# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:52:15 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (4S,7S)-4,7-dihydroxy-10-oxo-3,5,9-trioxa-4-phosphaundecan-1-aminium 4-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)OC[C@H](O)CO[P@](O)(=O)OCC[NH3+]
#
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
 LSP  LSP  '(4S,7S)-4,7-dihydroxy-10-oxo-3,5,9-trioxa-4-phosphaundecan-1-aminium 4-oxide'  ligand  32  16  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LSP
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
 LSP  N     N  NT3    1  -0.772  -5.0031  -1.8796   0.8111
 LSP  C12   C  CH2    0  -0.345  -5.2815  -0.8007  -0.1724
 LSP  C11   C  CH2    0  -0.166  -4.4634   0.4295   0.1301
 LSP  P     P  P      0   1.340  -2.0085   1.3076  -0.0682
 LSP  O12   O  O      0  -0.793  -2.1840   2.2729   1.0622
 LSP  O14   O  OP    -1  -0.786  -1.9905   1.8027  -1.4801
 LSP  O11   O  O2     0  -0.611  -0.7299   0.3195   0.2066
 LSP  O13   O  O2     0  -0.620  -3.0986   0.0770   0.0740
 LSP  C1    C  CH2    0  -0.160   0.5531   0.9071   0.1676
 LSP  C2    C  CH1    0  -0.059   1.6002  -0.1925   0.0887
 LSP  O21   O  OH1    0  -0.653   1.4411  -1.0071  -1.0450
 LSP  C3    C  CH2    0  -0.183   2.9803   0.4402   0.1556
 LSP  O31   O  O2     0  -0.450   3.9401  -0.6143   0.1716
 LSP  C31   C  C      0   0.568   5.2269  -0.2825   0.1791
 LSP  O32   O  O      0  -0.456   5.6157   0.8591   0.1676
 LSP  C32   C  CH3    0  -0.770   6.1104  -1.4927   0.2326
 LSP  HN1   H  HNT3   0   0.468  -4.0098  -2.1103   0.8453
 LSP  HN2   H  HNT3   0   0.471  -5.2882  -1.6196   1.7552
 LSP  HN3   H  HNT3   0   0.480  -5.5017  -2.7362   0.5737
 LSP  H121  H  HCH2   0   0.303  -6.3438  -0.5771  -0.1163
 LSP  H122  H  HCH2   0   0.299  -5.0532  -1.1999  -1.1578
 LSP  H111  H  HCH2   0   0.239  -4.7296   0.8282   1.1147
 LSP  H112  H  HCH2   0   0.247  -4.7316   1.1867  -0.6138
 LSP  H11   H  HCH2   0   0.221   0.7297   1.5155   1.0616
 LSP  H12   H  HCH2   0   0.213   0.6591   1.5713  -0.7004
 LSP  H2    H  HCH1   0   0.244   1.4769  -0.8539   0.9526
 LSP  H21   H  HOH1   0   0.446   1.4856  -0.4557  -1.8342
 LSP  H31   H  HCH2   0   0.243   3.0728   1.0509   1.0577
 LSP  H32   H  HCH2   0   0.238   3.1463   1.0931  -0.7074
 LSP  H321  H  HCH3   0   0.278   6.1256  -1.8847   1.2514
 LSP  H322  H  HCH3   0   0.267   5.7453  -2.2874  -0.4159
 LSP  H323  H  HCH3   0   0.263   7.1272  -1.2314  -0.0475

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
 LSP  N    C12   single  1.486  0.020  1.486
 LSP  N    HN1   single  0.890  0.020  1.040
 LSP  N    HN2   single  0.890  0.020  1.040
 LSP  N    HN3   single  0.890  0.020  1.040
 LSP  C12  C11   single  1.508  0.020  1.508
 LSP  C12  H121  single  0.970  0.020  1.090
 LSP  C12  H122  single  0.970  0.020  1.090
 LSP  C11  O13   single  1.411  0.020  1.411
 LSP  C11  H111  single  0.970  0.020  1.090
 LSP  C11  H112  single  0.970  0.020  1.090
 LSP  P    O12   deloc   1.497  0.020  1.497
 LSP  P    O14   deloc   1.496  0.020  1.496
 LSP  P    O11   single  1.639  0.020  1.639
 LSP  P    O13   single  1.650  0.020  1.650
 LSP  O11  C1    single  1.412  0.020  1.412
 LSP  C1   C2    single  1.520  0.020  1.520
 LSP  C1   H11   single  0.970  0.020  1.090
 LSP  C1   H12   single  0.970  0.020  1.090
 LSP  C2   O21   single  1.405  0.020  1.405
 LSP  C2   C3    single  1.520  0.020  1.520
 LSP  C2   H2    single  0.970  0.020  1.090
 LSP  O21  H21   single  0.850  0.020  0.980
 LSP  C3   O31   single  1.426  0.020  1.426
 LSP  C3   H31   single  0.970  0.020  1.090
 LSP  C3   H32   single  0.970  0.020  1.090
 LSP  O31  C31   single  1.329  0.020  1.329
 LSP  C31  O32   double  1.206  0.020  1.206
 LSP  C31  C32   single  1.499  0.020  1.499
 LSP  C32  H321  single  0.970  0.020  1.090
 LSP  C32  H322  single  0.970  0.020  1.090
 LSP  C32  H323  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
 LSP  HN3   N    HN2   107.05  3.000
 LSP  HN3   N    HN1   107.10  3.000
 LSP  HN2   N    HN1   107.39  3.000
 LSP  HN3   N    C12   111.36  3.000
 LSP  HN2   N    C12   112.03  3.000
 LSP  HN1   N    C12   111.63  3.000
 LSP  H122  C12  H121  109.12  3.000
 LSP  H122  C12  C11   111.55  3.000
 LSP  H121  C12  C11   110.61  3.000
 LSP  H122  C12  N     107.09  3.000
 LSP  H121  C12  N     107.35  3.000
 LSP  C11   C12  N     110.97  3.000
 LSP  H112  C11  H111  107.44  3.000
 LSP  H112  C11  O13   112.51  3.000
 LSP  H111  C11  O13   111.21  3.000
 LSP  H112  C11  C12   107.16  3.000
 LSP  H111  C11  C12   110.21  3.000
 LSP  O13   C11  C12   108.24  3.000
 LSP  O13   P    O11    92.94  3.000
 LSP  O13   P    O14   109.64  3.000
 LSP  O11   P    O14   110.38  3.000
 LSP  O13   P    O12   109.78  3.000
 LSP  O11   P    O12   110.71  3.000
 LSP  O14   P    O12   120.04  3.000
 LSP  C1    O11  P     116.96  3.000
 LSP  P     O13  C11   117.14  3.000
 LSP  H12   C1   H11   107.07  3.000
 LSP  H12   C1   C2    109.27  3.000
 LSP  H11   C1   C2    109.45  3.000
 LSP  H12   C1   O11   111.18  3.000
 LSP  H11   C1   O11   110.80  3.000
 LSP  C2    C1   O11   109.04  3.000
 LSP  H2    C2   C3    108.60  3.000
 LSP  H2    C2   O21   105.88  3.000
 LSP  C3    C2   O21   112.32  3.000
 LSP  H2    C2   C1    108.57  3.000
 LSP  C3    C2   C1    108.79  3.000
 LSP  O21   C2   C1    112.53  3.000
 LSP  H21   O21  C2    108.89  3.000
 LSP  H32   C3   H31   107.73  3.000
 LSP  H32   C3   O31   110.35  3.000
 LSP  H31   C3   O31   110.30  3.000
 LSP  H32   C3   C2    110.56  3.000
 LSP  H31   C3   C2    110.23  3.000
 LSP  O31   C3   C2    107.69  3.000
 LSP  C31   O31  C3    117.85  3.000
 LSP  C32   C31  O32   125.06  3.000
 LSP  C32   C31  O31   111.67  3.000
 LSP  O32   C31  O31   123.26  3.000
 LSP  H323  C32  H322  109.62  3.000
 LSP  H323  C32  H321  108.29  3.000
 LSP  H322  C32  H321  107.36  3.000
 LSP  H323  C32  C31   110.37  3.000
 LSP  H322  C32  C31   111.74  3.000
 LSP  H321  C32  C31   109.35  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
 LSP  Var_01  O13   C11  C12  N      59.63  30.0  3
 LSP  Var_02  O12   P    O13  C11    56.76  30.0  1
 LSP  Var_03  C2    C1   O11  P    -165.73  30.0  3
 LSP  Var_04  O32   C31  O31  C3     -0.30  30.0  3
 LSP  Var_05  HN1   N    C12  C11   -56.25  30.0  3
 LSP  Var_06  H321  C32  C31  O31   -77.27  30.0  3
 LSP  Var_07  H31   C3   O31  C31   -62.10  30.0  1

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
 LSP  chir_02  C2  C1  O21  C3  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
 LSP  plan-1  O31  0.020
 LSP  plan-1  C31  0.020
 LSP  plan-1  O32  0.020
 LSP  plan-1  C32  0.020

