# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:54:38 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2R,4R)-2-(acetyloxy)-5-methyl-4-(methylamino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](C[C@@H](OC(C)=O)C(O)=O)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
 55N  55N  '(2R,4R)-2-(acetyloxy)-5-methyl-4-(methylamino)hexanoic acid'  peptide  34  15  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_55N
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
 55N  NAP  N  NH1   0  -0.597  -1.7149   0.3913  -1.4264
 55N  CAU  C  CH3   0  -0.532  -1.9536  -0.8671  -2.1020
 55N  CAQ  C  CH1   0  -0.047  -1.6443   0.3521   0.0245
 55N  CAV  C  CH1   0  -0.241  -3.0241   0.0428   0.6346
 55N  CAX  C  CH3   0  -0.665  -3.0028   0.1190   2.1605
 55N  CAW  C  CH3   0  -0.646  -4.0907   0.9868   0.0884
 55N  CAR  C  CH2   0  -0.502  -0.5710  -0.6067   0.5786
 55N  CAS  C  CH1   0  -0.080   0.7978  -0.4197  -0.0670
 55N  OAZ  O  O2    0  -0.455   1.2232   0.9051   0.2107
 55N  CBB  C  C     0   0.578   2.3275   1.3363  -0.4007
 55N  OBA  O  O     0  -0.451   2.9582   0.6519  -1.1663
 55N  CBC  C  CH3   0  -0.775   2.6755   2.7446  -0.0298
 55N  CAY  C  C     0   0.527   1.7923  -1.4052   0.5199
 55N  H25  H  HCH3  0   0.238  -1.9315  -0.7004  -3.1786
 55N  H26  H  HCH3  0   0.193  -1.2327  -1.6663  -1.8822
 55N  H27  H  HCH3  0   0.228  -2.9445  -1.2522  -1.8570
 55N  H28  H  HCH1  0   0.232  -1.3825   1.3679   0.3414
 55N  H29  H  HCH1  0   0.216  -3.3038  -0.9819   0.3615
 55N  H30  H  HCH3  0   0.216  -2.6498   1.0960   2.5004
 55N  H31  H  HCH3  0   0.231  -4.0077  -0.0251   2.5602
 55N  H32  H  HCH3  0   0.232  -2.3678  -0.6416   2.6141
 55N  H33  H  HCH3  0   0.232  -4.1816   0.9204  -0.9944
 55N  H34  H  HCH3  0   0.220  -5.0642   0.7548   0.5241
 55N  H35  H  HCH3  0   0.209  -3.8566   2.0248   0.3392
 55N  H36  H  HCH2  0   0.266  -0.4682  -0.4664   1.6566
 55N  H37  H  HCH2  0   0.256  -0.8806  -1.6449   0.4289
 55N  H38  H  HCH1  0   0.277   0.7359  -0.5825  -1.1468
 55N  H39  H  HCH3  0   0.264   1.9565   3.1945   0.6487
 55N  H40  H  HCH3  0   0.279   3.6602   2.7568   0.4378
 55N  H41  H  HCH3  0   0.278   2.7421   3.3490  -0.9341
 55N  H1   H  HNH1  0   0.350  -0.8987   0.8459  -1.8118
 55N  OXT  O  OH1   0  -0.587   1.6496  -2.6012  -0.0258
 55N  HXT  H  HOH1  0   0.489   2.2498  -3.2376   0.3921
 55N  O    O  O     0  -0.431   2.5735  -1.1396   1.3946

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
 55N  OBA  CBB  double  1.205  0.020  1.205
 55N  CBB  CBC  single  1.497  0.020  1.497
 55N  CBB  OAZ  single  1.334  0.020  1.334
 55N  CAY  CAS  single  1.518  0.020  1.518
 55N  CAS  OAZ  single  1.419  0.020  1.419
 55N  CAS  CAR  single  1.525  0.020  1.525
 55N  CAU  NAP  single  1.448  0.020  1.448
 55N  NAP  CAQ  single  1.453  0.020  1.453
 55N  CAR  CAQ  single  1.542  0.020  1.542
 55N  CAQ  CAV  single  1.540  0.020  1.540
 55N  CAV  CAX  single  1.528  0.020  1.528
 55N  CAV  CAW  single  1.525  0.020  1.525
 55N  CAU  H25  single  0.970  0.020  1.090
 55N  CAU  H26  single  0.970  0.020  1.090
 55N  CAU  H27  single  0.970  0.020  1.090
 55N  CAQ  H28  single  0.970  0.020  1.090
 55N  CAV  H29  single  0.970  0.020  1.090
 55N  CAX  H30  single  0.970  0.020  1.090
 55N  CAX  H31  single  0.970  0.020  1.090
 55N  CAX  H32  single  0.970  0.020  1.090
 55N  CAW  H33  single  0.970  0.020  1.090
 55N  CAW  H34  single  0.970  0.020  1.090
 55N  CAW  H35  single  0.970  0.020  1.090
 55N  CAR  H36  single  0.970  0.020  1.090
 55N  CAR  H37  single  0.970  0.020  1.090
 55N  CAS  H38  single  0.970  0.020  1.090
 55N  CBC  H39  single  0.970  0.020  1.090
 55N  CBC  H40  single  0.970  0.020  1.090
 55N  CBC  H41  single  0.970  0.020  1.090
 55N  NAP  H1   single  0.890  0.020  1.040
 55N  CAY  OXT  single  1.322  0.020  1.322
 55N  OXT  HXT  single  0.850  0.020  0.980
 55N  CAY  O    double  1.202  0.020  1.202

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
 55N  H1   NAP  CAQ  110.71  3.000
 55N  H1   NAP  CAU  110.25  3.000
 55N  CAQ  NAP  CAU  116.77  3.000
 55N  H27  CAU  H26  107.11  3.000
 55N  H27  CAU  H25  107.12  3.000
 55N  H26  CAU  H25  107.20  3.000
 55N  H27  CAU  NAP  110.59  3.000
 55N  H26  CAU  NAP  115.51  3.000
 55N  H25  CAU  NAP  108.95  3.000
 55N  H28  CAQ  CAR  107.83  3.000
 55N  H28  CAQ  CAV  106.59  3.000
 55N  CAR  CAQ  CAV  110.87  3.000
 55N  H28  CAQ  NAP  105.99  3.000
 55N  CAV  CAQ  NAP  110.94  3.000
 55N  CAR  CAQ  NAP  114.17  3.000
 55N  H29  CAV  CAW  108.10  3.000
 55N  H29  CAV  CAX  107.39  3.000
 55N  CAW  CAV  CAX  109.67  3.000
 55N  H29  CAV  CAQ  108.51  3.000
 55N  CAW  CAV  CAQ  111.12  3.000
 55N  CAX  CAV  CAQ  111.91  3.000
 55N  H32  CAX  H31  106.98  3.000
 55N  H32  CAX  H30  107.84  3.000
 55N  H31  CAX  H30  107.55  3.000
 55N  H32  CAX  CAV  112.89  3.000
 55N  H31  CAX  CAV  110.27  3.000
 55N  H30  CAX  CAV  111.08  3.000
 55N  H35  CAW  H34  107.53  3.000
 55N  H35  CAW  H33  107.70  3.000
 55N  H34  CAW  H33  108.04  3.000
 55N  H35  CAW  CAV  110.83  3.000
 55N  H34  CAW  CAV  110.43  3.000
 55N  H33  CAW  CAV  112.13  3.000
 55N  H37  CAR  H36  106.49  3.000
 55N  H37  CAR  CAS  108.21  3.000
 55N  H36  CAR  CAS  108.52  3.000
 55N  H37  CAR  CAQ  110.12  3.000
 55N  H36  CAR  CAQ  109.90  3.000
 55N  CAS  CAR  CAQ  113.34  3.000
 55N  H38  CAS  CAY  108.79  3.000
 55N  H38  CAS  OAZ  110.44  3.000
 55N  CAY  CAS  OAZ  109.52  3.000
 55N  H38  CAS  CAR  110.42  3.000
 55N  OAZ  CAS  CAR  107.50  3.000
 55N  CAY  CAS  CAR  110.17  3.000
 55N  CBB  OAZ  CAS  117.41  3.000
 55N  CBC  CBB  OBA  124.74  3.000
 55N  CBC  CBB  OAZ  112.52  3.000
 55N  OBA  CBB  OAZ  122.75  3.000
 55N  H41  CBC  H40  107.13  3.000
 55N  H41  CBC  H39  109.21  3.000
 55N  H40  CBC  H39  108.98  3.000
 55N  H41  CBC  CBB  109.29  3.000
 55N  H40  CBC  CBB  109.07  3.000
 55N  H39  CBC  CBB  112.98  3.000
 55N  O    CAY  OXT  124.76  3.000
 55N  O    CAY  CAS  124.29  3.000
 55N  OXT  CAY  CAS  110.91  3.000
 55N  HXT  OXT  CAY  110.43  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
 55N  CONST_01  HXT  OXT  CAY  CAS   180.00   0.0  0
 55N  Var_01    OBA  CBB  OAZ  CAS     0.18  30.0  1
 55N  Var_02    H25  CAU  NAP  CAQ  -177.14  30.0  3
 55N  Var_03    H30  CAX  CAV  CAQ    56.34  30.0  3
 55N  Var_04    H33  CAW  CAV  CAQ    59.18  30.0  3
 55N  Var_05    H39  CBC  CBB  OAZ    -1.89  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
 55N  chir_01  CAQ  NAP  CAR  CAV  positiv
 55N  chir_02  CAS  OAZ  CAY  CAR  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
 55N  plan-1  CAS  0.020
 55N  plan-1  CAY  0.020
 55N  plan-1  OXT  0.020
 55N  plan-1  HXT  0.020
 55N  plan-1  O    0.020
 55N  plan-2  OAZ  0.020
 55N  plan-2  CBB  0.020
 55N  plan-2  OBA  0.020
 55N  plan-2  CBC  0.020

