# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:06:33 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2S)-4-(methylamino)-4-oxo-2-[(4-phosphonooxyphenyl)methyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C[C@H](Cc1ccc(O[P](O)(O)=O)cc1)C(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
 FY0  FY0  '(2S)-4-(methylamino)-4-oxo-2-[(4-phosphonooxyphenyl)methyl]butanoic acid'  ligand  34  21  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FY0
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
 FY0  C1   C  CR16   0  -0.285  -0.2296  -0.9600   0.9620
 FY0  C2   C  CR16   0  -0.362  -1.4552  -1.3338   0.4326
 FY0  C3   C  CR6    0   0.373  -2.3193  -0.3895  -0.1350
 FY0  C4   C  CR16   0  -0.375  -1.9092   0.9493  -0.1348
 FY0  C5   C  CR16   0  -0.311  -0.6807   1.3050   0.4038
 FY0  C6   C  CR6    0   0.105   0.1860   0.3689   0.9626
 FY0  O1   O  O2     0  -0.658  -3.4673  -0.8254  -0.6570
 FY0  P1   P  P      0   1.230  -4.9371   0.1298  -0.7087
 FY0  O2   O  OP    -1  -0.875  -5.9087  -0.9495  -1.1482
 FY0  O3   O  O      0  -0.885  -5.0875   0.6213   0.7187
 FY0  O4   O  OP    -1  -0.881  -4.6581   1.2084  -1.7447
 FY0  C7   C  CH2    0  -0.492   1.5320   0.7736   1.4936
 FY0  C8   C  CH1    0  -0.328   2.6378   0.7193   0.4304
 FY0  C9   C  C      0   0.433   2.8156  -0.7174  -0.1018
 FY0  O5   O  O      0  -0.621   3.1909  -1.5683   0.7379
 FY0  O6   O  OC    -1  -0.600   2.5906  -0.9208  -1.3075
 FY0  C10  C  CH2    0  -0.548   3.9524   1.2368   1.0321
 FY0  C11  C  C      0   0.507   5.0801   1.2084   0.0247
 FY0  N1   N  NH1    0  -0.609   5.8035   0.0780   0.0084
 FY0  C12  C  CH3    0  -0.513   6.8218  -0.1780  -0.9805
 FY0  O7   O  O      0  -0.511   5.3084   2.1448  -0.7342
 FY0  H1   H  HCR6   0   0.228   0.4195  -1.7201   1.3816
 FY0  H2   H  HCR6   0   0.233  -1.7541  -2.3758   0.4507
 FY0  H3   H  HCR6   0   0.247  -2.5435   1.7033  -0.5798
 FY0  H4   H  HCR6   0   0.229  -0.3885   2.3503   0.3875
 FY0  H7   H  HCH2   0   0.228   1.4763   1.7916   1.8915
 FY0  H8   H  HCH2   0   0.227   1.8210   0.1292   2.3283
 FY0  H9   H  HCH1   0   0.215   2.3497   1.3765  -0.3967
 FY0  H11  H  HCH2   0   0.249   3.8220   2.2678   1.3675
 FY0  H12  H  HCH2   0   0.241   4.2058   0.6381   1.9101
 FY0  H13  H  HNH1   0   0.395   5.4717  -0.6975   0.5601
 FY0  H14  H  HCH3   0   0.245   7.2817  -1.1378  -0.7616
 FY0  H15  H  HCH3   0   0.231   6.4143  -0.2162  -1.9928
 FY0  H16  H  HCH3   0   0.235   7.5992   0.5850  -0.9555

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
 FY0  C1   C2   aromatic  1.386  0.020  1.386
 FY0  C1   C6   aromatic  1.392  0.020  1.392
 FY0  C2   C3   aromatic  1.400  0.020  1.400
 FY0  C3   C4   aromatic  1.400  0.020  1.400
 FY0  C4   C5   aromatic  1.388  0.020  1.388
 FY0  C5   C6   aromatic  1.393  0.020  1.393
 FY0  C3   O1   single    1.334  0.020  1.334
 FY0  O1   P1   single    1.754  0.020  1.754
 FY0  P1   O2   deloc     1.517  0.020  1.517
 FY0  P1   O3   deloc     1.517  0.020  1.517
 FY0  P1   O4   deloc     1.521  0.020  1.521
 FY0  C6   C7   single    1.503  0.020  1.503
 FY0  C7   C8   single    1.535  0.020  1.535
 FY0  C8   C9   single    1.542  0.020  1.542
 FY0  C9   O5   deloc     1.253  0.020  1.253
 FY0  C9   O6   deloc     1.243  0.020  1.243
 FY0  C8   C10  single    1.536  0.020  1.536
 FY0  C10  C11  single    1.512  0.020  1.512
 FY0  C11  N1   single    1.342  0.020  1.342
 FY0  N1   C12  single    1.442  0.020  1.442
 FY0  C11  O7   double    1.227  0.020  1.227
 FY0  C1   H1   single    0.930  0.020  1.080
 FY0  C2   H2   single    0.930  0.020  1.080
 FY0  C4   H3   single    0.930  0.020  1.080
 FY0  C5   H4   single    0.930  0.020  1.080
 FY0  C7   H7   single    0.970  0.020  1.090
 FY0  C7   H8   single    0.970  0.020  1.090
 FY0  C8   H9   single    0.970  0.020  1.090
 FY0  C10  H11  single    0.970  0.020  1.090
 FY0  C10  H12  single    0.970  0.020  1.090
 FY0  N1   H13  single    0.860  0.020  1.020
 FY0  C12  H14  single    0.970  0.020  1.090
 FY0  C12  H15  single    0.970  0.020  1.090
 FY0  C12  H16  single    0.970  0.020  1.090

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
 FY0  H1   C1   C6   119.36  3.000
 FY0  H1   C1   C2   119.22  3.000
 FY0  C6   C1   C2   121.42  3.000
 FY0  H2   C2   C3   119.00  3.000
 FY0  H2   C2   C1   119.77  3.000
 FY0  C3   C2   C1   121.23  3.000
 FY0  O1   C3   C4   124.36  3.000
 FY0  O1   C3   C2   117.98  3.000
 FY0  C4   C3   C2   117.65  3.000
 FY0  H3   C4   C5   120.02  3.000
 FY0  H3   C4   C3   119.67  3.000
 FY0  C5   C4   C3   120.29  3.000
 FY0  H4   C5   C6   119.06  3.000
 FY0  H4   C5   C4   118.64  3.000
 FY0  C6   C5   C4   122.30  3.000
 FY0  C7   C6   C5   121.21  3.000
 FY0  C7   C6   C1   121.64  3.000
 FY0  C5   C6   C1   117.10  3.000
 FY0  P1   O1   C3   123.69  3.000
 FY0  O4   P1   O3   115.41  3.000
 FY0  O4   P1   O2   115.12  3.000
 FY0  O3   P1   O2   116.08  3.000
 FY0  O4   P1   O1   104.63  3.000
 FY0  O3   P1   O1   103.41  3.000
 FY0  O2   P1   O1    99.08  3.000
 FY0  H8   C7   H7   106.51  3.000
 FY0  H8   C7   C8   108.51  3.000
 FY0  H7   C7   C8   108.75  3.000
 FY0  H8   C7   C6   110.35  3.000
 FY0  H7   C7   C6   109.48  3.000
 FY0  C8   C7   C6   113.01  3.000
 FY0  H9   C8   C10  108.60  3.000
 FY0  H9   C8   C9   109.20  3.000
 FY0  C10  C8   C9   110.51  3.000
 FY0  H9   C8   C7   108.20  3.000
 FY0  C10  C8   C7   109.47  3.000
 FY0  C9   C8   C7   110.79  3.000
 FY0  O6   C9   O5   126.37  3.000
 FY0  O6   C9   C8   117.78  3.000
 FY0  O5   C9   C8   115.84  3.000
 FY0  H12  C10  H11  107.36  3.000
 FY0  H12  C10  C11  110.61  3.000
 FY0  H11  C10  C11  108.13  3.000
 FY0  H12  C10  C8   109.20  3.000
 FY0  H11  C10  C8   109.65  3.000
 FY0  C11  C10  C8   111.77  3.000
 FY0  O7   C11  N1   122.34  3.000
 FY0  O7   C11  C10  122.45  3.000
 FY0  N1   C11  C10  115.20  3.000
 FY0  H13  N1   C12  118.11  3.000
 FY0  H13  N1   C11  117.64  3.000
 FY0  C12  N1   C11  122.57  3.000
 FY0  H16  C12  H15  108.18  3.000
 FY0  H16  C12  H14  108.17  3.000
 FY0  H15  C12  H14  108.29  3.000
 FY0  H16  C12  N1   111.33  3.000
 FY0  H15  C12  N1   112.23  3.000
 FY0  H14  C12  N1   108.51  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
 FY0  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 FY0  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 FY0  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 FY0  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 FY0  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 FY0  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 FY0  CONST_07  O1   C3   C2   C1    180.00   0.0  0
 FY0  CONST_08  C7   C6   C1   C2    180.00   0.0  0
 FY0  CONST_09  C7   C6   C5   C4    180.00   0.0  0
 FY0  CONST_10  O1   C3   C4   C5    180.00   0.0  0
 FY0  CONST_11  H4   C5   C6   C1    180.00   0.0  0
 FY0  CONST_12  H3   C4   C3   C2    180.00   0.0  0
 FY0  CONST_13  H1   C1   C2   C3    180.00   0.0  0
 FY0  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 FY0  CONST_15  C12  N1   C11  C10   180.00   0.0  0
 FY0  CONST_16  O7   C11  N1   C12     0.00   0.0  0
 FY0  CONST_17  H13  N1   C11  C10     0.00   0.0  0
 FY0  Var_01    C8   C7   C6   C1     88.23  30.0  2
 FY0  Var_02    O2   P1   O1   C3   -169.99  30.0  3
 FY0  Var_03    N1   C11  C10  C8    -91.02  30.0  3
 FY0  Var_04    H14  C12  N1   C11   178.20  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
 FY0  chir_01  C8  C7  C9  C10  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
 FY0  plan-1  C1   0.020
 FY0  plan-1  C2   0.020
 FY0  plan-1  C3   0.020
 FY0  plan-1  C4   0.020
 FY0  plan-1  C5   0.020
 FY0  plan-1  C6   0.020
 FY0  plan-1  O1   0.020
 FY0  plan-1  C7   0.020
 FY0  plan-1  H1   0.020
 FY0  plan-1  H2   0.020
 FY0  plan-1  H3   0.020
 FY0  plan-1  H4   0.020
 FY0  plan-2  C10  0.020
 FY0  plan-2  C11  0.020
 FY0  plan-2  N1   0.020
 FY0  plan-2  C12  0.020
 FY0  plan-2  O7   0.020
 FY0  plan-2  H13  0.020
 FY0  plan-3  C8   0.020
 FY0  plan-3  C9   0.020
 FY0  plan-3  O5   0.020
 FY0  plan-3  O6   0.020

