# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:04:59 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)cc(CNCCCNc2[nH]c3cccnc3n2)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
 4RP  4RP  N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine  ligand  40  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4RP
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
 4RP  C1   C   CR16  0  -0.193   6.4504  -0.1114   0.3792
 4RP  C2   C   CR6   0  -0.023   5.3841  -0.8785   0.8226
 4RP  C3   C   CR16  0  -0.247   4.1083  -0.7329   0.3058
 4RP  C4   C   CR6   0   0.065   3.8782   0.2106  -0.6910
 4RP  C5   C   CH2   0  -0.300   2.5085   0.3627  -1.3008
 4RP  C6   C   CH2   0  -0.251   0.1317   0.1595  -0.9154
 4RP  C7   C   CH2   0  -0.484  -0.9205  -0.1505   0.1368
 4RP  N1   N   NH1   0  -0.684  -3.2938  -0.4562   0.5759
 4RP  C8   C   CH2   0  -0.275  -2.3218  -0.1404  -0.4499
 4RP  C9   C   CR5   0   0.691  -4.6197  -0.3775   0.3931
 4RP  C10  C   CR56  0   0.269  -6.5333   0.1596  -0.5460
 4RP  C11  C   CR16  0  -0.227  -7.6088   0.5824  -1.2902
 4RP  N2   N   NR15  0  -0.738  -5.1698   0.2261  -0.6992
 4RP  C12  C   CR16  0  -0.347  -8.8625   0.2975  -0.7472
 4RP  C13  C   CR16  0  -0.109  -8.9570  -0.3688   0.4695
 4RP  C14  C   CR56  0   0.277  -6.7218  -0.5141   0.6816
 4RP  C15  C   CR16  0  -0.261   4.9313   0.9953  -1.1474
 4RP  N3   N   N     0  -0.438  -7.9132  -0.7782   1.1913
 4RP  CL1  CL  CL    0  -0.118   5.6655  -2.0539   2.0636
 4RP  C    C   CR6   0  -0.026   6.1974   0.8218  -0.6124
 4RP  CL   CL  CL    0  -0.117   7.5010   1.8056  -1.1872
 4RP  N    N   NH1   0  -0.601   1.4586   0.1476  -0.3302
 4RP  N4   N   N     0  -0.532  -5.5187  -0.8365   1.2401
 4RP  H1   H   HCR6  0   0.299   7.4405  -0.2334   0.7954
 4RP  H2   H   HCR6  0   0.275   3.2917  -1.3395   0.6722
 4RP  H3   H   HCH2  0   0.223   2.4477   1.3383  -1.8055
 4RP  H4   H   HCH2  0   0.253   2.3993  -0.3895  -2.0891
 4RP  H5   H   HCH2  0   0.226   0.0988  -0.6033  -1.6991
 4RP  H6   H   HCH2  0   0.198  -0.1080   1.1166  -1.4046
 4RP  H7   H   HCH2  0   0.239  -0.7090  -1.1305   0.5741
 4RP  H8   H   HCH2  0   0.239  -0.8667   0.5832   0.9466
 4RP  H9   H   HNH1  0   0.401  -3.0022  -1.0642   1.3251
 4RP  H10  H   HCH2  0   0.241  -2.5354   0.8538  -0.8519
 4RP  H11  H   HCH2  0   0.238  -2.3819  -0.8480  -1.2854
 4RP  H12  H   HCR6  0   0.274  -7.4993   1.1029  -2.2327
 4RP  H13  H   HNR5  0   0.428  -4.6775   0.6435  -1.4728
 4RP  H14  H   HCR6  0   0.262  -9.7643   0.5907  -1.2663
 4RP  H15  H   HCR6  0   0.249  -9.9362  -0.5821   0.8837
 4RP  H16  H   HCR6  0   0.279   4.7626   1.7403  -1.9141
 4RP  H17  H   HNH1  0   0.347   1.5141   0.8677   0.3810

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
 4RP  C12  C13  aromatic  1.390  0.020  1.390
 4RP  C12  C11  aromatic  1.396  0.020  1.396
 4RP  C13  N3   aromatic  1.333  0.020  1.333
 4RP  C11  C10  aromatic  1.375  0.020  1.375
 4RP  N3   C14  aromatic  1.322  0.020  1.322
 4RP  C10  C14  aromatic  1.413  0.020  1.413
 4RP  C10  N2   aromatic  1.374  0.020  1.374
 4RP  C14  N4   aromatic  1.365  0.020  1.365
 4RP  N2   C9   aromatic  1.364  0.020  1.364
 4RP  N4   C9   aromatic  1.318  0.020  1.318
 4RP  C9   N1   single    1.341  0.020  1.341
 4RP  N1   C8   single    1.448  0.020  1.448
 4RP  C8   C7   single    1.519  0.020  1.519
 4RP  C7   C6   single    1.520  0.020  1.520
 4RP  C6   N    single    1.450  0.020  1.450
 4RP  N    C5   single    1.446  0.020  1.446
 4RP  C15  C    aromatic  1.385  0.020  1.385
 4RP  C15  C4   aromatic  1.390  0.020  1.390
 4RP  C    C1   aromatic  1.385  0.020  1.385
 4RP  C    CL   single    1.731  0.020  1.731
 4RP  C1   C2   aromatic  1.386  0.020  1.386
 4RP  C4   C3   aromatic  1.392  0.020  1.392
 4RP  C4   C5   single    1.507  0.020  1.507
 4RP  C3   C2   aromatic  1.384  0.020  1.384
 4RP  C2   CL1  single    1.732  0.020  1.732
 4RP  C1   H1   single    0.930  0.020  1.080
 4RP  C3   H2   single    0.930  0.020  1.080
 4RP  C5   H3   single    0.970  0.020  1.090
 4RP  C5   H4   single    0.970  0.020  1.090
 4RP  C6   H5   single    0.970  0.020  1.090
 4RP  C6   H6   single    0.970  0.020  1.090
 4RP  C7   H7   single    0.970  0.020  1.090
 4RP  C7   H8   single    0.970  0.020  1.090
 4RP  N1   H9   single    0.890  0.020  1.040
 4RP  C8   H10  single    0.970  0.020  1.090
 4RP  C8   H11  single    0.970  0.020  1.090
 4RP  C11  H12  single    0.930  0.020  1.080
 4RP  N2   H13  single    0.860  0.020  1.020
 4RP  C12  H14  single    0.930  0.020  1.080
 4RP  C13  H15  single    0.930  0.020  1.080
 4RP  C15  H16  single    0.930  0.020  1.080
 4RP  N    H17  single    0.890  0.020  1.040

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
 4RP  H1   C1   C    121.27  3.000
 4RP  H1   C1   C2   121.25  3.000
 4RP  C    C1   C2   117.47  3.000
 4RP  CL1  C2   C3   119.25  3.000
 4RP  CL1  C2   C1   118.66  3.000
 4RP  C3   C2   C1   122.09  3.000
 4RP  H2   C3   C4   119.88  3.000
 4RP  H2   C3   C2   120.70  3.000
 4RP  C4   C3   C2   119.42  3.000
 4RP  C15  C4   C5   119.91  3.000
 4RP  C5   C4   C3   120.57  3.000
 4RP  C15  C4   C3   119.50  3.000
 4RP  H4   C5   H3   105.87  3.000
 4RP  H4   C5   N    107.97  3.000
 4RP  H3   C5   N    113.57  3.000
 4RP  H4   C5   C4   108.21  3.000
 4RP  H3   C5   C4   108.99  3.000
 4RP  N    C5   C4   111.92  3.000
 4RP  H6   C6   H5   106.33  3.000
 4RP  H6   C6   N    112.68  3.000
 4RP  H5   C6   N    108.11  3.000
 4RP  H6   C6   C7   109.52  3.000
 4RP  H5   C6   C7   109.44  3.000
 4RP  N    C6   C7   110.63  3.000
 4RP  H8   C7   H7   107.19  3.000
 4RP  H8   C7   C8   109.07  3.000
 4RP  H7   C7   C8   109.80  3.000
 4RP  H8   C7   C6   109.97  3.000
 4RP  H7   C7   C6   109.00  3.000
 4RP  C8   C7   C6   111.70  3.000
 4RP  H9   N1   C9   115.01  3.000
 4RP  H9   N1   C8   117.64  3.000
 4RP  C9   N1   C8   123.67  3.000
 4RP  H11  C8   H10  107.21  3.000
 4RP  H11  C8   N1   111.24  3.000
 4RP  H10  C8   N1   109.12  3.000
 4RP  H11  C8   C7   109.91  3.000
 4RP  H10  C8   C7   109.16  3.000
 4RP  N1   C8   C7   110.13  3.000
 4RP  N4   C9   N2   113.19  3.000
 4RP  N4   C9   N1   124.52  3.000
 4RP  N2   C9   N1   122.28  3.000
 4RP  C14  C10  N2   104.62  3.000
 4RP  N2   C10  C11  134.53  3.000
 4RP  C14  C10  C11  120.85  3.000
 4RP  H12  C11  C12  121.86  3.000
 4RP  H12  C11  C10  122.71  3.000
 4RP  C12  C11  C10  115.43  3.000
 4RP  H13  N2   C10  126.21  3.000
 4RP  H13  N2   C9   126.96  3.000
 4RP  C10  N2   C9   106.83  3.000
 4RP  H14  C12  C13  119.56  3.000
 4RP  H14  C12  C11  120.48  3.000
 4RP  C13  C12  C11  119.96  3.000
 4RP  H15  C13  N3   116.08  3.000
 4RP  H15  C13  C12  119.34  3.000
 4RP  N3   C13  C12  124.58  3.000
 4RP  N4   C14  N3   126.10  3.000
 4RP  N4   C14  C10  110.52  3.000
 4RP  N3   C14  C10  123.39  3.000
 4RP  H16  C15  C    120.14  3.000
 4RP  H16  C15  C4   120.20  3.000
 4RP  C    C15  C4   119.66  3.000
 4RP  C14  N3   C13  115.80  3.000
 4RP  CL   C    C15  119.26  3.000
 4RP  CL   C    C1   118.88  3.000
 4RP  C15  C    C1   121.86  3.000
 4RP  H17  N    C6   109.11  3.000
 4RP  H17  N    C5   108.99  3.000
 4RP  C6   N    C5   113.10  3.000
 4RP  C14  N4   C9   104.84  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
 4RP  CONST_01  C4   C15  C    C1      0.00   0.0  0
 4RP  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 4RP  CONST_03  C15  C    C1   C2      0.00   0.0  0
 4RP  CONST_04  C15  C4   C3   C2      0.00   0.0  0
 4RP  CONST_05  C    C15  C4   C3      0.00   0.0  0
 4RP  CONST_06  C    C1   C2   C3      0.00   0.0  0
 4RP  CONST_07  C11  C10  N2   C9    180.00   0.0  0
 4RP  CONST_08  C14  C10  N2   C9      0.00   0.0  0
 4RP  CONST_09  N3   C14  N4   C9    180.00   0.0  0
 4RP  CONST_10  C10  C14  N4   C9      0.00   0.0  0
 4RP  CONST_11  C13  C12  C11  C10     0.00   0.0  0
 4RP  CONST_12  C13  N3   C14  C10     0.00   0.0  0
 4RP  CONST_13  N4   C9   N2   C10     0.00   0.0  0
 4RP  CONST_14  N3   C13  C12  C11     0.00   0.0  0
 4RP  CONST_15  N3   C14  C10  C11     0.00   0.0  0
 4RP  CONST_16  N4   C14  C10  C11   180.00   0.0  0
 4RP  CONST_17  C12  C11  C10  N2    180.00   0.0  0
 4RP  CONST_18  N3   C14  C10  N2    180.00   0.0  0
 4RP  CONST_19  N4   C14  C10  N2      0.00   0.0  0
 4RP  CONST_20  C14  N4   C9   N2      0.00   0.0  0
 4RP  CONST_21  C14  N3   C13  C12     0.00   0.0  0
 4RP  CONST_22  C14  C10  C11  C12     0.00   0.0  0
 4RP  CONST_23  N4   C14  N3   C13   180.00   0.0  0
 4RP  CONST_24  CL   C    C1   C2    180.00   0.0  0
 4RP  CONST_25  C5   C4   C3   C2    180.00   0.0  0
 4RP  CONST_26  CL   C    C15  C4    180.00   0.0  0
 4RP  CONST_27  CL1  C2   C3   C4    180.00   0.0  0
 4RP  CONST_28  C    C15  C4   C5    180.00   0.0  0
 4RP  CONST_29  C10  N2   C9   N1    180.00   0.0  0
 4RP  CONST_30  C14  N4   C9   N1    180.00   0.0  0
 4RP  CONST_31  C    C1   C2   CL1   180.00   0.0  0
 4RP  CONST_32  H16  C15  C    C1    180.00   0.0  0
 4RP  CONST_33  H2   C3   C2   C1    180.00   0.0  0
 4RP  CONST_34  H1   C1   C2   C3    180.00   0.0  0
 4RP  CONST_35  H14  C12  C11  C10   180.00   0.0  0
 4RP  CONST_36  H15  C13  C12  C11   180.00   0.0  0
 4RP  CONST_37  H13  N2   C10  C11     0.00   0.0  0
 4RP  CONST_38  H12  C11  C10  N2      0.00   0.0  0
 4RP  CONST_39  N2   C9   N1   C8      0.00   0.0  0
 4RP  CONST_40  N4   C9   N1   C8    180.00   0.0  0
 4RP  CONST_41  H9   N1   C9   N2    180.00   0.0  0
 4RP  Var_01    N    C5   C4   C3     35.35  30.0  2
 4RP  Var_02    C6   N    C5   C4   -174.38  30.0  1
 4RP  Var_03    C9   N1   C8   C7    172.34  30.0  2
 4RP  Var_04    C7   C6   N    C5    176.74  30.0  2
 4RP  Var_05    N1   C8   C7   C6    179.26  30.0  1
 4RP  Var_06    N    C6   C7   C8    179.84  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
 4RP  plan-1  C1   0.020
 4RP  plan-1  C2   0.020
 4RP  plan-1  C3   0.020
 4RP  plan-1  C4   0.020
 4RP  plan-1  C5   0.020
 4RP  plan-1  C15  0.020
 4RP  plan-1  CL1  0.020
 4RP  plan-1  C    0.020
 4RP  plan-1  CL   0.020
 4RP  plan-1  H1   0.020
 4RP  plan-1  H2   0.020
 4RP  plan-1  H16  0.020
 4RP  plan-2  N1   0.020
 4RP  plan-2  C9   0.020
 4RP  plan-2  C10  0.020
 4RP  plan-2  C11  0.020
 4RP  plan-2  N2   0.020
 4RP  plan-2  C12  0.020
 4RP  plan-2  C13  0.020
 4RP  plan-2  C14  0.020
 4RP  plan-2  N3   0.020
 4RP  plan-2  N4   0.020
 4RP  plan-2  H12  0.020
 4RP  plan-2  H13  0.020
 4RP  plan-2  H14  0.020
 4RP  plan-2  H15  0.020
 4RP  plan-3  N1   0.020
 4RP  plan-3  C8   0.020
 4RP  plan-3  C9   0.020
 4RP  plan-3  H9   0.020

