# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:40:58 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: N-{(3S,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-[2-(3-fluorophenyl)ethyl]ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@H]2CNC[C@H]2NCCNCCc3cccc(F)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
 JI4  JI4  N-{(3S,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-[2-(3-fluorophenyl)ethyl]ethane-1,2-diamine  ligand  57  27  .  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_JI4
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
 JI4  C1    C  CH2   0  -0.283   0.4619   1.3375  -1.0048
 JI4  N1    N  NH1   0  -0.614  -0.8203   0.8141  -0.5702
 JI4  C2    C  CH2   0  -0.278   1.5981   0.6533  -0.2637
 JI4  N2    N  NH1   0  -0.603   2.8800   1.1714  -0.6980
 JI4  C3    C  CH2   0  -0.245   3.9987   0.5755   0.0025
 JI4  C4    C  CH2   0  -0.531   5.3187   1.1830  -0.4680
 JI4  N1'   N  NH1   0  -0.612  -3.5004   3.1133  -0.6540
 JI4  C11   C  CR6   0   0.139   6.4911   0.5664   0.2395
 JI4  C12   C  CR16  0  -0.464   7.0856  -0.5880  -0.2644
 JI4  C13   C  CR6   0   0.539   8.1359  -1.1637   0.4232
 JI4  F13   F  F     0  -0.319   8.7034  -2.2737  -0.0808
 JI4  C14   C  CR16  0  -0.427   8.6274  -0.6415   1.6036
 JI4  C15   C  CR16  0  -0.224   8.0299   0.5084   2.1028
 JI4  C16   C  CR16  0  -0.320   6.9733   1.1066   1.4301
 JI4  N11   N  N     0  -0.478  -5.0964  -0.8151   1.3237
 JI4  C2'   C  CH2   0  -0.287  -2.0740   2.9153  -0.8522
 JI4  C21   C  CR6   0   0.280  -4.6404  -1.0785   0.0980
 JI4  C3'   C  CH1   0  -0.074  -1.9396   1.4336  -1.2598
 JI4  C31   C  CR16  0  -0.423  -5.3863  -1.7645  -0.8453
 JI4  C4'   C  CH1   0  -0.242  -3.3157   0.8192  -0.8757
 JI4  C41   C  CR6   0   0.204  -6.6701  -2.2050  -0.5088
 JI4  C5'   C  CH2   0  -0.272  -3.9592   1.8978  -0.0083
 JI4  C51   C  CR16  0  -0.448  -7.1433  -1.9235   0.7573
 JI4  C61   C  CR6   0   0.440  -6.3205  -1.2178   1.6506
 JI4  N61   N  NH2   0  -0.840  -6.7715  -0.8793   2.8959
 JI4  C71   C  CH2   0  -0.529  -3.2670  -0.5661  -0.2326
 JI4  C81   C  CH3   0  -0.729  -7.4936  -2.9724  -1.4976
 JI4  H1    H  HCH2  0   0.192   0.6080   1.2275  -2.0931
 JI4  H1A   H  HCH2  0   0.229   0.5063   2.4094  -0.7964
 JI4  HN1   H  HNH1  0   0.347  -0.8253  -0.1793  -0.7728
 JI4  H2    H  HCH2  0   0.222   1.4901   0.8445   0.8076
 JI4  H2A   H  HCH2  0   0.190   1.5151  -0.4392  -0.3930
 JI4  HN2   H  HNH1  0   0.339   2.9856   0.9909  -1.6903
 JI4  H3    H  HCH2  0   0.225   3.8786   0.7646   1.0737
 JI4  H3A   H  HCH2  0   0.198   4.0419  -0.5194  -0.1138
 JI4  H4    H  HCH2  0   0.246   5.4163   1.0358  -1.5474
 JI4  H4A   H  HCH2  0   0.248   5.2966   2.2606  -0.2930
 JI4  HN1'  H  HNH1  0   0.348  -3.6818   3.9333  -0.0903
 JI4  H12   H  HCR6  0   0.269   6.7359  -1.0331  -1.1884
 JI4  H14   H  HCR6  0   0.277   9.4530  -1.1161   2.1173
 JI4  H15   H  HCR6  0   0.266   8.3969   0.9405   3.0245
 JI4  H16   H  HCR6  0   0.253   6.5192   2.0046   1.8311
 JI4  H2'   H  HCH2  0   0.225  -1.6808   3.6007  -1.6060
 JI4  H2'A  H  HCH2  0   0.199  -1.4964   3.0721   0.0714
 JI4  H3'   H  HCH1  0   0.211  -1.8120   1.3608  -2.3509
 JI4  H31   H  HCR6  0   0.240  -4.9742  -1.9650  -1.8272
 JI4  H4'   H  HCH1  0   0.243  -3.9026   0.7430  -1.7960
 JI4  H5'   H  HCH2  0   0.191  -3.6152   1.7964   1.0335
 JI4  H5'A  H  HCH2  0   0.227  -5.0489   1.8397   0.0010
 JI4  H51   H  HCR6  0   0.255  -8.1307  -2.2466   1.0649
 JI4  HN61  H  HNH2  0   0.378  -6.0624  -0.6407   3.5702
 JI4  HN6A  H  HNH2  0   0.386  -7.5281  -1.4228   3.2765
 JI4  H71   H  HCH2  0   0.243  -2.6715  -0.5338   0.6815
 JI4  H71A  H  HCH2  0   0.245  -2.7803  -1.2665  -0.9174
 JI4  H81   H  HCH3  0   0.252  -6.9971  -3.9047  -1.7706
 JI4  H81A  H  HCH3  0   0.247  -8.4780  -3.2174  -1.1028
 JI4  H81B  H  HCH3  0   0.251  -7.6284  -2.4034  -2.4183

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
 JI4  N1   C1    single    1.451  0.020  1.451
 JI4  C2   C1    single    1.519  0.020  1.519
 JI4  C1   H1    single    0.970  0.020  1.090
 JI4  C1   H1A   single    0.970  0.020  1.090
 JI4  N1   C3'   single    1.453  0.020  1.453
 JI4  N1   HN1   single    0.890  0.020  1.040
 JI4  N2   C2    single    1.449  0.020  1.449
 JI4  C2   H2    single    0.970  0.020  1.090
 JI4  C2   H2A   single    0.970  0.020  1.090
 JI4  C3   N2    single    1.448  0.020  1.448
 JI4  N2   HN2   single    0.890  0.020  1.040
 JI4  C4   C3    single    1.527  0.020  1.527
 JI4  C3   H3    single    0.970  0.020  1.090
 JI4  C3   H3A   single    0.970  0.020  1.090
 JI4  C11  C4    single    1.502  0.020  1.502
 JI4  C4   H4    single    0.970  0.020  1.090
 JI4  C4   H4A   single    0.970  0.020  1.090
 JI4  C2'  N1'   single    1.454  0.020  1.454
 JI4  N1'  C5'   single    1.451  0.020  1.451
 JI4  N1'  HN1'  single    0.890  0.020  1.040
 JI4  C12  C11   aromatic  1.393  0.020  1.393
 JI4  C16  C11   aromatic  1.393  0.020  1.393
 JI4  C13  C12   aromatic  1.381  0.020  1.381
 JI4  C12  H12   single    0.930  0.020  1.080
 JI4  F13  C13   single    1.345  0.020  1.345
 JI4  C14  C13   aromatic  1.381  0.020  1.381
 JI4  C14  C15   aromatic  1.389  0.020  1.389
 JI4  C14  H14   single    0.930  0.020  1.080
 JI4  C15  C16   aromatic  1.388  0.020  1.388
 JI4  C15  H15   single    0.930  0.020  1.080
 JI4  C16  H16   single    0.930  0.020  1.080
 JI4  N11  C21   aromatic  1.334  0.020  1.334
 JI4  N11  C61   aromatic  1.329  0.020  1.329
 JI4  C2'  C3'   single    1.543  0.020  1.543
 JI4  C2'  H2'   single    0.970  0.020  1.090
 JI4  C2'  H2'A  single    0.970  0.020  1.090
 JI4  C71  C21   single    1.503  0.020  1.503
 JI4  C21  C31   aromatic  1.384  0.020  1.384
 JI4  C3'  C4'   single    1.555  0.020  1.555
 JI4  C3'  H3'   single    0.970  0.020  1.090
 JI4  C31  C41   aromatic  1.398  0.020  1.398
 JI4  C31  H31   single    0.930  0.020  1.080
 JI4  C71  C4'   single    1.528  0.020  1.528
 JI4  C4'  C5'   single    1.526  0.020  1.526
 JI4  C4'  H4'   single    0.970  0.020  1.090
 JI4  C51  C41   aromatic  1.381  0.020  1.381
 JI4  C41  C81   single    1.498  0.020  1.498
 JI4  C5'  H5'   single    0.970  0.020  1.090
 JI4  C5'  H5'A  single    0.970  0.020  1.090
 JI4  C61  C51   aromatic  1.405  0.020  1.405
 JI4  C51  H51   single    0.930  0.020  1.080
 JI4  N61  C61   single    1.367  0.020  1.367
 JI4  N61  HN61  single    0.890  0.020  1.040
 JI4  N61  HN6A  single    0.890  0.020  1.040
 JI4  C71  H71   single    0.970  0.020  1.090
 JI4  C71  H71A  single    0.970  0.020  1.090
 JI4  C81  H81   single    0.970  0.020  1.090
 JI4  C81  H81A  single    0.970  0.020  1.090
 JI4  C81  H81B  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
 JI4  H1A   C1   H1    106.28  3.000
 JI4  H1A   C1   C2    108.56  3.000
 JI4  H1    C1   C2    109.70  3.000
 JI4  H1A   C1   N1    109.42  3.000
 JI4  H1    C1   N1    112.11  3.000
 JI4  C2    C1   N1    110.62  3.000
 JI4  HN1   N1   C3'   108.61  3.000
 JI4  HN1   N1   C1    107.33  3.000
 JI4  C3'   N1   C1    112.62  3.000
 JI4  H2A   C2   H2    106.29  3.000
 JI4  H2A   C2   N2    112.68  3.000
 JI4  H2    C2   N2    108.57  3.000
 JI4  H2A   C2   C1    109.42  3.000
 JI4  H2    C2   C1    108.98  3.000
 JI4  N2    C2   C1    110.75  3.000
 JI4  HN2   N2   C3    108.64  3.000
 JI4  HN2   N2   C2    108.76  3.000
 JI4  C3    N2   C2    113.03  3.000
 JI4  H3A   C3   H3    106.21  3.000
 JI4  H3A   C3   C4    109.20  3.000
 JI4  H3    C3   C4    109.13  3.000
 JI4  H3A   C3   N2    112.83  3.000
 JI4  H3    C3   N2    108.52  3.000
 JI4  C4    C3   N2    110.79  3.000
 JI4  H4A   C4   H4    107.02  3.000
 JI4  H4A   C4   C11   110.21  3.000
 JI4  H4    C4   C11   109.88  3.000
 JI4  H4A   C4   C3    109.00  3.000
 JI4  H4    C4   C3    109.12  3.000
 JI4  C11   C4   C3    111.49  3.000
 JI4  HN1'  N1'  C5'   111.99  3.000
 JI4  HN1'  N1'  C2'   111.25  3.000
 JI4  C5'   N1'  C2'   104.89  3.000
 JI4  C16   C11  C12   118.86  3.000
 JI4  C16   C11  C4    120.90  3.000
 JI4  C12   C11  C4    120.21  3.000
 JI4  H12   C12  C13   119.91  3.000
 JI4  H12   C12  C11   120.74  3.000
 JI4  C13   C12  C11   119.34  3.000
 JI4  C14   C13  F13   118.84  3.000
 JI4  C14   C13  C12   122.58  3.000
 JI4  F13   C13  C12   118.59  3.000
 JI4  H14   C14  C15   121.40  3.000
 JI4  H14   C14  C13   120.75  3.000
 JI4  C15   C14  C13   117.85  3.000
 JI4  H15   C15  C16   119.93  3.000
 JI4  H15   C15  C14   119.40  3.000
 JI4  C16   C15  C14   120.68  3.000
 JI4  H16   C16  C15   119.80  3.000
 JI4  H16   C16  C11   119.51  3.000
 JI4  C15   C16  C11   120.69  3.000
 JI4  C61   N11  C21   118.74  3.000
 JI4  H2'A  C2'  H2'   107.51  3.000
 JI4  H2'A  C2'  C3'   108.23  3.000
 JI4  H2'   C2'  C3'   112.90  3.000
 JI4  H2'A  C2'  N1'   112.40  3.000
 JI4  H2'   C2'  N1'   111.22  3.000
 JI4  C3'   C2'  N1'   104.62  3.000
 JI4  C71   C21  C31   120.76  3.000
 JI4  C31   C21  N11   122.67  3.000
 JI4  C71   C21  N11   116.56  3.000
 JI4  H3'   C3'  C4'   108.74  3.000
 JI4  H3'   C3'  C2'   109.60  3.000
 JI4  C4'   C3'  C2'   103.72  3.000
 JI4  H3'   C3'  N1    110.65  3.000
 JI4  C4'   C3'  N1    113.32  3.000
 JI4  C2'   C3'  N1    110.56  3.000
 JI4  H31   C31  C41   120.59  3.000
 JI4  H31   C31  C21   120.28  3.000
 JI4  C41   C31  C21   119.13  3.000
 JI4  H4'   C4'  C71   107.93  3.000
 JI4  H4'   C4'  C5'   107.52  3.000
 JI4  C71   C4'  C5'   114.52  3.000
 JI4  H4'   C4'  C3'   107.12  3.000
 JI4  C5'   C4'  C3'   103.54  3.000
 JI4  C71   C4'  C3'   115.71  3.000
 JI4  C81   C41  C51   121.42  3.000
 JI4  C81   C41  C31   120.47  3.000
 JI4  C51   C41  C31   118.11  3.000
 JI4  H5'A  C5'  H5'   107.39  3.000
 JI4  H5'A  C5'  C4'   112.84  3.000
 JI4  H5'   C5'  C4'   109.92  3.000
 JI4  H5'A  C5'  N1'   111.36  3.000
 JI4  H5'   C5'  N1'   113.53  3.000
 JI4  C4'   C5'  N1'   101.87  3.000
 JI4  H51   C51  C61   120.20  3.000
 JI4  H51   C51  C41   120.79  3.000
 JI4  C61   C51  C41   119.01  3.000
 JI4  N61   C61  C51   120.70  3.000
 JI4  N61   C61  N11   116.92  3.000
 JI4  C51   C61  N11   122.35  3.000
 JI4  HN6A  N61  HN61  113.84  3.000
 JI4  HN6A  N61  C61   117.31  3.000
 JI4  HN61  N61  C61   115.87  3.000
 JI4  H71A  C71  H71   107.49  3.000
 JI4  H71A  C71  C4'   109.34  3.000
 JI4  H71   C71  C4'   110.06  3.000
 JI4  H71A  C71  C21   109.03  3.000
 JI4  H71   C71  C21   108.94  3.000
 JI4  C4'   C71  C21   111.87  3.000
 JI4  H81B  C81  H81A  108.16  3.000
 JI4  H81B  C81  H81   106.91  3.000
 JI4  H81A  C81  H81   108.06  3.000
 JI4  H81B  C81  C41   110.97  3.000
 JI4  H81A  C81  C41   111.90  3.000
 JI4  H81   C81  C41   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
 JI4  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 JI4  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 JI4  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 JI4  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 JI4  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 JI4  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 JI4  CONST_07  C41  C31  C21  N11     0.00   0.0  0
 JI4  CONST_08  C41  C51  C61  N11     0.00   0.0  0
 JI4  CONST_09  C51  C61  N11  C21     0.00   0.0  0
 JI4  CONST_10  C51  C41  C31  C21     0.00   0.0  0
 JI4  CONST_11  C61  N11  C21  C31     0.00   0.0  0
 JI4  CONST_12  C61  C51  C41  C31     0.00   0.0  0
 JI4  CONST_13  C13  C12  C11  C4    180.00   0.0  0
 JI4  CONST_14  C15  C16  C11  C4    180.00   0.0  0
 JI4  CONST_15  F13  C13  C12  C11   180.00   0.0  0
 JI4  CONST_16  C15  C14  C13  F13   180.00   0.0  0
 JI4  CONST_17  N61  C61  N11  C21   180.00   0.0  0
 JI4  CONST_18  C81  C41  C31  C21   180.00   0.0  0
 JI4  CONST_19  C71  C21  C31  C41   180.00   0.0  0
 JI4  CONST_20  N61  C61  C51  C41   180.00   0.0  0
 JI4  CONST_21  C71  C21  N11  C61   180.00   0.0  0
 JI4  CONST_22  C81  C41  C51  C61   180.00   0.0  0
 JI4  CONST_23  H15  C15  C16  C11   180.00   0.0  0
 JI4  CONST_24  H16  C16  C11  C12   180.00   0.0  0
 JI4  CONST_25  H14  C14  C13  C12   180.00   0.0  0
 JI4  CONST_26  H12  C12  C13  C14   180.00   0.0  0
 JI4  CONST_27  H31  C31  C21  N11   180.00   0.0  0
 JI4  CONST_28  H51  C51  C61  N11   180.00   0.0  0
 JI4  Var_01    C4'  C5'  N1'  C2'   -47.39  30.0  1
 JI4  Var_02    C5'  N1'  C2'  C3'    39.23  30.0  1
 JI4  Var_03    C4'  C71  C21  N11   -92.08  30.0  2
 JI4  Var_04    C12  C11  C4   C3     87.61  30.0  2
 JI4  Var_05    H81  C81  C41  C31    61.27  30.0  2
 JI4  Var_06    C3'  N1   C1   C2   -179.61  30.0  1
 JI4  Var_07    C11  C4   C3   N2   -179.46  30.0  1
 JI4  Var_08    C3   N2   C2   C1    178.55  30.0  1
 JI4  Var_09    N2   C2   C1   N1    179.85  30.0  2
 JI4  Var_10    C4   C3   N2   C2   -178.53  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
 JI4  chir_01  C3'  N1   C2'  C4'  positiv
 JI4  chir_02  C4'  C3'  C71  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
 JI4  plan-1  C4    0.020
 JI4  plan-1  C11   0.020
 JI4  plan-1  C12   0.020
 JI4  plan-1  C13   0.020
 JI4  plan-1  F13   0.020
 JI4  plan-1  C14   0.020
 JI4  plan-1  C15   0.020
 JI4  plan-1  C16   0.020
 JI4  plan-1  H12   0.020
 JI4  plan-1  H14   0.020
 JI4  plan-1  H15   0.020
 JI4  plan-1  H16   0.020
 JI4  plan-2  N11   0.020
 JI4  plan-2  C21   0.020
 JI4  plan-2  C31   0.020
 JI4  plan-2  C41   0.020
 JI4  plan-2  C51   0.020
 JI4  plan-2  C61   0.020
 JI4  plan-2  N61   0.020
 JI4  plan-2  C71   0.020
 JI4  plan-2  C81   0.020
 JI4  plan-2  H31   0.020
 JI4  plan-2  H51   0.020
 JI4  plan-3  C61   0.020
 JI4  plan-3  N61   0.020
 JI4  plan-3  HN61  0.020
 JI4  plan-3  HN6A  0.020

