# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 14:36:14 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)-2-methylpropane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CNCc1cc(Cl)cc(Cl)c1)CNc2[nH]c3cccnc3n2
#
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
 4RN  4RN  (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)-2-methylpropane-1,3-diamine  ligand  43  24  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4RN
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
 4RN  C1   C   CH1   0  -0.300  -0.9066  -0.0132   0.2342
 4RN  C2   C   CH2   0  -0.239   0.1405  -0.1593  -0.8664
 4RN  C3   C   CH2   0  -0.301   2.4990  -0.2160  -1.3655
 4RN  C4   C   CR6   0   0.063   3.8898  -0.1283  -0.7928
 4RN  C5   C   CR16  0  -0.261   4.9329  -0.8238  -1.3936
 4RN  C6   C   CR6   0  -0.026   6.2160  -0.7097  -0.8837
 4RN  C7   C   CR16  0  -0.193   6.4963   0.0766   0.2213
 4RN  N1   N   NH1   0  -0.685  -3.2851   0.4473   0.5742
 4RN  N2   N   NR15  0  -0.738  -5.1457  -0.2281  -0.7315
 4RN  N3   N   N     0  -0.438  -7.9086   0.8439   1.0924
 4RN  N4   N   N     0  -0.533  -5.5153   0.8648   1.1868
 4RN  C8   C   CR6   0  -0.024   5.4397   0.7570   0.8069
 4RN  CL1  CL  CL    0  -0.118   5.7543   1.7476   2.1928
 4RN  CL   CL  CL    0  -0.117   7.5081  -1.5807  -1.6387
 4RN  C9   C   CR16  0  -0.247   4.1473   0.6669   0.3200
 4RN  N    N   NH1   0  -0.609   1.4880  -0.1740  -0.3320
 4RN  C    C   CH3   0  -0.672  -0.8563  -1.1576   1.2415
 4RN  C10  C   CH2   0  -0.262  -2.2850   0.1004  -0.4119
 4RN  C11  C   CR5   0   0.694  -4.6071   0.3814   0.3635
 4RN  C16  C   CR56  0   0.277  -6.7122   0.5541   0.6094
 4RN  C12  C   CR56  0   0.269  -6.5109  -0.1383  -0.6058
 4RN  C15  C   CR16  0  -0.109  -8.9448   0.4421   0.3555
 4RN  C14  C   CR16  0  -0.347  -8.8377  -0.2407  -0.8509
 4RN  C13  C   CR16  0  -0.227  -7.5785  -0.5528  -1.3658
 4RN  H1   H   HCH1  0   0.238  -0.6999   0.9295   0.7552
 4RN  H2   H   HCH2  0   0.195  -0.0846  -1.0558  -1.4683
 4RN  H3   H   HCH2  0   0.232   0.0600   0.6942  -1.5465
 4RN  H4   H   HCH2  0   0.253   2.3432   0.6417  -2.0285
 4RN  H5   H   HCH2  0   0.224   2.4314  -1.1067  -2.0077
 4RN  H6   H   HCR6  0   0.279   4.7431  -1.4533  -2.2533
 4RN  H7   H   HCR6  0   0.299   7.5000   0.1540   0.6147
 4RN  H8   H   HNH1  0   0.400  -3.0056   1.0613   1.3233
 4RN  H9   H   HNR5  0   0.427  -4.6463  -0.6605  -1.4921
 4RN  H11  H   HCR6  0   0.276   3.3391   1.2026   0.7984
 4RN  H12  H   HNH1  0   0.354   1.6055  -0.9818   0.2680
 4RN  H14  H   HCH3  0   0.222  -0.9454  -2.1236   0.7388
 4RN  H15  H   HCH3  0   0.236   0.0758  -1.1574   1.8072
 4RN  H16  H   HCH3  0   0.241  -1.6667  -1.0837   1.9660
 4RN  H17  H   HCH2  0   0.246  -2.2567   0.8417  -1.2195
 4RN  H18  H   HCH2  0   0.237  -2.5450  -0.8610  -0.8641
 4RN  H19  H   HCR6  0   0.249  -9.9281   0.6760   0.7481
 4RN  H20  H   HCR6  0   0.262  -9.7339  -0.5258  -1.3839
 4RN  H21  H   HCR6  0   0.274  -7.4596  -1.0863  -2.2997

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
 4RN  CL1  C8   single    1.732  0.020  1.732
 4RN  C8   C9   aromatic  1.384  0.020  1.384
 4RN  C8   C7   aromatic  1.386  0.020  1.386
 4RN  C9   C4   aromatic  1.392  0.020  1.392
 4RN  C7   C6   aromatic  1.385  0.020  1.385
 4RN  C3   C4   single    1.507  0.020  1.507
 4RN  C3   N    single    1.446  0.020  1.446
 4RN  C4   C5   aromatic  1.390  0.020  1.390
 4RN  CL   C6   single    1.732  0.020  1.732
 4RN  C6   C5   aromatic  1.385  0.020  1.385
 4RN  N    C2   single    1.450  0.020  1.450
 4RN  C2   C1   single    1.526  0.020  1.526
 4RN  C    C1   single    1.525  0.020  1.525
 4RN  C1   C10  single    1.527  0.020  1.527
 4RN  C10  N1   single    1.447  0.020  1.447
 4RN  N1   C11  single    1.340  0.020  1.340
 4RN  C11  N4   aromatic  1.318  0.020  1.318
 4RN  C11  N2   aromatic  1.364  0.020  1.364
 4RN  N4   C16  aromatic  1.365  0.020  1.365
 4RN  N2   C12  aromatic  1.374  0.020  1.374
 4RN  C16  C12  aromatic  1.413  0.020  1.413
 4RN  C16  N3   aromatic  1.322  0.020  1.322
 4RN  C12  C13  aromatic  1.374  0.020  1.374
 4RN  N3   C15  aromatic  1.333  0.020  1.333
 4RN  C13  C14  aromatic  1.396  0.020  1.396
 4RN  C15  C14  aromatic  1.390  0.020  1.390
 4RN  C1   H1   single    0.970  0.020  1.090
 4RN  C2   H2   single    0.970  0.020  1.090
 4RN  C2   H3   single    0.970  0.020  1.090
 4RN  C3   H4   single    0.970  0.020  1.090
 4RN  C3   H5   single    0.970  0.020  1.090
 4RN  C5   H6   single    0.930  0.020  1.080
 4RN  C7   H7   single    0.930  0.020  1.080
 4RN  N1   H8   single    0.890  0.020  1.040
 4RN  N2   H9   single    0.860  0.020  1.020
 4RN  C9   H11  single    0.930  0.020  1.080
 4RN  N    H12  single    0.890  0.020  1.040
 4RN  C    H14  single    0.970  0.020  1.090
 4RN  C    H15  single    0.970  0.020  1.090
 4RN  C    H16  single    0.970  0.020  1.090
 4RN  C10  H17  single    0.970  0.020  1.090
 4RN  C10  H18  single    0.970  0.020  1.090
 4RN  C15  H19  single    0.930  0.020  1.080
 4RN  C14  H20  single    0.930  0.020  1.080
 4RN  C13  H21  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
 4RN  H1   C1   C10  107.89  3.000
 4RN  H1   C1   C    108.96  3.000
 4RN  C10  C1   C    111.41  3.000
 4RN  H1   C1   C2   107.20  3.000
 4RN  C10  C1   C2   108.75  3.000
 4RN  C    C1   C2   112.44  3.000
 4RN  H3   C2   H2   106.25  3.000
 4RN  H3   C2   N    107.78  3.000
 4RN  H2   C2   N    112.49  3.000
 4RN  H3   C2   C1   108.85  3.000
 4RN  H2   C2   C1   109.35  3.000
 4RN  N    C2   C1   111.90  3.000
 4RN  H5   C3   H4   105.78  3.000
 4RN  H5   C3   N    113.43  3.000
 4RN  H4   C3   N    108.08  3.000
 4RN  H5   C3   C4   109.01  3.000
 4RN  H4   C3   C4   108.41  3.000
 4RN  N    C3   C4   111.84  3.000
 4RN  C9   C4   C5   119.51  3.000
 4RN  C5   C4   C3   119.95  3.000
 4RN  C9   C4   C3   120.53  3.000
 4RN  H6   C5   C6   120.18  3.000
 4RN  H6   C5   C4   120.17  3.000
 4RN  C6   C5   C4   119.64  3.000
 4RN  CL   C6   C7   118.85  3.000
 4RN  CL   C6   C5   119.28  3.000
 4RN  C7   C6   C5   121.86  3.000
 4RN  H7   C7   C8   121.26  3.000
 4RN  H7   C7   C6   121.26  3.000
 4RN  C8   C7   C6   117.48  3.000
 4RN  H8   N1   C11  114.85  3.000
 4RN  H8   N1   C10  117.45  3.000
 4RN  C11  N1   C10  124.25  3.000
 4RN  H9   N2   C12  126.14  3.000
 4RN  H9   N2   C11  127.02  3.000
 4RN  C12  N2   C11  106.84  3.000
 4RN  C15  N3   C16  115.79  3.000
 4RN  C16  N4   C11  104.87  3.000
 4RN  C9   C8   CL1  119.22  3.000
 4RN  C9   C8   C7   122.08  3.000
 4RN  CL1  C8   C7   118.70  3.000
 4RN  H11  C9   C8   120.67  3.000
 4RN  H11  C9   C4   119.91  3.000
 4RN  C8   C9   C4   119.42  3.000
 4RN  H12  N    C3   108.60  3.000
 4RN  H12  N    C2   109.53  3.000
 4RN  C3   N    C2   112.75  3.000
 4RN  H16  C    H15  106.91  3.000
 4RN  H16  C    H14  107.77  3.000
 4RN  H15  C    H14  107.97  3.000
 4RN  H16  C    C1   111.33  3.000
 4RN  H15  C    C1   111.76  3.000
 4RN  H14  C    C1   110.90  3.000
 4RN  H18  C10  H17  107.21  3.000
 4RN  H18  C10  N1   109.16  3.000
 4RN  H17  C10  N1   110.96  3.000
 4RN  H18  C10  C1   108.92  3.000
 4RN  H17  C10  C1   109.80  3.000
 4RN  N1   C10  C1   110.70  3.000
 4RN  N4   C11  N2   113.16  3.000
 4RN  N2   C11  N1   122.53  3.000
 4RN  N4   C11  N1   124.30  3.000
 4RN  C12  C16  N4   110.52  3.000
 4RN  C12  C16  N3   123.40  3.000
 4RN  N4   C16  N3   126.09  3.000
 4RN  C13  C12  C16  120.84  3.000
 4RN  C13  C12  N2   134.54  3.000
 4RN  C16  C12  N2   104.61  3.000
 4RN  H19  C15  C14  119.34  3.000
 4RN  H19  C15  N3   116.07  3.000
 4RN  C14  C15  N3   124.59  3.000
 4RN  H20  C14  C13  120.47  3.000
 4RN  H20  C14  C15  119.57  3.000
 4RN  C13  C14  C15  119.96  3.000
 4RN  H21  C13  C14  121.85  3.000
 4RN  H21  C13  C12  122.73  3.000
 4RN  C14  C13  C12  115.42  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
 4RN  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 4RN  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 4RN  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 4RN  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 4RN  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 4RN  CONST_06  C9   C4   C5   C6      0.00   0.0  0
 4RN  CONST_07  C16  N4   C11  N2      0.00   0.0  0
 4RN  CONST_08  N4   C16  C12  N2      0.00   0.0  0
 4RN  CONST_09  N3   C16  C12  N2    180.00   0.0  0
 4RN  CONST_10  C14  C13  C12  N2    180.00   0.0  0
 4RN  CONST_11  C11  N4   C16  N3    180.00   0.0  0
 4RN  CONST_12  C13  C12  C16  N3      0.00   0.0  0
 4RN  CONST_13  C13  C14  C15  N3      0.00   0.0  0
 4RN  CONST_14  C12  N2   C11  N4      0.00   0.0  0
 4RN  CONST_15  C13  C12  C16  N4    180.00   0.0  0
 4RN  CONST_16  C15  N3   C16  N4    180.00   0.0  0
 4RN  CONST_17  C12  C16  N4   C11     0.00   0.0  0
 4RN  CONST_18  C16  C12  N2   C11     0.00   0.0  0
 4RN  CONST_19  C13  C12  N2   C11   180.00   0.0  0
 4RN  CONST_20  C14  C13  C12  C16     0.00   0.0  0
 4RN  CONST_21  C14  C15  N3   C16     0.00   0.0  0
 4RN  CONST_22  C15  N3   C16  C12     0.00   0.0  0
 4RN  CONST_23  C15  C14  C13  C12     0.00   0.0  0
 4RN  CONST_24  C8   C9   C4   C3    180.00   0.0  0
 4RN  CONST_25  C6   C5   C4   C3    180.00   0.0  0
 4RN  CONST_26  CL1  C8   C9   C4    180.00   0.0  0
 4RN  CONST_27  CL   C6   C5   C4    180.00   0.0  0
 4RN  CONST_28  CL1  C8   C7   C6    180.00   0.0  0
 4RN  CONST_29  C16  N4   C11  N1    180.00   0.0  0
 4RN  CONST_30  C12  N2   C11  N1    180.00   0.0  0
 4RN  CONST_31  CL   C6   C7   C8    180.00   0.0  0
 4RN  CONST_32  H11  C9   C4   C5    180.00   0.0  0
 4RN  CONST_33  H7   C7   C6   C5    180.00   0.0  0
 4RN  CONST_34  H6   C5   C6   C7    180.00   0.0  0
 4RN  CONST_35  H21  C13  C12  N2      0.00   0.0  0
 4RN  CONST_36  H20  C14  C15  N3    180.00   0.0  0
 4RN  CONST_37  H9   N2   C11  N4    180.00   0.0  0
 4RN  CONST_38  H19  C15  N3   C16   180.00   0.0  0
 4RN  CONST_39  C10  N1   C11  N2      0.00   0.0  0
 4RN  CONST_40  C10  N1   C11  N4    180.00   0.0  0
 4RN  CONST_41  H8   N1   C11  N2    180.00   0.0  0
 4RN  Var_01    N    C3   C4   C5    145.40  30.0  2
 4RN  Var_02    C11  N1   C10  C1   -167.38  30.0  3
 4RN  Var_03    C4   C3   N    C2    175.80  30.0  1
 4RN  Var_04    C3   N    C2   C1   -175.87  30.0  1

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
 4RN  chir_01  C1  C2  C  C10  positiv

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
 4RN  plan-1  C3   0.020
 4RN  plan-1  C4   0.020
 4RN  plan-1  C5   0.020
 4RN  plan-1  C6   0.020
 4RN  plan-1  C7   0.020
 4RN  plan-1  C8   0.020
 4RN  plan-1  CL1  0.020
 4RN  plan-1  CL   0.020
 4RN  plan-1  C9   0.020
 4RN  plan-1  H6   0.020
 4RN  plan-1  H7   0.020
 4RN  plan-1  H11  0.020
 4RN  plan-2  N1   0.020
 4RN  plan-2  N2   0.020
 4RN  plan-2  N3   0.020
 4RN  plan-2  N4   0.020
 4RN  plan-2  C11  0.020
 4RN  plan-2  C16  0.020
 4RN  plan-2  C12  0.020
 4RN  plan-2  C15  0.020
 4RN  plan-2  C14  0.020
 4RN  plan-2  C13  0.020
 4RN  plan-2  H9   0.020
 4RN  plan-2  H19  0.020
 4RN  plan-2  H20  0.020
 4RN  plan-2  H21  0.020
 4RN  plan-3  N1   0.020
 4RN  plan-3  C10  0.020
 4RN  plan-3  C11  0.020
 4RN  plan-3  H8   0.020

