# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 21:12:09 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: [(1R)-1,5-diaminopentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N)[P](O)(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
 KPH  KPH  '[(1R)-1,5-diaminopentyl]phosphonic acid'  ligand  24  11  .  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_KPH
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
 KPH  O1   O  O      0  -0.913   2.0379   0.4190   1.6356
 KPH  P1   P  P      0   1.151   2.0021   0.5595   0.1040
 KPH  O2   O  OP    -1  -0.913   3.3943   0.4652  -0.5497
 KPH  C1   C  CH1    0  -0.335   1.1360  -0.9872  -0.4898
 KPH  N1   N  NH2    0  -0.814   1.9527  -2.1810  -0.1943
 KPH  C2   C  CH2    0  -0.408  -0.2567  -1.2049   0.0918
 KPH  C3   C  CH2    0  -0.422  -1.3230  -0.2351  -0.4012
 KPH  C4   C  CH2    0  -0.421  -2.7012  -0.5241   0.1796
 KPH  C5   C  CH2    0  -0.270  -3.7597   0.4613  -0.2909
 KPH  N2   N  NH2    0  -0.801  -5.0663   0.1398   0.2693
 KPH  O3   O  OP    -1  -0.897   1.1940   1.7721  -0.3862
 KPH  H2   H  HCH1   0   0.167   1.0359  -0.9357  -1.5838
 KPH  H3   H  HNH2   0   0.318   2.8937  -1.9711  -0.5119
 KPH  H4   H  HNH2   0   0.312   2.0512  -2.2191   0.8164
 KPH  H5   H  HCH2   0   0.184  -0.5770  -2.2295  -0.1390
 KPH  H6   H  HCH2   0   0.187  -0.1917  -1.1475   1.1851
 KPH  H7   H  HCH2   0   0.219  -1.0151   0.7845  -0.1654
 KPH  H8   H  HCH2   0   0.187  -1.3774  -0.2874  -1.4954
 KPH  H9   H  HCH2   0   0.202  -3.0166  -1.5388  -0.0857
 KPH  H10  H  HCH2   0   0.202  -2.6473  -0.4961   1.2746
 KPH  H11  H  HCH2   0   0.183  -3.4230   1.4818  -0.0552
 KPH  H12  H  HCH2   0   0.206  -3.8352   0.4112  -1.3813
 KPH  H13  H  HNH2   0   0.335  -5.0344   0.2654   1.2741
 KPH  H14  H  HNH2   0   0.343  -5.7496   0.8090  -0.0623

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
 KPH  O1  P1   deloc   1.538  0.020  1.538
 KPH  P1  O2   deloc   1.541  0.020  1.541
 KPH  P1  C1   single  1.869  0.020  1.869
 KPH  C1  N1   single  1.476  0.020  1.476
 KPH  C1  C2   single  1.525  0.020  1.525
 KPH  C2  C3   single  1.523  0.020  1.523
 KPH  C3  C4   single  1.523  0.020  1.523
 KPH  C4  C5   single  1.521  0.020  1.521
 KPH  C5  N2   single  1.458  0.020  1.458
 KPH  P1  O3   deloc   1.537  0.020  1.537
 KPH  C1  H2   single  0.970  0.020  1.090
 KPH  N1  H3   single  0.890  0.020  1.040
 KPH  N1  H4   single  0.890  0.020  1.040
 KPH  C2  H5   single  0.970  0.020  1.090
 KPH  C2  H6   single  0.970  0.020  1.090
 KPH  C3  H7   single  0.970  0.020  1.090
 KPH  C3  H8   single  0.970  0.020  1.090
 KPH  C4  H9   single  0.970  0.020  1.090
 KPH  C4  H10  single  0.970  0.020  1.090
 KPH  C5  H11  single  0.970  0.020  1.090
 KPH  C5  H12  single  0.970  0.020  1.090
 KPH  N2  H13  single  0.890  0.020  1.040
 KPH  N2  H14  single  0.890  0.020  1.040

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
 KPH  O3   P1  C1   107.93  3.000
 KPH  O3   P1  O2   112.82  3.000
 KPH  C1   P1  O2   103.48  3.000
 KPH  O3   P1  O1   113.69  3.000
 KPH  C1   P1  O1   104.56  3.000
 KPH  O2   P1  O1   113.31  3.000
 KPH  H2   C1  C2   107.63  3.000
 KPH  H2   C1  N1   106.70  3.000
 KPH  C2   C1  N1   108.27  3.000
 KPH  H2   C1  P1   108.63  3.000
 KPH  C2   C1  P1   114.84  3.000
 KPH  N1   C1  P1   110.44  3.000
 KPH  H4   N1  H3   103.24  3.000
 KPH  H4   N1  C1   106.44  3.000
 KPH  H3   N1  C1   106.44  3.000
 KPH  H6   C2  H5   106.00  3.000
 KPH  H6   C2  C3   109.32  3.000
 KPH  H5   C2  C3   108.77  3.000
 KPH  H6   C2  C1   108.58  3.000
 KPH  H5   C2  C1   108.63  3.000
 KPH  C3   C2  C1   115.15  3.000
 KPH  H8   C3  H7   105.92  3.000
 KPH  H8   C3  C4   109.06  3.000
 KPH  H7   C3  C4   110.50  3.000
 KPH  H8   C3  C2   109.10  3.000
 KPH  H7   C3  C2   109.11  3.000
 KPH  C4   C3  C2   112.90  3.000
 KPH  H10  C4  H9   106.24  3.000
 KPH  H10  C4  C5   109.06  3.000
 KPH  H9   C4  C5   108.96  3.000
 KPH  H10  C4  C3   109.36  3.000
 KPH  H9   C4  C3   110.12  3.000
 KPH  C5   C4  C3   112.89  3.000
 KPH  H12  C5  H11  106.09  3.000
 KPH  H12  C5  N2   108.12  3.000
 KPH  H11  C5  N2   113.37  3.000
 KPH  H12  C5  C4   109.07  3.000
 KPH  H11  C5  C4   108.77  3.000
 KPH  N2   C5  C4   111.23  3.000
 KPH  H14  N2  H13  105.32  3.000
 KPH  H14  N2  C5   109.47  3.000
 KPH  H13  N2  C5   109.00  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
 KPH  Var_01  C4   C3  C2  C1  178.30  30.0  3
 KPH  Var_02  C5   C4  C3  C2  178.84  30.0  3
 KPH  Var_03  N2   C5  C4  C3  179.13  30.0  3
 KPH  Var_04  H13  N2  C5  C4   65.44  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
 KPH  chir_01  C1  P1  N1  C2  negativ

