# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 17:40:26 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2S)-2-azanyl-4-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxy-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(\C=N\OCC[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
 P00  P00  '(2S)-2-azanyl-4-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxy-butanoic acid'  ligand  42  24  .  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_P00
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
 P00  O23  O  OH1   0  -0.729   6.1202   1.5943   0.2331
 P00  P21  P  P     0   1.454   4.6593   1.6306  -0.3975
 P00  O24  O  OH1   0  -0.734   4.2251   3.1584  -0.5587
 P00  O22  O  O     0  -0.701   4.4233   0.9109  -1.6610
 P00  O20  O  O2    0  -0.587   3.8903   1.0703   0.8929
 P00  C19  C  CH2   0  -0.252   2.5074   0.7566   0.7915
 P00  C5   C  CR6   0  -0.063   2.2737  -0.7056   0.5126
 P00  C6   C  CR16  0  -0.132   3.3114  -1.6157   0.4814
 P00  N1   N  N     0  -0.402   3.1385  -2.9163   0.2528
 P00  C2   C  CR6   0   0.132   1.9281  -3.3948   0.0410
 P00  C7   C  CH3   0  -0.719   1.7686  -4.8610  -0.2149
 P00  C3   C  CR6   0   0.294   0.8007  -2.5549   0.0563
 P00  O8   O  OH1   0  -0.623  -0.3846  -3.1232  -0.1649
 P00  C4   C  CR6   0  -0.017   0.9690  -1.1864   0.3024
 P00  C9   C  C1    0   0.009  -0.1694  -0.2744   0.3452
 P00  N10  N  N     0  -0.155  -1.3493  -0.7129   0.1515
 P00  O11  O  O2    0  -0.390  -2.3053   0.2351   0.2224
 P00  C12  C  CH2   0  -0.122  -3.5978  -0.3316   0.0137
 P00  C13  C  CH2   0  -0.493  -4.5956   0.8041   0.1098
 P00  C14  C  CH1   0  -0.218  -6.0344   0.2809   0.0203
 P00  N16  N  NH2   0  -0.777  -6.2411  -0.4323  -1.2153
 P00  C15  C  C     0   0.526  -7.0087   1.4345   0.2342
 P00  O18  O  O     0  -0.436  -7.7585   1.8599  -0.6078
 P00  O17  O  OH1   0  -0.593  -6.9392   1.9236   1.4663
 P00  H1   H  HOH1  0   0.506   6.8266   1.7946  -0.3962
 P00  H2   H  HOH1  0   0.498   4.3872   3.7262   0.2071
 P00  H3   H  HCH2  0   0.289   2.0619   1.0337   1.7489
 P00  H4   H  HCH2  0   0.256   2.0221   1.3736   0.0289
 P00  H5   H  HCR6  0   0.255   4.3327  -1.3028   0.6506
 P00  H6   H  HCH3  0   0.248   1.1022  -5.3268   0.5130
 P00  H7   H  HCH3  0   0.249   1.3444  -5.0527  -1.2023
 P00  H8   H  HCH3  0   0.248   2.7366  -5.3539  -0.1582
 P00  H9   H  HOH1  0   0.473  -1.0890  -2.4408  -0.1213
 P00  H10  H  H     0   0.273  -0.0062   0.7812   0.5481
 P00  H11  H  HCH2  0   0.233  -3.6403  -0.8173  -0.9627
 P00  H12  H  HCH2  0   0.223  -3.8011  -1.0855   0.7813
 P00  H13  H  HCH2  0   0.261  -4.4553   1.3269   1.0574
 P00  H14  H  HCH2  0   0.251  -4.4189   1.5293  -0.6905
 P00  H15  H  HCH1  0   0.278  -6.1893  -0.4204   0.8478
 P00  H16  H  HNH2  0   0.358  -7.1700  -0.8323  -1.2425
 P00  H17  H  HNH2  0   0.347  -6.1783   0.2011  -2.0030
 P00  H18  H  HOH1  0   0.483  -7.5551   2.6646   1.5691

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
 P00  O22  P21  double    1.473  0.020  1.473
 P00  O23  P21  single    1.592  0.020  1.592
 P00  O18  C15  double    1.205  0.020  1.205
 P00  P21  O24  single    1.596  0.020  1.596
 P00  P21  O20  single    1.603  0.020  1.603
 P00  C15  O17  single    1.328  0.020  1.328
 P00  C15  C14  single    1.525  0.020  1.525
 P00  O20  C19  single    1.422  0.020  1.422
 P00  N16  C14  single    1.442  0.020  1.442
 P00  C14  C13  single    1.534  0.020  1.534
 P00  C19  C5   single    1.507  0.020  1.507
 P00  C13  C12  single    1.515  0.020  1.515
 P00  C5   C6   aromatic  1.381  0.020  1.381
 P00  C5   C4   aromatic  1.406  0.020  1.406
 P00  C6   N1   aromatic  1.332  0.020  1.332
 P00  C9   C4   single    1.459  0.020  1.459
 P00  C9   N10  double    1.274  0.020  1.274
 P00  O11  C12  single    1.427  0.020  1.427
 P00  O11  N10  single    1.348  0.020  1.348
 P00  C4   C3   aromatic  1.401  0.020  1.401
 P00  N1   C2   aromatic  1.319  0.020  1.319
 P00  C3   C2   aromatic  1.406  0.020  1.406
 P00  C3   O8   single    1.333  0.020  1.333
 P00  C2   C7   single    1.497  0.020  1.497
 P00  O23  H1   single    0.850  0.020  0.980
 P00  O24  H2   single    0.850  0.020  0.980
 P00  C19  H3   single    0.970  0.020  1.090
 P00  C19  H4   single    0.970  0.020  1.090
 P00  C6   H5   single    0.930  0.020  1.080
 P00  C7   H6   single    0.970  0.020  1.090
 P00  C7   H7   single    0.970  0.020  1.090
 P00  C7   H8   single    0.970  0.020  1.090
 P00  O8   H9   single    0.850  0.020  0.980
 P00  C9   H10  single    0.930  0.020  1.080
 P00  C12  H11  single    0.970  0.020  1.090
 P00  C12  H12  single    0.970  0.020  1.090
 P00  C13  H13  single    0.970  0.020  1.090
 P00  C13  H14  single    0.970  0.020  1.090
 P00  C14  H15  single    0.970  0.020  1.090
 P00  N16  H16  single    0.890  0.020  1.040
 P00  N16  H17  single    0.890  0.020  1.040
 P00  O17  H18  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
 P00  H1   O23  P21  114.08  3.000
 P00  O20  P21  O22  116.28  3.000
 P00  O20  P21  O24  106.57  3.000
 P00  O22  P21  O24  109.72  3.000
 P00  O20  P21  O23   96.51  3.000
 P00  O24  P21  O23  108.15  3.000
 P00  O22  P21  O23  118.41  3.000
 P00  H2   O24  P21  115.87  3.000
 P00  C19  O20  P21  119.09  3.000
 P00  H4   C19  H3   106.68  3.000
 P00  H4   C19  C5   110.45  3.000
 P00  H3   C19  C5   110.21  3.000
 P00  H4   C19  O20  110.90  3.000
 P00  H3   C19  O20  106.16  3.000
 P00  C5   C19  O20  112.22  3.000
 P00  C4   C5   C6   117.94  3.000
 P00  C4   C5   C19  120.22  3.000
 P00  C6   C5   C19  121.82  3.000
 P00  H5   C6   N1   115.59  3.000
 P00  H5   C6   C5   121.03  3.000
 P00  N1   C6   C5   123.37  3.000
 P00  C2   N1   C6   120.08  3.000
 P00  C3   C2   C7   120.10  3.000
 P00  C7   C2   N1   118.73  3.000
 P00  C3   C2   N1   121.16  3.000
 P00  H8   C7   H7   108.26  3.000
 P00  H8   C7   H6   108.38  3.000
 P00  H7   C7   H6   106.92  3.000
 P00  H8   C7   C2   109.88  3.000
 P00  H7   C7   C2   111.60  3.000
 P00  H6   C7   C2   111.66  3.000
 P00  C4   C3   O8   123.54  3.000
 P00  O8   C3   C2   117.16  3.000
 P00  C4   C3   C2   119.30  3.000
 P00  H9   O8   C3   109.53  3.000
 P00  C9   C4   C3   121.48  3.000
 P00  C3   C4   C5   118.15  3.000
 P00  C9   C4   C5   120.38  3.000
 P00  H10  C9   N10  120.12  3.000
 P00  H10  C9   C4   119.68  3.000
 P00  N10  C9   C4   120.20  3.000
 P00  O11  N10  C9   114.00  3.000
 P00  C12  O11  N10  110.82  3.000
 P00  H12  C12  H11  108.27  3.000
 P00  H12  C12  C13  110.45  3.000
 P00  H11  C12  C13  111.39  3.000
 P00  H12  C12  O11  109.82  3.000
 P00  H11  C12  O11  110.05  3.000
 P00  C13  C12  O11  106.84  3.000
 P00  H14  C13  H13  107.27  3.000
 P00  H14  C13  C14  109.57  3.000
 P00  H13  C13  C14  109.56  3.000
 P00  H14  C13  C12  110.12  3.000
 P00  H13  C13  C12  109.24  3.000
 P00  C14  C13  C12  111.01  3.000
 P00  H15  C14  C15  106.73  3.000
 P00  H15  C14  N16  108.08  3.000
 P00  C15  C14  N16  113.75  3.000
 P00  H15  C14  C13  107.88  3.000
 P00  N16  C14  C13  110.70  3.000
 P00  C15  C14  C13  109.46  3.000
 P00  H17  N16  H16  106.45  3.000
 P00  H17  N16  C14  110.38  3.000
 P00  H16  N16  C14  110.51  3.000
 P00  O17  C15  O18  123.44  3.000
 P00  O17  C15  C14  112.05  3.000
 P00  O18  C15  C14  124.51  3.000
 P00  H18  O17  C15  110.30  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
 P00  CONST_01  C2   N1   C6   C5      0.00   0.0  0
 P00  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 P00  CONST_03  C3   C4   C5   C6      0.00   0.0  0
 P00  CONST_04  C3   C2   N1   C6      0.00   0.0  0
 P00  CONST_05  C4   C5   C6   N1      0.00   0.0  0
 P00  CONST_06  C4   C3   C2   N1      0.00   0.0  0
 P00  CONST_07  N1   C6   C5   C19   180.00   0.0  0
 P00  CONST_08  C3   C4   C5   C19   180.00   0.0  0
 P00  CONST_09  O8   C3   C4   C5    180.00   0.0  0
 P00  CONST_10  C9   C4   C5   C6    180.00   0.0  0
 P00  CONST_11  C7   C2   N1   C6    180.00   0.0  0
 P00  CONST_12  O8   C3   C2   N1    180.00   0.0  0
 P00  CONST_13  C9   C4   C3   C2    180.00   0.0  0
 P00  CONST_14  C4   C3   C2   C7    180.00   0.0  0
 P00  CONST_15  H5   C6   N1   C2    180.00   0.0  0
 P00  CONST_16  H18  O17  C15  C14   180.00   0.0  0
 P00  Var_01    C6   C5   C19  O20     5.07  30.0  2
 P00  Var_02    N10  C9   C4   C5    179.85  30.0  2
 P00  Var_03    H6   C7   C2   N1    121.91  30.0  2
 P00  Var_04    C5   C19  O20  P21    95.72  30.0  3
 P00  Var_05    C13  C12  O11  N10  -179.93  30.0  3
 P00  Var_06    C14  C13  C12  O11  -175.07  30.0  1

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
 P00  chir_01  C14  C15  N16  C13  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
 P00  plan-1  C19  0.020
 P00  plan-1  C5   0.020
 P00  plan-1  C6   0.020
 P00  plan-1  N1   0.020
 P00  plan-1  C2   0.020
 P00  plan-1  C7   0.020
 P00  plan-1  C3   0.020
 P00  plan-1  O8   0.020
 P00  plan-1  C4   0.020
 P00  plan-1  C9   0.020
 P00  plan-1  H5   0.020
 P00  plan-2  C14  0.020
 P00  plan-2  C15  0.020
 P00  plan-2  O18  0.020
 P00  plan-2  O17  0.020
 P00  plan-2  H18  0.020
 P00  plan-3  C4   0.020
 P00  plan-3  C9   0.020
 P00  plan-3  N10  0.020
 P00  plan-3  O11  0.020
 P00  plan-3  H10  0.020

