# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 15:26:19 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2S)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]hexanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CCCC(O)=O)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
 N5F  N5F  '(2S)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]hexanedioic acid'  ligand  47  26  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N5F
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
 N5F  OAM   O  OH1   0  -0.775   3.2950  -0.2891   0.4476
 N5F  PAT   P  P     0   1.463   2.1591  -1.3645   0.2232
 N5F  OAZ   O  OH1   0  -0.744   1.4050  -0.9774  -1.1367
 N5F  OAU   O  O     0  -0.709   2.6284  -2.7618   0.3185
 N5F  OAS   O  O2    0  -0.585   1.0771  -0.9351   1.3239
 N5F  CAR   C  CH2   0  -0.301   0.1271  -1.8936   1.8164
 N5F  CAQ   C  CR6   0  -0.017  -0.9559  -2.1891   0.8226
 N5F  CAY   C  CR16  0  -0.129  -0.9598  -3.4239   0.1917
 N5F  NAX   N  N     0  -0.408  -1.8659  -3.7864  -0.7039
 N5F  CAW   C  CR6   0   0.127  -2.8241  -2.9334  -1.0341
 N5F  CAV   C  CH3   0  -0.786  -3.8407  -3.3699  -2.0457
 N5F  CAO   C  CR6   0   0.271  -2.8966  -1.6571  -0.4557
 N5F  OAN   O  OH1   0  -0.611  -3.8603  -0.7795  -0.7873
 N5F  CAP   C  CR6   0   0.039  -1.9565  -1.2693   0.4960
 N5F  CAK   C  CH2   0  -0.321  -2.0093   0.1093   1.0935
 N5F  N     N  NH1   0  -0.600  -1.3827   1.0653   0.1892
 N5F  CA    C  CH1   0  -0.185  -1.1102   2.3403   0.8094
 N5F  C     C  C     0   0.540  -2.4025   3.1081   1.0226
 N5F  OXT   O  OH1   0  -0.595  -2.2575   4.0496   1.9494
 N5F  O     O  O     0  -0.429  -3.4263   2.9262   0.4168
 N5F  CB    C  CH2   0  -0.435  -0.1903   3.2000  -0.0706
 N5F  CAG   C  CH2   0  -0.472   1.1632   2.5481  -0.3336
 N5F  CAH   C  CH2   0  -0.577   2.1045   3.5111  -1.0361
 N5F  CAI   C  C     0   0.601   3.4268   2.9056  -1.4035
 N5F  OAB   O  O     0  -0.474   3.7930   1.7818  -1.1230
 N5F  OAJ   O  OH1   0  -0.576   4.1871   3.7363  -2.0882
 N5F  HOAM  H  HOH1  0   0.505   3.3444   0.4962  -0.1504
 N5F  HOAZ  H  HOH1  0   0.499   1.7944  -1.3635  -1.9331
 N5F  HAR   H  HCH2  0   0.268   0.6379  -2.8179   2.0919
 N5F  HARA  H  HCH2  0   0.271  -0.2724  -1.4589   2.7312
 N5F  HAY   H  HCR6  0   0.257  -0.1907  -4.1526   0.4273
 N5F  HAV   H  HCH3  0   0.259  -4.8454  -3.4210  -1.6174
 N5F  HAVA  H  HCH3  0   0.259  -3.8845  -2.6956  -2.9043
 N5F  HAVB  H  HCH3  0   0.272  -3.5920  -4.3615  -2.4157
 N5F  HOAN  H  HOH1  0   0.486  -4.5088  -1.1806  -1.3761
 N5F  HAK   H  HCH2  0   0.254  -3.0476   0.3970   1.2615
 N5F  HAKA  H  HCH2  0   0.221  -1.5291   0.1046   2.0810
 N5F  HN    H  HNH1  0   0.361  -0.5057   0.6666  -0.1175
 N5F  HA    H  HCH1  0   0.243  -0.6239   2.2298   1.7938
 N5F  HOXT  H  HOH1  0   0.481  -3.0741   4.5651   2.0290
 N5F  HB    H  HCH2  0   0.246  -0.6889   3.4130  -1.0205
 N5F  HBA   H  HCH2  0   0.251  -0.0322   4.1592   0.4274
 N5F  HAG   H  HCH2  0   0.243   1.5980   2.2170   0.6137
 N5F  HAGA  H  HCH2  0   0.240   1.0417   1.6670  -0.9647
 N5F  HAH   H  HCH2  0   0.289   1.6466   3.8947  -1.9528
 N5F  HAHA  H  HCH2  0   0.294   2.2994   4.3909  -0.4149
 N5F  HOAJ  H  HOH1  0   0.488   5.0368   3.3226  -2.3053

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
 N5F  OAM  PAT   single    1.580  0.020  1.580
 N5F  PAT  OAZ   single    1.602  0.020  1.602
 N5F  PAT  OAU   double    1.477  0.020  1.477
 N5F  PAT  OAS   single    1.602  0.020  1.602
 N5F  OAS  CAR   single    1.437  0.020  1.437
 N5F  CAR  CAQ   single    1.499  0.020  1.499
 N5F  CAQ  CAY   aromatic  1.387  0.020  1.387
 N5F  CAQ  CAP   aromatic  1.398  0.020  1.398
 N5F  CAY  NAX   aromatic  1.325  0.020  1.325
 N5F  NAX  CAW   aromatic  1.325  0.020  1.325
 N5F  CAW  CAV   single    1.499  0.020  1.499
 N5F  CAW  CAO   aromatic  1.403  0.020  1.403
 N5F  CAO  OAN   single    1.345  0.020  1.345
 N5F  CAO  CAP   aromatic  1.393  0.020  1.393
 N5F  CAP  CAK   single    1.503  0.020  1.503
 N5F  CAK  N     single    1.457  0.020  1.457
 N5F  N    CA    single    1.444  0.020  1.444
 N5F  CA   C     single    1.518  0.020  1.518
 N5F  CA   CB    single    1.536  0.020  1.536
 N5F  C    OXT   single    1.329  0.020  1.329
 N5F  C    O     double    1.203  0.020  1.203
 N5F  CB   CAG   single    1.525  0.020  1.525
 N5F  CAG  CAH   single    1.519  0.020  1.519
 N5F  CAH  CAI   single    1.500  0.020  1.500
 N5F  CAI  OAB   double    1.215  0.020  1.215
 N5F  CAI  OAJ   single    1.318  0.020  1.318
 N5F  OAM  HOAM  single    0.850  0.020  0.980
 N5F  OAZ  HOAZ  single    0.850  0.020  0.980
 N5F  CAR  HAR   single    0.970  0.020  1.090
 N5F  CAR  HARA  single    0.970  0.020  1.090
 N5F  CAY  HAY   single    0.930  0.020  1.080
 N5F  CAV  HAV   single    0.970  0.020  1.090
 N5F  CAV  HAVA  single    0.970  0.020  1.090
 N5F  CAV  HAVB  single    0.970  0.020  1.090
 N5F  OAN  HOAN  single    0.850  0.020  0.980
 N5F  CAK  HAK   single    0.970  0.020  1.090
 N5F  CAK  HAKA  single    0.970  0.020  1.090
 N5F  N    HN    single    0.890  0.020  1.040
 N5F  CA   HA    single    0.970  0.020  1.090
 N5F  OXT  HOXT  single    0.850  0.020  0.980
 N5F  CB   HB    single    0.970  0.020  1.090
 N5F  CB   HBA   single    0.970  0.020  1.090
 N5F  CAG  HAG   single    0.970  0.020  1.090
 N5F  CAG  HAGA  single    0.970  0.020  1.090
 N5F  CAH  HAH   single    0.970  0.020  1.090
 N5F  CAH  HAHA  single    0.970  0.020  1.090
 N5F  OAJ  HOAJ  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
 N5F  HOAM  OAM  PAT   119.38  3.000
 N5F  OAS   PAT  OAU   115.08  3.000
 N5F  OAS   PAT  OAZ   101.57  3.000
 N5F  OAU   PAT  OAZ   115.64  3.000
 N5F  OAS   PAT  OAM   101.86  3.000
 N5F  OAU   PAT  OAM   113.97  3.000
 N5F  OAZ   PAT  OAM   107.12  3.000
 N5F  HOAZ  OAZ  PAT   114.39  3.000
 N5F  CAR   OAS  PAT   120.22  3.000
 N5F  HARA  CAR  HAR   107.32  3.000
 N5F  HARA  CAR  CAQ   111.75  3.000
 N5F  HAR   CAR  CAQ   109.78  3.000
 N5F  HARA  CAR  OAS   105.33  3.000
 N5F  HAR   CAR  OAS   110.01  3.000
 N5F  CAQ   CAR  OAS   112.45  3.000
 N5F  CAP   CAQ  CAY   118.53  3.000
 N5F  CAP   CAQ  CAR   122.84  3.000
 N5F  CAY   CAQ  CAR   118.63  3.000
 N5F  HAY   CAY  NAX   116.60  3.000
 N5F  HAY   CAY  CAQ   119.80  3.000
 N5F  NAX   CAY  CAQ   123.59  3.000
 N5F  CAW   NAX  CAY   119.15  3.000
 N5F  CAO   CAW  CAV   120.54  3.000
 N5F  CAO   CAW  NAX   121.35  3.000
 N5F  CAV   CAW  NAX   118.11  3.000
 N5F  HAVB  CAV  HAVA  107.74  3.000
 N5F  HAVB  CAV  HAV   107.51  3.000
 N5F  HAVA  CAV  HAV   107.45  3.000
 N5F  HAVB  CAV  CAW   109.89  3.000
 N5F  HAVA  CAV  CAW   112.19  3.000
 N5F  HAV   CAV  CAW   111.86  3.000
 N5F  CAP   CAO  OAN   118.06  3.000
 N5F  CAP   CAO  CAW   120.00  3.000
 N5F  OAN   CAO  CAW   121.93  3.000
 N5F  HOAN  OAN  CAO   111.18  3.000
 N5F  CAK   CAP  CAO   120.21  3.000
 N5F  CAK   CAP  CAQ   122.39  3.000
 N5F  CAO   CAP  CAQ   117.36  3.000
 N5F  HAKA  CAK  HAK   106.20  3.000
 N5F  HAKA  CAK  N     111.89  3.000
 N5F  HAK   CAK  N     109.39  3.000
 N5F  HAKA  CAK  CAP   109.76  3.000
 N5F  HAK   CAK  CAP   109.67  3.000
 N5F  N     CAK  CAP   109.86  3.000
 N5F  HN    N    CA    108.35  3.000
 N5F  HN    N    CAK   107.61  3.000
 N5F  CA    N    CAK   113.19  3.000
 N5F  HA    CA   CB    107.65  3.000
 N5F  HA    CA   C     107.48  3.000
 N5F  CB    CA   C     107.89  3.000
 N5F  HA    CA   N     112.21  3.000
 N5F  CB    CA   N     111.17  3.000
 N5F  C     CA   N     110.26  3.000
 N5F  O     C    OXT   123.43  3.000
 N5F  O     C    CA    125.24  3.000
 N5F  OXT   C    CA    111.31  3.000
 N5F  HOXT  OXT  C     110.01  3.000
 N5F  HBA   CB   HB    106.91  3.000
 N5F  HBA   CB   CAG   109.00  3.000
 N5F  HB    CB   CAG   109.75  3.000
 N5F  HBA   CB   CA    108.48  3.000
 N5F  HB    CB   CA    109.48  3.000
 N5F  CAG   CB   CA    113.01  3.000
 N5F  HAGA  CAG  HAG   107.51  3.000
 N5F  HAGA  CAG  CAH   108.28  3.000
 N5F  HAG   CAG  CAH   110.25  3.000
 N5F  HAGA  CAG  CB    110.26  3.000
 N5F  HAG   CAG  CB    109.44  3.000
 N5F  CAH   CAG  CB    111.02  3.000
 N5F  HAHA  CAH  HAH   105.56  3.000
 N5F  HAHA  CAH  CAI   107.85  3.000
 N5F  HAH   CAH  CAI   107.77  3.000
 N5F  HAHA  CAH  CAG   110.95  3.000
 N5F  HAH   CAH  CAG   110.51  3.000
 N5F  CAI   CAH  CAG   113.80  3.000
 N5F  OAJ   CAI  OAB   121.95  3.000
 N5F  OAJ   CAI  CAH   112.42  3.000
 N5F  OAB   CAI  CAH   125.63  3.000
 N5F  HOAJ  OAJ  CAI   110.67  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
 N5F  CONST_01  CAW   NAX  CAY  CAQ     0.00   0.0  0
 N5F  CONST_02  CAW   CAO  CAP  CAQ     0.00   0.0  0
 N5F  CONST_03  CAO   CAP  CAQ  CAY     0.00   0.0  0
 N5F  CONST_04  CAO   CAW  NAX  CAY     0.00   0.0  0
 N5F  CONST_05  CAP   CAQ  CAY  NAX     0.00   0.0  0
 N5F  CONST_06  CAP   CAO  CAW  NAX     0.00   0.0  0
 N5F  CONST_07  NAX   CAY  CAQ  CAR   180.00   0.0  0
 N5F  CONST_08  CAO   CAP  CAQ  CAR   180.00   0.0  0
 N5F  CONST_09  OAN   CAO  CAP  CAQ   180.00   0.0  0
 N5F  CONST_10  CAK   CAP  CAQ  CAY   180.00   0.0  0
 N5F  CONST_11  CAV   CAW  NAX  CAY   180.00   0.0  0
 N5F  CONST_12  OAN   CAO  CAW  NAX   180.00   0.0  0
 N5F  CONST_13  CAK   CAP  CAO  CAW   180.00   0.0  0
 N5F  CONST_14  CAP   CAO  CAW  CAV   180.00   0.0  0
 N5F  CONST_15  HAY   CAY  NAX  CAW   180.00   0.0  0
 N5F  CONST_16  HOXT  OXT  C    CA    180.00   0.0  0
 N5F  CONST_17  HOAJ  OAJ  CAI  CAH   180.00   0.0  0
 N5F  Var_01    CAY   CAQ  CAR  OAS   108.47  30.0  2
 N5F  Var_02    N     CAK  CAP  CAQ    96.27  30.0  2
 N5F  Var_03    HAV   CAV  CAW  NAX   116.20  30.0  2
 N5F  Var_04    CAQ   CAR  OAS  PAT   -74.56  30.0  3
 N5F  Var_05    CA    N    CAK  CAP  -166.34  30.0  3
 N5F  Var_06    CAH   CAG  CB   CA   -171.95  30.0  3
 N5F  Var_07    CAI   CAH  CAG  CB   -176.33  30.0  3
 N5F  Var_08    OAB   CAI  CAH  CAG    -4.10  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
 N5F  chir_01  CA  N  C  CB  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
 N5F  plan-1  CAR   0.020
 N5F  plan-1  CAQ   0.020
 N5F  plan-1  CAY   0.020
 N5F  plan-1  NAX   0.020
 N5F  plan-1  CAW   0.020
 N5F  plan-1  CAV   0.020
 N5F  plan-1  CAO   0.020
 N5F  plan-1  OAN   0.020
 N5F  plan-1  CAP   0.020
 N5F  plan-1  CAK   0.020
 N5F  plan-1  HAY   0.020
 N5F  plan-2  CA    0.020
 N5F  plan-2  C     0.020
 N5F  plan-2  OXT   0.020
 N5F  plan-2  O     0.020
 N5F  plan-2  HOXT  0.020
 N5F  plan-3  CAH   0.020
 N5F  plan-3  CAI   0.020
 N5F  plan-3  OAB   0.020
 N5F  plan-3  OAJ   0.020
 N5F  plan-3  HOAJ  0.020

