# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 12:35:07 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-[(R)-hydroxy(oxido)-lambda~5~-phosphanyl]-N,N,N-trimethylpropan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCC[PH](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
 RTK  RTK  3-[(R)-hydroxy(oxido)-lambda~5~-phosphanyl]-N,N,N-trimethylpropan-1-aminium  ligand  26  10  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RTK
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
 RTK  O7    O  O      0  -0.818   2.7011  -1.4000  -0.0889
 RTK  P5    P  P      0   0.970   2.6532   0.1022  -0.2643
 RTK  O4    O  OP    -1  -0.816   3.7744   0.9608   0.2776
 RTK  C6    C  CH2    0  -0.718   1.0556   0.7307   0.3855
 RTK  C3    C  CH2    0  -0.474  -0.1460  -0.0241  -0.1730
 RTK  C2    C  CH2    0  -0.297  -1.4225   0.6035   0.3519
 RTK  N1    N  NT     1  -0.384  -2.7040  -0.0924  -0.0358
 RTK  C28   C  CH3    0  -0.547  -2.8038  -1.4193   0.6307
 RTK  C9    C  CH3    0  -0.544  -3.8381   0.7609   0.4182
 RTK  C8    C  CH3    0  -0.552  -2.7933  -0.2653  -1.5109
 RTK  H5    H  H      0  -0.061   2.4779   0.3897  -1.6602
 RTK  H61C  H  HCH2   0   0.251   1.0830   0.6500   1.4769
 RTK  H62C  H  HCH2   0   0.243   0.9821   1.7965   0.1502
 RTK  H31C  H  HCH2   0   0.249  -0.1219   0.0187  -1.2646
 RTK  H32C  H  HCH2   0   0.255  -0.0660  -1.0746   0.1108
 RTK  H21C  H  HCH2   0   0.294  -1.4170   0.6323   1.4418
 RTK  H22C  H  HCH2   0   0.297  -1.5165   1.6278  -0.0095
 RTK  H281  H  HCH3   0   0.293  -2.7355  -1.2810   1.7066
 RTK  H282  H  HCH3   0   0.295  -3.7589  -1.8712   0.3772
 RTK  H283  H  HCH3   0   0.294  -2.0003  -2.0642   0.2898
 RTK  H91C  H  HCH3   0   0.295  -3.7825   1.7215  -0.0868
 RTK  H92C  H  HCH3   0   0.293  -4.7757   0.2701   0.1723
 RTK  H93C  H  HCH3   0   0.294  -3.7675   0.9063   1.4928
 RTK  H81C  H  HCH3   0   0.295  -2.0519  -0.9850  -1.8430
 RTK  H82C  H  HCH3   0   0.297  -3.7857  -0.6308  -1.7595
 RTK  H83C  H  HCH3   0   0.295  -2.6210   0.6922  -1.9948

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
 RTK  O7   P5    deloc   1.513  0.020  1.513
 RTK  P5   O4    deloc   1.513  0.020  1.513
 RTK  P5   C6    single  1.836  0.020  1.836
 RTK  P5   H5    single  1.209  0.020  1.412
 RTK  C6   C3    single  1.525  0.020  1.525
 RTK  C3   C2    single  1.516  0.020  1.516
 RTK  C2   N1    single  1.509  0.020  1.509
 RTK  N1   C28   single  1.488  0.020  1.488
 RTK  N1   C9    single  1.490  0.020  1.490
 RTK  N1   C8    single  1.488  0.020  1.488
 RTK  C6   H61C  single  0.970  0.020  1.090
 RTK  C6   H62C  single  0.970  0.020  1.090
 RTK  C3   H31C  single  0.970  0.020  1.090
 RTK  C3   H32C  single  0.970  0.020  1.090
 RTK  C2   H21C  single  0.970  0.020  1.090
 RTK  C2   H22C  single  0.970  0.020  1.090
 RTK  C28  H281  single  0.970  0.020  1.090
 RTK  C28  H282  single  0.970  0.020  1.090
 RTK  C28  H283  single  0.970  0.020  1.090
 RTK  C9   H91C  single  0.970  0.020  1.090
 RTK  C9   H92C  single  0.970  0.020  1.090
 RTK  C9   H93C  single  0.970  0.020  1.090
 RTK  C8   H81C  single  0.970  0.020  1.090
 RTK  C8   H82C  single  0.970  0.020  1.090
 RTK  C8   H83C  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
 RTK  H5    P5   C6     99.75  3.000
 RTK  H5    P5   O4    108.97  3.000
 RTK  C6    P5   O4    108.90  3.000
 RTK  H5    P5   O7    108.38  3.000
 RTK  C6    P5   O7    109.05  3.000
 RTK  O4    P5   O7    119.90  3.000
 RTK  H62C  C6   H61C  106.73  3.000
 RTK  H62C  C6   C3    110.52  3.000
 RTK  H61C  C6   C3    110.39  3.000
 RTK  H62C  C6   P5    108.42  3.000
 RTK  H61C  C6   P5    107.81  3.000
 RTK  C3    C6   P5    112.75  3.000
 RTK  H32C  C3   H31C  107.21  3.000
 RTK  H32C  C3   C2    111.73  3.000
 RTK  H31C  C3   C2    110.38  3.000
 RTK  H32C  C3   C6    108.87  3.000
 RTK  H31C  C3   C6    109.21  3.000
 RTK  C2    C3   C6    109.37  3.000
 RTK  H22C  C2   H21C  107.88  3.000
 RTK  H22C  C2   N1    105.96  3.000
 RTK  H21C  C2   N1    105.86  3.000
 RTK  H22C  C2   C3    110.28  3.000
 RTK  H21C  C2   C3    110.66  3.000
 RTK  N1    C2   C3    115.80  3.000
 RTK  C8    N1   C9    108.84  3.000
 RTK  C8    N1   C28   109.65  3.000
 RTK  C9    N1   C28   108.85  3.000
 RTK  C8    N1   C2    111.06  3.000
 RTK  C9    N1   C2    107.70  3.000
 RTK  C28   N1   C2    110.68  3.000
 RTK  H283  C28  H282  109.29  3.000
 RTK  H283  C28  H281  109.88  3.000
 RTK  H282  C28  H281  109.82  3.000
 RTK  H283  C28  N1    109.84  3.000
 RTK  H282  C28  N1    108.98  3.000
 RTK  H281  C28  N1    109.00  3.000
 RTK  H93C  C9   H92C  109.89  3.000
 RTK  H93C  C9   H91C  109.76  3.000
 RTK  H92C  C9   H91C  109.78  3.000
 RTK  H93C  C9   N1    109.17  3.000
 RTK  H92C  C9   N1    109.22  3.000
 RTK  H91C  C9   N1    109.01  3.000
 RTK  H83C  C8   H82C  109.84  3.000
 RTK  H83C  C8   H81C  109.85  3.000
 RTK  H82C  C8   H81C  109.32  3.000
 RTK  H83C  C8   N1    109.25  3.000
 RTK  H82C  C8   N1    108.72  3.000
 RTK  H81C  C8   N1    109.85  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
 RTK  Var_01  C3    C6   P5  O7   -50.86  30.0  3
 RTK  Var_02  C2    C3   C6  P5  -176.92  30.0  3
 RTK  Var_03  N1    C2   C3  C6  -175.92  30.0  3
 RTK  Var_04  C28   N1   C2  C3    68.32  30.0  3
 RTK  Var_05  H281  C28  N1  C2    57.03  30.0  3
 RTK  Var_06  H91C  C9   N1  C2    61.43  30.0  3
 RTK  Var_07  H81C  C8   N1  C2    68.78  30.0  3

