# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 13:58:11 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-cyclopropyl-4-[4-(3,4-dichlorophenyl)-2-(1-methylpiperidin-4-yl)-1-propyl-1H-imidazol-5-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCn1c(nc(c2ccc(Cl)c(Cl)c2)c1c3ccnc(NC4CC4)n3)C5CCN(C)CC5
#
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
 984  984  N-cyclopropyl-4-[4-(3,4-dichlorophenyl)-2-(1-methylpiperidin-4-yl)-1-propyl-1H-imidazol-5-yl]pyrimidin-2-amine  ligand  63  33  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_984
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
 984  N1    N   NR5   0  -0.512   1.1837   0.4156   1.9560
 984  C2    C   CR5   0   0.528   0.0724   0.1632   2.6936
 984  N3    N   N     0  -0.457  -0.9648  -0.0569   1.9250
 984  C4    C   CR5   0   0.083  -0.5237   0.0347   0.6401
 984  C5    C   CR5   0   0.297   0.8223   0.3203   0.6335
 984  C6    C   CH2   0  -0.334   2.5409   0.5240   2.4690
 984  C7    C   CH2   0  -0.436   3.1552  -0.8323   2.7912
 984  C10   C   CH3   0  -0.667   4.5926  -0.6829   3.2664
 984  C16   C   CH1   0  -0.402   0.0272   0.1303   4.1857
 984  C17   C   CH2   0  -0.410  -0.9698   1.1530   4.7363
 984  C18   C   CH2   0  -0.282  -1.0451   1.0619   6.2516
 984  N19   N   NT    0  -0.409  -1.4087  -0.2747   6.6829
 984  C20   C   CH2   0  -0.281  -0.4487  -1.2576   6.2191
 984  C21   C   CH2   0  -0.418  -0.3481  -1.2623   4.7024
 984  C31   C   CH3   0  -0.518  -1.5764  -0.3372   8.1164
 984  C35   C   CR6   0   0.041  -1.4465  -0.1402  -0.4811
 984  C36   C   CR6   0   0.156   1.7347   0.5170  -0.4969
 984  C37   C   CR16  0  -0.280  -1.2468   0.4911  -1.7069
 984  C38   C   CR6   0   0.022  -2.1226   0.2863  -2.7589
 984  C39   C   CR6   0  -0.023  -3.2331  -0.5328  -2.5980
 984  C40   C   CR16  0  -0.204  -3.4577  -1.1420  -1.3722
 984  C41   C   CR16  0  -0.305  -2.5739  -0.9474  -0.3262
 984  CL45  CL  CL    0  -0.098  -1.8195   1.0716  -4.2640
 984  CL46  CL  CL    0  -0.100  -4.3320  -0.7959  -3.8978
 984  C47   C   CR16  0  -0.389   2.4808   1.6844  -0.6452
 984  C48   C   CR16  0  -0.011   3.2405   1.7731  -1.7988
 984  N49   N   N     0  -0.448   3.2563   0.8370  -2.7325
 984  C50   C   CR6   0   0.588   2.4890  -0.2346  -2.5042
 984  N51   N   N     0  -0.455   1.7510  -0.4444  -1.4077
 984  N54   N   NH1   0  -0.663   2.4462  -1.1939  -3.4470
 984  C55   C   CH1   0  -0.083   3.0530  -1.0678  -4.7270
 984  C56   C   CH2   0  -0.513   2.3197  -1.6481  -5.8915
 984  C57   C   CH2   0  -0.479   2.4258  -0.1611  -5.7406
 984  HC61  H   HCH2  0   0.273   2.5254   1.1627   3.3521
 984  HC62  H   HCH2  0   0.275   3.1488   1.0399   1.7284
 984  HC71  H   HCH2  0   0.237   3.1153  -1.4652   1.9010
 984  HC72  H   HCH2  0   0.237   2.5595  -1.3338   3.5585
 984  H101  H   HCH3  0   0.240   5.0243  -1.6511   3.5169
 984  H102  H   HCH3  0   0.227   5.2183  -0.2298   2.4957
 984  H103  H   HCH3  0   0.226   4.6518  -0.0534   4.1558
 984  H16   H   HCH1  0   0.255   1.0155   0.3833   4.5832
 984  H171  H   HCH2  0   0.242  -0.6772   2.1642   4.4454
 984  H172  H   HCH2  0   0.228  -1.9574   0.9624   4.3094
 984  H181  H   HCH2  0   0.186  -0.0784   1.3751   6.6870
 984  H182  H   HCH2  0   0.237  -1.7957   1.7644   6.6228
 984  H201  H   HCH2  0   0.185   0.5554  -1.0749   6.6452
 984  H202  H   HCH2  0   0.238  -0.7609  -2.2446   6.5691
 984  H211  H   HCH2  0   0.231  -1.3039  -1.5628   4.2662
 984  H212  H   HCH2  0   0.242   0.3966  -2.0001   4.3932
 984  H311  H   HCH3  0   0.232  -1.8894  -1.3393   8.4136
 984  H312  H   HCH3  0   0.190  -0.6573  -0.0951   8.6736
 984  H313  H   HCH3  0   0.232  -2.3497   0.3640   8.4347
 984  H37   H   HCR6  0   0.271  -0.4171   1.1674  -1.8527
 984  H40   H   HCR6  0   0.287  -4.3235  -1.7768  -1.2413
 984  H41   H   HCR6  0   0.264  -2.7575  -1.4365   0.6208
 984  H47   H   HCR6  0   0.281   2.4456   2.4915   0.0713
 984  H48   H   HCR6  0   0.271   3.8543   2.6485  -1.9825
 984  H54   H   HNH1  0   0.395   1.8818  -2.0037  -3.2466
 984  H55   H   HCH1  0   0.262   4.1360  -1.1430  -4.7406
 984  H561  H   HCH2  0   0.260   2.9031  -2.1381  -6.6594
 984  H562  H   HCH2  0   0.257   1.3574  -2.1068  -5.6994
 984  H571  H   HCH2  0   0.246   1.5354   0.3757  -5.4378
 984  H572  H   HCH2  0   0.254   3.0797   0.3855  -6.4073

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
 984  N1   C2    aromatic  1.358  0.020  1.358
 984  N1   C5    aromatic  1.374  0.020  1.374
 984  N1   C6    single    1.455  0.020  1.455
 984  C2   N3    aromatic  1.310  0.020  1.310
 984  C2   C16   single    1.493  0.020  1.493
 984  N3   C4    aromatic  1.362  0.020  1.362
 984  C4   C5    aromatic  1.376  0.020  1.376
 984  C4   C35   single    1.463  0.020  1.463
 984  C5   C36   single    1.466  0.020  1.466
 984  C6   C7    single    1.523  0.020  1.523
 984  C6   HC61  single    0.970  0.020  1.090
 984  C6   HC62  single    0.970  0.020  1.090
 984  C7   C10   single    1.521  0.020  1.521
 984  C7   HC71  single    0.970  0.020  1.090
 984  C7   HC72  single    0.970  0.020  1.090
 984  C10  H101  single    0.970  0.020  1.090
 984  C10  H102  single    0.970  0.020  1.090
 984  C10  H103  single    0.970  0.020  1.090
 984  C16  C17   single    1.531  0.020  1.531
 984  C16  C21   single    1.532  0.020  1.532
 984  C16  H16   single    0.970  0.020  1.090
 984  C17  C18   single    1.520  0.020  1.520
 984  C17  H171  single    0.970  0.020  1.090
 984  C17  H172  single    0.970  0.020  1.090
 984  C18  N19   single    1.451  0.020  1.451
 984  C18  H181  single    0.970  0.020  1.090
 984  C18  H182  single    0.970  0.020  1.090
 984  N19  C20   single    1.450  0.020  1.450
 984  N19  C31   single    1.445  0.020  1.445
 984  C20  C21   single    1.520  0.020  1.520
 984  C20  H201  single    0.970  0.020  1.090
 984  C20  H202  single    0.970  0.020  1.090
 984  C21  H211  single    0.970  0.020  1.090
 984  C21  H212  single    0.970  0.020  1.090
 984  C31  H311  single    0.970  0.020  1.090
 984  C31  H312  single    0.970  0.020  1.090
 984  C31  H313  single    0.970  0.020  1.090
 984  C35  C37   aromatic  1.393  0.020  1.393
 984  C35  C41   aromatic  1.395  0.020  1.395
 984  C36  C47   aromatic  1.393  0.020  1.393
 984  C36  N51   aromatic  1.324  0.020  1.324
 984  C37  C38   aromatic  1.384  0.020  1.384
 984  C37  H37   single    0.930  0.020  1.080
 984  C38  C39   aromatic  1.389  0.020  1.389
 984  C38  CL45  single    1.724  0.020  1.724
 984  C39  C40   aromatic  1.387  0.020  1.387
 984  C39  CL46  single    1.722  0.020  1.722
 984  C40  C41   aromatic  1.383  0.020  1.383
 984  C40  H40   single    0.930  0.020  1.080
 984  C41  H41   single    0.930  0.020  1.080
 984  C47  C48   aromatic  1.384  0.020  1.384
 984  C47  H47   single    0.930  0.020  1.080
 984  C48  N49   aromatic  1.322  0.020  1.322
 984  C48  H48   single    0.930  0.020  1.080
 984  N49  C50   aromatic  1.338  0.020  1.338
 984  C50  N51   aromatic  1.338  0.020  1.338
 984  C50  N54   single    1.346  0.020  1.346
 984  N54  C55   single    1.422  0.020  1.422
 984  N54  H54   single    0.860  0.020  1.020
 984  C55  C56   single    1.493  0.020  1.493
 984  C55  C57   single    1.498  0.020  1.498
 984  C55  H55   single    0.970  0.020  1.090
 984  C56  C57   single    1.498  0.020  1.498
 984  C56  H561  single    0.970  0.020  1.090
 984  C56  H562  single    0.970  0.020  1.090
 984  C57  H571  single    0.970  0.020  1.090
 984  C57  H572  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
 984  C6    N1   C5    126.15  3.000
 984  C6    N1   C2    125.86  3.000
 984  C5    N1   C2    107.14  3.000
 984  C16   C2   N3    123.98  3.000
 984  C16   C2   N1    124.88  3.000
 984  N3    C2   N1    111.14  3.000
 984  C4    N3   C2    106.62  3.000
 984  C35   C4   C5    129.67  3.000
 984  C35   C4   N3    120.73  3.000
 984  C5    C4   N3    109.60  3.000
 984  C36   C5   C4    129.82  3.000
 984  C36   C5   N1    124.68  3.000
 984  C4    C5   N1    105.49  3.000
 984  HC62  C6   HC61  106.35  3.000
 984  HC62  C6   C7    109.92  3.000
 984  HC61  C6   C7    110.86  3.000
 984  HC62  C6   N1    108.45  3.000
 984  HC61  C6   N1    108.43  3.000
 984  C7    C6   N1    112.61  3.000
 984  HC72  C7   HC71  106.63  3.000
 984  HC72  C7   C10   109.92  3.000
 984  HC71  C7   C10   110.23  3.000
 984  HC72  C7   C6    109.70  3.000
 984  HC71  C7   C6    109.18  3.000
 984  C10   C7   C6    111.08  3.000
 984  H103  C10  H102  107.76  3.000
 984  H103  C10  H101  107.69  3.000
 984  H102  C10  H101  107.72  3.000
 984  H103  C10  C7    111.25  3.000
 984  H102  C10  C7    111.22  3.000
 984  H101  C10  C7    111.04  3.000
 984  H16   C16  C21   107.98  3.000
 984  H16   C16  C17   107.64  3.000
 984  C21   C16  C17   109.05  3.000
 984  H16   C16  C2    109.29  3.000
 984  C21   C16  C2    111.37  3.000
 984  C17   C16  C2    111.37  3.000
 984  H172  C17  H171  107.44  3.000
 984  H172  C17  C18   109.53  3.000
 984  H171  C17  C18   109.53  3.000
 984  H172  C17  C16   109.37  3.000
 984  H171  C17  C16   110.38  3.000
 984  C18   C17  C16   110.54  3.000
 984  H182  C18  H181  106.54  3.000
 984  H182  C18  N19   108.61  3.000
 984  H181  C18  N19   111.29  3.000
 984  H182  C18  C17   109.52  3.000
 984  H181  C18  C17   109.41  3.000
 984  N19   C18  C17   111.35  3.000
 984  C31   N19  C20   111.40  3.000
 984  C31   N19  C18   111.34  3.000
 984  C20   N19  C18   111.32  3.000
 984  H202  C20  H201  106.57  3.000
 984  H202  C20  C21   109.61  3.000
 984  H201  C20  C21   108.96  3.000
 984  H202  C20  N19   108.70  3.000
 984  H201  C20  N19   111.46  3.000
 984  C21   C20  N19   111.41  3.000
 984  H212  C21  H211  107.30  3.000
 984  H212  C21  C20   109.23  3.000
 984  H211  C21  C20   109.95  3.000
 984  H212  C21  C16   110.57  3.000
 984  H211  C21  C16   109.25  3.000
 984  C20   C21  C16   110.48  3.000
 984  H313  C31  H312  107.60  3.000
 984  H313  C31  H311  107.90  3.000
 984  H312  C31  H311  107.66  3.000
 984  H313  C31  N19   110.11  3.000
 984  H312  C31  N19   113.30  3.000
 984  H311  C31  N19   110.08  3.000
 984  C41   C35  C37   118.40  3.000
 984  C41   C35  C4    119.60  3.000
 984  C37   C35  C4    122.00  3.000
 984  N51   C36  C47   121.90  3.000
 984  N51   C36  C5    116.14  3.000
 984  C47   C36  C5    121.86  3.000
 984  H37   C37  C38   118.43  3.000
 984  H37   C37  C35   120.83  3.000
 984  C38   C37  C35   120.73  3.000
 984  CL45  C38  C39   120.67  3.000
 984  CL45  C38  C37   119.00  3.000
 984  C39   C38  C37   120.33  3.000
 984  CL46  C39  C40   119.77  3.000
 984  CL46  C39  C38   120.84  3.000
 984  C40   C39  C38   119.39  3.000
 984  H40   C40  C41   120.17  3.000
 984  H40   C40  C39   119.63  3.000
 984  C41   C40  C39   120.20  3.000
 984  H41   C41  C40   119.35  3.000
 984  H41   C41  C35   119.73  3.000
 984  C40   C41  C35   120.91  3.000
 984  H47   C47  C48   121.53  3.000
 984  H47   C47  C36   122.56  3.000
 984  C48   C47  C36   115.87  3.000
 984  H48   C48  N49   116.42  3.000
 984  H48   C48  C47   120.23  3.000
 984  N49   C48  C47   123.35  3.000
 984  C50   N49  C48   116.09  3.000
 984  N54   C50  N51   116.40  3.000
 984  N54   C50  N49   118.02  3.000
 984  N51   C50  N49   125.58  3.000
 984  C50   N51  C36   117.16  3.000
 984  H54   N54  C55   119.30  3.000
 984  H54   N54  C50   116.85  3.000
 984  C55   N54  C50   123.63  3.000
 984  H55   C55  C57   116.82  3.000
 984  H55   C55  C56   116.94  3.000
 984  C57   C55  C56    60.13  3.000
 984  H55   C55  N54   115.52  3.000
 984  C57   C55  N54   118.96  3.000
 984  C56   C55  N54   117.25  3.000
 984  H562  C56  H561  114.41  3.000
 984  H562  C56  C57   117.74  3.000
 984  H561  C56  C57   118.86  3.000
 984  H562  C56  C55   117.55  3.000
 984  H561  C56  C55   117.69  3.000
 984  C57   C56  C55    60.07  3.000
 984  H572  C57  H571  114.75  3.000
 984  H572  C57  C56   118.83  3.000
 984  H571  C57  C56   117.51  3.000
 984  H572  C57  C55   118.02  3.000
 984  H571  C57  C55   117.08  3.000
 984  C56   C57  C55    59.80  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
 984  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 984  CONST_02  N3    C4   C5   N1      0.00   0.0  0
 984  CONST_03  C35   C4   C5   N1    180.00   0.0  0
 984  CONST_06  C4    C5   N1   C2      0.00   0.0  0
 984  CONST_07  C36   C5   N1   C2    180.00   0.0  0
 984  CONST_08  C5    C4   N3   C2      0.00   0.0  0
 984  CONST_09  C35   C4   N3   C2    180.00   0.0  0
 984  CONST_10  C5    N1   C2   N3      0.00   0.0  0
 984  CONST_11  C36   C5   C4   N3    180.00   0.0  0
 984  CONST_16  C38   C37  C35  C4    180.00   0.0  0
 984  CONST_17  C40   C41  C35  C4    180.00   0.0  0
 984  CONST_20  C48   C47  C36  C5    180.00   0.0  0
 984  CONST_21  C50   N51  C36  C5    180.00   0.0  0
 984  CONST_22  C36   C5   C4   C35     0.00   0.0  0
 984  CONST_23  C39   C38  C37  C35     0.00   0.0  0
 984  CONST_24  C39   C40  C41  C35     0.00   0.0  0
 984  CONST_25  N49   C48  C47  C36     0.00   0.0  0
 984  CONST_26  N49   C50  N51  C36     0.00   0.0  0
 984  CONST_27  C40   C41  C35  C37     0.00   0.0  0
 984  CONST_28  C40   C39  C38  C37     0.00   0.0  0
 984  CONST_29  C41   C35  C37  C38     0.00   0.0  0
 984  CONST_30  C41   C40  C39  C38     0.00   0.0  0
 984  CONST_31  C50   N51  C36  C47     0.00   0.0  0
 984  CONST_32  C50   N49  C48  C47     0.00   0.0  0
 984  CONST_33  N51   C36  C47  C48     0.00   0.0  0
 984  CONST_34  N51   C50  N49  C48     0.00   0.0  0
 984  CONST_35  C16   C2   N3   C4    180.00   0.0  0
 984  CONST_36  C16   C2   N1   C5    180.00   0.0  0
 984  CONST_37  C6    N1   C2   N3    180.00   0.0  0
 984  CONST_38  C6    N1   C5   C4    180.00   0.0  0
 984  CONST_39  C16   C2   N1   C6      0.00   0.0  0
 984  CONST_40  C36   C5   N1   C6      0.00   0.0  0
 984  CONST_41  CL45  C38  C37  C35   180.00   0.0  0
 984  CONST_42  N54   C50  N51  C36   180.00   0.0  0
 984  CONST_43  CL46  C39  C38  C37   180.00   0.0  0
 984  CONST_44  CL45  C38  C39  C40   180.00   0.0  0
 984  CONST_45  CL46  C39  C40  C41   180.00   0.0  0
 984  CONST_46  N54   C50  N49  C48   180.00   0.0  0
 984  CONST_47  C55   N54  C50  N49     0.00   0.0  0
 984  CONST_48  C55   N54  C50  N51   180.00   0.0  0
 984  CONST_49  H37   C37  C35  C4      0.00   0.0  0
 984  CONST_50  H41   C41  C35  C4      0.00   0.0  0
 984  CONST_51  H47   C47  C36  C5      0.00   0.0  0
 984  CONST_52  H40   C40  C41  C35   180.00   0.0  0
 984  CONST_53  H48   C48  C47  C36   180.00   0.0  0
 984  CONST_54  H54   N54  C50  N49   180.00   0.0  0
 984  Var_01    N19   C18  C17  C16   -57.15  30.0  1
 984  Var_02    N19   C20  C21  C16    57.09  30.0  1
 984  Var_03    C20   N19  C18  C17    59.27  30.0  1
 984  Var_04    C21   C20  N19  C18   -59.28  30.0  1
 984  Var_05    C56   C55  N54  C50  -142.24  30.0  3
 984  Var_06    C57   C56  C55  N54   109.41  30.0  1
 984  Var_07    H571  C57  C56  C55  -106.91  30.0  1
 984  Var_08    C7    C6   N1   C2     76.43  30.0  2
 984  Var_09    H311  C31  N19  C18   177.66  30.0  3
 984  Var_10    C10   C7   C6   N1    177.52  30.0  3
 984  Var_11    H101  C10  C7   C6    178.78  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 984  chir_01  C16  C2   C17  C21  negativ
 984  chir_02  C55  N54  C56  C57  both

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
 984  plan-1  N1    0.020
 984  plan-1  C2    0.020
 984  plan-1  N3    0.020
 984  plan-1  C4    0.020
 984  plan-1  C5    0.020
 984  plan-1  C6    0.020
 984  plan-1  C16   0.020
 984  plan-1  C35   0.020
 984  plan-1  C36   0.020
 984  plan-2  C50   0.020
 984  plan-2  N54   0.020
 984  plan-2  C55   0.020
 984  plan-2  H54   0.020
 984  plan-3  C4    0.020
 984  plan-3  C35   0.020
 984  plan-3  C37   0.020
 984  plan-3  C38   0.020
 984  plan-3  C39   0.020
 984  plan-3  C40   0.020
 984  plan-3  C41   0.020
 984  plan-3  CL45  0.020
 984  plan-3  CL46  0.020
 984  plan-3  H37   0.020
 984  plan-3  H40   0.020
 984  plan-3  H41   0.020
 984  plan-4  C5    0.020
 984  plan-4  C36   0.020
 984  plan-4  C47   0.020
 984  plan-4  C48   0.020
 984  plan-4  N49   0.020
 984  plan-4  C50   0.020
 984  plan-4  N51   0.020
 984  plan-4  N54   0.020
 984  plan-4  H47   0.020
 984  plan-4  H48   0.020

