# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 00:06:49 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2R)-2-hydroxy-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)C
#
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
 C0D  C0D  (2R)-2-hydroxy-3,3-dimethyl-N-[3-oxo-3-(pentylamino)propyl]butanamide  ligand  47  19  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C0D
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
 C0D  CAP  C  CH3   0  -0.643   5.9743   1.8556  -0.3253
 C0D  CAW  C  CT    0  -0.116   4.7661   1.1922   0.3418
 C0D  CAB  C  CH3   0  -0.658   5.1141   0.8613   1.7941
 C0D  CAC  C  CH3   0  -0.661   3.5981   2.1793   0.3156
 C0D  CAV  C  CH1   0  -0.030   4.4201  -0.0833  -0.4719
 C0D  OAG  O  OH1   0  -0.663   5.4834  -0.9979  -0.5092
 C0D  CAU  C  C     0   0.522   3.1807  -0.8093   0.0502
 C0D  OAE  O  O     0  -0.501   3.2821  -1.6524   0.9346
 C0D  NAR  N  NH1   0  -0.640   2.0118  -0.4846  -0.5088
 C0D  CAN  C  CH2   0  -0.234   0.7579  -1.0737  -0.0838
 C0D  CAO  C  CH2   0  -0.631  -0.3983  -0.4288  -0.8301
 C0D  CAT  C  C     0   0.567  -1.7228  -1.0575  -0.4476
 C0D  OAD  O  O     0  -0.506  -1.8297  -2.2563  -0.2211
 C0D  NAQ  N  NH1   0  -0.645  -2.7644  -0.2184  -0.4018
 C0D  CAM  C  CH2   0  -0.235  -4.1088  -0.6491  -0.0752
 C0D  CAL  C  CH2   0  -0.472  -5.0988   0.4910  -0.2473
 C0D  CAK  C  CH2   0  -0.411  -6.5116   0.0811   0.1462
 C0D  CAJ  C  CH2   0  -0.419  -7.5261   1.2054  -0.0208
 C0D  CAA  C  CH3   0  -0.663  -8.9325   0.7944   0.3916
 C0D  H1   H  HCH3  0   0.223   5.7498   2.1452  -1.3547
 C0D  H2   H  HCH3  0   0.227   6.2522   2.7611   0.2175
 C0D  H3   H  HCH3  0   0.232   6.8435   1.1981  -0.3420
 C0D  H4   H  HCH3  0   0.225   5.9422   0.1543   1.8695
 C0D  H5   H  HCH3  0   0.230   5.4252   1.7703   2.3124
 C0D  H6   H  HCH3  0   0.232   4.2661   0.4506   2.3425
 C0D  H7   H  HCH3  0   0.232   2.7252   1.8140   0.8582
 C0D  H8   H  HCH3  0   0.236   3.8999   3.1170   0.7858
 C0D  H9   H  HCH3  0   0.227   3.2868   2.4154  -0.7048
 C0D  H10  H  HCH1  0   0.246   4.2411   0.2316  -1.5066
 C0D  H11  H  HOH1  0   0.443   5.4487  -1.5173   0.3037
 C0D  H12  H  HNH1  0   0.405   2.0013   0.1744  -1.2705
 C0D  H13  H  HCH2  0   0.246   0.7686  -2.1493  -0.2667
 C0D  H14  H  HCH2  0   0.247   0.6343  -0.9304   0.9921
 C0D  H15  H  HCH2  0   0.267  -0.4118   0.6487  -0.6496
 C0D  H16  H  HCH2  0   0.285  -0.2673  -0.5653  -1.9087
 C0D  H17  H  HNH1  0   0.401  -2.6042   0.7648  -0.5503
 C0D  H18  H  HCH2  0   0.232  -4.3928  -1.4861  -0.7181
 C0D  H19  H  HCH2  0   0.229  -4.1439  -1.0169   0.9550
 C0D  H20  H  HCH2  0   0.227  -4.7843   1.3439   0.3636
 C0D  H21  H  HCH2  0   0.230  -5.0889   0.8299  -1.2879
 C0D  H22  H  HCH2  0   0.215  -6.8241  -0.7806  -0.4536
 C0D  H23  H  HCH2  0   0.214  -6.5141  -0.2574   1.1877
 C0D  H24  H  HCH2  0   0.213  -7.2072   2.0706   0.5685
 C0D  H25  H  HCH2  0   0.213  -7.5316   1.5354  -1.0639
 C0D  H26  H  HCH3  0   0.228  -9.6438   1.6096   0.2559
 C0D  H27  H  HCH3  0   0.217  -9.2845  -0.0525  -0.2004
 C0D  H28  H  HCH3  0   0.217  -8.9660   0.4974   1.4415

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
 C0D  CAA  CAJ  single  1.522  0.020  1.522
 C0D  CAJ  CAK  single  1.524  0.020  1.524
 C0D  CAK  CAL  single  1.523  0.020  1.523
 C0D  CAL  CAM  single  1.520  0.020  1.520
 C0D  CAM  NAQ  single  1.449  0.020  1.449
 C0D  NAQ  CAT  single  1.338  0.020  1.338
 C0D  OAD  CAT  double  1.225  0.020  1.225
 C0D  CAT  CAO  single  1.515  0.020  1.515
 C0D  CAO  CAN  single  1.520  0.020  1.520
 C0D  CAN  NAR  single  1.449  0.020  1.449
 C0D  OAE  CAU  double  1.226  0.020  1.226
 C0D  NAR  CAU  single  1.336  0.020  1.336
 C0D  CAC  CAW  single  1.530  0.020  1.530
 C0D  CAU  CAV  single  1.528  0.020  1.528
 C0D  CAB  CAW  single  1.530  0.020  1.530
 C0D  CAW  CAV  single  1.552  0.020  1.552
 C0D  CAW  CAP  single  1.531  0.020  1.531
 C0D  CAV  OAG  single  1.403  0.020  1.403
 C0D  CAP  H1   single  0.970  0.020  1.090
 C0D  CAP  H2   single  0.970  0.020  1.090
 C0D  CAP  H3   single  0.970  0.020  1.090
 C0D  CAB  H4   single  0.970  0.020  1.090
 C0D  CAB  H5   single  0.970  0.020  1.090
 C0D  CAB  H6   single  0.970  0.020  1.090
 C0D  CAC  H7   single  0.970  0.020  1.090
 C0D  CAC  H8   single  0.970  0.020  1.090
 C0D  CAC  H9   single  0.970  0.020  1.090
 C0D  CAV  H10  single  0.970  0.020  1.090
 C0D  OAG  H11  single  0.850  0.020  0.980
 C0D  NAR  H12  single  0.860  0.020  1.020
 C0D  CAN  H13  single  0.970  0.020  1.090
 C0D  CAN  H14  single  0.970  0.020  1.090
 C0D  CAO  H15  single  0.970  0.020  1.090
 C0D  CAO  H16  single  0.970  0.020  1.090
 C0D  NAQ  H17  single  0.860  0.020  1.020
 C0D  CAM  H18  single  0.970  0.020  1.090
 C0D  CAM  H19  single  0.970  0.020  1.090
 C0D  CAL  H20  single  0.970  0.020  1.090
 C0D  CAL  H21  single  0.970  0.020  1.090
 C0D  CAK  H22  single  0.970  0.020  1.090
 C0D  CAK  H23  single  0.970  0.020  1.090
 C0D  CAJ  H24  single  0.970  0.020  1.090
 C0D  CAJ  H25  single  0.970  0.020  1.090
 C0D  CAA  H26  single  0.970  0.020  1.090
 C0D  CAA  H27  single  0.970  0.020  1.090
 C0D  CAA  H28  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
 C0D  H3   CAP  H2   107.76  3.000
 C0D  H3   CAP  H1   108.01  3.000
 C0D  H2   CAP  H1   107.51  3.000
 C0D  H3   CAP  CAW  111.99  3.000
 C0D  H2   CAP  CAW  110.10  3.000
 C0D  H1   CAP  CAW  111.30  3.000
 C0D  CAV  CAW  CAC  110.56  3.000
 C0D  CAV  CAW  CAB  111.76  3.000
 C0D  CAC  CAW  CAB  109.24  3.000
 C0D  CAV  CAW  CAP  107.67  3.000
 C0D  CAB  CAW  CAP  109.14  3.000
 C0D  CAC  CAW  CAP  108.39  3.000
 C0D  H6   CAB  H5   107.25  3.000
 C0D  H6   CAB  H4   108.14  3.000
 C0D  H5   CAB  H4   106.88  3.000
 C0D  H6   CAB  CAW  112.47  3.000
 C0D  H5   CAB  CAW  109.60  3.000
 C0D  H4   CAB  CAW  112.23  3.000
 C0D  H9   CAC  H8   107.18  3.000
 C0D  H9   CAC  H7   107.99  3.000
 C0D  H8   CAC  H7   107.14  3.000
 C0D  H9   CAC  CAW  111.90  3.000
 C0D  H8   CAC  CAW  109.63  3.000
 C0D  H7   CAC  CAW  112.73  3.000
 C0D  H10  CAV  CAU  109.05  3.000
 C0D  H10  CAV  OAG  106.61  3.000
 C0D  CAU  CAV  OAG  108.30  3.000
 C0D  H10  CAV  CAW  107.17  3.000
 C0D  OAG  CAV  CAW  112.38  3.000
 C0D  CAU  CAV  CAW  113.09  3.000
 C0D  H11  OAG  CAV  107.52  3.000
 C0D  NAR  CAU  OAE  122.78  3.000
 C0D  NAR  CAU  CAV  116.82  3.000
 C0D  OAE  CAU  CAV  120.40  3.000
 C0D  H12  NAR  CAN  118.60  3.000
 C0D  H12  NAR  CAU  118.99  3.000
 C0D  CAN  NAR  CAU  122.39  3.000
 C0D  H14  CAN  H13  107.18  3.000
 C0D  H14  CAN  CAO  109.99  3.000
 C0D  H13  CAN  CAO  110.09  3.000
 C0D  H14  CAN  NAR  109.47  3.000
 C0D  H13  CAN  NAR  110.07  3.000
 C0D  CAO  CAN  NAR  109.99  3.000
 C0D  H16  CAO  H15  106.68  3.000
 C0D  H16  CAO  CAT  107.55  3.000
 C0D  H15  CAO  CAT  110.89  3.000
 C0D  H16  CAO  CAN  109.87  3.000
 C0D  H15  CAO  CAN  110.29  3.000
 C0D  CAT  CAO  CAN  111.41  3.000
 C0D  NAQ  CAT  OAD  122.65  3.000
 C0D  OAD  CAT  CAO  121.94  3.000
 C0D  NAQ  CAT  CAO  115.40  3.000
 C0D  H17  NAQ  CAM  118.10  3.000
 C0D  H17  NAQ  CAT  118.89  3.000
 C0D  CAM  NAQ  CAT  122.92  3.000
 C0D  H19  CAM  H18  106.74  3.000
 C0D  H19  CAM  CAL  109.74  3.000
 C0D  H18  CAM  CAL  109.80  3.000
 C0D  H19  CAM  NAQ  109.99  3.000
 C0D  H18  CAM  NAQ  109.64  3.000
 C0D  CAL  CAM  NAQ  110.85  3.000
 C0D  H21  CAL  H20  106.66  3.000
 C0D  H21  CAL  CAK  109.72  3.000
 C0D  H20  CAL  CAK  109.39  3.000
 C0D  H21  CAL  CAM  109.51  3.000
 C0D  H20  CAL  CAM  109.51  3.000
 C0D  CAK  CAL  CAM  111.91  3.000
 C0D  H23  CAK  H22  106.08  3.000
 C0D  H23  CAK  CAJ  109.31  3.000
 C0D  H22  CAK  CAJ  109.30  3.000
 C0D  H23  CAK  CAL  109.34  3.000
 C0D  H22  CAK  CAL  109.57  3.000
 C0D  CAJ  CAK  CAL  113.01  3.000
 C0D  H25  CAJ  H24  106.05  3.000
 C0D  H25  CAJ  CAA  109.58  3.000
 C0D  H24  CAJ  CAA  109.68  3.000
 C0D  H25  CAJ  CAK  109.29  3.000
 C0D  H24  CAJ  CAK  109.29  3.000
 C0D  CAA  CAJ  CAK  112.73  3.000
 C0D  H28  CAA  H27  107.50  3.000
 C0D  H28  CAA  H26  107.64  3.000
 C0D  H27  CAA  H26  107.58  3.000
 C0D  H28  CAA  CAJ  111.25  3.000
 C0D  H27  CAA  CAJ  111.13  3.000
 C0D  H26  CAA  CAJ  111.54  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
 C0D  CONST_01  CAN  NAR  CAU  CAV   180.00   0.0  0
 C0D  CONST_02  CAN  NAR  CAU  OAE     0.00   0.0  0
 C0D  CONST_03  CAM  NAQ  CAT  CAO   180.00   0.0  0
 C0D  CONST_04  CAM  NAQ  CAT  OAD     0.00   0.0  0
 C0D  CONST_05  H12  NAR  CAU  CAV     0.00   0.0  0
 C0D  CONST_06  H17  NAQ  CAT  CAO     0.00   0.0  0
 C0D  Var_01    CAO  CAN  NAR  CAU   175.68  30.0  1
 C0D  Var_02    CAT  CAO  CAN  NAR   177.88  30.0  1
 C0D  Var_03    NAQ  CAT  CAO  CAN   144.52  30.0  2
 C0D  Var_04    CAL  CAM  NAQ  CAT  -173.93  30.0  2
 C0D  Var_05    CAK  CAL  CAM  NAQ  -177.59  30.0  1
 C0D  Var_06    CAJ  CAK  CAL  CAM  -179.83  30.0  1
 C0D  Var_07    CAA  CAJ  CAK  CAL  -179.24  30.0  1
 C0D  Var_08    H7   CAC  CAW  CAP  -174.57  30.0  3
 C0D  Var_09    H4   CAB  CAW  CAP   -61.90  30.0  3
 C0D  Var_10    H1   CAP  CAW  CAB  -177.64  30.0  3
 C0D  Var_11    H26  CAA  CAJ  CAK  -179.48  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
 C0D  chir_01  CAV  CAU  CAW  OAG  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
 C0D  plan-1  CAV  0.020
 C0D  plan-1  CAU  0.020
 C0D  plan-1  OAE  0.020
 C0D  plan-1  NAR  0.020
 C0D  plan-1  CAN  0.020
 C0D  plan-1  H12  0.020
 C0D  plan-2  CAO  0.020
 C0D  plan-2  CAT  0.020
 C0D  plan-2  OAD  0.020
 C0D  plan-2  NAQ  0.020
 C0D  plan-2  CAM  0.020
 C0D  plan-2  H17  0.020

