# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 24 04:44:38 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: N~2~-acetyl-N-{(1R)-1-[(S)-[(2S)-3-{[(2S)-1-amino-1-oxopropan-2-yl]amino}-2-methyl-3-oxopropyl](hydroxy)phosphoryl]-2-phenylethyl}-L-alpha-asparagine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C[P](O)(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(O)=O)NC(C)=O)C(=O)N[C@@H](C)C(N)=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
 RX4  RX4  N~2~-acetyl-N-{(1R)-1-[(S)-[(2S)-3-{[(2S)-1-amino-1-oxopropan-2-yl]amino}-2-methyl-3-oxopropyl](hydroxy)phosphoryl]-2-phenylethyl}-L-alpha-asparagine  peptide  63  34  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RX4
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
 RX4  CAX   C  C      0   0.510  -6.2133   0.1933   0.6765
 RX4  CAA   C  CH3    0  -0.780  -7.1616   0.8389   1.6587
 RX4  OAE   O  O      0  -0.510  -6.3372  -0.9784   0.3410
 RX4  CBB   C  C      0   0.580  -2.9614   0.1906   0.3193
 RX4  OAI   O  O      0  -0.497  -3.1364  -0.1109   1.4893
 RX4  CBF   C  CH1    0  -0.211  -4.1410   0.5612  -0.5881
 RX4  CAR   C  CH2    0  -0.631  -3.8153   1.5872  -1.6706
 RX4  CAZ   C  C      0   0.446  -3.2808   2.9319  -1.1426
 RX4  OAK   O  OC    -1  -0.611  -2.7073   3.6644  -1.9667
 RX4  OAG   O  O      0  -0.603  -3.5056   3.1928   0.0596
 RX4  NAU   N  NH1    0  -0.607  -5.2502   1.0021   0.2123
 RX4  CAP   C  CR16   0  -0.311  -2.1215  -2.7534  -1.4243
 RX4  CAN   C  CR16   0  -0.233  -3.1654  -3.6684  -1.4023
 RX4  CAM   C  CR16   0  -0.274  -3.3029  -4.5437  -0.3335
 RX4  CAO   C  CR16   0  -0.243  -2.3885  -4.4956   0.7110
 RX4  CAQ   C  CR16   0  -0.308  -1.3509  -3.5736   0.6864
 RX4  CBC   C  CR6    0   0.168  -1.2021  -2.6890  -0.3792
 RX4  CAS   C  CH2    0  -0.541  -0.1122  -1.6565  -0.3719
 RX4  CBG   C  CH1    0  -0.314  -0.5547  -0.3580   0.3211
 RX4  P1    P  P      0   1.202   0.7027   1.0119   0.2222
 RX4  O4    O  OP    -1  -0.794   0.2514   2.1261   1.1394
 RX4  O3    O  O      0  -0.816   0.9249   1.2981  -1.2506
 RX4  CAT   C  CH2    0  -0.712   2.2275   0.2180   0.8905
 RX4  CBD   C  CH1    0  -0.373   3.4353   1.1690   0.9215
 RX4  CAB   C  CH3    0  -0.656   3.3836   2.1592   2.0805
 RX4  CBA   C  C      0   0.577   4.6981   0.3311   1.0163
 RX4  OAH   O  O      0  -0.507   4.9812  -0.3082   2.0217
 RX4  N     N  NH1    0  -0.637   5.4662   0.3309  -0.0860
 RX4  CA    C  CH1    0  -0.196   6.6514  -0.4761  -0.2278
 RX4  CB    C  CH3    0  -0.651   6.3235  -1.8985  -0.6908
 RX4  C     C  C      0   0.518   7.5747   0.1918  -1.2419
 RX4  O     O  O      0  -0.485   7.1416   0.9391  -2.1070
 RX4  NAD   N  NH2    0  -0.797   8.8630  -0.1449  -1.1293
 RX4  HAA1  H  HCH3   0   0.245  -7.0959   1.9255   1.6707
 RX4  HAA2  H  HCH3   0   0.256  -8.1867   0.5505   1.4327
 RX4  HAA3  H  HCH3   0   0.263  -6.9344   0.4775   2.6630
 RX4  HBF   H  HCH1   0   0.283  -4.4367  -0.3756  -1.0702
 RX4  HAR1  H  HCH2   0   0.234  -3.1315   1.1675  -2.4134
 RX4  HAR2  H  HCH2   0   0.265  -4.7360   1.7822  -2.2303
 RX4  HAU   H  HNH1   0   0.391  -5.1379   1.9319   0.5905
 RX4  HAM   H  HCR6   0   0.248  -4.1144  -5.2597  -0.3159
 RX4  HAO   H  HCR6   0   0.248  -2.4831  -5.1775   1.5467
 RX4  HAQ   H  HCR6   0   0.240  -0.6441  -3.5430   1.5081
 RX4  HAS1  H  HCH2   0   0.253   0.7665  -2.0508   0.1422
 RX4  HAS2  H  HCH2   0   0.241   0.1967  -1.4259  -1.3951
 RX4  HBG   H  HCH1   0   0.257  -0.7683  -0.5669   1.3702
 RX4  HAT1  H  HCH2   0   0.241   2.0422  -0.1830   1.8914
 RX4  HAT2  H  HCH2   0   0.249   2.4621  -0.6353   0.2473
 RX4  HBD   H  HCH1   0   0.244   3.4555   1.7283  -0.0199
 RX4  HAB1  H  HCH3   0   0.245   2.4881   2.7708   2.0105
 RX4  HAB2  H  HCH3   0   0.219   3.3608   1.6357   3.0367
 RX4  HAB3  H  HCH3   0   0.225   4.2532   2.8179   2.0757
 RX4  H     H  HNH1   0   0.396   5.1712   0.8585  -0.8937
 RX4  HA    H  HCH1   0   0.274   7.1555  -0.5263   0.7396
 RX4  HB1C  H  HCH3   0   0.250   5.6395  -2.3680   0.0146
 RX4  HB2C  H  HCH3   0   0.235   5.8501  -1.8864  -1.6730
 RX4  HB3C  H  HCH3   0   0.239   7.2211  -2.5134  -0.7476
 RX4  HAD1  H  HNH2   0   0.412   9.1955  -0.7432  -0.3926
 RX4  HAD2  H  HNH2   0   0.406   9.5387   0.1826  -1.8006
 RX4  HAP   H  HCR6   0   0.238  -2.0192  -2.0815  -2.2686
 RX4  NAW   N  NH1    0  -0.635  -1.7652   0.1440  -0.2856
 RX4  HAN   H  HCR6   0   0.247  -3.8709  -3.6983  -2.2231
 RX4  HAW   H  HNH1   0   0.386  -1.6747   0.4788  -1.2310

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
 RX4  CAP  CAN   aromatic  1.388  0.020  1.388
 RX4  CAP  CBC   aromatic  1.393  0.020  1.393
 RX4  CAN  CAM   aromatic  1.388  0.020  1.388
 RX4  CAM  CAO   aromatic  1.389  0.020  1.389
 RX4  CAO  CAQ   aromatic  1.388  0.020  1.388
 RX4  CAQ  CBC   aromatic  1.393  0.020  1.393
 RX4  CBC  CAS   single    1.501  0.020  1.501
 RX4  CAS  CBG   single    1.537  0.020  1.537
 RX4  CBG  NAW   single    1.444  0.020  1.444
 RX4  CBG  P1    single    1.862  0.020  1.862
 RX4  NAW  CBB   single    1.341  0.020  1.341
 RX4  CBB  OAI   double    1.221  0.020  1.221
 RX4  CBB  CBF   single    1.534  0.020  1.534
 RX4  CBF  CAR   single    1.527  0.020  1.527
 RX4  CBF  NAU   single    1.437  0.020  1.437
 RX4  CAR  CAZ   single    1.540  0.020  1.540
 RX4  CAZ  OAK   deloc     1.243  0.020  1.243
 RX4  CAZ  OAG   deloc     1.251  0.020  1.251
 RX4  NAU  CAX   single    1.341  0.020  1.341
 RX4  CAX  CAA   single    1.510  0.020  1.510
 RX4  CAX  OAE   double    1.225  0.020  1.225
 RX4  P1   O4    deloc     1.512  0.020  1.512
 RX4  P1   O3    deloc     1.517  0.020  1.517
 RX4  P1   CAT   single    1.844  0.020  1.844
 RX4  CAT  CBD   single    1.538  0.020  1.538
 RX4  CBD  CAB   single    1.525  0.020  1.525
 RX4  CBD  CBA   single    1.518  0.020  1.518
 RX4  CBA  OAH   double    1.225  0.020  1.225
 RX4  CBA  N     single    1.343  0.020  1.343
 RX4  N    CA    single    1.458  0.019  1.458
 RX4  CA   CB    single    1.521  0.033  1.521
 RX4  CA   C     single    1.525  0.021  1.525
 RX4  C    O     double    1.231  0.020  1.231
 RX4  C    NAD   single    1.336  0.020  1.336
 RX4  CAP  HAP   single    0.930  0.020  1.080
 RX4  CAN  HAN   single    0.930  0.020  1.080
 RX4  CAM  HAM   single    0.930  0.020  1.080
 RX4  CAO  HAO   single    0.930  0.020  1.080
 RX4  CAQ  HAQ   single    0.930  0.020  1.080
 RX4  CAS  HAS1  single    0.970  0.020  1.090
 RX4  CAS  HAS2  single    0.970  0.020  1.090
 RX4  CBG  HBG   single    0.970  0.020  1.090
 RX4  NAW  HAW   single    0.860  0.020  1.020
 RX4  CBF  HBF   single    0.970  0.020  1.090
 RX4  CAR  HAR1  single    0.970  0.020  1.090
 RX4  CAR  HAR2  single    0.970  0.020  1.090
 RX4  NAU  HAU   single    0.860  0.020  1.020
 RX4  CAA  HAA1  single    0.970  0.020  1.090
 RX4  CAA  HAA2  single    0.970  0.020  1.090
 RX4  CAA  HAA3  single    0.970  0.020  1.090
 RX4  CAT  HAT1  single    0.970  0.020  1.090
 RX4  CAT  HAT2  single    0.970  0.020  1.090
 RX4  CBD  HBD   single    0.970  0.020  1.090
 RX4  CAB  HAB1  single    0.970  0.020  1.090
 RX4  CAB  HAB2  single    0.970  0.020  1.090
 RX4  CAB  HAB3  single    0.970  0.020  1.090
 RX4  N    H     single    0.860  0.020  0.860
 RX4  CA   HA    single    0.970  0.020  0.970
 RX4  CB   HB1C  single    0.970  0.020  1.090
 RX4  CB   HB2C  single    0.970  0.020  1.090
 RX4  CB   HB3C  single    0.970  0.020  1.090
 RX4  NAD  HAD1  single    0.860  0.020  1.020
 RX4  NAD  HAD2  single    0.860  0.020  1.020

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
 RX4  NAU   CAX  OAE   123.70  3.000
 RX4  OAE   CAX  CAA   121.56  3.000
 RX4  NAU   CAX  CAA   114.73  3.000
 RX4  HAA3  CAA  HAA2  107.43  3.000
 RX4  HAA3  CAA  HAA1  107.93  3.000
 RX4  HAA2  CAA  HAA1  108.88  3.000
 RX4  HAA3  CAA  CAX   109.04  3.000
 RX4  HAA2  CAA  CAX   110.06  3.000
 RX4  HAA1  CAA  CAX   113.32  3.000
 RX4  NAW   CBB  CBF   115.31  3.000
 RX4  CBF   CBB  OAI   121.10  3.000
 RX4  NAW   CBB  OAI   123.47  3.000
 RX4  HBF   CBF  NAU   107.42  3.000
 RX4  HBF   CBF  CAR   108.70  3.000
 RX4  NAU   CBF  CAR   110.70  3.000
 RX4  HBF   CBF  CBB   105.17  3.000
 RX4  NAU   CBF  CBB   109.77  3.000
 RX4  CAR   CBF  CBB   114.70  3.000
 RX4  HAR2  CAR  HAR1  104.30  3.000
 RX4  HAR2  CAR  CAZ   108.15  3.000
 RX4  HAR1  CAR  CAZ   110.55  3.000
 RX4  HAR2  CAR  CBF   107.62  3.000
 RX4  HAR1  CAR  CBF   110.92  3.000
 RX4  CAZ   CAR  CBF   114.69  3.000
 RX4  OAG   CAZ  OAK   126.69  3.000
 RX4  OAG   CAZ  CAR   116.70  3.000
 RX4  OAK   CAZ  CAR   116.57  3.000
 RX4  HAU   NAU  CBF   113.90  3.000
 RX4  HAU   NAU  CAX   120.38  3.000
 RX4  CBF   NAU  CAX   124.21  3.000
 RX4  HAP   CAP  CBC   119.56  3.000
 RX4  HAP   CAP  CAN   119.46  3.000
 RX4  CBC   CAP  CAN   120.98  3.000
 RX4  HAN   CAN  CAM   120.11  3.000
 RX4  HAN   CAN  CAP   119.74  3.000
 RX4  CAM   CAN  CAP   120.14  3.000
 RX4  HAM   CAM  CAO   120.28  3.000
 RX4  HAM   CAM  CAN   120.25  3.000
 RX4  CAO   CAM  CAN   119.46  3.000
 RX4  HAO   CAO  CAQ   119.81  3.000
 RX4  HAO   CAO  CAM   120.07  3.000
 RX4  CAQ   CAO  CAM   120.11  3.000
 RX4  HAQ   CAQ  CBC   119.49  3.000
 RX4  HAQ   CAQ  CAO   119.50  3.000
 RX4  CBC   CAQ  CAO   121.01  3.000
 RX4  CAS   CBC  CAQ   120.70  3.000
 RX4  CAS   CBC  CAP   120.96  3.000
 RX4  CAQ   CBC  CAP   118.29  3.000
 RX4  HAS2  CAS  HAS1  106.83  3.000
 RX4  HAS2  CAS  CBG   108.97  3.000
 RX4  HAS1  CAS  CBG   108.93  3.000
 RX4  HAS2  CAS  CBC   110.22  3.000
 RX4  HAS1  CAS  CBC   109.76  3.000
 RX4  CBG   CAS  CBC   111.98  3.000
 RX4  HBG   CBG  NAW   107.85  3.000
 RX4  HBG   CBG  P1    108.92  3.000
 RX4  NAW   CBG  P1    106.73  3.000
 RX4  HBG   CBG  CAS   109.17  3.000
 RX4  P1    CBG  CAS   113.78  3.000
 RX4  NAW   CBG  CAS   110.22  3.000
 RX4  CAT   P1   O3    108.17  3.000
 RX4  CAT   P1   O4    110.13  3.000
 RX4  O3    P1   O4    119.59  3.000
 RX4  CAT   P1   CBG   102.84  3.000
 RX4  O3    P1   CBG   106.82  3.000
 RX4  O4    P1   CBG   107.96  3.000
 RX4  HAT2  CAT  HAT1  106.76  3.000
 RX4  HAT2  CAT  CBD   109.01  3.000
 RX4  HAT1  CAT  CBD   109.95  3.000
 RX4  HAT2  CAT  P1    107.46  3.000
 RX4  HAT1  CAT  P1    110.44  3.000
 RX4  CBD   CAT  P1    112.98  3.000
 RX4  HBD   CBD  CBA   108.67  3.000
 RX4  HBD   CBD  CAB   108.80  3.000
 RX4  CBA   CBD  CAB   109.81  3.000
 RX4  HBD   CBD  CAT   108.24  3.000
 RX4  CBA   CBD  CAT   108.25  3.000
 RX4  CAB   CBD  CAT   112.97  3.000
 RX4  HAB3  CAB  HAB2  108.09  3.000
 RX4  HAB3  CAB  HAB1  108.46  3.000
 RX4  HAB2  CAB  HAB1  108.03  3.000
 RX4  HAB3  CAB  CBD   111.20  3.000
 RX4  HAB2  CAB  CBD   110.82  3.000
 RX4  HAB1  CAB  CBD   110.14  3.000
 RX4  N     CBA  OAH   122.78  3.000
 RX4  N     CBA  CBD   115.11  3.000
 RX4  OAH   CBA  CBD   122.11  3.000
 RX4  H     N    CA    114.00  3.000
 RX4  H     N    CBA   119.32  3.000
 RX4  CA    N    CBA   123.45  3.000
 RX4  HA    CA   C     110.00  3.000
 RX4  HA    CA   CB    109.00  3.000
 RX4  C     CA   CB    110.50  1.500
 RX4  HA    CA   N     110.00  3.000
 RX4  C     CA   N     111.00  2.800
 RX4  CB    CA   N     110.40  1.500
 RX4  HB3C  CB   HB2C  108.48  3.000
 RX4  HB3C  CB   HB1C  107.94  3.000
 RX4  HB2C  CB   HB1C  108.39  3.000
 RX4  HB3C  CB   CA    111.32  3.000
 RX4  HB2C  CB   CA    110.79  3.000
 RX4  HB1C  CB   CA    109.82  3.000
 RX4  NAD   C    O     123.73  3.000
 RX4  NAD   C    CA    114.65  3.000
 RX4  O     C    CA    120.80  1.700
 RX4  HAD2  NAD  HAD1  117.38  3.000
 RX4  HAD2  NAD  C     120.57  3.000
 RX4  HAD1  NAD  C     122.03  3.000
 RX4  HAW   NAW  CBG   115.76  3.000
 RX4  HAW   NAW  CBB   119.47  3.000
 RX4  CBG   NAW  CBB   124.76  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
 RX4  CONST_01  CAO   CAM  CAN  CAP     0.00   0.0  0
 RX4  CONST_02  CAO   CAQ  CBC  CAP     0.00   0.0  0
 RX4  CONST_03  CAQ   CBC  CAP  CAN     0.00   0.0  0
 RX4  CONST_04  CAQ   CAO  CAM  CAN     0.00   0.0  0
 RX4  CONST_05  CBC   CAP  CAN  CAM     0.00   0.0  0
 RX4  CONST_06  CBC   CAQ  CAO  CAM     0.00   0.0  0
 RX4  CONST_07  CAS   CBC  CAP  CAN   180.00   0.0  0
 RX4  CONST_08  CAS   CBC  CAQ  CAO   180.00   0.0  0
 RX4  CONST_09  HAM   CAM  CAN  CAP   180.00   0.0  0
 RX4  CONST_10  HAQ   CAQ  CBC  CAP   180.00   0.0  0
 RX4  CONST_11  HAO   CAO  CAM  CAN   180.00   0.0  0
 RX4  CONST_12  HAP   CAP  CAN  CAM   180.00   0.0  0
 RX4  CONST_13  HAN   CAN  CAM  CAO   180.00   0.0  0
 RX4  CONST_14  CBF   NAU  CAX  CAA   180.00   0.0  0
 RX4  CONST_15  CBF   NAU  CAX  OAE     0.00   0.0  0
 RX4  CONST_16  CBG   NAW  CBB  OAI     0.00   0.0  0
 RX4  CONST_17  CBG   NAW  CBB  CBF   180.00   0.0  0
 RX4  CONST_18  CA    N    CBA  CBD   180.00   0.0  0
 RX4  CONST_19  CA    N    CBA  OAH     0.00   0.0  0
 RX4  CONST_20  HAU   NAU  CAX  CAA     0.00   0.0  0
 RX4  CONST_21  HAW   NAW  CBB  OAI   180.00   0.0  0
 RX4  CONST_22  H     N    CBA  CBD     0.00   0.0  0
 RX4  CONST_23  HAD1  NAD  C    CA      0.00   0.0  0
 RX4  CONST_24  HAD2  NAD  C    CA    180.00   0.0  0
 RX4  Var_01    CBG   CAS  CBC  CAP    89.62  30.0  2
 RX4  Var_02    OAK   CAZ  CAR  CBF   163.19  30.0  3
 RX4  Var_03    CBD   CAT  P1   CBG  -179.67  30.0  3
 RX4  Var_04    HAA1  CAA  CAX  OAE  -165.21  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
 RX4  chir_01  CBF  CBB  CAR  NAU  positiv
 RX4  chir_02  CBG  P1   NAW  CAS  negativ
 RX4  chir_04  CBD  CAT  CAB  CBA  negativ
 RX4  chir_05  CA   N    CB   C    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
 RX4  plan-1  CAP   0.020
 RX4  plan-1  CAN   0.020
 RX4  plan-1  CAM   0.020
 RX4  plan-1  CAO   0.020
 RX4  plan-1  CAQ   0.020
 RX4  plan-1  CBC   0.020
 RX4  plan-1  CAS   0.020
 RX4  plan-1  HAM   0.020
 RX4  plan-1  HAO   0.020
 RX4  plan-1  HAQ   0.020
 RX4  plan-1  HAP   0.020
 RX4  plan-1  HAN   0.020
 RX4  plan-2  CAR   0.020
 RX4  plan-2  CAZ   0.020
 RX4  plan-2  OAK   0.020
 RX4  plan-2  OAG   0.020
 RX4  plan-3  CAX   0.020
 RX4  plan-3  CAA   0.020
 RX4  plan-3  OAE   0.020
 RX4  plan-3  CBF   0.020
 RX4  plan-3  NAU   0.020
 RX4  plan-3  HAU   0.020
 RX4  plan-4  CBB   0.020
 RX4  plan-4  OAI   0.020
 RX4  plan-4  CBF   0.020
 RX4  plan-4  CBG   0.020
 RX4  plan-4  NAW   0.020
 RX4  plan-4  HAW   0.020
 RX4  plan-5  CBD   0.020
 RX4  plan-5  CBA   0.020
 RX4  plan-5  OAH   0.020
 RX4  plan-5  N     0.020
 RX4  plan-5  CA    0.020
 RX4  plan-5  H     0.020
 RX4  plan-6  CA    0.020
 RX4  plan-6  C     0.020
 RX4  plan-6  O     0.020
 RX4  plan-6  NAD   0.020
 RX4  plan-6  HAD1  0.020
 RX4  plan-6  HAD2  0.020

