# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:55:22 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-{(3R,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
 J11  J11  N-{(3R,4S)-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_J11
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
 J11  C1    C  CH2   0  -0.281   0.4946  -1.0983  -0.9065
 J11  N1    N  NH1   0  -0.600  -0.7525  -0.7227  -0.2718
 J11  C2    C  CH2   0  -0.275   1.6472  -0.2769  -0.3520
 J11  N2    N  NH1   0  -0.604   2.8996  -0.6675  -0.9693
 J11  C3    C  CH2   0  -0.245   4.0381   0.0535  -0.4381
 J11  C4    C  CH2   0  -0.531   5.3285  -0.3835  -1.1289
 J11  N1'   N  NR15  0  -0.607  -2.8010  -2.9344   0.8519
 J11  C11   C  CR6   0   0.138   6.5235   0.3201  -0.5524
 J11  N11   N  N     0  -0.475  -6.3559  -0.2583  -0.5140
 J11  C12   C  CR16  0  -0.464   7.2002  -0.2270   0.5349
 J11  C13   C  CR6   0   0.538   8.2677   0.4576   1.0824
 J11  F13   F  F     0  -0.319   8.9113  -0.0868   2.1301
 J11  C14   C  CR16  0  -0.427   8.6990   1.6755   0.5944
 J11  C15   C  CR16  0  -0.225   8.0204   2.2170  -0.4896
 J11  C16   C  CR16  0  -0.319   6.9444   1.5489  -1.0574
 J11  C2'   C  CH2   0  -0.305  -1.9626  -2.9515  -0.3347
 J11  C21   C  CR6   0   0.273  -5.2679   0.5125  -0.5690
 J11  C3'   C  CR15  0  -0.077  -1.9061  -1.4668  -0.7448
 J11  C31   C  CR16  0  -0.427  -5.2414   1.8040  -0.0709
 J11  C4'   C  CR15  0  -0.237  -3.2071  -0.8759  -0.1461
 J11  C41   C  CR6   0   0.204  -6.3957   2.3316   0.5164
 J11  C5'   C  CH2   0  -0.276  -3.9150  -2.0776   0.4825
 J11  C51   C  CR16  0  -0.449  -7.5183   1.5307   0.5764
 J11  C61   C  CR6   0   0.441  -7.4571   0.2304   0.0473
 J11  N61   N  NH2   0  -0.839  -8.5623  -0.5737   0.0452
 J11  C71   C  CH2   0  -0.510  -4.0344  -0.1003  -1.1687
 J11  C81   C  CH3   0  -0.727  -6.4045   3.7301   1.0536
 J11  H1    H  HCH2  0   0.189   0.7337  -2.1691  -0.7928
 J11  H1A   H  HCH2  0   0.222   0.4068  -0.9160  -1.9815
 J11  HN1   H  HNH1  0   0.334  -0.6707  -0.8556   0.7312
 J11  H2    H  HCH2  0   0.221   1.4697   0.7819  -0.5598
 J11  H2A   H  HCH2  0   0.188   1.6691  -0.3785   0.7465
 J11  HN2   H  HNH1  0   0.339   3.0434  -1.6585  -0.8084
 J11  H3    H  HCH2  0   0.224   3.8853   1.1237  -0.6087
 J11  H3A   H  HCH2  0   0.198   4.1498  -0.0719   0.6510
 J11  H4    H  HCH2  0   0.245   5.4458  -1.4652  -1.0171
 J11  H4A   H  HCH2  0   0.249   5.2476  -0.1794  -2.1986
 J11  HN1'  H  HNR5  0   0.347  -3.1087  -3.8629   1.1104
 J11  H12   H  HCR6  0   0.270   6.9004  -1.1818   0.9503
 J11  H14   H  HCR6  0   0.277   9.5397   2.1861   1.0452
 J11  H15   H  HCR6  0   0.266   8.3379   3.1696  -0.8929
 J11  H16   H  HCR6  0   0.253   6.4253   1.9844  -1.9026
 J11  H2'   H  HCH2  0   0.227  -0.9763  -3.3730  -0.1238
 J11  H2'A  H  HCH2  0   0.195  -2.4012  -3.5429  -1.1535
 J11  H3'   H  HCR5  0   0.233  -1.9142  -1.3833  -1.8360
 J11  H31   H  HCR6  0   0.240  -4.3378   2.3977  -0.1398
 J11  H4'   H  HCR5  0   0.240  -2.9209  -0.1857   0.6547
 J11  H5'   H  HCH2  0   0.192  -4.5903  -2.5462  -0.2506
 J11  H5'A  H  HCH2  0   0.226  -4.5159  -1.8057   1.3520
 J11  H51   H  HCR6  0   0.254  -8.4381   1.8951   1.0186
 J11  HN61  H  HNH2  0   0.378  -8.3893  -1.5584  -0.0748
 J11  HN6A  H  HNH2  0   0.386  -9.2867  -0.3658   0.7121
 J11  H71   H  HCH2  0   0.237  -4.3231  -0.7672  -1.9858
 J11  H71A  H  HCH2  0   0.245  -3.4083   0.6860  -1.5979
 J11  H81   H  HCH3  0   0.251  -6.1559   4.4456   0.2684
 J11  H81A  H  HCH3  0   0.246  -7.3767   4.0016   1.4618
 J11  H81B  H  HCH3  0   0.251  -5.6597   3.8506   1.8415

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
 J11  C1   N1    single    1.449  0.020  1.449
 J11  C1   C2    single    1.520  0.020  1.520
 J11  N1   C3'   single    1.452  0.020  1.452
 J11  C2   N2    single    1.450  0.020  1.450
 J11  N2   C3    single    1.448  0.020  1.448
 J11  C3   C4    single    1.528  0.020  1.528
 J11  C4   C11   single    1.502  0.020  1.502
 J11  N1'  C2'   single    1.453  0.020  1.453
 J11  N1'  C5'   single    1.453  0.020  1.453
 J11  C11  C12   aromatic  1.393  0.020  1.393
 J11  C11  C16   aromatic  1.394  0.020  1.394
 J11  N11  C21   aromatic  1.334  0.020  1.334
 J11  N11  C61   aromatic  1.329  0.020  1.329
 J11  C12  C13   aromatic  1.381  0.020  1.381
 J11  C13  F13   single    1.345  0.020  1.345
 J11  C13  C14   aromatic  1.381  0.020  1.381
 J11  C14  C15   aromatic  1.389  0.020  1.389
 J11  C15  C16   aromatic  1.388  0.020  1.388
 J11  C2'  C3'   single    1.541  0.020  1.541
 J11  C21  C31   aromatic  1.384  0.020  1.384
 J11  C21  C71   single    1.502  0.020  1.502
 J11  C3'  C4'   single    1.549  0.020  1.549
 J11  C31  C41   aromatic  1.398  0.020  1.398
 J11  C4'  C5'   single    1.530  0.020  1.530
 J11  C4'  C71   single    1.527  0.020  1.527
 J11  C41  C51   aromatic  1.380  0.020  1.380
 J11  C41  C81   single    1.498  0.020  1.498
 J11  C51  C61   aromatic  1.405  0.020  1.405
 J11  C61  N61   single    1.367  0.020  1.367
 J11  C1   H1    single    0.970  0.020  1.090
 J11  C1   H1A   single    0.970  0.020  1.090
 J11  N1   HN1   single    0.890  0.020  1.040
 J11  C2   H2    single    0.970  0.020  1.090
 J11  C2   H2A   single    0.970  0.020  1.090
 J11  N2   HN2   single    0.890  0.020  1.040
 J11  C3   H3    single    0.970  0.020  1.090
 J11  C3   H3A   single    0.970  0.020  1.090
 J11  C4   H4    single    0.970  0.020  1.090
 J11  C4   H4A   single    0.970  0.020  1.090
 J11  N1'  HN1'  single    0.890  0.020  1.040
 J11  C12  H12   single    0.930  0.020  1.080
 J11  C14  H14   single    0.930  0.020  1.080
 J11  C15  H15   single    0.930  0.020  1.080
 J11  C16  H16   single    0.930  0.020  1.080
 J11  C2'  H2'   single    0.970  0.020  1.090
 J11  C2'  H2'A  single    0.970  0.020  1.090
 J11  C3'  H3'   single    0.970  0.020  1.090
 J11  C31  H31   single    0.930  0.020  1.080
 J11  C4'  H4'   single    0.970  0.020  1.090
 J11  C5'  H5'   single    0.970  0.020  1.090
 J11  C5'  H5'A  single    0.970  0.020  1.090
 J11  C51  H51   single    0.930  0.020  1.080
 J11  N61  HN61  single    0.890  0.020  1.040
 J11  N61  HN6A  single    0.890  0.020  1.040
 J11  C71  H71   single    0.970  0.020  1.090
 J11  C71  H71A  single    0.970  0.020  1.090
 J11  C81  H81   single    0.970  0.020  1.090
 J11  C81  H81A  single    0.970  0.020  1.090
 J11  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
 J11  H1A   C1   H1    106.29  3.000
 J11  H1A   C1   C2    109.23  3.000
 J11  H1    C1   C2    108.82  3.000
 J11  H1A   C1   N1    108.55  3.000
 J11  H1    C1   N1    113.15  3.000
 J11  C2    C1   N1    110.66  3.000
 J11  HN1   N1   C3'   108.59  3.000
 J11  HN1   N1   C1    109.24  3.000
 J11  C3'   N1   C1    114.10  3.000
 J11  H2A   C2   H2    106.35  3.000
 J11  H2A   C2   N2    112.46  3.000
 J11  H2    C2   N2    108.67  3.000
 J11  H2A   C2   C1    109.17  3.000
 J11  H2    C2   C1    109.32  3.000
 J11  N2    C2   C1    110.74  3.000
 J11  HN2   N2   C3    108.46  3.000
 J11  HN2   N2   C2    108.55  3.000
 J11  C3    N2   C2    112.87  3.000
 J11  H3A   C3   H3    106.23  3.000
 J11  H3A   C3   C4    109.19  3.000
 J11  H3    C3   C4    109.10  3.000
 J11  H3A   C3   N2    112.68  3.000
 J11  H3    C3   N2    108.65  3.000
 J11  C4    C3   N2    110.84  3.000
 J11  H4A   C4   H4    107.04  3.000
 J11  H4A   C4   C11   110.33  3.000
 J11  H4    C4   C11   109.80  3.000
 J11  H4A   C4   C3    109.09  3.000
 J11  H4    C4   C3    109.10  3.000
 J11  C11   C4   C3    111.38  3.000
 J11  HN1'  N1'  C5'   111.90  3.000
 J11  HN1'  N1'  C2'   111.92  3.000
 J11  C5'   N1'  C2'   103.99  3.000
 J11  C16   C11  C12   118.85  3.000
 J11  C16   C11  C4    120.95  3.000
 J11  C12   C11  C4    120.15  3.000
 J11  C61   N11  C21   118.72  3.000
 J11  H12   C12  C13   119.91  3.000
 J11  H12   C12  C11   120.73  3.000
 J11  C13   C12  C11   119.36  3.000
 J11  C14   C13  F13   118.87  3.000
 J11  C14   C13  C12   122.57  3.000
 J11  F13   C13  C12   118.56  3.000
 J11  H14   C14  C15   121.39  3.000
 J11  H14   C14  C13   120.76  3.000
 J11  C15   C14  C13   117.84  3.000
 J11  H15   C15  C16   119.92  3.000
 J11  H15   C15  C14   119.39  3.000
 J11  C16   C15  C14   120.69  3.000
 J11  H16   C16  C15   119.81  3.000
 J11  H16   C16  C11   119.51  3.000
 J11  C15   C16  C11   120.68  3.000
 J11  H2'A  C2'  H2'   107.21  3.000
 J11  H2'A  C2'  C3'   109.52  3.000
 J11  H2'   C2'  C3'   112.94  3.000
 J11  H2'A  C2'  N1'   112.56  3.000
 J11  H2'   C2'  N1'   111.57  3.000
 J11  C3'   C2'  N1'   103.12  3.000
 J11  C71   C21  C31   120.56  3.000
 J11  C71   C21  N11   116.76  3.000
 J11  C31   C21  N11   122.66  3.000
 J11  H3'   C3'  C4'   110.48  3.000
 J11  H3'   C3'  C2'   109.79  3.000
 J11  C4'   C3'  C2'   103.52  3.000
 J11  H3'   C3'  N1    106.95  3.000
 J11  C4'   C3'  N1    110.23  3.000
 J11  C2'   C3'  N1    115.86  3.000
 J11  H31   C31  C41   120.55  3.000
 J11  H31   C31  C21   120.29  3.000
 J11  C41   C31  C21   119.16  3.000
 J11  H4'   C4'  C71   108.13  3.000
 J11  H4'   C4'  C5'   108.38  3.000
 J11  C71   C4'  C5'   115.05  3.000
 J11  H4'   C4'  C3'   107.67  3.000
 J11  C71   C4'  C3'   112.95  3.000
 J11  C5'   C4'  C3'   104.35  3.000
 J11  C81   C41  C51   121.41  3.000
 J11  C81   C41  C31   120.51  3.000
 J11  C51   C41  C31   118.08  3.000
 J11  H5'A  C5'  H5'   107.38  3.000
 J11  H5'A  C5'  C4'   112.74  3.000
 J11  H5'   C5'  C4'   110.14  3.000
 J11  H5'A  C5'  N1'   111.50  3.000
 J11  H5'   C5'  N1'   112.85  3.000
 J11  C4'   C5'  N1'   102.29  3.000
 J11  H51   C51  C61   120.12  3.000
 J11  H51   C51  C41   120.86  3.000
 J11  C61   C51  C41   119.02  3.000
 J11  N61   C61  C51   120.65  3.000
 J11  N61   C61  N11   116.94  3.000
 J11  C51   C61  N11   122.37  3.000
 J11  HN6A  N61  HN61  113.87  3.000
 J11  HN6A  N61  C61   117.36  3.000
 J11  HN61  N61  C61   115.89  3.000
 J11  H71A  C71  H71   107.26  3.000
 J11  H71A  C71  C4'   108.54  3.000
 J11  H71   C71  C4'   109.49  3.000
 J11  H71A  C71  C21   109.49  3.000
 J11  H71   C71  C21   109.29  3.000
 J11  C4'   C71  C21   112.63  3.000
 J11  H81B  C81  H81A  108.13  3.000
 J11  H81B  C81  H81   106.96  3.000
 J11  H81A  C81  H81   108.04  3.000
 J11  H81B  C81  C41   110.98  3.000
 J11  H81A  C81  C41   111.87  3.000
 J11  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
 J11  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 J11  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 J11  CONST_03  C41  C31  C21  N11     0.00   0.0  0
 J11  CONST_04  C41  C51  C61  N11     0.00   0.0  0
 J11  CONST_05  C15  C16  C11  C12     0.00   0.0  0
 J11  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 J11  CONST_07  C16  C11  C12  C13     0.00   0.0  0
 J11  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 J11  CONST_09  C51  C61  N11  C21     0.00   0.0  0
 J11  CONST_10  C51  C41  C31  C21     0.00   0.0  0
 J11  CONST_11  C61  N11  C21  C31     0.00   0.0  0
 J11  CONST_12  C61  C51  C41  C31     0.00   0.0  0
 J11  CONST_13  C13  C12  C11  C4    180.00   0.0  0
 J11  CONST_14  C15  C16  C11  C4    180.00   0.0  0
 J11  CONST_15  F13  C13  C12  C11   180.00   0.0  0
 J11  CONST_16  C15  C14  C13  F13   180.00   0.0  0
 J11  CONST_17  N61  C61  N11  C21   180.00   0.0  0
 J11  CONST_18  C81  C41  C31  C21   180.00   0.0  0
 J11  CONST_19  C71  C21  C31  C41   180.00   0.0  0
 J11  CONST_20  N61  C61  C51  C41   180.00   0.0  0
 J11  CONST_21  C71  C21  N11  C61   180.00   0.0  0
 J11  CONST_22  C81  C41  C51  C61   180.00   0.0  0
 J11  CONST_23  H15  C15  C16  C11   180.00   0.0  0
 J11  CONST_24  H31  C31  C21  N11   180.00   0.0  0
 J11  CONST_25  H51  C51  C61  N11   180.00   0.0  0
 J11  CONST_26  H16  C16  C11  C12   180.00   0.0  0
 J11  CONST_27  H14  C14  C13  C12   180.00   0.0  0
 J11  CONST_28  H12  C12  C13  C14   180.00   0.0  0
 J11  Var_01    C4'  C5'  N1'  C2'   -47.15  30.0  1
 J11  Var_02    C5'  N1'  C2'  C3'    45.49  30.0  1
 J11  Var_03    C4'  C71  C21  N11   -86.35  30.0  2
 J11  Var_04    C12  C11  C4   C3     89.06  30.0  2
 J11  Var_05    H81  C81  C41  C31    58.43  30.0  2
 J11  Var_06    C3'  N1   C1   C2   -179.82  30.0  3
 J11  Var_07    C11  C4   C3   N2   -177.92  30.0  3
 J11  Var_08    C3   N2   C2   C1   -177.86  30.0  3
 J11  Var_09    N2   C2   C1   N1    179.02  30.0  3
 J11  Var_10    C4   C3   N2   C2   -179.45  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
 J11  chir_01  C3'  N1   C2'  C4'  negativ
 J11  chir_02  C4'  C3'  C5'  C71  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
 J11  plan-1  C4    0.020
 J11  plan-1  C11   0.020
 J11  plan-1  C12   0.020
 J11  plan-1  C13   0.020
 J11  plan-1  F13   0.020
 J11  plan-1  C14   0.020
 J11  plan-1  C15   0.020
 J11  plan-1  C16   0.020
 J11  plan-1  H12   0.020
 J11  plan-1  H14   0.020
 J11  plan-1  H15   0.020
 J11  plan-1  H16   0.020
 J11  plan-2  N11   0.020
 J11  plan-2  C21   0.020
 J11  plan-2  C31   0.020
 J11  plan-2  C41   0.020
 J11  plan-2  C51   0.020
 J11  plan-2  C61   0.020
 J11  plan-2  N61   0.020
 J11  plan-2  C71   0.020
 J11  plan-2  C81   0.020
 J11  plan-2  H31   0.020
 J11  plan-2  H51   0.020
 J11  plan-3  C61   0.020
 J11  plan-3  N61   0.020
 J11  plan-3  HN61  0.020
 J11  plan-3  HN6A  0.020

