# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:48:34 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 3-({(3S,4S)-4-[(6-aminopyridin-2-yl)methyl]pyrrolidin-3-yl}amino)propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(C[C@H]2CNC[C@H]2NCCCO)n1
#
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
 JI1  JI1  3-({(3S,4S)-4-[(6-aminopyridin-2-yl)methyl]pyrrolidin-3-yl}amino)propan-1-ol  ligand  40  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JI1
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
 JI1  N1    N  N     0  -0.472  -2.8173   0.4026  -0.9343
 JI1  C2    C  CR6   0   0.430  -4.1428   0.5256  -0.9478
 JI1  N2    N  NH2   0  -0.837  -4.8034  -0.0221  -2.0113
 JI1  C3    C  CR16  0  -0.393  -4.8466   1.1480   0.0962
 JI1  C4    C  CR16  0  -0.149  -4.1225   1.6400   1.1604
 JI1  C5    C  CR16  0  -0.380  -2.7376   1.5088   1.1765
 JI1  C6    C  CR6   0   0.263  -2.1263   0.8766   0.1021
 JI1  N1'   N  NH1   0  -0.585   0.0365  -2.9728   0.7618
 JI1  C2'   C  CH2   0  -0.323   1.3839  -2.4171   0.7448
 JI1  C3'   C  CH1   0  -0.090   1.2785  -0.8744   0.9334
 JI1  C4'   C  CH1   0  -0.271  -0.2474  -0.6061   0.8280
 JI1  C5'   C  CH2   0  -0.308  -0.8000  -1.9058   0.2315
 JI1  C7    C  CH2   0  -0.490  -0.6388   0.6665   0.0785
 JI1  C10   C  CH2   0  -0.477   4.2754   0.7407  -0.6741
 JI1  C11   C  CH2   0  -0.141   5.7712   0.6411  -0.4494
 JI1  O12   O  OH1   0  -0.675   6.4265   1.5465  -1.3127
 JI1  HN21  H  HNH2  0   0.379  -4.2471  -0.1968  -2.8322
 JI1  HN22  H  HNH2  0   0.387  -5.7267   0.3246  -2.2109
 JI1  H3    H  HCR6  0   0.261  -5.9245   1.2383   0.0580
 JI1  H4    H  HCR6  0   0.261  -4.6337   2.1311   1.9788
 JI1  H5    H  HCR6  0   0.248  -2.1488   1.8927   1.9988
 JI1  HN1'  H  HNH1  0   0.342  -0.2354  -3.1429   1.7228
 JI1  H2'1  H  HCH2  0   0.237   2.0073  -2.9038   1.4956
 JI1  H2'2  H  HCH2  0   0.214   1.8384  -2.6199  -0.2326
 JI1  H3'   H  HCH1  0   0.234   1.6159  -0.5999   1.9367
 JI1  H4'   H  HCH1  0   0.243  -0.6330  -0.5240   1.8500
 JI1  H5'1  H  HCH2  0   0.214  -0.7125  -1.8863  -0.8613
 JI1  H5'2  H  HCH2  0   0.238  -1.8498  -2.0813   0.4667
 JI1  H71   H  HCH2  0   0.233  -0.3096   0.6078  -0.9605
 JI1  H72   H  HCH2  0   0.243  -0.1335   1.5224   0.5301
 JI1  HN8   H  HNH1  0   0.334   1.8683  -0.3659  -0.9416
 JI1  H91   H  HCH2  0   0.217   3.7040   0.0481   1.2787
 JI1  H92   H  HCH2  0   0.193   3.8790  -1.2312   0.0911
 JI1  H101  H  HCH2  0   0.223   4.0498   0.5102  -1.7206
 JI1  H102  H  HCH2  0   0.224   3.9407   1.7653  -0.4888
 JI1  H111  H  HCH2  0   0.190   5.9950   0.8613   0.6030
 JI1  H112  H  HCH2  0   0.189   6.1000  -0.3912  -0.6304
 JI1  HO12  H  HOH1  0   0.452   7.3718   1.4809  -1.1519
 JI1  N8    N  NH1   0  -0.596   2.0736  -0.0867   0.0120
 JI1  C9    C  CH2   0  -0.260   3.5034  -0.2055   0.2328

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
 JI1  C4   C3    aromatic  1.378  0.020  1.378
 JI1  C4   C5    aromatic  1.391  0.020  1.391
 JI1  C3   C2    aromatic  1.405  0.020  1.405
 JI1  C5   C6    aromatic  1.388  0.020  1.388
 JI1  C2   N2    single    1.367  0.020  1.367
 JI1  C2   N1    aromatic  1.331  0.020  1.331
 JI1  C5'  C4'   single    1.533  0.020  1.533
 JI1  C5'  N1'   single    1.456  0.020  1.456
 JI1  C4'  C3'   single    1.553  0.020  1.553
 JI1  C4'  C7    single    1.528  0.020  1.528
 JI1  C6   N1    aromatic  1.333  0.020  1.333
 JI1  C6   C7    single    1.503  0.020  1.503
 JI1  C3'  N8    single    1.450  0.020  1.450
 JI1  C3'  C2'   single    1.558  0.020  1.558
 JI1  N1'  C2'   single    1.458  0.020  1.458
 JI1  N8   C9    single    1.452  0.020  1.452
 JI1  C9   C10   single    1.521  0.020  1.521
 JI1  O12  C11   single    1.412  0.020  1.412
 JI1  C10  C11   single    1.516  0.020  1.516
 JI1  N2   HN21  single    0.890  0.020  1.040
 JI1  N2   HN22  single    0.890  0.020  1.040
 JI1  C3   H3    single    0.930  0.020  1.080
 JI1  C4   H4    single    0.930  0.020  1.080
 JI1  C5   H5    single    0.930  0.020  1.080
 JI1  N1'  HN1'  single    0.890  0.020  1.040
 JI1  C2'  H2'1  single    0.970  0.020  1.090
 JI1  C2'  H2'2  single    0.970  0.020  1.090
 JI1  C3'  H3'   single    0.970  0.020  1.090
 JI1  C4'  H4'   single    0.970  0.020  1.090
 JI1  C5'  H5'1  single    0.970  0.020  1.090
 JI1  C5'  H5'2  single    0.970  0.020  1.090
 JI1  C7   H71   single    0.970  0.020  1.090
 JI1  C7   H72   single    0.970  0.020  1.090
 JI1  N8   HN8   single    0.890  0.020  1.040
 JI1  C9   H91   single    0.970  0.020  1.090
 JI1  C9   H92   single    0.970  0.020  1.090
 JI1  C10  H101  single    0.970  0.020  1.090
 JI1  C10  H102  single    0.970  0.020  1.090
 JI1  C11  H111  single    0.970  0.020  1.090
 JI1  C11  H112  single    0.970  0.020  1.090
 JI1  O12  HO12  single    0.850  0.020  0.980

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
 JI1  C6    N1   C2    119.42  3.000
 JI1  C3    C2   N2    120.92  3.000
 JI1  N2    C2   N1    116.88  3.000
 JI1  C3    C2   N1    122.17  3.000
 JI1  HN22  N2   HN21  113.89  3.000
 JI1  HN22  N2   C2    117.38  3.000
 JI1  HN21  N2   C2    115.91  3.000
 JI1  H3    C3   C4    121.38  3.000
 JI1  H3    C3   C2    120.65  3.000
 JI1  C4    C3   C2    117.97  3.000
 JI1  H4    C4   C5    120.27  3.000
 JI1  H4    C4   C3    119.84  3.000
 JI1  C5    C4   C3    119.89  3.000
 JI1  H5    C5   C6    120.67  3.000
 JI1  H5    C5   C4    121.15  3.000
 JI1  C6    C5   C4    118.18  3.000
 JI1  C7    C6   C5    120.78  3.000
 JI1  C7    C6   N1    116.83  3.000
 JI1  C5    C6   N1    122.37  3.000
 JI1  HN1'  N1'  C5'   108.32  3.000
 JI1  HN1'  N1'  C2'   108.86  3.000
 JI1  C5'   N1'  C2'   104.33  3.000
 JI1  H2'2  C2'  H2'1  107.11  3.000
 JI1  H2'2  C2'  C3'   108.60  3.000
 JI1  H2'1  C2'  C3'   113.41  3.000
 JI1  H2'2  C2'  N1'   108.85  3.000
 JI1  H2'1  C2'  N1'   110.50  3.000
 JI1  C3'   C2'  N1'   108.27  3.000
 JI1  H3'   C3'  N8    106.11  3.000
 JI1  H3'   C3'  C4'   108.79  3.000
 JI1  N8    C3'  C4'   113.70  3.000
 JI1  H3'   C3'  C2'   109.80  3.000
 JI1  N8    C3'  C2'   115.09  3.000
 JI1  C4'   C3'  C2'   103.26  3.000
 JI1  H4'   C4'  C7    107.76  3.000
 JI1  H4'   C4'  C5'   107.44  3.000
 JI1  C7    C4'  C5'   115.02  3.000
 JI1  H4'   C4'  C3'   107.19  3.000
 JI1  C7    C4'  C3'   115.39  3.000
 JI1  C5'   C4'  C3'   103.54  3.000
 JI1  H5'2  C5'  H5'1  107.14  3.000
 JI1  H5'2  C5'  C4'   113.56  3.000
 JI1  H5'1  C5'  C4'   110.11  3.000
 JI1  H5'2  C5'  N1'   110.90  3.000
 JI1  H5'1  C5'  N1'   109.28  3.000
 JI1  C4'   C5'  N1'   105.81  3.000
 JI1  H72   C7   H71   107.24  3.000
 JI1  H72   C7   C4'   109.36  3.000
 JI1  H71   C7   C4'   110.18  3.000
 JI1  H72   C7   C6    110.00  3.000
 JI1  H71   C7   C6    108.72  3.000
 JI1  C4'   C7   C6    111.25  3.000
 JI1  H102  C10  H101  107.22  3.000
 JI1  H102  C10  C11   109.78  3.000
 JI1  H101  C10  C11   109.34  3.000
 JI1  H102  C10  C9    109.05  3.000
 JI1  H101  C10  C9    109.53  3.000
 JI1  C11   C10  C9    111.81  3.000
 JI1  H112  C11  H111  106.58  3.000
 JI1  H112  C11  O12   111.28  3.000
 JI1  H111  C11  O12   111.27  3.000
 JI1  H112  C11  C10   109.43  3.000
 JI1  H111  C11  C10   109.26  3.000
 JI1  O12   C11  C10   108.97  3.000
 JI1  HO12  O12  C11   108.08  3.000
 JI1  HN8   N8   C9    108.65  3.000
 JI1  HN8   N8   C3'   109.69  3.000
 JI1  C9    N8   C3'   113.52  3.000
 JI1  H92   C9   H91   106.03  3.000
 JI1  H92   C9   C10   109.24  3.000
 JI1  H91   C9   C10   109.43  3.000
 JI1  H92   C9   N8    113.11  3.000
 JI1  H91   C9   N8    107.86  3.000
 JI1  C10   C9   N8    111.00  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
 JI1  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 JI1  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 JI1  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 JI1  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 JI1  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 JI1  CONST_06  C6   N1   C2   C3      0.00   0.0  0
 JI1  CONST_07  C7   C6   N1   C2    180.00   0.0  0
 JI1  CONST_08  C4   C3   C2   N2    180.00   0.0  0
 JI1  CONST_09  C6   N1   C2   N2    180.00   0.0  0
 JI1  CONST_10  C7   C6   C5   C4    180.00   0.0  0
 JI1  CONST_11  H3   C3   C2   N1    180.00   0.0  0
 JI1  CONST_12  H5   C5   C6   N1    180.00   0.0  0
 JI1  CONST_13  H4   C4   C3   C2    180.00   0.0  0
 JI1  Var_01    C4'  C5'  N1'  C2'   -39.50  30.0  1
 JI1  Var_02    C5'  N1'  C2'  C3'    29.82  30.0  1
 JI1  Var_03    C4'  C7   C6   N1    -93.75  30.0  2
 JI1  Var_04    C10  C9   N8   C3'  -174.64  30.0  3
 JI1  Var_05    C11  C10  C9   N8    179.46  30.0  3
 JI1  Var_06    O12  C11  C10  C9   -179.66  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
 JI1  chir_01  C3'  C4'  N8   C2'  positiv
 JI1  chir_02  C4'  C7   C3'  C5'  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
 JI1  plan-1  N1    0.020
 JI1  plan-1  C2    0.020
 JI1  plan-1  N2    0.020
 JI1  plan-1  C3    0.020
 JI1  plan-1  C4    0.020
 JI1  plan-1  C5    0.020
 JI1  plan-1  C6    0.020
 JI1  plan-1  C7    0.020
 JI1  plan-1  H3    0.020
 JI1  plan-1  H4    0.020
 JI1  plan-1  H5    0.020
 JI1  plan-2  C2    0.020
 JI1  plan-2  N2    0.020
 JI1  plan-2  HN21  0.020
 JI1  plan-2  HN22  0.020

