# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 01:12:56 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(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
 PAZ  PAZ  N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanine  ligand  37  19  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PAZ
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
 PAZ  O8    O  OH1   0  -0.743   4.8831  -0.0733  -1.1037
 PAZ  P1    P  P     0   1.453   3.9815  -1.1624  -0.3555
 PAZ  O6    O  O     0  -0.711   3.5006  -2.1546  -1.3345
 PAZ  O7    O  OH1   0  -0.732   4.8034  -1.6929   0.9029
 PAZ  O2    O  O2    0  -0.588   2.8744  -0.3643   0.4657
 PAZ  C2    C  CH2   0  -0.151   1.8270   0.3191  -0.2375
 PAZ  C1    C  CT    0  -0.165   1.0450   1.1708   0.7616
 PAZ  C4    C  CH3   0  -0.668   0.3835   0.2799   1.8147
 PAZ  C3    C  CH3   0  -0.649   1.9800   2.1633   1.4584
 PAZ  C5    C  CH1   0  -0.032  -0.0382   1.9927   0.0083
 PAZ  O5'   O  OH1   0  -0.660   0.5046   2.8395  -0.9696
 PAZ  C6    C  C     0   0.522  -1.1150   1.1215  -0.6396
 PAZ  O6'   O  O     0  -0.496  -0.9438   0.6576  -1.7615
 PAZ  N     N  NH1   0  -0.639  -2.2234   0.9179   0.0745
 PAZ  C8    C  CH2   0  -0.238  -3.3187   0.0954  -0.3992
 PAZ  C9    C  CH2   0  -0.632  -4.3722  -0.0096   0.6880
 PAZ  C     C  C     0   0.559  -5.5502  -0.8418   0.2645
 PAZ  O     O  O     0  -0.441  -5.6542  -1.3996  -0.7988
 PAZ  OXT   O  OH1   0  -0.592  -6.4776  -0.8948   1.2122
 PAZ  HO8   H  HOH1  0   0.494   5.3080   0.5870  -0.5405
 PAZ  HO7   H  HOH1  0   0.504   5.4913  -2.3353   0.6825
 PAZ  H2    H  HCH2  0   0.238   2.2627   0.9532  -1.0146
 PAZ  H2A   H  HCH2  0   0.252   1.1806  -0.4188  -0.7168
 PAZ  H4    H  HCH3  0   0.248   1.1355  -0.2091   2.4329
 PAZ  H4A   H  HCH3  0   0.236  -0.2480   0.8669   2.4846
 PAZ  H4B   H  HCH3  0   0.236  -0.2357  -0.5019   1.3725
 PAZ  H3    H  HCH3  0   0.236   2.5249   2.7828   0.7463
 PAZ  H3A   H  HCH3  0   0.231   1.4113   2.8265   2.1136
 PAZ  H3B   H  HCH3  0   0.240   2.7099   1.6453   2.0798
 PAZ  H5    H  HCH1  0   0.257  -0.5104   2.6359   0.7597
 PAZ  HO5'  H  HOH1  0   0.447   0.5205   2.3601  -1.8074
 PAZ  HN    H  HNH1  0   0.409  -2.3280   1.3983   0.9540
 PAZ  H8    H  HCH2  0   0.252  -3.7481   0.5312  -1.3040
 PAZ  H8A   H  HCH2  0   0.253  -2.9446  -0.8953  -0.6618
 PAZ  H9    H  HCH2  0   0.296  -3.9491  -0.4515   1.5956
 PAZ  H9A   H  HCH2  0   0.295  -4.7344   0.9828   0.9735
 PAZ  HOXT  H  HOH1  0   0.482  -7.2245  -1.4370   0.9171

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
 PAZ  O8   P1    single  1.600  0.020  1.600
 PAZ  O8   HO8   single  0.850  0.020  0.980
 PAZ  O6   P1    double  1.475  0.020  1.475
 PAZ  P1   O7    single  1.594  0.020  1.594
 PAZ  P1   O2    single  1.593  0.020  1.593
 PAZ  O7   HO7   single  0.850  0.020  0.980
 PAZ  O2   C2    single  1.435  0.020  1.435
 PAZ  C2   C1    single  1.528  0.020  1.528
 PAZ  C2   H2    single  0.970  0.020  1.090
 PAZ  C2   H2A   single  0.970  0.020  1.090
 PAZ  C4   C1    single  1.530  0.020  1.530
 PAZ  C1   C5    single  1.554  0.020  1.554
 PAZ  C1   C3    single  1.531  0.020  1.531
 PAZ  C4   H4    single  0.970  0.020  1.090
 PAZ  C4   H4A   single  0.970  0.020  1.090
 PAZ  C4   H4B   single  0.970  0.020  1.090
 PAZ  C3   H3    single  0.970  0.020  1.090
 PAZ  C3   H3A   single  0.970  0.020  1.090
 PAZ  C3   H3B   single  0.970  0.020  1.090
 PAZ  C5   C6    single  1.529  0.020  1.529
 PAZ  C5   O5'   single  1.403  0.020  1.403
 PAZ  C5   H5    single  0.970  0.020  1.090
 PAZ  O5'  HO5'  single  0.850  0.020  0.980
 PAZ  O6'  C6    double  1.226  0.020  1.226
 PAZ  C6   N     single  1.334  0.020  1.334
 PAZ  N    C8    single  1.449  0.020  1.449
 PAZ  N    HN    single  0.860  0.020  1.020
 PAZ  C8   C9    single  1.518  0.020  1.518
 PAZ  C8   H8    single  0.970  0.020  1.090
 PAZ  C8   H8A   single  0.970  0.020  1.090
 PAZ  C9   C     single  1.503  0.020  1.503
 PAZ  C9   H9    single  0.970  0.020  1.090
 PAZ  C9   H9A   single  0.970  0.020  1.090
 PAZ  O    C     double  1.205  0.020  1.205
 PAZ  C    OXT   single  1.327  0.020  1.327
 PAZ  OXT  HOXT  single  0.850  0.020  0.980

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
 PAZ  HO8   O8   P1   116.14  3.000
 PAZ  O2    P1   O7    96.79  3.000
 PAZ  O2    P1   O6   116.92  3.000
 PAZ  O7    P1   O6   117.93  3.000
 PAZ  O2    P1   O8   106.96  3.000
 PAZ  O7    P1   O8   107.77  3.000
 PAZ  O6    P1   O8   109.35  3.000
 PAZ  HO7   O7   P1   114.09  3.000
 PAZ  C2    O2   P1   119.56  3.000
 PAZ  H2A   C2   H2   108.41  3.000
 PAZ  H2A   C2   C1   111.15  3.000
 PAZ  H2    C2   C1   110.20  3.000
 PAZ  H2A   C2   O2   108.99  3.000
 PAZ  H2    C2   O2   109.49  3.000
 PAZ  C1    C2   O2   108.58  3.000
 PAZ  C5    C1   C3   107.66  3.000
 PAZ  C3    C1   C4   109.16  3.000
 PAZ  C5    C1   C4   109.89  3.000
 PAZ  C3    C1   C2   110.26  3.000
 PAZ  C5    C1   C2   109.54  3.000
 PAZ  C4    C1   C2   110.29  3.000
 PAZ  H4B   C4   H4A  107.80  3.000
 PAZ  H4B   C4   H4   107.47  3.000
 PAZ  H4A   C4   H4   107.01  3.000
 PAZ  H4B   C4   C1   112.56  3.000
 PAZ  H4A   C4   C1   111.06  3.000
 PAZ  H4    C4   C1   110.71  3.000
 PAZ  H3B   C3   H3A  107.19  3.000
 PAZ  H3B   C3   H3   107.93  3.000
 PAZ  H3A   C3   H3   107.89  3.000
 PAZ  H3B   C3   C1   111.13  3.000
 PAZ  H3A   C3   C1   110.40  3.000
 PAZ  H3    C3   C1   112.11  3.000
 PAZ  H5    C5   C6   108.75  3.000
 PAZ  H5    C5   O5'  106.87  3.000
 PAZ  C6    C5   O5'  108.72  3.000
 PAZ  H5    C5   C1   106.16  3.000
 PAZ  O5'   C5   C1   112.79  3.000
 PAZ  C6    C5   C1   113.25  3.000
 PAZ  HO5'  O5'  C5   108.15  3.000
 PAZ  N     C6   O6'  123.23  3.000
 PAZ  N     C6   C5   116.44  3.000
 PAZ  O6'   C6   C5   120.33  3.000
 PAZ  HN    N    C8   118.52  3.000
 PAZ  HN    N    C6   118.73  3.000
 PAZ  C8    N    C6   122.65  3.000
 PAZ  H8A   C8   H8   107.32  3.000
 PAZ  H8A   C8   C9   110.34  3.000
 PAZ  H8    C8   C9   110.38  3.000
 PAZ  H8A   C8   N    109.56  3.000
 PAZ  H8    C8   N    109.97  3.000
 PAZ  C9    C8   N    109.25  3.000
 PAZ  H9A   C9   H9   106.13  3.000
 PAZ  H9A   C9   C    108.44  3.000
 PAZ  H9    C9   C    108.25  3.000
 PAZ  H9A   C9   C8   110.72  3.000
 PAZ  H9    C9   C8   110.71  3.000
 PAZ  C     C9   C8   112.36  3.000
 PAZ  OXT   C    O    123.45  3.000
 PAZ  OXT   C    C9   111.62  3.000
 PAZ  O     C    C9   124.92  3.000
 PAZ  HOXT  OXT  C    110.09  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
 PAZ  CONST_01  C8    N    C6  C5    180.00   0.0  0
 PAZ  CONST_02  C8    N    C6  O6'     0.00   0.0  0
 PAZ  CONST_03  HN    N    C6  C5      0.00   0.0  0
 PAZ  CONST_04  HOXT  OXT  C   C9    180.00   0.0  0
 PAZ  Var_01    C1    C2   O2  P1   -171.23  30.0  3
 PAZ  Var_02    C4    C1   C2  O2    -62.56  30.0  3
 PAZ  Var_03    C9    C8   N   C6    175.93  30.0  3
 PAZ  Var_04    C     C9   C8  N     179.53  30.0  3
 PAZ  Var_05    O     C    C9  C8      1.75  30.0  3
 PAZ  Var_06    H4    C4   C1  C2     66.12  30.0  3
 PAZ  Var_07    H3    C3   C1  C2     55.16  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
 PAZ  chir_01  C5  C1  C6  O5'  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
 PAZ  plan-1  C5    0.020
 PAZ  plan-1  C6    0.020
 PAZ  plan-1  O6'   0.020
 PAZ  plan-1  N     0.020
 PAZ  plan-1  C8    0.020
 PAZ  plan-1  HN    0.020
 PAZ  plan-2  C9    0.020
 PAZ  plan-2  C     0.020
 PAZ  plan-2  O     0.020
 PAZ  plan-2  OXT   0.020
 PAZ  plan-2  HOXT  0.020

