.020  1.090
 NI5  CAB  H8   single    0.970  0.020  1.090
 NI5  CAO  H9   single    0.970  0.020  1.090
 NI5  CAO  H10  single    0.970  0.020  1.090
 NI5  CAQ  H11  single    0.970  0.020  1.090
 NI5  CAQ  H12  single    0.970  0.020  1.090
 NI5  CAH  H13  single    0.930  0.020  1.080
 NI5  CAF  H14  single    0.930  0.020  1.080
 NI5  CAG  H15  single    0.930  0.020  1.080
 NI5  CAK  H16  single    0.970  0.020  1.090
 NI5  CAK  H17  single    0.970  0.020  1.090
 NI5  CAI  H18  single    0.970  0.020  1.090
 NI5  CAI  H19  single    0.970  0.020  1.090
 NI5  CAA  H20  single    0.970  0.020  1.090
 NI5  CAA  H21  single    0.970  0.020  1.090
 NI5  CAA  H22  single    0.970  0.020  1.090
 NI5  CAL  H23  single    0.970  0.020  1.090
 NI5  CAL  H24  single    0.970  0.020  1.090
 NI5  CAJ  H25  single    0.970  0.020  1.090
 NI5  CAJ  H26  single    0.970  0.020  1.090
 NI5  CAM  H27  single    0.970  0.020  1.090
 NI5  CAM  H28  single    0.970  0.020  1.090
 NI5  NAS  H29  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
 NI5  H2   CAP  H1   107.04  3.000
 NI5  H2   CAP  NBC  110.59  3.000
 NI5  H1   CAP  NBC  106.80  3.000
 NI5  H2   CAP  CAN  110.57  3.000
 NI5  H1   CAP  CAN  109.44  3.000
 NI5  NBC  CAP  CAN  112.19  3.000
 NI5  H4   CAN  H3   107.00  3.000
 NI5  H4   CAN  NBB  109.29  3.000
 NI5  H3   CAN  NBB  111.51  3.000
 NI5  H4   CAN  CAP  108.28  3.000
 NI5  H3   CAN  CAP  109.91  3.000
 NI5  NBB  CAN  CAP  110.73  3.000
 NI5  CAO  NBB  CAB  111.39  3.000
 NI5  CAO  NBB  CAN  110.24  3.000
 NI5  CAB  NBB  CAN  111.44  3.000
 NI5  H8   CAB  H7   107.80  3.000
 NI5  H8   CAB  H6   107.88  3.000
 NI5  H7   CAB  H6   107.89  3.000
 NI5  H8   CAB  NBB  113.09  3.000
 NI5  H7   CAB  NBB  109.97  3.000
 NI5  H6   CAB  NBB  110.04  3.000
 NI5  H10  CAO  H9   106.95  3.000
 NI5  H10  CAO  CAQ  108.15  3.000
 NI5  H9   CAO  CAQ  110.15  3.000
 NI5  H10  CAO  NBB  109.30  3.000
 NI5  H9   CAO  NBB  111.52  3.000
 NI5  CAQ  CAO  NBB  110.63  3.000
 NI5  H12  CAQ  H11  107.07  3.000
 NI5  H12  CAQ  NBC  106.98  3.000
 NI5  H11  CAQ  NBC  110.59  3.000
 NI5  H12  CAQ  CAO  109.29  3.000
 NI5  H11  CAQ  CAO  110.61  3.000
 NI5  NBC  CAQ  CAO  112.10  3.000
 NI5  SBD  NBC  CAQ  119.84  3.000
 NI5  CAQ  NBC  CAP  112.92  3.000
 NI5  SBD  NBC  CAP  120.72  3.000
 NI5  CAU  SBD  OAE  107.61  3.000
 NI5  CAU  SBD  OAD  107.21  3.000
 NI5  OAE  SBD  OAD  119.69  3.000
 NI5  CAU  SBD  NBC  108.19  3.000
 NI5  OAD  SBD  NBC  106.76  3.000
 NI5  OAE  SBD  NBC  106.95  3.000
 NI5  CAF  CAU  CAH  120.14  3.000
 NI5  CAH  CAU  SBD  119.65  3.000
 NI5  CAF  CAU  SBD  120.10  3.000
 NI5  H13  CAH  CAX  119.31  3.000
 NI5  H13  CAH  CAU  120.48  3.000
 NI5  CAX  CAH  CAU  120.20  3.000
 NI5  H14  CAF  CAG  118.82  3.000
 NI5  H14  CAF  CAU  121.04  3.000
 NI5  CAG  CAF  CAU  120.14  3.000
 NI5  H15  CAG  CAW  121.07  3.000
 NI5  H15  CAG  CAF  118.55  3.000
 NI5  CAW  CAG  CAF  120.37  3.000
 NI5  CAX  CAW  OAT  116.70  3.000
 NI5  CAX  CAW  CAG  119.17  3.000
 NI5  OAT  CAW  CAG  124.12  3.000
 NI5  CAK  OAT  CAW  119.78  3.000
 NI5  H17  CAK  H16  107.84  3.000
 NI5  H17  CAK  CAI  110.47  3.000
 NI5  H16  CAK  CAI  110.48  3.000
 NI5  H17  CAK  OAT  109.95  3.000
 NI5  H16  CAK  OAT  109.99  3.000
 NI5  CAI  CAK  OAT  108.11  3.000
 NI5  H19  CAI  H18  107.07  3.000
 NI5  H19  CAI  CAA  109.87  3.000
 NI5  H18  CAI  CAA  109.96  3.000
 NI5  H19  CAI  CAK  109.47  3.000
 NI5  H18  CAI  CAK  109.47  3.000
 NI5  CAA  CAI  CAK  110.92  3.000
 NI5  H22  CAA  H21  107.64  3.000
 NI5  H22  CAA  H20  107.63  3.000
 NI5  H21  CAA  H20  107.67  3.000
 NI5  H22  CAA  CAI  111.48  3.000
 NI5  H21  CAA  CAI  111.46  3.000
 NI5  H20  CAA  CAI  110.78  3.000
 NI5  CAY  CAX  CAW  120.72  3.000
 NI5  CAY  CAX  CAH  119.32  3.000
 NI5  CAW  CAX  CAH  119.96  3.000
 NI5  NAS  CAY  NAR  123.10  3.000
 NI5  NAR  CAY  CAX  120.46  3.000
 NI5  NAS  CAY  CAX  116.40  3.000
 NI5  CAV  NAR  CAY  115.42  3.000
 NI5  CAZ  CAV  CAL  111.06  3.000
 NI5  CAL  CAV  NAR  123.61  3.000
 NI5  CAZ  CAV  NAR  125.32  3.000
 NI5  H24  CAL  H23  106.84  3.000
 NI5  H24  CAL  CAJ  113.42  3.000
 NI5  H23  CAL  CAJ  112.04  3.000
 NI5  H24  CAL  CAV  112.49  3.000
 NI5  H23  CAL  CAV  109.15  3.000
 NI5  CAJ  CAL  CAV  102.92  3.000
 NI5  H26  CAJ  H25  107.42  3.000
 NI5  H26  CAJ  CAM  109.21  3.000
 NI5  H25  CAJ  CAM  112.42  3.000
 NI5  H26  CAJ  CAL  109.24  3.000
 NI5  H25  CAJ  CAL  112.59  3.000
 NI5  CAM  CAJ  CAL  105.90  3.000
 NI5  H28  CAM  H27  106.79  3.000
 NI5  H28  CAM  CAZ  113.13  3.000
 NI5  H27  CAM  CAZ  110.57  3.000
 NI5  H28  CAM  CAJ  112.34  3.000
 NI5  H27  CAM  CAJ  111.72  3.000
 NI5  CAZ  CAM  CAJ  102.38  3.000
 NI5  CBA  CAZ  CAM  128.04  3.000
 NI5  CAM  CAZ  CAV  112.04  3.000
 NI5  CBA  CAZ  CAV  119.88  3.000
 NI5  NAS  CBA  OAC  120.79  3.000
 NI5  OAC  CBA  CAZ  127.79  3.000
 NI5  NAS  CBA  CAZ  111.41  3.000
 NI5  H29  NAS  CBA  116.62  3.000
 NI5  H29  NAS  CAY  118.50  3.000
 NI5  CBA  NAS  CAY  124.85  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
 NI5  CONST_01  CAW  CAG  CAF  CAU     0.00   0.0  0
 NI5  CONST_02  CAW  CAX  CAH  CAU     0.00   0.0  0
 NI5  CONST_03  CAG  CAF  CAU  CAH     0.00   0.0  0
 NI5  CONST_04  CAG  CAW  CAX  CAH     0.00   0.0  0
 NI5  CONST_05  CAX  CAW  CAG  CAF     0.00   0.0  0
 NI5  CONST_06  CAX  CAH  CAU  CAF     0.00   0.0  0
 NI5  CONST_07  CAY  CAX  CAH  CAU   180.00   0.0  0
 NI5  CONST_08  CAY  CAX  CAW  CAG   180.00   0.0  0
 NI5  CONST_09  CBA  NAS  CAY  CAX   180.00   0.0  0
 NI5  CONST_10  CAV  NAR  CAY  CAX   180.00   0.0  0
 NI5  CONST_11  CAZ  CBA  NAS  CAY     0.00   0.0  0
 NI5  CONST_12  CBA  NAS  CAY  NAR     0.00   0.0  0
 NI5  CONST_13  NAS  CAY  NAR  CAV     0.00   0.0  0
 NI5  CONST_14  CAG  CAF  CAU  SBD   180.00   0.0  0
 NI5  CONST_15  CAX  CAH  CAU  SBD   180.00   0.0  0
 NI5  CONST_16  OAT  CAW  CAX  CAH   180.00   0.0  0
 NI5  CONST_17  OAT  CAW  CAG  CAF   180.00   0.0  0
 NI5  CONST_18  CAY  CAX  CAW  OAT     0.00   0.0  0
 NI5  CONST_19  OAC  CBA  NAS  CAY   180.00   0.0  0
 NI5  CONST_20  H15  CAG  CAF  CAU   180.00   0.0  0
 NI5  CONST_21  H14  CAF  CAU  CAH   180.00   0.0  0
 NI5  CONST_22  H13  CAH  CAU  CAF   180.00   0.0  0
 NI5  CONST_23  H29  NAS  CAY  CAX     0.00   0.0  0
 NI5  Var_01    CAO  NBB  CAN  CAP    59.56  30.0  1
 NI5  Var_02    CAO  CAQ  NBC  CAP   -49.43  30.0  1
 NI5  Var_03    CAQ  NBC  CAP  CAN    49.24  30.0  1
 NI5  Var_04    CAQ  CAO  NBB  CAN   -59.74  30.0  1
 NI5  Var_05    NBC  CAP  CAN  NBB   -54.17  30.0  1
 NI5  Var_06    NBC  CAQ  CAO  NBB    54.55  30.0  1
 NI5  Var_07    NAS  CAY  CAX  CAH    55.51  30.0  2
 NI5  Var_08    CAJ  CAL  CAV  NAR   166.40  30.0  1
 NI5  Var_09    CAJ  CAM  CAZ  CAV    14.39  30.0  1
 NI5  Var_10    CAM  CAJ  CAL  CAV    22.84  30.0  1
 NI5  Var_11    CAZ  CAM  CAJ  CAL   -22.67  30.0  1
 NI5  Var_12    CAU  SBD  NBC  CAP    78.79  30.0  1
 NI5  Var_13    CAF  CAU  SBD  NBC   -86.53  30.0  2
 NI5  Var_14    CAX  CAW  OAT  CAK   179.65  30.0  1
 NI5  Var_15    H6   CAB  NBB  CAN    59.06  30.0  3
 NI5  Var_16    CAI  CAK  OAT  CAW   179.92  30.0  1
 NI5  Var_17    CAA  CAI  CAK  OAT  -179.28  30.0  3
 NI5  Var_18    H20  CAA  CAI  CAK  -179.71  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
 NI5  plan-1  SBD  0.020
 NI5  plan-1  CAU  0.020
 NI5  plan-1  CAH  0.020
 NI5  plan-1  CAF  0.020
 NI5  plan-1  CAG  0.020
 NI5  plan-1  CAW  0.020
 NI5  plan-1  OAT  0.020
 NI5  plan-1  CAX  0.020
 NI5  plan-1  CAY  0.020
 NI5  plan-1  H13  0.020
 NI5  plan-1  H14  0.020
 NI5  plan-1  H15  0.020
 NI5  plan-2  CAX  0.020
 NI5  plan-2  CAY  0.020
 NI5  plan-2  NAR  0.020
 NI5  plan-2  CAV  0.020
 NI5  plan-2  CAL  0.020
 NI5  plan-2  CAM  0.020
 NI5  plan-2  CAZ  0.020
 NI5  plan-2  CBA  0.020
 NI5  plan-2  OAC  0.020
 NI5  plan-2  NAS  0.020
 NI5  plan-2  H29  0.020

