# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 06:12:48 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3
#
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
 88G  88G  Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide  ligand  49  27  .  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_88G
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
 88G  CAA  C  CH3   0  -0.744   4.4035   0.6575   2.3023
 88G  CAW  C  CR6   0   0.062   4.8858   0.0186   1.0330
 88G  CAL  C  CR16  0  -0.308   6.2043  -0.4084   0.9055
 88G  CAJ  C  CR16  0  -0.248   6.6573  -1.0296  -0.2495
 88G  CAK  C  CR16  0  -0.275   5.7861  -1.2207  -1.3118
 88G  CAQ  C  CR16  0  -0.275   4.4723  -0.7877  -1.2175
 88G  CAZ  C  CR6   0   0.301   4.0219  -0.1764  -0.0516
 88G  NAS  N  NH1   0  -0.743   2.6954   0.2874   0.0549
 88G  C    C  C     0   0.547   1.5849  -0.3881  -0.3164
 88G  O    O  O     0  -0.456   1.5885  -1.5088  -0.7889
 88G  CA   C  CH1   0  -0.225   0.2963   0.4108  -0.1475
 88G  CB   C  CH2   0  -0.520   0.1361   1.3689  -1.3496
 88G  CG   C  CR6   0   0.144  -1.1475   2.1414  -1.2621
 88G  CD1  C  CR16  0  -0.291  -1.2291   3.2927  -0.4828
 88G  CE1  C  CR16  0  -0.242  -2.4251   3.9844  -0.3609
 88G  CZ   C  CR16  0  -0.271  -3.5636   3.5287  -1.0145
 88G  CE2  C  CR16  0  -0.239  -3.4935   2.3825  -1.7942
 88G  CD2  C  CR16  0  -0.306  -2.2922   1.6966  -1.9168
 88G  N    N  NH1   0  -0.652  -0.8156  -0.4893  -0.0369
 88G  CAU  C  C     0   0.551  -1.7934  -0.3501   0.8791
 88G  OAB  O  O     0  -0.477  -1.7643   0.4886   1.7670
 88G  CAY  C  CR6   0  -0.029  -2.9338  -1.3107   0.7645
 88G  CAO  C  CR16  0  -0.270  -3.6702  -1.5919   1.9137
 88G  CAH  C  CR16  0  -0.242  -4.7484  -2.4611   1.8612
 88G  CAE  C  CR16  0  -0.251  -5.1149  -3.0448   0.6549
 88G  CAI  C  CR16  0  -0.241  -4.3971  -2.7560  -0.4974
 88G  CAP  C  CR16  0  -0.294  -3.3101  -1.8951  -0.4435
 88G  H1   H  HCH3  0   0.249   4.1042   1.6983   2.1560
 88G  H2   H  HCH3  0   0.252   3.5407   0.1296   2.7121
 88G  H3   H  HCH3  0   0.259   5.1857   0.6529   3.0587
 88G  H4   H  HCR6  0   0.253   6.8848  -0.2613   1.7354
 88G  H5   H  HCR6  0   0.256   7.6853  -1.3605  -0.3182
 88G  H6   H  HCR6  0   0.258   6.1276  -1.6974  -2.2211
 88G  H7   H  HCR6  0   0.265   3.8053  -0.9129  -2.0586
 88G  H8   H  HNH1  0   0.414   2.5601   1.1687   0.5272
 88G  H9   H  HCH1  0   0.295   0.3399   1.0012   0.7693
 88G  H10  H  HCH2  0   0.268   0.9902   2.0492  -1.3736
 88G  H11  H  HCH2  0   0.267   0.1650   0.7859  -2.2737
 88G  H12  H  HCR6  0   0.245  -0.3468   3.6536   0.0336
 88G  H13  H  HCR6  0   0.253  -2.4696   4.8809   0.2444
 88G  H14  H  HCR6  0   0.253  -4.4977   4.0672  -0.9197
 88G  H15  H  HCR6  0   0.252  -4.3736   2.0215  -2.3112
 88G  H16  H  HCR6  0   0.245  -2.2427   0.8102  -2.5380
 88G  H17  H  HNH1  0   0.403  -0.8483  -1.2589  -0.6865
 88G  H18  H  HCR6  0   0.261  -3.3940  -1.1342   2.8543
 88G  H19  H  HCR6  0   0.263  -5.3064  -2.6798   2.7622
 88G  H20  H  HCR6  0   0.265  -5.9609  -3.7183   0.6126
 88G  H21  H  HCR6  0   0.265  -4.6848  -3.1964  -1.4428
 88G  H22  H  HCR6  0   0.254  -2.7823  -1.6708  -1.3622

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
 88G  CAE  CAH  aromatic  1.389  0.020  1.389
 88G  CAE  CAI  aromatic  1.388  0.020  1.388
 88G  CAH  CAO  aromatic  1.386  0.020  1.386
 88G  CAI  CAP  aromatic  1.388  0.020  1.388
 88G  CAO  CAY  aromatic  1.394  0.020  1.394
 88G  CAP  CAY  aromatic  1.394  0.020  1.394
 88G  CAY  CAU  single    1.495  0.020  1.495
 88G  CAU  N    single    1.347  0.020  1.347
 88G  CAU  OAB  double    1.222  0.020  1.222
 88G  N    CA   single    1.435  0.020  1.435
 88G  O    C    double    1.216  0.020  1.216
 88G  CA   CB   single    1.546  0.020  1.546
 88G  CA   C    single    1.526  0.020  1.526
 88G  CB   CG   single    1.501  0.020  1.501
 88G  C    NAS  single    1.352  0.020  1.352
 88G  CAA  CAW  single    1.501  0.020  1.501
 88G  CAW  CAL  aromatic  1.392  0.020  1.392
 88G  CAW  CAZ  aromatic  1.400  0.020  1.400
 88G  NAS  CAZ  single    1.409  0.020  1.409
 88G  CG   CD1  aromatic  1.393  0.020  1.393
 88G  CG   CD2  aromatic  1.392  0.020  1.392
 88G  CAL  CAJ  aromatic  1.387  0.020  1.387
 88G  CAZ  CAQ  aromatic  1.391  0.020  1.391
 88G  CD1  CE1  aromatic  1.387  0.020  1.387
 88G  CAJ  CAK  aromatic  1.387  0.020  1.387
 88G  CAQ  CAK  aromatic  1.386  0.020  1.386
 88G  CD2  CE2  aromatic  1.389  0.020  1.389
 88G  CE1  CZ   aromatic  1.390  0.020  1.390
 88G  CE2  CZ   aromatic  1.388  0.020  1.388
 88G  CAA  H1   single    0.970  0.020  1.090
 88G  CAA  H2   single    0.970  0.020  1.090
 88G  CAA  H3   single    0.970  0.020  1.090
 88G  CAL  H4   single    0.930  0.020  1.080
 88G  CAJ  H5   single    0.930  0.020  1.080
 88G  CAK  H6   single    0.930  0.020  1.080
 88G  CAQ  H7   single    0.930  0.020  1.080
 88G  NAS  H8   single    0.860  0.020  1.020
 88G  CA   H9   single    0.970  0.020  1.090
 88G  CB   H10  single    0.970  0.020  1.090
 88G  CB   H11  single    0.970  0.020  1.090
 88G  CD1  H12  single    0.930  0.020  1.080
 88G  CE1  H13  single    0.930  0.020  1.080
 88G  CZ   H14  single    0.930  0.020  1.080
 88G  CE2  H15  single    0.930  0.020  1.080
 88G  CD2  H16  single    0.930  0.020  1.080
 88G  N    H17  single    0.860  0.020  1.020
 88G  CAO  H18  single    0.930  0.020  1.080
 88G  CAH  H19  single    0.930  0.020  1.080
 88G  CAE  H20  single    0.930  0.020  1.080
 88G  CAI  H21  single    0.930  0.020  1.080
 88G  CAP  H22  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
 88G  H3   CAA  H2   107.77  3.000
 88G  H3   CAA  H1   107.10  3.000
 88G  H2   CAA  H1   107.13  3.000
 88G  H3   CAA  CAW  110.80  3.000
 88G  H2   CAA  CAW  111.45  3.000
 88G  H1   CAA  CAW  112.35  3.000
 88G  CAZ  CAW  CAL  118.09  3.000
 88G  CAZ  CAW  CAA  121.08  3.000
 88G  CAL  CAW  CAA  120.84  3.000
 88G  H4   CAL  CAJ  119.56  3.000
 88G  H4   CAL  CAW  118.90  3.000
 88G  CAJ  CAL  CAW  121.53  3.000
 88G  H5   CAJ  CAK  120.39  3.000
 88G  H5   CAJ  CAL  120.00  3.000
 88G  CAK  CAJ  CAL  119.61  3.000
 88G  H6   CAK  CAQ  119.59  3.000
 88G  H6   CAK  CAJ  120.40  3.000
 88G  CAQ  CAK  CAJ  120.00  3.000
 88G  H7   CAQ  CAZ  120.22  3.000
 88G  H7   CAQ  CAK  119.72  3.000
 88G  CAZ  CAQ  CAK  120.06  3.000
 88G  NAS  CAZ  CAQ  120.84  3.000
 88G  CAQ  CAZ  CAW  120.70  3.000
 88G  NAS  CAZ  CAW  118.45  3.000
 88G  H8   NAS  C    117.06  3.000
 88G  H8   NAS  CAZ  116.68  3.000
 88G  C    NAS  CAZ  126.02  3.000
 88G  CA   C    O    121.88  3.000
 88G  CA   C    NAS  113.69  3.000
 88G  O    C    NAS  124.38  3.000
 88G  H9   CA   N    107.80  3.000
 88G  H9   CA   CB   108.80  3.000
 88G  N    CA   CB   111.62  3.000
 88G  H9   CA   C    110.03  3.000
 88G  CB   CA   C    109.03  3.000
 88G  N    CA   C    109.54  3.000
 88G  H11  CB   H10  107.04  3.000
 88G  H11  CB   CG   110.28  3.000
 88G  H10  CB   CG   110.46  3.000
 88G  H11  CB   CA   108.92  3.000
 88G  H10  CB   CA   108.79  3.000
 88G  CG   CB   CA   111.25  3.000
 88G  CD2  CG   CD1  118.64  3.000
 88G  CD2  CG   CB   120.77  3.000
 88G  CD1  CG   CB   120.55  3.000
 88G  H12  CD1  CE1  119.59  3.000
 88G  H12  CD1  CG   119.61  3.000
 88G  CE1  CD1  CG   120.80  3.000
 88G  H13  CE1  CZ   120.06  3.000
 88G  H13  CE1  CD1  119.83  3.000
 88G  CZ   CE1  CD1  120.10  3.000
 88G  H14  CZ   CE2  120.24  3.000
 88G  H14  CZ   CE1  120.17  3.000
 88G  CE2  CZ   CE1  119.59  3.000
 88G  H15  CE2  CD2  119.77  3.000
 88G  H15  CE2  CZ   120.17  3.000
 88G  CD2  CE2  CZ   120.07  3.000
 88G  H16  CD2  CE2  119.61  3.000
 88G  H16  CD2  CG   119.58  3.000
 88G  CE2  CD2  CG   120.81  3.000
 88G  H17  N    CAU  119.59  3.000
 88G  H17  N    CA   117.04  3.000
 88G  CAU  N    CA   123.37  3.000
 88G  CAY  CAU  OAB  120.99  3.000
 88G  OAB  CAU  N    123.22  3.000
 88G  CAY  CAU  N    115.79  3.000
 88G  CAP  CAY  CAO  119.18  3.000
 88G  CAP  CAY  CAU  122.80  3.000
 88G  CAO  CAY  CAU  117.99  3.000
 88G  H18  CAO  CAH  119.79  3.000
 88G  H18  CAO  CAY  119.78  3.000
 88G  CAH  CAO  CAY  120.42  3.000
 88G  H19  CAH  CAE  120.13  3.000
 88G  H19  CAH  CAO  119.76  3.000
 88G  CAE  CAH  CAO  120.11  3.000
 88G  H20  CAE  CAI  120.09  3.000
 88G  H20  CAE  CAH  120.11  3.000
 88G  CAI  CAE  CAH  119.80  3.000
 88G  H21  CAI  CAP  119.65  3.000
 88G  H21  CAI  CAE  120.21  3.000
 88G  CAP  CAI  CAE  120.13  3.000
 88G  H22  CAP  CAI  118.51  3.000
 88G  H22  CAP  CAY  121.11  3.000
 88G  CAI  CAP  CAY  120.35  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
 88G  CONST_01  CAK  CAJ  CAL  CAW    0.00   0.0  0
 88G  CONST_02  CAK  CAQ  CAZ  CAW    0.00   0.0  0
 88G  CONST_03  CAQ  CAZ  CAW  CAL    0.00   0.0  0
 88G  CONST_04  CAQ  CAK  CAJ  CAL    0.00   0.0  0
 88G  CONST_05  CAZ  CAW  CAL  CAJ    0.00   0.0  0
 88G  CONST_06  CAZ  CAQ  CAK  CAJ    0.00   0.0  0
 88G  CONST_07  CZ   CE1  CD1  CG     0.00   0.0  0
 88G  CONST_08  CZ   CE2  CD2  CG     0.00   0.0  0
 88G  CONST_09  CE2  CD2  CG   CD1    0.00   0.0  0
 88G  CONST_10  CE2  CZ   CE1  CD1    0.00   0.0  0
 88G  CONST_11  CD2  CG   CD1  CE1    0.00   0.0  0
 88G  CONST_12  CD2  CE2  CZ   CE1    0.00   0.0  0
 88G  CONST_13  CAE  CAH  CAO  CAY    0.00   0.0  0
 88G  CONST_14  CAE  CAI  CAP  CAY    0.00   0.0  0
 88G  CONST_15  CAI  CAE  CAH  CAO    0.00   0.0  0
 88G  CONST_16  CAI  CAP  CAY  CAO    0.00   0.0  0
 88G  CONST_17  CAP  CAI  CAE  CAH    0.00   0.0  0
 88G  CONST_18  CAP  CAY  CAO  CAH    0.00   0.0  0
 88G  CONST_19  CAJ  CAL  CAW  CAA  180.00   0.0  0
 88G  CONST_20  CAQ  CAZ  CAW  CAA  180.00   0.0  0
 88G  CONST_21  NAS  CAZ  CAW  CAL  180.00   0.0  0
 88G  CONST_22  NAS  CAZ  CAQ  CAK  180.00   0.0  0
 88G  CONST_23  CE1  CD1  CG   CB   180.00   0.0  0
 88G  CONST_24  CE2  CD2  CG   CB   180.00   0.0  0
 88G  CONST_25  CAH  CAO  CAY  CAU  180.00   0.0  0
 88G  CONST_26  CAI  CAP  CAY  CAU  180.00   0.0  0
 88G  CONST_27  H5   CAJ  CAL  CAW  180.00   0.0  0
 88G  CONST_28  H7   CAQ  CAZ  CAW  180.00   0.0  0
 88G  CONST_29  H6   CAK  CAJ  CAL  180.00   0.0  0
 88G  CONST_30  H4   CAL  CAJ  CAK  180.00   0.0  0
 88G  CONST_31  H13  CE1  CD1  CG   180.00   0.0  0
 88G  CONST_32  H15  CE2  CD2  CG   180.00   0.0  0
 88G  CONST_33  H16  CD2  CG   CD1  180.00   0.0  0
 88G  CONST_34  H14  CZ   CE1  CD1  180.00   0.0  0
 88G  CONST_35  H12  CD1  CE1  CZ   180.00   0.0  0
 88G  CONST_36  H19  CAH  CAO  CAY  180.00   0.0  0
 88G  CONST_37  H21  CAI  CAP  CAY  180.00   0.0  0
 88G  CONST_38  H20  CAE  CAH  CAO  180.00   0.0  0
 88G  CONST_39  H22  CAP  CAY  CAO  180.00   0.0  0
 88G  CONST_40  H18  CAO  CAH  CAE  180.00   0.0  0
 88G  CONST_44  O    C    NAS  CAZ    0.00   0.0  0
 88G  CONST_45  CA   C    NAS  CAZ  180.00   0.0  0
 88G  CONST_46  CAY  CAU  N    CA   180.00   0.0  0
 88G  CONST_47  H17  N    CAU  CAY    0.00   0.0  0
 88G  CONST_48  OAB  CAU  N    CA     0.00   0.0  0
 88G  Var_01    CD1  CG   CB   CA    82.78  30.0  2
 88G  Var_02    CAO  CAY  CAU  N    154.78  30.0  2
 88G  Var_03    H1   CAA  CAW  CAL  115.71  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
 88G  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
 88G  plan-1  CAA  0.020
 88G  plan-1  CAW  0.020
 88G  plan-1  CAL  0.020
 88G  plan-1  CAJ  0.020
 88G  plan-1  CAK  0.020
 88G  plan-1  CAQ  0.020
 88G  plan-1  CAZ  0.020
 88G  plan-1  NAS  0.020
 88G  plan-1  H4   0.020
 88G  plan-1  H5   0.020
 88G  plan-1  H6   0.020
 88G  plan-1  H7   0.020
 88G  plan-2  CB   0.020
 88G  plan-2  CG   0.020
 88G  plan-2  CD1  0.020
 88G  plan-2  CE1  0.020
 88G  plan-2  CZ   0.020
 88G  plan-2  CE2  0.020
 88G  plan-2  CD2  0.020
 88G  plan-2  H12  0.020
 88G  plan-2  H13  0.020
 88G  plan-2  H14  0.020
 88G  plan-2  H15  0.020
 88G  plan-2  H16  0.020
 88G  plan-3  CAU  0.020
 88G  plan-3  CAY  0.020
 88G  plan-3  CAO  0.020
 88G  plan-3  CAH  0.020
 88G  plan-3  CAE  0.020
 88G  plan-3  CAI  0.020
 88G  plan-3  CAP  0.020
 88G  plan-3  H18  0.020
 88G  plan-3  H19  0.020
 88G  plan-3  H20  0.020
 88G  plan-3  H21  0.020
 88G  plan-3  H22  0.020
 88G  plan-4  CAZ  0.020
 88G  plan-4  NAS  0.020
 88G  plan-4  C    0.020
 88G  plan-4  O    0.020
 88G  plan-4  CA   0.020
 88G  plan-4  H8   0.020
 88G  plan-5  CA   0.020
 88G  plan-5  N    0.020
 88G  plan-5  CAU  0.020
 88G  plan-5  OAB  0.020
 88G  plan-5  CAY  0.020
 88G  plan-5  H17  0.020

