# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:04:35 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 6-(benzyloxy)-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCOCc1ccccc1)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
 NLB  NLB  6-(benzyloxy)-L-norleucine  L-peptide  35  17  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_NLB
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
 NLB  N    N  NH2    0  -0.785  -42.0212  106.8121  -3.9388
 NLB  CA   C  CH1    0  -0.213  -42.8132  105.5944  -3.8259
 NLB  CB   C  CH2    0  -0.412  -43.7031  105.4302  -5.0612
 NLB  CG   C  CH2    0  -0.412  -44.6859  106.5717  -5.2889
 NLB  CD   C  CH2    0  -0.460  -45.5751  106.3405  -6.5047
 NLB  CE   C  CH2    0  -0.122  -46.5781  107.4610  -6.6884
 NLB  C    C  C      0   0.381  -42.0008  104.2913  -3.5928
 NLB  O    O  O      0  -0.602  -40.7614  104.3556  -3.7156
 NLB  O1   O  O2     0  -0.480  -47.3554  107.2122  -7.8402
 NLB  C2   C  CH2    0  -0.217  -48.3594  108.1697  -8.0563
 NLB  C3   C  CR6    0   0.049  -49.4922  108.0891  -7.0618
 NLB  C4   C  CR16   0  -0.281  -50.0340  106.8544  -6.7081
 NLB  C5   C  CR16   0  -0.240  -51.0926  106.7785  -5.8155
 NLB  C6   C  CR16   0  -0.267  -51.6290  107.9370  -5.2651
 NLB  C7   C  CR16   0  -0.239  -51.0959  109.1702  -5.6117
 NLB  C8   C  CR16   0  -0.300  -50.0294  109.2417  -6.5002
 NLB  H1   H  HNH2   0   0.330  -41.4972  106.9366  -3.0808
 NLB  H2   H  HNH2   0   0.320  -41.3091  106.6539  -4.6433
 NLB  H4   H  HCH1   0   0.202  -43.4788  105.7200  -2.9623
 NLB  H5   H  HCH2   0   0.213  -44.2614  104.4964  -4.9656
 NLB  H6   H  HCH2   0   0.201  -43.0671  105.3169  -5.9487
 NLB  H7   H  HCH2   0   0.213  -44.1421  107.5123  -5.4047
 NLB  H8   H  HCH2   0   0.204  -45.3114  106.6880  -4.3964
 NLB  H9   H  HCH2   0   0.216  -46.1114  105.3925  -6.3955
 NLB  H10  H  HCH2   0   0.217  -44.9551  106.2513  -7.4023
 NLB  H11  H  HCH2   0   0.194  -46.0552  108.4241  -6.7849
 NLB  H12  H  HCH2   0   0.197  -47.2115  107.5342  -5.7941
 NLB  OXT  O  OC    -1  -0.618  -42.6710  103.2748  -3.3123
 NLB  H14  H  HCH2   0   0.215  -47.9450  109.1877  -8.0566
 NLB  H15  H  HCH2   0   0.245  -48.7452  107.9849  -9.0629
 NLB  H16  H  HCR6   0   0.248  -49.6244  105.9445  -7.1295
 NLB  H17  H  HCR6   0   0.252  -51.5025  105.8125  -5.5492
 NLB  H18  H  HCR6   0   0.252  -52.4557  107.8766  -4.5690
 NLB  H19  H  HCR6   0   0.252  -51.5023  110.0778  -5.1842
 NLB  H20  H  HCR6   0   0.248  -49.6091  110.2078  -6.7559

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
 NLB  C2  O1   single    1.404  0.020  1.404
 NLB  C2  C3   single    1.510  0.020  1.510
 NLB  O1  CE   single    1.412  0.020  1.412
 NLB  C3  C8   aromatic  1.390  0.020  1.390
 NLB  C3  C4   aromatic  1.394  0.020  1.394
 NLB  CE  CD   single    1.515  0.020  1.515
 NLB  C8  C7   aromatic  1.390  0.020  1.390
 NLB  CD  CG   single    1.524  0.020  1.524
 NLB  C4  C5   aromatic  1.387  0.020  1.387
 NLB  C7  C6   aromatic  1.387  0.020  1.387
 NLB  C5  C6   aromatic  1.390  0.020  1.390
 NLB  CG  CB   single    1.523  0.020  1.523
 NLB  CB  CA   single    1.530  0.020  1.530
 NLB  O   C    deloc     1.231  0.020  1.231
 NLB  CA  N    single    1.458  0.019  1.458
 NLB  CA  C    single    1.525  0.021  1.525
 NLB  N   H1   single    0.890  0.020  1.040
 NLB  N   H2   single    0.890  0.020  1.040
 NLB  CA  H4   single    0.970  0.020  1.090
 NLB  CB  H5   single    0.970  0.020  1.090
 NLB  CB  H6   single    0.970  0.020  1.090
 NLB  CG  H7   single    0.970  0.020  1.090
 NLB  CG  H8   single    0.970  0.020  1.090
 NLB  CD  H9   single    0.970  0.020  1.090
 NLB  CD  H10  single    0.970  0.020  1.090
 NLB  CE  H11  single    0.970  0.020  1.090
 NLB  CE  H12  single    0.970  0.020  1.090
 NLB  C   OXT  deloc     1.250  0.020  1.250
 NLB  C2  H14  single    0.970  0.020  1.090
 NLB  C2  H15  single    0.970  0.020  1.090
 NLB  C4  H16  single    0.930  0.020  1.080
 NLB  C5  H17  single    0.930  0.020  1.080
 NLB  C6  H18  single    0.930  0.020  1.080
 NLB  C7  H19  single    0.930  0.020  1.080
 NLB  C8  H20  single    0.930  0.020  1.080

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
 NLB  H2   N   H1   104.14  3.000
 NLB  H2   N   CA   107.77  3.000
 NLB  H1   N   CA   108.56  3.000
 NLB  H4   CA  C    107.16  3.000
 NLB  H4   CA  CB   107.13  3.000
 NLB  C    CA  CB   110.10  1.900
 NLB  H4   CA  N    107.16  3.000
 NLB  C    CA  N    111.00  2.800
 NLB  CB   CA  N    110.50  1.700
 NLB  H6   CB  H5   106.18  3.000
 NLB  H6   CB  CG   109.28  3.000
 NLB  H5   CB  CG   108.90  3.000
 NLB  H6   CB  CA   109.06  3.000
 NLB  H5   CB  CA   108.55  3.000
 NLB  CG   CB  CA   114.53  3.000
 NLB  H8   CG  H7   106.20  3.000
 NLB  H8   CG  CD   109.43  3.000
 NLB  H7   CG  CD   109.66  3.000
 NLB  H8   CG  CB   109.02  3.000
 NLB  H7   CG  CB   109.87  3.000
 NLB  CD   CG  CB   112.46  3.000
 NLB  H10  CD  H9   106.78  3.000
 NLB  H10  CD  CE   109.62  3.000
 NLB  H9   CD  CE   109.16  3.000
 NLB  H10  CD  CG   109.64  3.000
 NLB  H9   CD  CG   109.74  3.000
 NLB  CE   CD  CG   111.77  3.000
 NLB  H12  CE  H11  106.69  3.000
 NLB  H12  CE  O1   111.01  3.000
 NLB  H11  CE  O1   110.15  3.000
 NLB  H12  CE  CD   109.41  3.000
 NLB  H11  CE  CD   110.09  3.000
 NLB  O1   CE  CD   109.46  3.000
 NLB  OXT  C   O    126.66  3.000
 NLB  OXT  C   CA   115.83  3.000
 NLB  O    C   CA   120.80  1.700
 NLB  C2   O1  CE   113.52  3.000
 NLB  H15  C2  H14  106.81  3.000
 NLB  H15  C2  C3   109.43  3.000
 NLB  H14  C2  C3   109.43  3.000
 NLB  H15  C2  O1   106.17  3.000
 NLB  H14  C2  O1   111.23  3.000
 NLB  C3   C2  O1   113.50  3.000
 NLB  C8   C3  C4   118.79  3.000
 NLB  C4   C3  C2   120.41  3.000
 NLB  C8   C3  C2   120.79  3.000
 NLB  H16  C4  C5   119.54  3.000
 NLB  H16  C4  C3   119.89  3.000
 NLB  C5   C4  C3   120.57  3.000
 NLB  H17  C5  C6   120.01  3.000
 NLB  H17  C5  C4   119.75  3.000
 NLB  C6   C5  C4   120.25  3.000
 NLB  H18  C6  C7   120.25  3.000
 NLB  H18  C6  C5   120.18  3.000
 NLB  C7   C6  C5   119.57  3.000
 NLB  H19  C7  C8   119.83  3.000
 NLB  H19  C7  C6   120.15  3.000
 NLB  C8   C7  C6   120.02  3.000
 NLB  H20  C8  C7   119.61  3.000
 NLB  H20  C8  C3   119.58  3.000
 NLB  C7   C8  C3   120.80  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
 NLB  CONST_01  C6   C7  C8  C3     0.00   0.0  0
 NLB  CONST_02  C6   C5  C4  C3     0.00   0.0  0
 NLB  CONST_03  C7   C8  C3  C4     0.00   0.0  0
 NLB  CONST_04  C7   C6  C5  C4     0.00   0.0  0
 NLB  CONST_05  C8   C3  C4  C5     0.00   0.0  0
 NLB  CONST_06  C8   C7  C6  C5     0.00   0.0  0
 NLB  CONST_07  C7   C8  C3  C2   180.00   0.0  0
 NLB  CONST_08  C5   C4  C3  C2   180.00   0.0  0
 NLB  CONST_09  H19  C7  C8  C3   180.00   0.0  0
 NLB  CONST_10  H17  C5  C4  C3   180.00   0.0  0
 NLB  CONST_11  H20  C8  C3  C4   180.00   0.0  0
 NLB  CONST_12  H18  C6  C5  C4   180.00   0.0  0
 NLB  CONST_13  H16  C4  C5  C6   180.00   0.0  0
 NLB  Var_01    C8   C3  C2  O1   136.93  30.0  2
 NLB  Var_02    C3   C2  O1  CE   -70.98  30.0  1
 NLB  Var_03    CD   CG  CB  CA  -178.28  30.0  1
 NLB  Var_04    CE   CD  CG  CB   178.02  30.0  1
 NLB  Var_05    O1   CE  CD  CG   178.80  30.0  2

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
 NLB  chir_01  CA  CB  N  C  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
 NLB  plan-1  C2   0.020
 NLB  plan-1  C3   0.020
 NLB  plan-1  C4   0.020
 NLB  plan-1  C5   0.020
 NLB  plan-1  C6   0.020
 NLB  plan-1  C7   0.020
 NLB  plan-1  C8   0.020
 NLB  plan-1  H16  0.020
 NLB  plan-1  H17  0.020
 NLB  plan-1  H18  0.020
 NLB  plan-1  H19  0.020
 NLB  plan-1  H20  0.020
 NLB  plan-2  CA   0.020
 NLB  plan-2  C    0.020
 NLB  plan-2  O    0.020
 NLB  plan-2  OXT  0.020

