# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 17:06:41 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (2R)-2-hydroxy-4,5-dioxoheptyl hydrogen (R)-phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)C(=O)C[C@@H](O)CO[P@@H](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
 LI5  LI5  '(2R)-2-hydroxy-4,5-dioxoheptyl hydrogen (R)-phosphonate'  ligand  27  14  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LI5
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
 LI5  O2P   O  OH1   0  -0.746  -3.2462   -7.3180   3.4489
 LI5  P     P  P     0   1.155  -1.7535   -7.9020   3.4531
 LI5  O1P   O  O     0  -0.704  -1.4007   -8.8348   4.5452
 LI5  O3P   O  O2    0  -0.586  -1.5161   -8.5934   2.0261
 LI5  C1    C  CH2   0  -0.211  -1.7023   -7.8548   0.8168
 LI5  C2    C  CH1   0   0.025  -0.8056   -8.4274  -0.2663
 LI5  O2    O  OH1   0  -0.666  -1.1154   -9.7691  -0.5561
 LI5  C3    C  CH2   0  -0.616   0.6574   -8.3795   0.1369
 LI5  C4    C  C     0   0.336   1.6072   -8.6543  -0.9919
 LI5  O30   O  O     0  -0.355   1.2814   -8.7482  -2.1458
 LI5  C30   C  C     0   0.343   3.1163   -8.7755  -0.6588
 LI5  O5    O  O     0  -0.360   3.8988   -8.5793  -1.5521
 LI5  C31   C  CH2   0  -0.592   3.5122   -9.1421   0.7381
 LI5  C32   C  CH3   0  -0.660   5.0088   -9.2844   0.9422
 LI5  H2P   H  HOH1  0   0.497  -3.9414   -7.9797   3.5729
 LI5  H11   H  HCH2  0   0.239  -1.4585   -6.7955   0.9553
 LI5  H12   H  HCH2  0   0.261  -2.7499   -7.9165   0.5096
 LI5  H2    H  HCH1  0   0.236  -0.9548   -7.7816  -1.1418
 LI5  HO2   H  HOH1  0   0.457  -1.9532   -9.7962  -1.0286
 LI5  H31   H  HCH2  0   0.292   0.8537   -9.0786   0.9546
 LI5  H32   H  HCH2  0   0.302   0.9135   -7.3896   0.5343
 LI5  H311  H  HCH2  0   0.282   3.0959   -8.3888   1.4159
 LI5  H312  H  HCH2  0   0.283   2.9906  -10.0695   1.0009
 LI5  H321  H  HCH3  0   0.243   5.2192   -9.5403   1.9794
 LI5  H322  H  HCH3  0   0.234   5.5341   -8.3580   0.7137
 LI5  H323  H  HCH3  0   0.235   5.4253  -10.0712   0.3142
 LI5  HP1   H  H     0   0.076  -1.0453   -6.6962   3.3906

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
 LI5  O2P  P     single  1.603  0.020  1.603
 LI5  O2P  H2P   single  0.832  0.020  0.971
 LI5  P    O1P   double  1.479  0.020  1.479
 LI5  P    O3P   single  1.603  0.020  1.603
 LI5  O3P  C1    single  1.429  0.020  1.429
 LI5  C1   C2    single  1.518  0.020  1.518
 LI5  C1   H11   single  0.939  0.020  1.096
 LI5  C1   H12   single  0.939  0.020  1.096
 LI5  C2   O2    single  1.407  0.020  1.407
 LI5  C2   C3    single  1.518  0.020  1.518
 LI5  C2   H2    single  0.939  0.020  1.096
 LI5  O2   HO2   single  0.832  0.020  0.971
 LI5  C3   C4    single  1.501  0.020  1.501
 LI5  C3   H31   single  0.939  0.020  1.096
 LI5  C3   H32   single  0.939  0.020  1.096
 LI5  C4   O30   double  1.203  0.020  1.203
 LI5  C4   C30   single  1.550  0.020  1.550
 LI5  C30  O5    double  1.204  0.020  1.204
 LI5  C30  C31   single  1.497  0.020  1.497
 LI5  C31  C32   single  1.517  0.020  1.517
 LI5  C31  H311  single  0.939  0.020  1.096
 LI5  C31  H312  single  0.939  0.020  1.096
 LI5  C32  H321  single  0.939  0.020  1.096
 LI5  C32  H322  single  0.939  0.020  1.096
 LI5  C32  H323  single  0.939  0.020  1.096
 LI5  HP1  P     single  1.209  0.020  1.412

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
 LI5  H2P   O2P  P     114.81  3.000
 LI5  HP1   P    O3P   104.88  3.000
 LI5  HP1   P    O1P   117.11  3.000
 LI5  O3P   P    O1P   110.48  3.000
 LI5  HP1   P    O2P    99.05  3.000
 LI5  O3P   P    O2P   107.02  3.000
 LI5  O1P   P    O2P   116.99  3.000
 LI5  C1    O3P  P     120.73  3.000
 LI5  H12   C1   H11   107.65  3.000
 LI5  H12   C1   C2    110.14  3.000
 LI5  H11   C1   C2    108.87  3.000
 LI5  H12   C1   O3P   109.47  3.000
 LI5  H11   C1   O3P   111.32  3.000
 LI5  C2    C1   O3P   109.38  3.000
 LI5  H2    C2   C3    108.91  3.000
 LI5  H2    C2   O2    111.51  3.000
 LI5  C3    C2   O2    107.27  3.000
 LI5  H2    C2   C1    105.47  3.000
 LI5  C3    C2   C1    111.58  3.000
 LI5  O2    C2   C1    112.12  3.000
 LI5  HO2   O2   C2    108.65  3.000
 LI5  H32   C3   H31   105.31  3.000
 LI5  H32   C3   C4    106.85  3.000
 LI5  H31   C3   C4    109.38  3.000
 LI5  H32   C3   C2    110.47  3.000
 LI5  H31   C3   C2    110.57  3.000
 LI5  C4    C3   C2    113.85  3.000
 LI5  C30   C4   O30   117.63  3.000
 LI5  C30   C4   C3    117.96  3.000
 LI5  O30   C4   C3    124.37  3.000
 LI5  C31   C30  O5    124.08  3.000
 LI5  C31   C30  C4    118.49  3.000
 LI5  O5    C30  C4    117.43  3.000
 LI5  H312  C31  H311  104.63  3.000
 LI5  H312  C31  C32   110.97  3.000
 LI5  H311  C31  C32   110.87  3.000
 LI5  H312  C31  C30   107.76  3.000
 LI5  H311  C31  C30   107.96  3.000
 LI5  C32   C31  C30   114.16  3.000
 LI5  H323  C32  H322  107.99  3.000
 LI5  H323  C32  H321  107.80  3.000
 LI5  H322  C32  H321  107.86  3.000
 LI5  H323  C32  C31   111.55  3.000
 LI5  H322  C32  C31   111.57  3.000
 LI5  H321  C32  C31   109.92  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
 LI5  Var_01  C2    C1   O3P  P     151.92  30.0  3
 LI5  Var_02  O30   C4   C3   C2      8.53  30.0  3
 LI5  Var_03  O5    C30  C4   C3   -157.43  30.0  2
 LI5  Var_04  C32   C31  C30  C4    177.82  30.0  3
 LI5  Var_05  HP1   P    O3P  C1    -48.71  30.0  1
 LI5  Var_06  H321  C32  C31  C30   179.39  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
 LI5  chir_02  C2  C1   O2   C3   positiv
 LI5  chir_03  P   O2P  O1P  O3P  both

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
 LI5  plan-1  C3   0.020
 LI5  plan-1  C4   0.020
 LI5  plan-1  O30  0.020
 LI5  plan-1  C30  0.020
 LI5  plan-2  C4   0.020
 LI5  plan-2  C30  0.020
 LI5  plan-2  O5   0.020
 LI5  plan-2  C31  0.020

