# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 09:50:46 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{S})-5-[4-(aminomethyl)-1,2,3-triazol-1-yl]-2-azanyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cn(CCC[C@H](N)C(O)=O)nn1
#
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
 5MW  5MW  '(2~{S})-5-[4-(aminomethyl)-1,2,3-triazol-1-yl]-2-azanyl-pentanoic acid'  L-peptide  29  15  .  2022-07-23  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_5MW
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
 5MW  N    N  NH2    0  -0.785  -2.9004   1.8649  -0.4851
 5MW  CA   C  CH1    0  -0.213  -3.1257   0.4281  -0.4921
 5MW  C    C  C      0   0.385  -4.5402  -0.0322  -0.0536
 5MW  O    O  O      0  -0.607  -5.3224   0.8329   0.3863
 5MW  CB   C  CH2    0  -0.430  -2.0707  -0.2752   0.3633
 5MW  CG   C  CH2    0  -0.421  -0.6409  -0.0017  -0.0813
 5MW  CD   C  CH2    0  -0.291   0.3521  -0.7742   0.7749
 5MW  N1   N  N      0  -0.319   3.4345  -1.0201  -0.8347
 5MW  C1   C  CR5    0   0.150   3.6910   0.1096  -0.1399
 5MW  C2   C  CR15   0  -0.084   2.5797   0.3887   0.6162
 5MW  N2   N  NR5    0  -0.247   1.7212  -0.6019   0.3260
 5MW  N3   N  N      0  -0.113   2.2471  -1.4366  -0.5514
 5MW  N5   N  NH2    0  -0.793   5.9284   0.2812   0.7870
 5MW  H1   H  HNH2   0   0.334  -3.5890   2.3012  -1.0862
 5MW  H2   H  HNH2   0   0.322  -3.1203   2.2176   0.4401
 5MW  H4   H  HCH1   0   0.212  -2.9860   0.0843  -1.5252
 5MW  H6   H  HCH2   0   0.213  -2.1928   0.0303   1.4101
 5MW  H7   H  HCH2   0   0.226  -2.2610  -1.3499   0.3336
 5MW  H8   H  HCH2   0   0.226  -0.5166  -0.2979  -1.1272
 5MW  H9   H  HCH2   0   0.235  -0.4269   1.0671  -0.0251
 5MW  H10  H  HCH2   0   0.266   0.3010  -0.4562   1.8162
 5MW  H11  H  HCH2   0   0.268   0.1424  -1.8432   0.7478
 5MW  H12  H  HCR5   0   0.304   2.3517   1.1825   1.3075
 5MW  H13  H  HCH2   0   0.218   5.3761   0.7501  -1.2382
 5MW  H14  H  HCH2   0   0.239   4.8479   1.8726   0.0026
 5MW  H15  H  HNH2   0   0.342   6.1593  -0.6751   0.5464
 5MW  H16  H  HNH2   0   0.351   6.8002   0.7936   0.7318
 5MW  OXT  O  OC    -1  -0.623  -4.7779  -1.2525  -0.1774
 5MW  C8   C  CH2    0  -0.365   5.0032   0.8134  -0.2083

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
 5MW  C8  C1   single    1.491  0.020  1.491
 5MW  C8  N5   single    1.459  0.020  1.459
 5MW  C1  C2   aromatic  1.373  0.020  1.373
 5MW  C1  N1   aromatic  1.351  0.020  1.351
 5MW  C2  N2   aromatic  1.343  0.020  1.343
 5MW  N1  N3   aromatic  1.290  0.020  1.290
 5MW  N2  N3   aromatic  1.320  0.020  1.320
 5MW  N2  CD   single    1.451  0.020  1.451
 5MW  CG  CD   single    1.522  0.020  1.522
 5MW  CG  CB   single    1.522  0.020  1.522
 5MW  CB  CA   single    1.530  0.020  1.530
 5MW  CA  C    single    1.525  0.021  1.525
 5MW  CA  N    single    1.458  0.019  1.458
 5MW  C   O    deloc     1.231  0.020  1.231
 5MW  N   H1   single    0.890  0.020  1.040
 5MW  N   H2   single    0.890  0.020  1.040
 5MW  CA  H4   single    0.970  0.020  1.090
 5MW  CB  H6   single    0.970  0.020  1.090
 5MW  CB  H7   single    0.970  0.020  1.090
 5MW  CG  H8   single    0.970  0.020  1.090
 5MW  CG  H9   single    0.970  0.020  1.090
 5MW  CD  H10  single    0.970  0.020  1.090
 5MW  CD  H11  single    0.970  0.020  1.090
 5MW  C2  H12  single    0.930  0.020  1.080
 5MW  C8  H13  single    0.970  0.020  1.090
 5MW  C8  H14  single    0.970  0.020  1.090
 5MW  N5  H15  single    0.890  0.020  1.040
 5MW  N5  H16  single    0.890  0.020  1.040
 5MW  C   OXT  deloc     1.249  0.020  1.249

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
 5MW  H2   N   H1   104.13  3.000
 5MW  H2   N   CA   108.32  3.000
 5MW  H1   N   CA   108.50  3.000
 5MW  H4   CA  CB   107.13  3.000
 5MW  H4   CA  C    106.82  3.000
 5MW  CB   CA  C    110.10  1.900
 5MW  H4   CA  N    107.11  3.000
 5MW  C    CA  N    111.00  2.800
 5MW  CB   CA  N    110.50  1.700
 5MW  OXT  C   O    126.40  3.000
 5MW  OXT  C   CA   115.81  3.000
 5MW  O    C   CA   120.80  1.700
 5MW  H7   CB  H6   106.30  3.000
 5MW  H7   CB  CG   109.43  3.000
 5MW  H6   CB  CG   109.45  3.000
 5MW  H7   CB  CA   108.50  3.000
 5MW  H6   CB  CA   109.20  3.000
 5MW  CG   CB  CA   113.70  3.000
 5MW  H9   CG  H8   106.98  3.000
 5MW  H9   CG  CD   109.89  3.000
 5MW  H8   CG  CD   109.05  3.000
 5MW  H9   CG  CB   110.19  3.000
 5MW  H8   CG  CB   109.71  3.000
 5MW  CD   CG  CB   110.94  3.000
 5MW  H11  CD  H10  107.52  3.000
 5MW  H11  CD  N2   106.88  3.000
 5MW  H10  CD  N2   107.77  3.000
 5MW  H11  CD  CG   111.00  3.000
 5MW  H10  CD  CG   111.03  3.000
 5MW  N2   CD  CG   112.41  3.000
 5MW  N3   N1  C1   109.38  3.000
 5MW  C8   C1  C2   129.93  3.000
 5MW  C2   C1  N1   107.43  3.000
 5MW  C8   C1  N1   122.58  3.000
 5MW  H12  C2  N2   123.17  3.000
 5MW  H12  C2  C1   132.44  3.000
 5MW  N2   C2  C1   104.39  3.000
 5MW  N3   N2  C2   110.82  3.000
 5MW  N3   N2  CD   120.42  3.000
 5MW  C2   N2  CD   128.61  3.000
 5MW  N2   N3  N1   107.97  3.000
 5MW  H16  N5  H15  105.58  3.000
 5MW  H16  N5  C8   108.91  3.000
 5MW  H15  N5  C8   109.08  3.000
 5MW  H14  C8  H13  106.61  3.000
 5MW  H14  C8  N5   108.21  3.000
 5MW  H13  C8  N5   113.81  3.000
 5MW  H14  C8  C1   108.91  3.000
 5MW  H13  C8  C1   108.36  3.000
 5MW  N5   C8  C1   110.77  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
 5MW  CONST_01  N2   C2  C1  N1     0.00   0.0  0
 5MW  CONST_02  C2   N2  N3  N1     0.00   0.0  0
 5MW  CONST_03  N3   N2  C2  C1     0.00   0.0  0
 5MW  CONST_04  N2   N3  N1  C1     0.00   0.0  0
 5MW  CONST_05  N3   N1  C1  C2     0.00   0.0  0
 5MW  CONST_06  C1   C2  N2  CD   180.00   0.0  0
 5MW  CONST_07  N1   N3  N2  CD   180.00   0.0  0
 5MW  CONST_08  C8   C1  C2  N2   180.00   0.0  0
 5MW  CONST_09  C8   C1  N1  N3   180.00   0.0  0
 5MW  CONST_10  H12  C2  C1  N1   180.00   0.0  0
 5MW  Var_01    C2   N2  CD  CG    84.15  30.0  1
 5MW  Var_02    N5   C8  C1  N1   -88.20  30.0  1
 5MW  Var_03    N2   CD  CG  CB   176.42  30.0  3
 5MW  Var_04    H15  N5  C8  C1    66.66  30.0  3
 5MW  Var_05    CD   CG  CB  CA  -177.71  30.0  1

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
 5MW  chir_01  CA  CB  C  N  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
 5MW  plan-1  CD   0.020
 5MW  plan-1  N1   0.020
 5MW  plan-1  C1   0.020
 5MW  plan-1  C2   0.020
 5MW  plan-1  N2   0.020
 5MW  plan-1  N3   0.020
 5MW  plan-1  H12  0.020
 5MW  plan-1  C8   0.020
 5MW  plan-2  CA   0.020
 5MW  plan-2  C    0.020
 5MW  plan-2  O    0.020
 5MW  plan-2  OXT  0.020

