# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:39:44 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-{(3R,4R)-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
 JI5  JI5  N-{(3R,4R)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-[2-(3-fluorophenyl)ethyl]ethane-1,2-diamine  ligand  57  27  .  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_JI5
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
 JI5  C1    C  CH2   0  -0.278   0.4795  -1.7487  -0.2416
 JI5  N1    N  NH1   0  -0.604  -0.8047  -1.1118  -0.0166
 JI5  C2    C  CH2   0  -0.272   1.5986  -0.7239  -0.1463
 JI5  N2    N  NH1   0  -0.605   2.8922  -1.3454  -0.3524
 JI5  C3    C  CH2   0  -0.244   3.9835  -0.3940  -0.3110
 JI5  C4    C  CH2   0  -0.530   5.3234  -1.0835  -0.5586
 JI5  N1'   N  NH1   0  -0.584  -3.5936  -3.4334   0.6150
 JI5  C11   C  CR6   0   0.138   6.4549  -0.0956  -0.5373
 JI5  N11   N  N     0  -0.486  -5.1363   1.0736  -1.0520
 JI5  C12   C  CR16  0  -0.466   7.1277   0.1795   0.6506
 JI5  C13   C  CR6   0   0.539   8.1340   1.1260   0.6546
 JI5  F13   F  F     0  -0.319   8.7778   1.3758   1.8086
 JI5  C14   C  CR16  0  -0.427   8.5058   1.8209  -0.4793
 JI5  C15   C  CR16  0  -0.225   7.8309   1.5436  -1.6609
 JI5  C16   C  CR16  0  -0.318   6.8172   0.5964  -1.6916
 JI5  C2'   C  CH2   0  -0.329  -2.1627  -3.1795   0.5723
 JI5  C21   C  CR6   0   0.289  -4.6068   0.8942   0.1606
 JI5  C3'   C  CH1   0  -0.078  -1.9444  -1.9453  -0.3343
 JI5  C31   C  CR16  0  -0.435  -5.2601   1.2647   1.3224
 JI5  C4'   C  CH1   0  -0.273  -3.3142  -1.2052  -0.2772
 JI5  C41   C  CR6   0   0.205  -6.5276   1.8526   1.2345
 JI5  C5'   C  CH2   0  -0.305  -4.1815  -2.1001   0.6278
 JI5  C51   C  CR16  0  -0.449  -7.0748   2.0303  -0.0189
 JI5  C61   C  CR6   0   0.439  -6.3417   1.6223  -1.1477
 JI5  N61   N  NH2   0  -0.840  -6.8739   1.7399  -2.3998
 JI5  C71   C  CH2   0  -0.502  -3.2530   0.2428   0.2038
 JI5  C81   C  CH3   0  -0.726  -7.2532   2.2850   2.4719
 JI5  H1    H  HCH2  0   0.196   0.6838  -2.5778   0.4541
 JI5  H1A   H  HCH2  0   0.221   0.4797  -2.1825  -1.2454
 JI5  HN1   H  HNH1  0   0.337  -0.8586  -0.8133   0.9510
 JI5  H2    H  HCH2  0   0.219   1.4482   0.0324  -0.9218
 JI5  H2A   H  HCH2  0   0.189   1.5321  -0.1953   0.8196
 JI5  HN2   H  HNH1  0   0.339   3.0395  -2.0407   0.3709
 JI5  H3    H  HCH2  0   0.224   3.8183   0.3539  -1.0922
 JI5  H3A   H  HCH2  0   0.197   4.0321   0.1600   0.6405
 JI5  H4    H  HCH2  0   0.246   5.4834  -1.8492   0.2054
 JI5  H4A   H  HCH2  0   0.247   5.2883  -1.5942  -1.5237
 JI5  HN1'  H  HNH1  0   0.342  -3.8677  -3.9014  -0.2411
 JI5  H12   H  HCR6  0   0.269   6.8730  -0.3443   1.5645
 JI5  H14   H  HCR6  0   0.277   9.3003   2.5541  -0.4429
 JI5  H15   H  HCR6  0   0.266   8.1025   2.0736  -2.5644
 JI5  H16   H  HCR6  0   0.252   6.3038   0.3895  -2.6228
 JI5  H2'   H  HCH2  0   0.213  -1.8104  -2.9453   1.5851
 JI5  H2'A  H  HCH2  0   0.238  -1.6183  -4.0633   0.2368
 JI5  H3'   H  HCH1  0   0.232  -1.7924  -2.2953  -1.3598
 JI5  H31   H  HCR6  0   0.240  -4.7934   1.0998   2.2857
 JI5  H4'   H  HCH1  0   0.241  -3.7431  -1.1955  -1.2820
 JI5  H5'   H  HCH2  0   0.238  -5.2282  -2.1333   0.3242
 JI5  H5'A  H  HCH2  0   0.215  -4.1573  -1.7174   1.6552
 JI5  H51   H  HCR6  0   0.253  -8.0537   2.4784  -0.1407
 JI5  HN61  H  HNH2  0   0.378  -6.2237   1.6885  -3.1666
 JI5  HN6A  H  HNH2  0   0.387  -7.6168   2.4054  -2.5321
 JI5  H71   H  HCH2  0   0.247  -2.5580   0.8068  -0.4221
 JI5  H71A  H  HCH2  0   0.232  -2.8712   0.2845   1.2275
 JI5  H81   H  HCH3  0   0.252  -6.7442   3.1302   2.9390
 JI5  H81A  H  HCH3  0   0.246  -8.2770   2.5877   2.2577
 JI5  H81B  H  HCH3  0   0.249  -7.2815   1.4835   3.2106

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
 JI5  C1   N1    single    1.451  0.020  1.451
 JI5  C1   C2    single    1.520  0.020  1.520
 JI5  N1   C3'   single    1.447  0.020  1.447
 JI5  C2   N2    single    1.450  0.020  1.450
 JI5  N2   C3    single    1.448  0.020  1.448
 JI5  C3   C4    single    1.527  0.020  1.527
 JI5  C4   C11   single    1.502  0.020  1.502
 JI5  N1'  C2'   single    1.454  0.020  1.454
 JI5  N1'  C5'   single    1.457  0.020  1.457
 JI5  C11  C12   aromatic  1.393  0.020  1.393
 JI5  C11  C16   aromatic  1.394  0.020  1.394
 JI5  N11  C21   aromatic  1.335  0.020  1.335
 JI5  N11  C61   aromatic  1.328  0.020  1.328
 JI5  C12  C13   aromatic  1.381  0.020  1.381
 JI5  C13  F13   single    1.345  0.020  1.345
 JI5  C13  C14   aromatic  1.381  0.020  1.381
 JI5  C14  C15   aromatic  1.389  0.020  1.389
 JI5  C15  C16   aromatic  1.388  0.020  1.388
 JI5  C2'  C3'   single    1.547  0.020  1.547
 JI5  C21  C31   aromatic  1.383  0.020  1.383
 JI5  C21  C71   single    1.503  0.020  1.503
 JI5  C3'  C4'   single    1.558  0.020  1.558
 JI5  C31  C41   aromatic  1.400  0.020  1.400
 JI5  C4'  C5'   single    1.540  0.020  1.540
 JI5  C4'  C71   single    1.527  0.020  1.527
 JI5  C41  C51   aromatic  1.379  0.020  1.379
 JI5  C41  C81   single    1.498  0.020  1.498
 JI5  C51  C61   aromatic  1.406  0.020  1.406
 JI5  C61  N61   single    1.366  0.020  1.366
 JI5  C1   H1    single    0.970  0.020  1.090
 JI5  C1   H1A   single    0.970  0.020  1.090
 JI5  N1   HN1   single    0.890  0.020  1.040
 JI5  C2   H2    single    0.970  0.020  1.090
 JI5  C2   H2A   single    0.970  0.020  1.090
 JI5  N2   HN2   single    0.890  0.020  1.040
 JI5  C3   H3    single    0.970  0.020  1.090
 JI5  C3   H3A   single    0.970  0.020  1.090
 JI5  C4   H4    single    0.970  0.020  1.090
 JI5  C4   H4A   single    0.970  0.020  1.090
 JI5  N1'  HN1'  single    0.890  0.020  1.040
 JI5  C12  H12   single    0.930  0.020  1.080
 JI5  C14  H14   single    0.930  0.020  1.080
 JI5  C15  H15   single    0.930  0.020  1.080
 JI5  C16  H16   single    0.930  0.020  1.080
 JI5  C2'  H2'   single    0.970  0.020  1.090
 JI5  C2'  H2'A  single    0.970  0.020  1.090
 JI5  C3'  H3'   single    0.970  0.020  1.090
 JI5  C31  H31   single    0.930  0.020  1.080
 JI5  C4'  H4'   single    0.970  0.020  1.090
 JI5  C5'  H5'   single    0.970  0.020  1.090
 JI5  C5'  H5'A  single    0.970  0.020  1.090
 JI5  C51  H51   single    0.930  0.020  1.080
 JI5  N61  HN61  single    0.890  0.020  1.040
 JI5  N61  HN6A  single    0.890  0.020  1.040
 JI5  C71  H71   single    0.970  0.020  1.090
 JI5  C71  H71A  single    0.970  0.020  1.090
 JI5  C81  H81   single    0.970  0.020  1.090
 JI5  C81  H81A  single    0.970  0.020  1.090
 JI5  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
 JI5  H1A   C1   H1    106.33  3.000
 JI5  H1A   C1   C2    108.95  3.000
 JI5  H1    C1   C2    109.35  3.000
 JI5  H1A   C1   N1    108.45  3.000
 JI5  H1    C1   N1    113.37  3.000
 JI5  C2    C1   N1    110.23  3.000
 JI5  HN1   N1   C3'   109.70  3.000
 JI5  HN1   N1   C1    108.92  3.000
 JI5  C3'   N1   C1    114.22  3.000
 JI5  H2A   C2   H2    106.33  3.000
 JI5  H2A   C2   N2    112.56  3.000
 JI5  H2    C2   N2    108.57  3.000
 JI5  H2A   C2   C1    109.48  3.000
 JI5  H2    C2   C1    108.69  3.000
 JI5  N2    C2   C1    111.03  3.000
 JI5  HN2   N2   C3    108.70  3.000
 JI5  HN2   N2   C2    108.80  3.000
 JI5  C3    N2   C2    112.74  3.000
 JI5  H3A   C3   H3    106.23  3.000
 JI5  H3A   C3   C4    109.16  3.000
 JI5  H3    C3   C4    108.99  3.000
 JI5  H3A   C3   N2    112.83  3.000
 JI5  H3    C3   N2    108.36  3.000
 JI5  C4    C3   N2    111.09  3.000
 JI5  H4A   C4   H4    107.14  3.000
 JI5  H4A   C4   C11   110.13  3.000
 JI5  H4    C4   C11   109.90  3.000
 JI5  H4A   C4   C3    109.03  3.000
 JI5  H4    C4   C3    109.34  3.000
 JI5  C11   C4   C3    111.20  3.000
 JI5  HN1'  N1'  C5'   108.71  3.000
 JI5  HN1'  N1'  C2'   108.78  3.000
 JI5  C5'   N1'  C2'   103.74  3.000
 JI5  C16   C11  C12   118.86  3.000
 JI5  C16   C11  C4    120.70  3.000
 JI5  C12   C11  C4    120.39  3.000
 JI5  C61   N11  C21   118.74  3.000
 JI5  H12   C12  C13   119.99  3.000
 JI5  H12   C12  C11   120.68  3.000
 JI5  C13   C12  C11   119.33  3.000
 JI5  C14   C13  F13   118.83  3.000
 JI5  C14   C13  C12   122.58  3.000
 JI5  F13   C13  C12   118.59  3.000
 JI5  H14   C14  C15   121.39  3.000
 JI5  H14   C14  C13   120.74  3.000
 JI5  C15   C14  C13   117.86  3.000
 JI5  H15   C15  C16   119.95  3.000
 JI5  H15   C15  C14   119.38  3.000
 JI5  C16   C15  C14   120.67  3.000
 JI5  H16   C16  C15   119.71  3.000
 JI5  H16   C16  C11   119.59  3.000
 JI5  C15   C16  C11   120.70  3.000
 JI5  H2'A  C2'  H2'   107.25  3.000
 JI5  H2'A  C2'  C3'   113.31  3.000
 JI5  H2'   C2'  C3'   108.98  3.000
 JI5  H2'A  C2'  N1'   111.02  3.000
 JI5  H2'   C2'  N1'   109.03  3.000
 JI5  C3'   C2'  N1'   107.18  3.000
 JI5  C71   C21  C31   121.15  3.000
 JI5  C71   C21  N11   116.20  3.000
 JI5  C31   C21  N11   122.64  3.000
 JI5  H3'   C3'  C4'   107.96  3.000
 JI5  H3'   C3'  C2'   108.28  3.000
 JI5  C4'   C3'  C2'   103.50  3.000
 JI5  H3'   C3'  N1    106.29  3.000
 JI5  C4'   C3'  N1    114.25  3.000
 JI5  C2'   C3'  N1    116.23  3.000
 JI5  H31   C31  C41   120.66  3.000
 JI5  H31   C31  C21   120.17  3.000
 JI5  C41   C31  C21   119.16  3.000
 JI5  H4'   C4'  C71   107.28  3.000
 JI5  H4'   C4'  C5'   108.93  3.000
 JI5  C71   C4'  C5'   112.85  3.000
 JI5  H4'   C4'  C3'   108.41  3.000
 JI5  C71   C4'  C3'   115.26  3.000
 JI5  C5'   C4'  C3'   103.92  3.000
 JI5  C81   C41  C51   121.41  3.000
 JI5  C81   C41  C31   120.52  3.000
 JI5  C51   C41  C31   118.06  3.000
 JI5  H5'A  C5'  H5'   107.01  3.000
 JI5  H5'A  C5'  C4'   109.60  3.000
 JI5  H5'   C5'  C4'   113.25  3.000
 JI5  H5'A  C5'  N1'   108.58  3.000
 JI5  H5'   C5'  N1'   110.91  3.000
 JI5  C4'   C5'  N1'   107.41  3.000
 JI5  H51   C51  C61   120.05  3.000
 JI5  H51   C51  C41   120.92  3.000
 JI5  C61   C51  C41   119.03  3.000
 JI5  N61   C61  C51   120.51  3.000
 JI5  N61   C61  N11   117.09  3.000
 JI5  C51   C61  N11   122.36  3.000
 JI5  HN6A  N61  HN61  114.23  3.000
 JI5  HN6A  N61  C61   117.73  3.000
 JI5  HN61  N61  C61   116.25  3.000
 JI5  H71A  C71  H71   107.14  3.000
 JI5  H71A  C71  C4'   110.19  3.000
 JI5  H71   C71  C4'   109.55  3.000
 JI5  H71A  C71  C21   108.96  3.000
 JI5  H71   C71  C21   109.45  3.000
 JI5  C4'   C71  C21   111.46  3.000
 JI5  H81B  C81  H81A  108.25  3.000
 JI5  H81B  C81  H81   106.93  3.000
 JI5  H81A  C81  H81   107.90  3.000
 JI5  H81B  C81  C41   111.10  3.000
 JI5  H81A  C81  C41   111.91  3.000
 JI5  H81   C81  C41   110.55  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
 JI5  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 JI5  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 JI5  CONST_03  C41  C31  C21  N11     0.00   0.0  0
 JI5  CONST_04  C41  C51  C61  N11     0.00   0.0  0
 JI5  CONST_05  C15  C16  C11  C12     0.00   0.0  0
 JI5  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 JI5  CONST_07  C16  C11  C12  C13     0.00   0.0  0
 JI5  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 JI5  CONST_09  C51  C61  N11  C21     0.00   0.0  0
 JI5  CONST_10  C51  C41  C31  C21     0.00   0.0  0
 JI5  CONST_11  C61  N11  C21  C31     0.00   0.0  0
 JI5  CONST_12  C61  C51  C41  C31     0.00   0.0  0
 JI5  CONST_13  C13  C12  C11  C4    180.00   0.0  0
 JI5  CONST_14  C15  C16  C11  C4    180.00   0.0  0
 JI5  CONST_15  F13  C13  C12  C11   180.00   0.0  0
 JI5  CONST_16  C15  C14  C13  F13   180.00   0.0  0
 JI5  CONST_17  N61  C61  N11  C21   180.00   0.0  0
 JI5  CONST_18  C81  C41  C31  C21   180.00   0.0  0
 JI5  CONST_19  C71  C21  C31  C41   180.00   0.0  0
 JI5  CONST_20  N61  C61  C51  C41   180.00   0.0  0
 JI5  CONST_21  C71  C21  N11  C61   180.00   0.0  0
 JI5  CONST_22  C81  C41  C51  C61   180.00   0.0  0
 JI5  CONST_23  H15  C15  C16  C11   180.00   0.0  0
 JI5  CONST_24  H31  C31  C21  N11   180.00   0.0  0
 JI5  CONST_25  H51  C51  C61  N11   180.00   0.0  0
 JI5  CONST_26  H16  C16  C11  C12   180.00   0.0  0
 JI5  CONST_27  H14  C14  C13  C12   180.00   0.0  0
 JI5  CONST_28  H12  C12  C13  C14   180.00   0.0  0
 JI5  Var_01    C4'  C5'  N1'  C2'    36.60  30.0  1
 JI5  Var_02    C5'  N1'  C2'  C3'   -37.31  30.0  1
 JI5  Var_03    C4'  C71  C21  N11   -66.26  30.0  2
 JI5  Var_04    C12  C11  C4   C3     90.95  30.0  2
 JI5  Var_05    H81  C81  C41  C31    68.00  30.0  2
 JI5  Var_06    C3'  N1   C1   C2    168.90  30.0  3
 JI5  Var_07    C11  C4   C3   N2    179.12  30.0  3
 JI5  Var_08    C3   N2   C2   C1    178.18  30.0  3
 JI5  Var_09    N2   C2   C1   N1    179.30  30.0  3
 JI5  Var_10    C4   C3   N2   C2   -178.91  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
 JI5  chir_01  C3'  N1   C2'  C4'  negativ
 JI5  chir_02  C4'  C3'  C5'  C71  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
 JI5  plan-1  C4    0.020
 JI5  plan-1  C11   0.020
 JI5  plan-1  C12   0.020
 JI5  plan-1  C13   0.020
 JI5  plan-1  F13   0.020
 JI5  plan-1  C14   0.020
 JI5  plan-1  C15   0.020
 JI5  plan-1  C16   0.020
 JI5  plan-1  H12   0.020
 JI5  plan-1  H14   0.020
 JI5  plan-1  H15   0.020
 JI5  plan-1  H16   0.020
 JI5  plan-2  N11   0.020
 JI5  plan-2  C21   0.020
 JI5  plan-2  C31   0.020
 JI5  plan-2  C41   0.020
 JI5  plan-2  C51   0.020
 JI5  plan-2  C61   0.020
 JI5  plan-2  N61   0.020
 JI5  plan-2  C71   0.020
 JI5  plan-2  C81   0.020
 JI5  plan-2  H31   0.020
 JI5  plan-2  H51   0.020
 JI5  plan-3  C61   0.020
 JI5  plan-3  N61   0.020
 JI5  plan-3  HN61  0.020
 JI5  plan-3  HN6A  0.020

