# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:47:10 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N~1~-(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)-N~2~-[(3,5-dichlorophenyl)methyl]-N~1~-methylethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCNCc1cc(Cl)cc(Cl)c1)c2[nH]c3ccc(Cl)nc3n2
#
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
 N93  N93  N~1~-(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)-N~2~-[(3,5-dichlorophenyl)methyl]-N~1~-methylethane-1,2-diamine  ligand  40  24  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N93
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
 N93  CL2  CL  CL    0  -0.134   6.8031  -2.7125  -0.7951
 N93  C14  C   CR6   0   0.117   6.1089  -1.1481  -0.4562
 N93  C13  C   CR16  0  -0.292   6.9332  -0.1715   0.0857
 N93  C12  C   CR16  0  -0.214   6.3861   1.0822   0.3617
 N93  N3   N   N     0  -0.427   4.8330  -1.0146  -0.7461
 N93  C15  C   CR56  0   0.290   4.3091   0.1748  -0.4860
 N93  C11  C   CR56  0   0.266   5.0535   1.2390   0.0661
 N93  N2   N   NR15  0  -0.752   4.1530   2.2679   0.1763
 N93  N4   N   N     0  -0.532   3.0202   0.5451  -0.6975
 N93  C10  C   CR5   0   0.757   2.9594   1.8037  -0.2989
 N93  N    N   NT    0  -0.511   1.8667   2.5770  -0.3589
 N93  C    C   CH3   0  -0.563   1.8729   3.8934   0.2459
 N93  C1   C   CH2   0  -0.337   0.5994   1.9855  -0.7400
 N93  C2   C   CH2   0  -0.261  -0.1359   1.3601   0.4403
 N93  N1   N   NH1   0  -0.603  -1.4137   0.8409  -0.0012
 N93  C3   C   CH2   0  -0.295  -2.2170   0.3108   1.0773
 N93  C4   C   CR6   0   0.058  -3.5959  -0.0840   0.6146
 N93  C9   C   CR16  0  -0.249  -4.2157   0.5923  -0.4312
 N93  C8   C   CR6   0  -0.023  -5.4986   0.2323  -0.8082
 N93  CL1  CL  CL    0  -0.118  -6.2641   1.0764  -2.1130
 N93  C7   C   CR16  0  -0.192  -6.1940  -0.7857  -0.1754
 N93  C6   C   CR6   0  -0.027  -5.5555  -1.4464   0.8616
 N93  CL   CL  CL    0  -0.117  -6.3870  -2.7329   1.6690
 N93  C5   C   CR16  0  -0.257  -4.2717  -1.1143   1.2605
 N93  H1   H   HCR6  0   0.284   7.9739  -0.3761   0.2887
 N93  H2   H   HCR6  0   0.285   6.9913   1.8736   0.7830
 N93  H3   H   HNR5  0   0.431   4.3476   3.1891   0.5346
 N93  H5   H   HCH3  0   0.256   2.6784   4.5099  -0.1564
 N93  H6   H   HCH3  0   0.270   0.9378   4.3916   0.0053
 N93  H7   H   HCH3  0   0.251   1.9692   3.8574   1.3338
 N93  H8   H   HCH2  0   0.257  -0.0178   2.7671  -1.1848
 N93  H9   H   HCH2  0   0.260   0.7781   1.2358  -1.5113
 N93  H10  H   HCH2  0   0.206   0.5047   0.5971   0.9067
 N93  H11  H   HCH2  0   0.232  -0.3186   2.1258   1.2001
 N93  H12  H   HNH1  0   0.350  -1.2575   0.1092  -0.6857
 N93  H14  H   HCH2  0   0.225  -1.7517  -0.5450   1.5875
 N93  H15  H   HCH2  0   0.256  -2.3212   1.0920   1.8377
 N93  H16  H   HCR6  0   0.276  -3.6919   1.3862  -0.9455
 N93  H17  H   HCR6  0   0.300  -7.1945  -1.0567  -0.4813
 N93  H18  H   HCR6  0   0.278  -3.7960  -1.6570   2.0676

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
 N93  CL1  C8   single    1.732  0.020  1.732
 N93  C8   C7   aromatic  1.386  0.020  1.386
 N93  C8   C9   aromatic  1.385  0.020  1.385
 N93  C7   C6   aromatic  1.386  0.020  1.386
 N93  CL   C6   single    1.732  0.020  1.732
 N93  C9   C4   aromatic  1.391  0.020  1.391
 N93  C6   C5   aromatic  1.385  0.020  1.385
 N93  C4   C5   aromatic  1.391  0.020  1.391
 N93  C4   C3   single    1.507  0.020  1.507
 N93  C3   N1   single    1.446  0.020  1.446
 N93  N1   C2   single    1.448  0.020  1.448
 N93  C2   C1   single    1.525  0.020  1.525
 N93  C1   N    single    1.450  0.020  1.450
 N93  C    N    single    1.449  0.020  1.449
 N93  N    C10  single    1.340  0.020  1.340
 N93  C10  N2   aromatic  1.366  0.020  1.366
 N93  C10  N4   aromatic  1.322  0.020  1.322
 N93  N2   C11  aromatic  1.372  0.020  1.372
 N93  N4   C15  aromatic  1.358  0.020  1.358
 N93  C11  C15  aromatic  1.411  0.020  1.411
 N93  C11  C12  aromatic  1.374  0.020  1.374
 N93  C15  N3   aromatic  1.325  0.020  1.325
 N93  C12  C13  aromatic  1.395  0.020  1.395
 N93  N3   C14  aromatic  1.315  0.020  1.315
 N93  C13  C14  aromatic  1.388  0.020  1.388
 N93  C14  CL2  single    1.745  0.020  1.745
 N93  C13  H1   single    0.930  0.020  1.080
 N93  C12  H2   single    0.930  0.020  1.080
 N93  N2   H3   single    0.860  0.020  1.020
 N93  C    H5   single    0.970  0.020  1.090
 N93  C    H6   single    0.970  0.020  1.090
 N93  C    H7   single    0.970  0.020  1.090
 N93  C1   H8   single    0.970  0.020  1.090
 N93  C1   H9   single    0.970  0.020  1.090
 N93  C2   H10  single    0.970  0.020  1.090
 N93  C2   H11  single    0.970  0.020  1.090
 N93  N1   H12  single    0.890  0.020  1.040
 N93  C3   H14  single    0.970  0.020  1.090
 N93  C3   H15  single    0.970  0.020  1.090
 N93  C9   H16  single    0.930  0.020  1.080
 N93  C7   H17  single    0.930  0.020  1.080
 N93  C5   H18  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
 N93  N3   C14  C13  126.21  3.000
 N93  C13  C14  CL2  118.05  3.000
 N93  N3   C14  CL2  115.74  3.000
 N93  H1   C13  C12  120.72  3.000
 N93  H1   C13  C14  120.82  3.000
 N93  C12  C13  C14  118.45  3.000
 N93  H2   C12  C11  122.88  3.000
 N93  H2   C12  C13  121.00  3.000
 N93  C11  C12  C13  116.12  3.000
 N93  C15  N3   C14  115.55  3.000
 N93  N4   C15  C11  110.86  3.000
 N93  C11  C15  N3   123.02  3.000
 N93  N4   C15  N3   126.11  3.000
 N93  N2   C11  C15  104.52  3.000
 N93  C15  C11  C12  120.65  3.000
 N93  N2   C11  C12  134.83  3.000
 N93  H3   N2   C10  127.11  3.000
 N93  H3   N2   C11  125.98  3.000
 N93  C10  N2   C11  106.90  3.000
 N93  C10  N4   C15  104.86  3.000
 N93  N    C10  N4   125.01  3.000
 N93  N4   C10  N2   112.85  3.000
 N93  N    C10  N2   122.13  3.000
 N93  C1   N    C    118.96  3.000
 N93  C    N    C10  120.15  3.000
 N93  C1   N    C10  119.29  3.000
 N93  H7   C    H6   108.15  3.000
 N93  H7   C    H5   108.70  3.000
 N93  H6   C    H5   107.13  3.000
 N93  H7   C    N    112.71  3.000
 N93  H6   C    N    108.69  3.000
 N93  H5   C    N    111.26  3.000
 N93  H9   C1   H8   107.27  3.000
 N93  H9   C1   C2   110.16  3.000
 N93  H8   C1   C2   109.68  3.000
 N93  H9   C1   N    108.85  3.000
 N93  H8   C1   N    108.03  3.000
 N93  C2   C1   N    112.67  3.000
 N93  H11  C2   H10  106.75  3.000
 N93  H11  C2   N1   108.38  3.000
 N93  H10  C2   N1   113.22  3.000
 N93  H11  C2   C1   109.34  3.000
 N93  H10  C2   C1   109.38  3.000
 N93  N1   C2   C1   109.67  3.000
 N93  H12  N1   C3   108.94  3.000
 N93  H12  N1   C2   109.19  3.000
 N93  C3   N1   C2   113.23  3.000
 N93  H15  C3   H14  105.86  3.000
 N93  H15  C3   C4   108.24  3.000
 N93  H14  C3   C4   109.01  3.000
 N93  H15  C3   N1   108.02  3.000
 N93  H14  C3   N1   113.35  3.000
 N93  C4   C3   N1   112.06  3.000
 N93  C5   C4   C9   119.51  3.000
 N93  C5   C4   C3   119.73  3.000
 N93  C9   C4   C3   120.73  3.000
 N93  H16  C9   C8   120.68  3.000
 N93  H16  C9   C4   119.91  3.000
 N93  C8   C9   C4   119.41  3.000
 N93  C7   C8   CL1  118.70  3.000
 N93  C7   C8   C9   122.11  3.000
 N93  CL1  C8   C9   119.20  3.000
 N93  H17  C7   C6   121.26  3.000
 N93  H17  C7   C8   121.30  3.000
 N93  C6   C7   C8   117.44  3.000
 N93  C5   C6   CL   119.28  3.000
 N93  C5   C6   C7   121.90  3.000
 N93  CL   C6   C7   118.82  3.000
 N93  H18  C5   C6   120.12  3.000
 N93  H18  C5   C4   120.26  3.000
 N93  C6   C5   C4   119.62  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
 N93  CONST_01  N4   C15  N3   C14   180.00   0.0  0
 N93  CONST_02  C11  C15  N3   C14     0.00   0.0  0
 N93  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 N93  CONST_04  N2   C11  C12  C13   180.00   0.0  0
 N93  CONST_05  C15  C11  C12  C13     0.00   0.0  0
 N93  CONST_06  C15  N3   C14  C13     0.00   0.0  0
 N93  CONST_07  C10  N2   C11  C12   180.00   0.0  0
 N93  CONST_08  N4   C15  C11  C12   180.00   0.0  0
 N93  CONST_09  N3   C15  C11  C12     0.00   0.0  0
 N93  CONST_10  N3   C14  C13  C12     0.00   0.0  0
 N93  CONST_11  C10  N4   C15  N3    180.00   0.0  0
 N93  CONST_12  N2   C11  C15  N3    180.00   0.0  0
 N93  CONST_13  N2   C10  N4   C15     0.00   0.0  0
 N93  CONST_14  C10  N2   C11  C15     0.00   0.0  0
 N93  CONST_15  N4   C10  N2   C11     0.00   0.0  0
 N93  CONST_16  C10  N4   C15  C11     0.00   0.0  0
 N93  CONST_17  N4   C15  C11  N2      0.00   0.0  0
 N93  CONST_18  C7   C8   C9   C4      0.00   0.0  0
 N93  CONST_19  C7   C6   C5   C4      0.00   0.0  0
 N93  CONST_20  C6   C7   C8   C9      0.00   0.0  0
 N93  CONST_21  C6   C5   C4   C9      0.00   0.0  0
 N93  CONST_22  C5   C6   C7   C8      0.00   0.0  0
 N93  CONST_23  C5   C4   C9   C8      0.00   0.0  0
 N93  CONST_24  C15  N3   C14  CL2   180.00   0.0  0
 N93  CONST_25  C12  C13  C14  CL2   180.00   0.0  0
 N93  CONST_26  N    C10  N4   C15   180.00   0.0  0
 N93  CONST_27  N    C10  N2   C11   180.00   0.0  0
 N93  CONST_28  C8   C9   C4   C3    180.00   0.0  0
 N93  CONST_29  C6   C5   C4   C3    180.00   0.0  0
 N93  CONST_30  CL1  C8   C9   C4    180.00   0.0  0
 N93  CONST_31  CL   C6   C5   C4    180.00   0.0  0
 N93  CONST_32  CL   C6   C7   C8    180.00   0.0  0
 N93  CONST_33  C6   C7   C8   CL1   180.00   0.0  0
 N93  CONST_34  H2   C12  C13  C14   180.00   0.0  0
 N93  CONST_35  H3   N2   C11  C12     0.00   0.0  0
 N93  CONST_36  H1   C13  C14  N3    180.00   0.0  0
 N93  CONST_37  H17  C7   C8   C9    180.00   0.0  0
 N93  CONST_38  H18  C5   C4   C9    180.00   0.0  0
 N93  CONST_39  H16  C9   C8   C7    180.00   0.0  0
 N93  CONST_40  C1   N    C10  N2    180.00   0.0  0
 N93  CONST_41  C    N    C10  N2      0.00   0.0  0
 N93  CONST_42  C1   N    C10  N4      0.00   0.0  0
 N93  CONST_43  C    N    C10  N4    180.00   0.0  0
 N93  Var_01    C9   C4   C3   N1    -30.92  30.0  2
 N93  Var_02    C2   C1   N    C10    85.25  30.0  2
 N93  Var_03    C4   C3   N1   C2    173.80  30.0  1
 N93  Var_04    H5   C    N    C10    56.78  30.0  3
 N93  Var_05    N1   C2   C1   N     177.60  30.0  1
 N93  Var_06    C3   N1   C2   C1   -176.00  30.0  1

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
 N93  plan-1  C3   0.020
 N93  plan-1  C4   0.020
 N93  plan-1  C9   0.020
 N93  plan-1  C8   0.020
 N93  plan-1  CL1  0.020
 N93  plan-1  C7   0.020
 N93  plan-1  C6   0.020
 N93  plan-1  CL   0.020
 N93  plan-1  C5   0.020
 N93  plan-1  H16  0.020
 N93  plan-1  H17  0.020
 N93  plan-1  H18  0.020
 N93  plan-2  CL2  0.020
 N93  plan-2  C14  0.020
 N93  plan-2  C13  0.020
 N93  plan-2  C12  0.020
 N93  plan-2  N3   0.020
 N93  plan-2  C15  0.020
 N93  plan-2  C11  0.020
 N93  plan-2  N2   0.020
 N93  plan-2  N4   0.020
 N93  plan-2  C10  0.020
 N93  plan-2  N    0.020
 N93  plan-2  H1   0.020
 N93  plan-2  H2   0.020
 N93  plan-2  H3   0.020
 N93  plan-3  C10  0.020
 N93  plan-3  N    0.020
 N93  plan-3  C    0.020
 N93  plan-3  C1   0.020

