# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 13:46:23 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-[(3R)-5-chloro-8-hydroxy-3-methyl-1-oxo-3,4-dihydro-1H-2-benzopyran-7-carbonyl]-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1Cc2c(Cl)cc(c(O)c2C(=O)O1)C(=O)N[C@H](Cc3ccccc3)C(O)=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
 B2U  B2U  N-[(3R)-5-chloro-8-hydroxy-3-methyl-1-oxo-3,4-dihydro-1H-2-benzopyran-7-carbonyl]-D-phenylalanine  ligand  45  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B2U
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
 B2U  CD1  C   CR16   0  -0.327  -3.5069  -2.3295  -0.1560
 B2U  CE1  C   CR16   0  -0.239  -3.2857  -3.3748   0.7327
 B2U  CZ   C   CR16   0  -0.275  -3.6772  -3.2550   2.0586
 B2U  CE2  C   CR16   0  -0.240  -4.2941  -2.0850   2.4866
 B2U  CD2  C   CR16   0  -0.304  -4.5118  -1.0449   1.5947
 B2U  CG   C   CR6    0   0.164  -4.1208  -1.1521   0.2609
 B2U  CB   C   CH2    0  -0.558  -4.3281  -0.0078  -0.6910
 B2U  CA   C   CH1    0  -0.207  -3.3557   1.1484  -0.4390
 B2U  C    C   C      0   0.424  -3.6428   2.3605  -1.3697
 B2U  OXT  O   OC     0  -0.607  -4.8195   2.7675  -1.3419
 B2U  O    O   O     -1  -0.585  -2.6953   2.8128  -2.0298
 B2U  N    N   NH1    0  -0.637  -2.0002   0.6618  -0.5634
 B2U  CAN  C   C      0   0.659  -0.9742   1.1821   0.0931
 B2U  OAX  O   O      0  -0.555  -1.1331   2.0600   0.9613
 B2U  CAA  C   CR6    0  -0.223   0.3964   0.6687  -0.1790
 B2U  CAB  C   CR16   0  -0.233   0.6685  -0.2584  -1.1757
 B2U  CAC  C   CR6    0  -0.159   1.9451  -0.7435  -1.3737
 B2U  CLA  CL  CL     0  -0.117   2.2088  -1.8961  -2.6413
 B2U  CAD  C   CR6    0   0.236   3.0012  -0.3189  -0.5778
 B2U  CAG  C   CH2    0  -0.523   4.3868  -0.8637  -0.7131
 B2U  CAH  C   CH1    0   0.027   5.0847  -0.8113   0.6271
 B2U  CAL  C   CH3    0  -0.684   6.5348  -1.2271   0.5576
 B2U  OAI  O   O2     0  -0.447   5.0515   0.5336   1.1326
 B2U  CAJ  C   C      0   0.571   3.9196   1.2335   1.1225
 B2U  OAK  O   O      0  -0.419   3.9164   2.3094   1.6643
 B2U  CAE  C   CR6    0  -0.286   2.7639   0.6580   0.3928
 B2U  CAF  C   CR6    0   0.388   1.4633   1.1580   0.6116
 B2U  OBB  O   OH1    0  -0.600   1.2537   2.0502   1.5541
 B2U  HD1  H   HCR6   0   0.246  -3.2043  -2.4359  -1.1918
 B2U  HE1  H   HCR6   0   0.252  -2.8080  -4.2826   0.3866
 B2U  HZ   H   HCR6   0   0.252  -3.5065  -4.0665   2.7543
 B2U  HE2  H   HCR6   0   0.252  -4.6082  -1.9842   3.5178
 B2U  HD2  H   HCR6   0   0.246  -4.9940  -0.1375   1.9405
 B2U  HB1  H   HCH2   0   0.252  -4.2187  -0.3608  -1.7213
 B2U  HB2  H   HCH2   0   0.265  -5.3397   0.3875  -0.6013
 B2U  HAM  H   HCH1   0   0.263  -3.4912   1.4897   0.5902
 B2U  H    H   HNH1   0   0.408  -1.8274   0.0274  -1.3250
 B2U  HAB  H   HCR6   0   0.281  -0.1150  -0.6313  -1.8215
 B2U  HAH  H   HCH2   0   0.280   4.3611  -1.8969  -1.0584
 B2U  HAG  H   HCH2   0   0.286   4.9464  -0.2927  -1.4622
 B2U  HAI  H   HCH1   0   0.256   4.5505  -1.4534   1.3360
 B2U  HA2  H   HCH3   0   0.238   7.0849  -0.6257  -0.1669
 B2U  HA3  H   HCH3   0   0.252   7.0178  -1.1341   1.5299
 B2U  HA1  H   HCH3   0   0.244   6.6009  -2.2710   0.2529
 B2U  H2   H   HOH1   0   0.485   0.2689   2.2597   1.5192

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
 B2U  OAK  CAJ  double    1.205  0.020  1.205
 B2U  OAI  CAJ  single    1.331  0.020  1.331
 B2U  OAI  CAH  single    1.437  0.020  1.437
 B2U  CAJ  CAE  single    1.483  0.020  1.483
 B2U  CAL  CAH  single    1.510  0.020  1.510
 B2U  CAH  CAG  single    1.512  0.020  1.512
 B2U  OBB  CAF  single    1.315  0.020  1.315
 B2U  CAE  CAF  aromatic  1.410  0.020  1.410
 B2U  CAE  CAD  aromatic  1.397  0.020  1.397
 B2U  CAF  CAA  aromatic  1.415  0.020  1.415
 B2U  CAG  CAD  single    1.495  0.020  1.495
 B2U  CAD  CAC  aromatic  1.389  0.020  1.389
 B2U  OAX  CAN  double    1.245  0.020  1.245
 B2U  CAA  CAN  single    1.489  0.020  1.489
 B2U  CAA  CAB  aromatic  1.388  0.020  1.388
 B2U  CAN  N    single    1.325  0.020  1.325
 B2U  CAC  CAB  aromatic  1.380  0.020  1.380
 B2U  CAC  CLA  single    1.733  0.020  1.733
 B2U  O    C    deloc     1.240  0.020  1.240
 B2U  N    CA   single    1.446  0.020  1.446
 B2U  C    CA   single    1.555  0.020  1.555
 B2U  C    OXT  deloc     1.245  0.020  1.245
 B2U  CA   CB   single    1.532  0.020  1.532
 B2U  CB   CG   single    1.503  0.020  1.503
 B2U  CD2  CG   aromatic  1.394  0.020  1.394
 B2U  CD2  CE2  aromatic  1.387  0.020  1.387
 B2U  CG   CD1  aromatic  1.392  0.020  1.392
 B2U  CE2  CZ   aromatic  1.390  0.020  1.390
 B2U  CD1  CE1  aromatic  1.390  0.020  1.390
 B2U  CZ   CE1  aromatic  1.388  0.020  1.388
 B2U  CD1  HD1  single    0.930  0.020  1.080
 B2U  CE1  HE1  single    0.930  0.020  1.080
 B2U  CZ   HZ   single    0.930  0.020  1.080
 B2U  CE2  HE2  single    0.930  0.020  1.080
 B2U  CD2  HD2  single    0.930  0.020  1.080
 B2U  CB   HB1  single    0.970  0.020  1.090
 B2U  CB   HB2  single    0.970  0.020  1.090
 B2U  CA   HAM  single    0.970  0.020  1.090
 B2U  N    H    single    0.860  0.020  1.020
 B2U  CAB  HAB  single    0.930  0.020  1.080
 B2U  CAG  HAH  single    0.970  0.020  1.090
 B2U  CAG  HAG  single    0.970  0.020  1.090
 B2U  CAH  HAI  single    0.970  0.020  1.090
 B2U  CAL  HA2  single    0.970  0.020  1.090
 B2U  CAL  HA3  single    0.970  0.020  1.090
 B2U  CAL  HA1  single    0.970  0.020  1.090
 B2U  OBB  H2   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
 B2U  HD1  CD1  CG   119.49  3.000
 B2U  HD1  CD1  CE1  119.51  3.000
 B2U  CG   CD1  CE1  121.00  3.000
 B2U  HE1  CE1  CZ   120.15  3.000
 B2U  HE1  CE1  CD1  119.77  3.000
 B2U  CZ   CE1  CD1  120.08  3.000
 B2U  HZ   CZ   CE2  120.20  3.000
 B2U  HZ   CZ   CE1  120.33  3.000
 B2U  CE2  CZ   CE1  119.47  3.000
 B2U  HE2  CE2  CD2  119.80  3.000
 B2U  HE2  CE2  CZ   120.02  3.000
 B2U  CD2  CE2  CZ   120.18  3.000
 B2U  HD2  CD2  CG   119.62  3.000
 B2U  HD2  CD2  CE2  119.48  3.000
 B2U  CG   CD2  CE2  120.89  3.000
 B2U  CB   CG   CD2  120.58  3.000
 B2U  CD2  CG   CD1  118.38  3.000
 B2U  CB   CG   CD1  121.02  3.000
 B2U  HB2  CB   HB1  106.69  3.000
 B2U  HB2  CB   CA   107.58  3.000
 B2U  HB1  CB   CA   109.56  3.000
 B2U  HB2  CB   CG   110.62  3.000
 B2U  HB1  CB   CG   109.68  3.000
 B2U  CA   CB   CG   112.52  3.000
 B2U  HAM  CA   N    107.61  3.000
 B2U  HAM  CA   C    107.30  3.000
 B2U  N    CA   C    112.58  3.000
 B2U  HAM  CA   CB   108.18  3.000
 B2U  C    CA   CB   111.88  3.000
 B2U  N    CA   CB   109.09  3.000
 B2U  O    C    OXT  127.92  3.000
 B2U  OXT  C    CA   114.57  3.000
 B2U  O    C    CA   117.51  3.000
 B2U  H    N    CAN  119.33  3.000
 B2U  H    N    CA   116.01  3.000
 B2U  CAN  N    CA   123.47  3.000
 B2U  CAA  CAN  OAX  119.22  3.000
 B2U  CAA  CAN  N    119.15  3.000
 B2U  OAX  CAN  N    121.59  3.000
 B2U  CAF  CAA  CAB  118.97  3.000
 B2U  CAB  CAA  CAN  122.82  3.000
 B2U  CAF  CAA  CAN  118.22  3.000
 B2U  HAB  CAB  CAC  117.60  3.000
 B2U  HAB  CAB  CAA  121.13  3.000
 B2U  CAC  CAB  CAA  121.27  3.000
 B2U  CAD  CAC  CLA  120.44  3.000
 B2U  CLA  CAC  CAB  118.64  3.000
 B2U  CAD  CAC  CAB  120.92  3.000
 B2U  CAE  CAD  CAG  118.36  3.000
 B2U  CAG  CAD  CAC  122.78  3.000
 B2U  CAE  CAD  CAC  118.86  3.000
 B2U  HAG  CAG  HAH  106.82  3.000
 B2U  HAG  CAG  CAH  110.63  3.000
 B2U  HAH  CAG  CAH  108.94  3.000
 B2U  HAG  CAG  CAD  110.20  3.000
 B2U  HAH  CAG  CAD  110.64  3.000
 B2U  CAH  CAG  CAD  109.57  3.000
 B2U  HAI  CAH  OAI  108.04  3.000
 B2U  HAI  CAH  CAL  109.67  3.000
 B2U  OAI  CAH  CAL  107.22  3.000
 B2U  HAI  CAH  CAG  109.16  3.000
 B2U  CAL  CAH  CAG  113.14  3.000
 B2U  OAI  CAH  CAG  109.48  3.000
 B2U  HA1  CAL  HA3  107.73  3.000
 B2U  HA1  CAL  HA2  108.18  3.000
 B2U  HA3  CAL  HA2  108.79  3.000
 B2U  HA1  CAL  CAH  109.57  3.000
 B2U  HA3  CAL  CAH  111.17  3.000
 B2U  HA2  CAL  CAH  111.29  3.000
 B2U  CAJ  OAI  CAH  120.61  3.000
 B2U  CAE  CAJ  OAK  124.45  3.000
 B2U  CAE  CAJ  OAI  117.55  3.000
 B2U  OAK  CAJ  OAI  117.95  3.000
 B2U  CAF  CAE  CAJ  120.31  3.000
 B2U  CAF  CAE  CAD  120.81  3.000
 B2U  CAJ  CAE  CAD  118.73  3.000
 B2U  OBB  CAF  CAE  119.92  3.000
 B2U  CAE  CAF  CAA  119.08  3.000
 B2U  OBB  CAF  CAA  120.99  3.000
 B2U  H2   OBB  CAF  105.79  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
 B2U  CONST_01  CE2  CD2  CG   CD1     0.00   0.0  0
 B2U  CONST_02  CE2  CZ   CE1  CD1     0.00   0.0  0
 B2U  CONST_03  CD2  CG   CD1  CE1     0.00   0.0  0
 B2U  CONST_04  CD2  CE2  CZ   CE1     0.00   0.0  0
 B2U  CONST_05  CG   CD2  CE2  CZ      0.00   0.0  0
 B2U  CONST_06  CG   CD1  CE1  CZ      0.00   0.0  0
 B2U  CONST_07  CAD  CAE  CAF  CAA     0.00   0.0  0
 B2U  CONST_08  CAD  CAC  CAB  CAA     0.00   0.0  0
 B2U  CONST_09  CAE  CAF  CAA  CAB     0.00   0.0  0
 B2U  CONST_10  CAE  CAD  CAC  CAB     0.00   0.0  0
 B2U  CONST_11  CAF  CAE  CAD  CAC     0.00   0.0  0
 B2U  CONST_12  CAF  CAA  CAB  CAC     0.00   0.0  0
 B2U  CONST_13  CB   CG   CD1  CE1   180.00   0.0  0
 B2U  CONST_14  CB   CG   CD2  CE2   180.00   0.0  0
 B2U  CONST_15  CAE  CAF  CAA  CAN   180.00   0.0  0
 B2U  CONST_16  CAC  CAB  CAA  CAN   180.00   0.0  0
 B2U  CONST_17  CLA  CAC  CAB  CAA   180.00   0.0  0
 B2U  CONST_18  OBB  CAF  CAA  CAB   180.00   0.0  0
 B2U  CONST_19  CAE  CAD  CAC  CLA   180.00   0.0  0
 B2U  CONST_20  CAG  CAD  CAC  CLA     0.00   0.0  0
 B2U  CONST_21  OBB  CAF  CAE  CAD   180.00   0.0  0
 B2U  CONST_22  OBB  CAF  CAE  CAJ     0.00   0.0  0
 B2U  CONST_23  HD2  CD2  CG   CD1   180.00   0.0  0
 B2U  CONST_24  HZ   CZ   CE1  CD1   180.00   0.0  0
 B2U  CONST_25  HE2  CE2  CZ   CE1   180.00   0.0  0
 B2U  CONST_26  HD1  CD1  CE1  CZ    180.00   0.0  0
 B2U  CONST_27  HE1  CE1  CZ   CE2   180.00   0.0  0
 B2U  CONST_28  HAB  CAB  CAC  CAD   180.00   0.0  0
 B2U  CONST_29  CAA  CAN  N    CA    180.00   0.0  0
 B2U  CONST_30  H    N    CAN  CAA     0.00   0.0  0
 B2U  CONST_31  OAX  CAN  N    CA      0.00   0.0  0
 B2U  Var_01    CAH  CAG  CAD  CAC  -150.30  30.0  1
 B2U  Var_02    OAI  CAJ  CAE  CAD   -20.31  30.0  1
 B2U  Var_03    CAE  CAJ  OAI  CAH    -9.04  30.0  1
 B2U  Var_04    CA   CB   CG   CD1  -105.42  30.0  2
 B2U  Var_05    CAF  CAA  CAN  N    -174.80  30.0  2

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
 B2U  chir_01  CA   N    C    CB   negativ
 B2U  chir_02  CAH  OAI  CAL  CAG  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
 B2U  plan-1  CD1  0.020
 B2U  plan-1  CE1  0.020
 B2U  plan-1  CZ   0.020
 B2U  plan-1  CE2  0.020
 B2U  plan-1  CD2  0.020
 B2U  plan-1  CG   0.020
 B2U  plan-1  CB   0.020
 B2U  plan-1  HD1  0.020
 B2U  plan-1  HE1  0.020
 B2U  plan-1  HZ   0.020
 B2U  plan-1  HE2  0.020
 B2U  plan-1  HD2  0.020
 B2U  plan-2  CAN  0.020
 B2U  plan-2  CAA  0.020
 B2U  plan-2  CAB  0.020
 B2U  plan-2  CAC  0.020
 B2U  plan-2  CLA  0.020
 B2U  plan-2  CAD  0.020
 B2U  plan-2  CAG  0.020
 B2U  plan-2  CAJ  0.020
 B2U  plan-2  CAE  0.020
 B2U  plan-2  CAF  0.020
 B2U  plan-2  OBB  0.020
 B2U  plan-2  HAB  0.020
 B2U  plan-3  CA   0.020
 B2U  plan-3  N    0.020
 B2U  plan-3  CAN  0.020
 B2U  plan-3  OAX  0.020
 B2U  plan-3  CAA  0.020
 B2U  plan-3  H    0.020
 B2U  plan-4  CA   0.020
 B2U  plan-4  C    0.020
 B2U  plan-4  OXT  0.020
 B2U  plan-4  O    0.020
 B2U  plan-5  OAI  0.020
 B2U  plan-5  CAJ  0.020
 B2U  plan-5  OAK  0.020
 B2U  plan-5  CAE  0.020

