# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 02:47:48 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (2S,4S,5S)-5-amino-4-hydroxy-7-methyl-2-(propan-2-yl)octanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@@H](O)C[C@@H](C(C)C)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
 LOV  LOV  '(2S,4S,5S)-5-amino-4-hydroxy-7-methyl-2-(propan-2-yl)octanoic acid'  peptide  41  16  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LOV
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
 LOV  CD1   C  CH3   0  -0.651   5.3271   0.9004  -0.5756
 LOV  CD2   C  CH3   0  -0.660   4.3483   0.2046   1.6277
 LOV  C1G   C  CH1   0  -0.232   4.2662   0.0468   0.1127
 LOV  C1B   C  CH2   0  -0.425   2.8794   0.4015  -0.4271
 LOV  C1A   C  CH1   0  -0.108   1.7288  -0.4489   0.1115
 LOV  CS    C  CH1   0   0.051   0.3823   0.0039  -0.4785
 LOV  N     N  NH2   0  -0.817   1.8919  -1.8793  -0.1490
 LOV  OS    O  OH1   0  -0.672   0.2765  -0.3792  -1.8333
 LOV  CT    C  CH2   0  -0.459  -0.7801  -0.5367   0.3519
 LOV  CA    C  CH1   0  -0.317  -2.1702  -0.2026  -0.1956
 LOV  CB    C  CH1   0  -0.226  -3.3042  -0.7446   0.7032
 LOV  CG1   C  CH3   0  -0.667  -4.6793  -0.2722   0.2326
 LOV  CG2   C  CH3   0  -0.663  -3.2867  -2.2702   0.7529
 LOV  C     C  C     0   0.534  -2.3071   1.2962  -0.3226
 LOV  O     O  O     0  -0.451  -2.1285   2.0706   0.5878
 LOV  OXT   O  OH1   0  -0.587  -2.6557   1.6898  -1.5420
 LOV  HD11  H  HCH3  0   0.224   6.3312   0.6320  -0.2430
 LOV  HD12  H  HCH3  0   0.223   5.2922   0.7784  -1.6600
 LOV  HD13  H  HCH3  0   0.212   5.1797   1.9614  -0.3584
 LOV  HD21  H  HCH3  0   0.213   4.0963   1.2250   1.9284
 LOV  HD22  H  HCH3  0   0.226   3.6695  -0.4707   2.1509
 LOV  HD23  H  HCH3  0   0.226   5.3561  -0.0062   1.9901
 LOV  H1G   H  HCH1  0   0.207   4.4763  -1.0009  -0.1312
 LOV  H1B1  H  HCH2  0   0.214   2.6767   1.4554  -0.2035
 LOV  H1B2  H  HCH2  0   0.220   2.8897   0.3173  -1.5202
 LOV  H1A   H  HCH1  0   0.229   1.6610  -0.3046   1.1943
 LOV  HS1   H  HCH1  0   0.223   0.3590   1.1000  -0.4695
 LOV  H     H  HNH2  0   0.349   2.5287  -2.0279  -0.9220
 LOV  H2    H  HNH2  0   0.357   2.3058  -2.3466   0.6453
 LOV  HOS   H  HOH1  0   0.436   0.3870  -1.3389  -1.8488
 LOV  HT1   H  HCH2  0   0.244  -0.6715  -1.6214   0.4195
 LOV  HT2   H  HCH2  0   0.227  -0.6895  -0.1531   1.3725
 LOV  HA    H  HCH1  0   0.246  -2.2854  -0.6476  -1.1874
 LOV  HB    H  HCH1  0   0.226  -3.1368  -0.3654   1.7173
 LOV  HG11  H  HCH3  0   0.221  -4.8615  -0.5686  -0.8026
 LOV  HG12  H  HCH3  0   0.235  -5.4632  -0.7192   0.8451
 LOV  HG13  H  HCH3  0   0.232  -4.8025   0.8097   0.2996
 LOV  HG21  H  HCH3  0   0.218  -3.4646  -2.6932  -0.2389
 LOV  HG22  H  HCH3  0   0.235  -2.3449  -2.6729   1.1240
 LOV  HG23  H  HCH3  0   0.234  -4.0769  -2.6341   1.4114
 LOV  HXT   H  HOH1  0   0.475  -2.7403   2.6554  -1.5653

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
 LOV  CD1  C1G   single  1.526  0.020  1.526
 LOV  CD1  HD11  single  0.970  0.020  1.090
 LOV  CD1  HD12  single  0.970  0.020  1.090
 LOV  CD1  HD13  single  0.970  0.020  1.090
 LOV  CD2  C1G   single  1.525  0.020  1.525
 LOV  CD2  HD21  single  0.970  0.020  1.090
 LOV  CD2  HD22  single  0.970  0.020  1.090
 LOV  CD2  HD23  single  0.970  0.020  1.090
 LOV  C1G  C1B   single  1.530  0.020  1.530
 LOV  C1G  H1G   single  0.970  0.020  1.090
 LOV  C1B  C1A   single  1.529  0.020  1.529
 LOV  C1B  H1B1  single  0.970  0.020  1.090
 LOV  C1B  H1B2  single  0.970  0.020  1.090
 LOV  C1A  CS    single  1.538  0.020  1.538
 LOV  C1A  N     single  1.463  0.020  1.463
 LOV  C1A  H1A   single  0.970  0.020  1.090
 LOV  CS   OS    single  1.412  0.020  1.412
 LOV  CS   CT    single  1.527  0.020  1.527
 LOV  CS   HS1   single  0.970  0.020  1.090
 LOV  N    H     single  0.860  0.020  0.860
 LOV  N    H2    single  0.890  0.020  1.040
 LOV  OS   HOS   single  0.850  0.020  0.980
 LOV  CT   CA    single  1.531  0.020  1.531
 LOV  CT   HT1   single  0.970  0.020  1.090
 LOV  CT   HT2   single  0.970  0.020  1.090
 LOV  CA   CB    single  1.521  0.033  1.521
 LOV  CA   C     single  1.525  0.021  1.525
 LOV  CA   HA    single  0.970  0.020  0.970
 LOV  CB   CG1   single  1.528  0.020  1.528
 LOV  CB   CG2   single  1.526  0.020  1.526
 LOV  CB   HB    single  0.970  0.020  1.090
 LOV  CG1  HG11  single  0.970  0.020  1.090
 LOV  CG1  HG12  single  0.970  0.020  1.090
 LOV  CG1  HG13  single  0.970  0.020  1.090
 LOV  CG2  HG21  single  0.970  0.020  1.090
 LOV  CG2  HG22  single  0.970  0.020  1.090
 LOV  CG2  HG23  single  0.970  0.020  1.090
 LOV  C    O     double  1.231  0.020  1.231
 LOV  C    OXT   single  1.328  0.020  1.328
 LOV  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
 LOV  HD13  CD1  HD12  107.55  3.000
 LOV  HD13  CD1  HD11  107.59  3.000
 LOV  HD12  CD1  HD11  107.74  3.000
 LOV  HD13  CD1  C1G   111.08  3.000
 LOV  HD12  CD1  C1G   111.31  3.000
 LOV  HD11  CD1  C1G   111.39  3.000
 LOV  HD23  CD2  HD22  107.20  3.000
 LOV  HD23  CD2  HD21  107.57  3.000
 LOV  HD22  CD2  HD21  107.60  3.000
 LOV  HD23  CD2  C1G   111.06  3.000
 LOV  HD22  CD2  C1G   112.25  3.000
 LOV  HD21  CD2  C1G   110.94  3.000
 LOV  H1G   C1G  C1B   108.47  3.000
 LOV  H1G   C1G  CD2   108.04  3.000
 LOV  C1B   C1G  CD2   112.04  3.000
 LOV  H1G   C1G  CD1   107.52  3.000
 LOV  C1B   C1G  CD1   109.96  3.000
 LOV  CD2   C1G  CD1   110.66  3.000
 LOV  H1B2  C1B  H1B1  106.20  3.000
 LOV  H1B2  C1B  C1A   108.40  3.000
 LOV  H1B1  C1B  C1A   108.89  3.000
 LOV  H1B2  C1B  C1G   108.99  3.000
 LOV  H1B1  C1B  C1G   108.57  3.000
 LOV  C1A   C1B  C1G   115.40  3.000
 LOV  H1A   C1A  N     108.18  3.000
 LOV  H1A   C1A  CS    106.65  3.000
 LOV  N     C1A  CS    108.49  3.000
 LOV  H1A   C1A  C1B   108.77  3.000
 LOV  N     C1A  C1B   113.40  3.000
 LOV  CS    C1A  C1B   111.09  3.000
 LOV  HS1   CS   CT    109.46  3.000
 LOV  HS1   CS   OS    106.12  3.000
 LOV  CT    CS   OS    111.63  3.000
 LOV  HS1   CS   C1A   108.05  3.000
 LOV  CT    CS   C1A   110.70  3.000
 LOV  OS    CS   C1A   110.72  3.000
 LOV  H2    N    H     105.95  3.000
 LOV  H2    N    C1A   110.97  3.000
 LOV  H     N    C1A   110.46  3.000
 LOV  HOS   OS   CS    106.05  3.000
 LOV  HT2   CT   HT1   106.39  3.000
 LOV  HT2   CT   CA    109.41  3.000
 LOV  HT1   CT   CA    109.22  3.000
 LOV  HT2   CT   CS    108.67  3.000
 LOV  HT1   CT   CS    108.03  3.000
 LOV  CA    CT   CS    114.79  3.000
 LOV  HA    CA   C     110.00  3.000
 LOV  HA    CA   CB    109.00  3.000
 LOV  C     CA   CB    110.50  1.500
 LOV  HA    CA   CT    109.35  3.000
 LOV  C     CA   CT    109.20  3.000
 LOV  CB    CA   CT    112.45  3.000
 LOV  HB    CB   CG2   108.31  3.000
 LOV  HB    CB   CG1   108.39  3.000
 LOV  CG2   CB   CG1   109.23  3.000
 LOV  HB    CB   CA    107.75  3.000
 LOV  CG2   CB   CA    111.17  3.000
 LOV  CG1   CB   CA    111.89  3.000
 LOV  HG13  CG1  HG12  106.90  3.000
 LOV  HG13  CG1  HG11  107.97  3.000
 LOV  HG12  CG1  HG11  107.53  3.000
 LOV  HG13  CG1  CB    112.91  3.000
 LOV  HG12  CG1  CB    110.31  3.000
 LOV  HG11  CG1  CB    110.99  3.000
 LOV  HG23  CG2  HG22  107.29  3.000
 LOV  HG23  CG2  HG21  107.50  3.000
 LOV  HG22  CG2  HG21  107.86  3.000
 LOV  HG23  CG2  CB    110.17  3.000
 LOV  HG22  CG2  CB    112.98  3.000
 LOV  HG21  CG2  CB    110.82  3.000
 LOV  OXT   C    O     122.73  3.000
 LOV  OXT   C    CA    120.80  1.700
 LOV  O     C    CA    120.80  1.700
 LOV  HXT   OXT  C     109.89  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
 LOV  CONST_01  HXT   OXT  C    CA   180.00   0.0  0
 LOV  Var_01    C1A   C1B  C1G  CD1  176.04  30.0  3
 LOV  Var_02    HD21  CD2  C1G  CD1   65.40  30.0  3
 LOV  Var_03    HD11  CD1  C1G  CD2   58.48  30.0  3
 LOV  Var_04    HG11  CG1  CB   CA    57.37  30.0  3
 LOV  Var_05    HG21  CG2  CB   CA   -62.60  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
 LOV  chir_01  C1A  C1B  CS   N   negativ
 LOV  chir_02  CS   OS   C1A  CT  positiv
 LOV  chir_03  CA   C    CB   CT  positiv

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
 LOV  plan-1  CA   0.020
 LOV  plan-1  C    0.020
 LOV  plan-1  O    0.020
 LOV  plan-1  OXT  0.020
 LOV  plan-1  HXT  0.020

