# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 07:29:44 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N-[(2S)-2-amino-1,1-dihydroxy-4-methylpentyl]-L-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(O)(O)N[C@@H]([C@@H](C)O)C(O)=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
 LNT  LNT  N-[(2S)-2-amino-1,1-dihydroxy-4-methylpentyl]-L-threonine  peptide  39  17  .  2022-09-22  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_LNT
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
 LNT  N14   N  NH2   0  -0.790  -1.7643   1.6488   0.7096
 LNT  CA    C  CH1   0  -0.202  -1.6537   0.2821   0.2287
 LNT  C16   C  CT    0   0.660  -0.3873   0.0290  -0.6346
 LNT  C17   C  CH2   0  -0.402  -2.9352  -0.0970  -0.5099
 LNT  C18   C  CH1   0  -0.225  -4.2068  -0.0242   0.3395
 LNT  C19   C  CH3   0  -0.652  -5.4300  -0.2607  -0.5409
 LNT  C20   C  CH3   0  -0.663  -4.1835  -1.0267   1.4887
 LNT  O21   O  OH1   0  -0.662  -0.3504  -1.2845  -1.1239
 LNT  O22   O  OH1   0  -0.660  -0.3961   0.7765  -1.8121
 LNT  N23   N  NH1   0  -0.656   0.7598   0.3924   0.1538
 LNT  C24   C  CH1   0  -0.225   2.0600   0.0963  -0.3844
 LNT  C     C  C     0   0.548   2.5356  -1.3036  -0.0191
 LNT  O     O  O     0  -0.443   2.0106  -2.0195   0.7961
 LNT  C27   C  CH1   0   0.049   3.1058   1.1234   0.0742
 LNT  OG1   O  OH1   0  -0.674   3.2558   0.9452   1.4683
 LNT  C29   C  CH3   0  -0.690   2.7004   2.5405  -0.2897
 LNT  H     H  HNH2  0   0.349  -0.8766   1.9864   1.0592
 LNT  H2    H  HNH2  0   0.338  -2.0406   2.2694  -0.0422
 LNT  H15   H  HCH1  0   0.224  -1.5545  -0.3695   1.1076
 LNT  H17   H  HCH2  0   0.218  -3.0439   0.5668  -1.3747
 LNT  H17A  H  HCH2  0   0.221  -2.8461  -1.1098  -0.9118
 LNT  H18   H  HCH1  0   0.216  -4.2807   0.9815   0.7633
 LNT  H19   H  HCH3  0   0.210  -5.3981  -1.2533  -0.9979
 LNT  H19A  H  HCH3  0   0.223  -6.3537  -0.1973   0.0376
 LNT  H19B  H  HCH3  0   0.222  -5.4927   0.4724  -1.3474
 LNT  H20   H  HCH3  0   0.228  -3.3610  -0.8470   2.1823
 LNT  H20A  H  HCH3  0   0.225  -5.1081  -0.9821   2.0669
 LNT  H20B  H  HCH3  0   0.211  -4.0800  -2.0470   1.1100
 LNT  HO21  H  HOH1  0   0.449  -0.3789  -1.8918  -0.3763
 LNT  HO22  H  HOH1  0   0.445  -0.2985   1.7038  -1.5700
 LNT  HN23  H  HNH1  0   0.359   0.6735   0.1016   1.1187
 LNT  H24   H  HCH1  0   0.292   2.0196   0.1620  -1.4749
 LNT  OXT   O  OH1   0  -0.593   3.6205  -1.6474  -0.7004
 LNT  H27   H  HCH1  0   0.218   4.0458   0.8946  -0.4444
 LNT  HOG1  H  HOH1  0   0.455   3.9275   1.5590   1.7818
 LNT  H29   H  HCH3  0   0.236   3.4726   3.2476   0.0192
 LNT  H29A  H  HCH3  0   0.226   2.5795   2.6418  -1.3694
 LNT  H29B  H  HCH3  0   0.234   1.7626   2.8207   0.1882
 LNT  HXT   H  HOH1  0   0.482   3.9180  -2.5304  -0.4340

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
 LNT  N14  CA    single  1.453  0.020  1.453
 LNT  N14  H     single  0.890  0.020  1.040
 LNT  N14  H2    single  0.890  0.020  1.040
 LNT  CA   C17   single  1.527  0.020  1.527
 LNT  CA   H15   single  0.970  0.020  1.090
 LNT  C16  CA    single  1.553  0.020  1.553
 LNT  C16  O22   single  1.395  0.020  1.395
 LNT  C16  O21   single  1.402  0.020  1.402
 LNT  C17  C18   single  1.531  0.020  1.531
 LNT  C17  H17   single  0.970  0.020  1.090
 LNT  C17  H17A  single  0.970  0.020  1.090
 LNT  C18  C20   single  1.525  0.020  1.525
 LNT  C18  H18   single  0.970  0.020  1.090
 LNT  C19  C18   single  1.526  0.020  1.526
 LNT  C19  H19   single  0.970  0.020  1.090
 LNT  C19  H19A  single  0.970  0.020  1.090
 LNT  C19  H19B  single  0.970  0.020  1.090
 LNT  C20  H20   single  0.970  0.020  1.090
 LNT  C20  H20A  single  0.970  0.020  1.090
 LNT  C20  H20B  single  0.970  0.020  1.090
 LNT  O21  HO21  single  0.850  0.020  0.980
 LNT  O22  HO22  single  0.850  0.020  0.980
 LNT  N23  C16   single  1.438  0.020  1.438
 LNT  N23  HN23  single  0.890  0.020  1.040
 LNT  C24  N23   single  1.438  0.020  1.438
 LNT  C24  C     single  1.523  0.020  1.523
 LNT  C24  H24   single  0.970  0.020  1.090
 LNT  C    O     double  1.231  0.020  1.231
 LNT  C    OXT   single  1.326  0.020  1.326
 LNT  C27  C24   single  1.536  0.020  1.536
 LNT  C27  H27   single  0.970  0.020  1.090
 LNT  OG1  C27   single  1.413  0.020  1.413
 LNT  OG1  HOG1  single  0.850  0.020  0.980
 LNT  C29  C27   single  1.518  0.020  1.518
 LNT  C29  H29   single  0.970  0.020  1.090
 LNT  C29  H29A  single  0.970  0.020  1.090
 LNT  C29  H29B  single  0.970  0.020  1.090
 LNT  OXT  HXT   single  0.850  0.020  0.980

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
 LNT  H2    N14  H     106.93  3.000
 LNT  H2    N14  CA    110.57  3.000
 LNT  H     N14  CA    111.19  3.000
 LNT  H15   CA   C17   108.39  3.000
 LNT  H15   CA   C16   105.92  3.000
 LNT  C17   CA   C16   112.02  3.000
 LNT  C16   CA   N14   113.53  3.000
 LNT  H15   CA   N14   107.46  3.000
 LNT  C17   CA   N14   109.26  3.000
 LNT  N23   C16  O22   109.41  3.000
 LNT  N23   C16  O21   114.01  3.000
 LNT  O22   C16  O21   101.98  3.000
 LNT  N23   C16  CA    107.72  3.000
 LNT  O21   C16  CA    111.59  3.000
 LNT  O22   C16  CA    112.13  3.000
 LNT  H17A  C17  H17   106.22  3.000
 LNT  H17A  C17  C18   108.40  3.000
 LNT  H17   C17  C18   109.07  3.000
 LNT  H17A  C17  CA    109.85  3.000
 LNT  H17   C17  CA    108.34  3.000
 LNT  C18   C17  CA    114.64  3.000
 LNT  H18   C18  C20   108.27  3.000
 LNT  H18   C18  C19   108.18  3.000
 LNT  C20   C18  C19   110.20  3.000
 LNT  C19   C18  C17   109.78  3.000
 LNT  H18   C18  C17   108.35  3.000
 LNT  C20   C18  C17   111.97  3.000
 LNT  H19B  C19  H19A  107.69  3.000
 LNT  H19B  C19  H19   107.61  3.000
 LNT  H19A  C19  H19   107.40  3.000
 LNT  H19B  C19  C18   111.61  3.000
 LNT  H19A  C19  C18   111.32  3.000
 LNT  H19   C19  C18   111.01  3.000
 LNT  H20B  C20  H20A  107.57  3.000
 LNT  H20B  C20  H20   107.62  3.000
 LNT  H20A  C20  H20   107.17  3.000
 LNT  H20B  C20  C18   110.72  3.000
 LNT  H20A  C20  C18   111.06  3.000
 LNT  H20   C20  C18   112.48  3.000
 LNT  HO21  O21  C16   108.60  3.000
 LNT  HO22  O22  C16   107.64  3.000
 LNT  HN23  N23  C24   112.02  3.000
 LNT  C24   N23  C16   117.64  3.000
 LNT  HN23  N23  C16   112.47  3.000
 LNT  H24   C24  C27   106.43  3.000
 LNT  C27   C24  C     109.29  3.000
 LNT  H24   C24  C     107.83  3.000
 LNT  C27   C24  N23   111.48  3.000
 LNT  H24   C24  N23   109.12  3.000
 LNT  C     C24  N23   112.45  3.000
 LNT  OXT   C    O     123.35  3.000
 LNT  OXT   C    C24   111.75  3.000
 LNT  O     C    C24   124.90  3.000
 LNT  H27   C27  C29   108.06  3.000
 LNT  C29   C27  OG1   112.49  3.000
 LNT  H27   C27  OG1   110.41  3.000
 LNT  C29   C27  C24   111.76  3.000
 LNT  OG1   C27  C24   106.41  3.000
 LNT  H27   C27  C24   107.61  3.000
 LNT  HOG1  OG1  C27   108.37  3.000
 LNT  H29B  C29  H29A  108.36  3.000
 LNT  H29B  C29  H29   108.56  3.000
 LNT  H29A  C29  H29   107.35  3.000
 LNT  H29B  C29  C27   111.40  3.000
 LNT  H29A  C29  C27   110.70  3.000
 LNT  H29   C29  C27   110.35  3.000
 LNT  HXT   OXT  C     110.25  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
 LNT  CONST_01  HXT  OXT  C    C24  180.00   0.0  0
 LNT  Var_01    C20  C18  C17  CA   -63.96  30.0  3
 LNT  Var_02    C24  N23  C16  CA   172.94  30.0  1
 LNT  Var_03    H20  C20  C18  C17   61.52  30.0  3
 LNT  Var_04    H19  C19  C18  C17   61.38  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
 LNT  chir_01  CA   N14  C17  C16  negativ
 LNT  chir_02  C24  N23  C27  C    negativ
 LNT  chir_03  C27  OG1  C24  C29  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
 LNT  plan-1  C24  0.020
 LNT  plan-1  C    0.020
 LNT  plan-1  O    0.020
 LNT  plan-1  OXT  0.020
 LNT  plan-1  HXT  0.020

