# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:41:28 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: N-{(3R,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-(3-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]2NCCNCc3cccc(Cl)c3)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
 JI7  JI7  N-{(3R,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-(3-chlorobenzyl)ethane-1,2-diamine  ligand  54  26  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JI7
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
 JI7  C5    C   CR16  0  -0.447   7.6665   0.9802  -0.0246
 JI7  C4    C   CR6   0   0.204   6.6802   1.7538  -0.6049
 JI7  C3    C   CR16  0  -0.420   5.3498   1.4757  -0.2805
 JI7  C2    C   CR6   0   0.278   5.0718   0.4347   0.5900
 JI7  N1    N   N     0  -0.482   6.0250  -0.3096   1.1513
 JI7  C6    C   CR6   0   0.442   7.2961  -0.0460   0.8591
 JI7  C7    C   CH2   0  -0.512   3.6486   0.0632   0.9041
 JI7  C4'   C   CH1   0  -0.284   3.0216  -0.7702  -0.2119
 JI7  C3'   C   CH1   0  -0.053   1.5670  -1.1742   0.0257
 JI7  C2'   C   CH2   0  -0.302   1.4350  -2.3450  -0.9485
 JI7  N1'   N   NH1   0  -0.603   2.6909  -3.0793  -0.8545
 JI7  C5'   C   CH2   0  -0.267   3.7294  -2.1140  -0.4630
 JI7  N8    N   NH1   0  -0.612   0.6451  -0.0904  -0.2352
 JI7  C9    C   CH2   0  -0.283  -0.7289  -0.4011   0.1098
 JI7  C10   C   CH2   0  -0.275  -1.6335   0.7817  -0.1926
 JI7  N11   N   NH1   0  -0.604  -3.0063   0.4774   0.1564
 JI7  C12   C   CH2   0  -0.293  -3.9240   1.5460  -0.1688
 JI7  C26   C   CR6   0   0.065  -5.3612   1.1661   0.0803
 JI7  C25   C   CR16  0  -0.295  -6.3060   2.1462   0.3726
 JI7  C24   C   CR16  0  -0.247  -7.6394   1.8112   0.5573
 JI7  C23   C   CR16  0  -0.232  -8.0556   0.4905   0.4629
 JI7  C22   C   CR6   0  -0.018  -7.1067  -0.4784   0.1792
 JI7  C21   C   CR16  0  -0.261  -5.7719  -0.1604  -0.0138
 JI7  CL    CL  CL    0  -0.136  -7.6021  -2.1396   0.0626
 JI7  C8    C   CH3   0  -0.727   7.0168   2.8549  -1.5636
 JI7  N6    N   NH2   0  -0.839   8.2448  -0.7934   1.4978
 JI7  H5    H   HCR6  0   0.255   8.7130   1.1596  -0.2415
 JI7  H3    H   HCR6  0   0.240   4.5434   2.0601  -0.7078
 JI7  H71   H   HCH2  0   0.239   3.6230  -0.5011   1.8395
 JI7  H72   H   HCH2  0   0.243   3.0638   0.9752   1.0558
 JI7  H4'   H   HCH1  0   0.237   3.0344  -0.1781  -1.1351
 JI7  H3'   H   HCH1  0   0.192   1.4661  -1.5671   1.0546
 JI7  H2'1  H   HCH2  0   0.236   0.5938  -3.0080  -0.7416
 JI7  H2'2  H   HCH2  0   0.207   1.2929  -1.9425  -1.9586
 JI7  HN1'  H   HNH1  0   0.349   2.6019  -3.7759  -0.1285
 JI7  H5'1  H   HCH2  0   0.216   4.4897  -2.0080  -1.2411
 JI7  H5'2  H   HCH2  0   0.222   4.2478  -2.4556   0.4361
 JI7  HN8   H   HNH1  0   0.342   0.9317   0.7216   0.3001
 JI7  H91   H   HCH2  0   0.227  -1.0630  -1.2565  -0.4825
 JI7  H92   H   HCH2  0   0.192  -0.8433  -0.6917   1.1678
 JI7  H101  H   HCH2  0   0.193  -1.2518   1.6774   0.3250
 JI7  H102  H   HCH2  0   0.225  -1.5863   1.0013  -1.2629
 JI7  HN11  H   HNH1  0   0.345  -3.0629   0.2832   1.1497
 JI7  H121  H   HCH2  0   0.218  -3.7027   2.4851   0.3610
 JI7  H122  H   HCH2  0   0.248  -3.8073   1.7750  -1.2338
 JI7  H25   H   HCR6  0   0.254  -5.9969   3.1810   0.4595
 JI7  H24   H   HCR6  0   0.266  -8.3646   2.5819   0.7836
 JI7  H23   H   HCR6  0   0.277  -9.0931   0.2243   0.6125
 JI7  H21   H   HCR6  0   0.269  -5.0475  -0.9341  -0.2297
 JI7  H81   H   HCH3  0   0.252   6.6575   2.6152  -2.5657
 JI7  H82   H   HCH3  0   0.250   6.5389   3.7895  -1.2685
 JI7  H83   H   HCH3  0   0.246   8.0904   3.0258  -1.6244
 JI7  HN61  H   HNH2  0   0.378   7.9324  -1.6688   1.8849
 JI7  HN62  H   HNH2  0   0.387   9.1601  -0.8343   1.0818

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
 JI7  CL   C22   single    1.737  0.020  1.737
 JI7  C22  C23   aromatic  1.385  0.020  1.385
 JI7  C22  C21   aromatic  1.386  0.020  1.386
 JI7  C23  C24   aromatic  1.388  0.020  1.388
 JI7  C21  C26   aromatic  1.392  0.020  1.392
 JI7  C24  C25   aromatic  1.387  0.020  1.387
 JI7  C26  C25   aromatic  1.392  0.020  1.392
 JI7  C26  C12   single    1.507  0.020  1.507
 JI7  C12  N11   single    1.446  0.020  1.446
 JI7  N11  C10   single    1.449  0.020  1.449
 JI7  C10  C9    single    1.519  0.020  1.519
 JI7  C2'  N1'   single    1.458  0.020  1.458
 JI7  C2'  C3'   single    1.529  0.020  1.529
 JI7  N1'  C5'   single    1.471  0.020  1.471
 JI7  C3'  N8    single    1.447  0.020  1.447
 JI7  C3'  C4'   single    1.528  0.020  1.528
 JI7  C9   N8    single    1.450  0.020  1.450
 JI7  C7   C4'   single    1.527  0.020  1.527
 JI7  C7   C2    single    1.504  0.020  1.504
 JI7  N1   C2    aromatic  1.333  0.020  1.333
 JI7  N1   C6    aromatic  1.331  0.020  1.331
 JI7  C4'  C5'   single    1.539  0.020  1.539
 JI7  N6   C6    single    1.366  0.020  1.366
 JI7  C2   C3    aromatic  1.385  0.020  1.385
 JI7  C6   C5    aromatic  1.404  0.020  1.404
 JI7  C3   C4    aromatic  1.397  0.020  1.397
 JI7  C5   C4    aromatic  1.381  0.020  1.381
 JI7  C4   C8    single    1.498  0.020  1.498
 JI7  C5   H5    single    0.930  0.020  1.080
 JI7  C3   H3    single    0.930  0.020  1.080
 JI7  C7   H71   single    0.970  0.020  1.090
 JI7  C7   H72   single    0.970  0.020  1.090
 JI7  C4'  H4'   single    0.970  0.020  1.090
 JI7  C3'  H3'   single    0.970  0.020  1.090
 JI7  C2'  H2'1  single    0.970  0.020  1.090
 JI7  C2'  H2'2  single    0.970  0.020  1.090
 JI7  N1'  HN1'  single    0.890  0.020  1.040
 JI7  C5'  H5'1  single    0.970  0.020  1.090
 JI7  C5'  H5'2  single    0.970  0.020  1.090
 JI7  N8   HN8   single    0.890  0.020  1.040
 JI7  C9   H91   single    0.970  0.020  1.090
 JI7  C9   H92   single    0.970  0.020  1.090
 JI7  C10  H101  single    0.970  0.020  1.090
 JI7  C10  H102  single    0.970  0.020  1.090
 JI7  N11  HN11  single    0.890  0.020  1.040
 JI7  C12  H121  single    0.970  0.020  1.090
 JI7  C12  H122  single    0.970  0.020  1.090
 JI7  C25  H25   single    0.930  0.020  1.080
 JI7  C24  H24   single    0.930  0.020  1.080
 JI7  C23  H23   single    0.930  0.020  1.080
 JI7  C21  H21   single    0.930  0.020  1.080
 JI7  C8   H81   single    0.970  0.020  1.090
 JI7  C8   H82   single    0.970  0.020  1.090
 JI7  C8   H83   single    0.970  0.020  1.090
 JI7  N6   HN61  single    0.890  0.020  1.040
 JI7  N6   HN62  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
 JI7  H5    C5   C6    120.12  3.000
 JI7  H5    C5   C4    120.84  3.000
 JI7  C6    C5   C4    119.04  3.000
 JI7  C8    C4   C3    120.58  3.000
 JI7  C8    C4   C5    121.33  3.000
 JI7  C3    C4   C5    118.09  3.000
 JI7  H3    C3   C2    120.25  3.000
 JI7  H3    C3   C4    120.64  3.000
 JI7  C2    C3   C4    119.11  3.000
 JI7  C7    C2   N1    116.79  3.000
 JI7  N1    C2   C3    122.72  3.000
 JI7  C7    C2   C3    120.45  3.000
 JI7  C6    N1   C2    118.68  3.000
 JI7  N6    C6   N1    116.89  3.000
 JI7  N6    C6   C5    120.72  3.000
 JI7  N1    C6   C5    122.35  3.000
 JI7  H72   C7   H71   107.41  3.000
 JI7  H72   C7   C4'   109.68  3.000
 JI7  H71   C7   C4'   109.51  3.000
 JI7  H72   C7   C2    109.20  3.000
 JI7  H71   C7   C2    109.18  3.000
 JI7  C4'   C7   C2    111.75  3.000
 JI7  H4'   C4'  C5'   109.18  3.000
 JI7  H4'   C4'  C3'   106.53  3.000
 JI7  C5'   C4'  C3'   103.43  3.000
 JI7  H4'   C4'  C7    108.40  3.000
 JI7  C5'   C4'  C7    114.00  3.000
 JI7  C3'   C4'  C7    114.92  3.000
 JI7  H3'   C3'  N8    112.07  3.000
 JI7  H3'   C3'  C2'   108.23  3.000
 JI7  N8    C3'  C2'   113.81  3.000
 JI7  H3'   C3'  C4'   108.99  3.000
 JI7  N8    C3'  C4'   112.36  3.000
 JI7  C2'   C3'  C4'   100.70  3.000
 JI7  H2'2  C2'  H2'1  107.33  3.000
 JI7  H2'2  C2'  N1'   110.85  3.000
 JI7  H2'1  C2'  N1'   110.24  3.000
 JI7  H2'2  C2'  C3'   108.49  3.000
 JI7  H2'1  C2'  C3'   114.28  3.000
 JI7  N1'   C2'  C3'   105.68  3.000
 JI7  HN1'  N1'  C5'   108.88  3.000
 JI7  HN1'  N1'  C2'   108.53  3.000
 JI7  C5'   N1'  C2'   107.14  3.000
 JI7  H5'2  C5'  H5'1  106.62  3.000
 JI7  H5'2  C5'  N1'   110.41  3.000
 JI7  H5'1  C5'  N1'   111.43  3.000
 JI7  H5'2  C5'  C4'   110.90  3.000
 JI7  H5'1  C5'  C4'   110.57  3.000
 JI7  N1'   C5'  C4'   106.96  3.000
 JI7  HN8   N8   C9    108.28  3.000
 JI7  HN8   N8   C3'   108.94  3.000
 JI7  C9    N8   C3'   113.60  3.000
 JI7  H92   C9   H91   106.37  3.000
 JI7  H92   C9   C10   109.53  3.000
 JI7  H91   C9   C10   108.63  3.000
 JI7  H92   C9   N8    112.51  3.000
 JI7  H91   C9   N8    109.17  3.000
 JI7  C10   C9   N8    110.48  3.000
 JI7  H102  C10  H101  106.35  3.000
 JI7  H102  C10  N11   108.59  3.000
 JI7  H101  C10  N11   112.67  3.000
 JI7  H102  C10  C9    108.99  3.000
 JI7  H101  C10  C9    109.44  3.000
 JI7  N11   C10  C9    110.65  3.000
 JI7  HN11  N11  C12   109.06  3.000
 JI7  HN11  N11  C10   109.22  3.000
 JI7  C12   N11  C10   113.08  3.000
 JI7  H122  C12  H121  105.55  3.000
 JI7  H122  C12  C26   108.36  3.000
 JI7  H121  C12  C26   109.10  3.000
 JI7  H122  C12  N11   107.79  3.000
 JI7  H121  C12  N11   113.25  3.000
 JI7  C26   C12  N11   112.45  3.000
 JI7  C21   C26  C25   119.00  3.000
 JI7  C25   C26  C12   120.29  3.000
 JI7  C21   C26  C12   120.69  3.000
 JI7  H25   C25  C24   119.62  3.000
 JI7  H25   C25  C26   119.71  3.000
 JI7  C24   C25  C26   120.68  3.000
 JI7  H24   C24  C23   119.41  3.000
 JI7  H24   C24  C25   119.99  3.000
 JI7  C23   C24  C25   120.60  3.000
 JI7  H23   C23  C22   120.88  3.000
 JI7  H23   C23  C24   120.83  3.000
 JI7  C22   C23  C24   118.29  3.000
 JI7  CL    C22  C21   119.00  3.000
 JI7  C21   C22  C23   121.86  3.000
 JI7  CL    C22  C23   119.15  3.000
 JI7  H21   C21  C22   120.58  3.000
 JI7  H21   C21  C26   119.84  3.000
 JI7  C22   C21  C26   119.58  3.000
 JI7  H83   C8   H82   108.22  3.000
 JI7  H83   C8   H81   107.93  3.000
 JI7  H82   C8   H81   107.00  3.000
 JI7  H83   C8   C4    111.88  3.000
 JI7  H82   C8   C4    110.99  3.000
 JI7  H81   C8   C4    110.63  3.000
 JI7  HN62  N6   HN61  113.94  3.000
 JI7  HN62  N6   C6    117.42  3.000
 JI7  HN61  N6   C6    116.10  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
 JI7  CONST_01  C2   N1   C6   C5      0.00   0.0  0
 JI7  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 JI7  CONST_03  N1   C2   C3   C4      0.00   0.0  0
 JI7  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 JI7  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 JI7  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 JI7  CONST_07  C23  C22  C21  C26     0.00   0.0  0
 JI7  CONST_08  C23  C24  C25  C26     0.00   0.0  0
 JI7  CONST_09  C22  C23  C24  C25     0.00   0.0  0
 JI7  CONST_10  C22  C21  C26  C25     0.00   0.0  0
 JI7  CONST_11  C21  C22  C23  C24     0.00   0.0  0
 JI7  CONST_12  C21  C26  C25  C24     0.00   0.0  0
 JI7  CONST_13  C7   C2   C3   C4    180.00   0.0  0
 JI7  CONST_14  N6   C6   C5   C4    180.00   0.0  0
 JI7  CONST_15  N6   C6   N1   C2    180.00   0.0  0
 JI7  CONST_16  C8   C4   C3   C2    180.00   0.0  0
 JI7  CONST_17  C7   C2   N1   C6    180.00   0.0  0
 JI7  CONST_18  C8   C4   C5   C6    180.00   0.0  0
 JI7  CONST_19  C22  C21  C26  C12   180.00   0.0  0
 JI7  CONST_20  C24  C25  C26  C12   180.00   0.0  0
 JI7  CONST_21  CL   C22  C21  C26   180.00   0.0  0
 JI7  CONST_22  CL   C22  C23  C24   180.00   0.0  0
 JI7  CONST_23  H3   C3   C4   C5    180.00   0.0  0
 JI7  CONST_24  H5   C5   C4   C3    180.00   0.0  0
 JI7  CONST_25  H24  C24  C25  C26   180.00   0.0  0
 JI7  CONST_26  H23  C23  C24  C25   180.00   0.0  0
 JI7  CONST_27  H21  C21  C26  C25   180.00   0.0  0
 JI7  CONST_28  H25  C25  C24  C23   180.00   0.0  0
 JI7  Var_01    C2'  N1'  C5'  C4'     4.45  30.0  1
 JI7  Var_02    C5'  N1'  C2'  C3'   -27.93  30.0  1
 JI7  Var_03    C4'  C7   C2   C3     78.88  30.0  2
 JI7  Var_04    C21  C26  C12  N11   -28.75  30.0  2
 JI7  Var_05    H81  C8   C4   C5    113.19  30.0  2
 JI7  Var_06    C10  C9   N8   C3'  -179.96  30.0  1
 JI7  Var_07    C26  C12  N11  C10   174.65  30.0  1
 JI7  Var_08    N11  C10  C9   N8   -179.74  30.0  1
 JI7  Var_09    C12  N11  C10  C9   -177.26  30.0  2

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
 JI7  chir_01  C4'  C3'  C7   C5'  negativ
 JI7  chir_02  C3'  N8   C4'  C2'  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
 JI7  plan-1  C5    0.020
 JI7  plan-1  C4    0.020
 JI7  plan-1  C3    0.020
 JI7  plan-1  C2    0.020
 JI7  plan-1  N1    0.020
 JI7  plan-1  C6    0.020
 JI7  plan-1  C7    0.020
 JI7  plan-1  C8    0.020
 JI7  plan-1  N6    0.020
 JI7  plan-1  H5    0.020
 JI7  plan-1  H3    0.020
 JI7  plan-2  C12   0.020
 JI7  plan-2  C26   0.020
 JI7  plan-2  C25   0.020
 JI7  plan-2  C24   0.020
 JI7  plan-2  C23   0.020
 JI7  plan-2  C22   0.020
 JI7  plan-2  C21   0.020
 JI7  plan-2  CL    0.020
 JI7  plan-2  H25   0.020
 JI7  plan-2  H24   0.020
 JI7  plan-2  H23   0.020
 JI7  plan-2  H21   0.020
 JI7  plan-3  C6    0.020
 JI7  plan-3  N6    0.020
 JI7  plan-3  HN61  0.020
 JI7  plan-3  HN62  0.020

