# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 22:05:12 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (1S)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-3-ene-1,3-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNC2=C(C[C@@H](C2)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
 RW2  RW2  '(1S)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-3-ene-1,3-dicarboxylic acid'  ligand  46  27  .  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_RW2
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
 RW2  O2   O  O     0  -0.698   0.5248  -3.2827   0.1190
 RW2  P    P  P     0   1.465   1.8725  -2.8346   0.5155
 RW2  O4   O  OH1   0  -0.738   2.0774  -3.0650   2.0816
 RW2  O3   O  OH1   0  -0.726   3.1304  -3.4428  -0.2449
 RW2  O    O  O2    0  -0.592   2.2100  -1.2959   0.2258
 RW2  C6   C  CH2   0  -0.210   1.2327  -0.3215   0.5625
 RW2  C3   C  CR6   0  -0.061   1.7750   1.0592   0.3387
 RW2  C2   C  CR16  0  -0.135   3.0667   1.2820  -0.1069
 RW2  N    N  N     0  -0.404   3.5676   2.4978  -0.2978
 RW2  C1   C  CR6   0   0.131   2.8195   3.5614  -0.0640
 RW2  C7   C  CH3   0  -0.784   3.4190   4.9167  -0.2904
 RW2  C    C  CR6   0   0.263   1.4959   3.4312   0.3857
 RW2  O1   O  OH1   0  -0.620   0.7132   4.5016   0.6148
 RW2  C4   C  CR6   0   0.088   0.9602   2.1660   0.5998
 RW2  C5   C  CH2   0  -0.396  -0.4677   2.0055   1.0669
 RW2  N1   N  NH1   0  -0.645  -1.3266   1.6111  -0.0295
 RW2  C8   C  CR5   0   0.400  -2.1066   0.5309  -0.0908
 RW2  C12  C  CR5   0  -0.223  -2.8798   0.1311  -1.1540
 RW2  C15  C  C     0   0.498  -2.9837   0.8767  -2.3715
 RW2  O6   O  O     0  -0.505  -2.3649   1.9027  -2.6316
 RW2  O7   O  OH1   0  -0.612  -3.8461   0.3455  -3.2462
 RW2  C9   C  CH2   0  -0.519  -2.2929  -0.4063   1.0698
 RW2  C10  C  CR15  0  -0.404  -2.8908  -1.6450   0.4079
 RW2  C11  C  CH2   0  -0.449  -3.6462  -1.1239  -0.8306
 RW2  C13  C  C     0   0.563  -3.7273  -2.4857   1.3293
 RW2  O5   O  O     0  -0.438  -3.8883  -2.2798   2.5066
 RW2  O14  O  OH1   0  -0.594  -4.2779  -3.5098   0.6882
 RW2  H1   H  HOH1  0   0.498   2.9423  -2.8131   2.4333
 RW2  H2   H  HOH1  0   0.507   3.1769  -4.4083  -0.2312
 RW2  H3   H  HCH2  0   0.261   0.3409  -0.4834  -0.0483
 RW2  H4   H  HCH2  0   0.254   0.9427  -0.4263   1.6145
 RW2  H5   H  HCR6  0   0.261   3.7335   0.4563  -0.3182
 RW2  H6   H  HCH3  0   0.260   2.8649   5.4908  -1.0376
 RW2  H7   H  HCH3  0   0.258   3.4465   5.5114   0.6264
 RW2  H8   H  HCH3  0   0.273   4.4420   4.8135  -0.6440
 RW2  H9   H  HOH1  0   0.490   1.1998   5.3250   0.4999
 RW2  H10  H  HCH2  0   0.277  -0.5240   1.2566   1.8568
 RW2  H11  H  HCH2  0   0.290  -0.8330   2.9318   1.5090
 RW2  H12  H  HNH1  0   0.405  -1.3214   2.1946  -0.8552
 RW2  H13  H  HOH1  0   0.475  -3.8673   0.8915  -4.0448
 RW2  H14  H  HCH2  0   0.266  -1.3756  -0.6360   1.6114
 RW2  H15  H  HCH2  0   0.291  -2.9774   0.0535   1.7893
 RW2  H16  H  HCR5  0   0.307  -2.0633  -2.2716   0.0554
 RW2  H17  H  HCH2  0   0.241  -4.6966  -0.9138  -0.5986
 RW2  H18  H  HCH2  0   0.252  -3.6385  -1.8592  -1.6354
 RW2  H19  H  HOH1  0   0.482  -4.8141  -4.0372   1.2993

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
 RW2  O6   C15  double    1.226  0.020  1.226
 RW2  O7   C15  single    1.338  0.020  1.338
 RW2  C15  C12  single    1.431  0.020  1.431
 RW2  O1   C    single    1.346  0.020  1.346
 RW2  C12  C11  single    1.506  0.020  1.506
 RW2  C12  C8   double    1.374  0.020  1.374
 RW2  N1   C8   single    1.334  0.020  1.334
 RW2  N1   C5   single    1.447  0.020  1.447
 RW2  C7   C1   single    1.499  0.020  1.499
 RW2  C11  C10  single    1.541  0.020  1.541
 RW2  C8   C9   single    1.503  0.020  1.503
 RW2  C    C1   aromatic  1.404  0.020  1.404
 RW2  C    C4   aromatic  1.390  0.020  1.390
 RW2  C5   C4   single    1.511  0.020  1.511
 RW2  C1   N    aromatic  1.321  0.020  1.321
 RW2  C4   C3   aromatic  1.399  0.020  1.399
 RW2  C10  C9   single    1.526  0.020  1.526
 RW2  C10  C13  single    1.502  0.020  1.502
 RW2  N    C2   aromatic  1.329  0.020  1.329
 RW2  O2   P    double    1.475  0.020  1.475
 RW2  C3   C2   aromatic  1.384  0.020  1.384
 RW2  C3   C6   single    1.500  0.020  1.500
 RW2  O5   C13  double    1.206  0.020  1.206
 RW2  C13  O14  single    1.328  0.020  1.328
 RW2  O    P    single    1.602  0.020  1.602
 RW2  O    C6   single    1.421  0.020  1.421
 RW2  O3   P    single    1.591  0.020  1.591
 RW2  P    O4   single    1.596  0.020  1.596
 RW2  O4   H1   single    0.850  0.020  0.980
 RW2  O3   H2   single    0.850  0.020  0.980
 RW2  C6   H3   single    0.970  0.020  1.090
 RW2  C6   H4   single    0.970  0.020  1.090
 RW2  C2   H5   single    0.930  0.020  1.080
 RW2  C7   H6   single    0.970  0.020  1.090
 RW2  C7   H7   single    0.970  0.020  1.090
 RW2  C7   H8   single    0.970  0.020  1.090
 RW2  O1   H9   single    0.850  0.020  0.980
 RW2  C5   H10  single    0.970  0.020  1.090
 RW2  C5   H11  single    0.970  0.020  1.090
 RW2  N1   H12  single    0.860  0.020  1.020
 RW2  O7   H13  single    0.850  0.020  0.980
 RW2  C9   H14  single    0.970  0.020  1.090
 RW2  C9   H15  single    0.970  0.020  1.090
 RW2  C10  H16  single    0.970  0.020  1.090
 RW2  C11  H17  single    0.970  0.020  1.090
 RW2  C11  H18  single    0.970  0.020  1.090
 RW2  O14  H19  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
 RW2  O    P    O3    96.56  3.000
 RW2  O3   P    O4   108.20  3.000
 RW2  O    P    O4   106.80  3.000
 RW2  O4   P    O2   109.71  3.000
 RW2  O3   P    O2   118.56  3.000
 RW2  O    P    O2   115.84  3.000
 RW2  H1   O4   P    115.72  3.000
 RW2  H2   O3   P    114.40  3.000
 RW2  C6   O    P    118.11  3.000
 RW2  H4   C6   H3   107.84  3.000
 RW2  H4   C6   C3   109.07  3.000
 RW2  H3   C6   C3   110.36  3.000
 RW2  H4   C6   O    110.11  3.000
 RW2  H3   C6   O    109.11  3.000
 RW2  C3   C6   O    110.32  3.000
 RW2  C4   C3   C2   118.44  3.000
 RW2  C2   C3   C6   122.23  3.000
 RW2  C4   C3   C6   119.33  3.000
 RW2  H5   C2   N    115.96  3.000
 RW2  H5   C2   C3   121.00  3.000
 RW2  N    C2   C3   123.04  3.000
 RW2  C1   N    C2   119.85  3.000
 RW2  C    C1   C7   120.61  3.000
 RW2  C    C1   N    121.05  3.000
 RW2  C7   C1   N    118.34  3.000
 RW2  H8   C7   H7   107.50  3.000
 RW2  H8   C7   H6   107.73  3.000
 RW2  H7   C7   H6   107.48  3.000
 RW2  H8   C7   C1   109.85  3.000
 RW2  H7   C7   C1   112.04  3.000
 RW2  H6   C7   C1   112.04  3.000
 RW2  C4   C    O1   118.26  3.000
 RW2  C4   C    C1   119.80  3.000
 RW2  O1   C    C1   121.95  3.000
 RW2  H9   O1   C    111.46  3.000
 RW2  C5   C4   C    120.56  3.000
 RW2  C5   C4   C3   121.60  3.000
 RW2  C    C4   C3   117.82  3.000
 RW2  H11  C5   H10  105.83  3.000
 RW2  H11  C5   N1   109.88  3.000
 RW2  H10  C5   N1   109.34  3.000
 RW2  H11  C5   C4   110.61  3.000
 RW2  H10  C5   C4   110.23  3.000
 RW2  N1   C5   C4   110.83  3.000
 RW2  H12  N1   C8   115.65  3.000
 RW2  H12  N1   C5   117.28  3.000
 RW2  C8   N1   C5   127.05  3.000
 RW2  C9   C8   C12  110.25  3.000
 RW2  C9   C8   N1   122.82  3.000
 RW2  C12  C8   N1   126.89  3.000
 RW2  C11  C12  C15  125.44  3.000
 RW2  C11  C12  C8   111.27  3.000
 RW2  C15  C12  C8   123.19  3.000
 RW2  O7   C15  O6   121.25  3.000
 RW2  O7   C15  C12  113.33  3.000
 RW2  O6   C15  C12  125.43  3.000
 RW2  H13  O7   C15  109.24  3.000
 RW2  H15  C9   H14  106.75  3.000
 RW2  H15  C9   C10  112.40  3.000
 RW2  H14  C9   C10  111.97  3.000
 RW2  H15  C9   C8   108.85  3.000
 RW2  H14  C9   C8   114.25  3.000
 RW2  C10  C9   C8   102.69  3.000
 RW2  H16  C10  C13  107.33  3.000
 RW2  H16  C10  C11  107.74  3.000
 RW2  C13  C10  C11  114.16  3.000
 RW2  H16  C10  C9   107.92  3.000
 RW2  C13  C10  C9   113.98  3.000
 RW2  C11  C10  C9   105.43  3.000
 RW2  H18  C11  H17  106.99  3.000
 RW2  H18  C11  C10  111.21  3.000
 RW2  H17  C11  C10  111.37  3.000
 RW2  H18  C11  C12  113.58  3.000
 RW2  H17  C11  C12  111.93  3.000
 RW2  C10  C11  C12  101.83  3.000
 RW2  O14  C13  O5   123.21  3.000
 RW2  O14  C13  C10  111.50  3.000
 RW2  O5   C13  C10  125.29  3.000
 RW2  H19  O14  C13  110.16  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
 RW2  CONST_01  C1   C    C4   C3      0.00   0.0  0
 RW2  CONST_02  C1   N    C2   C3      0.00   0.0  0
 RW2  CONST_03  C    C1   N    C2      0.00   0.0  0
 RW2  CONST_04  C    C4   C3   C2      0.00   0.0  0
 RW2  CONST_05  C4   C    C1   N       0.00   0.0  0
 RW2  CONST_06  C4   C3   C2   N       0.00   0.0  0
 RW2  CONST_07  C    C4   C3   C6    180.00   0.0  0
 RW2  CONST_08  N    C2   C3   C6    180.00   0.0  0
 RW2  CONST_09  O1   C    C4   C3    180.00   0.0  0
 RW2  CONST_10  C7   C1   N    C2    180.00   0.0  0
 RW2  CONST_11  C5   C4   C3   C2    180.00   0.0  0
 RW2  CONST_12  O1   C    C1   N     180.00   0.0  0
 RW2  CONST_13  C5   C4   C    C1    180.00   0.0  0
 RW2  CONST_14  C4   C    C1   C7    180.00   0.0  0
 RW2  CONST_15  H5   C2   N    C1    180.00   0.0  0
 RW2  CONST_16  H13  O7   C15  C12   180.00   0.0  0
 RW2  CONST_17  H19  O14  C13  C10   180.00   0.0  0
 RW2  Var_01    C10  C11  C12  C8    -16.75  30.0  1
 RW2  Var_02    C10  C9   C8   C12    18.46  30.0  1
 RW2  Var_03    C11  C12  C8   C9     -0.95  30.0  1
 RW2  Var_04    C4   C3   C6   O     179.39  30.0  1
 RW2  Var_05    N1   C5   C4   C3    -75.62  30.0  3
 RW2  Var_06    C8   N1   C5   C4    123.37  30.0  2
 RW2  Var_07    C12  C8   N1   C5   -177.18  30.0  2
 RW2  Var_08    O6   C15  C12  C8      3.48  30.0  2
 RW2  Var_09    H6   C7   C1   N     120.23  30.0  2
 RW2  Var_10    C3   C6   O    P     174.76  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
 RW2  chir_01  C10  C11  C9  C13  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
 RW2  plan-1  C6   0.020
 RW2  plan-1  C3   0.020
 RW2  plan-1  C2   0.020
 RW2  plan-1  N    0.020
 RW2  plan-1  C1   0.020
 RW2  plan-1  C7   0.020
 RW2  plan-1  C    0.020
 RW2  plan-1  O1   0.020
 RW2  plan-1  C4   0.020
 RW2  plan-1  C5   0.020
 RW2  plan-1  H5   0.020
 RW2  plan-2  C10  0.020
 RW2  plan-2  C13  0.020
 RW2  plan-2  O5   0.020
 RW2  plan-2  O14  0.020
 RW2  plan-2  H19  0.020
 RW2  plan-3  C12  0.020
 RW2  plan-3  C15  0.020
 RW2  plan-3  O6   0.020
 RW2  plan-3  O7   0.020
 RW2  plan-3  H13  0.020

