# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:30:59 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: [(1R,2S)-1-amino-2-methylpentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](C)[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
 Q07  Q07  '[(1R,2S)-1-amino-2-methylpentyl]phosphonic acid'  ligand  25  11  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q07
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
 Q07  O2   O  OP    -1  -0.890  -2.1435  -1.4447   0.2565
 Q07  P    P  P      0   1.173  -1.9511   0.0805   0.3007
 Q07  O    O  OP    -1  -0.910  -3.0153   0.8290  -0.5109
 Q07  O1   O  O      0  -0.914  -1.7638   0.6281   1.7279
 Q07  C5   C  CH1    0  -0.324  -0.3073   0.4806  -0.5304
 Q07  N    N  NH2    0  -0.809  -0.1701   1.9353  -0.4551
 Q07  C3   C  CH1    0  -0.210   0.8830  -0.3244   0.0509
 Q07  C4   C  CH3    0  -0.695   0.8511  -1.7664  -0.4521
 Q07  C2   C  CH2    0  -0.406   2.2456   0.3087  -0.2520
 Q07  C1   C  CH2    0  -0.419   3.4413  -0.4419   0.3255
 Q07  C    C  CH3    0  -0.658   4.7496   0.3151   0.1364
 Q07  H3   H  HCH1   0   0.159  -0.3826   0.2192  -1.5969
 Q07  H4   H  HNH2   0   0.312  -0.2267   2.2091   0.5190
 Q07  H5   H  HNH2   0   0.326   0.7400   2.2343  -0.7825
 Q07  H7   H  HCH1   0   0.175   0.7672  -0.3350   1.1437
 Q07  H8   H  HCH3   0   0.205   1.5565  -2.4062   0.0811
 Q07  H9   H  HCH3   0   0.249  -0.1477  -2.1762  -0.3260
 Q07  H10  H  HCH3   0   0.188   1.1134  -1.8087  -1.5143
 Q07  H11  H  HCH2   0   0.191   2.3697   0.4029  -1.3395
 Q07  H12  H  HCH2   0   0.196   2.2816   1.3275   0.1460
 Q07  H13  H  HCH2   0   0.203   3.2725  -0.6182   1.3935
 Q07  H14  H  HCH2   0   0.213   3.5314  -1.4299  -0.1324
 Q07  H15  H  HCH3   0   0.213   4.9551   0.4884  -0.9219
 Q07  H16  H  HCH3   0   0.212   4.7172   1.2897   0.6276
 Q07  H17  H  HCH3   0   0.222   5.5966  -0.2348   0.5493

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
 Q07  N   C5   single  1.463  0.020  1.463
 Q07  C2  C1   single  1.525  0.020  1.525
 Q07  C2  C3   single  1.533  0.020  1.533
 Q07  C5  C3   single  1.550  0.020  1.550
 Q07  C5  P    single  1.885  0.020  1.885
 Q07  O1  P    deloc   1.540  0.020  1.540
 Q07  C   C1   single  1.523  0.020  1.523
 Q07  C3  C4   single  1.528  0.020  1.528
 Q07  P   O    deloc   1.533  0.020  1.533
 Q07  P   O2   deloc   1.538  0.020  1.538
 Q07  C5  H3   single  0.970  0.020  1.090
 Q07  N   H4   single  0.890  0.020  1.040
 Q07  N   H5   single  0.890  0.020  1.040
 Q07  C3  H7   single  0.970  0.020  1.090
 Q07  C4  H8   single  0.970  0.020  1.090
 Q07  C4  H9   single  0.970  0.020  1.090
 Q07  C4  H10  single  0.970  0.020  1.090
 Q07  C2  H11  single  0.970  0.020  1.090
 Q07  C2  H12  single  0.970  0.020  1.090
 Q07  C1  H13  single  0.970  0.020  1.090
 Q07  C1  H14  single  0.970  0.020  1.090
 Q07  C   H15  single  0.970  0.020  1.090
 Q07  C   H16  single  0.970  0.020  1.090
 Q07  C   H17  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
 Q07  C5   P   O1   103.12  3.000
 Q07  O1   P   O    113.66  3.000
 Q07  C5   P   O    105.56  3.000
 Q07  O    P   O2   112.46  3.000
 Q07  O1   P   O2   113.23  3.000
 Q07  C5   P   O2   107.88  3.000
 Q07  H3   C5  C3   107.01  3.000
 Q07  H3   C5  N    107.00  3.000
 Q07  C3   C5  N    115.15  3.000
 Q07  H3   C5  P    108.49  3.000
 Q07  C3   C5  P    113.21  3.000
 Q07  N    C5  P    105.68  3.000
 Q07  H5   N   H4   106.34  3.000
 Q07  H5   N   C5   111.18  3.000
 Q07  H4   N   C5   108.23  3.000
 Q07  H7   C3  C2   107.10  3.000
 Q07  H7   C3  C4   108.43  3.000
 Q07  C2   C3  C4   110.08  3.000
 Q07  H7   C3  C5   107.28  3.000
 Q07  C4   C3  C5   110.53  3.000
 Q07  C2   C3  C5   113.21  3.000
 Q07  H10  C4  H9   108.55  3.000
 Q07  H10  C4  H8   107.25  3.000
 Q07  H9   C4  H8   108.43  3.000
 Q07  H10  C4  C3   110.55  3.000
 Q07  H9   C4  C3   109.68  3.000
 Q07  H8   C4  C3   112.27  3.000
 Q07  H12  C2  H11  106.05  3.000
 Q07  H12  C2  C1   107.14  3.000
 Q07  H11  C2  C1   109.17  3.000
 Q07  H12  C2  C3   110.00  3.000
 Q07  H11  C2  C3   109.36  3.000
 Q07  C1   C2  C3   114.76  3.000
 Q07  H14  C1  H13  106.00  3.000
 Q07  H14  C1  C    109.06  3.000
 Q07  H13  C1  C    109.48  3.000
 Q07  H14  C1  C2   110.54  3.000
 Q07  H13  C1  C2   109.11  3.000
 Q07  C    C1  C2   112.44  3.000
 Q07  H17  C   H16  107.62  3.000
 Q07  H17  C   H15  107.50  3.000
 Q07  H16  C   H15  107.45  3.000
 Q07  H17  C   C1   111.68  3.000
 Q07  H16  C   C1   111.24  3.000
 Q07  H15  C   C1   111.15  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
 Q07  Var_01  C    C1  C2  C3  -173.23  30.0  3
 Q07  Var_02  H15  C   C1  C2   -59.67  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
 Q07  chir_01  C5  N   C3  P   negativ
 Q07  chir_02  C3  C2  C5  C4  negativ

