# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 19:29:43 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (2~{S})-2-azanyl-6,6-bis(fluoranyl)-5-oxidanylidene-6-phosphono-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)C(F)(F)[P](O)(O)=O)C(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
 DV9  DV9  "(2S)-2-azanyl-6,6-bis(fluoranyl)-5-oxidanylidene-6-phosphono-hexanoic acid"  L-peptide  23  16  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_DV9
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
 DV9  CA   C  CH1    0  -0.169   9.3731  -6.3428  -33.0403
 DV9  C    C  C      0   0.390   8.0926  -7.1908  -32.8415
 DV9  CB   C  CH2    0  -0.446   9.4213  -5.2244  -31.9842
 DV9  CG   C  CH2    0  -0.580   9.9436  -5.6709  -30.6285
 DV9  CD   C  C      0   0.270  11.4460  -5.7160  -30.5332
 DV9  C45  C  CT     0   0.395  12.0545  -6.4119  -29.3341
 DV9  F01  F  F      0  -0.376  13.0862  -5.6337  -28.8594
 DV9  F02  F  F      0  -0.373  11.1227  -6.4212  -28.3159
 DV9  N    N  NH2    0  -0.807   9.4054  -5.7251  -34.3592
 DV9  O    O  O      0  -0.610   8.1287  -8.0260  -31.9123
 DV9  OE1  O  O      0  -0.412  12.1795  -5.2351  -31.3680
 DV9  O14  O  OP    -1  -0.865  13.8905  -7.9461  -30.5804
 DV9  O15  O  O      0  -0.865  11.4272  -8.6976  -30.5390
 DV9  O16  O  OP    -1  -0.866  12.8505  -8.8200  -28.3911
 DV9  P01  P  P      0   1.111  12.6327  -8.1830  -29.7569
 DV9  H40  H  HCH1   0   0.180  10.2330  -7.0094  -32.8679
 DV9  H42  H  HCH2   0   0.221  10.0457  -4.4094  -32.3599
 DV9  H41  H  HCH2   0   0.223   8.4208  -4.7984  -31.8689
 DV9  H43  H  HCH2   0   0.261   9.6059  -4.9840  -29.8437
 DV9  H44  H  HCH2   0   0.266   9.5366  -6.6463  -30.3619
 DV9  H2   H  HNH2   0   0.327  10.3339  -5.3528  -34.5197
 DV9  H3   H  HNH2   0   0.328   9.2630  -6.4302  -35.0708
 DV9  OXT  O  OC    -1  -0.601   7.1250  -6.9644  -33.5925

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
 DV9  N    CA   single  1.458  0.019  1.458
 DV9  O    C    deloc   1.231  0.020  1.231
 DV9  CA   C    single  1.525  0.021  1.525
 DV9  CA   CB   single  1.530  0.020  1.530
 DV9  CB   CG   single  1.520  0.020  1.520
 DV9  OE1  CD   double  1.211  0.020  1.211
 DV9  CG   CD   single  1.506  0.020  1.506
 DV9  CD   C45  single  1.514  0.020  1.514
 DV9  O14  P01  deloc   1.522  0.020  1.522
 DV9  C45  F01  single  1.377  0.020  1.377
 DV9  C45  P01  single  1.910  0.020  1.910
 DV9  C45  F02  single  1.380  0.020  1.380
 DV9  P01  O15  deloc   1.526  0.020  1.526
 DV9  P01  O16  deloc   1.523  0.020  1.523
 DV9  CA   H40  single  0.970  0.020  1.090
 DV9  CB   H42  single  0.970  0.020  1.090
 DV9  CB   H41  single  0.970  0.020  1.090
 DV9  CG   H43  single  0.970  0.020  1.090
 DV9  CG   H44  single  0.970  0.020  1.090
 DV9  N    H2   single  0.890  0.020  1.040
 DV9  N    H3   single  0.890  0.020  1.040
 DV9  C    OXT  deloc   1.246  0.020  1.246

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
 DV9  H40  CA   N    112.39  3.000
 DV9  H40  CA   CB   107.94  3.000
 DV9  N    CA   CB   110.50  1.700
 DV9  H40  CA   C    107.10  3.000
 DV9  CB   CA   C    110.10  1.900
 DV9  N    CA   C    111.00  2.800
 DV9  OXT  C    O    126.30  3.000
 DV9  OXT  C    CA   117.74  3.000
 DV9  O    C    CA   120.80  1.700
 DV9  H41  CB   H42  105.57  3.000
 DV9  H41  CB   CG   109.56  3.000
 DV9  H42  CB   CG   109.22  3.000
 DV9  H41  CB   CA   109.08  3.000
 DV9  H42  CB   CA   108.89  3.000
 DV9  CG   CB   CA   114.17  3.000
 DV9  H44  CG   H43  105.70  3.000
 DV9  H44  CG   CD   109.28  3.000
 DV9  H43  CG   CD   106.31  3.000
 DV9  H44  CG   CB   110.65  3.000
 DV9  H43  CG   CB   110.41  3.000
 DV9  CD   CG   CB   114.08  3.000
 DV9  OE1  CD   C45  119.02  3.000
 DV9  C45  CD   CG   117.69  3.000
 DV9  OE1  CD   CG   123.29  3.000
 DV9  P01  C45  F02  111.19  3.000
 DV9  F02  C45  F01  104.79  3.000
 DV9  P01  C45  F01  111.93  3.000
 DV9  F02  C45  CD   108.42  3.000
 DV9  P01  C45  CD   111.87  3.000
 DV9  F01  C45  CD   108.32  3.000
 DV9  H3   N    H2   105.88  3.000
 DV9  H3   N    CA   109.76  3.000
 DV9  H2   N    CA   108.63  3.000
 DV9  O16  P01  O15  115.56  3.000
 DV9  O16  P01  O14  115.61  3.000
 DV9  O15  P01  O14  115.34  3.000
 DV9  O16  P01  C45  103.45  3.000
 DV9  O15  P01  C45  100.77  3.000
 DV9  O14  P01  C45  103.04  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
 DV9  Var_01  CD   CG   CB   CA     82.12  30.0  3
 DV9  Var_02  OE1  CD   CG   CB     11.70  30.0  3
 DV9  Var_03  C45  CD   CG   CB   -167.73  30.0  3
 DV9  Var_04  F01  C45  CD   CG   -136.16  30.0  3
 DV9  Var_05  P01  C45  CD   CG    100.00  30.0  3
 DV9  Var_06  F02  C45  CD   CG    -22.97  30.0  3
 DV9  Var_07  O14  P01  C45  CD     73.82  30.0  3
 DV9  Var_08  O15  P01  C45  CD    -45.60  30.0  3
 DV9  Var_09  O16  P01  C45  CD   -165.41  30.0  3
 DV9  Var_10  OE1  CD   C45  F01    44.38  30.0  1
 DV9  Var_11  O14  P01  C45  F01   -47.97  30.0  3
 DV9  Var_12  O15  P01  C45  F01  -167.39  30.0  3
 DV9  Var_13  O16  P01  C45  F01    72.80  30.0  3
 DV9  Var_14  OE1  CD   C45  F02   157.57  30.0  1
 DV9  Var_15  O14  P01  C45  F02  -164.80  30.0  3
 DV9  Var_16  O15  P01  C45  F02    75.78  30.0  3
 DV9  Var_17  O16  P01  C45  F02   -44.03  30.0  3
 DV9  Var_18  P01  C45  CD   OE1   -79.46  30.0  3
 DV9  Var_19  H43  CG   CB   CA   -158.25  30.0  3
 DV9  Var_20  H44  CG   CB   CA    -41.59  30.0  3
 DV9  Var_21  H42  CB   CG   CD    -40.04  30.0  1
 DV9  Var_22  H41  CB   CG   CD   -155.22  30.0  1
 DV9  Var_23  H43  CG   CD   C45    70.36  30.0  2
 DV9  Var_24  H44  CG   CD   C45   -43.29  30.0  2
 DV9  Var_25  H43  CG   CD   OE1  -110.21  30.0  2
 DV9  Var_26  H44  CG   CD   OE1   136.14  30.0  2

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
 DV9  chir_01  CA  N  C  CB  positiv

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
 DV9  plan-1  CG   0.020
 DV9  plan-1  CD   0.020
 DV9  plan-1  C45  0.020
 DV9  plan-1  OE1  0.020
 DV9  plan-2  CA   0.020
 DV9  plan-2  C    0.020
 DV9  plan-2  O    0.020
 DV9  plan-2  OXT  0.020

