# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 06:33:09 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-(2-methylphenyl)-Nalpha-(selenophene-2-carbonyl)-D-phenylalaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3[se]ccc3
#
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
 88D  88D  N-(2-methylphenyl)-Nalpha-(selenophene-2-carbonyl)-D-phenylalaninamide  ligand  46  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_88D
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
 88D  CAA  C   CH3   0  -0.747   4.9757   0.6489   2.1183
 88D  CAW  C   CR6   0   0.061   5.2671  -0.2129   0.9244
 88D  CAM  C   CR16  0  -0.307   6.4939  -0.8564   0.7924
 88D  CAG  C   CR16  0  -0.249   6.7750  -1.6669  -0.2981
 88D  CAH  C   CR16  0  -0.274   5.8214  -1.8325  -1.2916
 88D  CAN  C   CR16  0  -0.277   4.5967  -1.1901  -1.1921
 88D  CAX  C   CR6   0   0.303   4.3161  -0.3904  -0.0882
 88D  NAQ  N   NH1   0  -0.744   3.0842   0.2836   0.0240
 88D  C    C   C     0   0.550   1.8654  -0.2344  -0.2512
 88D  O    O   O     0  -0.454   1.6724  -1.3727  -0.6312
 88D  CA   C   CH1   0  -0.232   0.7244   0.7679  -0.0958
 88D  CB   C   CH2   0  -0.524   0.6831   1.6988  -1.3284
 88D  CG   C   CR6   0   0.147  -0.4765   2.6485  -1.2436
 88D  CD1  C   CR16  0  -0.294  -0.3914   3.8020  -0.4682
 88D  CE1  C   CR16  0  -0.241  -1.4796   4.6537  -0.3423
 88D  CZ   C   CR16  0  -0.271  -2.6738   4.3593  -0.9888
 88D  CE2  C   CR16  0  -0.238  -2.7689   3.2128  -1.7657
 88D  CD2  C   CR16  0  -0.310  -1.6757   2.3655  -1.8910
 88D  N    N   NH1   0  -0.649  -0.5209   0.0738   0.0672
 88D  CAT  C   C     0   0.552  -1.3575   0.2858   1.1039
 88D  OAB  O   O     0  -0.470  -1.0761   0.9847   2.0652
 88D  CAY  C   CR5   0  -0.339  -2.6706  -0.3909   1.0261
 88D  SE   SE  SE    0   0.329  -3.5543  -0.8138  -0.5569
 88D  CAJ  C   CR15  0  -0.492  -4.9228  -1.4869   0.4819
 88D  CAI  C   CR15  0  -0.175  -4.6639  -1.3528   1.8098
 88D  CAO  C   CR15  0  -0.209  -3.4201  -0.7357   2.1111
 88D  H1   H   HCH3  0   0.250   4.8864   1.7042   1.8480
 88D  H2   H   HCH3  0   0.251   4.0436   0.3606   2.6070
 88D  H3   H   HCH3  0   0.260   5.7743   0.5736   2.8533
 88D  H4   H   HCR6  0   0.252   7.2393  -0.7255   1.5674
 88D  H5   H   HCR6  0   0.255   7.7339  -2.1631  -0.3706
 88D  H6   H   HCR6  0   0.258   6.0298  -2.4537  -2.1529
 88D  H7   H   HCR6  0   0.266   3.8691  -1.3015  -1.9828
 88D  H8   H   HNH1  0   0.415   3.1100   1.2078   0.4282
 88D  H9   H   HCH1  0   0.298   0.8844   1.3761   0.7957
 88D  H10  H   HCH2  0   0.270   1.6241   2.2494  -1.3875
 88D  H11  H   HCH2  0   0.270   0.6106   1.0902  -2.2333
 88D  H12  H   HCR6  0   0.247   0.5360   4.0383   0.0414
 88D  H13  H   HCR6  0   0.253  -1.3958   5.5488   0.2610
 88D  H14  H   HCR6  0   0.254  -3.5238   5.0219  -0.8898
 88D  H15  H   HCR6  0   0.253  -3.6940   2.9766  -2.2762
 88D  H16  H   HCR6  0   0.247  -1.7527   1.4771  -2.5071
 88D  H17  H   HNH1  0   0.401  -0.7355  -0.6339  -0.6182
 88D  H18  H   HCR5  0   0.304  -5.8104  -1.9116   0.0344
 88D  H19  H   HCR5  0   0.275  -5.3540  -1.6841   2.5736
 88D  H20  H   HCR5  0   0.274  -3.0826  -0.5620   3.1239

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
 88D  CAJ  CAI  aromatic  1.360  0.020  1.360
 88D  CAJ  SE   aromatic  1.845  0.020  1.845
 88D  CAI  CAO  aromatic  1.421  0.020  1.421
 88D  SE   CAY  aromatic  1.862  0.020  1.862
 88D  CAO  CAY  aromatic  1.363  0.020  1.363
 88D  CAY  CAT  single    1.479  0.020  1.479
 88D  CAT  N    single    1.349  0.020  1.349
 88D  CAT  OAB  double    1.221  0.020  1.221
 88D  N    CA   single    1.435  0.020  1.435
 88D  O    C    double    1.215  0.020  1.215
 88D  CA   CB   single    1.545  0.020  1.545
 88D  CA   C    single    1.527  0.020  1.527
 88D  CB   CG   single    1.501  0.020  1.501
 88D  C    NAQ  single    1.353  0.020  1.353
 88D  NAQ  CAX  single    1.409  0.020  1.409
 88D  CG   CD1  aromatic  1.393  0.020  1.393
 88D  CG   CD2  aromatic  1.392  0.020  1.392
 88D  CAA  CAW  single    1.501  0.020  1.501
 88D  CAX  CAW  aromatic  1.400  0.020  1.400
 88D  CAX  CAN  aromatic  1.392  0.020  1.392
 88D  CAW  CAM  aromatic  1.392  0.020  1.392
 88D  CD1  CE1  aromatic  1.388  0.020  1.388
 88D  CAN  CAH  aromatic  1.386  0.020  1.386
 88D  CAM  CAG  aromatic  1.387  0.020  1.387
 88D  CD2  CE2  aromatic  1.389  0.020  1.389
 88D  CAH  CAG  aromatic  1.387  0.020  1.387
 88D  CE1  CZ   aromatic  1.390  0.020  1.390
 88D  CE2  CZ   aromatic  1.388  0.020  1.388
 88D  CAA  H1   single    0.970  0.020  1.090
 88D  CAA  H2   single    0.970  0.020  1.090
 88D  CAA  H3   single    0.970  0.020  1.090
 88D  CAM  H4   single    0.930  0.020  1.080
 88D  CAG  H5   single    0.930  0.020  1.080
 88D  CAH  H6   single    0.930  0.020  1.080
 88D  CAN  H7   single    0.930  0.020  1.080
 88D  NAQ  H8   single    0.860  0.020  1.020
 88D  CA   H9   single    0.970  0.020  1.090
 88D  CB   H10  single    0.970  0.020  1.090
 88D  CB   H11  single    0.970  0.020  1.090
 88D  CD1  H12  single    0.930  0.020  1.080
 88D  CE1  H13  single    0.930  0.020  1.080
 88D  CZ   H14  single    0.930  0.020  1.080
 88D  CE2  H15  single    0.930  0.020  1.080
 88D  CD2  H16  single    0.930  0.020  1.080
 88D  N    H17  single    0.860  0.020  1.020
 88D  CAJ  H18  single    0.930  0.020  1.080
 88D  CAI  H19  single    0.930  0.020  1.080
 88D  CAO  H20  single    0.930  0.020  1.080

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
 88D  H3   CAA  H2   107.83  3.000
 88D  H3   CAA  H1   107.09  3.000
 88D  H2   CAA  H1   107.22  3.000
 88D  H3   CAA  CAW  110.80  3.000
 88D  H2   CAA  CAW  111.74  3.000
 88D  H1   CAA  CAW  111.93  3.000
 88D  CAX  CAW  CAM  118.13  3.000
 88D  CAM  CAW  CAA  120.80  3.000
 88D  CAX  CAW  CAA  121.07  3.000
 88D  H4   CAM  CAG  119.57  3.000
 88D  H4   CAM  CAW  118.87  3.000
 88D  CAG  CAM  CAW  121.55  3.000
 88D  H5   CAG  CAH  120.43  3.000
 88D  H5   CAG  CAM  120.01  3.000
 88D  CAH  CAG  CAM  119.56  3.000
 88D  H6   CAH  CAN  119.55  3.000
 88D  H6   CAH  CAG  120.41  3.000
 88D  CAN  CAH  CAG  120.04  3.000
 88D  H7   CAN  CAX  120.26  3.000
 88D  H7   CAN  CAH  119.65  3.000
 88D  CAX  CAN  CAH  120.08  3.000
 88D  NAQ  CAX  CAN  120.96  3.000
 88D  CAN  CAX  CAW  120.63  3.000
 88D  NAQ  CAX  CAW  118.40  3.000
 88D  H8   NAQ  C    117.09  3.000
 88D  H8   NAQ  CAX  116.59  3.000
 88D  C    NAQ  CAX  126.06  3.000
 88D  CA   C    O    121.87  3.000
 88D  CA   C    NAQ  113.66  3.000
 88D  O    C    NAQ  124.43  3.000
 88D  H9   CA   N    107.71  3.000
 88D  H9   CA   CB   108.66  3.000
 88D  N    CA   CB   111.03  3.000
 88D  H9   CA   C    109.85  3.000
 88D  CB   CA   C    109.53  3.000
 88D  N    CA   C    110.03  3.000
 88D  H11  CB   H10  107.05  3.000
 88D  H11  CB   CG   110.35  3.000
 88D  H10  CB   CG   110.47  3.000
 88D  H11  CB   CA   109.08  3.000
 88D  H10  CB   CA   108.91  3.000
 88D  CG   CB   CA   110.90  3.000
 88D  CD2  CG   CD1  118.69  3.000
 88D  CD2  CG   CB   120.71  3.000
 88D  CD1  CG   CB   120.55  3.000
 88D  H12  CD1  CE1  119.63  3.000
 88D  H12  CD1  CG   119.64  3.000
 88D  CE1  CD1  CG   120.74  3.000
 88D  H13  CE1  CZ   120.07  3.000
 88D  H13  CE1  CD1  119.82  3.000
 88D  CZ   CE1  CD1  120.11  3.000
 88D  H14  CZ   CE2  120.20  3.000
 88D  H14  CZ   CE1  120.18  3.000
 88D  CE2  CZ   CE1  119.62  3.000
 88D  H15  CE2  CD2  119.80  3.000
 88D  H15  CE2  CZ   120.17  3.000
 88D  CD2  CE2  CZ   120.03  3.000
 88D  H16  CD2  CE2  119.70  3.000
 88D  H16  CD2  CG   119.49  3.000
 88D  CE2  CD2  CG   120.81  3.000
 88D  H17  N    CAT  120.05  3.000
 88D  H17  N    CA   116.55  3.000
 88D  CAT  N    CA   123.33  3.000
 88D  CAY  CAT  OAB  120.51  3.000
 88D  OAB  CAT  N    123.50  3.000
 88D  CAY  CAT  N    115.99  3.000
 88D  CAO  CAY  SE   111.00  3.000
 88D  CAO  CAY  CAT  124.19  3.000
 88D  SE   CAY  CAT  124.75  3.000
 88D  CAJ  SE   CAY   87.49  3.000
 88D  H18  CAJ  CAI  126.84  3.000
 88D  H18  CAJ  SE   121.28  3.000
 88D  CAI  CAJ  SE   111.87  3.000
 88D  H19  CAI  CAO  122.82  3.000
 88D  H19  CAI  CAJ  122.55  3.000
 88D  CAO  CAI  CAJ  114.63  3.000
 88D  H20  CAO  CAI  122.78  3.000
 88D  H20  CAO  CAY  122.22  3.000
 88D  CAI  CAO  CAY  114.99  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
 88D  CONST_01  CAH  CAN  CAX  CAW    0.00   0.0  0
 88D  CONST_02  CAH  CAG  CAM  CAW    0.00   0.0  0
 88D  CONST_03  CAN  CAX  CAW  CAM    0.00   0.0  0
 88D  CONST_04  CAN  CAH  CAG  CAM    0.00   0.0  0
 88D  CONST_05  CAX  CAW  CAM  CAG    0.00   0.0  0
 88D  CONST_06  CAX  CAN  CAH  CAG    0.00   0.0  0
 88D  CONST_07  CZ   CE1  CD1  CG     0.00   0.0  0
 88D  CONST_08  CZ   CE2  CD2  CG     0.00   0.0  0
 88D  CONST_09  CE2  CD2  CG   CD1    0.00   0.0  0
 88D  CONST_10  CE2  CZ   CE1  CD1    0.00   0.0  0
 88D  CONST_11  CD2  CG   CD1  CE1    0.00   0.0  0
 88D  CONST_12  CD2  CE2  CZ   CE1    0.00   0.0  0
 88D  CONST_13  CAI  CAJ  SE   CAY    0.00   0.0  0
 88D  CONST_14  CAJ  CAI  CAO  CAY    0.00   0.0  0
 88D  CONST_15  CAO  CAI  CAJ  SE     0.00   0.0  0
 88D  CONST_16  CAI  CAO  CAY  SE     0.00   0.0  0
 88D  CONST_17  CAO  CAY  SE   CAJ    0.00   0.0  0
 88D  CONST_18  CAN  CAX  CAW  CAA  180.00   0.0  0
 88D  CONST_19  CAG  CAM  CAW  CAA  180.00   0.0  0
 88D  CONST_20  NAQ  CAX  CAW  CAM  180.00   0.0  0
 88D  CONST_21  NAQ  CAX  CAN  CAH  180.00   0.0  0
 88D  CONST_22  CE1  CD1  CG   CB   180.00   0.0  0
 88D  CONST_23  CE2  CD2  CG   CB   180.00   0.0  0
 88D  CONST_24  CAJ  SE   CAY  CAT  180.00   0.0  0
 88D  CONST_25  CAI  CAO  CAY  CAT  180.00   0.0  0
 88D  CONST_26  H7   CAN  CAX  CAW  180.00   0.0  0
 88D  CONST_27  H5   CAG  CAM  CAW  180.00   0.0  0
 88D  CONST_28  H6   CAH  CAG  CAM  180.00   0.0  0
 88D  CONST_29  H4   CAM  CAG  CAH  180.00   0.0  0
 88D  CONST_30  H13  CE1  CD1  CG   180.00   0.0  0
 88D  CONST_31  H15  CE2  CD2  CG   180.00   0.0  0
 88D  CONST_32  H16  CD2  CG   CD1  180.00   0.0  0
 88D  CONST_33  H14  CZ   CE1  CD1  180.00   0.0  0
 88D  CONST_34  H12  CD1  CE1  CZ   180.00   0.0  0
 88D  CONST_35  H18  CAJ  SE   CAY  180.00   0.0  0
 88D  CONST_36  H19  CAI  CAO  CAY  180.00   0.0  0
 88D  CONST_37  H20  CAO  CAY  SE   180.00   0.0  0
 88D  CONST_41  O    C    NAQ  CAX    0.00   0.0  0
 88D  CONST_42  CA   C    NAQ  CAX  180.00   0.0  0
 88D  CONST_43  CAY  CAT  N    CA   180.00   0.0  0
 88D  CONST_44  H17  N    CAT  CAY    0.00   0.0  0
 88D  CONST_45  OAB  CAT  N    CA     0.00   0.0  0
 88D  Var_01    CD1  CG   CB   CA    80.84  30.0  2
 88D  Var_02    SE   CAY  CAT  N    -29.21  30.0  1
 88D  Var_03    H1   CAA  CAW  CAM  112.41  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
 88D  chir_01  CA  N  CB  C  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
 88D  plan-1  CAT  0.020
 88D  plan-1  CAY  0.020
 88D  plan-1  SE   0.020
 88D  plan-1  CAJ  0.020
 88D  plan-1  CAI  0.020
 88D  plan-1  CAO  0.020
 88D  plan-1  H18  0.020
 88D  plan-1  H19  0.020
 88D  plan-1  H20  0.020
 88D  plan-2  CAA  0.020
 88D  plan-2  CAW  0.020
 88D  plan-2  CAM  0.020
 88D  plan-2  CAG  0.020
 88D  plan-2  CAH  0.020
 88D  plan-2  CAN  0.020
 88D  plan-2  CAX  0.020
 88D  plan-2  NAQ  0.020
 88D  plan-2  H4   0.020
 88D  plan-2  H5   0.020
 88D  plan-2  H6   0.020
 88D  plan-2  H7   0.020
 88D  plan-3  CB   0.020
 88D  plan-3  CG   0.020
 88D  plan-3  CD1  0.020
 88D  plan-3  CE1  0.020
 88D  plan-3  CZ   0.020
 88D  plan-3  CE2  0.020
 88D  plan-3  CD2  0.020
 88D  plan-3  H12  0.020
 88D  plan-3  H13  0.020
 88D  plan-3  H14  0.020
 88D  plan-3  H15  0.020
 88D  plan-3  H16  0.020
 88D  plan-4  CAX  0.020
 88D  plan-4  NAQ  0.020
 88D  plan-4  C    0.020
 88D  plan-4  O    0.020
 88D  plan-4  CA   0.020
 88D  plan-4  H8   0.020
 88D  plan-5  CA   0.020
 88D  plan-5  N    0.020
 88D  plan-5  CAT  0.020
 88D  plan-5  OAB  0.020
 88D  plan-5  CAY  0.020
 88D  plan-5  H17  0.020

