# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:47:47 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (4R)-4-amino-6-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CC[C@@H](N)CCC(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
 77E  77E  '(4R)-4-amino-6-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}hexanoic acid'  ligand  44  23  .  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_77E
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
 77E  O7   O  OH1   0  -0.739  -3.8543  -2.6504  -1.6415
 77E  P1   P  P     0   1.459  -3.2011  -2.8238  -0.1942
 77E  O5   O  OH1   0  -0.728  -4.3732  -3.0794   0.8522
 77E  O6   O  O     0  -0.707  -2.1029  -3.8048  -0.2614
 77E  O4   O  O2    0  -0.592  -2.8179  -1.3587   0.3164
 77E  C17  C  CH2   0  -0.211  -1.7227  -0.6727  -0.2810
 77E  C16  C  CR6   0  -0.089  -1.8235   0.7979   0.0168
 77E  C15  C  CR16  0  -0.134  -2.9160   1.3407   0.6764
 77E  N3   N  N     0  -0.412  -3.0329   2.6354   0.9452
 77E  C13  C  CR6   0   0.126  -2.0723   3.4681   0.5755
 77E  C14  C  CH3   0  -0.785  -2.2342   4.9240   0.8974
 77E  C12  C  CR6   0   0.243  -0.9335   3.0062  -0.0959
 77E  O3   O  OH1   0  -0.620   0.0592   3.8357  -0.4768
 77E  C11  C  CR6   0   0.112  -0.7945   1.6523  -0.3906
 77E  C5   C  CH2   0  -0.509   0.4389   1.1465  -1.0828
 77E  C6   C  CH2   0  -0.411   1.5829   0.8878  -0.0998
 77E  C7   C  CH1   0  -0.098   2.8135   0.2773  -0.7654
 77E  C8   C  CH2   0  -0.418   3.8366  -0.1326   0.3008
 77E  C9   C  CH2   0  -0.591   5.0527  -0.8229  -0.2936
 77E  C10  C  C     0   0.553   6.0445  -1.2923   0.7337
 77E  O2   O  O     0  -0.446   5.9744  -1.0838   1.9195
 77E  O1   O  OH1   0  -0.598   7.0429  -1.9756   0.1794
 77E  N2   N  NH2   0  -0.791   3.3217   1.1965  -1.7743
 77E  H1   H  HOH1  0   0.497  -4.6268  -2.0713  -1.6903
 77E  H2   H  HOH1  0   0.506  -4.7252  -3.9796   0.8385
 77E  H3   H  HCH2  0   0.261  -0.7866  -1.0810   0.1095
 77E  H4   H  HCH2  0   0.254  -1.7156  -0.8263  -1.3655
 77E  H5   H  HCR6  0   0.255  -3.7358   0.7155   1.0058
 77E  H6   H  HCH3  0   0.254  -2.2061   5.5499   0.0015
 77E  H7   H  HCH3  0   0.270  -3.1922   5.0908   1.3838
 77E  H8   H  HCH3  0   0.257  -1.4533   5.2833   1.5727
 77E  H9   H  HOH1  0   0.484  -0.1353   4.7485  -0.2376
 77E  H10  H  HCH2  0   0.238   0.2173   0.2224  -1.6219
 77E  H11  H  HCH2  0   0.261   0.7704   1.8552  -1.8408
 77E  H12  H  HCH2  0   0.230   1.8674   1.8237   0.3918
 77E  H13  H  HCH2  0   0.231   1.2403   0.2196   0.6957
 77E  H14  H  HCH1  0   0.222   2.4939  -0.6307  -1.2922
 77E  H15  H  HCH2  0   0.224   4.1469   0.7570   0.8585
 77E  H16  H  HCH2  0   0.229   3.3524  -0.8007   1.0177
 77E  H17  H  HCH2  0   0.276   4.7495  -1.6847  -0.8969
 77E  H18  H  HCH2  0   0.273   5.5865  -0.1570  -0.9793
 77E  H19  H  HOH1  0   0.478   7.6702  -2.2545   0.8629
 77E  H20  H  HNH2  0   0.336   3.7431   1.9985  -1.3183
 77E  H21  H  HNH2  0   0.351   4.0561   0.7630  -2.3196

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
 77E  C14  C13  single    1.500  0.020  1.500
 77E  O3   C12  single    1.349  0.020  1.349
 77E  C13  C12  aromatic  1.400  0.020  1.400
 77E  C13  N3   aromatic  1.324  0.020  1.324
 77E  C12  C11  aromatic  1.393  0.020  1.393
 77E  N3   C15  aromatic  1.327  0.020  1.327
 77E  C11  C5   single    1.502  0.020  1.502
 77E  C11  C16  aromatic  1.398  0.020  1.398
 77E  C6   C5   single    1.530  0.020  1.530
 77E  C6   C7   single    1.527  0.020  1.527
 77E  C15  C16  aromatic  1.387  0.020  1.387
 77E  C16  C17  single    1.504  0.020  1.504
 77E  C8   C7   single    1.533  0.020  1.533
 77E  C8   C9   single    1.519  0.020  1.519
 77E  C7   N2   single    1.456  0.020  1.456
 77E  C17  O4   single    1.424  0.020  1.424
 77E  O4   P1   single    1.598  0.020  1.598
 77E  C9   C10  single    1.503  0.020  1.503
 77E  O2   C10  double    1.206  0.020  1.206
 77E  O6   P1   double    1.474  0.020  1.474
 77E  C10  O1   single    1.331  0.020  1.331
 77E  P1   O5   single    1.592  0.020  1.592
 77E  P1   O7   single    1.597  0.020  1.597
 77E  O7   H1   single    0.850  0.020  0.980
 77E  O5   H2   single    0.850  0.020  0.980
 77E  C17  H3   single    0.970  0.020  1.090
 77E  C17  H4   single    0.970  0.020  1.090
 77E  C15  H5   single    0.930  0.020  1.080
 77E  C14  H6   single    0.970  0.020  1.090
 77E  C14  H7   single    0.970  0.020  1.090
 77E  C14  H8   single    0.970  0.020  1.090
 77E  O3   H9   single    0.850  0.020  0.980
 77E  C5   H10  single    0.970  0.020  1.090
 77E  C5   H11  single    0.970  0.020  1.090
 77E  C6   H12  single    0.970  0.020  1.090
 77E  C6   H13  single    0.970  0.020  1.090
 77E  C7   H14  single    0.970  0.020  1.090
 77E  C8   H15  single    0.970  0.020  1.090
 77E  C8   H16  single    0.970  0.020  1.090
 77E  C9   H17  single    0.970  0.020  1.090
 77E  C9   H18  single    0.970  0.020  1.090
 77E  O1   H19  single    0.850  0.020  0.980
 77E  N2   H20  single    0.890  0.020  1.040
 77E  N2   H21  single    0.890  0.020  1.040

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
 77E  H1   O7   P1   115.95  3.000
 77E  O4   P1   O6   116.49  3.000
 77E  O6   P1   O5   118.14  3.000
 77E  O4   P1   O5    96.53  3.000
 77E  O5   P1   O7   108.18  3.000
 77E  O6   P1   O7   109.61  3.000
 77E  O4   P1   O7   106.74  3.000
 77E  H2   O5   P1   114.09  3.000
 77E  C17  O4   P1   119.48  3.000
 77E  H4   C17  H3   107.19  3.000
 77E  H4   C17  C16  109.49  3.000
 77E  H3   C17  C16  110.60  3.000
 77E  H4   C17  O4   110.66  3.000
 77E  H3   C17  O4   109.20  3.000
 77E  C16  C17  O4   109.67  3.000
 77E  C11  C16  C15  118.63  3.000
 77E  C15  C16  C17  121.99  3.000
 77E  C11  C16  C17  119.38  3.000
 77E  H5   C15  N3   115.79  3.000
 77E  H5   C15  C16  121.02  3.000
 77E  N3   C15  C16  123.19  3.000
 77E  C13  N3   C15  119.53  3.000
 77E  C12  C13  C14  120.72  3.000
 77E  C12  C13  N3   121.10  3.000
 77E  C14  C13  N3   118.18  3.000
 77E  H8   C14  H7   107.62  3.000
 77E  H8   C14  H6   107.44  3.000
 77E  H7   C14  H6   107.54  3.000
 77E  H8   C14  C13  112.00  3.000
 77E  H7   C14  C13  109.88  3.000
 77E  H6   C14  C13  112.16  3.000
 77E  C11  C12  O3   117.69  3.000
 77E  C11  C12  C13  120.22  3.000
 77E  O3   C12  C13  122.09  3.000
 77E  H9   O3   C12  111.34  3.000
 77E  C5   C11  C12  120.45  3.000
 77E  C5   C11  C16  122.20  3.000
 77E  C12  C11  C16  117.32  3.000
 77E  H11  C5   H10  105.59  3.000
 77E  H11  C5   C6   109.24  3.000
 77E  H10  C5   C6   109.00  3.000
 77E  H11  C5   C11  110.57  3.000
 77E  H10  C5   C11  110.22  3.000
 77E  C6   C5   C11  112.01  3.000
 77E  H13  C6   H12  106.08  3.000
 77E  H13  C6   C7   108.99  3.000
 77E  H12  C6   C7   109.16  3.000
 77E  H13  C6   C5   109.65  3.000
 77E  H12  C6   C5   109.77  3.000
 77E  C7   C6   C5   112.96  3.000
 77E  H14  C7   N2   106.94  3.000
 77E  H14  C7   C8   107.87  3.000
 77E  N2   C7   C8   114.68  3.000
 77E  H14  C7   C6   107.78  3.000
 77E  N2   C7   C6   109.33  3.000
 77E  C8   C7   C6   109.97  3.000
 77E  H16  C8   H15  106.74  3.000
 77E  H16  C8   C9   109.48  3.000
 77E  H15  C8   C9   109.97  3.000
 77E  H16  C8   C7   108.89  3.000
 77E  H15  C8   C7   109.03  3.000
 77E  C9   C8   C7   112.55  3.000
 77E  H18  C9   H17  105.58  3.000
 77E  H18  C9   C10  107.23  3.000
 77E  H17  C9   C10  108.27  3.000
 77E  H18  C9   C8   111.04  3.000
 77E  H17  C9   C8   110.58  3.000
 77E  C10  C9   C8   113.75  3.000
 77E  O1   C10  O2   122.82  3.000
 77E  O1   C10  C9   111.76  3.000
 77E  O2   C10  C9   125.42  3.000
 77E  H19  O1   C10  109.86  3.000
 77E  H21  N2   H20  106.23  3.000
 77E  H21  N2   C7   110.86  3.000
 77E  H20  N2   C7   109.43  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
 77E  CONST_01  C13  C12  C11  C16     0.00   0.0  0
 77E  CONST_02  C13  N3   C15  C16     0.00   0.0  0
 77E  CONST_03  C12  C13  N3   C15     0.00   0.0  0
 77E  CONST_04  C12  C11  C16  C15     0.00   0.0  0
 77E  CONST_05  C11  C12  C13  N3      0.00   0.0  0
 77E  CONST_06  C11  C16  C15  N3      0.00   0.0  0
 77E  CONST_07  C12  C11  C16  C17   180.00   0.0  0
 77E  CONST_08  N3   C15  C16  C17   180.00   0.0  0
 77E  CONST_09  O3   C12  C11  C16   180.00   0.0  0
 77E  CONST_10  C14  C13  N3   C15   180.00   0.0  0
 77E  CONST_11  C5   C11  C16  C15   180.00   0.0  0
 77E  CONST_12  O3   C12  C13  N3    180.00   0.0  0
 77E  CONST_13  C5   C11  C12  C13   180.00   0.0  0
 77E  CONST_14  C11  C12  C13  C14   180.00   0.0  0
 77E  CONST_15  H5   C15  N3   C13   180.00   0.0  0
 77E  CONST_16  H19  O1   C10  C9    180.00   0.0  0
 77E  Var_01    C11  C16  C17  O4    175.27  30.0  1
 77E  Var_02    C6   C5   C11  C16   -94.39  30.0  2
 77E  Var_03    H6   C14  C13  N3   -121.73  30.0  2
 77E  Var_04    C16  C17  O4   P1    161.65  30.0  1
 77E  Var_05    C7   C6   C5   C11   175.82  30.0  1
 77E  Var_06    C10  C9   C8   C7   -177.37  30.0  3
 77E  Var_07    O2   C10  C9   C8     -5.00  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
 77E  chir_01  C7  C6  C8  N2  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
 77E  plan-1  C17  0.020
 77E  plan-1  C16  0.020
 77E  plan-1  C15  0.020
 77E  plan-1  N3   0.020
 77E  plan-1  C13  0.020
 77E  plan-1  C14  0.020
 77E  plan-1  C12  0.020
 77E  plan-1  O3   0.020
 77E  plan-1  C11  0.020
 77E  plan-1  C5   0.020
 77E  plan-1  H5   0.020
 77E  plan-2  C9   0.020
 77E  plan-2  C10  0.020
 77E  plan-2  O2   0.020
 77E  plan-2  O1   0.020
 77E  plan-2  H19  0.020

