# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 23:29:30 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(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
 4RO  4RO  N-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine  ligand  40  25  .  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_4RO
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
 4RO  C4   C   CR16  0  -0.318  -4.4869   1.2931  -1.0423
 4RO  C2   C   CH2   0  -0.328  -2.4018  -0.0083  -1.5650
 4RO  C3   C   CR6   0   0.171  -3.5191   0.3850  -0.6339
 4RO  C1   C   CH2   0  -0.373  -0.0785  -0.6823  -1.6296
 4RO  C7   C   CR6   0   0.077  -4.6524   0.1544   1.4644
 4RO  C8   C   CR16  0  -0.256  -3.5998  -0.1843   0.6339
 4RO  C11  C   CR56  0   0.352   6.3065  -0.6308   0.3947
 4RO  C15  C   CR56  0   0.204   5.7093   0.5087  -0.1878
 4RO  C14  C   CR16  0  -0.236   6.3541   1.7231  -0.1844
 4RO  C12  C   CR16  0  -0.038   8.1238   0.5580   0.9677
 4RO  CL1  CL  CL    0  -0.134  -4.7551  -0.5599   3.0381
 4RO  C6   C   CR16  0  -0.227  -5.6330   1.0557   1.0763
 4RO  C5   C   CR6   0   0.012  -5.5291   1.6142  -0.1858
 4RO  CL   CL  CL    0  -0.050  -6.7267   2.7529  -0.6996
 4RO  N    N   NH1   0  -0.598  -1.1404  -0.0818  -0.8609
 4RO  C    C   CT    0   0.730   1.0960  -1.0433  -0.7455
 4RO  F    F   F     0  -0.411   1.5300   0.0763  -0.0772
 4RO  F1   F   F     0  -0.303   0.7048  -1.9103   0.2275
 4RO  C9   C   CH2   0  -0.324   2.2678  -1.6452  -1.5042
 4RO  N1   N   NH1   0  -0.651   3.3538  -2.0251  -0.6481
 4RO  C10  C   CR5   0   0.716   4.4184  -1.2601  -0.3420
 4RO  N4   N   NR15  0  -0.725   4.4977   0.0641  -0.6601
 4RO  N2   N   N     0  -0.473   5.4808  -1.7143   0.2778
 4RO  C13  C   CR16  0  -0.303   7.6091   1.7303   0.4225
 4RO  N3   N   N     0  -0.445   7.4985  -0.6175   0.9647
 4RO  H1   H   HCR6  0   0.230  -4.4268   1.7509  -2.0212
 4RO  H2   H   HCH2  0   0.259  -2.6242  -1.0009  -1.9685
 4RO  H3   H   HCH2  0   0.178  -2.3885   0.6745  -2.4260
 4RO  H4   H   HCH2  0   0.282  -0.4481  -1.6065  -2.0812
 4RO  H5   H   HCH2  0   0.237   0.2851  -0.0605  -2.4607
 4RO  H6   H   HCR6  0   0.257  -2.8382  -0.8786   0.9611
 4RO  H8   H   HCR6  0   0.252   9.1015   0.5766   1.4372
 4RO  H9   H   HCR6  0   0.257  -6.4453   1.3170   1.7395
 4RO  H10  H   HNH1  0   0.356  -0.8717   0.8468  -0.5616
 4RO  H12  H   HCH2  0   0.220   1.9196  -2.5347  -2.0300
 4RO  H13  H   HCH2  0   0.219   2.5998  -0.9505  -2.2806
 4RO  H14  H   HNH1  0   0.380   3.4374  -2.9938  -0.3922
 4RO  H15  H   HNR5  0   0.361   3.7666   0.6411  -1.0405
 4RO  H17  H   HCR6  0   0.203   8.1869   2.6422   0.4759
 4RO  H7   H   HCR6  0   0.243   5.9251   2.6167  -0.6179

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
 4RO  C6   C5   aromatic  1.384  0.020  1.384
 4RO  C6   C7   aromatic  1.387  0.020  1.387
 4RO  C5   C4   aromatic  1.387  0.020  1.387
 4RO  C5   CL   single    1.731  0.020  1.731
 4RO  C4   C3   aromatic  1.389  0.020  1.389
 4RO  C7   CL1  single    1.731  0.020  1.731
 4RO  C7   C8   aromatic  1.383  0.020  1.383
 4RO  C3   C8   aromatic  1.392  0.020  1.392
 4RO  C3   C2   single    1.507  0.020  1.507
 4RO  C2   N    single    1.446  0.020  1.446
 4RO  N    C1   single    1.442  0.020  1.442
 4RO  C1   C    single    1.514  0.020  1.514
 4RO  F    C    single    1.374  0.020  1.374
 4RO  F1   C    single    1.361  0.020  1.361
 4RO  C    C9   single    1.520  0.020  1.520
 4RO  C9   N1   single    1.434  0.020  1.434
 4RO  N1   C10  single    1.346  0.020  1.346
 4RO  C10  N4   aromatic  1.364  0.020  1.364
 4RO  C10  N2   aromatic  1.311  0.020  1.311
 4RO  N4   C15  aromatic  1.374  0.020  1.374
 4RO  N2   C11  aromatic  1.367  0.020  1.367
 4RO  C15  C11  aromatic  1.412  0.020  1.412
 4RO  C15  C14  aromatic  1.375  0.020  1.375
 4RO  C11  N3   aromatic  1.321  0.020  1.321
 4RO  N3   C12  aromatic  1.331  0.020  1.331
 4RO  C14  C13  aromatic  1.394  0.020  1.394
 4RO  C12  C13  aromatic  1.392  0.020  1.392
 4RO  C4   H1   single    0.930  0.020  1.080
 4RO  C2   H2   single    0.970  0.020  1.090
 4RO  C2   H3   single    0.970  0.020  1.090
 4RO  C1   H4   single    0.970  0.020  1.090
 4RO  C1   H5   single    0.970  0.020  1.090
 4RO  C8   H6   single    0.930  0.020  1.080
 4RO  C14  H7   single    0.930  0.020  1.080
 4RO  C12  H8   single    0.930  0.020  1.080
 4RO  C6   H9   single    0.930  0.020  1.080
 4RO  N    H10  single    0.890  0.020  1.040
 4RO  C9   H12  single    0.970  0.020  1.090
 4RO  C9   H13  single    0.970  0.020  1.090
 4RO  N1   H14  single    0.860  0.020  1.020
 4RO  N4   H15  single    0.860  0.020  1.020
 4RO  C13  H17  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
 4RO  H1   C4   C5   120.16  3.000
 4RO  H1   C4   C3   120.26  3.000
 4RO  C5   C4   C3   119.58  3.000
 4RO  H3   C2   H2   106.09  3.000
 4RO  H3   C2   N    113.73  3.000
 4RO  H2   C2   N    108.10  3.000
 4RO  H3   C2   C3   109.33  3.000
 4RO  H2   C2   C3   108.29  3.000
 4RO  N    C2   C3   111.05  3.000
 4RO  C8   C3   C2   119.93  3.000
 4RO  C2   C3   C4   120.39  3.000
 4RO  C8   C3   C4   119.67  3.000
 4RO  H5   C1   H4   106.12  3.000
 4RO  H5   C1   C    108.64  3.000
 4RO  H4   C1   C    107.58  3.000
 4RO  H5   C1   N    114.26  3.000
 4RO  H4   C1   N    108.87  3.000
 4RO  C    C1   N    111.07  3.000
 4RO  C6   C7   CL1  118.71  3.000
 4RO  CL1  C7   C8   119.34  3.000
 4RO  C6   C7   C8   121.95  3.000
 4RO  H6   C8   C7   120.77  3.000
 4RO  H6   C8   C3   119.83  3.000
 4RO  C7   C8   C3   119.40  3.000
 4RO  N3   C11  N2   126.13  3.000
 4RO  N3   C11  C15  123.45  3.000
 4RO  N2   C11  C15  110.41  3.000
 4RO  N4   C15  C14  134.42  3.000
 4RO  C14  C15  C11  120.89  3.000
 4RO  N4   C15  C11  104.69  3.000
 4RO  H7   C14  C13  121.81  3.000
 4RO  H7   C14  C15  122.86  3.000
 4RO  C13  C14  C15  115.33  3.000
 4RO  H8   C12  N3   116.07  3.000
 4RO  H8   C12  C13  119.24  3.000
 4RO  N3   C12  C13  124.70  3.000
 4RO  H9   C6   C5   121.23  3.000
 4RO  H9   C6   C7   121.11  3.000
 4RO  C5   C6   C7   117.66  3.000
 4RO  CL   C5   C6   118.96  3.000
 4RO  CL   C5   C4   119.28  3.000
 4RO  C6   C5   C4   121.75  3.000
 4RO  H10  N    C1   110.14  3.000
 4RO  H10  N    C2   109.20  3.000
 4RO  C1   N    C2   113.82  3.000
 4RO  C9   C    F1   109.04  3.000
 4RO  C9   C    F    108.77  3.000
 4RO  F1   C    F    105.19  3.000
 4RO  C9   C    C1   113.64  3.000
 4RO  F1   C    C1   110.27  3.000
 4RO  F    C    C1   109.56  3.000
 4RO  H13  C9   H12  105.84  3.000
 4RO  H13  C9   N1   111.24  3.000
 4RO  H12  C9   N1   108.27  3.000
 4RO  H13  C9   C    109.69  3.000
 4RO  H12  C9   C    108.51  3.000
 4RO  N1   C9   C    112.99  3.000
 4RO  H14  N1   C10  115.08  3.000
 4RO  H14  N1   C9   118.04  3.000
 4RO  C10  N1   C9   125.74  3.000
 4RO  N2   C10  N4   113.54  3.000
 4RO  N2   C10  N1   123.46  3.000
 4RO  N4   C10  N1   122.99  3.000
 4RO  H15  N4   C10  127.06  3.000
 4RO  H15  N4   C15  125.81  3.000
 4RO  C10  N4   C15  106.56  3.000
 4RO  C10  N2   C11  104.79  3.000
 4RO  H17  C13  C12  119.59  3.000
 4RO  H17  C13  C14  120.47  3.000
 4RO  C12  C13  C14  119.94  3.000
 4RO  C12  N3   C11  115.69  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
 4RO  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 4RO  CONST_02  C7   C8   C3   C4      0.00   0.0  0
 4RO  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 4RO  CONST_04  C6   C7   C8   C3      0.00   0.0  0
 4RO  CONST_05  C5   C6   C7   C8      0.00   0.0  0
 4RO  CONST_06  C5   C4   C3   C8      0.00   0.0  0
 4RO  CONST_07  N4   C10  N2   C11     0.00   0.0  0
 4RO  CONST_08  C10  N4   C15  C11     0.00   0.0  0
 4RO  CONST_09  C13  C14  C15  C11     0.00   0.0  0
 4RO  CONST_10  C13  C12  N3   C11     0.00   0.0  0
 4RO  CONST_11  N2   C10  N4   C15     0.00   0.0  0
 4RO  CONST_12  C10  N2   C11  C15     0.00   0.0  0
 4RO  CONST_13  C12  N3   C11  C15     0.00   0.0  0
 4RO  CONST_14  C12  C13  C14  C15     0.00   0.0  0
 4RO  CONST_15  C10  N4   C15  C14   180.00   0.0  0
 4RO  CONST_16  N2   C11  C15  C14   180.00   0.0  0
 4RO  CONST_17  N3   C11  C15  C14     0.00   0.0  0
 4RO  CONST_18  N3   C12  C13  C14     0.00   0.0  0
 4RO  CONST_19  N2   C11  N3   C12   180.00   0.0  0
 4RO  CONST_20  N3   C11  N2   C10   180.00   0.0  0
 4RO  CONST_21  N2   C11  C15  N4      0.00   0.0  0
 4RO  CONST_22  N3   C11  C15  N4    180.00   0.0  0
 4RO  CONST_23  C13  C14  C15  N4    180.00   0.0  0
 4RO  CONST_24  C5   C4   C3   C2    180.00   0.0  0
 4RO  CONST_25  C7   C8   C3   C2    180.00   0.0  0
 4RO  CONST_26  CL   C5   C4   C3    180.00   0.0  0
 4RO  CONST_27  CL1  C7   C8   C3    180.00   0.0  0
 4RO  CONST_28  CL   C5   C6   C7    180.00   0.0  0
 4RO  CONST_29  N1   C10  N2   C11   180.00   0.0  0
 4RO  CONST_30  N1   C10  N4   C15   180.00   0.0  0
 4RO  CONST_31  C5   C6   C7   CL1   180.00   0.0  0
 4RO  CONST_32  H9   C6   C5   C4    180.00   0.0  0
 4RO  CONST_33  H6   C8   C3   C4    180.00   0.0  0
 4RO  CONST_34  H1   C4   C3   C8    180.00   0.0  0
 4RO  CONST_35  H15  N4   C15  C11   180.00   0.0  0
 4RO  CONST_36  H7   C14  C15  C11   180.00   0.0  0
 4RO  CONST_37  H8   C12  N3   C11   180.00   0.0  0
 4RO  CONST_38  H17  C13  C14  C15   180.00   0.0  0
 4RO  CONST_39  N4   C10  N1   C9      0.00   0.0  0
 4RO  CONST_40  N2   C10  N1   C9    180.00   0.0  0
 4RO  CONST_41  H14  N1   C10  N4    180.00   0.0  0
 4RO  Var_01    N    C2   C3   C4    138.45  30.0  2
 4RO  Var_02    C1   N    C2   C3    169.42  30.0  3
 4RO  Var_03    C10  N1   C9   C     -93.30  30.0  3
 4RO  Var_04    C    C1   N    C2   -165.88  30.0  3
 4RO  Var_05    N1   C9   C    C1   -177.94  30.0  3
 4RO  Var_06    F    C    C1   N     -56.42  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
 4RO  plan-1  C4   0.020
 4RO  plan-1  C2   0.020
 4RO  plan-1  C3   0.020
 4RO  plan-1  C7   0.020
 4RO  plan-1  C8   0.020
 4RO  plan-1  CL1  0.020
 4RO  plan-1  C6   0.020
 4RO  plan-1  C5   0.020
 4RO  plan-1  CL   0.020
 4RO  plan-1  H1   0.020
 4RO  plan-1  H6   0.020
 4RO  plan-1  H9   0.020
 4RO  plan-2  C11  0.020
 4RO  plan-2  C15  0.020
 4RO  plan-2  C14  0.020
 4RO  plan-2  C12  0.020
 4RO  plan-2  N1   0.020
 4RO  plan-2  C10  0.020
 4RO  plan-2  N4   0.020
 4RO  plan-2  N2   0.020
 4RO  plan-2  C13  0.020
 4RO  plan-2  N3   0.020
 4RO  plan-2  H8   0.020
 4RO  plan-2  H15  0.020
 4RO  plan-2  H17  0.020
 4RO  plan-2  H7   0.020
 4RO  plan-3  C9   0.020
 4RO  plan-3  N1   0.020
 4RO  plan-3  C10  0.020
 4RO  plan-3  H14  0.020

