# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 03:14:36 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: (2R)-2,4-dihydroxy-3,3-dimethyl-N-[3-oxo-3-(pentylamino)propyl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)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
 PN4  PN4  "(2R)-2,4-dihydroxy-3,3-dimethyl-N-[3-oxo-3-(pentylamino)propyl]butanamide"  peptide  48  20  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_PN4
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
 PN4  CAU   C  C     0   0.519    2.8537  -0.9546   0.0941
 PN4  OAE   O  O     0  -0.502    3.0687  -1.6861   1.0550
 PN4  CAV   C  CH1   0  -0.034    4.0099  -0.5018  -0.8007
 PN4  OAG   O  OH1   0  -0.663    4.9603  -1.5321  -0.8403
 PN4  CAW   C  CT    0  -0.143    4.6234   0.8643  -0.3850
 PN4  CAC   C  CH3   0  -0.645    5.7404   1.1892  -1.3817
 PN4  CAB   C  CH3   0  -0.670    3.5566   1.9597  -0.4635
 PN4  CAP   C  CH2   0  -0.132    5.1831   0.7801   1.0369
 PN4  OAS   O  OH1   0  -0.672    5.8078   2.0023   1.3640
 PN4  NAR   N  NH1   0  -0.639    1.6349  -0.5294  -0.2411
 PN4  CAN   C  CH2   0  -0.233    0.4417  -0.8941   0.4982
 PN4  CAO   C  CH2   0  -0.639   -0.7566  -0.1804  -0.1000
 PN4  CAT   C  C     0   0.569   -2.0599  -0.5856   0.5605
 PN4  OAD   O  O     0  -0.503   -2.1036  -1.3348   1.5271
 PN4  CAA   C  CH3   0  -0.661   -9.4329   0.4289  -0.2947
 PN4  CAJ   C  CH2   0  -0.421   -8.0172   0.8071  -0.7076
 PN4  CAK   C  CH2   0  -0.411   -6.9552   0.0432   0.0735
 PN4  CAL   C  CH2   0  -0.474   -5.5349   0.4001  -0.3451
 PN4  CAM   C  CH2   0  -0.232   -4.4992  -0.3707   0.4571
 PN4  NAQ   N  NH1   0  -0.647   -3.1589  -0.0600   0.0024
 PN4  HAV   H  HCH1  0   0.249    3.6322  -0.3744  -1.8227
 PN4  HOAG  H  HOH1  0   0.443    4.9494  -1.9717   0.0197
 PN4  HAC   H  HCH3  0   0.222    5.3481   1.2203  -2.4010
 PN4  HACA  H  HCH3  0   0.234    6.1766   2.1649  -1.1717
 PN4  HACB  H  HCH3  0   0.230    6.5408   0.4503  -1.3547
 PN4  HAB   H  HCH3  0   0.230    2.7994   1.8566   0.3143
 PN4  HABA  H  HCH3  0   0.245    4.0098   2.9439  -0.3520
 PN4  HABB  H  HCH3  0   0.227    3.0493   1.9511  -1.4319
 PN4  HAP   H  HCH2  0   0.202    4.3686   0.5643   1.7414
 PN4  HAPA  H  HCH2  0   0.199    5.8989  -0.0494   1.1057
 PN4  HOAS  H  HOH1  0   0.454    6.1978   1.9088   2.2373
 PN4  HNAR  H  HNH1  0   0.407    1.5314   0.0199  -1.0794
 PN4  HAN   H  HCH2  0   0.246    0.2984  -1.9760   0.4572
 PN4  HANA  H  HCH2  0   0.248    0.5627  -0.6242   1.5483
 PN4  HAO   H  HCH2  0   0.285   -0.6365   0.9038  -0.0122
 PN4  HAOA  H  HCH2  0   0.278   -0.8251  -0.3944  -1.1710
 PN4  HAA   H  HCH3  0   0.227  -10.1788   0.9841  -0.8643
 PN4  HAAA  H  HCH3  0   0.217   -9.6183  -0.6346  -0.4556
 PN4  HAAB  H  HCH3  0   0.217   -9.6033   0.6362   0.7632
 PN4  HAJ   H  HCH2  0   0.213   -7.8850   0.6195  -1.7775
 PN4  HAJA  H  HCH2  0   0.214   -7.8683   1.8820  -0.5670
 PN4  HAK   H  HCH2  0   0.215   -7.0806   0.2404   1.1433
 PN4  HAKA  H  HCH2  0   0.214   -7.1108  -1.0327  -0.0595
 PN4  HAL   H  HCH2  0   0.228   -5.4065   0.1853  -1.4110
 PN4  HALA  H  HCH2  0   0.230   -5.3723   1.4749  -0.2183
 PN4  HAM   H  HCH2  0   0.231   -4.5972  -0.1270   1.5183
 PN4  HAMA  H  HCH2  0   0.227   -4.6839  -1.4453   0.3612
 PN4  HNAQ  H  HNH1  0   0.401   -3.0572   0.5281  -0.8094

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
 PN4  CAJ  CAA   single  1.522  0.020  1.522
 PN4  CAA  HAA   single  0.970  0.020  1.090
 PN4  CAA  HAAA  single  0.970  0.020  1.090
 PN4  CAA  HAAB  single  0.970  0.020  1.090
 PN4  CAB  CAW   single  1.531  0.020  1.531
 PN4  CAB  HAB   single  0.970  0.020  1.090
 PN4  CAB  HABA  single  0.970  0.020  1.090
 PN4  CAB  HABB  single  0.970  0.020  1.090
 PN4  CAW  CAC   single  1.532  0.020  1.532
 PN4  CAC  HAC   single  0.970  0.020  1.090
 PN4  CAC  HACA  single  0.970  0.020  1.090
 PN4  CAC  HACB  single  0.970  0.020  1.090
 PN4  OAD  CAT   double  1.224  0.020  1.224
 PN4  CAU  OAE   double  1.227  0.020  1.227
 PN4  CAV  OAG   single  1.402  0.020  1.402
 PN4  OAG  HOAG  single  0.850  0.020  0.980
 PN4  CAJ  CAK   single  1.524  0.020  1.524
 PN4  CAJ  HAJ   single  0.970  0.020  1.090
 PN4  CAJ  HAJA  single  0.970  0.020  1.090
 PN4  CAL  CAK   single  1.523  0.020  1.523
 PN4  CAK  HAK   single  0.970  0.020  1.090
 PN4  CAK  HAKA  single  0.970  0.020  1.090
 PN4  CAL  CAM   single  1.520  0.020  1.520
 PN4  CAL  HAL   single  0.970  0.020  1.090
 PN4  CAL  HALA  single  0.970  0.020  1.090
 PN4  CAM  NAQ   single  1.449  0.020  1.449
 PN4  CAM  HAM   single  0.970  0.020  1.090
 PN4  CAM  HAMA  single  0.970  0.020  1.090
 PN4  CAO  CAN   single  1.518  0.020  1.518
 PN4  NAR  CAN   single  1.450  0.020  1.450
 PN4  CAN  HAN   single  0.970  0.020  1.090
 PN4  CAN  HANA  single  0.970  0.020  1.090
 PN4  CAT  CAO   single  1.516  0.020  1.516
 PN4  CAO  HAO   single  0.970  0.020  1.090
 PN4  CAO  HAOA  single  0.970  0.020  1.090
 PN4  CAP  CAW   single  1.530  0.020  1.530
 PN4  CAP  OAS   single  1.411  0.020  1.411
 PN4  CAP  HAP   single  0.970  0.020  1.090
 PN4  CAP  HAPA  single  0.970  0.020  1.090
 PN4  CAT  NAQ   single  1.340  0.020  1.340
 PN4  NAQ  HNAQ  single  0.860  0.020  1.020
 PN4  NAR  CAU   single  1.334  0.020  1.334
 PN4  NAR  HNAR  single  0.860  0.020  1.020
 PN4  OAS  HOAS  single  0.850  0.020  0.980
 PN4  CAV  CAU   single  1.531  0.020  1.531
 PN4  CAV  CAW   single  1.554  0.020  1.554
 PN4  CAV  HAV   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
 PN4  NAR   CAU  CAV   116.68  3.000
 PN4  CAV   CAU  OAE   120.14  3.000
 PN4  NAR   CAU  OAE   123.18  3.000
 PN4  HAV   CAV  CAW   106.44  3.000
 PN4  HAV   CAV  OAG   107.00  3.000
 PN4  CAW   CAV  OAG   112.69  3.000
 PN4  HAV   CAV  CAU   108.60  3.000
 PN4  CAW   CAV  CAU   113.70  3.000
 PN4  OAG   CAV  CAU   108.13  3.000
 PN4  HOAG  OAG  CAV   107.55  3.000
 PN4  CAP   CAW  CAB   109.99  3.000
 PN4  CAP   CAW  CAC   110.46  3.000
 PN4  CAB   CAW  CAC   108.84  3.000
 PN4  CAP   CAW  CAV   110.15  3.000
 PN4  CAC   CAW  CAV   107.47  3.000
 PN4  CAB   CAW  CAV   109.88  3.000
 PN4  HACB  CAC  HACA  107.97  3.000
 PN4  HACB  CAC  HAC   107.83  3.000
 PN4  HACA  CAC  HAC   107.34  3.000
 PN4  HACB  CAC  CAW   112.06  3.000
 PN4  HACA  CAC  CAW   110.89  3.000
 PN4  HAC   CAC  CAW   110.57  3.000
 PN4  HABB  CAB  HABA  106.91  3.000
 PN4  HABB  CAB  HAB   107.99  3.000
 PN4  HABA  CAB  HAB   107.53  3.000
 PN4  HABB  CAB  CAW   111.30  3.000
 PN4  HABA  CAB  CAW   110.57  3.000
 PN4  HAB   CAB  CAW   112.31  3.000
 PN4  HAPA  CAP  HAP   107.15  3.000
 PN4  HAPA  CAP  OAS   110.56  3.000
 PN4  HAP   CAP  OAS   110.47  3.000
 PN4  HAPA  CAP  CAW   109.77  3.000
 PN4  HAP   CAP  CAW   109.61  3.000
 PN4  OAS   CAP  CAW   109.24  3.000
 PN4  HOAS  OAS  CAP   107.83  3.000
 PN4  HNAR  NAR  CAN   118.47  3.000
 PN4  HNAR  NAR  CAU   118.49  3.000
 PN4  CAN   NAR  CAU   122.92  3.000
 PN4  HANA  CAN  HAN   107.20  3.000
 PN4  HANA  CAN  CAO   110.52  3.000
 PN4  HAN   CAN  CAO   110.33  3.000
 PN4  HANA  CAN  NAR   109.71  3.000
 PN4  HAN   CAN  NAR   109.75  3.000
 PN4  CAO   CAN  NAR   109.30  3.000
 PN4  HAOA  CAO  HAO   106.21  3.000
 PN4  HAOA  CAO  CAT   108.68  3.000
 PN4  HAO   CAO  CAT   108.91  3.000
 PN4  HAOA  CAO  CAN   110.07  3.000
 PN4  HAO   CAO  CAN   110.34  3.000
 PN4  CAT   CAO  CAN   112.41  3.000
 PN4  NAQ   CAT  OAD   122.67  3.000
 PN4  NAQ   CAT  CAO   114.75  3.000
 PN4  OAD   CAT  CAO   122.58  3.000
 PN4  HAAB  CAA  HAAA  107.54  3.000
 PN4  HAAB  CAA  HAA   107.63  3.000
 PN4  HAAA  CAA  HAA   107.63  3.000
 PN4  HAAB  CAA  CAJ   111.15  3.000
 PN4  HAAA  CAA  CAJ   111.10  3.000
 PN4  HAA   CAA  CAJ   111.59  3.000
 PN4  HAJA  CAJ  HAJ   106.11  3.000
 PN4  HAJA  CAJ  CAK   109.38  3.000
 PN4  HAJ   CAJ  CAK   109.33  3.000
 PN4  HAJA  CAJ  CAA   109.62  3.000
 PN4  HAJ   CAJ  CAA   109.57  3.000
 PN4  CAK   CAJ  CAA   112.62  3.000
 PN4  HAKA  CAK  HAK   106.22  3.000
 PN4  HAKA  CAK  CAL   109.22  3.000
 PN4  HAK   CAK  CAL   109.46  3.000
 PN4  HAKA  CAK  CAJ   109.35  3.000
 PN4  HAK   CAK  CAJ   109.31  3.000
 PN4  CAL   CAK  CAJ   113.06  3.000
 PN4  HALA  CAL  HAL   106.74  3.000
 PN4  HALA  CAL  CAM   109.61  3.000
 PN4  HAL   CAL  CAM   109.54  3.000
 PN4  HALA  CAL  CAK   109.68  3.000
 PN4  HAL   CAL  CAK   109.33  3.000
 PN4  CAM   CAL  CAK   111.81  3.000
 PN4  HAMA  CAM  HAM   106.78  3.000
 PN4  HAMA  CAM  NAQ   109.82  3.000
 PN4  HAM   CAM  NAQ   109.86  3.000
 PN4  HAMA  CAM  CAL   109.68  3.000
 PN4  HAM   CAM  CAL   109.77  3.000
 PN4  NAQ   CAM  CAL   110.85  3.000
 PN4  HNAQ  NAQ  CAM   118.12  3.000
 PN4  HNAQ  NAQ  CAT   118.80  3.000
 PN4  CAM   NAQ  CAT   122.94  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
 PN4  CONST_01  CAN   NAR  CAU  OAE     0.00   0.0  0
 PN4  CONST_02  CAN   NAR  CAU  CAV   180.00   0.0  0
 PN4  CONST_03  CAM   NAQ  CAT  CAO   180.00   0.0  0
 PN4  CONST_04  CAM   NAQ  CAT  OAD     0.00   0.0  0
 PN4  CONST_05  HNAR  NAR  CAU  OAE   180.00   0.0  0
 PN4  CONST_06  HNAR  NAR  CAU  CAV     0.00   0.0  0
 PN4  CONST_07  HNAQ  NAQ  CAT  CAO     0.00   0.0  0
 PN4  CONST_08  HNAQ  NAQ  CAT  OAD   180.00   0.0  0
 PN4  Var_01    CAO   CAN  NAR  CAU   176.82  30.0  3
 PN4  Var_02    OAS   CAP  CAW  CAV   176.41  30.0  3
 PN4  Var_03    OAS   CAP  CAW  CAC    57.83  30.0  3
 PN4  Var_04    OAS   CAP  CAW  CAB   -62.33  30.0  3
 PN4  Var_05    CAT   CAO  CAN  NAR   176.06  30.0  1
 PN4  Var_06    OAD   CAT  CAO  CAN     4.74  30.0  1
 PN4  Var_07    NAQ   CAT  CAO  CAN  -175.21  30.0  1
 PN4  Var_08    CAL   CAM  NAQ  CAT   178.64  30.0  1
 PN4  Var_09    CAL   CAK  CAJ  CAA   179.21  30.0  3
 PN4  Var_10    CAM   CAL  CAK  CAJ   179.63  30.0  1
 PN4  Var_11    NAQ   CAM  CAL  CAK   177.47  30.0  3
 PN4  Var_12    HAN   CAN  NAR  CAU   -62.06  30.0  3
 PN4  Var_13    HANA  CAN  NAR  CAU    55.49  30.0  3
 PN4  Var_14    HAB   CAB  CAW  CAV    70.14  30.0  3
 PN4  Var_15    HABA  CAB  CAW  CAV  -169.74  30.0  3
 PN4  Var_16    HABB  CAB  CAW  CAV   -51.07  30.0  3
 PN4  Var_17    HAC   CAC  CAW  CAV    58.12  30.0  3
 PN4  Var_18    HACA  CAC  CAW  CAV   177.07  30.0  3
 PN4  Var_19    HACB  CAC  CAW  CAV   -62.21  30.0  3
 PN4  Var_20    HAP   CAP  CAW  CAV   -62.42  30.0  3
 PN4  Var_21    HAPA  CAP  CAW  CAV    55.02  30.0  3
 PN4  Var_22    HAB   CAB  CAW  CAC  -172.42  30.0  3
 PN4  Var_23    HABA  CAB  CAW  CAC   -52.30  30.0  3
 PN4  Var_24    HABB  CAB  CAW  CAC    66.36  30.0  3
 PN4  Var_25    HAP   CAP  CAW  CAC   179.01  30.0  3
 PN4  Var_26    HAPA  CAP  CAW  CAC   -63.55  30.0  3
 PN4  Var_27    HAC   CAC  CAW  CAB   -60.84  30.0  3
 PN4  Var_28    HACA  CAC  CAW  CAB    58.11  30.0  3
 PN4  Var_29    HACB  CAC  CAW  CAB   178.84  30.0  3
 PN4  Var_30    HAP   CAP  CAW  CAB    58.84  30.0  3
 PN4  Var_31    HAPA  CAP  CAW  CAB   176.28  30.0  3
 PN4  Var_32    HAB   CAB  CAW  CAP   -51.28  30.0  3
 PN4  Var_33    HABA  CAB  CAW  CAP    68.84  30.0  3
 PN4  Var_34    HABB  CAB  CAW  CAP  -172.49  30.0  3
 PN4  Var_35    HAC   CAC  CAW  CAP   178.31  30.0  3
 PN4  Var_36    HACA  CAC  CAW  CAP   -62.74  30.0  3
 PN4  Var_37    HACB  CAC  CAW  CAP    57.99  30.0  3
 PN4  Var_38    HAO   CAO  CAN  NAR   -62.15  30.0  1
 PN4  Var_39    HAOA  CAO  CAN  NAR    54.75  30.0  1
 PN4  Var_40    HNAR  NAR  CAN  CAO    -7.29  30.0  1
 PN4  Var_41    HAN   CAN  CAO  CAT    55.29  30.0  3
 PN4  Var_42    HANA  CAN  CAO  CAT   -63.11  30.0  3
 PN4  Var_43    HAM   CAM  NAQ  CAT    57.15  30.0  1
 PN4  Var_44    HAMA  CAM  NAQ  CAT   -60.01  30.0  1
 PN4  Var_45    HAO   CAO  CAT  OAD  -117.86  30.0  3
 PN4  Var_46    HAOA  CAO  CAT  OAD   126.84  30.0  3
 PN4  Var_47    HAK   CAK  CAJ  CAA   -58.60  30.0  3
 PN4  Var_48    HAKA  CAK  CAJ  CAA    57.29  30.0  3
 PN4  Var_49    HAL   CAL  CAK  CAJ   -58.89  30.0  1
 PN4  Var_50    HALA  CAL  CAK  CAJ    57.83  30.0  1
 PN4  Var_51    HAA   CAA  CAJ  CAK  -179.94  30.0  3
 PN4  Var_52    HAAA  CAA  CAJ  CAK   -59.81  30.0  3
 PN4  Var_53    HAAB  CAA  CAJ  CAK    59.91  30.0  3
 PN4  Var_54    HAM   CAM  CAL  CAK   -60.99  30.0  3
 PN4  Var_55    HAMA  CAM  CAL  CAK    56.04  30.0  3
 PN4  Var_56    HAJ   CAJ  CAK  CAL    57.15  30.0  1
 PN4  Var_57    HAJA  CAJ  CAK  CAL   -58.64  30.0  1
 PN4  Var_58    HNAQ  NAQ  CAM  CAL    -5.65  30.0  3
 PN4  Var_59    HAK   CAK  CAL  CAM    57.53  30.0  3
 PN4  Var_60    HAKA  CAK  CAL  CAM   -58.38  30.0  3
 PN4  Var_61    HAL   CAL  CAM  NAQ    56.12  30.0  1
 PN4  Var_62    HALA  CAL  CAM  NAQ   -60.68  30.0  1
 PN4  Var_63    HAO   CAO  CAT  NAQ    62.19  30.0  3
 PN4  Var_64    HAOA  CAO  CAT  NAQ   -53.11  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
 PN4  chir_01  CAV  OAG  CAU  CAW  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
 PN4  plan-1  CAU   0.020
 PN4  plan-1  OAE   0.020
 PN4  plan-1  CAV   0.020
 PN4  plan-1  NAR   0.020
 PN4  plan-1  CAN   0.020
 PN4  plan-1  HNAR  0.020
 PN4  plan-2  CAO   0.020
 PN4  plan-2  CAT   0.020
 PN4  plan-2  OAD   0.020
 PN4  plan-2  CAM   0.020
 PN4  plan-2  NAQ   0.020
 PN4  plan-2  HNAQ  0.020

