# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 00:28:45 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (4S)-5-fluoro-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CF)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
 76U  76U  '(4S)-5-fluoro-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid'  ligand  44  24  .  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_76U
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
 76U  C1   C  CR6   0  -0.041   0.7362   1.6190  -0.3387
 76U  C3   C  CR6   0   0.125   0.2404   3.9577   0.9992
 76U  C4   C  CH3   0  -0.786  -0.0041   5.2319   1.7503
 76U  C2   C  CR16  0  -0.110   1.7039   2.3154   0.3725
 76U  C5   C  CR6   0   0.273  -0.7976   3.3313   0.2976
 76U  C6   C  CR6   0   0.031  -0.5549   2.1472  -0.3982
 76U  O1   O  OH1   0  -0.726   3.0716  -2.3186   0.7766
 76U  O2   O  OH1   0  -0.737   3.8802  -1.2640  -1.4310
 76U  C11  C  CH2   0  -0.603  -1.1949  -2.3981   0.4055
 76U  C12  C  C     0   0.558  -1.1291  -3.5374   1.3839
 76U  O    O  O     0  -0.705   1.8100  -2.6796  -1.5099
 76U  P    P  P     0   1.475   2.5910  -1.7802  -0.6405
 76U  O3   O  O2    0  -0.588   1.8352  -0.4754  -0.1029
 76U  C    C  CH2   0  -0.265   1.1221   0.3447  -1.0353
 76U  N    N  N     0  -0.407   1.4621   3.4447   1.0197
 76U  O4   O  OH1   0  -0.618  -2.0457   3.8358   0.2731
 76U  C7   C  CH2   0  -0.335  -1.6717   1.4443  -1.1251
 76U  N1   N  NH1   0  -0.616  -2.2518   0.4112  -0.2712
 76U  C8   C  CH1   0  -0.142  -2.6578  -0.8181  -0.9302
 76U  C9   C  CH2   0   0.032  -4.0653  -0.6971  -1.4743
 76U  F1   F  F     0  -0.376  -4.1471   0.3434  -2.3992
 76U  C10  C  CH2   0  -0.460  -2.6162  -1.9870   0.0538
 76U  O5   O  O     0  -0.445  -2.0834  -4.1090   1.8502
 76U  O6   O  OH1   0  -0.588   0.1255  -3.8553   1.6831
 76U  H1   H  HCH3  0   0.257  -0.7800   5.1168   2.5115
 76U  H2   H  HCH3  0   0.273   0.9072   5.5444   2.2544
 76U  H3   H  HCH3  0   0.260  -0.3103   6.0458   1.0879
 76U  H4   H  HCR6  0   0.255   2.7214   1.9436   0.4254
 76U  H5   H  HOH1  0   0.505   3.3593  -3.2412   0.7734
 76U  H6   H  HOH1  0   0.495   4.4970  -0.7132  -0.9306
 76U  H7   H  HCH2  0   0.268  -0.6199  -1.5699   0.8297
 76U  H8   H  HCH2  0   0.287  -0.6452  -2.6953  -0.4922
 76U  H9   H  HCH2  0   0.259   0.2541  -0.2022  -1.4028
 76U  H10  H  HCH2  0   0.272   1.7509   0.5756  -1.9007
 76U  H11  H  HOH1  0   0.487  -2.1024   4.6567   0.7743
 76U  H12  H  HCH2  0   0.250  -2.4298   2.1658  -1.4281
 76U  H13  H  HCH2  0   0.226  -1.2850   1.0182  -2.0592
 76U  H14  H  HNH1  0   0.361  -1.6341   0.2135   0.5029
 76U  H16  H  HCH1  0   0.216  -1.9908  -1.0573  -1.7775
 76U  H17  H  HCH2  0   0.206  -4.3623  -1.6168  -1.9827
 76U  H18  H  HCH2  0   0.199  -4.7706  -0.4870  -0.6669
 76U  H19  H  HCH2  0   0.253  -3.1357  -2.8403  -0.3865
 76U  H20  H  HCH2  0   0.246  -3.1707  -1.7101   0.9544
 76U  H21  H  HOH1  0   0.478   0.1391  -4.5970   2.3062

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
 76U  O    P    double    1.475  0.020  1.475
 76U  O2   P    single    1.598  0.020  1.598
 76U  P    O1   single    1.590  0.020  1.590
 76U  P    O3   single    1.601  0.020  1.601
 76U  O3   C    single    1.432  0.020  1.432
 76U  C2   N    aromatic  1.324  0.020  1.324
 76U  C2   C1   aromatic  1.388  0.020  1.388
 76U  C    C1   single    1.503  0.020  1.503
 76U  N    C3   aromatic  1.325  0.020  1.325
 76U  C1   C6   aromatic  1.396  0.020  1.396
 76U  C3   C4   single    1.499  0.020  1.499
 76U  C3   C5   aromatic  1.401  0.020  1.401
 76U  C6   C5   aromatic  1.395  0.020  1.395
 76U  C6   C7   single    1.507  0.020  1.507
 76U  C5   O4   single    1.346  0.020  1.346
 76U  C7   N1   single    1.460  0.020  1.460
 76U  N1   C8   single    1.453  0.020  1.453
 76U  C8   C9   single    1.514  0.020  1.514
 76U  C8   C10  single    1.528  0.020  1.528
 76U  C9   F1   single    1.395  0.020  1.395
 76U  C10  C11  single    1.521  0.020  1.521
 76U  C11  C12  single    1.503  0.020  1.503
 76U  O5   C12  double    1.206  0.020  1.206
 76U  C12  O6   single    1.328  0.020  1.328
 76U  C4   H1   single    0.970  0.020  1.090
 76U  C4   H2   single    0.970  0.020  1.090
 76U  C4   H3   single    0.970  0.020  1.090
 76U  C2   H4   single    0.930  0.020  1.080
 76U  O1   H5   single    0.850  0.020  0.980
 76U  O2   H6   single    0.850  0.020  0.980
 76U  C11  H7   single    0.970  0.020  1.090
 76U  C11  H8   single    0.970  0.020  1.090
 76U  C    H9   single    0.970  0.020  1.090
 76U  C    H10  single    0.970  0.020  1.090
 76U  O4   H11  single    0.850  0.020  0.980
 76U  C7   H12  single    0.970  0.020  1.090
 76U  C7   H13  single    0.970  0.020  1.090
 76U  N1   H14  single    0.890  0.020  1.040
 76U  C8   H16  single    0.970  0.020  1.090
 76U  C9   H17  single    0.970  0.020  1.090
 76U  C9   H18  single    0.970  0.020  1.090
 76U  C10  H19  single    0.970  0.020  1.090
 76U  C10  H20  single    0.970  0.020  1.090
 76U  O6   H21  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
 76U  C    C1   C6   122.58  3.000
 76U  C6   C1   C2   118.47  3.000
 76U  C    C1   C2   118.94  3.000
 76U  N    C3   C5   121.18  3.000
 76U  C5   C3   C4   120.68  3.000
 76U  N    C3   C4   118.14  3.000
 76U  H3   C4   H2   107.56  3.000
 76U  H3   C4   H1   107.54  3.000
 76U  H2   C4   H1   107.60  3.000
 76U  H3   C4   C3   112.02  3.000
 76U  H2   C4   C3   109.87  3.000
 76U  H1   C4   C3   112.04  3.000
 76U  H4   C2   N    116.10  3.000
 76U  H4   C2   C1   120.46  3.000
 76U  N    C2   C1   123.44  3.000
 76U  O4   C5   C6   118.06  3.000
 76U  O4   C5   C3   121.90  3.000
 76U  C6   C5   C3   120.04  3.000
 76U  C7   C6   C5   120.52  3.000
 76U  C7   C6   C1   121.98  3.000
 76U  C5   C6   C1   117.44  3.000
 76U  H5   O1   P    114.22  3.000
 76U  H6   O2   P    116.28  3.000
 76U  H8   C11  H7   105.06  3.000
 76U  H8   C11  C10  110.69  3.000
 76U  H7   C11  C10  112.11  3.000
 76U  H8   C11  C12  107.83  3.000
 76U  H7   C11  C12  107.36  3.000
 76U  C10  C11  C12  113.35  3.000
 76U  O6   C12  O5   123.15  3.000
 76U  O6   C12  C11  111.67  3.000
 76U  O5   C12  C11  125.18  3.000
 76U  O3   P    O    116.43  3.000
 76U  O3   P    O2   106.48  3.000
 76U  O    P    O2   109.43  3.000
 76U  O3   P    O1    96.85  3.000
 76U  O2   P    O1   107.84  3.000
 76U  O    P    O1   118.61  3.000
 76U  C    O3   P    118.90  3.000
 76U  H10  C    H9   107.26  3.000
 76U  H10  C    O3   110.47  3.000
 76U  H9   C    O3   109.20  3.000
 76U  H10  C    C1   109.58  3.000
 76U  H9   C    C1   112.17  3.000
 76U  O3   C    C1   108.16  3.000
 76U  C2   N    C3   119.41  3.000
 76U  H11  O4   C5   111.37  3.000
 76U  H13  C7   H12  105.41  3.000
 76U  H13  C7   N1   111.29  3.000
 76U  H12  C7   N1   110.78  3.000
 76U  H13  C7   C6   109.31  3.000
 76U  H12  C7   C6   109.94  3.000
 76U  N1   C7   C6   110.02  3.000
 76U  H14  N1   C8   110.67  3.000
 76U  H14  N1   C7   110.11  3.000
 76U  C8   N1   C7   116.38  3.000
 76U  H16  C8   C10  108.17  3.000
 76U  H16  C8   C9   107.64  3.000
 76U  C10  C8   C9   108.53  3.000
 76U  H16  C8   N1   111.25  3.000
 76U  C10  C8   N1   110.33  3.000
 76U  C9   C8   N1   110.81  3.000
 76U  H18  C9   H17  109.30  3.000
 76U  H18  C9   F1   107.99  3.000
 76U  H17  C9   F1   107.68  3.000
 76U  H18  C9   C8   110.48  3.000
 76U  H17  C9   C8   110.66  3.000
 76U  F1   C9   C8   110.64  3.000
 76U  H20  C10  H19  106.79  3.000
 76U  H20  C10  C8   108.83  3.000
 76U  H19  C10  C8   108.97  3.000
 76U  H20  C10  C11  110.61  3.000
 76U  H19  C10  C11  109.07  3.000
 76U  C8   C10  C11  112.40  3.000
 76U  H21  O6   C12  109.96  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
 76U  CONST_01  C3   N    C2   C1      0.00   0.0  0
 76U  CONST_02  C3   C5   C6   C1      0.00   0.0  0
 76U  CONST_03  C5   C3   N    C2      0.00   0.0  0
 76U  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 76U  CONST_05  N    C2   C1   C6      0.00   0.0  0
 76U  CONST_06  N    C3   C5   C6      0.00   0.0  0
 76U  CONST_07  O4   C5   C6   C1    180.00   0.0  0
 76U  CONST_08  C7   C6   C5   C3    180.00   0.0  0
 76U  CONST_09  C2   N    C3   C4    180.00   0.0  0
 76U  CONST_10  C6   C5   C3   C4    180.00   0.0  0
 76U  CONST_11  C7   C6   C1   C2    180.00   0.0  0
 76U  CONST_12  C    C1   C6   C5    180.00   0.0  0
 76U  CONST_13  N    C2   C1   C     180.00   0.0  0
 76U  CONST_14  O4   C5   C3   N     180.00   0.0  0
 76U  CONST_15  H4   C2   N    C3    180.00   0.0  0
 76U  CONST_16  H21  O6   C12  C11   180.00   0.0  0
 76U  Var_01    N1   C7   C6   C1     82.32  30.0  2
 76U  Var_02    O3   C    C1   C2     49.11  30.0  2
 76U  Var_03    H1   C4   C3   C5     58.57  30.0  2
 76U  Var_04    C8   N1   C7   C6   -142.61  30.0  3
 76U  Var_05    C8   C10  C11  C12   179.39  30.0  1
 76U  Var_06    O5   C12  C11  C10     1.13  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
 76U  chir_01  C8  N1  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
 76U  plan-1  C1   0.020
 76U  plan-1  C3   0.020
 76U  plan-1  C4   0.020
 76U  plan-1  C2   0.020
 76U  plan-1  C5   0.020
 76U  plan-1  C6   0.020
 76U  plan-1  C    0.020
 76U  plan-1  N    0.020
 76U  plan-1  O4   0.020
 76U  plan-1  C7   0.020
 76U  plan-1  H4   0.020
 76U  plan-2  C11  0.020
 76U  plan-2  C12  0.020
 76U  plan-2  O5   0.020
 76U  plan-2  O6   0.020
 76U  plan-2  H21  0.020

