# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:52:12 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: [(1R)-1-aminopentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[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
 NLP  NLP  '[(1R)-1-aminopentyl]phosphonic acid'  L-peptide  22  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NLP
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
 NLP  N    N  NH2    0  -0.810  -2.2115   0.3099  -1.3574
 NLP  CA   C  CH1    0  -0.326  -0.9917   0.4987  -0.5665
 NLP  CB   C  CH2    0  -0.425  -1.0989  -0.1474   0.8205
 NLP  CG   C  CH2    0  -0.414  -0.1101   0.3604   1.8618
 NLP  CD   C  CH2    0  -0.414  -0.3133  -0.2640   3.2369
 NLP  CE   C  CH3    0  -0.660   0.6820   0.2441   4.2715
 NLP  P    P  P      0   1.165   0.4451  -0.1501  -1.5834
 NLP  O1   O  O      0  -0.913   0.0321  -1.6006  -1.8964
 NLP  O2   O  OP    -1  -0.912   0.5153   0.7489  -2.8246
 NLP  O3   O  OP    -1  -0.891   1.6986  -0.0495  -0.7004
 NLP  HN1  H  HNH2   0   0.313  -3.0244   0.3995  -0.7563
 NLP  HN2  H  HNH2   0   0.312  -2.2153  -0.6501  -1.6834
 NLP  HA   H  HCH1   0   0.161  -0.8542   1.5800  -0.4177
 NLP  HB1  H  HCH2   0   0.185  -1.0013  -1.2343   0.7120
 NLP  HB2  H  HCH2   0   0.179  -2.1149   0.0233   1.2054
 NLP  HG1  H  HCH2   0   0.182  -0.2084   1.4499   1.9498
 NLP  HG2  H  HCH2   0   0.221   0.9034   0.1720   1.5055
 NLP  HD1  H  HCH2   0   0.202  -0.2311  -1.3529   3.1571
 NLP  HD2  H  HCH2   0   0.200  -1.3328  -0.0642   3.5837
 NLP  HE1  H  HCH3   0   0.221   0.5080  -0.2000   5.2529
 NLP  HE2  H  HCH3   0   0.213   1.7075   0.0095   3.9800
 NLP  HE3  H  HCH3   0   0.212   0.6142   1.3283   4.3843

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
 NLP  N   CA   single  1.458  0.019  1.458
 NLP  N   HN1  single  0.890  0.020  1.040
 NLP  N   HN2  single  0.890  0.020  1.040
 NLP  CA  CB   single  1.530  0.020  1.530
 NLP  CA  P    single  1.876  0.020  1.876
 NLP  CA  HA   single  0.970  0.020  0.970
 NLP  CB  CG   single  1.523  0.020  1.523
 NLP  CB  HB1  single  0.970  0.020  1.090
 NLP  CB  HB2  single  0.970  0.020  1.090
 NLP  CG  CD   single  1.524  0.020  1.524
 NLP  CG  HG1  single  0.970  0.020  1.090
 NLP  CG  HG2  single  0.970  0.020  1.090
 NLP  CD  CE   single  1.523  0.020  1.523
 NLP  CD  HD1  single  0.970  0.020  1.090
 NLP  CD  HD2  single  0.970  0.020  1.090
 NLP  CE  HE1  single  0.970  0.020  1.090
 NLP  CE  HE2  single  0.970  0.020  1.090
 NLP  CE  HE3  single  0.970  0.020  1.090
 NLP  P   O1   deloc   1.540  0.020  1.540
 NLP  P   O2   deloc   1.534  0.020  1.534
 NLP  P   O3   deloc   1.537  0.020  1.537

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
 NLP  HN2  N   HN1  105.73  3.000
 NLP  HN2  N   CA   107.37  3.000
 NLP  HN1  N   CA   109.60  3.000
 NLP  HA   CA  P    108.51  3.000
 NLP  HA   CA  CB   109.00  3.000
 NLP  P    CA  CB   113.45  3.000
 NLP  HA   CA  N    110.00  3.000
 NLP  P    CA  N    107.47  3.000
 NLP  CB   CA  N    110.50  1.700
 NLP  HB2  CB  HB1  105.71  3.000
 NLP  HB2  CB  CG   107.98  3.000
 NLP  HB1  CB  CG   109.89  3.000
 NLP  HB2  CB  CA   108.40  3.000
 NLP  HB1  CB  CA   108.77  3.000
 NLP  CG   CB  CA   115.62  3.000
 NLP  HG2  CG  HG1  106.31  3.000
 NLP  HG2  CG  CD   110.36  3.000
 NLP  HG1  CG  CD   108.81  3.000
 NLP  HG2  CG  CB   108.80  3.000
 NLP  HG1  CG  CB   109.13  3.000
 NLP  CD   CG  CB   113.19  3.000
 NLP  HD2  CD  HD1  105.93  3.000
 NLP  HD2  CD  CE   109.41  3.000
 NLP  HD1  CD  CE   109.41  3.000
 NLP  HD2  CD  CG   109.58  3.000
 NLP  HD1  CD  CG   109.37  3.000
 NLP  CE   CD  CG   112.90  3.000
 NLP  HE3  CE  HE2  107.41  3.000
 NLP  HE3  CE  HE1  107.54  3.000
 NLP  HE2  CE  HE1  107.61  3.000
 NLP  HE3  CE  CD   111.15  3.000
 NLP  HE2  CE  CD   111.15  3.000
 NLP  HE1  CE  CD   111.77  3.000
 NLP  O3   P   O2   112.91  3.000
 NLP  O3   P   O1   113.40  3.000
 NLP  O2   P   O1   113.56  3.000
 NLP  O3   P   CA   106.90  3.000
 NLP  O2   P   CA   105.72  3.000
 NLP  O1   P   CA   103.32  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
 NLP  Var_01  CD   CG  CB  CA  176.94  30.0  3
 NLP  Var_02  CE   CD  CG  CB  179.78  30.0  3
 NLP  Var_03  HE1  CE  CD  CG  178.91  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
 NLP  chir_01  CA  N  CB  P  negativ

