# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:22:01 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: L-alanyl-N-[(1S,2R)-1-benzyl-2-hydroxypropyl]-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C(=O)N[C@@H](C)C(=O)N[C@@H](Cc1ccccc1)[C@@H](C)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
 K7I  K7I  L-alanyl-N-[(1S,2R)-1-benzyl-2-hydroxypropyl]-L-alaninamide  ligand  47  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K7I
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
 K7I  CAK   C  CR16  0  -0.313  -1.4022  -1.7027   0.5169
 K7I  CAI   C  CR16  0  -0.232  -0.7041  -2.7322  -0.0998
 K7I  CAH   C  CR16  0  -0.274  -0.9167  -3.0108  -1.4430
 K7I  CAJ   C  CR16  0  -0.243  -1.8332  -2.2532  -2.1616
 K7I  CAL   C  CR16  0  -0.298  -2.5223  -1.2204  -1.5416
 K7I  CAR   C  CR6   0   0.146  -2.3158  -0.9289  -0.1952
 K7I  CAM   C  CH2   0  -0.513  -3.0084   0.2377   0.4489
 K7I  CAV   C  CH1   0  -0.116  -2.2283   1.5442   0.2274
 K7I  OAG   O  OH1   0  -0.660  -4.2584   2.8473   0.5128
 K7I  NAO   N  NH1   0  -0.635  -0.8786   1.4000   0.7261
 K7I  CAQ   C  C     0   0.566   0.2079   1.2520  -0.0462
 K7I  OAF   O  O     0  -0.480   0.2121   1.3646  -1.2616
 K7I  CAU   C  CH1   0  -0.202   1.4939   0.9835   0.7312
 K7I  CAC   C  CH3   0  -0.647   2.1210   2.3080   1.1705
 K7I  NAN   N  NH1   0  -0.634   2.3721   0.2131  -0.1133
 K7I  C     C  C     0   0.564   3.2682  -0.6661   0.3570
 K7I  O     O  O     0  -0.502   3.4753  -0.8397   1.5503
 K7I  CA    C  CH1   0  -0.226   3.9755  -1.4937  -0.7066
 K7I  CB    C  CH3   0  -0.669   3.1660  -2.7730  -0.9445
 K7I  N     N  NH2   0  -0.784   5.3491  -1.7124  -0.2939
 K7I  CAT   C  CH1   0   0.047  -2.9018   2.7577   0.8902
 K7I  CAB   C  CH3   0  -0.687  -2.1510   4.0492   0.6010
 K7I  HAK   H  HCR6  0   0.243  -1.2343  -1.4996   1.5682
 K7I  HAI   H  HCR6  0   0.248   0.0060  -3.3161   0.4718
 K7I  HAH   H  HCR6  0   0.251  -0.3765  -3.8148  -1.9267
 K7I  HAJ   H  HCR6  0   0.251  -2.0108  -2.4666  -3.2081
 K7I  HAL   H  HCR6  0   0.242  -3.2291  -0.6302  -2.1139
 K7I  HAM   H  HCH2  0   0.257  -4.0126   0.3555   0.0409
 K7I  HAMA  H  HCH2  0   0.245  -3.1213   0.0647   1.5239
 K7I  HAV   H  HCH1  0   0.259  -2.1542   1.7292  -0.8476
 K7I  HOAG  H  HOH1  0   0.445  -4.2984   3.0780  -0.4219
 K7I  HNAO  H  HNH1  0   0.398  -0.7780   1.2089   1.7119
 K7I  HAU   H  HCH1  0   0.268   1.2614   0.3901   1.6188
 K7I  HAC   H  HCH3  0   0.251   3.0275   2.1199   1.7438
 K7I  HACA  H  HCH3  0   0.236   2.3802   2.9190   0.3056
 K7I  HACB  H  HCH3  0   0.236   1.4352   2.8759   1.8002
 K7I  HNAN  H  HNH1  0   0.398   2.2502   0.3159  -1.1098
 K7I  HA    H  HCH1  0   0.251   3.9973  -0.9244  -1.6405
 K7I  HB    H  HCH3  0   0.233   2.1425  -2.5565  -1.2552
 K7I  HBA   H  HCH3  0   0.240   3.6350  -3.3701  -1.7278
 K7I  HBB   H  HCH3  0   0.227   3.1240  -3.3781  -0.0370
 K7I  HN    H  HNH2  0   0.340   5.3601  -2.2546   0.5619
 K7I  HNA   H  HNH2  0   0.350   5.8144  -2.2813  -0.9905
 K7I  HAT   H  HCH1  0   0.224  -2.9132   2.5905   1.9734
 K7I  HAB   H  HCH3  0   0.224  -2.0984   4.2403  -0.4740
 K7I  HABA  H  HCH3  0   0.242  -2.6494   4.8952   1.0745
 K7I  HABB  H  HCH3  0   0.233  -1.1309   4.0092   0.9807

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
 K7I  CAK  CAI   aromatic  1.388  0.020  1.388
 K7I  CAK  CAR   aromatic  1.393  0.020  1.393
 K7I  CAI  CAH   aromatic  1.388  0.020  1.388
 K7I  CAH  CAJ   aromatic  1.389  0.020  1.389
 K7I  CAJ  CAL   aromatic  1.388  0.020  1.388
 K7I  CAL  CAR   aromatic  1.393  0.020  1.393
 K7I  CAR  CAM   single    1.502  0.020  1.502
 K7I  CAM  CAV   single    1.538  0.020  1.538
 K7I  CAV  NAO   single    1.446  0.020  1.446
 K7I  CAV  CAT   single    1.538  0.020  1.538
 K7I  OAG  CAT   single    1.411  0.020  1.411
 K7I  NAO  CAQ   single    1.341  0.020  1.341
 K7I  CAQ  OAF   double    1.221  0.020  1.221
 K7I  CAQ  CAU   single    1.526  0.020  1.526
 K7I  CAU  CAC   single    1.530  0.020  1.530
 K7I  CAU  NAN   single    1.442  0.020  1.442
 K7I  NAN  C     single    1.341  0.020  1.341
 K7I  C    O     double    1.224  0.020  1.224
 K7I  C    CA    single    1.522  0.020  1.522
 K7I  CA   CB    single    1.532  0.020  1.532
 K7I  CA   N     single    1.451  0.020  1.451
 K7I  CAT  CAB   single    1.522  0.020  1.522
 K7I  CAK  HAK   single    0.930  0.020  1.080
 K7I  CAI  HAI   single    0.930  0.020  1.080
 K7I  CAH  HAH   single    0.930  0.020  1.080
 K7I  CAJ  HAJ   single    0.930  0.020  1.080
 K7I  CAL  HAL   single    0.930  0.020  1.080
 K7I  CAM  HAM   single    0.970  0.020  1.090
 K7I  CAM  HAMA  single    0.970  0.020  1.090
 K7I  CAV  HAV   single    0.970  0.020  1.090
 K7I  OAG  HOAG  single    0.850  0.020  0.980
 K7I  NAO  HNAO  single    0.860  0.020  1.020
 K7I  CAU  HAU   single    0.970  0.020  1.090
 K7I  CAC  HAC   single    0.970  0.020  1.090
 K7I  CAC  HACA  single    0.970  0.020  1.090
 K7I  CAC  HACB  single    0.970  0.020  1.090
 K7I  NAN  HNAN  single    0.860  0.020  1.020
 K7I  CA   HA    single    0.970  0.020  1.090
 K7I  CB   HB    single    0.970  0.020  1.090
 K7I  CB   HBA   single    0.970  0.020  1.090
 K7I  CB   HBB   single    0.970  0.020  1.090
 K7I  N    HN    single    0.890  0.020  1.040
 K7I  N    HNA   single    0.890  0.020  1.040
 K7I  CAT  HAT   single    0.970  0.020  1.090
 K7I  CAB  HAB   single    0.970  0.020  1.090
 K7I  CAB  HABA  single    0.970  0.020  1.090
 K7I  CAB  HABB  single    0.970  0.020  1.090

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
 K7I  HAK   CAK  CAR   119.56  3.000
 K7I  HAK   CAK  CAI   119.47  3.000
 K7I  CAR   CAK  CAI   120.97  3.000
 K7I  HAI   CAI  CAH   120.21  3.000
 K7I  HAI   CAI  CAK   119.69  3.000
 K7I  CAH   CAI  CAK   120.10  3.000
 K7I  HAH   CAH  CAJ   120.20  3.000
 K7I  HAH   CAH  CAI   120.32  3.000
 K7I  CAJ   CAH  CAI   119.48  3.000
 K7I  HAJ   CAJ  CAL   119.80  3.000
 K7I  HAJ   CAJ  CAH   120.04  3.000
 K7I  CAL   CAJ  CAH   120.15  3.000
 K7I  HAL   CAL  CAR   119.53  3.000
 K7I  HAL   CAL  CAJ   119.54  3.000
 K7I  CAR   CAL  CAJ   120.93  3.000
 K7I  CAM   CAR  CAL   120.58  3.000
 K7I  CAM   CAR  CAK   120.98  3.000
 K7I  CAL   CAR  CAK   118.36  3.000
 K7I  HAMA  CAM  HAM   106.83  3.000
 K7I  HAMA  CAM  CAV   109.15  3.000
 K7I  HAM   CAM  CAV   108.76  3.000
 K7I  HAMA  CAM  CAR   110.24  3.000
 K7I  HAM   CAM  CAR   110.38  3.000
 K7I  CAV   CAM  CAR   111.36  3.000
 K7I  HAV   CAV  CAT   108.66  3.000
 K7I  HAV   CAV  NAO   107.02  3.000
 K7I  CAT   CAV  NAO   109.81  3.000
 K7I  HAV   CAV  CAM   108.65  3.000
 K7I  CAT   CAV  CAM   112.71  3.000
 K7I  NAO   CAV  CAM   109.82  3.000
 K7I  HOAG  OAG  CAT   108.34  3.000
 K7I  HNAO  NAO  CAQ   117.44  3.000
 K7I  HNAO  NAO  CAV   116.67  3.000
 K7I  CAQ   NAO  CAV   124.65  3.000
 K7I  CAU   CAQ  OAF   121.36  3.000
 K7I  CAU   CAQ  NAO   114.12  3.000
 K7I  OAF   CAQ  NAO   124.47  3.000
 K7I  HAU   CAU  NAN   108.38  3.000
 K7I  HAU   CAU  CAC   108.91  3.000
 K7I  NAN   CAU  CAC   112.41  3.000
 K7I  HAU   CAU  CAQ   109.26  3.000
 K7I  NAN   CAU  CAQ   108.00  3.000
 K7I  CAC   CAU  CAQ   109.83  3.000
 K7I  HACB  CAC  HACA  108.40  3.000
 K7I  HACB  CAC  HAC   108.03  3.000
 K7I  HACA  CAC  HAC   108.45  3.000
 K7I  HACB  CAC  CAU   111.03  3.000
 K7I  HACA  CAC  CAU   110.78  3.000
 K7I  HAC   CAC  CAU   110.05  3.000
 K7I  HNAN  NAN  C     119.61  3.000
 K7I  HNAN  NAN  CAU   116.77  3.000
 K7I  C     NAN  CAU   123.52  3.000
 K7I  CA    C    O     121.72  3.000
 K7I  CA    C    NAN   114.96  3.000
 K7I  O     C    NAN   123.26  3.000
 K7I  HA    CA   N     107.60  3.000
 K7I  HA    CA   CB    108.21  3.000
 K7I  N     CA   CB    114.73  3.000
 K7I  HA    CA   C     108.84  3.000
 K7I  N     CA   C     108.86  3.000
 K7I  CB    CA   C     108.48  3.000
 K7I  HBB   CB   HBA   108.06  3.000
 K7I  HBB   CB   HB    108.09  3.000
 K7I  HBA   CB   HB    107.90  3.000
 K7I  HBB   CB   CA    110.74  3.000
 K7I  HBA   CB   CA    109.96  3.000
 K7I  HB    CB   CA    111.96  3.000
 K7I  HNA   N    HN    105.99  3.000
 K7I  HNA   N    CA    108.91  3.000
 K7I  HN    N    CA    109.34  3.000
 K7I  HAT   CAT  CAB   108.81  3.000
 K7I  HAT   CAT  OAG   105.31  3.000
 K7I  CAB   CAT  OAG   111.70  3.000
 K7I  HAT   CAT  CAV   108.06  3.000
 K7I  CAB   CAT  CAV   111.81  3.000
 K7I  OAG   CAT  CAV   110.85  3.000
 K7I  HABB  CAB  HABA  107.77  3.000
 K7I  HABB  CAB  HAB   107.72  3.000
 K7I  HABA  CAB  HAB   108.27  3.000
 K7I  HABB  CAB  CAT   111.39  3.000
 K7I  HABA  CAB  CAT   110.52  3.000
 K7I  HAB   CAB  CAT   111.04  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
 K7I  CONST_01  CAJ   CAH  CAI  CAK    0.00   0.0  0
 K7I  CONST_02  CAJ   CAL  CAR  CAK    0.00   0.0  0
 K7I  CONST_03  CAL   CAR  CAK  CAI    0.00   0.0  0
 K7I  CONST_04  CAL   CAJ  CAH  CAI    0.00   0.0  0
 K7I  CONST_05  CAR   CAK  CAI  CAH    0.00   0.0  0
 K7I  CONST_06  CAR   CAL  CAJ  CAH    0.00   0.0  0
 K7I  CONST_07  CAM   CAR  CAK  CAI  180.00   0.0  0
 K7I  CONST_08  CAM   CAR  CAL  CAJ  180.00   0.0  0
 K7I  CONST_09  HAH   CAH  CAI  CAK  180.00   0.0  0
 K7I  CONST_10  HAL   CAL  CAR  CAK  180.00   0.0  0
 K7I  CONST_11  HAJ   CAJ  CAH  CAI  180.00   0.0  0
 K7I  CONST_12  HAK   CAK  CAI  CAH  180.00   0.0  0
 K7I  CONST_13  HAI   CAI  CAH  CAJ  180.00   0.0  0
 K7I  CONST_14  OAF   CAQ  NAO  CAV    0.00   0.0  0
 K7I  CONST_15  CAU   CAQ  NAO  CAV  180.00   0.0  0
 K7I  CONST_16  O     C    NAN  CAU    0.00   0.0  0
 K7I  CONST_17  CA    C    NAN  CAU  180.00   0.0  0
 K7I  CONST_18  HNAO  NAO  CAQ  OAF  180.00   0.0  0
 K7I  CONST_19  HNAN  NAN  C    O    180.00   0.0  0
 K7I  Var_01    CAV   CAM  CAR  CAK   91.82  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
 K7I  chir_01  CAV  CAM  NAO  CAT  positiv
 K7I  chir_02  CAU  NAN  CAQ  CAC  positiv
 K7I  chir_03  CA   N    C    CB   positiv
 K7I  chir_04  CAT  OAG  CAV  CAB  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
 K7I  plan-1  CAK   0.020
 K7I  plan-1  CAI   0.020
 K7I  plan-1  CAH   0.020
 K7I  plan-1  CAJ   0.020
 K7I  plan-1  CAL   0.020
 K7I  plan-1  CAR   0.020
 K7I  plan-1  CAM   0.020
 K7I  plan-1  HAK   0.020
 K7I  plan-1  HAI   0.020
 K7I  plan-1  HAH   0.020
 K7I  plan-1  HAJ   0.020
 K7I  plan-1  HAL   0.020
 K7I  plan-2  CAV   0.020
 K7I  plan-2  NAO   0.020
 K7I  plan-2  CAQ   0.020
 K7I  plan-2  OAF   0.020
 K7I  plan-2  CAU   0.020
 K7I  plan-2  HNAO  0.020
 K7I  plan-3  CAU   0.020
 K7I  plan-3  NAN   0.020
 K7I  plan-3  C     0.020
 K7I  plan-3  O     0.020
 K7I  plan-3  CA    0.020
 K7I  plan-3  HNAN  0.020

