# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 03:26:03 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](CCC(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
 PL6  PL6  '(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid'  ligand  42  25  .  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_PL6
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
 PL6  OAE   O  O     0  -0.721  -3.8946  -3.0321   0.1487
 PL6  PAY   P  P     0   1.478  -4.4383  -1.6628   0.1573
 PL6  OAI   O  OH1   0  -0.711  -5.6904  -1.3362  -0.7687
 PL6  OAD   O  OH1   0  -0.773  -4.8061  -1.2389   1.6527
 PL6  OAQ   O  O2    0  -0.634  -3.4823  -0.5175  -0.4208
 PL6  CAN   C  CH2   0  -0.250  -2.1331  -0.4491   0.0197
 PL6  CAU   C  CR6   0   0.163  -1.6009   0.9392  -0.2057
 PL6  CAK   C  CR16  0  -0.244  -2.4016   1.9698  -0.6516
 PL6  NAO   N  N     0  -0.420  -1.9493   3.2088  -0.8567
 PL6  CAT   C  CR6   0   0.148  -0.6849   3.5033  -0.6400
 PL6  CAA   C  CH3   0  -0.729  -0.2176   4.9049  -0.8777
 PL6  CAV   C  CR6   0   0.295   0.2212   2.5219  -0.1887
 PL6  OAH   O  OH1   0  -0.588   1.4830   2.8822   0.0091
 PL6  CAW   C  CR6   0  -0.070  -0.2450   1.2212   0.0388
 PL6  CAJ   C  C1    0  -0.077   0.6663   0.1975   0.5411
 PL6  N     N  N     0  -0.170   1.9020   0.4462   0.6981
 PL6  CA    C  CH1   0  -0.248   2.7773  -0.5747   1.2033
 PL6  C     C  C     0   0.457   3.4691  -0.0372   2.4442
 PL6  OXT   O  OH1   0  -0.440   4.1077  -1.0049   3.0845
 PL6  O     O  O     0  -0.457   3.4492   1.1107   2.7989
 PL6  CB    C  CH2   0  -0.439   3.8227  -0.9504   0.1425
 PL6  CG    C  CH2   0  -0.600   3.1726  -1.5697  -1.0822
 PL6  CD    C  C     0   0.584   4.1781  -2.0407  -2.0975
 PL6  OE2   O  OH1   0  -0.567   3.5903  -2.6347  -3.1310
 PL6  OE1   O  O     0  -0.510   5.3716  -1.9023  -2.0077
 PL6  HOAI  H  HOH1  0   0.514  -6.4238  -1.9589  -0.6773
 PL6  HOAD  H  HOH1  0   0.471  -5.2405  -0.3819   1.7552
 PL6  HAN   H  HCH2  0   0.273  -2.0554  -0.7016   1.0829
 PL6  HANA  H  HCH2  0   0.330  -1.5392  -1.1812  -0.5335
 PL6  HAK   H  HCR6  0   0.249  -3.4518   1.8137  -0.8566
 PL6  HAA   H  HCH3  0   0.278   0.1782   5.3559   0.0341
 PL6  HAAA  H  HCH3  0   0.250   0.5785   4.9437  -1.6232
 PL6  HAAB  H  HCH3  0   0.205  -1.0465   5.5157  -1.2288
 PL6  HOAH  H  HOH1  0   0.487   1.9860   2.0780   0.3155
 PL6  HAJ   H  H     0   0.207   0.2565  -0.7824   0.7957
 PL6  HA    H  HCH1  0   0.223   2.2234  -1.4801   1.4901
 PL6  HOXT  H  HOH1  0   0.493   4.5612  -0.6485   3.8631
 PL6  HB    H  HCH2  0   0.270   4.3867  -0.0576  -0.1350
 PL6  HBA   H  HCH2  0   0.204   4.5264  -1.6556   0.5846
 PL6  HG    H  HCH2  0   0.296   2.5445  -2.4203  -0.7989
 PL6  HGA   H  HCH2  0   0.289   2.5070  -0.8600  -1.5816
 PL6  HOE2  H  HOH1  0   0.485   4.2604  -2.9195  -3.7700

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
 PL6  OAE  PAY   double    1.473  0.020  1.473
 PL6  OAI  PAY   single    1.591  0.020  1.591
 PL6  PAY  OAQ   single    1.600  0.020  1.600
 PL6  PAY  OAD   single    1.597  0.020  1.597
 PL6  OAI  HOAI  single    0.850  0.020  0.980
 PL6  OAD  HOAD  single    0.850  0.020  0.980
 PL6  OAQ  CAN   single    1.421  0.020  1.421
 PL6  CAU  CAN   single    1.504  0.020  1.504
 PL6  CAN  HAN   single    0.970  0.020  1.090
 PL6  CAN  HANA  single    0.970  0.020  1.090
 PL6  CAW  CAU   aromatic  1.406  0.020  1.406
 PL6  CAU  CAK   aromatic  1.379  0.020  1.379
 PL6  CAK  NAO   aromatic  1.335  0.020  1.335
 PL6  CAK  HAK   single    0.930  0.020  1.080
 PL6  CAT  NAO   aromatic  1.316  0.020  1.316
 PL6  CAV  CAT   aromatic  1.410  0.020  1.410
 PL6  CAT  CAA   single    1.496  0.020  1.496
 PL6  CAA  HAA   single    0.970  0.020  1.090
 PL6  CAA  HAAA  single    0.970  0.020  1.090
 PL6  CAA  HAAB  single    0.970  0.020  1.090
 PL6  OAH  CAV   single    1.327  0.020  1.327
 PL6  CAW  CAV   aromatic  1.400  0.020  1.400
 PL6  OAH  HOAH  single    0.850  0.020  0.980
 PL6  CAJ  CAW   single    1.460  0.020  1.460
 PL6  N    CAJ   double    1.270  0.020  1.270
 PL6  CAJ  HAJ   single    0.930  0.020  1.080
 PL6  CA   N     single    1.437  0.020  1.437
 PL6  C    CA    single    1.519  0.020  1.519
 PL6  CA   CB    single    1.536  0.020  1.536
 PL6  CA   HA    single    0.970  0.020  1.090
 PL6  O    C     double    1.202  0.020  1.202
 PL6  C    OXT   single    1.324  0.020  1.324
 PL6  OXT  HOXT  single    0.850  0.020  0.980
 PL6  CB   CG    single    1.519  0.020  1.519
 PL6  CB   HB    single    0.970  0.020  1.090
 PL6  CB   HBA   single    0.970  0.020  1.090
 PL6  CG   CD    single    1.505  0.020  1.505
 PL6  CG   HG    single    0.970  0.020  1.090
 PL6  CG   HGA   single    0.970  0.020  1.090
 PL6  CD   OE1   double    1.205  0.020  1.205
 PL6  CD   OE2   single    1.329  0.020  1.329
 PL6  OE2  HOE2  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
 PL6  OAQ   PAY  OAD   106.61  3.000
 PL6  OAD   PAY  OAI   108.01  3.000
 PL6  OAQ   PAY  OAI    96.49  3.000
 PL6  OAD   PAY  OAE   109.70  3.000
 PL6  OAQ   PAY  OAE   116.28  3.000
 PL6  OAI   PAY  OAE   118.54  3.000
 PL6  HOAI  OAI  PAY   114.20  3.000
 PL6  HOAD  OAD  PAY   115.99  3.000
 PL6  CAN   OAQ  PAY   119.32  3.000
 PL6  HANA  CAN  HAN   107.36  3.000
 PL6  HANA  CAN  CAU   110.50  3.000
 PL6  HAN   CAN  CAU   109.46  3.000
 PL6  HANA  CAN  OAQ   109.07  3.000
 PL6  HAN   CAN  OAQ   110.92  3.000
 PL6  CAU   CAN  OAQ   109.51  3.000
 PL6  CAW   CAU  CAK   117.78  3.000
 PL6  CAK   CAU  CAN   122.20  3.000
 PL6  CAW   CAU  CAN   120.02  3.000
 PL6  HAK   CAK  NAO   115.72  3.000
 PL6  HAK   CAK  CAU   121.15  3.000
 PL6  NAO   CAK  CAU   123.13  3.000
 PL6  CAT   NAO  CAK   120.53  3.000
 PL6  CAV   CAT  CAA   120.14  3.000
 PL6  CAA   CAT  NAO   118.91  3.000
 PL6  CAV   CAT  NAO   120.95  3.000
 PL6  HAAB  CAA  HAAA  108.38  3.000
 PL6  HAAB  CAA  HAA   108.29  3.000
 PL6  HAAA  CAA  HAA   106.95  3.000
 PL6  HAAB  CAA  CAT   109.83  3.000
 PL6  HAAA  CAA  CAT   111.69  3.000
 PL6  HAA   CAA  CAT   111.56  3.000
 PL6  CAW   CAV  OAH   122.99  3.000
 PL6  CAW   CAV  CAT   118.99  3.000
 PL6  OAH   CAV  CAT   118.02  3.000
 PL6  HOAH  OAH  CAV   107.85  3.000
 PL6  CAJ   CAW  CAV   119.96  3.000
 PL6  CAJ   CAW  CAU   121.41  3.000
 PL6  CAV   CAW  CAU   118.62  3.000
 PL6  HAJ   CAJ  N     120.79  3.000
 PL6  HAJ   CAJ  CAW   118.36  3.000
 PL6  N     CAJ  CAW   120.83  3.000
 PL6  CA    N    CAJ   119.81  3.000
 PL6  HA    CA   CB    108.76  3.000
 PL6  HA    CA   C     107.92  3.000
 PL6  CB    CA   C     109.93  3.000
 PL6  HA    CA   N     111.71  3.000
 PL6  CB    CA   N     110.22  3.000
 PL6  C     CA   N     108.26  3.000
 PL6  O     C    OXT   124.29  3.000
 PL6  OXT   C    CA    110.85  3.000
 PL6  O     C    CA    124.86  3.000
 PL6  HOXT  OXT  C     110.20  3.000
 PL6  HBA   CB   HB    107.37  3.000
 PL6  HBA   CB   CG    109.86  3.000
 PL6  HB    CB   CG    110.46  3.000
 PL6  HBA   CB   CA    108.52  3.000
 PL6  HB    CB   CA    109.09  3.000
 PL6  CG    CB   CA    111.43  3.000
 PL6  HGA   CG   HG    105.86  3.000
 PL6  HGA   CG   CD    107.56  3.000
 PL6  HG    CG   CD    108.36  3.000
 PL6  HGA   CG   CB    111.36  3.000
 PL6  HG    CG   CB    110.72  3.000
 PL6  CD    CG   CB    112.69  3.000
 PL6  OE1   CD   OE2   123.19  3.000
 PL6  OE2   CD   CG    111.66  3.000
 PL6  OE1   CD   CG    125.15  3.000
 PL6  HOE2  OE2  CD    109.78  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
 PL6  CONST_01  CAT   CAV  CAW  CAU     0.00   0.0  0
 PL6  CONST_02  CAT   NAO  CAK  CAU     0.00   0.0  0
 PL6  CONST_03  CAV   CAW  CAU  CAK     0.00   0.0  0
 PL6  CONST_04  CAV   CAT  NAO  CAK     0.00   0.0  0
 PL6  CONST_05  CAW   CAU  CAK  NAO     0.00   0.0  0
 PL6  CONST_06  CAW   CAV  CAT  NAO     0.00   0.0  0
 PL6  CONST_07  CAV   CAW  CAU  CAN   180.00   0.0  0
 PL6  CONST_08  NAO   CAK  CAU  CAN   180.00   0.0  0
 PL6  CONST_09  OAH   CAV  CAW  CAU   180.00   0.0  0
 PL6  CONST_10  CAJ   CAW  CAU  CAK   180.00   0.0  0
 PL6  CONST_11  CAA   CAT  NAO  CAK   180.00   0.0  0
 PL6  CONST_12  OAH   CAV  CAT  NAO   180.00   0.0  0
 PL6  CONST_13  CAJ   CAW  CAV  CAT   180.00   0.0  0
 PL6  CONST_14  CAW   CAV  CAT  CAA   180.00   0.0  0
 PL6  CONST_15  HAK   CAK  NAO  CAT   180.00   0.0  0
 PL6  CONST_16  HOXT  OXT  C    CA    180.00   0.0  0
 PL6  CONST_17  HOE2  OE2  CD   CG    180.00   0.0  0
 PL6  Var_01    CAW   CAU  CAN  OAQ  -174.17  30.0  1
 PL6  Var_02    N     CAJ  CAW  CAU   176.63  30.0  1
 PL6  Var_03    HAA   CAA  CAT  NAO   119.48  30.0  2
 PL6  Var_04    CAU   CAN  OAQ  PAY  -158.18  30.0  3
 PL6  Var_05    CD    CG   CB   CA   -175.81  30.0  3
 PL6  Var_06    OE1   CD   CG   CB     -3.21  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
 PL6  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
 PL6  plan-1  CAN   0.020
 PL6  plan-1  CAU   0.020
 PL6  plan-1  CAK   0.020
 PL6  plan-1  NAO   0.020
 PL6  plan-1  CAT   0.020
 PL6  plan-1  CAA   0.020
 PL6  plan-1  CAV   0.020
 PL6  plan-1  OAH   0.020
 PL6  plan-1  CAW   0.020
 PL6  plan-1  CAJ   0.020
 PL6  plan-1  HAK   0.020
 PL6  plan-2  CA    0.020
 PL6  plan-2  C     0.020
 PL6  plan-2  OXT   0.020
 PL6  plan-2  O     0.020
 PL6  plan-2  HOXT  0.020
 PL6  plan-3  CG    0.020
 PL6  plan-3  CD    0.020
 PL6  plan-3  OE2   0.020
 PL6  plan-3  OE1   0.020
 PL6  plan-3  HOE2  0.020
 PL6  plan-4  CAW   0.020
 PL6  plan-4  CAJ   0.020
 PL6  plan-4  N     0.020
 PL6  plan-4  CA    0.020
 PL6  plan-4  HAJ   0.020

