# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:29:41 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: (4S,5R)-4,5-dihydroxy-5-[(3E,6E)-octa-3,6-dien-1-yl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C=C\C\C=C\CC[C@]1(O)NC(=O)C[C@@H]1O
#
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
 HVV  HVV  (4S,5R)-4,5-dihydroxy-5-[(3E,6E)-octa-3,6-dien-1-yl]pyrrolidin-2-one  ligand  35  16  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HVV
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
 HVV  CAP  C  CH3   0  -0.707   6.7950   1.4388   0.3818
 HVV  CAO  C  C1    0  -0.228   6.0125   0.1976   0.1017
 HVV  CAN  C  C1    0  -0.194   4.8192   0.1611  -0.4845
 HVV  CAM  C  CH2   0  -0.555   4.0367  -1.0913  -0.7542
 HVV  CAL  C  C1    0  -0.205   2.7339  -1.1020  -0.0095
 HVV  CAK  C  C1    0  -0.204   1.5352  -1.1201  -0.5835
 HVV  CAJ  C  CH2   0  -0.521   0.2314  -1.1066   0.1508
 HVV  CAI  C  CH2   0  -0.427  -0.5789   0.1470  -0.1955
 HVV  CAH  C  CT    0   0.381  -1.9697   0.1855   0.4300
 HVV  OAC  O  OH1   0  -0.665  -1.9121   0.0867   1.8338
 HVV  NAD  N  NH1   0  -0.664  -2.8460  -0.8151  -0.1387
 HVV  CAE  C  C     0   0.532  -4.1427  -0.4461  -0.2120
 HVV  OAB  O  O     0  -0.480  -5.0664  -1.1473  -0.5796
 HVV  CAF  C  CH2   0  -0.634  -4.2160   0.9909   0.2582
 HVV  CAG  C  CH1   0   0.030  -2.7723   1.4763   0.1543
 HVV  OAA  O  OH1   0  -0.663  -2.4700   1.9141  -1.1451
 HVV  H1   H  HCH3  0   0.235   6.9911   1.5470   1.4511
 HVV  H2   H  HCH3  0   0.235   7.7705   1.4087  -0.1085
 HVV  H3   H  HCH3  0   0.234   6.2725   2.3331   0.0424
 HVV  H4   H  H     0   0.230   6.4724  -0.7402   0.4056
 HVV  H5   H  H     0   0.232   4.3475   1.0931  -0.7884
 HVV  H6   H  HCH2  0   0.244   3.8382  -1.1835  -1.8265
 HVV  H7   H  HCH2  0   0.244   4.6363  -1.9602  -0.4655
 HVV  H8   H  H     0   0.236   2.8032  -1.0781   1.0761
 HVV  H10  H  H     0   0.235   1.4708  -1.1337  -1.6700
 HVV  H12  H  HCH2  0   0.237  -0.3307  -2.0069  -0.1229
 HVV  H13  H  HCH2  0   0.239   0.4231  -1.1645   1.2253
 HVV  H14  H  HCH2  0   0.245  -0.0254   1.0276   0.1402
 HVV  H15  H  HCH2  0   0.245  -0.6720   0.2247  -1.2796
 HVV  H16  H  HOH1  0   0.453  -1.5927  -0.7878   2.0814
 HVV  H17  H  HNH1  0   0.397  -2.5513  -1.7576  -0.3485
 HVV  H18  H  HCH2  0   0.281  -4.9205   1.5782  -0.3320
 HVV  H19  H  HCH2  0   0.285  -4.5678   1.0025   1.2929
 HVV  H20  H  HCH1  0   0.240  -2.5279   2.2363   0.9039
 HVV  H21  H  HOH1  0   0.459  -3.0276   2.6726  -1.3438

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
 HVV  CAP  CAO  single  1.494  0.020  1.494
 HVV  CAO  CAN  double  1.330  0.020  1.330
 HVV  OAC  CAH  single  1.408  0.020  1.408
 HVV  OAA  CAG  single  1.404  0.020  1.404
 HVV  CAG  CAH  single  1.545  0.020  1.545
 HVV  CAG  CAF  single  1.527  0.020  1.527
 HVV  CAN  CAM  single  1.501  0.020  1.501
 HVV  CAH  CAI  single  1.525  0.020  1.525
 HVV  CAH  NAD  single  1.447  0.020  1.447
 HVV  CAL  CAM  single  1.501  0.020  1.501
 HVV  CAL  CAK  double  1.329  0.020  1.329
 HVV  CAI  CAJ  single  1.532  0.020  1.532
 HVV  CAJ  CAK  single  1.496  0.020  1.496
 HVV  NAD  CAE  single  1.350  0.020  1.350
 HVV  CAF  CAE  single  1.514  0.020  1.514
 HVV  CAE  OAB  double  1.217  0.020  1.217
 HVV  CAP  H1   single  0.970  0.020  1.090
 HVV  CAP  H2   single  0.970  0.020  1.090
 HVV  CAP  H3   single  0.970  0.020  1.090
 HVV  CAO  H4   single  0.930  0.020  1.080
 HVV  CAN  H5   single  0.930  0.020  1.080
 HVV  CAM  H6   single  0.970  0.020  1.090
 HVV  CAM  H7   single  0.970  0.020  1.090
 HVV  CAL  H8   single  0.930  0.020  1.080
 HVV  CAK  H10  single  0.930  0.020  1.080
 HVV  CAJ  H12  single  0.970  0.020  1.090
 HVV  CAJ  H13  single  0.970  0.020  1.090
 HVV  CAI  H14  single  0.970  0.020  1.090
 HVV  CAI  H15  single  0.970  0.020  1.090
 HVV  OAC  H16  single  0.850  0.020  0.980
 HVV  NAD  H17  single  0.860  0.020  1.020
 HVV  CAF  H18  single  0.970  0.020  1.090
 HVV  CAF  H19  single  0.970  0.020  1.090
 HVV  CAG  H20  single  0.970  0.020  1.090
 HVV  OAA  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
 HVV  H3   CAP  H2   108.11  3.000
 HVV  H3   CAP  H1   108.03  3.000
 HVV  H2   CAP  H1   106.37  3.000
 HVV  H3   CAP  CAO  111.86  3.000
 HVV  H2   CAP  CAO  111.15  3.000
 HVV  H1   CAP  CAO  111.10  3.000
 HVV  H4   CAO  CAN  118.61  3.000
 HVV  H4   CAO  CAP  116.26  3.000
 HVV  CAN  CAO  CAP  125.13  3.000
 HVV  H5   CAN  CAM  116.01  3.000
 HVV  H5   CAN  CAO  119.25  3.000
 HVV  CAM  CAN  CAO  124.73  3.000
 HVV  H7   CAM  H6   106.91  3.000
 HVV  H7   CAM  CAL  109.82  3.000
 HVV  H6   CAM  CAL  109.15  3.000
 HVV  H7   CAM  CAN  109.24  3.000
 HVV  H6   CAM  CAN  109.93  3.000
 HVV  CAL  CAM  CAN  111.67  3.000
 HVV  H8   CAL  CAK  119.25  3.000
 HVV  H8   CAL  CAM  116.08  3.000
 HVV  CAK  CAL  CAM  124.66  3.000
 HVV  H10  CAK  CAJ  116.00  3.000
 HVV  H10  CAK  CAL  118.99  3.000
 HVV  CAJ  CAK  CAL  125.01  3.000
 HVV  H13  CAJ  H12  106.97  3.000
 HVV  H13  CAJ  CAI  110.99  3.000
 HVV  H12  CAJ  CAI  110.15  3.000
 HVV  H13  CAJ  CAK  109.21  3.000
 HVV  H12  CAJ  CAK  108.47  3.000
 HVV  CAI  CAJ  CAK  110.93  3.000
 HVV  H15  CAI  H14  106.93  3.000
 HVV  H15  CAI  CAH  109.14  3.000
 HVV  H14  CAI  CAH  108.39  3.000
 HVV  H15  CAI  CAJ  109.15  3.000
 HVV  H14  CAI  CAJ  108.78  3.000
 HVV  CAH  CAI  CAJ  114.21  3.000
 HVV  CAG  CAH  NAD  101.13  3.000
 HVV  NAD  CAH  OAC  111.60  3.000
 HVV  CAG  CAH  OAC  104.94  3.000
 HVV  NAD  CAH  CAI  111.94  3.000
 HVV  CAG  CAH  CAI  114.93  3.000
 HVV  OAC  CAH  CAI  111.70  3.000
 HVV  H16  OAC  CAH  109.47  3.000
 HVV  H17  NAD  CAE  121.62  3.000
 HVV  H17  NAD  CAH  123.41  3.000
 HVV  CAE  NAD  CAH  114.46  3.000
 HVV  CAF  CAE  OAB  127.18  3.000
 HVV  OAB  CAE  NAD  126.02  3.000
 HVV  CAF  CAE  NAD  106.80  3.000
 HVV  H19  CAF  H18  107.38  3.000
 HVV  H19  CAF  CAG  111.43  3.000
 HVV  H18  CAF  CAG  113.75  3.000
 HVV  H19  CAF  CAE  108.65  3.000
 HVV  H18  CAF  CAE  111.99  3.000
 HVV  CAG  CAF  CAE  103.58  3.000
 HVV  H20  CAG  OAA  111.66  3.000
 HVV  H20  CAG  CAF  112.65  3.000
 HVV  OAA  CAG  CAF  111.45  3.000
 HVV  H20  CAG  CAH  109.99  3.000
 HVV  CAF  CAG  CAH  102.33  3.000
 HVV  OAA  CAG  CAH  108.29  3.000
 HVV  H21  OAA  CAG  108.19  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
 HVV  CONST_01  CAF  CAE  NAD  CAH     0.00   0.0  0
 HVV  CONST_02  OAB  CAE  NAD  CAH   180.00   0.0  0
 HVV  CONST_03  H17  NAD  CAE  CAF   180.00   0.0  0
 HVV  CONST_04  CAM  CAN  CAO  CAP   180.00   0.0  0
 HVV  CONST_05  H5   CAN  CAO  CAP     0.00   0.0  0
 HVV  CONST_06  H4   CAO  CAN  CAM     0.00   0.0  0
 HVV  Var_01    CAG  CAF  CAE  NAD    17.89  30.0  1
 HVV  Var_02    CAH  CAI  CAJ  CAK   175.56  30.0  2
 HVV  Var_03    CAJ  CAK  CAL  CAM  -178.86   0.0  2
 HVV  Var_04    CAL  CAM  CAN  CAO   117.28  30.0  3
 HVV  Var_05    CAK  CAL  CAM  CAN   117.16  30.0  2
 HVV  Var_06    CAI  CAJ  CAK  CAL   117.94  30.0  1
 HVV  Var_07    H1   CAP  CAO  CAN   120.57  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
 HVV  chir_01  CAH  CAG  CAI  NAD  positiv
 HVV  chir_02  CAG  OAA  CAH  CAF  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
 HVV  plan-1  CAH  0.020
 HVV  plan-1  NAD  0.020
 HVV  plan-1  CAE  0.020
 HVV  plan-1  OAB  0.020
 HVV  plan-1  CAF  0.020
 HVV  plan-1  H17  0.020
 HVV  plan-2  CAP  0.020
 HVV  plan-2  CAO  0.020
 HVV  plan-2  CAN  0.020
 HVV  plan-2  CAM  0.020
 HVV  plan-2  H4   0.020
 HVV  plan-2  H5   0.020
 HVV  plan-3  CAM  0.020
 HVV  plan-3  CAL  0.020
 HVV  plan-3  CAK  0.020
 HVV  plan-3  CAJ  0.020
 HVV  plan-3  H8   0.020
 HVV  plan-3  H10  0.020

