# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 20:49:46 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (2S,6S)-2-amino-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]heptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CCC[C@H](N)C(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
 PL4  PL4  '(2S,6S)-2-amino-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]heptanedioic acid'  ligand  52  28  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PL4
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
 PL4  CB    C  CH2   0  -0.435   3.5496   1.3812  -0.2205
 PL4  CBA   C  CH1   0  -0.209   0.0516   2.6178   0.9347
 PL4  N     N  NH2   0  -0.777   4.8594   0.2181   1.4940
 PL4  OAI   O  O     0  -0.686   1.6277  -2.2910   0.3364
 PL4  PBB   P  P     0   1.455   0.4027  -2.7791  -0.3229
 PL4  OAJ   O  OH1   0  -0.732  -0.0145  -1.7917  -1.5065
 PL4  OAE   O  OH1   0  -0.730   0.4260  -4.2636  -0.9026
 PL4  OAS   O  O2    0  -0.582  -0.8892  -2.9636   0.6056
 PL4  CAW   C  CR6   0  -0.057  -2.5172  -1.1776   0.3941
 PL4  CAK   C  CR16  0  -0.132  -3.3412  -1.9494  -0.4094
 PL4  NAQ   N  N     0  -0.405  -4.2837  -1.4367  -1.1925
 PL4  CAV   C  CR6   0   0.139  -4.4442  -0.1246  -1.2511
 PL4  CAX   C  CR6   0   0.254  -3.6474   0.7393  -0.4836
 PL4  OAH   O  OH1   0  -0.648  -3.8628   2.0583  -0.6372
 PL4  CAY   C  CR6   0   0.048  -2.7083   0.2057   0.3970
 PL4  NAR   N  NH1   0  -0.570  -0.6455   1.4307   0.5343
 PL4  CAU   C  C     0   0.569  -0.7343   3.8903   0.6333
 PL4  OAG   O  OH1   0  -0.579  -0.1858   4.9659   1.1648
 PL4  OAD   O  O     0  -0.458  -1.7471   3.9311  -0.0316
 PL4  CAN   C  CH2   0  -0.439   1.4250   2.6680   0.2460
 PL4  CAL   C  CH2   0  -0.420   2.2980   1.4826   0.6391
 PL4  CA    C  CH1   0  -0.220   4.3951   0.1484   0.1287
 PL4  C     C  C     0   0.519   5.5220   0.0125  -0.8850
 PL4  O     O  O     0  -0.444   6.6824   0.2521  -0.6583
 PL4  OXT   O  OH1   0  -0.594   5.0837  -0.3910  -2.0732
 PL4  HB    H  HCH2  0   0.237   3.2544   1.3324  -1.2716
 PL4  HBA   H  HCH2  0   0.226   4.1658   2.2814  -0.1149
 PL4  HAA   H  HCH3  0   0.247  -6.2317   1.0208  -1.6250
 PL4  HAAA  H  HCH3  0   0.247  -5.0632   1.0694  -2.9311
 PL4  HAAB  H  HCH3  0   0.246  -6.0167  -0.3931  -2.6620
 PL4  HBAA  H  HCH1  0   0.280   0.2104   2.5841   2.0190
 PL4  HN    H  HNH2  0   0.352   5.3749  -0.6188   1.7340
 PL4  HNA   H  HNH2  0   0.341   5.5065   0.9895   1.6046
 PL4  HOAJ  H  HOH1  0   0.492  -0.8072  -2.0385  -2.0010
 PL4  HOAE  H  HOH1  0   0.504   1.2866  -4.5332  -1.2505
 PL4  HAP   H  HCH2  0   0.282  -1.8849  -2.1855   2.1865
 PL4  HAPA  H  HCH2  0   0.260  -0.6748  -1.1040   1.5050
 PL4  HAK   H  HCR6  0   0.259  -3.2401  -3.0289  -0.4313
 PL4  HOAH  H  HOH1  0   0.484  -3.1030   2.6009  -0.3640
 PL4  HAO   H  HCH2  0   0.236  -2.4584   1.9971   1.5350
 PL4  HAOA  H  HCH2  0   0.260  -1.6245   0.6320   2.1976
 PL4  HNAR  H  HNH1  0   0.356  -0.7787   1.4114  -0.4683
 PL4  HOAG  H  HOH1  0   0.487  -0.7019   5.7567   0.9439
 PL4  HAN   H  HCH2  0   0.230   1.2674   2.6767  -0.8385
 PL4  HANA  H  HCH2  0   0.247   1.9312   3.6022   0.4950
 PL4  HAL   H  HCH2  0   0.252   1.7231   0.5596   0.5396
 PL4  HALA  H  HCH2  0   0.222   2.5756   1.5699   1.6917
 PL4  HA    H  HCH1  0   0.277   3.7500  -0.7309   0.0307
 PL4  HO    H  HOH1  0   0.479   5.8206  -0.4391  -2.7006
 PL4  CAO   C  CH2   0  -0.389  -1.8689   1.1162   1.2490
 PL4  CAA   C  CH3   0  -0.721  -5.4961   0.4229  -2.1656
 PL4  CAP   C  CH2   0  -0.259  -1.4580  -1.8203   1.2515

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
 PL4  CAL  CB    single    1.522  0.020  1.522
 PL4  CB   CA    single    1.535  0.020  1.535
 PL4  CB   HB    single    0.970  0.020  1.090
 PL4  CB   HBA   single    0.970  0.020  1.090
 PL4  CAV  CAA   single    1.497  0.020  1.497
 PL4  CAA  HAA   single    0.970  0.020  1.090
 PL4  CAA  HAAA  single    0.970  0.020  1.090
 PL4  CAA  HAAB  single    0.970  0.020  1.090
 PL4  CAU  CBA   single    1.526  0.020  1.526
 PL4  CAN  CBA   single    1.537  0.020  1.537
 PL4  CBA  NAR   single    1.434  0.020  1.434
 PL4  CBA  HBAA  single    0.970  0.020  1.090
 PL4  CA   N     single    1.444  0.020  1.444
 PL4  N    HN    single    0.890  0.020  1.040
 PL4  N    HNA   single    0.890  0.020  1.040
 PL4  OAI  PBB   double    1.474  0.020  1.474
 PL4  OAJ  PBB   single    1.597  0.020  1.597
 PL4  PBB  OAS   single    1.602  0.020  1.602
 PL4  PBB  OAE   single    1.594  0.020  1.594
 PL4  OAJ  HOAJ  single    0.850  0.020  0.980
 PL4  OAE  HOAE  single    0.850  0.020  0.980
 PL4  OAS  CAP   single    1.431  0.020  1.431
 PL4  CAW  CAP   single    1.507  0.020  1.507
 PL4  CAP  HAP   single    0.970  0.020  1.090
 PL4  CAP  HAPA  single    0.970  0.020  1.090
 PL4  CAY  CAW   aromatic  1.396  0.020  1.396
 PL4  CAW  CAK   aromatic  1.386  0.020  1.386
 PL4  CAK  NAQ   aromatic  1.328  0.020  1.328
 PL4  CAK  HAK   single    0.930  0.020  1.080
 PL4  CAV  NAQ   aromatic  1.323  0.020  1.323
 PL4  CAX  CAV   aromatic  1.404  0.020  1.404
 PL4  OAH  CAX   single    1.345  0.020  1.345
 PL4  CAY  CAX   aromatic  1.394  0.020  1.394
 PL4  OAH  HOAH  single    0.850  0.020  0.980
 PL4  CAO  CAY   single    1.503  0.020  1.503
 PL4  CAO  NAR   single    1.451  0.020  1.451
 PL4  CAO  HAO   single    0.970  0.020  1.090
 PL4  CAO  HAOA  single    0.970  0.020  1.090
 PL4  NAR  HNAR  single    0.890  0.020  1.040
 PL4  OAD  CAU   double    1.212  0.020  1.212
 PL4  CAU  OAG   single    1.319  0.020  1.319
 PL4  OAG  HOAG  single    0.850  0.020  0.980
 PL4  CAN  CAL   single    1.524  0.020  1.524
 PL4  CAN  HAN   single    0.970  0.020  1.090
 PL4  CAN  HANA  single    0.970  0.020  1.090
 PL4  CAL  HAL   single    0.970  0.020  1.090
 PL4  CAL  HALA  single    0.970  0.020  1.090
 PL4  CA   C     single    1.522  0.020  1.522
 PL4  CA   HA    single    0.970  0.020  1.090
 PL4  C    O     double    1.206  0.020  1.206
 PL4  C    OXT   single    1.329  0.020  1.329
 PL4  OXT  HO    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
 PL4  HBA   CB   HB    106.33  3.000
 PL4  HBA   CB   CA    109.15  3.000
 PL4  HB    CB   CA    109.37  3.000
 PL4  HBA   CB   CAL   110.69  3.000
 PL4  HB    CB   CAL   108.91  3.000
 PL4  CA    CB   CAL   112.21  3.000
 PL4  HBAA  CBA  CAN   108.34  3.000
 PL4  HBAA  CBA  CAU   107.20  3.000
 PL4  CAN   CBA  CAU   110.15  3.000
 PL4  HBAA  CBA  NAR   108.74  3.000
 PL4  CAN   CBA  NAR   109.65  3.000
 PL4  CAU   CBA  NAR   112.64  3.000
 PL4  HNA   N    HN    106.17  3.000
 PL4  HNA   N    CA    110.21  3.000
 PL4  HN    N    CA    110.38  3.000
 PL4  OAS   PBB  OAE    96.63  3.000
 PL4  OAE   PBB  OAJ   108.07  3.000
 PL4  OAS   PBB  OAJ   106.87  3.000
 PL4  OAE   PBB  OAI   117.31  3.000
 PL4  OAS   PBB  OAI   116.68  3.000
 PL4  OAJ   PBB  OAI   110.11  3.000
 PL4  HOAJ  OAJ  PBB   115.83  3.000
 PL4  HOAE  OAE  PBB   113.81  3.000
 PL4  CAP   OAS  PBB   119.36  3.000
 PL4  CAY   CAW  CAK   118.13  3.000
 PL4  CAK   CAW  CAP   120.69  3.000
 PL4  CAY   CAW  CAP   121.17  3.000
 PL4  HAK   CAK  NAQ   116.00  3.000
 PL4  HAK   CAK  CAW   120.71  3.000
 PL4  NAQ   CAK  CAW   123.28  3.000
 PL4  CAV   NAQ  CAK   119.67  3.000
 PL4  CAX   CAV  NAQ   121.14  3.000
 PL4  CAX   CAV  CAA   120.51  3.000
 PL4  NAQ   CAV  CAA   118.35  3.000
 PL4  CAY   CAX  OAH   123.74  3.000
 PL4  CAY   CAX  CAV   119.50  3.000
 PL4  OAH   CAX  CAV   116.75  3.000
 PL4  HOAH  OAH  CAX   112.94  3.000
 PL4  CAO   CAY  CAX   120.16  3.000
 PL4  CAO   CAY  CAW   121.66  3.000
 PL4  CAX   CAY  CAW   118.05  3.000
 PL4  HNAR  NAR  CAO   111.90  3.000
 PL4  HNAR  NAR  CBA   110.90  3.000
 PL4  CAO   NAR  CBA   116.85  3.000
 PL4  OAD   CAU  OAG   122.75  3.000
 PL4  OAG   CAU  CBA   112.72  3.000
 PL4  OAD   CAU  CBA   124.53  3.000
 PL4  HOAG  OAG  CAU   110.60  3.000
 PL4  HANA  CAN  HAN   106.60  3.000
 PL4  HANA  CAN  CAL   109.96  3.000
 PL4  HAN   CAN  CAL   110.12  3.000
 PL4  HANA  CAN  CBA   109.88  3.000
 PL4  HAN   CAN  CBA   108.37  3.000
 PL4  CAL   CAN  CBA   111.77  3.000
 PL4  HALA  CAL  HAL   106.81  3.000
 PL4  HALA  CAL  CAN   109.40  3.000
 PL4  HAL   CAL  CAN   109.42  3.000
 PL4  HALA  CAL  CB    109.92  3.000
 PL4  HAL   CAL  CB    108.98  3.000
 PL4  CAN   CAL  CB    112.17  3.000
 PL4  HA    CA   C     107.75  3.000
 PL4  HA    CA   N     108.23  3.000
 PL4  C     CA   N     113.33  3.000
 PL4  HA    CA   CB    107.46  3.000
 PL4  C     CA   CB    109.15  3.000
 PL4  N     CA   CB    110.70  3.000
 PL4  OXT   C    O     123.05  3.000
 PL4  OXT   C    CA    112.24  3.000
 PL4  O     C    CA    124.71  3.000
 PL4  HO    OXT  C     110.07  3.000
 PL4  HAOA  CAO  HAO   104.45  3.000
 PL4  HAOA  CAO  NAR   109.57  3.000
 PL4  HAO   CAO  NAR   114.03  3.000
 PL4  HAOA  CAO  CAY   110.39  3.000
 PL4  HAO   CAO  CAY   109.50  3.000
 PL4  NAR   CAO  CAY   108.83  3.000
 PL4  HAAB  CAA  HAAA  108.30  3.000
 PL4  HAAB  CAA  HAA   108.33  3.000
 PL4  HAAA  CAA  HAA   106.88  3.000
 PL4  HAAB  CAA  CAV   109.91  3.000
 PL4  HAAA  CAA  CAV   111.49  3.000
 PL4  HAA   CAA  CAV   111.79  3.000
 PL4  HAPA  CAP  HAP   107.55  3.000
 PL4  HAPA  CAP  CAW   110.90  3.000
 PL4  HAP   CAP  CAW   110.82  3.000
 PL4  HAPA  CAP  OAS   110.12  3.000
 PL4  HAP   CAP  OAS   105.96  3.000
 PL4  CAW   CAP  OAS   111.31  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
 PL4  CONST_01  CAV   CAX  CAY  CAW     0.00   0.0  0
 PL4  CONST_02  CAV   NAQ  CAK  CAW     0.00   0.0  0
 PL4  CONST_03  CAX   CAY  CAW  CAK     0.00   0.0  0
 PL4  CONST_04  CAX   CAV  NAQ  CAK     0.00   0.0  0
 PL4  CONST_05  CAY   CAW  CAK  NAQ     0.00   0.0  0
 PL4  CONST_06  CAY   CAX  CAV  NAQ     0.00   0.0  0
 PL4  CONST_07  CAK   NAQ  CAV  CAA   180.00   0.0  0
 PL4  CONST_08  CAY   CAX  CAV  CAA   180.00   0.0  0
 PL4  CONST_09  CAX   CAY  CAW  CAP   180.00   0.0  0
 PL4  CONST_10  NAQ   CAK  CAW  CAP   180.00   0.0  0
 PL4  CONST_11  OAH   CAX  CAY  CAW   180.00   0.0  0
 PL4  CONST_12  CAO   CAY  CAW  CAK   180.00   0.0  0
 PL4  CONST_13  OAH   CAX  CAV  NAQ   180.00   0.0  0
 PL4  CONST_14  CAO   CAY  CAX  CAV   180.00   0.0  0
 PL4  CONST_15  HAK   CAK  NAQ  CAV   180.00   0.0  0
 PL4  CONST_16  HOAG  OAG  CAU  CBA   180.00   0.0  0
 PL4  CONST_17  HO    OXT  C    CA    180.00   0.0  0
 PL4  Var_01    CAY   CAW  CAP  OAS  -145.72  30.0  1
 PL4  Var_02    NAR   CAO  CAY  CAW    84.93  30.0  3
 PL4  Var_03    HAA   CAA  CAV  NAQ   121.49  30.0  2
 PL4  Var_04    CAY   CAO  NAR  CBA   158.49  30.0  1
 PL4  Var_05    CAW   CAP  OAS  PBB    90.69  30.0  3
 PL4  Var_06    CBA   CAN  CAL  CB    169.56  30.0  1
 PL4  Var_07    CA    CB   CAL  CAN  -177.20  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
 PL4  chir_01  CBA  CAU  CAN  NAR  positiv
 PL4  chir_02  CA   N    CB   C    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
 PL4  plan-1  CAW   0.020
 PL4  plan-1  CAK   0.020
 PL4  plan-1  NAQ   0.020
 PL4  plan-1  CAV   0.020
 PL4  plan-1  CAX   0.020
 PL4  plan-1  OAH   0.020
 PL4  plan-1  CAY   0.020
 PL4  plan-1  HAK   0.020
 PL4  plan-1  CAO   0.020
 PL4  plan-1  CAA   0.020
 PL4  plan-1  CAP   0.020
 PL4  plan-2  CBA   0.020
 PL4  plan-2  CAU   0.020
 PL4  plan-2  OAG   0.020
 PL4  plan-2  OAD   0.020
 PL4  plan-2  HOAG  0.020
 PL4  plan-3  CA    0.020
 PL4  plan-3  C     0.020
 PL4  plan-3  O     0.020
 PL4  plan-3  OXT   0.020
 PL4  plan-3  HO    0.020

