# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 00:09:55 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2S,3R,4S,5S)-2-methyl-5-(phenylethynyl)pyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@@H](C#Cc2ccccc2)[C@H](O)[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
 2M7  2M7  (2S,3R,4S,5S)-2-methyl-5-(phenylethynyl)pyrrolidine-3,4-diol  ligand  31  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2M7
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
 2M7  CAI  C  CR16  0  -0.294   3.4900   0.9177   0.7463
 2M7  CAJ  C  CR16  0  -0.249   4.8672   0.8233   0.6259
 2M7  CAK  C  CR16  0  -0.254   5.4350  -0.1854  -0.1431
 2M7  CAL  C  CR16  0  -0.248   4.6178  -1.1011  -0.7943
 2M7  CAM  C  CR16  0  -0.295   3.2393  -1.0117  -0.6809
 2M7  CAH  C  CR6   0  -0.128   2.6618  -0.0003   0.0926
 2M7  CAG  C  CSP   0   0.140   1.2441   0.0944   0.2174
 2M7  CAF  C  CSP   0   0.078   0.0454   0.1712   0.3272
 2M7  CAD  C  CH1   0  -0.249  -1.3991   0.2755   0.4734
 2M7  NAE  N  NH1   0  -0.627  -2.0553  -1.0107   0.7222
 2M7  CAA  C  CH1   0  -0.076  -3.1843  -1.1633  -0.2101
 2M7  CAN  C  CH3   0  -0.657  -4.3410  -1.9124   0.4240
 2M7  CAB  C  CH1   0  -0.028  -3.4938   0.2610  -0.6529
 2M7  OAO  O  OH1   0  -0.671  -4.2227   0.9219   0.3522
 2M7  CAC  C  CH1   0   0.018  -2.0897   0.8350  -0.7931
 2M7  OAP  O  OH1   0  -0.664  -2.1118   2.2284  -0.8805
 2M7  H1   H  HCR6  0   0.259   3.0489   1.7030   1.3459
 2M7  H2   H  HCR6  0   0.263   5.4990   1.5392   1.1350
 2M7  H3   H  HCR6  0   0.263   6.5108  -0.2573  -0.2351
 2M7  H4   H  HCR6  0   0.263   5.0559  -1.8888  -1.3930
 2M7  H5   H  HCR6  0   0.259   2.6043  -1.7259  -1.1886
 2M7  H6   H  HCH1  0   0.255  -1.5984   0.9695   1.3002
 2M7  H7   H  HNH1  0   0.359  -1.4091  -1.7822   0.6380
 2M7  H9   H  HCH1  0   0.228  -2.8782  -1.7059  -1.1145
 2M7  H10  H  HCH3  0   0.225  -4.6771  -1.4226   1.3364
 2M7  H11  H  HCH3  0   0.221  -5.1846  -1.9838  -0.2642
 2M7  H12  H  HCH3  0   0.229  -4.0378  -2.9287   0.6784
 2M7  H13  H  HCH1  0   0.240  -4.0337   0.2666  -1.6090
 2M7  H14  H  HOH1  0   0.451  -4.2730   1.8559   0.1237
 2M7  H15  H  HCH1  0   0.227  -1.6227   0.3806  -1.6771
 2M7  H16  H  HOH1  0   0.461  -1.2263   2.5465  -1.0815

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
 2M7  OAO  CAB  single    1.407  0.020  1.407
 2M7  OAP  CAC  single    1.396  0.020  1.396
 2M7  CAB  CAC  single    1.523  0.020  1.523
 2M7  CAB  CAA  single    1.523  0.020  1.523
 2M7  CAN  CAA  single    1.517  0.020  1.517
 2M7  CAC  CAD  single    1.547  0.020  1.547
 2M7  CAD  NAE  single    1.465  0.020  1.465
 2M7  CAD  CAF  single    1.456  0.020  1.456
 2M7  CAA  NAE  single    1.472  0.020  1.472
 2M7  CAF  CAG  triple    1.206  0.020  1.206
 2M7  CAG  CAH  single    1.426  0.020  1.426
 2M7  CAI  CAH  aromatic  1.398  0.020  1.398
 2M7  CAI  CAJ  aromatic  1.386  0.020  1.386
 2M7  CAH  CAM  aromatic  1.398  0.020  1.398
 2M7  CAJ  CAK  aromatic  1.390  0.020  1.390
 2M7  CAM  CAL  aromatic  1.386  0.020  1.386
 2M7  CAK  CAL  aromatic  1.389  0.020  1.389
 2M7  CAI  H1   single    0.930  0.020  1.080
 2M7  CAJ  H2   single    0.930  0.020  1.080
 2M7  CAK  H3   single    0.930  0.020  1.080
 2M7  CAL  H4   single    0.930  0.020  1.080
 2M7  CAM  H5   single    0.930  0.020  1.080
 2M7  CAD  H6   single    0.970  0.020  1.090
 2M7  NAE  H7   single    0.890  0.020  1.040
 2M7  CAA  H9   single    0.970  0.020  1.090
 2M7  CAN  H10  single    0.970  0.020  1.090
 2M7  CAN  H11  single    0.970  0.020  1.090
 2M7  CAN  H12  single    0.970  0.020  1.090
 2M7  CAB  H13  single    0.970  0.020  1.090
 2M7  OAO  H14  single    0.850  0.020  0.980
 2M7  CAC  H15  single    0.970  0.020  1.090
 2M7  OAP  H16  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
 2M7  H1   CAI  CAH  119.61  3.000
 2M7  H1   CAI  CAJ  120.18  3.000
 2M7  CAH  CAI  CAJ  120.21  3.000
 2M7  H2   CAJ  CAK  120.13  3.000
 2M7  H2   CAJ  CAI  119.63  3.000
 2M7  CAK  CAJ  CAI  120.24  3.000
 2M7  H3   CAK  CAL  120.07  3.000
 2M7  H3   CAK  CAJ  120.10  3.000
 2M7  CAL  CAK  CAJ  119.83  3.000
 2M7  H4   CAL  CAM  119.66  3.000
 2M7  H4   CAL  CAK  120.07  3.000
 2M7  CAM  CAL  CAK  120.27  3.000
 2M7  H5   CAM  CAH  119.64  3.000
 2M7  H5   CAM  CAL  120.18  3.000
 2M7  CAH  CAM  CAL  120.18  3.000
 2M7  CAG  CAH  CAM  120.46  3.000
 2M7  CAM  CAH  CAI  119.26  3.000
 2M7  CAG  CAH  CAI  120.27  3.000
 2M7  CAF  CAG  CAH  180.00  3.000
 2M7  CAD  CAF  CAG  180.00  3.000
 2M7  H6   CAD  CAC  107.87  3.000
 2M7  H6   CAD  NAE  110.23  3.000
 2M7  CAC  CAD  NAE  104.86  3.000
 2M7  H6   CAD  CAF  107.53  3.000
 2M7  NAE  CAD  CAF  113.49  3.000
 2M7  CAC  CAD  CAF  112.75  3.000
 2M7  H7   NAE  CAA  111.03  3.000
 2M7  H7   NAE  CAD  111.71  3.000
 2M7  CAA  NAE  CAD  109.08  3.000
 2M7  H9   CAA  CAB  106.21  3.000
 2M7  H9   CAA  CAN  108.22  3.000
 2M7  CAB  CAA  CAN  115.36  3.000
 2M7  H9   CAA  NAE  111.04  3.000
 2M7  CAN  CAA  NAE  111.79  3.000
 2M7  CAB  CAA  NAE  104.07  3.000
 2M7  H12  CAN  H11  107.52  3.000
 2M7  H12  CAN  H10  108.03  3.000
 2M7  H11  CAN  H10  108.62  3.000
 2M7  H12  CAN  CAA  110.23  3.000
 2M7  H11  CAN  CAA  111.00  3.000
 2M7  H10  CAN  CAA  111.32  3.000
 2M7  H13  CAB  CAC  111.79  3.000
 2M7  H13  CAB  OAO  111.41  3.000
 2M7  CAC  CAB  OAO  111.49  3.000
 2M7  H13  CAB  CAA  110.96  3.000
 2M7  CAC  CAB  CAA  101.06  3.000
 2M7  OAO  CAB  CAA  109.69  3.000
 2M7  H14  OAO  CAB  108.26  3.000
 2M7  H15  CAC  OAP  111.67  3.000
 2M7  H15  CAC  CAB  108.07  3.000
 2M7  OAP  CAC  CAB  111.54  3.000
 2M7  H15  CAC  CAD  108.63  3.000
 2M7  CAB  CAC  CAD  101.53  3.000
 2M7  OAP  CAC  CAD  114.78  3.000
 2M7  H16  OAP  CAC  109.17  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
 2M7  CONST_01  CAL  CAM  CAH  CAI    0.00  0.0  0
 2M7  CONST_02  CAL  CAK  CAJ  CAI    0.00  0.0  0
 2M7  CONST_03  CAM  CAH  CAI  CAJ    0.00  0.0  0
 2M7  CONST_04  CAM  CAL  CAK  CAJ    0.00  0.0  0
 2M7  CONST_05  CAH  CAI  CAJ  CAK    0.00  0.0  0
 2M7  CONST_06  CAH  CAM  CAL  CAK    0.00  0.0  0
 2M7  CONST_07  CAG  CAH  CAI  CAJ  180.00  0.0  0
 2M7  CONST_08  CAG  CAH  CAM  CAL  180.00  0.0  0
 2M7  CONST_09  H5   CAM  CAH  CAI  180.00  0.0  0
 2M7  CONST_10  H3   CAK  CAJ  CAI  180.00  0.0  0
 2M7  CONST_11  H4   CAL  CAK  CAJ  180.00  0.0  0
 2M7  CONST_12  H1   CAI  CAJ  CAK  180.00  0.0  0
 2M7  CONST_13  H2   CAJ  CAK  CAL  180.00  0.0  0

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
 2M7  chir_01  CAD  CAC  NAE  CAF  negativ
 2M7  chir_02  CAA  NAE  CAB  CAN  positiv
 2M7  chir_03  CAB  OAO  CAA  CAC  positiv
 2M7  chir_04  CAC  OAP  CAB  CAD  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
 2M7  plan-1  CAI  0.020
 2M7  plan-1  CAJ  0.020
 2M7  plan-1  CAK  0.020
 2M7  plan-1  CAL  0.020
 2M7  plan-1  CAM  0.020
 2M7  plan-1  CAH  0.020
 2M7  plan-1  CAG  0.020
 2M7  plan-1  CAF  0.020
 2M7  plan-1  H1   0.020
 2M7  plan-1  H2   0.020
 2M7  plan-1  H3   0.020
 2M7  plan-1  H4   0.020
 2M7  plan-1  H5   0.020

