# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 06:39:39 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2S)-2-azanyl-4-[(Z)-[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=NCC[C@H](N)C(O)=O)c1O
#
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
 Z98  Z98  '(2S)-2-azanyl-4-[(Z)-[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid'  ligand  41  23  .  2021-08-26  2021-08-26  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Z98
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
 Z98  C     C  C     0   0.524  -3.3838   3.1224   0.5742
 Z98  N     N  NH2   0  -0.776  -4.8930   1.2385  -0.0118
 Z98  OXT   O  OH1   0  -0.591  -2.2423   3.4015   1.1920
 Z98  P     P  P     0   1.466   3.3290   1.7510   0.0515
 Z98  N1    N  N     0  -0.403   0.8551  -3.0825   1.6215
 Z98  C2    C  CR6   0   0.131  -0.1329  -3.6714   0.9685
 Z98  C3    C  CR6   0   0.285  -0.6626  -3.1035  -0.1992
 Z98  O3    O  OH1   0  -0.610  -1.6679  -3.6610  -0.8951
 Z98  C4    C  CR6   0  -0.054  -0.1403  -1.9082  -0.6722
 Z98  C5    C  CR6   0  -0.050   0.9018  -1.3054   0.0319
 Z98  C6    C  CR16  0  -0.135   1.3598  -1.9369   1.1773
 Z98  CA    C  CH1   0  -0.210  -3.5447   1.6289   0.3189
 Z98  CB    C  CH2   0  -0.451  -2.5743   1.2097  -0.7928
 Z98  ND    N  N     0  -0.300  -1.6909  -0.6202  -2.1028
 Z98  CG    C  CH2   0  -0.300  -2.5500  -0.3026  -0.9870
 Z98  C4A   C  C1    0  -0.092  -0.6502  -1.3137  -1.9409
 Z98  C5A   C  CH2   0  -0.194   1.4614  -0.0044  -0.4675
 Z98  OP1   O  OH1   0  -0.729   4.2185   1.7514   1.3717
 Z98  OP2   O  O     0  -0.705   2.5168   2.9446  -0.2435
 Z98  OP3   O  OH1   0  -0.740   4.2808   1.4252  -1.1876
 Z98  OP4   O  O2    0  -0.590   2.5221   0.4092   0.3813
 Z98  O     O  O     0  -0.439  -4.1839   3.9620   0.2455
 Z98  HN    H  HNH2  0   0.357  -5.5185   1.4423   0.7567
 Z98  HNA   H  HNH2  0   0.345  -5.2283   1.7757  -0.8023
 Z98  HO    H  HOH1  0   0.481  -2.1473   4.3593   1.3050
 Z98  HO3   H  HOH1  0   0.487  -1.9519  -4.4927  -0.4993
 Z98  H6    H  HCR6  0   0.262   2.1633  -1.5129   1.7650
 Z98  HA    H  HCH1  0   0.273  -3.2521   1.1104   1.2380
 Z98  HB    H  HCH2  0   0.244  -2.8575   1.6977  -1.7304
 Z98  HBA   H  HCH2  0   0.248  -1.5668   1.5537  -0.5490
 Z98  HG    H  HCH2  0   0.214  -2.2571  -0.7827  -0.0454
 Z98  HGA   H  HCH2  0   0.253  -3.5557  -0.6479  -1.2315
 Z98  H2A   H  HCH3  0   0.260  -1.7348  -4.8886   1.7572
 Z98  H2AA  H  HCH3  0   0.259  -0.5672  -5.7802   0.7841
 Z98  H2AB  H  HCH3  0   0.273  -0.1364  -5.2452   2.4039
 Z98  H4A   H  H     0   0.270  -0.0317  -1.4961  -2.8216
 Z98  H5A   H  HCH2  0   0.260   1.8172  -0.1240  -1.4970
 Z98  H5AA  H  HCH2  0   0.255   0.6782   0.7595  -0.4834
 Z98  HOP1  H  HOH1  0   0.506   4.7657   2.5410   1.4793
 Z98  HOP3  H  HOH1  0   0.498   4.8983   0.6914  -1.0646
 Z98  C2A   C  CH3   0  -0.783  -0.6746  -4.9632   1.5023

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
 Z98  O    C     double    1.206  0.020  1.206
 Z98  CA   C     single    1.524  0.020  1.524
 Z98  C    OXT   single    1.328  0.020  1.328
 Z98  CA   N     single    1.442  0.020  1.442
 Z98  N    HN    single    0.890  0.020  1.040
 Z98  N    HNA   single    0.890  0.020  1.040
 Z98  OXT  HO    single    0.850  0.020  0.980
 Z98  OP2  P     double    1.474  0.020  1.474
 Z98  OP3  P     single    1.596  0.020  1.596
 Z98  P    OP1   single    1.592  0.020  1.592
 Z98  P    OP4   single    1.600  0.020  1.600
 Z98  C6   N1    aromatic  1.328  0.020  1.328
 Z98  N1   C2    aromatic  1.323  0.020  1.323
 Z98  C2   C2A   single    1.499  0.020  1.499
 Z98  C2   C3    aromatic  1.402  0.020  1.402
 Z98  C3   C4    aromatic  1.388  0.020  1.388
 Z98  C3   O3    single    1.344  0.020  1.344
 Z98  O3   HO3   single    0.850  0.020  0.980
 Z98  C5   C4    aromatic  1.395  0.020  1.395
 Z98  C4   C4A   single    1.491  0.020  1.491
 Z98  C6   C5    aromatic  1.386  0.020  1.386
 Z98  C5A  C5    single    1.502  0.020  1.502
 Z98  C6   H6    single    0.930  0.020  1.080
 Z98  CB   CA    single    1.534  0.020  1.534
 Z98  CA   HA    single    0.970  0.020  1.090
 Z98  CG   CB    single    1.525  0.020  1.525
 Z98  CB   HB    single    0.970  0.020  1.090
 Z98  CB   HBA   single    0.970  0.020  1.090
 Z98  C4A  ND    double    1.261  0.020  1.261
 Z98  ND   CG    single    1.444  0.020  1.444
 Z98  CG   HG    single    0.970  0.020  1.090
 Z98  CG   HGA   single    0.970  0.020  1.090
 Z98  C2A  H2A   single    0.970  0.020  1.090
 Z98  C2A  H2AA  single    0.970  0.020  1.090
 Z98  C2A  H2AB  single    0.970  0.020  1.090
 Z98  C4A  H4A   single    0.930  0.020  1.080
 Z98  OP4  C5A   single    1.420  0.020  1.420
 Z98  C5A  H5A   single    0.970  0.020  1.090
 Z98  C5A  H5AA  single    0.970  0.020  1.090
 Z98  OP1  HOP1  single    0.850  0.020  0.980
 Z98  OP3  HOP3  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
 Z98  O     C    CA    124.53  3.000
 Z98  CA    C    OXT   112.02  3.000
 Z98  O     C    OXT   123.45  3.000
 Z98  HNA   N    HN    106.34  3.000
 Z98  HNA   N    CA    110.18  3.000
 Z98  HN    N    CA    110.45  3.000
 Z98  HO    OXT  C     110.27  3.000
 Z98  OP4   P    OP3   106.83  3.000
 Z98  OP4   P    OP2   116.27  3.000
 Z98  OP3   P    OP2   109.79  3.000
 Z98  OP4   P    OP1    96.37  3.000
 Z98  OP3   P    OP1   108.10  3.000
 Z98  OP2   P    OP1   118.28  3.000
 Z98  C6    N1   C2    120.18  3.000
 Z98  C2A   C2   C3    120.60  3.000
 Z98  C3    C2   N1    120.86  3.000
 Z98  C2A   C2   N1    118.54  3.000
 Z98  C4    C3   O3    117.55  3.000
 Z98  O3    C3   C2    123.07  3.000
 Z98  C4    C3   C2    119.38  3.000
 Z98  HO3   O3   C3    111.46  3.000
 Z98  C4A   C4   C5    120.85  3.000
 Z98  C4A   C4   C3    120.32  3.000
 Z98  C5    C4   C3    118.78  3.000
 Z98  C5A   C5   C6    123.13  3.000
 Z98  C5A   C5   C4    119.01  3.000
 Z98  C6    C5   C4    117.86  3.000
 Z98  H6    C6   C5    121.05  3.000
 Z98  H6    C6   N1    116.00  3.000
 Z98  C5    C6   N1    122.95  3.000
 Z98  HA    CA   CB    108.05  3.000
 Z98  HA    CA   N     108.30  3.000
 Z98  CB    CA   N     110.57  3.000
 Z98  HA    CA   C     107.17  3.000
 Z98  CB    CA   C     108.82  3.000
 Z98  N     CA   C     113.73  3.000
 Z98  HBA   CB   HB    106.83  3.000
 Z98  HBA   CB   CG    109.03  3.000
 Z98  HB    CB   CG    109.71  3.000
 Z98  HBA   CB   CA    109.61  3.000
 Z98  HB    CB   CA    109.59  3.000
 Z98  CG    CB   CA    111.92  3.000
 Z98  C4A   ND   CG    120.86  3.000
 Z98  HGA   CG   HG    107.46  3.000
 Z98  HGA   CG   ND    107.80  3.000
 Z98  HG    CG   ND    114.10  3.000
 Z98  HGA   CG   CB    109.13  3.000
 Z98  HG    CG   CB    109.21  3.000
 Z98  ND    CG   CB    109.03  3.000
 Z98  H4A   C4A  ND    117.13  3.000
 Z98  H4A   C4A  C4    115.22  3.000
 Z98  ND    C4A  C4    127.64  3.000
 Z98  H5AA  C5A  H5A   107.15  3.000
 Z98  H5AA  C5A  OP4   109.88  3.000
 Z98  H5A   C5A  OP4   110.54  3.000
 Z98  H5AA  C5A  C5    110.05  3.000
 Z98  H5A   C5A  C5    109.81  3.000
 Z98  OP4   C5A  C5    109.38  3.000
 Z98  HOP1  OP1  P     114.13  3.000
 Z98  HOP3  OP3  P     115.91  3.000
 Z98  C5A   OP4  P     119.85  3.000
 Z98  H2AB  C2A  H2AA  107.59  3.000
 Z98  H2AB  C2A  H2A   107.73  3.000
 Z98  H2AA  C2A  H2A   107.43  3.000
 Z98  H2AB  C2A  C2    109.87  3.000
 Z98  H2AA  C2A  C2    112.00  3.000
 Z98  H2A   C2A  C2    112.01  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
 Z98  CONST_01  C4   C5   C6   N1      0.00   0.0  0
 Z98  CONST_02  C4   C3   C2   N1      0.00   0.0  0
 Z98  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 Z98  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 Z98  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 Z98  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 Z98  CONST_07  C5A  C5   C6   N1    180.00   0.0  0
 Z98  CONST_08  O3   C3   C2   N1    180.00   0.0  0
 Z98  CONST_09  C4A  C4   C3   C2    180.00   0.0  0
 Z98  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 Z98  CONST_11  C5   C4   C3   O3    180.00   0.0  0
 Z98  CONST_12  C2A  C2   C3   C4    180.00   0.0  0
 Z98  CONST_13  C2A  C2   N1   C6    180.00   0.0  0
 Z98  CONST_14  C4A  C4   C5   C6    180.00   0.0  0
 Z98  CONST_15  H6   C6   N1   C2    180.00   0.0  0
 Z98  CONST_16  HO   OXT  C    CA    180.00   0.0  0
 Z98  Var_01    ND   C4A  C4   C3     81.47  30.0  2
 Z98  Var_02    OP4  C5A  C5   C4   -178.87  30.0  2
 Z98  Var_03    H2A  C2A  C2   N1    119.41  30.0  2
 Z98  Var_04    C5   C5A  OP4  P     178.19  30.0  3
 Z98  Var_05    ND   CG   CB   CA    176.12  30.0  2
 Z98  Var_06    OP2  P    OP4  C5A    48.47  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
 Z98  chir_01  CA  C  N  CB  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
 Z98  plan-1  N1   0.020
 Z98  plan-1  C2   0.020
 Z98  plan-1  C3   0.020
 Z98  plan-1  O3   0.020
 Z98  plan-1  C4   0.020
 Z98  plan-1  C5   0.020
 Z98  plan-1  C6   0.020
 Z98  plan-1  C4A  0.020
 Z98  plan-1  C5A  0.020
 Z98  plan-1  H6   0.020
 Z98  plan-1  C2A  0.020
 Z98  plan-2  C    0.020
 Z98  plan-2  OXT  0.020
 Z98  plan-2  CA   0.020
 Z98  plan-2  O    0.020
 Z98  plan-2  HO   0.020
 Z98  plan-3  C4   0.020
 Z98  plan-3  ND   0.020
 Z98  plan-3  CG   0.020
 Z98  plan-3  C4A  0.020
 Z98  plan-3  H4A  0.020

