# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:00:30 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2S)-2-(3'-carbamimidoylbiphenyl-3-yl)-5-(pyridin-4-ylamino)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1cccc(c1)c2cccc(c2)[C@H](CCCNc3ccncc3)C(O)=O
#
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
 4PP  4PP  '(2S)-2-(3'-carbamimidoylbiphenyl-3-yl)-5-(pyridin-4-ylamino)pentanoic acid'  ligand  52  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4PP
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
 4PP  C1C   C  C      0   0.421  -3.0339  -0.0423  -0.9997
 4PP  O2    O  O      0  -0.601  -3.4015   0.9318  -1.6854
 4PP  O3    O  OC    -1  -0.605  -3.7594  -0.9334  -0.5201
 4PP  N1P   N  N      0  -0.444   2.6287  -0.1813  -8.6561
 4PP  C2P   C  CR16   0  -0.074   1.5946  -1.0250  -8.6381
 4PP  C3P   C  CR16   0  -0.417   0.7396  -1.1929  -7.5722
 4PP  C4P   C  CR6    0   0.474   0.9388  -0.4380  -6.3998
 4PP  C5P   C  CR16   0  -0.425   2.0231   0.4567  -6.4162
 4PP  C6P   C  CR16   0  -0.077   2.8116   0.5321  -7.5492
 4PP  N1    N  NH1    0  -0.691   0.1297  -0.5830  -5.3334
 4PP  C1    C  CH1    0  -0.429  -1.5224  -0.1343  -0.6587
 4PP  C2    C  CH2    0  -0.392  -0.6109   0.4204  -1.7526
 4PP  C3    C  CH2    0  -0.475  -0.7113  -0.3600  -3.0558
 4PP  C4    C  CH2    0  -0.245   0.2632   0.1576  -4.1010
 4PP  N1A   N  N      0  -0.639   2.0816   1.4025   7.4834
 4PP  N2A   N  NH2    0  -0.803   3.0152  -0.6825   7.6878
 4PP  C1A   C  C      0   0.326   2.1051   0.1716   7.1407
 4PP  C1D   C  C1     0  -0.335  -0.8648   1.8767   3.0946
 4PP  C2D   C  C1     0  -0.224  -1.2938   2.5907   1.9846
 4PP  C3D   C  C1     0  -0.314  -1.5142   1.9496   0.7748
 4PP  C4D   C  C      0   0.183  -1.3000   0.5760   0.6536
 4PP  C5D   C  C1     0  -0.412  -0.8741  -0.1269   1.7753
 4PP  C6D   C  C      0   0.111  -0.6515   0.5022   3.0017
 4PP  C1B   C  C1     0  -0.226  -0.2143  -2.3091   5.4802
 4PP  C2B   C  C1     0  -0.312  -0.6548  -1.5784   4.3882
 4PP  C3B   C  C      0   0.110  -0.1985  -0.2768   4.1721
 4PP  C4B   C  C1     0  -0.368   0.7018   0.2689   5.0854
 4PP  C5B   C  C      0   0.030   1.1503  -0.4578   6.1840
 4PP  C6B   C  C1     0  -0.295   0.6908  -1.7590   6.3757
 4PP  H5P   H  HCR6   0   0.270   2.2545   1.0873  -5.5687
 4PP  H6P   H  HCR6   0   0.252   3.6495   1.2221  -7.5551
 4PP  H1N   H  HNH1   0   0.391  -0.6511  -1.2127  -5.4191
 4PP  H1    H  HCH1   0   0.222  -1.2715  -1.1893  -0.5073
 4PP  H21   H  HCH2   0   0.219  -0.8484   1.4710  -1.9361
 4PP  H22   H  HCH2   0   0.218   0.4244   0.3917  -1.3970
 4PP  H31   H  HCH2   0   0.226  -0.5069  -1.4195  -2.8699
 4PP  H32   H  HCH2   0   0.233  -1.7306  -0.2929  -3.4448
 4PP  H41   H  HCH2   0   0.223   0.0883   1.2273  -4.2716
 4PP  H42   H  HCH2   0   0.226   1.2866   0.0634  -3.7221
 4PP  HN1   H  H      0   0.332   1.2857   1.8753   7.0716
 4PP  HN21  H  HNH2   0   0.385   3.7471  -0.2596   8.2367
 4PP  HN22  H  HNH2   0   0.393   3.3115  -1.4769   7.1453
 4PP  H1D   H  H      0   0.250  -0.7172   2.3904   4.0366
 4PP  H2D   H  H      0   0.252  -1.4674   3.6559   2.0697
 4PP  H3D   H  H      0   0.245  -1.8635   2.5166  -0.0787
 4PP  H5D   H  H      0   0.245  -0.6856  -1.1906   1.6816
 4PP  H1B   H  H      0   0.264  -0.5858  -3.3127   5.6402
 4PP  H2B   H  H      0   0.260  -1.3716  -2.0211   3.7080
 4PP  H4B   H  H      0   0.262   1.0938   1.2638   4.9107
 4PP  H6B   H  H      0   0.264   1.0222  -2.3373   7.2281
 4PP  H2P   H  HCR6   0   0.252   1.4352  -1.6108  -9.5377
 4PP  H3P   H  HCR6   0   0.265  -0.0754  -1.9031  -7.6377

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
 4PP  C1C  O2    deloc     1.247  0.020  1.247
 4PP  C1C  O3    deloc     1.245  0.020  1.245
 4PP  C1C  C1    single    1.552  0.020  1.552
 4PP  N1P  C2P   aromatic  1.335  0.020  1.335
 4PP  N1P  C6P   aromatic  1.330  0.020  1.330
 4PP  C2P  C3P   aromatic  1.377  0.020  1.377
 4PP  C2P  H2P   single    0.930  0.020  1.080
 4PP  C3P  C4P   aromatic  1.409  0.020  1.409
 4PP  C3P  H3P   single    0.930  0.020  1.080
 4PP  C4P  C5P   aromatic  1.406  0.020  1.406
 4PP  C4P  N1    single    1.346  0.020  1.346
 4PP  C5P  C6P   aromatic  1.383  0.020  1.383
 4PP  C5P  H5P   single    0.930  0.020  1.080
 4PP  C6P  H6P   single    0.930  0.020  1.080
 4PP  N1   C4    single    1.444  0.020  1.444
 4PP  N1   H1N   single    0.860  0.020  1.020
 4PP  C1   C2    single    1.528  0.020  1.528
 4PP  C1   C4D   single    1.509  0.020  1.509
 4PP  C1   H1    single    0.970  0.020  1.090
 4PP  C2   C3    single    1.522  0.020  1.522
 4PP  C2   H21   single    0.970  0.020  1.090
 4PP  C2   H22   single    0.970  0.020  1.090
 4PP  C3   C4    single    1.520  0.020  1.520
 4PP  C3   H31   single    0.970  0.020  1.090
 4PP  C3   H32   single    0.970  0.020  1.090
 4PP  C4   H41   single    0.970  0.020  1.090
 4PP  C4   H42   single    0.970  0.020  1.090
 4PP  N1A  C1A   double    1.278  0.020  1.278
 4PP  N1A  HN1   single    0.890  0.020  1.040
 4PP  N2A  C1A   single    1.363  0.020  1.363
 4PP  N2A  HN21  single    0.890  0.020  1.040
 4PP  N2A  HN22  single    0.890  0.020  1.040
 4PP  C1A  C5B   single    1.491  0.020  1.491
 4PP  C1D  C2D   aromatic  1.388  0.020  1.388
 4PP  C1D  C6D   aromatic  1.394  0.020  1.394
 4PP  C1D  H1D   single    0.930  0.020  1.080
 4PP  C2D  C3D   aromatic  1.387  0.020  1.387
 4PP  C2D  H2D   single    0.930  0.020  1.080
 4PP  C3D  C4D   aromatic  1.396  0.020  1.396
 4PP  C3D  H3D   single    0.930  0.020  1.080
 4PP  C4D  C5D   aromatic  1.391  0.020  1.391
 4PP  C5D  C6D   aromatic  1.396  0.020  1.396
 4PP  C5D  H5D   single    0.930  0.020  1.080
 4PP  C6D  C3B   single    1.477  0.020  1.477
 4PP  C1B  C2B   aromatic  1.386  0.020  1.386
 4PP  C1B  C6B   aromatic  1.387  0.020  1.387
 4PP  C1B  H1B   single    0.930  0.020  1.080
 4PP  C2B  C3B   aromatic  1.396  0.020  1.396
 4PP  C2B  H2B   single    0.930  0.020  1.080
 4PP  C3B  C4B   aromatic  1.394  0.020  1.394
 4PP  C4B  C5B   aromatic  1.391  0.020  1.391
 4PP  C4B  H4B   single    0.930  0.020  1.080
 4PP  C5B  C6B   aromatic  1.393  0.020  1.393
 4PP  C6B  H6B   single    0.930  0.020  1.080

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
 4PP  C1    C1C  O3    116.13  3.000
 4PP  C1    C1C  O2    117.02  3.000
 4PP  O3    C1C  O2    126.81  3.000
 4PP  C6P   N1P  C2P   115.76  3.000
 4PP  H2P   C2P  C3P   118.99  3.000
 4PP  H2P   C2P  N1P   116.34  3.000
 4PP  C3P   C2P  N1P   124.66  3.000
 4PP  H3P   C3P  C4P   120.55  3.000
 4PP  H3P   C3P  C2P   120.03  3.000
 4PP  C4P   C3P  C2P   119.42  3.000
 4PP  N1    C4P  C5P   122.77  3.000
 4PP  N1    C4P  C3P   121.10  3.000
 4PP  C5P   C4P  C3P   116.13  3.000
 4PP  H5P   C5P  C6P   119.24  3.000
 4PP  H5P   C5P  C4P   121.81  3.000
 4PP  C6P   C5P  C4P   118.96  3.000
 4PP  H6P   C6P  C5P   118.65  3.000
 4PP  H6P   C6P  N1P   116.28  3.000
 4PP  C5P   C6P  N1P   125.07  3.000
 4PP  H1N   N1   C4    117.72  3.000
 4PP  H1N   N1   C4P   117.78  3.000
 4PP  C4    N1   C4P   124.41  3.000
 4PP  H1    C1   C4D   107.43  3.000
 4PP  H1    C1   C2    108.19  3.000
 4PP  C4D   C1   C2    111.34  3.000
 4PP  H1    C1   C1C   108.09  3.000
 4PP  C4D   C1   C1C   107.86  3.000
 4PP  C2    C1   C1C   113.71  3.000
 4PP  H22   C2   H21   106.57  3.000
 4PP  H22   C2   C3    109.08  3.000
 4PP  H21   C2   C3    109.56  3.000
 4PP  H22   C2   C1    108.78  3.000
 4PP  H21   C2   C1    109.86  3.000
 4PP  C3    C2   C1    112.79  3.000
 4PP  H32   C3   H31   107.09  3.000
 4PP  H32   C3   C4    109.40  3.000
 4PP  H31   C3   C4    109.06  3.000
 4PP  H32   C3   C2    109.55  3.000
 4PP  H31   C3   C2    109.78  3.000
 4PP  C4    C3   C2    111.83  3.000
 4PP  H42   C4   H41   106.65  3.000
 4PP  H42   C4   C3    109.38  3.000
 4PP  H41   C4   C3    109.67  3.000
 4PP  H42   C4   N1    109.73  3.000
 4PP  H41   C4   N1    110.65  3.000
 4PP  C3    C4   N1    110.67  3.000
 4PP  HN1   N1A  C1A   110.79  3.000
 4PP  HN22  N2A  HN21  114.26  3.000
 4PP  HN22  N2A  C1A   118.35  3.000
 4PP  HN21  N2A  C1A   116.15  3.000
 4PP  C5B   C1A  N2A   114.88  3.000
 4PP  C5B   C1A  N1A   124.53  3.000
 4PP  N2A   C1A  N1A   120.55  3.000
 4PP  H1D   C1D  C6D   120.31  3.000
 4PP  H1D   C1D  C2D   119.59  3.000
 4PP  C6D   C1D  C2D   120.08  3.000
 4PP  H2D   C2D  C3D   119.87  3.000
 4PP  H2D   C2D  C1D   119.53  3.000
 4PP  C3D   C2D  C1D   120.61  3.000
 4PP  H3D   C3D  C4D   119.78  3.000
 4PP  H3D   C3D  C2D   119.80  3.000
 4PP  C4D   C3D  C2D   120.42  3.000
 4PP  C5D   C4D  C3D   118.33  3.000
 4PP  C5D   C4D  C1    120.59  3.000
 4PP  C3D   C4D  C1    121.08  3.000
 4PP  H5D   C5D  C6D   119.35  3.000
 4PP  H5D   C5D  C4D   118.65  3.000
 4PP  C6D   C5D  C4D   121.98  3.000
 4PP  C3B   C6D  C5D   120.48  3.000
 4PP  C3B   C6D  C1D   120.94  3.000
 4PP  C5D   C6D  C1D   118.58  3.000
 4PP  H1B   C1B  C6B   119.76  3.000
 4PP  H1B   C1B  C2B   119.76  3.000
 4PP  C6B   C1B  C2B   120.47  3.000
 4PP  H2B   C2B  C3B   120.02  3.000
 4PP  H2B   C2B  C1B   119.33  3.000
 4PP  C3B   C2B  C1B   120.64  3.000
 4PP  C4B   C3B  C2B   118.35  3.000
 4PP  C4B   C3B  C6D   120.72  3.000
 4PP  C2B   C3B  C6D   120.94  3.000
 4PP  H4B   C4B  C5B   119.36  3.000
 4PP  H4B   C4B  C3B   119.18  3.000
 4PP  C5B   C4B  C3B   121.41  3.000
 4PP  C6B   C5B  C4B   119.35  3.000
 4PP  C6B   C5B  C1A   121.15  3.000
 4PP  C4B   C5B  C1A   119.51  3.000
 4PP  H6B   C6B  C5B   120.43  3.000
 4PP  H6B   C6B  C1B   119.77  3.000
 4PP  C5B   C6B  C1B   119.79  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
 4PP  CONST_01  C4P   C3P  C2P  N1P     0.00   0.0  0
 4PP  CONST_02  C4P   C5P  C6P  N1P     0.00   0.0  0
 4PP  CONST_03  C5P   C6P  N1P  C2P     0.00   0.0  0
 4PP  CONST_04  C5P   C4P  C3P  C2P     0.00   0.0  0
 4PP  CONST_05  C6P   N1P  C2P  C3P     0.00   0.0  0
 4PP  CONST_06  C6P   C5P  C4P  C3P     0.00   0.0  0
 4PP  CONST_07  C4D   C3D  C2D  C1D     0.00   0.0  0
 4PP  CONST_08  C4D   C5D  C6D  C1D     0.00   0.0  0
 4PP  CONST_11  C5D   C6D  C1D  C2D     0.00   0.0  0
 4PP  CONST_12  C3B   C6D  C1D  C2D   180.00   0.0  0
 4PP  CONST_13  C5D   C4D  C3D  C2D     0.00   0.0  0
 4PP  CONST_14  C6D   C1D  C2D  C3D     0.00   0.0  0
 4PP  CONST_15  C6D   C5D  C4D  C3D     0.00   0.0  0
 4PP  CONST_16  C3B   C6D  C5D  C4D   180.00   0.0  0
 4PP  CONST_19  C1B   C2B  C3B  C6D   180.00   0.0  0
 4PP  CONST_20  C5B   C4B  C3B  C6D   180.00   0.0  0
 4PP  CONST_21  C4B   C3B  C2B  C1B     0.00   0.0  0
 4PP  CONST_22  C4B   C5B  C6B  C1B     0.00   0.0  0
 4PP  CONST_23  C5B   C6B  C1B  C2B     0.00   0.0  0
 4PP  CONST_24  C5B   C4B  C3B  C2B     0.00   0.0  0
 4PP  CONST_25  C6B   C1B  C2B  C3B     0.00   0.0  0
 4PP  CONST_26  C6B   C5B  C4B  C3B     0.00   0.0  0
 4PP  CONST_27  N1    C4P  C3P  C2P   180.00   0.0  0
 4PP  CONST_28  N1    C4P  C5P  C6P   180.00   0.0  0
 4PP  CONST_29  C2D   C3D  C4D  C1    180.00   0.0  0
 4PP  CONST_30  C6D   C5D  C4D  C1    180.00   0.0  0
 4PP  CONST_31  C3B   C4B  C5B  C1A   180.00   0.0  0
 4PP  CONST_32  C1B   C6B  C5B  C1A   180.00   0.0  0
 4PP  CONST_33  H3P   C3P  C2P  N1P   180.00   0.0  0
 4PP  CONST_34  H5P   C5P  C6P  N1P   180.00   0.0  0
 4PP  CONST_35  H6P   C6P  N1P  C2P   180.00   0.0  0
 4PP  CONST_36  H2P   C2P  C3P  C4P   180.00   0.0  0
 4PP  CONST_37  H3D   C3D  C2D  C1D   180.00   0.0  0
 4PP  CONST_38  H5D   C5D  C6D  C1D   180.00   0.0  0
 4PP  CONST_39  H1D   C1D  C2D  C3D   180.00   0.0  0
 4PP  CONST_40  H2D   C2D  C3D  C4D   180.00   0.0  0
 4PP  CONST_41  H2B   C2B  C3B  C6D     0.00   0.0  0
 4PP  CONST_42  H4B   C4B  C3B  C6D     0.00   0.0  0
 4PP  CONST_43  H6B   C6B  C1B  C2B   180.00   0.0  0
 4PP  CONST_44  H1B   C1B  C2B  C3B   180.00   0.0  0
 4PP  CONST_45  C4    N1   C4P  C3P   180.00   0.0  0
 4PP  CONST_46  C4    N1   C4P  C5P     0.00   0.0  0
 4PP  CONST_47  H1N   N1   C4P  C3P     0.00   0.0  0
 4PP  CONST_48  HN1   N1A  C1A  C5B     0.00   0.0  0
 4PP  CONST_49  HN21  N2A  C1A  C5B   180.00   0.0  0
 4PP  Var_01    C4B   C5B  C1A  N1A    36.48  30.0  2
 4PP  Var_02    C3    C4   N1   C4P  -173.66  30.0  3
 4PP  Var_03    C2    C3   C4   N1   -178.93  30.0  2
 4PP  Var_04    C4    C3   C2   C1   -176.60  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
 4PP  chir_01  C1  C1C  C2  C4D  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
 4PP  plan-1  N1P   0.020
 4PP  plan-1  C2P   0.020
 4PP  plan-1  C3P   0.020
 4PP  plan-1  C4P   0.020
 4PP  plan-1  C5P   0.020
 4PP  plan-1  C6P   0.020
 4PP  plan-1  N1    0.020
 4PP  plan-1  H5P   0.020
 4PP  plan-1  H6P   0.020
 4PP  plan-1  H2P   0.020
 4PP  plan-1  H3P   0.020
 4PP  plan-2  C1    0.020
 4PP  plan-2  C1D   0.020
 4PP  plan-2  C2D   0.020
 4PP  plan-2  C3D   0.020
 4PP  plan-2  C4D   0.020
 4PP  plan-2  C5D   0.020
 4PP  plan-2  C6D   0.020
 4PP  plan-2  C3B   0.020
 4PP  plan-2  H1D   0.020
 4PP  plan-2  H2D   0.020
 4PP  plan-2  H3D   0.020
 4PP  plan-2  H5D   0.020
 4PP  plan-3  C1A   0.020
 4PP  plan-3  C6D   0.020
 4PP  plan-3  C1B   0.020
 4PP  plan-3  C2B   0.020
 4PP  plan-3  C3B   0.020
 4PP  plan-3  C4B   0.020
 4PP  plan-3  C5B   0.020
 4PP  plan-3  C6B   0.020
 4PP  plan-3  H1B   0.020
 4PP  plan-3  H2B   0.020
 4PP  plan-3  H4B   0.020
 4PP  plan-3  H6B   0.020
 4PP  plan-4  C4P   0.020
 4PP  plan-4  N1    0.020
 4PP  plan-4  C4    0.020
 4PP  plan-4  H1N   0.020
 4PP  plan-5  N1A   0.020
 4PP  plan-5  N2A   0.020
 4PP  plan-5  C1A   0.020
 4PP  plan-5  C5B   0.020
 4PP  plan-5  HN1   0.020
 4PP  plan-5  HN21  0.020
 4PP  plan-5  HN22  0.020
 4PP  plan-6  C1C   0.020
 4PP  plan-6  O2    0.020
 4PP  plan-6  O3    0.020
 4PP  plan-6  C1    0.020

