# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:36:26 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: N-{(3S,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
 J14  J14  N-{(3S,4R)-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_J14
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
 J14  C1    C  CH2   0  -0.287   0.5101   1.2898  -0.5829
 J14  N1    N  NH1   0  -0.613  -0.7113   0.8501   0.0641
 J14  C2    C  CH2   0  -0.277   1.7228   0.5794  -0.0060
 J14  N2    N  NH1   0  -0.603   2.9349   1.0389  -0.6545
 J14  C3    C  CH2   0  -0.245   4.1353   0.4288  -0.1227
 J14  C4    C  CH2   0  -0.530   5.3788   1.0073  -0.7946
 J14  N1'   N  NH1   0  -0.582  -3.2386   3.0536   0.8962
 J14  C11   C  CR6   0   0.139   6.6379   0.4145  -0.2299
 J14  N11   N  N     0  -0.485  -4.9551  -1.5842   0.5526
 J14  C12   C  CR16  0  -0.467   7.2100  -0.7144  -0.8109
 J14  C13   C  CR6   0   0.539   8.3469  -1.2624  -0.2488
 J14  F13   F  F     0  -0.319   8.8921  -2.3471  -0.8272
 J14  C14   C  CR16  0  -0.427   8.9466  -0.7365   0.8785
 J14  C15   C  CR16  0  -0.224   8.3703   0.3877   1.4555
 J14  C16   C  CR16  0  -0.318   7.2291   0.9577   0.9096
 J14  C2'   C  CH2   0  -0.316  -2.0252   2.9766   0.0847
 J14  C21   C  CR6   0   0.284  -5.0454  -0.7619  -0.4944
 J14  C3'   C  CH1   0  -0.056  -1.8926   1.5260  -0.4473
 J14  C31   C  CR16  0  -0.433  -6.2526  -0.4355  -1.0872
 J14  C4'   C  CH1   0  -0.279  -3.1847   0.8390   0.0251
 J14  C41   C  CR6   0   0.204  -7.4338  -0.9766  -0.5696
 J14  C5'   C  CH2   0  -0.304  -4.1042   2.0194   0.3485
 J14  C51   C  CR16  0  -0.445  -7.3388  -1.8223   0.5172
 J14  C61   C  CR6   0   0.437  -6.0708  -2.1073   1.0509
 J14  N61   N  NH2   0  -0.840  -5.9356  -2.9823   2.0914
 J14  C71   C  CH2   0  -0.498  -3.7569  -0.1591  -0.9778
 J14  C81   C  CH3   0  -0.725  -8.7589  -0.6626  -1.1947
 J14  H1    H  HCH2  0   0.192   0.4818   1.1413  -1.6759
 J14  H1A   H  HCH2  0   0.225   0.6280   2.3650  -0.4249
 J14  HN1   H  HNH1  0   0.341  -0.8150  -0.1463  -0.0964
 J14  H2    H  HCH2  0   0.221   1.7939   0.8027   1.0623
 J14  H2A   H  HCH2  0   0.190   1.5844  -0.5121  -0.0864
 J14  HN2   H  HNH1  0   0.340   2.8748   0.8318  -1.6454
 J14  H3    H  HCH2  0   0.224   4.1804   0.6334   0.9513
 J14  H3A   H  HCH2  0   0.198   4.1433  -0.6682  -0.2263
 J14  H4    H  HCH2  0   0.246   5.3280   0.8195  -1.8706
 J14  H4A   H  HCH2  0   0.247   5.3803   2.0910  -0.6587
 J14  HN1'  H  HNH1  0   0.343  -3.0044   2.7935   1.8469
 J14  H12   H  HCR6  0   0.269   6.7754  -1.1610  -1.6974
 J14  H14   H  HCR6  0   0.277   9.8388  -1.1882   1.2917
 J14  H15   H  HCR6  0   0.265   8.8226   0.8222   2.3373
 J14  H16   H  HCR6  0   0.253   6.7951   1.8363   1.3715
 J14  H2'   H  HCH2  0   0.219  -2.1083   3.6710  -0.7553
 J14  H2'A  H  HCH2  0   0.234  -1.1574   3.2820   0.6710
 J14  H3'   H  HCH1  0   0.203  -1.8837   1.5500  -1.5509
 J14  H31   H  HCR6  0   0.241  -6.2825   0.2429  -1.9308
 J14  H4'   H  HCH1  0   0.236  -2.9632   0.3156   0.9624
 J14  H5'   H  HCH2  0   0.242  -4.9051   1.7691   1.0454
 J14  H5'A  H  HCH2  0   0.214  -4.5768   2.3907  -0.5696
 J14  H51   H  HCR6  0   0.253  -8.2250  -2.2635   0.9577
 J14  HN61  H  HNH2  0   0.378  -5.0654  -2.9389   2.5962
 J14  HN6A  H  HNH2  0   0.387  -6.7405  -3.1376   2.6754
 J14  H71   H  HCH2  0   0.246  -3.0300  -0.9573  -1.1563
 J14  H71A  H  HCH2  0   0.238  -3.9195   0.3465  -1.9334
 J14  H81   H  HCH3  0   0.255  -8.9524  -1.3335  -2.0340
 J14  H81A  H  HCH3  0   0.247  -9.5774  -0.7808  -0.4861
 J14  H81B  H  HCH3  0   0.247  -8.7837   0.3548  -1.5842

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
 J14  C1   N1    single    1.450  0.020  1.450
 J14  C1   C2    single    1.519  0.020  1.519
 J14  N1   C3'   single    1.454  0.020  1.454
 J14  C2   N2    single    1.449  0.020  1.449
 J14  N2   C3    single    1.448  0.020  1.448
 J14  C3   C4    single    1.527  0.020  1.527
 J14  C4   C11   single    1.502  0.020  1.502
 J14  N1'  C2'   single    1.462  0.020  1.462
 J14  N1'  C5'   single    1.456  0.020  1.456
 J14  C11  C12   aromatic  1.393  0.020  1.393
 J14  C11  C16   aromatic  1.394  0.020  1.394
 J14  N11  C21   aromatic  1.334  0.020  1.334
 J14  N11  C61   aromatic  1.329  0.020  1.329
 J14  C12  C13   aromatic  1.382  0.020  1.382
 J14  C13  F13   single    1.345  0.020  1.345
 J14  C13  C14   aromatic  1.381  0.020  1.381
 J14  C14  C15   aromatic  1.389  0.020  1.389
 J14  C15  C16   aromatic  1.388  0.020  1.388
 J14  C2'  C3'   single    1.551  0.020  1.551
 J14  C21  C31   aromatic  1.384  0.020  1.384
 J14  C21  C71   single    1.502  0.020  1.502
 J14  C3'  C4'   single    1.538  0.020  1.538
 J14  C31  C41   aromatic  1.399  0.020  1.399
 J14  C4'  C5'   single    1.531  0.020  1.531
 J14  C4'  C71   single    1.526  0.020  1.526
 J14  C41  C51   aromatic  1.380  0.020  1.380
 J14  C41  C81   single    1.498  0.020  1.498
 J14  C51  C61   aromatic  1.405  0.020  1.405
 J14  C61  N61   single    1.366  0.020  1.366
 J14  C1   H1    single    0.970  0.020  1.090
 J14  C1   H1A   single    0.970  0.020  1.090
 J14  N1   HN1   single    0.890  0.020  1.040
 J14  C2   H2    single    0.970  0.020  1.090
 J14  C2   H2A   single    0.970  0.020  1.090
 J14  N2   HN2   single    0.890  0.020  1.040
 J14  C3   H3    single    0.970  0.020  1.090
 J14  C3   H3A   single    0.970  0.020  1.090
 J14  C4   H4    single    0.970  0.020  1.090
 J14  C4   H4A   single    0.970  0.020  1.090
 J14  N1'  HN1'  single    0.890  0.020  1.040
 J14  C12  H12   single    0.930  0.020  1.080
 J14  C14  H14   single    0.930  0.020  1.080
 J14  C15  H15   single    0.930  0.020  1.080
 J14  C16  H16   single    0.930  0.020  1.080
 J14  C2'  H2'   single    0.970  0.020  1.090
 J14  C2'  H2'A  single    0.970  0.020  1.090
 J14  C3'  H3'   single    0.970  0.020  1.090
 J14  C31  H31   single    0.930  0.020  1.080
 J14  C4'  H4'   single    0.970  0.020  1.090
 J14  C5'  H5'   single    0.970  0.020  1.090
 J14  C5'  H5'A  single    0.970  0.020  1.090
 J14  C51  H51   single    0.930  0.020  1.080
 J14  N61  HN61  single    0.890  0.020  1.040
 J14  N61  HN6A  single    0.890  0.020  1.040
 J14  C71  H71   single    0.970  0.020  1.090
 J14  C71  H71A  single    0.970  0.020  1.090
 J14  C81  H81   single    0.970  0.020  1.090
 J14  C81  H81A  single    0.970  0.020  1.090
 J14  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
 J14  H1A   C1   H1    106.16  3.000
 J14  H1A   C1   C2    108.60  3.000
 J14  H1    C1   C2    109.50  3.000
 J14  H1A   C1   N1    108.93  3.000
 J14  H1    C1   N1    112.30  3.000
 J14  C2    C1   N1    111.17  3.000
 J14  HN1   N1   C3'   108.53  3.000
 J14  HN1   N1   C1    108.26  3.000
 J14  C3'   N1   C1    112.73  3.000
 J14  H2A   C2   H2    106.34  3.000
 J14  H2A   C2   N2    112.71  3.000
 J14  H2    C2   N2    108.54  3.000
 J14  H2A   C2   C1    109.56  3.000
 J14  H2    C2   C1    109.11  3.000
 J14  N2    C2   C1    110.45  3.000
 J14  HN2   N2   C3    108.79  3.000
 J14  HN2   N2   C2    108.84  3.000
 J14  C3    N2   C2    113.29  3.000
 J14  H3A   C3   H3    106.15  3.000
 J14  H3A   C3   C4    109.26  3.000
 J14  H3    C3   C4    109.11  3.000
 J14  H3A   C3   N2    113.02  3.000
 J14  H3    C3   N2    108.41  3.000
 J14  C4    C3   N2    110.72  3.000
 J14  H4A   C4   H4    107.03  3.000
 J14  H4A   C4   C11   110.10  3.000
 J14  H4    C4   C11   109.95  3.000
 J14  H4A   C4   C3    108.80  3.000
 J14  H4    C4   C3    109.27  3.000
 J14  C11   C4   C3    111.57  3.000
 J14  HN1'  N1'  C5'   107.95  3.000
 J14  HN1'  N1'  C2'   108.40  3.000
 J14  C5'   N1'  C2'   104.32  3.000
 J14  C16   C11  C12   118.86  3.000
 J14  C16   C11  C4    120.61  3.000
 J14  C12   C11  C4    120.50  3.000
 J14  C61   N11  C21   118.68  3.000
 J14  H12   C12  C13   119.96  3.000
 J14  H12   C12  C11   120.71  3.000
 J14  C13   C12  C11   119.33  3.000
 J14  C14   C13  F13   118.83  3.000
 J14  C14   C13  C12   122.58  3.000
 J14  F13   C13  C12   118.59  3.000
 J14  H14   C14  C15   121.43  3.000
 J14  H14   C14  C13   120.72  3.000
 J14  C15   C14  C13   117.85  3.000
 J14  H15   C15  C16   119.96  3.000
 J14  H15   C15  C14   119.35  3.000
 J14  C16   C15  C14   120.68  3.000
 J14  H16   C16  C15   119.66  3.000
 J14  H16   C16  C11   119.64  3.000
 J14  C15   C16  C11   120.69  3.000
 J14  H2'A  C2'  H2'   107.19  3.000
 J14  H2'A  C2'  C3'   112.22  3.000
 J14  H2'   C2'  C3'   109.71  3.000
 J14  H2'A  C2'  N1'   110.31  3.000
 J14  H2'   C2'  N1'   109.27  3.000
 J14  C3'   C2'  N1'   108.10  3.000
 J14  C71   C21  C31   121.04  3.000
 J14  C71   C21  N11   116.22  3.000
 J14  C31   C21  N11   122.71  3.000
 J14  H3'   C3'  C4'   108.89  3.000
 J14  H3'   C3'  C2'   108.86  3.000
 J14  C4'   C3'  C2'   103.93  3.000
 J14  H3'   C3'  N1    110.80  3.000
 J14  C4'   C3'  N1    111.53  3.000
 J14  C2'   C3'  N1    112.56  3.000
 J14  H31   C31  C41   120.49  3.000
 J14  H31   C31  C21   120.36  3.000
 J14  C41   C31  C21   119.14  3.000
 J14  H4'   C4'  C71   108.99  3.000
 J14  H4'   C4'  C5'   107.99  3.000
 J14  C71   C4'  C5'   114.70  3.000
 J14  H4'   C4'  C3'   107.84  3.000
 J14  C71   C4'  C3'   113.91  3.000
 J14  C5'   C4'  C3'   103.01  3.000
 J14  C81   C41  C51   121.18  3.000
 J14  C81   C41  C31   120.75  3.000
 J14  C51   C41  C31   118.06  3.000
 J14  H5'A  C5'  H5'   107.21  3.000
 J14  H5'A  C5'  C4'   110.05  3.000
 J14  H5'   C5'  C4'   113.52  3.000
 J14  H5'A  C5'  N1'   109.31  3.000
 J14  H5'   C5'  N1'   111.06  3.000
 J14  C4'   C5'  N1'   105.67  3.000
 J14  H51   C51  C61   120.07  3.000
 J14  H51   C51  C41   120.88  3.000
 J14  C61   C51  C41   119.04  3.000
 J14  N61   C61  C51   120.57  3.000
 J14  N61   C61  N11   117.03  3.000
 J14  C51   C61  N11   122.37  3.000
 J14  HN6A  N61  HN61  114.01  3.000
 J14  HN6A  N61  C61   117.49  3.000
 J14  HN61  N61  C61   116.09  3.000
 J14  H71A  C71  H71   107.07  3.000
 J14  H71A  C71  C4'   109.13  3.000
 J14  H71   C71  C4'   109.58  3.000
 J14  H71A  C71  C21   109.84  3.000
 J14  H71   C71  C21   109.24  3.000
 J14  C4'   C71  C21   111.87  3.000
 J14  H81B  C81  H81A  108.47  3.000
 J14  H81B  C81  H81   107.15  3.000
 J14  H81A  C81  H81   107.47  3.000
 J14  H81B  C81  C41   111.41  3.000
 J14  H81A  C81  C41   111.74  3.000
 J14  H81   C81  C41   110.41  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
 J14  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 J14  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 J14  CONST_03  C41  C31  C21  N11     0.00   0.0  0
 J14  CONST_04  C41  C51  C61  N11     0.00   0.0  0
 J14  CONST_05  C15  C16  C11  C12     0.00   0.0  0
 J14  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 J14  CONST_07  C16  C11  C12  C13     0.00   0.0  0
 J14  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 J14  CONST_09  C51  C61  N11  C21     0.00   0.0  0
 J14  CONST_10  C51  C41  C31  C21     0.00   0.0  0
 J14  CONST_11  C61  N11  C21  C31     0.00   0.0  0
 J14  CONST_12  C61  C51  C41  C31     0.00   0.0  0
 J14  CONST_13  C13  C12  C11  C4    180.00   0.0  0
 J14  CONST_14  C15  C16  C11  C4    180.00   0.0  0
 J14  CONST_15  F13  C13  C12  C11   180.00   0.0  0
 J14  CONST_16  C15  C14  C13  F13   180.00   0.0  0
 J14  CONST_17  N61  C61  N11  C21   180.00   0.0  0
 J14  CONST_18  C81  C41  C31  C21   180.00   0.0  0
 J14  CONST_19  C71  C21  C31  C41   180.00   0.0  0
 J14  CONST_20  N61  C61  C51  C41   180.00   0.0  0
 J14  CONST_21  C71  C21  N11  C61   180.00   0.0  0
 J14  CONST_22  C81  C41  C51  C61   180.00   0.0  0
 J14  CONST_23  H15  C15  C16  C11   180.00   0.0  0
 J14  CONST_24  H31  C31  C21  N11   180.00   0.0  0
 J14  CONST_25  H51  C51  C61  N11   180.00   0.0  0
 J14  CONST_26  H16  C16  C11  C12   180.00   0.0  0
 J14  CONST_27  H14  C14  C13  C12   180.00   0.0  0
 J14  CONST_28  H12  C12  C13  C14   180.00   0.0  0
 J14  Var_01    C4'  C5'  N1'  C2'    39.17  30.0  1
 J14  Var_02    C5'  N1'  C2'  C3'   -27.13  30.0  1
 J14  Var_03    C4'  C71  C21  N11   -68.69  30.0  2
 J14  Var_04    C12  C11  C4   C3     91.74  30.0  2
 J14  Var_05    H81  C81  C41  C31    84.63  30.0  2
 J14  Var_06    C3'  N1   C1   C2    179.03  30.0  3
 J14  Var_07    C11  C4   C3   N2    178.43  30.0  3
 J14  Var_08    C3   N2   C2   C1    178.28  30.0  3
 J14  Var_09    N2   C2   C1   N1   -179.48  30.0  3
 J14  Var_10    C4   C3   N2   C2   -177.00  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
 J14  chir_01  C3'  N1   C2'  C4'  positiv
 J14  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
 J14  plan-1  C4    0.020
 J14  plan-1  C11   0.020
 J14  plan-1  C12   0.020
 J14  plan-1  C13   0.020
 J14  plan-1  F13   0.020
 J14  plan-1  C14   0.020
 J14  plan-1  C15   0.020
 J14  plan-1  C16   0.020
 J14  plan-1  H12   0.020
 J14  plan-1  H14   0.020
 J14  plan-1  H15   0.020
 J14  plan-1  H16   0.020
 J14  plan-2  N11   0.020
 J14  plan-2  C21   0.020
 J14  plan-2  C31   0.020
 J14  plan-2  C41   0.020
 J14  plan-2  C51   0.020
 J14  plan-2  C61   0.020
 J14  plan-2  N61   0.020
 J14  plan-2  C71   0.020
 J14  plan-2  C81   0.020
 J14  plan-2  H31   0.020
 J14  plan-2  H51   0.020
 J14  plan-3  C61   0.020
 J14  plan-3  N61   0.020
 J14  plan-3  HN61  0.020
 J14  plan-3  HN6A  0.020

