# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:59:08 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  40  16  .  2022-03-22  2022-09-22
;
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  -0.650   5.3287   0.8417  -0.6398
 LOV  CD2   C  CH3    0  -0.660   4.3316   0.3563   1.6086
 LOV  C1G   C  CH1    0  -0.236   4.2657   0.0491   0.1152
 LOV  C1B   C  CH2    0  -0.413   2.8821   0.3335  -0.4708
 LOV  C1A   C  CH1    0  -0.108   1.7300  -0.4661   0.1441
 LOV  CS    C  CH1    0   0.055   0.3963  -0.1221  -0.5395
 LOV  N     N  NH2    0  -0.806   1.9303  -1.9127   0.1175
 LOV  OS    O  OH1    0  -0.676   0.3582  -0.6352  -1.8599
 LOV  CT    C  CH2    0  -0.452  -0.7959  -0.5927   0.2868
 LOV  CA    C  CH1    0  -0.286  -2.1636  -0.2167  -0.2838
 LOV  CB    C  CH1    0  -0.219  -3.3103  -0.7381   0.6024
 LOV  CG1   C  CH3    0  -0.658  -4.6708  -0.2279   0.1286
 LOV  CG2   C  CH3    0  -0.660  -3.3458  -2.2647   0.6563
 LOV  C     C  C      0   0.406  -2.2664   1.3113  -0.4530
 LOV  O     O  O      0  -0.624  -2.0637   1.9981   0.5728
 LOV  OXT   O  OC    -1  -0.619  -2.5494   1.7552  -1.5844
 LOV  HD11  H  HCH3   0   0.223   6.3327   0.5957  -0.2900
 LOV  HD12  H  HCH3   0   0.222   5.2906   0.6370  -1.7114
 LOV  HD13  H  HCH3   0   0.211   5.1860   1.9171  -0.5047
 LOV  HD21  H  HCH3   0   0.213   4.0684   1.3996   1.8003
 LOV  HD22  H  HCH3   0   0.225   3.6510  -0.2657   2.1922
 LOV  HD23  H  HCH3   0   0.225   5.3369   0.1907   2.0005
 LOV  H1G   H  HCH1   0   0.204   4.4859  -1.0155  -0.0255
 LOV  H1B1  H  HCH2   0   0.206   2.6703   1.4044  -0.3624
 LOV  H1B2  H  HCH2   0   0.215   2.9078   0.1352  -1.5486
 LOV  H1A   H  HCH1   0   0.221   1.6211  -0.1761   1.1942
 LOV  HS1   H  HCH1   0   0.216   0.3508   0.9675  -0.6435
 LOV  H     H  HNH2   0   0.338   2.3713  -2.1846  -0.7535
 LOV  H2    H  HNH2   0   0.350   2.5775  -2.1878   0.8446
 LOV  HOS   H  HOH1   0   0.435   0.2734  -1.5925  -1.7882
 LOV  HT1   H  HCH2   0   0.217  -0.7078  -1.6760   0.4097
 LOV  HT2   H  HCH2   0   0.205  -0.7031  -0.1669   1.2904
 LOV  HA    H  HCH1   0   0.178  -2.2795  -0.6809  -1.2698
 LOV  HB    H  HCH1   0   0.199  -3.1428  -0.3653   1.6198
 LOV  HG11  H  HCH3   0   0.208  -4.8507  -0.5104  -0.9116
 LOV  HG12  H  HCH3   0   0.217  -5.4753  -0.6576   0.7288
 LOV  HG13  H  HCH3   0   0.226  -4.7563   0.8566   0.1995
 LOV  HG21  H  HCH3   0   0.208  -3.5267  -2.6828  -0.3379
 LOV  HG22  H  HCH3   0   0.225  -2.4192  -2.6982   1.0328
 LOV  HG23  H  HCH3   0   0.221  -4.1520  -2.6104   1.3066

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  1.526  0.020  1.526
 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  1.529  0.020  1.529
 LOV  C1G  H1G   single  0.970  0.020  1.090
 LOV  C1B  C1A   single  1.531  0.020  1.531
 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  1.461  0.020  1.461
 LOV  C1A  H1A   single  0.970  0.020  1.090
 LOV  CS   OS    single  1.417  0.020  1.417
 LOV  CS   CT    single  1.525  0.020  1.525
 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  1.529  0.020  1.529
 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  1.528  0.020  1.528
 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     deloc   1.231  0.020  1.231
 LOV  C    OXT   deloc   1.248  0.020  1.248

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  107.53  3.000
 LOV  HD13  CD1  HD11  107.59  3.000
 LOV  HD12  CD1  HD11  107.72  3.000
 LOV  HD13  CD1  C1G   111.04  3.000
 LOV  HD12  CD1  C1G   111.35  3.000
 LOV  HD11  CD1  C1G   111.43  3.000
 LOV  HD23  CD2  HD22  107.21  3.000
 LOV  HD23  CD2  HD21  107.68  3.000
 LOV  HD22  CD2  HD21  107.47  3.000
 LOV  HD23  CD2  C1G   111.14  3.000
 LOV  HD22  CD2  C1G   112.44  3.000
 LOV  HD21  CD2  C1G   110.70  3.000
 LOV  H1G   C1G  C1B   108.25  3.000
 LOV  H1G   C1G  CD2   108.20  3.000
 LOV  C1B   C1G  CD2   112.12  3.000
 LOV  H1G   C1G  CD1   107.52  3.000
 LOV  C1B   C1G  CD1   110.13  3.000
 LOV  CD2   C1G  CD1   110.46  3.000
 LOV  H1B2  C1B  H1B1  106.16  3.000
 LOV  H1B2  C1B  C1A   108.54  3.000
 LOV  H1B1  C1B  C1A   108.96  3.000
 LOV  H1B2  C1B  C1G   108.78  3.000
 LOV  H1B1  C1B  C1G   108.56  3.000
 LOV  C1A   C1B  C1G   115.45  3.000
 LOV  H1A   C1A  N     107.06  3.000
 LOV  H1A   C1A  CS    106.31  3.000
 LOV  N     C1A  CS    109.41  3.000
 LOV  H1A   C1A  C1B   108.76  3.000
 LOV  N     C1A  C1B   114.00  3.000
 LOV  CS    C1A  C1B   110.93  3.000
 LOV  HS1   CS   CT    109.01  3.000
 LOV  HS1   CS   OS    105.70  3.000
 LOV  CT    CS   OS    111.85  3.000
 LOV  HS1   CS   C1A   107.50  3.000
 LOV  CT    CS   C1A   111.60  3.000
 LOV  OS    CS   C1A   110.89  3.000
 LOV  H2    N    H     105.45  3.000
 LOV  H2    N    C1A   110.12  3.000
 LOV  H     N    C1A   109.94  3.000
 LOV  HOS   OS   CS    107.02  3.000
 LOV  HT2   CT   HT1   105.99  3.000
 LOV  HT2   CT   CA    108.82  3.000
 LOV  HT1   CT   CA    110.95  3.000
 LOV  HT2   CT   CS    108.10  3.000
 LOV  HT1   CT   CS    107.67  3.000
 LOV  CA    CT   CS    114.91  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    109.04  3.000
 LOV  C     CA   CT    110.15  3.000
 LOV  CB    CA   CT    111.59  3.000
 LOV  HB    CB   CG2   108.09  3.000
 LOV  HB    CB   CG1   108.07  3.000
 LOV  CG2   CB   CG1   108.89  3.000
 LOV  HB    CB   CA    107.76  3.000
 LOV  CG2   CB   CA    112.07  3.000
 LOV  CG1   CB   CA    111.80  3.000
 LOV  HG13  CG1  HG12  107.34  3.000
 LOV  HG13  CG1  HG11  107.83  3.000
 LOV  HG12  CG1  HG11  107.47  3.000
 LOV  HG13  CG1  CB    112.44  3.000
 LOV  HG12  CG1  CB    110.74  3.000
 LOV  HG11  CG1  CB    110.82  3.000
 LOV  HG23  CG2  HG22  107.22  3.000
 LOV  HG23  CG2  HG21  107.35  3.000
 LOV  HG22  CG2  HG21  107.61  3.000
 LOV  HG23  CG2  CB    110.76  3.000
 LOV  HG22  CG2  CB    112.94  3.000
 LOV  HG21  CG2  CB    110.72  3.000
 LOV  OXT   C    O     125.80  3.000
 LOV  OXT   C    CA    120.80  1.700
 LOV  O     C    CA    120.80  1.700

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  Var_01  C1A   C1B  C1G  CD1  176.49  30.0  3
 LOV  Var_02  HD21  CD2  C1G  CD1   65.41  30.0  3
 LOV  Var_03  HD11  CD1  C1G  CD2   60.03  30.0  3
 LOV  Var_04  HG11  CG1  CB   CA    57.24  30.0  3
 LOV  Var_05  HG21  CG2  CB   CA   -62.26  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

