# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:09:09 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (1S,3S,4E)-3-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-4-iminocyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C[C@@H]2C[C@@H](CC2=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
 9QJ  9QJ  '(1S,3S,4E)-3-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-4-iminocyclopentane-1-carboxylic acid'  ligand  43  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9QJ
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
 9QJ  C4A  C  CH2   0  -0.585   0.8847   0.2828   1.0180
 9QJ  CGF  C  CR15  0  -0.330   1.5869  -0.4971  -0.1056
 9QJ  CDF  C  CR5   0   0.233   2.4830   0.3458  -1.0033
 9QJ  NF   N  N     0  -0.567   2.1502   1.2687  -1.7993
 9QJ  CEF  C  CH2   0  -0.495   3.8971  -0.1543  -0.8834
 9QJ  CAF  C  CR15  0  -0.405   3.6931  -1.6270  -0.5074
 9QJ  CF   C  C     0   0.566   4.9134  -2.3094   0.0433
 9QJ  O1F  O  O     0  -0.437   4.9523  -2.9267   1.0781
 9QJ  O2F  O  OH1   0  -0.593   5.9623  -2.1669  -0.7584
 9QJ  CBF  C  CH2   0  -0.430   2.5135  -1.5818   0.4615
 9QJ  C4   C  CR6   0   0.094  -0.0688   1.3580   0.5676
 9QJ  C3   C  CR6   0   0.242   0.3083   2.6986   0.5282
 9QJ  O3   O  OH1   0  -0.616   1.5273   3.1505   0.8784
 9QJ  C2   C  CR6   0   0.141  -0.6043   3.6748   0.0989
 9QJ  C2A  C  CH3   0  -0.721  -0.2064   5.1179   0.0467
 9QJ  N1   N  N     0  -0.406  -1.8291   3.3479  -0.2706
 9QJ  C6   C  CR16  0  -0.135  -2.2105   2.0748  -0.2321
 9QJ  C5   C  CR6   0  -0.089  -1.3800   1.0467   0.1775
 9QJ  C5A  C  CH2   0  -0.202  -1.8492  -0.3802   0.2270
 9QJ  O4P  O  O2    0  -0.592  -3.2030  -0.4507  -0.2011
 9QJ  P    P  P     0   1.465  -3.9911  -1.8390  -0.1039
 9QJ  O2P  O  OH1   0  -0.740  -4.2715  -2.0998   1.4461
 9QJ  O3P  O  OH1   0  -0.728  -5.3417  -1.3281  -0.7730
 9QJ  O1P  O  O     0  -0.707  -3.3232  -3.0130  -0.6939
 9QJ  H1   H  HCH2  0   0.293   0.3490  -0.4411   1.6373
 9QJ  H2   H  HCH2  0   0.267   1.6491   0.6829   1.6907
 9QJ  H3   H  HCR5  0   0.297   0.8321  -0.9632  -0.7462
 9QJ  H4   H  H     0   0.338   1.1474   1.4382  -1.7680
 9QJ  H5   H  HCH2  0   0.276   4.4728   0.0122  -1.7915
 9QJ  H6   H  HCH2  0   0.272   4.3977   0.3739  -0.0638
 9QJ  H7   H  HCR5  0   0.305   3.4029  -2.1755  -1.4121
 9QJ  H8   H  HOH1  0   0.482   6.7295  -2.6300  -0.3890
 9QJ  H9   H  HCH2  0   0.245   2.8670  -1.2887   1.4540
 9QJ  H10  H  HCH2  0   0.265   2.0094  -2.5415   0.5663
 9QJ  H11  H  HOH1  0   0.474   2.1048   2.4381   1.1703
 9QJ  H12  H  HCH3  0   0.248   0.6292   5.2820  -0.6363
 9QJ  H13  H  HCH3  0   0.248  -1.0475   5.7186  -0.2931
 9QJ  H14  H  HCH3  0   0.248   0.1051   5.4882   1.0250
 9QJ  H15  H  HCR6  0   0.258  -3.2283   1.8783  -0.5420
 9QJ  H16  H  HCH2  0   0.259  -1.2304  -1.0110  -0.4173
 9QJ  H17  H  HCH2  0   0.258  -1.7528  -0.7637   1.2485
 9QJ  H18  H  HOH1  0   0.497  -4.7529  -1.4025   1.9116
 9QJ  H19  H  HOH1  0   0.506  -5.9710  -2.0321  -0.9802

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
 9QJ  O1F  CF   double    1.206  0.020  1.206
 9QJ  O1P  P    double    1.474  0.020  1.474
 9QJ  O2P  P    single    1.597  0.020  1.597
 9QJ  O3P  P    single    1.591  0.020  1.591
 9QJ  P    O4P  single    1.599  0.020  1.599
 9QJ  CF   O2F  single    1.328  0.020  1.328
 9QJ  CF   CAF  single    1.503  0.020  1.503
 9QJ  CEF  CDF  single    1.505  0.020  1.505
 9QJ  CEF  CAF  single    1.534  0.020  1.534
 9QJ  NF   CDF  double    1.263  0.020  1.263
 9QJ  CDF  CGF  single    1.523  0.020  1.523
 9QJ  CAF  CBF  single    1.527  0.020  1.527
 9QJ  O4P  C5A  single    1.422  0.020  1.422
 9QJ  CBF  CGF  single    1.535  0.020  1.535
 9QJ  C5A  C5   single    1.503  0.020  1.503
 9QJ  CGF  C4A  single    1.537  0.020  1.537
 9QJ  C4A  C4   single    1.506  0.020  1.506
 9QJ  C5   C4   aromatic  1.403  0.020  1.403
 9QJ  C5   C6   aromatic  1.384  0.020  1.384
 9QJ  C4   C3   aromatic  1.393  0.020  1.393
 9QJ  C6   N1   aromatic  1.330  0.020  1.330
 9QJ  C3   O3   single    1.346  0.020  1.346
 9QJ  C3   C2   aromatic  1.404  0.020  1.404
 9QJ  N1   C2   aromatic  1.320  0.020  1.320
 9QJ  C2   C2A  single    1.498  0.020  1.498
 9QJ  C4A  H1   single    0.970  0.020  1.090
 9QJ  C4A  H2   single    0.970  0.020  1.090
 9QJ  CGF  H3   single    0.970  0.020  1.090
 9QJ  NF   H4   single    0.890  0.020  1.040
 9QJ  CEF  H5   single    0.970  0.020  1.090
 9QJ  CEF  H6   single    0.970  0.020  1.090
 9QJ  CAF  H7   single    0.970  0.020  1.090
 9QJ  O2F  H8   single    0.850  0.020  0.980
 9QJ  CBF  H9   single    0.970  0.020  1.090
 9QJ  CBF  H10  single    0.970  0.020  1.090
 9QJ  O3   H11  single    0.850  0.020  0.980
 9QJ  C2A  H12  single    0.970  0.020  1.090
 9QJ  C2A  H13  single    0.970  0.020  1.090
 9QJ  C2A  H14  single    0.970  0.020  1.090
 9QJ  C6   H15  single    0.930  0.020  1.080
 9QJ  C5A  H16  single    0.970  0.020  1.090
 9QJ  C5A  H17  single    0.970  0.020  1.090
 9QJ  O2P  H18  single    0.850  0.020  0.980
 9QJ  O3P  H19  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
 9QJ  H2   C4A  H1   103.66  3.000
 9QJ  H2   C4A  C4   111.42  3.000
 9QJ  H1   C4A  C4   109.39  3.000
 9QJ  H2   C4A  CGF  108.41  3.000
 9QJ  H1   C4A  CGF  107.57  3.000
 9QJ  C4   C4A  CGF  115.64  3.000
 9QJ  H3   CGF  CBF  109.37  3.000
 9QJ  H3   CGF  CDF  107.25  3.000
 9QJ  CBF  CGF  CDF  104.70  3.000
 9QJ  H3   CGF  C4A  109.20  3.000
 9QJ  CBF  CGF  C4A  111.35  3.000
 9QJ  CDF  CGF  C4A  114.75  3.000
 9QJ  CEF  CDF  NF   122.72  3.000
 9QJ  NF   CDF  CGF  128.37  3.000
 9QJ  CEF  CDF  CGF  108.79  3.000
 9QJ  H4   NF   CDF  111.22  3.000
 9QJ  H6   CEF  H5   107.98  3.000
 9QJ  H6   CEF  CAF  109.89  3.000
 9QJ  H5   CEF  CAF  114.96  3.000
 9QJ  H6   CEF  CDF  109.18  3.000
 9QJ  H5   CEF  CDF  112.33  3.000
 9QJ  CAF  CEF  CDF  102.34  3.000
 9QJ  H7   CAF  CBF  109.49  3.000
 9QJ  H7   CAF  CF   106.86  3.000
 9QJ  CBF  CAF  CF   114.09  3.000
 9QJ  H7   CAF  CEF  108.25  3.000
 9QJ  CBF  CAF  CEF  103.29  3.000
 9QJ  CF   CAF  CEF  114.70  3.000
 9QJ  O2F  CF   O1F  123.21  3.000
 9QJ  O2F  CF   CAF  111.81  3.000
 9QJ  O1F  CF   CAF  124.98  3.000
 9QJ  H8   O2F  CF   110.11  3.000
 9QJ  H10  CBF  H9   107.36  3.000
 9QJ  H10  CBF  CAF  113.11  3.000
 9QJ  H9   CBF  CAF  109.52  3.000
 9QJ  H10  CBF  CGF  112.26  3.000
 9QJ  H9   CBF  CGF  109.94  3.000
 9QJ  CAF  CBF  CGF  104.64  3.000
 9QJ  C5   C4   C3   117.30  3.000
 9QJ  C3   C4   C4A  121.60  3.000
 9QJ  C5   C4   C4A  121.10  3.000
 9QJ  C2   C3   O3   115.77  3.000
 9QJ  C2   C3   C4   120.13  3.000
 9QJ  O3   C3   C4   124.10  3.000
 9QJ  H11  O3   C3   111.95  3.000
 9QJ  N1   C2   C2A  118.37  3.000
 9QJ  C2A  C2   C3   120.53  3.000
 9QJ  N1   C2   C3   121.10  3.000
 9QJ  H14  C2A  H13  108.26  3.000
 9QJ  H14  C2A  H12  106.94  3.000
 9QJ  H13  C2A  H12  108.26  3.000
 9QJ  H14  C2A  C2   111.81  3.000
 9QJ  H13  C2A  C2   109.72  3.000
 9QJ  H12  C2A  C2   111.71  3.000
 9QJ  C6   N1   C2   119.67  3.000
 9QJ  H15  C6   C5   120.96  3.000
 9QJ  H15  C6   N1   115.81  3.000
 9QJ  C5   C6   N1   123.22  3.000
 9QJ  C5A  C5   C6   121.86  3.000
 9QJ  C6   C5   C4   118.58  3.000
 9QJ  C5A  C5   C4   119.56  3.000
 9QJ  H17  C5A  H16  107.32  3.000
 9QJ  H17  C5A  O4P  110.32  3.000
 9QJ  H16  C5A  O4P  109.44  3.000
 9QJ  H17  C5A  C5   109.62  3.000
 9QJ  H16  C5A  C5   110.58  3.000
 9QJ  O4P  C5A  C5   109.54  3.000
 9QJ  P    O4P  C5A  119.60  3.000
 9QJ  O1P  P    O3P  118.16  3.000
 9QJ  O3P  P    O2P  108.15  3.000
 9QJ  O1P  P    O2P  109.76  3.000
 9QJ  O3P  P    O4P   96.54  3.000
 9QJ  O2P  P    O4P  106.70  3.000
 9QJ  O1P  P    O4P  116.34  3.000
 9QJ  H18  O2P  P    115.92  3.000
 9QJ  H19  O3P  P    114.13  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
 9QJ  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 9QJ  CONST_02  N1   C2   C3   C4     0.00   0.0  0
 9QJ  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 9QJ  CONST_04  C6   N1   C2   C3     0.00   0.0  0
 9QJ  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 9QJ  CONST_06  C5   C6   N1   C2     0.00   0.0  0
 9QJ  CONST_07  C6   C5   C4   C4A  180.00   0.0  0
 9QJ  CONST_08  C2   C3   C4   C4A  180.00   0.0  0
 9QJ  CONST_09  C2A  C2   C3   C4   180.00   0.0  0
 9QJ  CONST_10  C5A  C5   C4   C3   180.00   0.0  0
 9QJ  CONST_11  C5   C4   C3   O3   180.00   0.0  0
 9QJ  CONST_12  N1   C2   C3   O3   180.00   0.0  0
 9QJ  CONST_13  C6   N1   C2   C2A  180.00   0.0  0
 9QJ  CONST_14  C5A  C5   C6   N1   180.00   0.0  0
 9QJ  CONST_15  H15  C6   C5   C4   180.00   0.0  0
 9QJ  CONST_16  H8   O2F  CF   CAF  180.00   0.0  0
 9QJ  Var_01    CAF  CEF  CDF  CGF   27.13  30.0  1
 9QJ  Var_02    C5   C4   C4A  CGF   81.62  30.0  2
 9QJ  Var_03    O4P  C5A  C5   C4   179.57  30.0  1
 9QJ  Var_04    H12  C2A  C2   C3    60.86  30.0  2
 9QJ  Var_05    O1P  P    O4P  C5A  -50.97  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
 9QJ  chir_01  CGF  CDF  CBF  C4A  negativ
 9QJ  chir_02  CAF  CBF  CEF  CF   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
 9QJ  plan-1  C4A  0.020
 9QJ  plan-1  C4   0.020
 9QJ  plan-1  C3   0.020
 9QJ  plan-1  O3   0.020
 9QJ  plan-1  C2   0.020
 9QJ  plan-1  C2A  0.020
 9QJ  plan-1  N1   0.020
 9QJ  plan-1  C6   0.020
 9QJ  plan-1  C5   0.020
 9QJ  plan-1  C5A  0.020
 9QJ  plan-1  H15  0.020
 9QJ  plan-2  CAF  0.020
 9QJ  plan-2  CF   0.020
 9QJ  plan-2  O1F  0.020
 9QJ  plan-2  O2F  0.020
 9QJ  plan-2  H8   0.020

