# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 17:10:23 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  33  15  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.596  -1.7158   0.3631  -1.4287
 55N  CAU  C  CH3    0  -0.532  -1.9508  -0.9072  -2.0841
 55N  CAQ  C  CH1    0  -0.045  -1.6298   0.3311   0.0256
 55N  CAV  C  CH1    0  -0.237  -3.0052   0.0272   0.6474
 55N  CAX  C  CH3    0  -0.663  -2.9719   0.1219   2.1721
 55N  CAW  C  CH3    0  -0.646  -4.0818   0.9594   0.0998
 55N  CAR  C  CH2    0  -0.491  -0.5448  -0.6158   0.5709
 55N  CAS  C  CH1    0  -0.092   0.8225  -0.4538  -0.0770
 55N  OAZ  O  O2     0  -0.457   1.2382   0.8930   0.1734
 55N  CBB  C  C      0   0.574   2.3054   1.3433  -0.4628
 55N  OBA  O  O      0  -0.474   2.8772   0.7362  -1.3373
 55N  CBC  C  CH3    0  -0.777   2.7119   2.7143  -0.0031
 55N  CAY  C  C      0   0.398   1.8297  -1.4719   0.5035
 55N  H25  H  HCH3   0   0.232  -1.9520  -0.7549  -3.1637
 55N  H26  H  HCH3   0   0.196  -1.2150  -1.6927  -1.8663
 55N  H27  H  HCH3   0   0.224  -2.9328  -1.3007  -1.8167
 55N  H28  H  HCH1   0   0.217  -1.3712   1.3527   0.3292
 55N  H29  H  HCH1   0   0.210  -3.2848  -1.0021   0.3905
 55N  H30  H  HCH3   0   0.213  -2.6183   1.1040   2.4964
 55N  H31  H  HCH3   0   0.227  -3.9729  -0.0193   2.5832
 55N  H32  H  HCH3   0   0.231  -2.3296  -0.6311   2.6277
 55N  H33  H  HCH3   0   0.231  -4.1774   0.8831  -0.9820
 55N  H34  H  HCH3   0   0.217  -5.0521   0.7261   0.5422
 55N  H35  H  HCH3   0   0.207  -3.8527   2.0012   0.3399
 55N  H36  H  HCH2   0   0.240  -0.4380  -0.4673   1.6487
 55N  H37  H  HCH2   0   0.234  -0.8501  -1.6562   0.4337
 55N  H38  H  HCH1   0   0.226   0.7476  -0.6195  -1.1558
 55N  H39  H  HCH3   0   0.254   2.0640   3.1116   0.7737
 55N  H40  H  HCH3   0   0.269   3.7333   2.6768   0.3765
 55N  H41  H  HCH3   0   0.268   2.7104   3.3982  -0.8515
 55N  H1   H  HNH1   0   0.346  -0.8819   0.7898  -1.8096
 55N  OXT  O  OC    -1  -0.610   1.6241  -2.6499   0.1555
 55N  O    O  O      0  -0.593   2.7105  -1.0430   1.2659

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  1.208  0.020  1.208
 55N  CBB  CBC  single  1.502  0.020  1.502
 55N  CBB  OAZ  single  1.321  0.020  1.321
 55N  CAY  CAS  single  1.545  0.020  1.545
 55N  CAS  OAZ  single  1.432  0.020  1.432
 55N  CAS  CAR  single  1.522  0.020  1.522
 55N  CAU  NAP  single  1.449  0.020  1.449
 55N  NAP  CAQ  single  1.457  0.020  1.457
 55N  CAR  CAQ  single  1.540  0.020  1.540
 55N  CAQ  CAV  single  1.540  0.020  1.540
 55N  CAV  CAX  single  1.528  0.020  1.528
 55N  CAV  CAW  single  1.526  0.020  1.526
 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  deloc   1.245  0.020  1.245
 55N  CAY  O    deloc   1.241  0.020  1.241

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  109.67  3.000
 55N  H1   NAP  CAU  109.47  3.000
 55N  CAQ  NAP  CAU  116.22  3.000
 55N  H27  CAU  H26  107.25  3.000
 55N  H27  CAU  H25  106.98  3.000
 55N  H26  CAU  H25  107.28  3.000
 55N  H27  CAU  NAP  110.56  3.000
 55N  H26  CAU  NAP  115.39  3.000
 55N  H25  CAU  NAP  109.01  3.000
 55N  H28  CAQ  CAR  107.98  3.000
 55N  H28  CAQ  CAV  106.42  3.000
 55N  CAR  CAQ  CAV  111.41  3.000
 55N  H28  CAQ  NAP  105.65  3.000
 55N  CAV  CAQ  NAP  110.77  3.000
 55N  CAR  CAQ  NAP  114.11  3.000
 55N  H29  CAV  CAW  108.01  3.000
 55N  H29  CAV  CAX  107.30  3.000
 55N  CAW  CAV  CAX  109.61  3.000
 55N  H29  CAV  CAQ  108.56  3.000
 55N  CAW  CAV  CAQ  111.39  3.000
 55N  CAX  CAV  CAQ  111.80  3.000
 55N  H32  CAX  H31  107.08  3.000
 55N  H32  CAX  H30  107.83  3.000
 55N  H31  CAX  H30  107.53  3.000
 55N  H32  CAX  CAV  112.79  3.000
 55N  H31  CAX  CAV  110.36  3.000
 55N  H30  CAX  CAV  111.02  3.000
 55N  H35  CAW  H34  107.51  3.000
 55N  H35  CAW  H33  107.67  3.000
 55N  H34  CAW  H33  108.04  3.000
 55N  H35  CAW  CAV  110.82  3.000
 55N  H34  CAW  CAV  110.56  3.000
 55N  H33  CAW  CAV  112.07  3.000
 55N  H37  CAR  H36  106.28  3.000
 55N  H37  CAR  CAS  107.39  3.000
 55N  H36  CAR  CAS  108.51  3.000
 55N  H37  CAR  CAQ  110.13  3.000
 55N  H36  CAR  CAQ  109.54  3.000
 55N  CAS  CAR  CAQ  114.64  3.000
 55N  H38  CAS  CAY  108.37  3.000
 55N  H38  CAS  OAZ  109.56  3.000
 55N  CAY  CAS  OAZ  111.40  3.000
 55N  H38  CAS  CAR  110.01  3.000
 55N  OAZ  CAS  CAR  106.66  3.000
 55N  CAY  CAS  CAR  110.83  3.000
 55N  CBB  OAZ  CAS  118.09  3.000
 55N  CBC  CBB  OBA  123.50  3.000
 55N  CBC  CBB  OAZ  112.47  3.000
 55N  OBA  CBB  OAZ  124.01  3.000
 55N  H41  CBC  H40  107.09  3.000
 55N  H41  CBC  H39  109.04  3.000
 55N  H40  CBC  H39  108.80  3.000
 55N  H41  CBC  CBB  109.52  3.000
 55N  H40  CBC  CBB  109.19  3.000
 55N  H39  CBC  CBB  113.03  3.000
 55N  O    CAY  OXT  127.99  3.000
 55N  O    CAY  CAS  117.74  3.000
 55N  OXT  CAY  CAS  114.25  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  Var_01  OBA  CBB  OAZ  CAS     7.43  30.0  1
 55N  Var_02  H25  CAU  NAP  CAQ  -177.64  30.0  3
 55N  Var_03  H30  CAX  CAV  CAQ    56.39  30.0  3
 55N  Var_04  H33  CAW  CAV  CAQ    58.87  30.0  3
 55N  Var_05  H39  CBC  CBB  OAZ    -0.08  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  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

