# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:18:32 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-[({2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}amino)methyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1cccc(CNCCc2ccnc(n2)n3ccnc3)c1
#
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
 OLW  OLW  3-[({2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}amino)methyl]benzonitrile  ligand  39  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OLW
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
 OLW  N01   N  N     0  -0.443   5.7726  -2.4362   0.8462
 OLW  C02   C  CR15  0   0.115   4.7148  -1.6831   0.7972
 OLW  N03   N  NR5   0  -0.528   4.9864  -0.4744   0.2255
 OLW  C04   C  CR15  0  -0.094   6.3222  -0.4792  -0.1069
 OLW  C05   C  CR15  0  -0.209   6.7837  -1.6946   0.2851
 OLW  C1'   C  CR6   0   0.101  -3.7836  -0.8325  -0.3121
 OLW  N11   N  N     0  -0.439   4.5492   1.6494  -0.5676
 OLW  C12   C  CR6   0   0.636   4.0779   0.5688   0.0223
 OLW  N13   N  N     0  -0.452   2.8484   0.3588   0.4479
 OLW  C14   C  CR6   0   0.313   1.9704   1.3416   0.2666
 OLW  C15   C  CR16  0  -0.382   2.3531   2.5279  -0.3506
 OLW  C16   C  CR16  0   0.004   3.6717   2.6292  -0.7511
 OLW  C17   C  CH2   0  -0.525   0.5673   1.0980   0.7195
 OLW  C18   C  CH2   0  -0.255  -0.2071   0.2739  -0.3089
 OLW  N19   N  NH1   0  -0.598  -1.5551   0.0317   0.1612
 OLW  C2'   C  CR16  0  -0.283  -4.4608   0.2844   0.1642
 OLW  C20   C  CH2   0  -0.317  -2.3621  -0.7049  -0.7902
 OLW  C3'   C  CR6   0   0.025  -5.7837   0.1709   0.5835
 OLW  C4'   C  CR16  0  -0.257  -6.4484  -1.0558   0.5409
 OLW  C5'   C  CR16  0  -0.229  -5.7698  -2.1660   0.0734
 OLW  C6'   C  CR16  0  -0.292  -4.4493  -2.0533  -0.3463
 OLW  C7'   C  CSP   0   0.053  -6.4690   1.3286   1.0627
 OLW  N8'   N  NS    0  -0.253  -7.0222   2.2638   1.4466
 OLW  H02   H  HCR5  0   0.294   3.7299  -1.9416   1.1502
 OLW  H04   H  HCR5  0   0.300   6.8019   0.3614  -0.5751
 OLW  H05   H  HCR5  0   0.261   7.7882  -2.0774   0.1959
 OLW  H15   H  HCR6  0   0.284   1.6539   3.3363  -0.5067
 OLW  H16   H  HCR6  0   0.287   4.0404   3.5264  -1.2333
 OLW  H17   H  HCH2  0   0.262   0.5933   0.5628   1.6718
 OLW  H17A  H  HCH2  0   0.259   0.0547   2.0472   0.8813
 OLW  H18   H  HCH2  0   0.235  -0.2660   0.8311  -1.2487
 OLW  H18A  H  HCH2  0   0.211   0.3467  -0.6508  -0.5288
 OLW  HN19  H  HNH1  0   0.349  -1.5159  -0.4889   1.0305
 OLW  H2'   H  HCR6  0   0.272  -3.9568   1.2408   0.2109
 OLW  H20   H  HCH2  0   0.225  -1.9632  -1.7038  -1.0196
 OLW  H20A  H  HCH2  0   0.249  -2.3562  -0.1526  -1.7353
 OLW  H4'   H  HCR6  0   0.280  -7.4754  -1.1336   0.8710
 OLW  H5'   H  HCR6  0   0.273  -6.2668  -3.1259   0.0415
 OLW  H6'   H  HCR6  0   0.267  -3.9293  -2.9339  -0.7030

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
 OLW  N01  C02   aromatic  1.299  0.020  1.299
 OLW  N01  C05   aromatic  1.374  0.020  1.374
 OLW  C02  N03   aromatic  1.364  0.020  1.364
 OLW  N03  C04   aromatic  1.377  0.020  1.377
 OLW  N03  C12   single    1.398  0.020  1.398
 OLW  C04  C05   aromatic  1.358  0.020  1.358
 OLW  C1'  C2'   aromatic  1.390  0.020  1.390
 OLW  C1'  C20   single    1.505  0.020  1.505
 OLW  C1'  C6'   aromatic  1.391  0.020  1.391
 OLW  N11  C12   aromatic  1.318  0.020  1.318
 OLW  N11  C16   aromatic  1.328  0.020  1.328
 OLW  C12  N13   aromatic  1.318  0.020  1.318
 OLW  N13  C14   aromatic  1.330  0.020  1.330
 OLW  C14  C15   aromatic  1.391  0.020  1.391
 OLW  C14  C17   single    1.494  0.020  1.494
 OLW  C15  C16   aromatic  1.382  0.020  1.382
 OLW  C17  C18   single    1.529  0.020  1.529
 OLW  C18  N19   single    1.448  0.020  1.448
 OLW  N19  C20   single    1.449  0.020  1.449
 OLW  C2'  C3'   aromatic  1.392  0.020  1.392
 OLW  C3'  C4'   aromatic  1.396  0.020  1.396
 OLW  C3'  C7'   single    1.428  0.020  1.428
 OLW  C4'  C5'   aromatic  1.383  0.020  1.383
 OLW  C5'  C6'   aromatic  1.390  0.020  1.390
 OLW  C7'  N8'   triple    1.152  0.020  1.152
 OLW  C02  H02   single    0.930  0.020  1.080
 OLW  C04  H04   single    0.930  0.020  1.080
 OLW  C05  H05   single    0.930  0.020  1.080
 OLW  C15  H15   single    0.930  0.020  1.080
 OLW  C16  H16   single    0.930  0.020  1.080
 OLW  C17  H17   single    0.970  0.020  1.090
 OLW  C17  H17A  single    0.970  0.020  1.090
 OLW  C18  H18   single    0.970  0.020  1.090
 OLW  C18  H18A  single    0.970  0.020  1.090
 OLW  N19  HN19  single    0.890  0.020  1.040
 OLW  C2'  H2'   single    0.930  0.020  1.080
 OLW  C20  H20   single    0.970  0.020  1.090
 OLW  C20  H20A  single    0.970  0.020  1.090
 OLW  C4'  H4'   single    0.930  0.020  1.080
 OLW  C5'  H5'   single    0.930  0.020  1.080
 OLW  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
 OLW  C05   N01  C02  105.72  3.000
 OLW  H02   C02  N03  122.12  3.000
 OLW  H02   C02  N01  126.34  3.000
 OLW  N03   C02  N01  111.54  3.000
 OLW  C12   N03  C04  126.72  3.000
 OLW  C12   N03  C02  126.34  3.000
 OLW  C04   N03  C02  106.94  3.000
 OLW  H04   C04  C05  132.37  3.000
 OLW  H04   C04  N03  122.38  3.000
 OLW  C05   C04  N03  105.26  3.000
 OLW  H05   C05  C04  127.61  3.000
 OLW  H05   C05  N01  121.85  3.000
 OLW  C04   C05  N01  110.55  3.000
 OLW  C6'   C1'  C20  121.23  3.000
 OLW  C6'   C1'  C2'  118.71  3.000
 OLW  C20   C1'  C2'  120.05  3.000
 OLW  C16   N11  C12  115.49  3.000
 OLW  N13   C12  N11  127.49  3.000
 OLW  N13   C12  N03  116.12  3.000
 OLW  N11   C12  N03  116.38  3.000
 OLW  C14   N13  C12  117.00  3.000
 OLW  C17   C14  C15  122.13  3.000
 OLW  C17   C14  N13  117.26  3.000
 OLW  C15   C14  N13  120.59  3.000
 OLW  H15   C15  C16  121.40  3.000
 OLW  H15   C15  C14  121.62  3.000
 OLW  C16   C15  C14  116.98  3.000
 OLW  H16   C16  C15  120.97  3.000
 OLW  H16   C16  N11  116.60  3.000
 OLW  C15   C16  N11  122.44  3.000
 OLW  H17A  C17  H17  107.95  3.000
 OLW  H17A  C17  C18  109.32  3.000
 OLW  H17   C17  C18  109.53  3.000
 OLW  H17A  C17  C14  110.15  3.000
 OLW  H17   C17  C14  108.76  3.000
 OLW  C18   C17  C14  111.07  3.000
 OLW  H18A  C18  H18  106.47  3.000
 OLW  H18A  C18  N19  113.14  3.000
 OLW  H18   C18  N19  108.30  3.000
 OLW  H18A  C18  C17  109.43  3.000
 OLW  H18   C18  C17  109.31  3.000
 OLW  N19   C18  C17  110.08  3.000
 OLW  HN19  N19  C20  108.87  3.000
 OLW  HN19  N19  C18  109.17  3.000
 OLW  C20   N19  C18  112.98  3.000
 OLW  H2'   C2'  C3'  120.10  3.000
 OLW  H2'   C2'  C1'  119.86  3.000
 OLW  C3'   C2'  C1'  120.03  3.000
 OLW  H20A  C20  H20  106.04  3.000
 OLW  H20A  C20  N19  107.91  3.000
 OLW  H20   C20  N19  113.37  3.000
 OLW  H20A  C20  C1'  108.78  3.000
 OLW  H20   C20  C1'  109.38  3.000
 OLW  N19   C20  C1'  111.14  3.000
 OLW  C7'   C3'  C4'  119.61  3.000
 OLW  C7'   C3'  C2'  119.40  3.000
 OLW  C4'   C3'  C2'  120.99  3.000
 OLW  H4'   C4'  C5'  120.77  3.000
 OLW  H4'   C4'  C3'  120.40  3.000
 OLW  C5'   C4'  C3'  118.83  3.000
 OLW  H5'   C5'  C6'  119.97  3.000
 OLW  H5'   C5'  C4'  119.81  3.000
 OLW  C6'   C5'  C4'  120.22  3.000
 OLW  H6'   C6'  C5'  119.31  3.000
 OLW  H6'   C6'  C1'  119.47  3.000
 OLW  C5'   C6'  C1'  121.22  3.000
 OLW  N8'   C7'  C3'  180.00  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
 OLW  CONST_01  C04  N03  C02  N01     0.00   0.0  0
 OLW  CONST_02  C12  N03  C02  N01   180.00   0.0  0
 OLW  CONST_03  N03  C04  C05  N01     0.00   0.0  0
 OLW  CONST_04  C04  C05  N01  C02     0.00   0.0  0
 OLW  CONST_05  C05  C04  N03  C02     0.00   0.0  0
 OLW  CONST_06  N11  C12  N03  C02   180.00   0.0  0
 OLW  CONST_07  N13  C12  N03  C02     0.00   0.0  0
 OLW  CONST_08  C05  N01  C02  N03     0.00   0.0  0
 OLW  CONST_09  C16  N11  C12  N03   180.00   0.0  0
 OLW  CONST_10  C14  N13  C12  N03   180.00   0.0  0
 OLW  CONST_11  N11  C12  N03  C04     0.00   0.0  0
 OLW  CONST_12  N13  C12  N03  C04   180.00   0.0  0
 OLW  CONST_13  C12  N03  C04  C05   180.00   0.0  0
 OLW  CONST_14  C4'  C3'  C2'  C1'     0.00   0.0  0
 OLW  CONST_15  C4'  C5'  C6'  C1'     0.00   0.0  0
 OLW  CONST_16  C14  N13  C12  N11     0.00   0.0  0
 OLW  CONST_17  C14  C15  C16  N11     0.00   0.0  0
 OLW  CONST_18  C15  C16  N11  C12     0.00   0.0  0
 OLW  CONST_19  C15  C14  N13  C12     0.00   0.0  0
 OLW  CONST_20  C16  N11  C12  N13     0.00   0.0  0
 OLW  CONST_21  C16  C15  C14  N13     0.00   0.0  0
 OLW  CONST_22  C5'  C6'  C1'  C2'     0.00   0.0  0
 OLW  CONST_23  C5'  C4'  C3'  C2'     0.00   0.0  0
 OLW  CONST_24  C6'  C1'  C2'  C3'     0.00   0.0  0
 OLW  CONST_25  C6'  C5'  C4'  C3'     0.00   0.0  0
 OLW  CONST_26  C7'  C3'  C2'  C1'   180.00   0.0  0
 OLW  CONST_27  C17  C14  N13  C12   180.00   0.0  0
 OLW  CONST_28  C17  C14  C15  C16   180.00   0.0  0
 OLW  CONST_29  C3'  C2'  C1'  C20   180.00   0.0  0
 OLW  CONST_30  C5'  C6'  C1'  C20   180.00   0.0  0
 OLW  CONST_31  C7'  C3'  C4'  C5'   180.00   0.0  0
 OLW  CONST_32  H04  C04  C05  N01   180.00   0.0  0
 OLW  CONST_33  H05  C05  N01  C02   180.00   0.0  0
 OLW  CONST_34  H02  C02  N03  C04   180.00   0.0  0
 OLW  CONST_35  H5'  C5'  C6'  C1'   180.00   0.0  0
 OLW  CONST_36  H15  C15  C16  N11   180.00   0.0  0
 OLW  CONST_37  H16  C16  N11  C12   180.00   0.0  0
 OLW  CONST_38  H6'  C6'  C1'  C2'   180.00   0.0  0
 OLW  CONST_39  H4'  C4'  C3'  C2'   180.00   0.0  0
 OLW  CONST_40  H2'  C2'  C3'  C4'   180.00   0.0  0
 OLW  Var_01    C18  C17  C14  N13   -80.50  30.0  2
 OLW  Var_02    C2'  C1'  C20  N19    47.77  30.0  2
 OLW  Var_03    C18  N19  C20  C1'  -175.20  30.0  1
 OLW  Var_04    N19  C18  C17  C14   179.04  30.0  3
 OLW  Var_05    C20  N19  C18  C17   177.87  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
 OLW  plan-1  N01  0.020
 OLW  plan-1  C02  0.020
 OLW  plan-1  N03  0.020
 OLW  plan-1  C04  0.020
 OLW  plan-1  C05  0.020
 OLW  plan-1  C12  0.020
 OLW  plan-1  H02  0.020
 OLW  plan-1  H04  0.020
 OLW  plan-1  H05  0.020
 OLW  plan-2  C1'  0.020
 OLW  plan-2  C2'  0.020
 OLW  plan-2  C20  0.020
 OLW  plan-2  C3'  0.020
 OLW  plan-2  C4'  0.020
 OLW  plan-2  C5'  0.020
 OLW  plan-2  C6'  0.020
 OLW  plan-2  C7'  0.020
 OLW  plan-2  N8'  0.020
 OLW  plan-2  H2'  0.020
 OLW  plan-2  H4'  0.020
 OLW  plan-2  H5'  0.020
 OLW  plan-2  H6'  0.020
 OLW  plan-3  N03  0.020
 OLW  plan-3  N11  0.020
 OLW  plan-3  C12  0.020
 OLW  plan-3  N13  0.020
 OLW  plan-3  C14  0.020
 OLW  plan-3  C15  0.020
 OLW  plan-3  C16  0.020
 OLW  plan-3  C17  0.020
 OLW  plan-3  H15  0.020
 OLW  plan-3  H16  0.020

