# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 12:16:19 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-[(3S,4R,4aR,5S,6R)-3-(dichloromethyl)-5,8-dihydroxy-3,6-dimethyl-1-oxo-3,4,4a,5,6,7-hexahydro-1H-isochromen-4-yl]-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C(=O)N[C@@H]1[C@@H]2[C@@H](O)[C@H](C)CC(=C2C(=O)O[C@]1(C)C(Cl)Cl)O
#
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
 3V6  3V6  N-[(3S,4R,4aR,5S,6R)-3-(dichloromethyl)-5,8-dihydroxy-3,6-dimethyl-1-oxo-3,4,4a,5,6,7-hexahydro-1H-isochromen-4-yl]-L-alaninamide  ligand  46  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3V6
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
 3V6  CLI  CL  CL    0  -0.068  -4.2109  -1.0003   0.5585
 3V6  CAT  C   CH1   0  -0.307  -2.7909   0.0681   0.5067
 3V6  CLJ  CL  CL    0  -0.064  -3.0932   1.4959   1.5141
 3V6  CAX  C   CR6   0   0.227  -1.5104  -0.6638   0.9548
 3V6  CAC  C   CH3   0  -0.660  -1.6328  -1.2207   2.3654
 3V6  OAM  O   O     0  -0.469  -1.4323  -1.7551   0.0340
 3V6  CAO  C   CR6   0   0.563  -0.3234  -2.1939  -0.6018
 3V6  OAE  O   O     0  -0.432  -0.4920  -3.1053  -1.3751
 3V6  CAQ  C   CR6   0  -0.257   0.9464  -1.5438  -0.2965
 3V6  CAN  C   C     0   0.381   2.0553  -1.8008  -1.0339
 3V6  OAG  O   OH1   0  -0.573   2.0180  -2.5968  -2.0944
 3V6  CAK  C   CH2   0  -0.575   3.3827  -1.1849  -0.7202
 3V6  CAS  C   CH1   0  -0.281   3.4746  -0.5971   0.6809
 3V6  CAB  C   CH3   0  -0.675   4.7690   0.1864   0.8465
 3V6  CAU  C   CH1   0   0.098   2.2404   0.2675   0.9160
 3V6  OAH  O   OH1   0  -0.670   2.2517   0.9029   2.1716
 3V6  CAW  C   CR16  0  -0.300   0.9832  -0.5911   0.8716
 3V6  CAV  C   CR16  0  -0.126  -0.2892   0.2661   0.8321
 3V6  NAL  N   NH1   0  -0.652  -0.3319   1.0736  -0.3643
 3V6  C    C   C     0   0.558  -0.1777   2.4188  -0.3737
 3V6  O    O   O     0  -0.471  -0.1167   3.0968   0.6352
 3V6  CA   C   CH1   0  -0.231  -0.0225   3.0190  -1.7650
 3V6  CB   C   CH3   0  -0.672   1.4456   2.8886  -2.1912
 3V6  N    N   NH2   0  -0.782  -0.5322   4.3754  -1.7558
 3V6  H1   H   HCH1  0   0.358  -2.7030   0.4145  -0.5196
 3V6  H2   H   HCH3  0   0.260  -2.4706  -1.9108   2.4455
 3V6  H3   H   HCH3  0   0.264  -0.7342  -1.7644   2.6504
 3V6  H4   H   HCH3  0   0.249  -1.7754  -0.4199   3.0890
 3V6  H5   H   HOH1  0   0.488   2.8908  -2.6484  -2.5040
 3V6  H6   H   HCH2  0   0.288   4.1602  -1.9440  -0.8560
 3V6  H7   H   HCH2  0   0.279   3.5852  -0.4109  -1.4721
 3V6  H8   H   HCH1  0   0.246   3.4626  -1.4227   1.4026
 3V6  H9   H   HCH3  0   0.223   4.7932   1.0512   0.1784
 3V6  H10  H   HCH3  0   0.240   4.8986   0.5412   1.8687
 3V6  H11  H   HCH3  0   0.242   5.6329  -0.4365   0.6111
 3V6  H12  H   HCH1  0   0.206   2.2024   1.0106   0.1042
 3V6  H13  H   HOH1  0   0.457   2.8000   1.6906   2.1206
 3V6  H14  H   HCR6  0   0.277   0.9774  -1.1647   1.8058
 3V6  H15  H   HCR6  0   0.302  -0.2938   0.9417   1.6859
 3V6  H16  H   HNH1  0   0.404  -0.2876   0.6001  -1.2548
 3V6  H17  H   HCH1  0   0.257  -0.6321   2.4402  -2.4657
 3V6  H18  H   HCH3  0   0.221   1.7702   1.8473  -2.2440
 3V6  H19  H   HCH3  0   0.251   1.5840   3.3212  -3.1824
 3V6  H20  H   HCH3  0   0.233   2.1021   3.4159  -1.4966
 3V6  H21  H   HNH2  0   0.342   0.0231   4.9430  -1.1268
 3V6  H22  H   HNH2  0   0.352  -0.4062   4.7751  -2.6773

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
 3V6  CLJ  CAT  single  1.773  0.020  1.773
 3V6  CAT  CLI  single  1.778  0.020  1.778
 3V6  CAT  CAX  single  1.541  0.020  1.541
 3V6  CB   CA   single  1.534  0.020  1.534
 3V6  CA   N    single  1.449  0.020  1.449
 3V6  CA   C    single  1.523  0.020  1.523
 3V6  OAM  CAX  single  1.430  0.020  1.430
 3V6  OAM  CAO  single  1.351  0.020  1.351
 3V6  OAE  CAO  double  1.207  0.020  1.207
 3V6  CAX  CAC  single  1.521  0.020  1.521
 3V6  CAX  CAV  single  1.540  0.020  1.540
 3V6  C    NAL  single  1.354  0.020  1.354
 3V6  C    O    double  1.217  0.020  1.217
 3V6  CAO  CAQ  single  1.459  0.020  1.459
 3V6  NAL  CAV  single  1.444  0.020  1.444
 3V6  CAV  CAW  single  1.535  0.020  1.535
 3V6  OAG  CAN  single  1.326  0.020  1.326
 3V6  CAQ  CAW  single  1.508  0.020  1.508
 3V6  CAQ  CAN  double  1.356  0.020  1.356
 3V6  CAW  CAU  single  1.523  0.020  1.523
 3V6  CAN  CAK  single  1.497  0.020  1.497
 3V6  CAU  OAH  single  1.407  0.020  1.407
 3V6  CAU  CAS  single  1.525  0.020  1.525
 3V6  CAK  CAS  single  1.522  0.020  1.522
 3V6  CAS  CAB  single  1.522  0.020  1.522
 3V6  CAT  H1   single  0.970  0.020  1.090
 3V6  CAC  H2   single  0.970  0.020  1.090
 3V6  CAC  H3   single  0.970  0.020  1.090
 3V6  CAC  H4   single  0.970  0.020  1.090
 3V6  OAG  H5   single  0.850  0.020  0.980
 3V6  CAK  H6   single  0.970  0.020  1.090
 3V6  CAK  H7   single  0.970  0.020  1.090
 3V6  CAS  H8   single  0.970  0.020  1.090
 3V6  CAB  H9   single  0.970  0.020  1.090
 3V6  CAB  H10  single  0.970  0.020  1.090
 3V6  CAB  H11  single  0.970  0.020  1.090
 3V6  CAU  H12  single  0.970  0.020  1.090
 3V6  OAH  H13  single  0.850  0.020  0.980
 3V6  CAW  H14  single  0.970  0.020  1.090
 3V6  CAV  H15  single  0.970  0.020  1.090
 3V6  NAL  H16  single  0.860  0.020  1.020
 3V6  CA   H17  single  0.970  0.020  1.090
 3V6  CB   H18  single  0.970  0.020  1.090
 3V6  CB   H19  single  0.970  0.020  1.090
 3V6  CB   H20  single  0.970  0.020  1.090
 3V6  N    H21  single  0.890  0.020  1.040
 3V6  N    H22  single  0.890  0.020  1.040

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
 3V6  H1   CAT  CAX  111.02  3.000
 3V6  H1   CAT  CLJ  107.07  3.000
 3V6  CAX  CAT  CLJ  111.02  3.000
 3V6  H1   CAT  CLI  106.48  3.000
 3V6  CAX  CAT  CLI  111.70  3.000
 3V6  CLJ  CAT  CLI  109.34  3.000
 3V6  CAV  CAX  OAM  111.49  3.000
 3V6  CAV  CAX  CAC  111.02  3.000
 3V6  OAM  CAX  CAC  108.78  3.000
 3V6  CAV  CAX  CAT  110.42  3.000
 3V6  CAC  CAX  CAT  112.12  3.000
 3V6  OAM  CAX  CAT  102.74  3.000
 3V6  H4   CAC  H3   107.55  3.000
 3V6  H4   CAC  H2   108.46  3.000
 3V6  H3   CAC  H2   107.43  3.000
 3V6  H4   CAC  CAX  110.95  3.000
 3V6  H3   CAC  CAX  111.06  3.000
 3V6  H2   CAC  CAX  111.24  3.000
 3V6  CAO  OAM  CAX  126.55  3.000
 3V6  CAQ  CAO  OAE  126.31  3.000
 3V6  CAQ  CAO  OAM  118.10  3.000
 3V6  OAE  CAO  OAM  115.59  3.000
 3V6  CAW  CAQ  CAN  121.40  3.000
 3V6  CAN  CAQ  CAO  120.89  3.000
 3V6  CAW  CAQ  CAO  117.71  3.000
 3V6  CAK  CAN  OAG  116.07  3.000
 3V6  CAK  CAN  CAQ  122.22  3.000
 3V6  OAG  CAN  CAQ  121.70  3.000
 3V6  H5   OAG  CAN  110.23  3.000
 3V6  H7   CAK  H6   105.83  3.000
 3V6  H7   CAK  CAS  110.30  3.000
 3V6  H6   CAK  CAS  109.81  3.000
 3V6  H7   CAK  CAN  108.07  3.000
 3V6  H6   CAK  CAN  108.57  3.000
 3V6  CAS  CAK  CAN  113.92  3.000
 3V6  H8   CAS  CAU  108.45  3.000
 3V6  H8   CAS  CAB  108.98  3.000
 3V6  CAU  CAS  CAB  112.31  3.000
 3V6  H8   CAS  CAK  108.32  3.000
 3V6  CAB  CAS  CAK  110.51  3.000
 3V6  CAU  CAS  CAK  108.17  3.000
 3V6  H11  CAB  H10  107.11  3.000
 3V6  H11  CAB  H9   107.60  3.000
 3V6  H10  CAB  H9   108.24  3.000
 3V6  H11  CAB  CAS  110.86  3.000
 3V6  H10  CAB  CAS  111.76  3.000
 3V6  H9   CAB  CAS  111.08  3.000
 3V6  H12  CAU  CAW  109.30  3.000
 3V6  H12  CAU  OAH  110.69  3.000
 3V6  CAW  CAU  OAH  106.69  3.000
 3V6  H12  CAU  CAS  107.27  3.000
 3V6  OAH  CAU  CAS  112.77  3.000
 3V6  CAW  CAU  CAS  110.11  3.000
 3V6  H13  OAH  CAU  109.11  3.000
 3V6  H14  CAW  CAV  108.05  3.000
 3V6  H14  CAW  CAU  105.93  3.000
 3V6  CAV  CAW  CAU  111.73  3.000
 3V6  H14  CAW  CAQ  109.24  3.000
 3V6  CAU  CAW  CAQ  113.51  3.000
 3V6  CAV  CAW  CAQ  108.23  3.000
 3V6  H15  CAV  NAL  107.62  3.000
 3V6  H15  CAV  CAW  109.26  3.000
 3V6  NAL  CAV  CAW  110.99  3.000
 3V6  H15  CAV  CAX  107.99  3.000
 3V6  CAW  CAV  CAX  108.55  3.000
 3V6  NAL  CAV  CAX  112.35  3.000
 3V6  H16  NAL  C    117.05  3.000
 3V6  H16  NAL  CAV  117.86  3.000
 3V6  C    NAL  CAV  123.91  3.000
 3V6  CA   C    O    122.18  3.000
 3V6  O    C    NAL  123.60  3.000
 3V6  CA   C    NAL  114.17  3.000
 3V6  H17  CA   N    107.65  3.000
 3V6  H17  CA   CB   108.07  3.000
 3V6  N    CA   CB   114.70  3.000
 3V6  H17  CA   C    108.64  3.000
 3V6  N    CA   C    109.10  3.000
 3V6  CB   CA   C    108.53  3.000
 3V6  H20  CB   H19  108.09  3.000
 3V6  H20  CB   H18  108.22  3.000
 3V6  H19  CB   H18  107.26  3.000
 3V6  H20  CB   CA   110.96  3.000
 3V6  H19  CB   CA   109.89  3.000
 3V6  H18  CB   CA   112.27  3.000
 3V6  H22  N    H21  106.01  3.000
 3V6  H22  N    CA   108.67  3.000
 3V6  H21  N    CA   109.61  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
 3V6  CONST_01  CA   C    NAL  CAV   180.00   0.0  0
 3V6  CONST_02  O    C    NAL  CAV     0.00   0.0  0
 3V6  CONST_03  H16  NAL  C    O     180.00   0.0  0
 3V6  Var_01    CAQ  CAO  OAM  CAX     2.74  30.0  1
 3V6  Var_02    CAW  CAQ  CAO  OAM    10.21  30.0  1
 3V6  Var_03    CAK  CAN  CAQ  CAO  -177.99  30.0  1
 3V6  Var_04    CAS  CAK  CAN  CAQ    16.77  30.0  1

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
 3V6  chir_01  CAX  OAM  CAC  CAV  negativ
 3V6  chir_02  CAS  CAU  CAK  CAB  negativ
 3V6  chir_03  CAU  OAH  CAW  CAS  positiv
 3V6  chir_04  CAW  CAU  CAQ  CAV  positiv
 3V6  chir_05  CAV  NAL  CAW  CAX  positiv
 3V6  chir_06  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
 3V6  plan-1  CAV  0.020
 3V6  plan-1  NAL  0.020
 3V6  plan-1  C    0.020
 3V6  plan-1  O    0.020
 3V6  plan-1  CA   0.020
 3V6  plan-1  H16  0.020
 3V6  plan-2  OAM  0.020
 3V6  plan-2  CAO  0.020
 3V6  plan-2  OAE  0.020
 3V6  plan-2  CAQ  0.020

