# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:22:31 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}-3-(pyridin-3-yl)propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(CNCCc1ccnc(n1)n2ccnc2)Cc3cccnc3
#
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
 EG8  EG8  N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}-3-(pyridin-3-yl)propan-1-amine  ligand  43  23  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EG8
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
 EG8  N01   N  N     0  -0.444   5.3855  -3.0305   0.0219
 EG8  C02   C  CR15  0   0.115   4.5459  -2.0537   0.1930
 EG8  N03   N  NR5   0  -0.528   5.1278  -0.8448  -0.0548
 EG8  C04   C  CR15  0  -0.094   6.4348  -1.0930  -0.4089
 EG8  C05   C  CR15  0  -0.209   6.5690  -2.4433  -0.3534
 EG8  N1'   N  N     0  -0.401  -7.9009   0.4683  -0.7314
 EG8  N11   N  N     0  -0.456   3.2524   0.4038   0.4321
 EG8  C12   C  CR6   0   0.633   4.5047   0.4045   0.0236
 EG8  N13   N  N     0  -0.440   5.2364   1.4461  -0.3214
 EG8  C14   C  CR16  0   0.004   4.6248   2.6221  -0.2478
 EG8  C15   C  CR16  0  -0.386   3.3084   2.7494   0.1535
 EG8  C16   C  CR6   0   0.327   2.6358   1.5815   0.4966
 EG8  C17   C  CH2   0  -0.525   1.2059   1.5858   0.9339
 EG8  C18   C  CH2   0  -0.250   0.3225   0.7572   0.0028
 EG8  N19   N  NH1   0  -0.603  -1.0645   0.8405   0.4108
 EG8  C2'   C  CR16  0  -0.110  -6.6335   0.2783  -1.0790
 EG8  C20   C  CH2   0  -0.254  -1.9383   0.0311  -0.4175
 EG8  C21   C  CH2   0  -0.437  -3.3903   0.1713   0.0089
 EG8  C22   C  CH2   0  -0.512  -4.3226  -0.7002  -0.8338
 EG8  C3'   C  CR6   0   0.041  -5.7546  -0.5671  -0.4085
 EG8  C4'   C  CR16  0  -0.194  -6.2576  -1.2508   0.6940
 EG8  C5'   C  CR16  0  -0.318  -7.5783  -1.0641   1.0686
 EG8  C6'   C  CR16  0  -0.077  -8.3600  -0.1921   0.3246
 EG8  H02   H  HCR5  0   0.294   3.5127  -2.1417   0.4872
 EG8  H04   H  HCR5  0   0.300   7.1241  -0.3063  -0.6586
 EG8  H05   H  HCR5  0   0.261   7.4517  -3.0264  -0.5648
 EG8  H14   H  HCR6  0   0.287   5.2097   3.4917  -0.5227
 EG8  H15   H  HCR6  0   0.284   2.8271   3.7151   0.2033
 EG8  H17   H  HCH2  0   0.263   1.1492   1.1761   1.9473
 EG8  H17A  H  HCH2  0   0.256   0.8377   2.6114   0.9782
 EG8  H18   H  HCH2  0   0.227   0.4047   1.1484  -1.0160
 EG8  H18A  H  HCH2  0   0.204   0.7002  -0.2753  -0.0290
 EG8  HN19  H  HNH1  0   0.340  -1.1427   0.5218   1.3705
 EG8  H20   H  HCH2  0   0.219  -1.8328   0.3656  -1.4545
 EG8  H20A  H  HCH2  0   0.191  -1.6555  -1.0345  -0.4104
 EG8  H21   H  HCH2  0   0.227  -3.4928  -0.1067   1.0632
 EG8  H21A  H  HCH2  0   0.230  -3.6935   1.2190  -0.0699
 EG8  H22   H  HCH2  0   0.244  -4.2249  -0.4247  -1.8873
 EG8  H22A  H  HCH2  0   0.246  -4.0129  -1.7459  -0.7544
 EG8  H4'   H  HCR6  0   0.265  -5.6200  -1.9277   1.2506
 EG8  H5'   H  HCR6  0   0.269  -7.9989  -1.5842   1.9184
 EG8  H6'   H  HCR6  0   0.261  -9.3978  -0.0242   0.5907
 EG8  H2'   H  HCR6  0   0.253  -6.2870   0.8267  -1.9505

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
 EG8  N01  C02   aromatic  1.299  0.020  1.299
 EG8  N01  C05   aromatic  1.374  0.020  1.374
 EG8  C02  N03   aromatic  1.364  0.020  1.364
 EG8  N03  C04   aromatic  1.377  0.020  1.377
 EG8  N03  C12   single    1.398  0.020  1.398
 EG8  C04  C05   aromatic  1.358  0.020  1.358
 EG8  N1'  C2'   aromatic  1.328  0.020  1.328
 EG8  N1'  C6'   aromatic  1.327  0.020  1.327
 EG8  N11  C12   aromatic  1.317  0.020  1.317
 EG8  N11  C16   aromatic  1.331  0.020  1.331
 EG8  C12  N13   aromatic  1.319  0.020  1.319
 EG8  N13  C14   aromatic  1.328  0.020  1.328
 EG8  C14  C15   aromatic  1.382  0.020  1.382
 EG8  C15  C16   aromatic  1.391  0.020  1.391
 EG8  C16  C17   single    1.495  0.020  1.495
 EG8  C17  C18   single    1.528  0.020  1.528
 EG8  C18  N19   single    1.448  0.020  1.448
 EG8  N19  C20   single    1.451  0.020  1.451
 EG8  C2'  C3'   aromatic  1.392  0.020  1.392
 EG8  C20  C21   single    1.520  0.020  1.520
 EG8  C21  C22   single    1.529  0.020  1.529
 EG8  C22  C3'   single    1.500  0.020  1.500
 EG8  C3'  C4'   aromatic  1.391  0.020  1.391
 EG8  C4'  C5'   aromatic  1.385  0.020  1.385
 EG8  C5'  C6'   aromatic  1.387  0.020  1.387
 EG8  C02  H02   single    0.930  0.020  1.080
 EG8  C04  H04   single    0.930  0.020  1.080
 EG8  C05  H05   single    0.930  0.020  1.080
 EG8  C14  H14   single    0.930  0.020  1.080
 EG8  C15  H15   single    0.930  0.020  1.080
 EG8  C17  H17   single    0.970  0.020  1.090
 EG8  C17  H17A  single    0.970  0.020  1.090
 EG8  C18  H18   single    0.970  0.020  1.090
 EG8  C18  H18A  single    0.970  0.020  1.090
 EG8  N19  HN19  single    0.890  0.020  1.040
 EG8  C2'  H2'   single    0.930  0.020  1.080
 EG8  C20  H20   single    0.970  0.020  1.090
 EG8  C20  H20A  single    0.970  0.020  1.090
 EG8  C21  H21   single    0.970  0.020  1.090
 EG8  C21  H21A  single    0.970  0.020  1.090
 EG8  C22  H22   single    0.970  0.020  1.090
 EG8  C22  H22A  single    0.970  0.020  1.090
 EG8  C4'  H4'   single    0.930  0.020  1.080
 EG8  C5'  H5'   single    0.930  0.020  1.080
 EG8  C6'  H6'   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
 EG8  C05   N01  C02  105.75  3.000
 EG8  H02   C02  N03  122.06  3.000
 EG8  H02   C02  N01  126.44  3.000
 EG8  N03   C02  N01  111.51  3.000
 EG8  C12   N03  C04  126.77  3.000
 EG8  C12   N03  C02  126.26  3.000
 EG8  C04   N03  C02  106.97  3.000
 EG8  H04   C04  C05  132.34  3.000
 EG8  H04   C04  N03  122.44  3.000
 EG8  C05   C04  N03  105.23  3.000
 EG8  H05   C05  C04  127.61  3.000
 EG8  H05   C05  N01  121.84  3.000
 EG8  C04   C05  N01  110.55  3.000
 EG8  C6'   N1'  C2'  117.85  3.000
 EG8  C16   N11  C12  117.06  3.000
 EG8  N13   C12  N11  127.52  3.000
 EG8  N13   C12  N03  116.34  3.000
 EG8  N11   C12  N03  116.14  3.000
 EG8  C14   N13  C12  115.43  3.000
 EG8  H14   C14  C15  120.93  3.000
 EG8  H14   C14  N13  116.63  3.000
 EG8  C15   C14  N13  122.44  3.000
 EG8  H15   C15  C16  121.59  3.000
 EG8  H15   C15  C14  121.34  3.000
 EG8  C16   C15  C14  117.07  3.000
 EG8  C17   C16  C15  122.16  3.000
 EG8  C17   C16  N11  117.37  3.000
 EG8  C15   C16  N11  120.47  3.000
 EG8  H17A  C17  H17  107.27  3.000
 EG8  H17A  C17  C18  109.85  3.000
 EG8  H17   C17  C18  109.35  3.000
 EG8  H17A  C17  C16  109.72  3.000
 EG8  H17   C17  C16  108.62  3.000
 EG8  C18   C17  C16  111.91  3.000
 EG8  H18A  C18  H18  106.43  3.000
 EG8  H18A  C18  N19  113.02  3.000
 EG8  H18   C18  N19  108.28  3.000
 EG8  H18A  C18  C17  109.16  3.000
 EG8  H18   C18  C17  109.27  3.000
 EG8  N19   C18  C17  110.54  3.000
 EG8  HN19  N19  C20  108.57  3.000
 EG8  HN19  N19  C18  108.81  3.000
 EG8  C20   N19  C18  112.57  3.000
 EG8  H2'   C2'  C3'  119.45  3.000
 EG8  H2'   C2'  N1'  116.24  3.000
 EG8  C3'   C2'  N1'  124.31  3.000
 EG8  H20A  C20  H20  106.06  3.000
 EG8  H20A  C20  C21  109.42  3.000
 EG8  H20   C20  C21  109.25  3.000
 EG8  H20A  C20  N19  112.40  3.000
 EG8  H20   C20  N19  108.20  3.000
 EG8  C21   C20  N19  111.33  3.000
 EG8  H21A  C21  H21  106.66  3.000
 EG8  H21A  C21  C22  109.71  3.000
 EG8  H21   C21  C22  109.19  3.000
 EG8  H21A  C21  C20  109.45  3.000
 EG8  H21   C21  C20  109.64  3.000
 EG8  C22   C21  C20  112.04  3.000
 EG8  H22A  C22  H22  106.60  3.000
 EG8  H22A  C22  C3'  109.55  3.000
 EG8  H22   C22  C3'  109.64  3.000
 EG8  H22A  C22  C21  109.41  3.000
 EG8  H22   C22  C21  109.45  3.000
 EG8  C3'   C22  C21  112.04  3.000
 EG8  C4'   C3'  C22  121.75  3.000
 EG8  C4'   C3'  C2'  116.87  3.000
 EG8  C22   C3'  C2'  121.35  3.000
 EG8  H4'   C4'  C5'  120.41  3.000
 EG8  H4'   C4'  C3'  120.08  3.000
 EG8  C5'   C4'  C3'  119.51  3.000
 EG8  H5'   C5'  C6'  120.30  3.000
 EG8  H5'   C5'  C4'  121.22  3.000
 EG8  C6'   C5'  C4'  118.48  3.000
 EG8  H6'   C6'  C5'  120.32  3.000
 EG8  H6'   C6'  N1'  116.69  3.000
 EG8  C5'   C6'  N1'  122.98  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
 EG8  CONST_01  C04  N03  C02  N01     0.00   0.0  0
 EG8  CONST_02  C12  N03  C02  N01   180.00   0.0  0
 EG8  CONST_03  N03  C04  C05  N01     0.00   0.0  0
 EG8  CONST_04  C04  C05  N01  C02     0.00   0.0  0
 EG8  CONST_05  C05  C04  N03  C02     0.00   0.0  0
 EG8  CONST_06  N11  C12  N03  C02     0.00   0.0  0
 EG8  CONST_07  N13  C12  N03  C02   180.00   0.0  0
 EG8  CONST_08  C05  N01  C02  N03     0.00   0.0  0
 EG8  CONST_09  C16  N11  C12  N03   180.00   0.0  0
 EG8  CONST_10  C14  N13  C12  N03   180.00   0.0  0
 EG8  CONST_11  N11  C12  N03  C04   180.00   0.0  0
 EG8  CONST_12  N13  C12  N03  C04     0.00   0.0  0
 EG8  CONST_13  C12  N03  C04  C05   180.00   0.0  0
 EG8  CONST_14  C4'  C3'  C2'  N1'     0.00   0.0  0
 EG8  CONST_15  C4'  C5'  C6'  N1'     0.00   0.0  0
 EG8  CONST_16  C14  N13  C12  N11     0.00   0.0  0
 EG8  CONST_17  C14  C15  C16  N11     0.00   0.0  0
 EG8  CONST_18  C15  C16  N11  C12     0.00   0.0  0
 EG8  CONST_19  C15  C14  N13  C12     0.00   0.0  0
 EG8  CONST_20  C16  N11  C12  N13     0.00   0.0  0
 EG8  CONST_21  C16  C15  C14  N13     0.00   0.0  0
 EG8  CONST_22  C5'  C6'  N1'  C2'     0.00   0.0  0
 EG8  CONST_23  C5'  C4'  C3'  C2'     0.00   0.0  0
 EG8  CONST_24  C6'  N1'  C2'  C3'     0.00   0.0  0
 EG8  CONST_25  C6'  C5'  C4'  C3'     0.00   0.0  0
 EG8  CONST_26  C22  C3'  C2'  N1'   180.00   0.0  0
 EG8  CONST_27  C17  C16  N11  C12   180.00   0.0  0
 EG8  CONST_28  C17  C16  C15  C14   180.00   0.0  0
 EG8  CONST_29  C5'  C4'  C3'  C22   180.00   0.0  0
 EG8  CONST_30  H04  C04  C05  N01   180.00   0.0  0
 EG8  CONST_31  H05  C05  N01  C02   180.00   0.0  0
 EG8  CONST_32  H02  C02  N03  C04   180.00   0.0  0
 EG8  CONST_33  H5'  C5'  C6'  N1'   180.00   0.0  0
 EG8  CONST_34  H15  C15  C16  N11   180.00   0.0  0
 EG8  CONST_35  H14  C14  N13  C12   180.00   0.0  0
 EG8  CONST_36  H6'  C6'  N1'  C2'   180.00   0.0  0
 EG8  CONST_37  H4'  C4'  C3'  C2'   180.00   0.0  0
 EG8  CONST_38  H2'  C2'  C3'  C4'   180.00   0.0  0
 EG8  Var_01    C18  C17  C16  N11   -59.90  30.0  2
 EG8  Var_02    C21  C22  C3'  C2'    97.92  30.0  2
 EG8  Var_03    N19  C18  C17  C16  -176.91  30.0  3
 EG8  Var_04    C3'  C22  C21  C20   179.71  30.0  3
 EG8  Var_05    C20  N19  C18  C17  -178.01  30.0  3
 EG8  Var_06    C21  C20  N19  C18  -178.31  30.0  3
 EG8  Var_07    C22  C21  C20  N19  -178.70  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
 EG8  plan-1  N01  0.020
 EG8  plan-1  C02  0.020
 EG8  plan-1  N03  0.020
 EG8  plan-1  C04  0.020
 EG8  plan-1  C05  0.020
 EG8  plan-1  C12  0.020
 EG8  plan-1  H02  0.020
 EG8  plan-1  H04  0.020
 EG8  plan-1  H05  0.020
 EG8  plan-2  N1'  0.020
 EG8  plan-2  C2'  0.020
 EG8  plan-2  C22  0.020
 EG8  plan-2  C3'  0.020
 EG8  plan-2  C4'  0.020
 EG8  plan-2  C5'  0.020
 EG8  plan-2  C6'  0.020
 EG8  plan-2  H4'  0.020
 EG8  plan-2  H5'  0.020
 EG8  plan-2  H6'  0.020
 EG8  plan-2  H2'  0.020
 EG8  plan-3  N03  0.020
 EG8  plan-3  N11  0.020
 EG8  plan-3  C12  0.020
 EG8  plan-3  N13  0.020
 EG8  plan-3  C14  0.020
 EG8  plan-3  C15  0.020
 EG8  plan-3  C16  0.020
 EG8  plan-3  C17  0.020
 EG8  plan-3  H14  0.020
 EG8  plan-3  H15  0.020

