# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 23:49:29 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-(3-fluorophenyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(CCNCCc2ccnc(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
 E2Z  E2Z  2-(3-fluorophenyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}ethanamine  ligand  41  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E2Z
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
 E2Z  N01   N  N     0  -0.434   5.0215   3.1857  -0.6798
 E2Z  C02   C  CR15  0   0.132   4.2840   2.1170  -0.7298
 E2Z  N03   N  NR5   0  -0.530   4.8196   1.1042   0.0113
 E2Z  C04   C  CR15  0  -0.082   5.9840   1.5853   0.5663
 E2Z  C05   C  CR15  0  -0.192   6.0862   2.8662   0.1271
 E2Z  C1'   C  CR6   0   0.161  -4.7073  -0.5876  -0.1707
 E2Z  N11   N  N     0  -0.418   4.9583  -0.9984   0.9532
 E2Z  C12   C  CR6   0   0.633   4.2788  -0.1742   0.1801
 E2Z  N13   N  N     0  -0.439   3.1481  -0.4152  -0.4519
 E2Z  C14   C  CR6   0   0.319   2.6148  -1.6247  -0.2965
 E2Z  C15   C  CR16  0  -0.370   3.2441  -2.5777   0.4974
 E2Z  C16   C  CR16  0   0.016   4.4287  -2.2063   1.1045
 E2Z  C17   C  CH2   0  -0.510   1.3078  -1.8902  -0.9704
 E2Z  C18   C  CH2   0  -0.246   0.1725  -1.1327  -0.2810
 E2Z  N19   N  NH1   0  -0.570  -1.0990  -1.4528  -0.8950
 E2Z  C2'   C  CR16  0  -0.445  -5.1269   0.6867  -0.5460
 E2Z  C20   C  CH2   0  -0.245  -2.2151  -0.7947  -0.2456
 E2Z  C21   C  CH2   0  -0.522  -3.5414  -1.2354  -0.8608
 E2Z  C3'   C  CR6   0   0.558  -6.1723   1.2818   0.1322
 E2Z  C4'   C  CR16  0  -0.402  -6.8283   0.6631   1.1787
 E2Z  C5'   C  CR16  0  -0.194  -6.4058  -0.6064   1.5492
 E2Z  C6'   C  CR16  0  -0.300  -5.3568  -1.2259   0.8838
 E2Z  F7'   F  F     0  -0.310  -6.5667   2.5110  -0.2440
 E2Z  H02   H  HCR5  0   0.278   3.3600   2.0019  -1.2726
 E2Z  H04   H  HCR5  0   0.288   6.6086   0.9860   1.2040
 E2Z  H05   H  HCR5  0   0.245   6.8661   3.5776   0.3488
 E2Z  H15   H  HCR6  0   0.251   2.8292  -3.5656   0.6340
 E2Z  H16   H  HCR6  0   0.258   4.9726  -2.8991   1.7354
 E2Z  H17   H  HCH2  0   0.247   1.3751  -1.5777  -2.0160
 E2Z  H17A  H  HCH2  0   0.246   1.0923  -2.9593  -0.9561
 E2Z  H18   H  HCH2  0   0.221   0.1270  -1.4313   0.7707
 E2Z  H18A  H  HCH2  0   0.207   0.3985  -0.0559  -0.2896
 E2Z  HN19  H  HNH1  0   0.317  -1.0751  -1.1737  -1.8697
 E2Z  H2'   H  HCR6  0   0.237  -4.6442   1.2107  -1.3626
 E2Z  H20   H  HCH2  0   0.223  -2.2045  -1.0664   0.8142
 E2Z  H20A  H  HCH2  0   0.196  -2.1432   0.3040  -0.2809
 E2Z  H21   H  HCH2  0   0.245  -3.6201  -2.3222  -0.7902
 E2Z  H21A  H  HCH2  0   0.226  -3.5489  -0.9822  -1.9247
 E2Z  H4'   H  HCR6  0   0.252  -7.6456   1.1569   1.6874
 E2Z  H5'   H  HCR6  0   0.235  -6.9043  -1.1165   2.3629
 E2Z  H6'   H  HCR6  0   0.222  -5.0421  -2.2182   1.1830

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
 E2Z  N01  C02   aromatic  1.299  0.020  1.299
 E2Z  N01  C05   aromatic  1.374  0.020  1.374
 E2Z  C02  N03   aromatic  1.364  0.020  1.364
 E2Z  N03  C04   aromatic  1.377  0.020  1.377
 E2Z  N03  C12   single    1.398  0.020  1.398
 E2Z  C04  C05   aromatic  1.358  0.020  1.358
 E2Z  C1'  C2'   aromatic  1.393  0.020  1.393
 E2Z  C1'  C21   single    1.502  0.020  1.502
 E2Z  C1'  C6'   aromatic  1.393  0.020  1.393
 E2Z  N11  C12   aromatic  1.319  0.020  1.319
 E2Z  N11  C16   aromatic  1.328  0.020  1.328
 E2Z  C12  N13   aromatic  1.318  0.020  1.318
 E2Z  N13  C14   aromatic  1.331  0.020  1.331
 E2Z  C14  C15   aromatic  1.391  0.020  1.391
 E2Z  C14  C17   single    1.494  0.020  1.494
 E2Z  C15  C16   aromatic  1.382  0.020  1.382
 E2Z  C17  C18   single    1.529  0.020  1.529
 E2Z  C18  N19   single    1.448  0.020  1.448
 E2Z  N19  C20   single    1.449  0.020  1.449
 E2Z  C2'  C3'   aromatic  1.381  0.020  1.381
 E2Z  C20  C21   single    1.527  0.020  1.527
 E2Z  C3'  C4'   aromatic  1.381  0.020  1.381
 E2Z  C3'  F7'   single    1.345  0.020  1.345
 E2Z  C4'  C5'   aromatic  1.388  0.020  1.388
 E2Z  C5'  C6'   aromatic  1.388  0.020  1.388
 E2Z  C02  H02   single    0.930  0.020  1.080
 E2Z  C04  H04   single    0.930  0.020  1.080
 E2Z  C05  H05   single    0.930  0.020  1.080
 E2Z  C15  H15   single    0.930  0.020  1.080
 E2Z  C16  H16   single    0.930  0.020  1.080
 E2Z  C17  H17   single    0.970  0.020  1.090
 E2Z  C17  H17A  single    0.970  0.020  1.090
 E2Z  C18  H18   single    0.970  0.020  1.090
 E2Z  C18  H18A  single    0.970  0.020  1.090
 E2Z  N19  HN19  single    0.890  0.020  1.040
 E2Z  C2'  H2'   single    0.930  0.020  1.080
 E2Z  C20  H20   single    0.970  0.020  1.090
 E2Z  C20  H20A  single    0.970  0.020  1.090
 E2Z  C21  H21   single    0.970  0.020  1.090
 E2Z  C21  H21A  single    0.970  0.020  1.090
 E2Z  C4'  H4'   single    0.930  0.020  1.080
 E2Z  C5'  H5'   single    0.930  0.020  1.080
 E2Z  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
 E2Z  C05   N01  C02  105.74  3.000
 E2Z  H02   C02  N03  122.06  3.000
 E2Z  H02   C02  N01  126.43  3.000
 E2Z  N03   C02  N01  111.51  3.000
 E2Z  C12   N03  C04  126.71  3.000
 E2Z  C12   N03  C02  126.33  3.000
 E2Z  C04   N03  C02  106.96  3.000
 E2Z  H04   C04  C05  132.37  3.000
 E2Z  H04   C04  N03  122.40  3.000
 E2Z  C05   C04  N03  105.24  3.000
 E2Z  H05   C05  C04  127.59  3.000
 E2Z  H05   C05  N01  121.85  3.000
 E2Z  C04   C05  N01  110.55  3.000
 E2Z  C6'   C1'  C21  120.81  3.000
 E2Z  C6'   C1'  C2'  118.85  3.000
 E2Z  C21   C1'  C2'  120.30  3.000
 E2Z  C16   N11  C12  115.46  3.000
 E2Z  N13   C12  N11  127.53  3.000
 E2Z  N13   C12  N03  116.18  3.000
 E2Z  N11   C12  N03  116.29  3.000
 E2Z  C14   N13  C12  117.00  3.000
 E2Z  C17   C14  C15  122.11  3.000
 E2Z  C17   C14  N13  117.34  3.000
 E2Z  C15   C14  N13  120.53  3.000
 E2Z  H15   C15  C16  121.30  3.000
 E2Z  H15   C15  C14  121.67  3.000
 E2Z  C16   C15  C14  117.03  3.000
 E2Z  H16   C16  C15  120.95  3.000
 E2Z  H16   C16  N11  116.61  3.000
 E2Z  C15   C16  N11  122.44  3.000
 E2Z  H17A  C17  H17  107.75  3.000
 E2Z  H17A  C17  C18  109.45  3.000
 E2Z  H17   C17  C18  109.59  3.000
 E2Z  H17A  C17  C14  109.94  3.000
 E2Z  H17   C17  C14  109.07  3.000
 E2Z  C18   C17  C14  110.98  3.000
 E2Z  H18A  C18  H18  106.44  3.000
 E2Z  H18A  C18  N19  113.16  3.000
 E2Z  H18   C18  N19  108.10  3.000
 E2Z  H18A  C18  C17  109.20  3.000
 E2Z  H18   C18  C17  109.22  3.000
 E2Z  N19   C18  C17  110.57  3.000
 E2Z  HN19  N19  C20  108.90  3.000
 E2Z  HN19  N19  C18  109.03  3.000
 E2Z  C20   N19  C18  112.70  3.000
 E2Z  H2'   C2'  C3'  119.92  3.000
 E2Z  H2'   C2'  C1'  120.75  3.000
 E2Z  C3'   C2'  C1'  119.33  3.000
 E2Z  H20A  C20  H20  106.15  3.000
 E2Z  H20A  C20  C21  109.37  3.000
 E2Z  H20   C20  C21  109.09  3.000
 E2Z  H20A  C20  N19  112.84  3.000
 E2Z  H20   C20  N19  108.29  3.000
 E2Z  C21   C20  N19  110.93  3.000
 E2Z  H21A  C21  H21  107.03  3.000
 E2Z  H21A  C21  C20  109.34  3.000
 E2Z  H21   C21  C20  108.89  3.000
 E2Z  H21A  C21  C1'  109.99  3.000
 E2Z  H21   C21  C1'  110.10  3.000
 E2Z  C20   C21  C1'  111.39  3.000
 E2Z  F7'   C3'  C4'  118.82  3.000
 E2Z  F7'   C3'  C2'  118.59  3.000
 E2Z  C4'   C3'  C2'  122.59  3.000
 E2Z  H4'   C4'  C5'  121.45  3.000
 E2Z  H4'   C4'  C3'  120.70  3.000
 E2Z  C5'   C4'  C3'  117.85  3.000
 E2Z  H5'   C5'  C6'  119.89  3.000
 E2Z  H5'   C5'  C4'  119.45  3.000
 E2Z  C6'   C5'  C4'  120.67  3.000
 E2Z  H6'   C6'  C5'  119.73  3.000
 E2Z  H6'   C6'  C1'  119.56  3.000
 E2Z  C5'   C6'  C1'  120.71  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
 E2Z  CONST_01  C04  N03  C02  N01     0.00   0.0  0
 E2Z  CONST_02  C12  N03  C02  N01   180.00   0.0  0
 E2Z  CONST_03  N03  C04  C05  N01     0.00   0.0  0
 E2Z  CONST_04  C04  C05  N01  C02     0.00   0.0  0
 E2Z  CONST_05  C05  C04  N03  C02     0.00   0.0  0
 E2Z  CONST_06  N11  C12  N03  C02   180.00   0.0  0
 E2Z  CONST_07  N13  C12  N03  C02     0.00   0.0  0
 E2Z  CONST_08  C05  N01  C02  N03     0.00   0.0  0
 E2Z  CONST_09  C16  N11  C12  N03   180.00   0.0  0
 E2Z  CONST_10  C14  N13  C12  N03   180.00   0.0  0
 E2Z  CONST_11  N11  C12  N03  C04     0.00   0.0  0
 E2Z  CONST_12  N13  C12  N03  C04   180.00   0.0  0
 E2Z  CONST_13  C12  N03  C04  C05   180.00   0.0  0
 E2Z  CONST_14  C4'  C3'  C2'  C1'     0.00   0.0  0
 E2Z  CONST_15  C4'  C5'  C6'  C1'     0.00   0.0  0
 E2Z  CONST_16  C14  N13  C12  N11     0.00   0.0  0
 E2Z  CONST_17  C14  C15  C16  N11     0.00   0.0  0
 E2Z  CONST_18  C15  C16  N11  C12     0.00   0.0  0
 E2Z  CONST_19  C15  C14  N13  C12     0.00   0.0  0
 E2Z  CONST_20  C16  N11  C12  N13     0.00   0.0  0
 E2Z  CONST_21  C16  C15  C14  N13     0.00   0.0  0
 E2Z  CONST_22  C5'  C6'  C1'  C2'     0.00   0.0  0
 E2Z  CONST_23  C5'  C4'  C3'  C2'     0.00   0.0  0
 E2Z  CONST_24  C6'  C1'  C2'  C3'     0.00   0.0  0
 E2Z  CONST_25  C6'  C5'  C4'  C3'     0.00   0.0  0
 E2Z  CONST_26  F7'  C3'  C2'  C1'   180.00   0.0  0
 E2Z  CONST_27  C17  C14  N13  C12   180.00   0.0  0
 E2Z  CONST_28  C17  C14  C15  C16   180.00   0.0  0
 E2Z  CONST_29  C3'  C2'  C1'  C21   180.00   0.0  0
 E2Z  CONST_30  C5'  C6'  C1'  C21   180.00   0.0  0
 E2Z  CONST_31  F7'  C3'  C4'  C5'   180.00   0.0  0
 E2Z  CONST_32  H04  C04  C05  N01   180.00   0.0  0
 E2Z  CONST_33  H05  C05  N01  C02   180.00   0.0  0
 E2Z  CONST_34  H02  C02  N03  C04   180.00   0.0  0
 E2Z  CONST_35  H5'  C5'  C6'  C1'   180.00   0.0  0
 E2Z  CONST_36  H15  C15  C16  N11   180.00   0.0  0
 E2Z  CONST_37  H16  C16  N11  C12   180.00   0.0  0
 E2Z  CONST_38  H6'  C6'  C1'  C2'   180.00   0.0  0
 E2Z  CONST_39  H4'  C4'  C3'  C2'   180.00   0.0  0
 E2Z  CONST_40  H2'  C2'  C3'  C4'   180.00   0.0  0
 E2Z  Var_01    C18  C17  C14  N13   -71.40  30.0  2
 E2Z  Var_02    C20  C21  C1'  C2'    84.44  30.0  2
 E2Z  Var_03    N19  C20  C21  C1'   178.46  30.0  1
 E2Z  Var_04    N19  C18  C17  C14  -176.89  30.0  3
 E2Z  Var_05    C20  N19  C18  C17   177.96  30.0  3
 E2Z  Var_06    C21  C20  N19  C18  -176.02  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
 E2Z  plan-1  N01  0.020
 E2Z  plan-1  C02  0.020
 E2Z  plan-1  N03  0.020
 E2Z  plan-1  C04  0.020
 E2Z  plan-1  C05  0.020
 E2Z  plan-1  C12  0.020
 E2Z  plan-1  H02  0.020
 E2Z  plan-1  H04  0.020
 E2Z  plan-1  H05  0.020
 E2Z  plan-2  C1'  0.020
 E2Z  plan-2  C2'  0.020
 E2Z  plan-2  C21  0.020
 E2Z  plan-2  C3'  0.020
 E2Z  plan-2  C4'  0.020
 E2Z  plan-2  C5'  0.020
 E2Z  plan-2  C6'  0.020
 E2Z  plan-2  F7'  0.020
 E2Z  plan-2  H2'  0.020
 E2Z  plan-2  H4'  0.020
 E2Z  plan-2  H5'  0.020
 E2Z  plan-2  H6'  0.020
 E2Z  plan-3  N03  0.020
 E2Z  plan-3  N11  0.020
 E2Z  plan-3  C12  0.020
 E2Z  plan-3  N13  0.020
 E2Z  plan-3  C14  0.020
 E2Z  plan-3  C15  0.020
 E2Z  plan-3  C16  0.020
 E2Z  plan-3  C17  0.020
 E2Z  plan-3  H15  0.020
 E2Z  plan-3  H16  0.020

