# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:41:16 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: N-{(3S,4S)-4-[(6-aminopyridin-2-yl)methyl]pyrrolidin-3-yl}ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN[C@@H]1CNC[C@@H]1Cc2cccc(N)n2
#
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
 JI2  JI2  N-{(3S,4S)-4-[(6-aminopyridin-2-yl)methyl]pyrrolidin-3-yl}ethane-1,2-diamine  ligand  38  17  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JI2
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
 JI2  C6    C  CR6   0   0.430  -3.8255   0.1660  -0.8195
 JI2  N6    N  NH2   0  -0.837  -4.5070  -0.5438  -1.7674
 JI2  C5    C  CR16  0  -0.393  -4.5071   0.8428   0.2050
 JI2  C4    C  CR16  0  -0.150  -3.7573   1.4980   1.1577
 JI2  C3    C  CR16  0  -0.380  -2.3683   1.4723   1.0846
 JI2  C2    C  CR6   0   0.265  -1.7796   0.7779   0.0360
 JI2  N1    N  N     0  -0.472  -2.4963   0.1468  -0.8937
 JI2  N1'   N  NH1   0  -0.585   0.7601  -2.8117   0.8220
 JI2  C2'   C  CH2   0  -0.326   2.0308  -2.1418   0.5895
 JI2  C3'   C  CH1   0  -0.085   1.8121  -0.6149   0.7775
 JI2  C4'   C  CH1   0  -0.273   0.2622  -0.4701   0.7695
 JI2  C5'   C  CH2   0  -0.308  -0.2333  -1.8600   0.3453
 JI2  C7    C  CH2   0  -0.494  -0.2841   0.6813  -0.0744
 JI2  C10   C  CH2   0  -0.296   4.5594   1.2563  -0.9813
 JI2  N11   N  NH2   0  -0.802   6.0108   1.2168  -0.8844
 JI2  HN61  H  HNH2  0   0.379  -3.9935  -0.7685  -2.6038
 JI2  HN62  H  HNH2  0   0.387  -5.4679  -0.2950  -1.9328
 JI2  H5    H  HCR6  0   0.261  -5.5889   0.8470   0.2389
 JI2  H4    H  HCR6  0   0.261  -4.2526   2.0328   1.9583
 JI2  H3    H  HCR6  0   0.248  -1.7579   1.9788   1.8201
 JI2  HN1'  H  HNH1  0   0.342   0.6321  -2.9374   1.8193
 JI2  H2'1  H  HCH2  0   0.237   2.8085  -2.5509   1.2352
 JI2  H2'2  H  HCH2  0   0.213   2.3437  -2.3237  -0.4461
 JI2  H3'   H  HCH1  0   0.233   2.1832  -0.3129   1.7611
 JI2  H4'   H  HCH1  0   0.243  -0.0584  -0.3054   1.8033
 JI2  H5'1  H  HCH2  0   0.215  -0.2941  -1.9208  -0.7474
 JI2  H5'2  H  HCH2  0   0.237  -1.2219  -2.1029   0.7348
 JI2  H71   H  HCH2  0   0.233  -0.0182   0.5394  -1.1241
 JI2  H72   H  HCH2  0   0.243   0.1716   1.6180   0.2520
 JI2  HN8   H  HNH1  0   0.335   2.2378  -0.0564  -1.1260
 JI2  H91   H  HCH2  0   0.214   4.1899   0.4487   0.9736
 JI2  H92   H  HCH2  0   0.194   4.3875  -0.7637  -0.2835
 JI2  H101  H  HCH2  0   0.215   4.2803   1.0334  -2.0154
 JI2  H102  H  HCH2  0   0.192   4.1210   2.2355  -0.7448
 JI2  H111  H  HNH2  0   0.349   6.4081   1.8857  -1.5311
 JI2  H112  H  HNH2  0   0.338   6.2937   1.5315   0.0358
 JI2  N8    N  NH1   0  -0.601   2.4882   0.2306  -0.1857
 JI2  C9    C  CH2   0  -0.265   3.9342   0.2153  -0.0659

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
 JI2  C4   C5    aromatic  1.378  0.020  1.378
 JI2  C4   C3    aromatic  1.391  0.020  1.391
 JI2  C5   C6    aromatic  1.404  0.020  1.404
 JI2  C3   C2    aromatic  1.389  0.020  1.389
 JI2  C6   N6    single    1.366  0.020  1.366
 JI2  C6   N1    aromatic  1.331  0.020  1.331
 JI2  C4'  C5'   single    1.535  0.020  1.535
 JI2  C4'  C7    single    1.528  0.020  1.528
 JI2  C4'  C3'   single    1.557  0.020  1.557
 JI2  C2   N1    aromatic  1.333  0.020  1.333
 JI2  C2   C7    single    1.503  0.020  1.503
 JI2  C5'  N1'   single    1.456  0.020  1.456
 JI2  C3'  N8    single    1.449  0.020  1.449
 JI2  C3'  C2'   single    1.554  0.020  1.554
 JI2  N11  C10   single    1.455  0.020  1.455
 JI2  N8   C9    single    1.451  0.020  1.451
 JI2  N1'  C2'   single    1.455  0.020  1.455
 JI2  C9   C10   single    1.521  0.020  1.521
 JI2  N6   HN61  single    0.890  0.020  1.040
 JI2  N6   HN62  single    0.890  0.020  1.040
 JI2  C5   H5    single    0.930  0.020  1.080
 JI2  C4   H4    single    0.930  0.020  1.080
 JI2  C3   H3    single    0.930  0.020  1.080
 JI2  N1'  HN1'  single    0.890  0.020  1.040
 JI2  C2'  H2'1  single    0.970  0.020  1.090
 JI2  C2'  H2'2  single    0.970  0.020  1.090
 JI2  C3'  H3'   single    0.970  0.020  1.090
 JI2  C4'  H4'   single    0.970  0.020  1.090
 JI2  C5'  H5'1  single    0.970  0.020  1.090
 JI2  C5'  H5'2  single    0.970  0.020  1.090
 JI2  C7   H71   single    0.970  0.020  1.090
 JI2  C7   H72   single    0.970  0.020  1.090
 JI2  N8   HN8   single    0.890  0.020  1.040
 JI2  C9   H91   single    0.970  0.020  1.090
 JI2  C9   H92   single    0.970  0.020  1.090
 JI2  C10  H101  single    0.970  0.020  1.090
 JI2  C10  H102  single    0.970  0.020  1.090
 JI2  N11  H111  single    0.890  0.020  1.040
 JI2  N11  H112  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
 JI2  N1    C6   C5    122.15  3.000
 JI2  N1    C6   N6    116.86  3.000
 JI2  C5    C6   N6    120.96  3.000
 JI2  HN62  N6   HN61  113.93  3.000
 JI2  HN62  N6   C6    117.51  3.000
 JI2  HN61  N6   C6    115.97  3.000
 JI2  H5    C5   C4    121.35  3.000
 JI2  H5    C5   C6    120.65  3.000
 JI2  C4    C5   C6    118.00  3.000
 JI2  H4    C4   C3    120.32  3.000
 JI2  H4    C4   C5    119.81  3.000
 JI2  C3    C4   C5    119.87  3.000
 JI2  H3    C3   C2    120.56  3.000
 JI2  H3    C3   C4    121.26  3.000
 JI2  C2    C3   C4    118.18  3.000
 JI2  C7    C2   N1    116.97  3.000
 JI2  C7    C2   C3    120.63  3.000
 JI2  N1    C2   C3    122.38  3.000
 JI2  C2    N1   C6    119.42  3.000
 JI2  HN1'  N1'  C5'   108.49  3.000
 JI2  HN1'  N1'  C2'   108.94  3.000
 JI2  C5'   N1'  C2'   104.04  3.000
 JI2  H2'2  C2'  H2'1  107.06  3.000
 JI2  H2'2  C2'  C3'   108.50  3.000
 JI2  H2'1  C2'  C3'   113.41  3.000
 JI2  H2'2  C2'  N1'   108.88  3.000
 JI2  H2'1  C2'  N1'   110.83  3.000
 JI2  C3'   C2'  N1'   108.07  3.000
 JI2  H3'   C3'  N8    106.16  3.000
 JI2  H3'   C3'  C4'   108.47  3.000
 JI2  N8    C3'  C4'   114.01  3.000
 JI2  H3'   C3'  C2'   109.41  3.000
 JI2  N8    C3'  C2'   115.29  3.000
 JI2  C4'   C3'  C2'   103.35  3.000
 JI2  H4'   C4'  C7    107.66  3.000
 JI2  H4'   C4'  C5'   107.61  3.000
 JI2  C7    C4'  C5'   114.46  3.000
 JI2  H4'   C4'  C3'   107.50  3.000
 JI2  C7    C4'  C3'   115.39  3.000
 JI2  C5'   C4'  C3'   103.80  3.000
 JI2  H5'2  C5'  H5'1  107.07  3.000
 JI2  H5'2  C5'  C4'   113.31  3.000
 JI2  H5'1  C5'  C4'   110.09  3.000
 JI2  H5'2  C5'  N1'   110.87  3.000
 JI2  H5'1  C5'  N1'   109.15  3.000
 JI2  C4'   C5'  N1'   106.33  3.000
 JI2  H72   C7   H71   107.29  3.000
 JI2  H72   C7   C4'   109.40  3.000
 JI2  H71   C7   C4'   110.23  3.000
 JI2  H72   C7   C2    109.78  3.000
 JI2  H71   C7   C2    108.74  3.000
 JI2  C4'   C7   C2    111.32  3.000
 JI2  H102  C10  H101  106.45  3.000
 JI2  H102  C10  N11   114.07  3.000
 JI2  H101  C10  N11   108.17  3.000
 JI2  H102  C10  C9    108.45  3.000
 JI2  H101  C10  C9    108.94  3.000
 JI2  N11   C10  C9    110.57  3.000
 JI2  H112  N11  H111  105.40  3.000
 JI2  H112  N11  C10   109.31  3.000
 JI2  H111  N11  C10   109.35  3.000
 JI2  HN8   N8   C9    108.63  3.000
 JI2  HN8   N8   C3'   109.63  3.000
 JI2  C9    N8   C3'   113.83  3.000
 JI2  H92   C9   H91   106.32  3.000
 JI2  H92   C9   C10   108.70  3.000
 JI2  H91   C9   C10   109.23  3.000
 JI2  H92   C9   N8    113.80  3.000
 JI2  H91   C9   N8    107.98  3.000
 JI2  C10   C9   N8    110.66  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
 JI2  CONST_01  C3    C4   C5   C6      0.00   0.0  0
 JI2  CONST_02  C3    C2   N1   C6      0.00   0.0  0
 JI2  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 JI2  CONST_04  C2    N1   C6   C5      0.00   0.0  0
 JI2  CONST_05  N1    C6   C5   C4      0.00   0.0  0
 JI2  CONST_06  N1    C2   C3   C4      0.00   0.0  0
 JI2  CONST_07  C7    C2   N1   C6    180.00   0.0  0
 JI2  CONST_08  C4    C5   C6   N6    180.00   0.0  0
 JI2  CONST_09  C2    N1   C6   N6    180.00   0.0  0
 JI2  CONST_10  C7    C2   C3   C4    180.00   0.0  0
 JI2  CONST_11  H4    C4   C5   C6    180.00   0.0  0
 JI2  CONST_12  H3    C3   C4   C5    180.00   0.0  0
 JI2  CONST_13  H5    C5   C4   C3    180.00   0.0  0
 JI2  Var_01    C4'   C5'  N1'  C2'   -39.09  30.0  1
 JI2  Var_02    C5'   N1'  C2'  C3'    32.95  30.0  1
 JI2  Var_03    C4'   C7   C2   C3     84.71  30.0  2
 JI2  Var_04    C10   C9   N8   C3'  -172.62  30.0  3
 JI2  Var_05    N11   C10  C9   N8   -178.59  30.0  3
 JI2  Var_06    H111  N11  C10  C9    177.41  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
 JI2  chir_01  C3'  C4'  N8  C2'  positiv
 JI2  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
 JI2  plan-1  C6    0.020
 JI2  plan-1  N6    0.020
 JI2  plan-1  C5    0.020
 JI2  plan-1  C4    0.020
 JI2  plan-1  C3    0.020
 JI2  plan-1  C2    0.020
 JI2  plan-1  N1    0.020
 JI2  plan-1  C7    0.020
 JI2  plan-1  H5    0.020
 JI2  plan-1  H4    0.020
 JI2  plan-1  H3    0.020
 JI2  plan-2  C6    0.020
 JI2  plan-2  N6    0.020
 JI2  plan-2  HN61  0.020
 JI2  plan-2  HN62  0.020

