# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 05:10:09 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (2~{S},3~{S})-3-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](NCc1c(O)c(C)ncc1CO[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
 7VO  7VO  '(2~{S},3~{S})-3-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic acid'  ligand  47  24  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7VO
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
 7VO  P    P  P     0   1.464   2.8552   2.2476   0.0052
 7VO  C5A  C  CH2   0  -0.217   1.3896   0.1555   0.4886
 7VO  C5   C  CR6   0  -0.067   1.2574  -1.3057   0.1726
 7VO  C6   C  CR16  0  -0.138   2.2876  -2.0414  -0.3816
 7VO  N1   N  N     0  -0.407   2.1896  -3.3422  -0.6481
 7VO  C2   C  CR6   0   0.139   1.0678  -3.9834  -0.3799
 7VO  C2A  C  CH3   0  -0.721   0.9906  -5.4468  -0.6898
 7VO  C3   C  CR6   0   0.255  -0.0348  -3.3153   0.1807
 7VO  C4   C  CR6   0   0.070   0.0527  -1.9594   0.4709
 7VO  C4A  C  CH2   0  -0.392  -1.1111  -1.1735   1.0228
 7VO  N    N  NH1   0  -0.581  -1.6459  -0.3139  -0.0153
 7VO  CA   C  CH1   0  -0.187  -2.5756   0.6949   0.4350
 7VO  CB   C  CH1   0  -0.231  -2.6810   1.8205  -0.6211
 7VO  C    C  C     0   0.535  -3.9349   0.1071   0.7888
 7VO  OXT  O  OH1   0  -0.584  -4.5831   0.8189   1.7003
 7VO  O    O  O     0  -0.441  -4.3812  -0.8985   0.2929
 7VO  O3P  O  OH1   0  -0.729   4.2060   2.2533  -0.8366
 7VO  O1P  O  O     0  -0.709   2.8786   2.8265   1.3607
 7VO  O2P  O  OH1   0  -0.741   1.7221   2.9662  -0.8625
 7VO  O4P  O  O2    0  -0.592   2.5846   0.6748  -0.0901
 7VO  O3   O  OH1   0  -0.621  -1.1325  -4.0670   0.3914
 7VO  CG2  C  CH3   0  -0.681  -3.2480   1.3282  -1.9492
 7VO  CG1  C  CH2   0  -0.419  -3.4180   3.0590  -0.1036
 7VO  CD1  C  CH3   0  -0.668  -3.1584   4.2995  -0.9500
 7VO  H1   H  HCH2  0   0.263   0.5164   0.6833   0.0966
 7VO  H2   H  HCH2  0   0.261   1.4093   0.3015   1.5739
 7VO  H3   H  HCR6  0   0.256   3.2346  -1.5787  -0.6281
 7VO  H4   H  HCH3  0   0.247   0.7393  -6.0336   0.1953
 7VO  H5   H  HCH3  0   0.248   0.2265  -5.6607  -1.4396
 7VO  H6   H  HCH3  0   0.247   1.9483  -5.7939  -1.0712
 7VO  H7   H  HCH2  0   0.226  -1.8642  -1.8241   1.4911
 7VO  H8   H  HCH2  0   0.271  -0.7564  -0.5440   1.8433
 7VO  H9   H  HNH1  0   0.359  -2.0486  -0.8742  -0.7558
 7VO  H11  H  HCH1  0   0.276  -2.1604   1.1497   1.3403
 7VO  H12  H  HCH1  0   0.235  -1.6364   2.1084  -0.7872
 7VO  H13  H  HOH1  0   0.480  -5.4564   0.4324   1.8687
 7VO  H14  H  HOH1  0   0.505   4.6596   3.1069  -0.8517
 7VO  H15  H  HOH1  0   0.497   1.6683   2.7021  -1.7907
 7VO  H16  H  HOH1  0   0.473  -1.8179  -3.5777   0.8586
 7VO  H17  H  HCH3  0   0.224  -4.2968   1.0380  -1.8638
 7VO  H18  H  HCH3  0   0.244  -3.1883   2.1108  -2.7048
 7VO  H19  H  HCH3  0   0.232  -2.6928   0.4749  -2.3399
 7VO  H20  H  HCH2  0   0.219  -4.4940   2.8712  -0.0606
 7VO  H21  H  HCH2  0   0.226  -3.0989   3.2630   0.9224
 7VO  H22  H  HCH3  0   0.218  -2.0932   4.5348  -0.9846
 7VO  H23  H  HCH3  0   0.223  -3.5020   4.1762  -1.9777
 7VO  H24  H  HCH3  0   0.232  -3.6749   5.1661  -0.5369

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
 7VO  CD1  CG1  single    1.524  0.020  1.524
 7VO  CG1  CB   single    1.531  0.020  1.531
 7VO  CG2  CB   single    1.526  0.020  1.526
 7VO  CB   CA   single    1.547  0.020  1.547
 7VO  N    CA   single    1.444  0.020  1.444
 7VO  N    C4A  single    1.450  0.020  1.450
 7VO  O1P  P    double    1.474  0.020  1.474
 7VO  C5A  C5   single    1.501  0.020  1.501
 7VO  C5A  O4P  single    1.426  0.020  1.426
 7VO  CA   C    single    1.523  0.020  1.523
 7VO  O2P  P    single    1.598  0.020  1.598
 7VO  C6   C5   aromatic  1.382  0.020  1.382
 7VO  C6   N1   aromatic  1.331  0.020  1.331
 7VO  C5   C4   aromatic  1.403  0.020  1.403
 7VO  C4   C4A  single    1.509  0.020  1.509
 7VO  C4   C3   aromatic  1.389  0.020  1.389
 7VO  N1   C2   aromatic  1.320  0.020  1.320
 7VO  C    O    double    1.207  0.020  1.207
 7VO  C    OXT  single    1.326  0.020  1.326
 7VO  P    O4P  single    1.599  0.020  1.599
 7VO  P    O3P  single    1.592  0.020  1.592
 7VO  C3   C2   aromatic  1.406  0.020  1.406
 7VO  C3   O3   single    1.347  0.020  1.347
 7VO  C2   C2A  single    1.498  0.020  1.498
 7VO  C5A  H1   single    0.970  0.020  1.090
 7VO  C5A  H2   single    0.970  0.020  1.090
 7VO  C6   H3   single    0.930  0.020  1.080
 7VO  C2A  H4   single    0.970  0.020  1.090
 7VO  C2A  H5   single    0.970  0.020  1.090
 7VO  C2A  H6   single    0.970  0.020  1.090
 7VO  C4A  H7   single    0.970  0.020  1.090
 7VO  C4A  H8   single    0.970  0.020  1.090
 7VO  N    H9   single    0.890  0.020  1.040
 7VO  CA   H11  single    0.970  0.020  1.090
 7VO  CB   H12  single    0.970  0.020  1.090
 7VO  OXT  H13  single    0.850  0.020  0.980
 7VO  O3P  H14  single    0.850  0.020  0.980
 7VO  O2P  H15  single    0.850  0.020  0.980
 7VO  O3   H16  single    0.850  0.020  0.980
 7VO  CG2  H17  single    0.970  0.020  1.090
 7VO  CG2  H18  single    0.970  0.020  1.090
 7VO  CG2  H19  single    0.970  0.020  1.090
 7VO  CG1  H20  single    0.970  0.020  1.090
 7VO  CG1  H21  single    0.970  0.020  1.090
 7VO  CD1  H22  single    0.970  0.020  1.090
 7VO  CD1  H23  single    0.970  0.020  1.090
 7VO  CD1  H24  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
 7VO  O4P  P    O2P  106.86  3.000
 7VO  O4P  P    O1P  116.35  3.000
 7VO  O2P  P    O1P  109.51  3.000
 7VO  O4P  P    O3P   96.64  3.000
 7VO  O2P  P    O3P  108.24  3.000
 7VO  O1P  P    O3P  118.13  3.000
 7VO  H2   C5A  H1   107.78  3.000
 7VO  H2   C5A  O4P  109.79  3.000
 7VO  H1   C5A  O4P  110.37  3.000
 7VO  H2   C5A  C5   109.88  3.000
 7VO  H1   C5A  C5   108.92  3.000
 7VO  O4P  C5A  C5   110.06  3.000
 7VO  C4   C5   C6   118.52  3.000
 7VO  C4   C5   C5A  118.98  3.000
 7VO  C6   C5   C5A  122.48  3.000
 7VO  H3   C6   N1   115.88  3.000
 7VO  H3   C6   C5   121.06  3.000
 7VO  N1   C6   C5   123.06  3.000
 7VO  C2   N1   C6   119.78  3.000
 7VO  C3   C2   C2A  120.42  3.000
 7VO  C2A  C2   N1   118.46  3.000
 7VO  C3   C2   N1   121.12  3.000
 7VO  H6   C2A  H5   108.23  3.000
 7VO  H6   C2A  H4   108.39  3.000
 7VO  H5   C2A  H4   106.89  3.000
 7VO  H6   C2A  C2   109.81  3.000
 7VO  H5   C2A  C2   111.69  3.000
 7VO  H4   C2A  C2   111.68  3.000
 7VO  O3   C3   C4   124.28  3.000
 7VO  O3   C3   C2   115.87  3.000
 7VO  C4   C3   C2   119.85  3.000
 7VO  C4A  C4   C3   122.42  3.000
 7VO  C3   C4   C5   117.68  3.000
 7VO  C4A  C4   C5   119.84  3.000
 7VO  H8   C4A  H7   104.08  3.000
 7VO  H8   C4A  N    108.39  3.000
 7VO  H7   C4A  N    113.76  3.000
 7VO  H8   C4A  C4   108.92  3.000
 7VO  H7   C4A  C4   112.07  3.000
 7VO  N    C4A  C4   109.35  3.000
 7VO  H9   N    CA   111.03  3.000
 7VO  H9   N    C4A  110.01  3.000
 7VO  CA   N    C4A  115.36  3.000
 7VO  H11  CA   C    107.87  3.000
 7VO  H11  CA   CB   106.74  3.000
 7VO  C    CA   CB   112.25  3.000
 7VO  H11  CA   N    107.69  3.000
 7VO  C    CA   N    112.18  3.000
 7VO  CB   CA   N    109.83  3.000
 7VO  H12  CB   CG1  107.30  3.000
 7VO  H12  CB   CG2  107.88  3.000
 7VO  CG1  CB   CG2  112.11  3.000
 7VO  H12  CB   CA   103.27  3.000
 7VO  CG2  CB   CA   112.63  3.000
 7VO  CG1  CB   CA   112.98  3.000
 7VO  O    C    OXT  123.30  3.000
 7VO  OXT  C    CA   112.89  3.000
 7VO  O    C    CA   123.81  3.000
 7VO  H13  OXT  C    110.23  3.000
 7VO  H14  O3P  P    114.18  3.000
 7VO  H15  O2P  P    115.98  3.000
 7VO  C5A  O4P  P    118.43  3.000
 7VO  H16  O3   C3   111.86  3.000
 7VO  H19  CG2  H18  106.60  3.000
 7VO  H19  CG2  H17  108.01  3.000
 7VO  H18  CG2  H17  107.33  3.000
 7VO  H19  CG2  CB   112.04  3.000
 7VO  H18  CG2  CB   110.59  3.000
 7VO  H17  CG2  CB   112.01  3.000
 7VO  H21  CG1  H20  106.40  3.000
 7VO  H21  CG1  CD1  108.64  3.000
 7VO  H20  CG1  CD1  109.23  3.000
 7VO  H21  CG1  CB   109.12  3.000
 7VO  H20  CG1  CB   110.37  3.000
 7VO  CD1  CG1  CB   112.87  3.000
 7VO  H24  CD1  H23  107.32  3.000
 7VO  H24  CD1  H22  107.64  3.000
 7VO  H23  CD1  H22  107.58  3.000
 7VO  H24  CD1  CG1  110.85  3.000
 7VO  H23  CD1  CG1  112.19  3.000
 7VO  H22  CD1  CG1  111.06  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
 7VO  CONST_01  C2   N1   C6   C5      0.00   0.0  0
 7VO  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 7VO  CONST_03  C3   C4   C5   C6      0.00   0.0  0
 7VO  CONST_04  C3   C2   N1   C6      0.00   0.0  0
 7VO  CONST_05  C4   C5   C6   N1      0.00   0.0  0
 7VO  CONST_06  C4   C3   C2   N1      0.00   0.0  0
 7VO  CONST_07  N1   C6   C5   C5A   180.00   0.0  0
 7VO  CONST_08  C3   C4   C5   C5A   180.00   0.0  0
 7VO  CONST_09  O3   C3   C4   C5    180.00   0.0  0
 7VO  CONST_10  C4A  C4   C5   C6    180.00   0.0  0
 7VO  CONST_11  C2A  C2   N1   C6    180.00   0.0  0
 7VO  CONST_12  O3   C3   C2   N1    180.00   0.0  0
 7VO  CONST_13  C4A  C4   C3   C2    180.00   0.0  0
 7VO  CONST_14  C4   C3   C2   C2A   180.00   0.0  0
 7VO  CONST_15  H3   C6   N1   C2    180.00   0.0  0
 7VO  CONST_16  H13  OXT  C    CA    180.00   0.0  0
 7VO  Var_01    N    C4A  C4   C5     70.25  30.0  2
 7VO  Var_02    O4P  C5A  C5   C6     10.94  30.0  1
 7VO  Var_03    H4   C2A  C2   N1    123.07  30.0  2
 7VO  Var_04    C5   C5A  O4P  P     174.29  30.0  1
 7VO  Var_05    CA   N    C4A  C4   -167.60  30.0  1
 7VO  Var_06    O1P  P    O4P  C5A    57.09  30.0  1
 7VO  Var_07    H22  CD1  CG1  CB    -58.78  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
 7VO  chir_01  CA  CB  N    C    positiv
 7VO  chir_02  CB  CA  CG2  CG1  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
 7VO  plan-1  C5A  0.020
 7VO  plan-1  C5   0.020
 7VO  plan-1  C6   0.020
 7VO  plan-1  N1   0.020
 7VO  plan-1  C2   0.020
 7VO  plan-1  C2A  0.020
 7VO  plan-1  C3   0.020
 7VO  plan-1  C4   0.020
 7VO  plan-1  C4A  0.020
 7VO  plan-1  O3   0.020
 7VO  plan-1  H3   0.020
 7VO  plan-2  CA   0.020
 7VO  plan-2  C    0.020
 7VO  plan-2  OXT  0.020
 7VO  plan-2  O    0.020
 7VO  plan-2  H13  0.020

