# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:40:35 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  53  29  .  2021-08-05  2021-08-05  
;
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   0.563  -3.0445   0.0369  -1.0590
 4PP  O2    O  O     0  -0.436  -3.5095   0.8257  -1.8432
 4PP  O3    O  OH1   0  -0.586  -3.7797  -0.8199  -0.3630
 4PP  N1P   N  N     0  -0.442   2.7708  -0.0800  -8.6030
 4PP  C2P   C  CR16  0  -0.073   1.8334  -1.0288  -8.5621
 4PP  C3P   C  CR16  0  -0.417   0.9909  -1.2509  -7.4960
 4PP  C4P   C  CR6   0   0.472   1.0966  -0.4395  -6.3504
 4PP  C5P   C  CR16  0  -0.423   2.0778   0.5655  -6.3911
 4PP  C6P   C  CR16  0  -0.076   2.8652   0.6868  -7.5211
 4PP  N1    N  NH1   0  -0.691   0.2993  -0.6424  -5.2815
 4PP  C1    C  CH1   0  -0.460  -1.5749  -0.0707  -0.7047
 4PP  C2    C  CH2   0  -0.405  -0.6688   0.4891  -1.8003
 4PP  C3    C  CH2   0  -0.477  -0.6574  -0.3669  -3.0598
 4PP  C4    C  CH2   0  -0.247   0.2819   0.2018  -4.1109
 4PP  N1A   N  N     0  -0.639   2.1075   1.3546   7.4086
 4PP  N2A   N  NH2   0  -0.803   3.0134  -0.7456   7.5790
 4PP  C1A   C  C     0   0.327   2.1084   0.1270   7.0538
 4PP  C1D   C  CR16  0  -0.323  -0.9120   1.9007   3.0625
 4PP  C2D   C  CR16  0  -0.224  -1.3467   2.6289   1.9650
 4PP  C3D   C  CR16  0  -0.304  -1.5752   2.0010   0.7495
 4PP  C4D   C  CR6   0   0.180  -1.3649   0.6300   0.6227
 4PP  C5D   C  CR16  0  -0.395  -0.9344  -0.0914   1.7282
 4PP  C6D   C  CR6   0   0.110  -0.7014   0.5266   2.9572
 4PP  C1B   C  CR16  0  -0.226  -0.2751  -2.3047   5.4112
 4PP  C2B   C  CR16  0  -0.310  -0.7189  -1.5605   4.3298
 4PP  C3B   C  CR6   0   0.108  -0.2441  -0.2654   4.1168
 4PP  C4B   C  CR16  0  -0.365   0.6772   0.2620   5.0193
 4PP  C5B   C  CR6   0   0.030   1.1298  -0.4794   6.1062
 4PP  C6B   C  CR16  0  -0.292   0.6516  -1.7740   6.2961
 4PP  HO3   H  HOH1  0   0.481  -4.7186  -0.6993  -0.5714
 4PP  H3P   H  HCR6  0   0.266   0.2568  -2.0457  -7.5432
 4PP  H5P   H  HCR6  0   0.271   2.2315   1.2464  -5.5652
 4PP  H6P   H  HCR6  0   0.253   3.6225   1.4638  -7.5469
 4PP  H1N   H  HNH1  0   0.391  -0.4506  -1.3060  -5.3850
 4PP  H1    H  HCH1  0   0.291  -1.3408  -1.1298  -0.5619
 4PP  H21   H  HCH2  0   0.238  -0.9602   1.5142  -2.0417
 4PP  H22   H  HCH2  0   0.248   0.3455   0.5425  -1.3967
 4PP  H31   H  HCH2  0   0.239  -0.3418  -1.3838  -2.8082
 4PP  H32   H  HCH2  0   0.240  -1.6639  -0.4413  -3.4817
 4PP  H41   H  HCH2  0   0.227  -0.0249   1.2239  -4.3669
 4PP  H42   H  HCH2  0   0.231   1.2913   0.2728  -3.6933
 4PP  HN1   H  H     0   0.332   1.3124   1.8424   7.0133
 4PP  HN21  H  HNH2  0   0.385   3.7595  -0.3391   8.1212
 4PP  HN22  H  HNH2  0   0.393   3.2918  -1.5386   7.0252
 4PP  H1D   H  HCR6  0   0.257  -0.7559   2.4036   4.0087
 4PP  H2D   H  HCR6  0   0.261  -1.5158   3.6934   2.0614
 4PP  H3D   H  HCR6  0   0.256  -1.9172   2.5845  -0.0968
 4PP  H5D   H  HCR6  0   0.257  -0.7526  -1.1548   1.6234
 4PP  H1B   H  HCR6  0   0.265  -0.6601  -3.3030   5.5705
 4PP  H2B   H  HCR6  0   0.261  -1.4523  -1.9865   3.6567
 4PP  H4B   H  HCR6  0   0.264   1.0810   1.2521   4.8444
 4PP  H6B   H  HCR6  0   0.265   0.9862  -2.3627   7.1401
 4PP  H2P   H  HCR6  0   0.253   1.7457  -1.6578  -9.4419

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    double    1.206  0.020  1.206
 4PP  C1C  O3    single    1.326  0.020  1.326
 4PP  C1C  C1    single    1.516  0.020  1.516
 4PP  O3   HO3   single    0.850  0.020  0.980
 4PP  N1P  C2P   aromatic  1.334  0.020  1.334
 4PP  N1P  C6P   aromatic  1.329  0.020  1.329
 4PP  C2P  C3P   aromatic  1.377  0.020  1.377
 4PP  C2P  H2P   single    0.930  0.020  1.080
 4PP  C3P  C4P   aromatic  1.408  0.020  1.408
 4PP  C3P  H3P   single    0.930  0.020  1.080
 4PP  C4P  C5P   aromatic  1.405  0.020  1.405
 4PP  C4P  N1    single    1.349  0.020  1.349
 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    1.443  0.020  1.443
 4PP  N1   H1N   single    0.860  0.020  1.020
 4PP  C1   C2    single    1.528  0.020  1.528
 4PP  C1   C4D   single    1.516  0.020  1.516
 4PP  C1   H1    single    0.970  0.020  1.090
 4PP  C2   C3    single    1.523  0.020  1.523
 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    1.362  0.020  1.362
 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  1.387  0.020  1.387
 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  1.393  0.020  1.393
 4PP  C3D  H3D   single    0.930  0.020  1.080
 4PP  C4D  C5D   aromatic  1.388  0.020  1.388
 4PP  C5D  C6D   aromatic  1.395  0.020  1.395
 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  1.393  0.020  1.393
 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    111.65  3.000
 4PP  C1    C1C  O2    124.93  3.000
 4PP  O3    C1C  O2    123.38  3.000
 4PP  HO3   O3   C1C   110.10  3.000
 4PP  C6P   N1P  C2P   115.79  3.000
 4PP  H2P   C2P  C3P   119.00  3.000
 4PP  H2P   C2P  N1P   116.36  3.000
 4PP  C3P   C2P  N1P   124.63  3.000
 4PP  H3P   C3P  C4P   120.62  3.000
 4PP  H3P   C3P  C2P   119.96  3.000
 4PP  C4P   C3P  C2P   119.42  3.000
 4PP  N1    C4P  C5P   122.91  3.000
 4PP  N1    C4P  C3P   120.92  3.000
 4PP  C5P   C4P  C3P   116.17  3.000
 4PP  H5P   C5P  C6P   119.21  3.000
 4PP  H5P   C5P  C4P   121.84  3.000
 4PP  C6P   C5P  C4P   118.95  3.000
 4PP  H6P   C6P  C5P   118.66  3.000
 4PP  H6P   C6P  N1P   116.31  3.000
 4PP  C5P   C6P  N1P   125.03  3.000
 4PP  H1N   N1   C4    117.38  3.000
 4PP  H1N   N1   C4P   117.26  3.000
 4PP  C4    N1   C4P   124.19  3.000
 4PP  H1    C1   C4D   107.67  3.000
 4PP  H1    C1   C2    108.75  3.000
 4PP  C4D   C1   C2    112.11  3.000
 4PP  H1    C1   C1C   107.86  3.000
 4PP  C4D   C1   C1C   107.84  3.000
 4PP  C2    C1   C1C   112.42  3.000
 4PP  H22   C2   H21   106.45  3.000
 4PP  H22   C2   C3    109.02  3.000
 4PP  H21   C2   C3    110.28  3.000
 4PP  H22   C2   C1    107.66  3.000
 4PP  H21   C2   C1    110.12  3.000
 4PP  C3    C2   C1    113.05  3.000
 4PP  H32   C3   H31   106.92  3.000
 4PP  H32   C3   C4    109.10  3.000
 4PP  H31   C3   C4    109.18  3.000
 4PP  H32   C3   C2    110.51  3.000
 4PP  H31   C3   C2    109.54  3.000
 4PP  C4    C3   C2    111.48  3.000
 4PP  H42   C4   H41   106.64  3.000
 4PP  H42   C4   C3    109.29  3.000
 4PP  H41   C4   C3    109.70  3.000
 4PP  H42   C4   N1    109.65  3.000
 4PP  H41   C4   N1    111.03  3.000
 4PP  C3    C4   N1    110.45  3.000
 4PP  HN1   N1A  C1A   110.78  3.000
 4PP  HN22  N2A  HN21  114.14  3.000
 4PP  HN22  N2A  C1A   118.44  3.000
 4PP  HN21  N2A  C1A   116.15  3.000
 4PP  C5B   C1A  N2A   114.86  3.000
 4PP  C5B   C1A  N1A   124.52  3.000
 4PP  N2A   C1A  N1A   120.58  3.000
 4PP  H1D   C1D  C6D   120.13  3.000
 4PP  H1D   C1D  C2D   119.53  3.000
 4PP  C6D   C1D  C2D   120.33  3.000
 4PP  H2D   C2D  C3D   119.84  3.000
 4PP  H2D   C2D  C1D   119.67  3.000
 4PP  C3D   C2D  C1D   120.49  3.000
 4PP  H3D   C3D  C4D   120.45  3.000
 4PP  H3D   C3D  C2D   119.52  3.000
 4PP  C4D   C3D  C2D   120.03  3.000
 4PP  C5D   C4D  C3D   119.07  3.000
 4PP  C5D   C4D  C1    120.00  3.000
 4PP  C3D   C4D  C1    120.92  3.000
 4PP  H5D   C5D  C6D   119.46  3.000
 4PP  H5D   C5D  C4D   119.00  3.000
 4PP  C6D   C5D  C4D   121.53  3.000
 4PP  C3B   C6D  C5D   120.38  3.000
 4PP  C3B   C6D  C1D   121.07  3.000
 4PP  C5D   C6D  C1D   118.55  3.000
 4PP  H1B   C1B  C6B   119.79  3.000
 4PP  H1B   C1B  C2B   119.78  3.000
 4PP  C6B   C1B  C2B   120.43  3.000
 4PP  H2B   C2B  C3B   120.04  3.000
 4PP  H2B   C2B  C1B   119.39  3.000
 4PP  C3B   C2B  C1B   120.56  3.000
 4PP  C4B   C3B  C2B   118.51  3.000
 4PP  C4B   C3B  C6D   120.69  3.000
 4PP  C2B   C3B  C6D   120.80  3.000
 4PP  H4B   C4B  C5B   119.46  3.000
 4PP  H4B   C4B  C3B   119.19  3.000
 4PP  C5B   C4B  C3B   121.29  3.000
 4PP  C6B   C5B  C4B   119.34  3.000
 4PP  C6B   C5B  C1A   121.11  3.000
 4PP  C4B   C5B  C1A   119.55  3.000
 4PP  H6B   C6B  C5B   120.38  3.000
 4PP  H6B   C6B  C1B   119.75  3.000
 4PP  C5B   C6B  C1B   119.87  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  CONST_51  HO3   O3   C1C  O2      0.00   0.0  0
 4PP  Var_01    C4B   C5B  C1A  N1A    36.69  30.0  2
 4PP  Var_02    C3    C4   N1   C4P  -175.98  30.0  3
 4PP  Var_03    C2    C3   C4   N1    178.66  30.0  1
 4PP  Var_04    C4    C3   C2   C1   -178.50  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  H3P   0.020
 4PP  plan-1  H5P   0.020
 4PP  plan-1  H6P   0.020
 4PP  plan-1  H2P   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
 4PP  plan-6  HO3   0.020

