# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:40:31 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: N-{(3S,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-(4-chlorobenzyl)ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@H]2CNC[C@H]2NCCNCc3ccc(Cl)cc3)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
 JI3  JI3  N-{(3S,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-(4-chlorobenzyl)ethane-1,2-diamine  ligand  54  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JI3
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
 JI3  C21   C   CR16  0  -0.319  -0.7318   8.7082  -6.2433
 JI3  C22   C   CR16  0  -0.197  -1.2870   8.9869  -7.4855
 JI3  C23   C   CR6   0  -0.056  -2.4829   8.3843  -7.8364
 JI3  CL    CL  CL    0  -0.136  -3.1885   8.7183  -9.3864
 JI3  C24   C   CR16  0  -0.197  -3.1255   7.5137  -6.9681
 JI3  C25   C   CR16  0  -0.295  -2.5573   7.2509  -5.7319
 JI3  C26   C   CR6   0   0.094  -1.3567   7.8464  -5.3489
 JI3  C6    C   CR6   0   0.439   4.7639  -0.1803  -2.1039
 JI3  N6    N   NH2   0  -0.839   5.6300  -0.9627  -1.3915
 JI3  C5    C   CR16  0  -0.447   4.7303  -0.2400  -3.5060
 JI3  C4    C   CR6   0   0.203   3.8795   0.6049  -4.1922
 JI3  C3    C   CR16  0  -0.420   3.0882   1.4857  -3.4507
 JI3  C2    C   CR6   0   0.277   3.1755   1.4736  -2.0675
 JI3  N1    N   N     0  -0.482   3.9998   0.6576  -1.4080
 JI3  N1'   N   NH1   0  -0.614   0.8885   1.1241   1.1915
 JI3  C2'   C   CH2   0  -0.283   0.3494   2.4836   1.1530
 JI3  C3'   C   CH1   0  -0.064  -0.0521   2.7329  -0.3031
 JI3  C4'   C   CH1   0  -0.314   0.8875   1.7906  -1.0721
 JI3  C5'   C   CH2   0  -0.265   0.8499   0.5671  -0.1618
 JI3  C7    C   CH2   0  -0.499   2.2969   2.3725  -1.2467
 JI3  N8    N   NH1   0  -0.611   0.0479   4.1264  -0.6714
 JI3  C9    C   CH2   0  -0.282  -0.4680   4.4124  -1.9949
 JI3  C10   C   CH2   0  -0.278  -0.3366   5.8918  -2.3147
 JI3  N11   N   NH1   0  -0.598  -0.8352   6.1738  -3.6461
 JI3  C12   C   CH2   0  -0.310  -0.7645   7.5787  -3.9912
 JI3  H21   H   HCR6  0   0.260   0.2097   9.1722  -5.9750
 JI3  H22   H   HCR6  0   0.277  -0.7866   9.6605  -8.1679
 JI3  H24   H   HCR6  0   0.276  -4.0591   7.0465  -7.2512
 JI3  H25   H   HCR6  0   0.257  -3.0537   6.5662  -5.0569
 JI3  HN61  H   HNH2  0   0.386   5.9721  -1.7965  -1.8392
 JI3  HN62  H   HNH2  0   0.378   5.4057  -1.0879  -0.4178
 JI3  H5    H   HCR6  0   0.254   5.3646  -0.9405  -4.0363
 JI3  H3    H   HCR6  0   0.237   2.4094   2.1693  -3.9478
 JI3  HN1'  H   HNH1  0   0.348   0.3757   0.5431   1.8370
 JI3  H2'1  H   HCH2  0   0.201   1.1107   3.2160   1.4481
 JI3  H2'2  H   HCH2  0   0.229  -0.4969   2.6104   1.8325
 JI3  H3'   H   HCH1  0   0.211  -1.0761   2.3478  -0.4544
 JI3  H4'   H   HCH1  0   0.251   0.4835   1.5436  -2.0579
 JI3  H5'1  H   HCH2  0   0.209  -0.0680  -0.0018  -0.3578
 JI3  H5'2  H   HCH2  0   0.225   1.6899  -0.1095  -0.3342
 JI3  H71   H   HCH2  0   0.243   2.7599   2.5407  -0.2720
 JI3  H72   H   HCH2  0   0.250   2.2181   3.3468  -1.7335
 JI3  H81   H   HCH3  0   0.246   4.4768  -0.1513  -6.1197
 JI3  H82   H   HCH3  0   0.251   2.7882   0.3487  -6.0200
 JI3  H83   H   HCH3  0   0.251   4.0526   1.5609  -6.1043
 JI3  HN8   H   HNH1  0   0.346  -0.4654   4.6796   0.0055
 JI3  H91   H   HCH2  0   0.217   0.1142   3.8392  -2.7242
 JI3  H92   H   HCH2  0   0.200  -1.5174   4.1050  -2.1245
 JI3  H101  H   HCH2  0   0.220  -0.9298   6.4711  -1.5990
 JI3  H102  H   HCH2  0   0.196   0.7110   6.1984  -2.1718
 JI3  HN11  H   HNH1  0   0.343  -0.2937   5.6451  -4.3203
 JI3  H121  H   HCH2  0   0.216   0.2584   7.9836  -3.9545
 JI3  H122  H   HCH2  0   0.242  -1.3331   8.1376  -3.2403
 JI3  C8    C   CH3   0  -0.727   3.8003   0.5845  -5.6883

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
 JI3  C21  C26   aromatic  1.390  0.020  1.390
 JI3  C21  C22   aromatic  1.389  0.020  1.389
 JI3  C21  H21   single    0.930  0.020  1.080
 JI3  C22  C23   aromatic  1.384  0.020  1.384
 JI3  C22  H22   single    0.930  0.020  1.080
 JI3  C23  C24   aromatic  1.387  0.020  1.387
 JI3  C23  CL    single    1.736  0.020  1.736
 JI3  C24  C25   aromatic  1.386  0.020  1.386
 JI3  C24  H24   single    0.930  0.020  1.080
 JI3  C25  C26   aromatic  1.394  0.020  1.394
 JI3  C25  H25   single    0.930  0.020  1.080
 JI3  C26  C12   single    1.505  0.020  1.505
 JI3  C6   N1    aromatic  1.330  0.020  1.330
 JI3  C6   N6    single    1.367  0.020  1.367
 JI3  C6   C5    aromatic  1.404  0.020  1.404
 JI3  N6   HN61  single    0.890  0.020  1.040
 JI3  N6   HN62  single    0.890  0.020  1.040
 JI3  C5   C4    aromatic  1.381  0.020  1.381
 JI3  C5   H5    single    0.930  0.020  1.080
 JI3  C4   C3    aromatic  1.397  0.020  1.397
 JI3  C4   C8    single    1.498  0.020  1.498
 JI3  C3   C2    aromatic  1.386  0.020  1.386
 JI3  C3   H3    single    0.930  0.020  1.080
 JI3  C2   C7    single    1.501  0.020  1.501
 JI3  C2   N1    aromatic  1.334  0.020  1.334
 JI3  N1'  C2'   single    1.463  0.020  1.463
 JI3  N1'  C5'   single    1.464  0.020  1.464
 JI3  N1'  HN1'  single    0.890  0.020  1.040
 JI3  C2'  C3'   single    1.531  0.020  1.531
 JI3  C2'  H2'1  single    0.970  0.020  1.090
 JI3  C2'  H2'2  single    0.970  0.020  1.090
 JI3  C3'  N8    single    1.445  0.020  1.445
 JI3  C3'  C4'   single    1.537  0.020  1.537
 JI3  C3'  H3'   single    0.970  0.020  1.090
 JI3  C4'  C7    single    1.535  0.020  1.535
 JI3  C4'  C5'   single    1.525  0.020  1.525
 JI3  C4'  H4'   single    0.970  0.020  1.090
 JI3  C5'  H5'1  single    0.970  0.020  1.090
 JI3  C5'  H5'2  single    0.970  0.020  1.090
 JI3  C7   H71   single    0.970  0.020  1.090
 JI3  C7   H72   single    0.970  0.020  1.090
 JI3  C8   H81   single    0.970  0.020  1.090
 JI3  C8   H82   single    0.970  0.020  1.090
 JI3  C8   H83   single    0.970  0.020  1.090
 JI3  N8   C9    single    1.449  0.020  1.449
 JI3  N8   HN8   single    0.890  0.020  1.040
 JI3  C9   C10   single    1.519  0.020  1.519
 JI3  C9   H91   single    0.970  0.020  1.090
 JI3  C9   H92   single    0.970  0.020  1.090
 JI3  C10  N11   single    1.449  0.020  1.449
 JI3  C10  H101  single    0.970  0.020  1.090
 JI3  C10  H102  single    0.970  0.020  1.090
 JI3  N11  C12   single    1.448  0.020  1.448
 JI3  N11  HN11  single    0.890  0.020  1.040
 JI3  C12  H121  single    0.970  0.020  1.090
 JI3  C12  H122  single    0.970  0.020  1.090

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
 JI3  H21   C21  C26   119.78  3.000
 JI3  H21   C21  C22   118.88  3.000
 JI3  C26   C21  C22   121.34  3.000
 JI3  H22   C22  C23   120.72  3.000
 JI3  H22   C22  C21   120.29  3.000
 JI3  C23   C22  C21   118.99  3.000
 JI3  C24   C23  CL    119.43  3.000
 JI3  CL    C23  C22   119.59  3.000
 JI3  C24   C23  C22   120.98  3.000
 JI3  H24   C24  C25   120.36  3.000
 JI3  H24   C24  C23   120.47  3.000
 JI3  C25   C24  C23   119.17  3.000
 JI3  H25   C25  C26   119.61  3.000
 JI3  H25   C25  C24   119.24  3.000
 JI3  C26   C25  C24   121.15  3.000
 JI3  C12   C26  C25   120.71  3.000
 JI3  C12   C26  C21   120.91  3.000
 JI3  C25   C26  C21   118.37  3.000
 JI3  N1    C6   C5    122.38  3.000
 JI3  C5    C6   N6    120.74  3.000
 JI3  N1    C6   N6    116.85  3.000
 JI3  HN62  N6   HN61  113.76  3.000
 JI3  HN62  N6   C6    115.71  3.000
 JI3  HN61  N6   C6    117.23  3.000
 JI3  H5    C5   C4    120.85  3.000
 JI3  H5    C5   C6    120.15  3.000
 JI3  C4    C5   C6    119.00  3.000
 JI3  C8    C4   C3    120.57  3.000
 JI3  C8    C4   C5    121.35  3.000
 JI3  C3    C4   C5    118.08  3.000
 JI3  H3    C3   C2    120.17  3.000
 JI3  H3    C3   C4    120.59  3.000
 JI3  C2    C3   C4    119.24  3.000
 JI3  C7    C2   N1    117.22  3.000
 JI3  N1    C2   C3    122.52  3.000
 JI3  C7    C2   C3    120.23  3.000
 JI3  C2    N1   C6    118.77  3.000
 JI3  HN1'  N1'  C5'   111.04  3.000
 JI3  HN1'  N1'  C2'   111.39  3.000
 JI3  C5'   N1'  C2'   108.63  3.000
 JI3  H2'2  C2'  H2'1  107.03  3.000
 JI3  H2'2  C2'  C3'   111.69  3.000
 JI3  H2'1  C2'  C3'   109.22  3.000
 JI3  H2'2  C2'  N1'   112.14  3.000
 JI3  H2'1  C2'  N1'   110.96  3.000
 JI3  C3'   C2'  N1'   105.84  3.000
 JI3  H3'   C3'  N8    111.44  3.000
 JI3  H3'   C3'  C4'   106.53  3.000
 JI3  N8    C3'  C4'   114.93  3.000
 JI3  H3'   C3'  C2'   108.46  3.000
 JI3  C4'   C3'  C2'   102.46  3.000
 JI3  N8    C3'  C2'   112.42  3.000
 JI3  H4'   C4'  C7    108.80  3.000
 JI3  H4'   C4'  C5'   110.35  3.000
 JI3  C7    C4'  C5'   113.24  3.000
 JI3  H4'   C4'  C3'   111.33  3.000
 JI3  C5'   C4'  C3'   100.26  3.000
 JI3  C7    C4'  C3'   112.70  3.000
 JI3  H5'2  C5'  H5'1  107.09  3.000
 JI3  H5'2  C5'  C4'   112.56  3.000
 JI3  H5'1  C5'  C4'   109.26  3.000
 JI3  H5'2  C5'  N1'   111.18  3.000
 JI3  H5'1  C5'  N1'   112.60  3.000
 JI3  C4'   C5'  N1'   104.23  3.000
 JI3  H72   C7   H71   106.92  3.000
 JI3  H72   C7   C4'   108.83  3.000
 JI3  H71   C7   C4'   110.26  3.000
 JI3  H72   C7   C2    109.43  3.000
 JI3  H71   C7   C2    109.39  3.000
 JI3  C4'   C7   C2    111.88  3.000
 JI3  HN8   N8   C9    108.77  3.000
 JI3  HN8   N8   C3'   108.73  3.000
 JI3  C9    N8   C3'   113.49  3.000
 JI3  H92   C9   H91   106.39  3.000
 JI3  H92   C9   C10   109.24  3.000
 JI3  H91   C9   C10   108.88  3.000
 JI3  H92   C9   N8    113.06  3.000
 JI3  H91   C9   N8    108.41  3.000
 JI3  C10   C9   N8    110.71  3.000
 JI3  H102  C10  H101  106.45  3.000
 JI3  H102  C10  N11   113.11  3.000
 JI3  H101  C10  N11   108.12  3.000
 JI3  H102  C10  C9    109.04  3.000
 JI3  H101  C10  C9    109.30  3.000
 JI3  N11   C10  C9    110.67  3.000
 JI3  HN11  N11  C12   108.74  3.000
 JI3  HN11  N11  C10   109.01  3.000
 JI3  C12   N11  C10   113.00  3.000
 JI3  H122  C12  H121  105.77  3.000
 JI3  H122  C12  N11   107.83  3.000
 JI3  H121  C12  N11   113.22  3.000
 JI3  H122  C12  C26   108.86  3.000
 JI3  H121  C12  C26   109.28  3.000
 JI3  N11   C12  C26   111.61  3.000
 JI3  H83   C8   H82   106.98  3.000
 JI3  H83   C8   H81   108.06  3.000
 JI3  H82   C8   H81   108.06  3.000
 JI3  H83   C8   C4    110.88  3.000
 JI3  H82   C8   C4    110.83  3.000
 JI3  H81   C8   C4    111.84  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
 JI3  CONST_01  C24  C25  C26  C21     0.00   0.0  0
 JI3  CONST_02  C24  C23  C22  C21     0.00   0.0  0
 JI3  CONST_03  C25  C26  C21  C22     0.00   0.0  0
 JI3  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 JI3  CONST_05  C26  C21  C22  C23     0.00   0.0  0
 JI3  CONST_06  C26  C25  C24  C23     0.00   0.0  0
 JI3  CONST_07  C3   C2   N1   C6      0.00   0.0  0
 JI3  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 JI3  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 JI3  CONST_10  C2   C3   C4   C5      0.00   0.0  0
 JI3  CONST_11  N1   C6   C5   C4      0.00   0.0  0
 JI3  CONST_12  N1   C2   C3   C4      0.00   0.0  0
 JI3  CONST_13  CL   C23  C22  C21   180.00   0.0  0
 JI3  CONST_14  C12  C26  C21  C22   180.00   0.0  0
 JI3  CONST_15  C25  C24  C23  CL    180.00   0.0  0
 JI3  CONST_16  C12  C26  C25  C24   180.00   0.0  0
 JI3  CONST_17  C7   C2   N1   C6    180.00   0.0  0
 JI3  CONST_18  C8   C4   C5   C6    180.00   0.0  0
 JI3  CONST_19  C2   N1   C6   N6    180.00   0.0  0
 JI3  CONST_20  C4   C5   C6   N6    180.00   0.0  0
 JI3  CONST_21  C7   C2   C3   C4    180.00   0.0  0
 JI3  CONST_22  C8   C4   C3   C2    180.00   0.0  0
 JI3  CONST_23  H25  C25  C26  C21   180.00   0.0  0
 JI3  CONST_24  H24  C24  C23  C22   180.00   0.0  0
 JI3  CONST_25  H21  C21  C22  C23   180.00   0.0  0
 JI3  CONST_26  H22  C22  C23  C24   180.00   0.0  0
 JI3  CONST_27  H3   C3   C4   C5    180.00   0.0  0
 JI3  CONST_28  H5   C5   C4   C3    180.00   0.0  0
 JI3  Var_01    C4'  C5'  N1'  C2'    25.29  30.0  1
 JI3  Var_02    C5'  N1'  C2'  C3'     1.00  30.0  1
 JI3  Var_03    C4'  C7   C2   C3     80.76  30.0  2
 JI3  Var_04    N11  C12  C26  C21  -137.41  30.0  2
 JI3  Var_05    H81  C8   C4   C5     -0.14  30.0  2
 JI3  Var_06    C10  N11  C12  C26  -176.96  30.0  2
 JI3  Var_07    C10  C9   N8   C3'   179.81  30.0  3
 JI3  Var_08    N11  C10  C9   N8    179.18  30.0  3
 JI3  Var_09    C12  N11  C10  C9    178.55  30.0  3

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
 JI3  chir_01  C3'  C2'  N8  C4'  negativ
 JI3  chir_02  C4'  C3'  C7  C5'  negativ

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
 JI3  plan-1  C21   0.020
 JI3  plan-1  C22   0.020
 JI3  plan-1  C23   0.020
 JI3  plan-1  CL    0.020
 JI3  plan-1  C24   0.020
 JI3  plan-1  C25   0.020
 JI3  plan-1  C26   0.020
 JI3  plan-1  C12   0.020
 JI3  plan-1  H21   0.020
 JI3  plan-1  H22   0.020
 JI3  plan-1  H24   0.020
 JI3  plan-1  H25   0.020
 JI3  plan-2  C6    0.020
 JI3  plan-2  N6    0.020
 JI3  plan-2  C5    0.020
 JI3  plan-2  C4    0.020
 JI3  plan-2  C3    0.020
 JI3  plan-2  C2    0.020
 JI3  plan-2  N1    0.020
 JI3  plan-2  C7    0.020
 JI3  plan-2  H5    0.020
 JI3  plan-2  H3    0.020
 JI3  plan-2  C8    0.020
 JI3  plan-3  C6    0.020
 JI3  plan-3  N6    0.020
 JI3  plan-3  HN61  0.020
 JI3  plan-3  HN62  0.020

