# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 19:57:54 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-acetylglycyl-N-[(3S)-1-hydroxy-5-methyl-2-oxohexan-3-yl]-L-serinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](CO)NC(=O)CNC(C)=O)C(=O)CO
#
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
 621  621  N-acetylglycyl-N-[(3S)-1-hydroxy-5-methyl-2-oxohexan-3-yl]-L-serinamide  ligand  48  23  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_621
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
 621  CAT   C  C     0   0.535   6.5863  -0.7134   0.9353
 621  OAV   O  O     0  -0.501   6.5821  -0.9321   2.1385
 621  CAU   C  CH3   0  -0.748   7.8637  -0.5323   0.1559
 621  NAS   N  NH1   0  -0.630   5.4537  -0.6094   0.2229
 621  CAQ   C  CH2   0  -0.351   4.1560  -0.7387   0.8160
 621  CAP   C  C     0   0.541   3.0898  -0.5371  -0.2480
 621  OAR   O  O     0  -0.480   3.3711  -0.3107  -1.4141
 621  NAM   N  NH1   0  -0.635   1.8349  -0.6262   0.2094
 621  CAK   C  CH1   0  -0.236   0.6806  -0.4377  -0.6269
 621  CAJ   C  C     0   0.586  -0.4853  -0.0109   0.2573
 621  OAL   O  O     0  -0.466  -0.4723  -0.1498   1.4670
 621  CAN   C  CH2   0  -0.135   0.2808  -1.7119  -1.3737
 621  OAO   O  OH1   0  -0.651  -0.1462  -2.6671  -0.4376
 621  C     C  C     0   0.380  -3.4750  -0.6831   0.4735
 621  N     N  NH1   0  -0.625  -1.5339   0.4997  -0.4104
 621  CA    C  CH1   0  -0.210  -2.8150   0.6741   0.2212
 621  CB    C  CH2   0  -0.431  -3.7258   1.5371  -0.6534
 621  CG    C  CH1   0  -0.225  -3.1883   2.9414  -0.9422
 621  CAC   C  CH2   0  -0.229  -4.3501  -0.7276   1.6974
 621  CD1   C  CH3   0  -0.626  -4.1811   3.6953  -1.8198
 621  CD2   C  CH3   0  -0.641  -2.8968   3.7189   0.3359
 621  OXT   O  OH1   0  -0.616  -5.0853  -1.9048   1.7328
 621  HAU   H  HCH3  0   0.230   7.7130  -0.4069  -0.9145
 621  HAUA  H  HCH3  0   0.260   8.3927   0.3438   0.5305
 621  HAUB  H  HCH3  0   0.259   8.5116  -1.3934   0.3119
 621  HNAS  H  HNH1  0   0.383   5.4809  -0.4356  -0.7689
 621  HAQ   H  HCH2  0   0.264   4.0101  -0.0027   1.6125
 621  HAQA  H  HCH2  0   0.264   4.0239  -1.7247   1.2722
 621  HNAM  H  HNH1  0   0.391   1.6628  -0.8015   1.1878
 621  HAK   H  HCH1  0   0.280   0.8921   0.3406  -1.3658
 621  HAN   H  HCH2  0   0.203  -0.5011  -1.4672  -2.0999
 621  HANA  H  HCH2  0   0.227   1.1414  -2.0651  -1.9517
 621  HOAO  H  HOH1  0   0.450  -0.8787  -3.1618  -0.8095
 621  HN    H  HNH1  0   0.377  -1.5035   0.5219  -1.4168
 621  HA    H  HCH1  0   0.266  -2.6688   1.1759   1.1818
 621  HB    H  HCH2  0   0.240  -3.9187   1.0151  -1.5969
 621  HBA   H  HCH2  0   0.232  -4.6990   1.6267  -0.1605
 621  HG    H  HCH1  0   0.216  -2.2516   2.8496  -1.5026
 621  HAC   H  HCH2  0   0.207  -4.9762   0.1786   1.7090
 621  HACA  H  HCH2  0   0.228  -3.6674  -0.6144   2.5551
 621  HD1   H  HCH3  0   0.208  -5.1285   3.8509  -1.2991
 621  HD1A  H  HCH3  0   0.226  -3.7929   4.6762  -2.0945
 621  HD1B  H  HCH3  0   0.221  -4.3965   3.1543  -2.7422
 621  HD2   H  HCH3  0   0.207  -3.7785   3.7667   0.9793
 621  HD2A  H  HCH3  0   0.226  -2.0847   3.2780   0.9148
 621  HD2B  H  HCH3  0   0.231  -2.6027   4.7437   0.1076
 621  HXT   H  HOH1  0   0.438  -5.5683  -1.9242   2.5619
 621  O     O  O     0  -0.342  -3.2954  -1.6202  -0.2557

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
 621  C    CAC   single  1.505  0.020  1.505
 621  C    CA    single  1.530  0.020  1.530
 621  N    CAJ   single  1.344  0.020  1.344
 621  N    HN    single  0.890  0.020  1.040
 621  O    C     double  1.201  0.020  1.201
 621  CA   N     single  1.439  0.020  1.439
 621  CA   HA    single  0.970  0.020  1.090
 621  CB   CA    single  1.529  0.020  1.529
 621  CB   HB    single  0.970  0.020  1.090
 621  CB   HBA   single  0.970  0.020  1.090
 621  CG   CB    single  1.531  0.020  1.531
 621  CG   CD2   single  1.524  0.020  1.524
 621  CG   CD1   single  1.525  0.020  1.525
 621  CG   HG    single  0.970  0.020  1.090
 621  CAC  HAC   single  0.970  0.020  1.090
 621  CAC  OXT   single  1.388  0.020  1.388
 621  CAC  HACA  single  0.970  0.020  1.090
 621  CAJ  OAL   double  1.218  0.020  1.218
 621  CAJ  CAK   single  1.524  0.020  1.524
 621  CAK  CAN   single  1.530  0.020  1.530
 621  CAK  NAM   single  1.438  0.020  1.438
 621  CAK  HAK   single  0.970  0.020  1.090
 621  NAM  CAP   single  1.339  0.020  1.339
 621  NAM  HNAM  single  0.860  0.020  1.020
 621  CAN  HAN   single  0.970  0.020  1.090
 621  CAN  HANA  single  0.970  0.020  1.090
 621  OAO  CAN   single  1.404  0.020  1.404
 621  OAO  HOAO  single  0.850  0.020  0.980
 621  CAP  CAQ   single  1.520  0.020  1.520
 621  CAQ  NAS   single  1.433  0.020  1.433
 621  CAQ  HAQ   single  0.970  0.020  1.090
 621  CAQ  HAQA  single  0.970  0.020  1.090
 621  OAR  CAP   double  1.221  0.020  1.221
 621  NAS  CAT   single  1.342  0.020  1.342
 621  NAS  HNAS  single  0.860  0.020  1.020
 621  CAT  CAU   single  1.507  0.020  1.507
 621  CAT  OAV   double  1.223  0.020  1.223
 621  CAU  HAU   single  0.970  0.020  1.090
 621  CAU  HAUA  single  0.970  0.020  1.090
 621  CAU  HAUB  single  0.970  0.020  1.090
 621  CD1  HD1   single  0.970  0.020  1.090
 621  CD1  HD1A  single  0.970  0.020  1.090
 621  CD1  HD1B  single  0.970  0.020  1.090
 621  CD2  HD2   single  0.970  0.020  1.090
 621  CD2  HD2A  single  0.970  0.020  1.090
 621  CD2  HD2B  single  0.970  0.020  1.090
 621  OXT  HXT   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
 621  NAS   CAT  CAU   115.56  3.000
 621  CAU   CAT  OAV   122.22  3.000
 621  NAS   CAT  OAV   122.22  3.000
 621  HAUB  CAU  HAUA  107.32  3.000
 621  HAUB  CAU  HAU   108.33  3.000
 621  HAUA  CAU  HAU   108.22  3.000
 621  HAUB  CAU  CAT   109.58  3.000
 621  HAUA  CAU  CAT   109.28  3.000
 621  HAU   CAU  CAT   113.90  3.000
 621  HNAS  NAS  CAQ   116.60  3.000
 621  HNAS  NAS  CAT   120.88  3.000
 621  CAQ   NAS  CAT   122.53  3.000
 621  HAQA  CAQ  HAQ   106.64  3.000
 621  HAQA  CAQ  CAP   109.06  3.000
 621  HAQ   CAQ  CAP   109.08  3.000
 621  HAQA  CAQ  NAS   111.29  3.000
 621  HAQ   CAQ  NAS   111.19  3.000
 621  CAP   CAQ  NAS   109.49  3.000
 621  NAM   CAP  OAR   123.69  3.000
 621  OAR   CAP  CAQ   122.13  3.000
 621  NAM   CAP  CAQ   114.18  3.000
 621  HNAM  NAM  CAK   116.74  3.000
 621  HNAM  NAM  CAP   120.19  3.000
 621  CAK   NAM  CAP   123.03  3.000
 621  HAK   CAK  CAN   108.26  3.000
 621  HAK   CAK  CAJ   109.91  3.000
 621  CAN   CAK  CAJ   108.45  3.000
 621  HAK   CAK  NAM   109.33  3.000
 621  CAN   CAK  NAM   112.61  3.000
 621  CAJ   CAK  NAM   108.27  3.000
 621  N     CAJ  OAL   123.04  3.000
 621  OAL   CAJ  CAK   122.42  3.000
 621  N     CAJ  CAK   114.53  3.000
 621  HANA  CAN  HAN   106.45  3.000
 621  HANA  CAN  OAO   111.80  3.000
 621  HAN   CAN  OAO   112.16  3.000
 621  OAO   CAN  CAK   108.70  3.000
 621  HANA  CAN  CAK   108.71  3.000
 621  HAN   CAN  CAK   108.92  3.000
 621  HOAO  OAO  CAN   108.95  3.000
 621  CAC   C    CA    114.27  3.000
 621  CA    C    O     121.84  3.000
 621  CAC   C    O     123.89  3.000
 621  HN    N    CA    117.57  3.000
 621  CA    N    CAJ   121.52  3.000
 621  HN    N    CAJ   118.77  3.000
 621  HA    CA   CB    108.85  3.000
 621  CB    CA   N     110.34  3.000
 621  HA    CA   N     108.79  3.000
 621  CB    CA   C     109.75  3.000
 621  HA    CA   C     108.65  3.000
 621  N     CA   C     110.42  3.000
 621  HBA   CB   HB    105.69  3.000
 621  HBA   CB   CG    108.78  3.000
 621  HB    CB   CG    109.67  3.000
 621  CG    CB   CA    114.60  3.000
 621  HBA   CB   CA    108.54  3.000
 621  HB    CB   CA    109.17  3.000
 621  HG    CG   CD2   107.95  3.000
 621  HG    CG   CD1   107.68  3.000
 621  CD2   CG   CD1   110.80  3.000
 621  HG    CG   CB    108.65  3.000
 621  CD1   CG   CB    109.48  3.000
 621  CD2   CG   CB    112.14  3.000
 621  HACA  CAC  HAC   105.04  3.000
 621  HACA  CAC  OXT   113.28  3.000
 621  HAC   CAC  OXT   113.34  3.000
 621  HACA  CAC  C     105.64  3.000
 621  OXT   CAC  C     110.71  3.000
 621  HAC   CAC  C     108.35  3.000
 621  HD1B  CD1  HD1A  107.67  3.000
 621  HD1B  CD1  HD1   107.60  3.000
 621  HD1A  CD1  HD1   107.51  3.000
 621  HD1B  CD1  CG    111.72  3.000
 621  HD1A  CD1  CG    110.99  3.000
 621  HD1   CD1  CG    111.15  3.000
 621  HD2B  CD2  HD2A  106.88  3.000
 621  HD2B  CD2  HD2   107.45  3.000
 621  HD2A  CD2  HD2   107.82  3.000
 621  HD2B  CD2  CG    110.82  3.000
 621  HD2A  CD2  CG    112.42  3.000
 621  HD2   CD2  CG    111.21  3.000
 621  HXT   OXT  CAC   107.80  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
 621  CONST_01  CAQ   NAS  CAT  OAV     0.00   0.0  0
 621  CONST_02  CAQ   NAS  CAT  CAU   180.00   0.0  0
 621  CONST_03  CAK   NAM  CAP  CAQ   180.00   0.0  0
 621  CONST_04  CAK   NAM  CAP  OAR     0.00   0.0  0
 621  CONST_05  CA    N    CAJ  CAK   180.00   0.0  0
 621  CONST_06  CA    N    CAJ  OAL     0.00   0.0  0
 621  CONST_07  HNAS  NAS  CAT  OAV   180.00   0.0  0
 621  CONST_08  HNAM  NAM  CAP  CAQ     0.00   0.0  0
 621  CONST_09  HN    N    CAJ  CAK     0.00   0.0  0
 621  Var_01    CAP   CAQ  NAS  CAT   178.65  30.0  2
 621  Var_02    NAM   CAP  CAQ  NAS  -179.41  30.0  1
 621  Var_03    OXT   CAC  C    O     -10.21  30.0  3
 621  Var_04    CD2   CG   CB   CA    -56.69  30.0  1
 621  Var_05    HAU   CAU  CAT  OAV   176.35  30.0  3
 621  Var_06    HD2   CD2  CG   CB    -55.38  30.0  3
 621  Var_07    HD1   CD1  CG   CB     64.10  30.0  3

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
 621  chir_01  CAK  CAJ  CAN  NAM  positiv
 621  chir_02  CA   N    C    CB   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
 621  plan-1  CAT   0.020
 621  plan-1  OAV   0.020
 621  plan-1  CAU   0.020
 621  plan-1  NAS   0.020
 621  plan-1  CAQ   0.020
 621  plan-1  HNAS  0.020
 621  plan-2  CAQ   0.020
 621  plan-2  CAP   0.020
 621  plan-2  OAR   0.020
 621  plan-2  NAM   0.020
 621  plan-2  CAK   0.020
 621  plan-2  HNAM  0.020
 621  plan-3  CAK   0.020
 621  plan-3  CAJ   0.020
 621  plan-3  OAL   0.020
 621  plan-3  N     0.020
 621  plan-3  CA    0.020
 621  plan-3  HN    0.020
 621  plan-4  C     0.020
 621  plan-4  CA    0.020
 621  plan-4  CAC   0.020
 621  plan-4  O     0.020

