# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:07:41 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  30  15  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.776  -2.9552   1.8059  -0.5708
 5MW  CA   C  CH1   0  -0.208  -3.1421   0.3793  -0.4764
 5MW  C    C  C     0   0.523  -4.5311  -0.0223   0.0065
 5MW  O    O  O     0  -0.439  -5.3310   0.7360   0.4952
 5MW  CB   C  CH2   0  -0.444  -2.0839  -0.2542   0.4366
 5MW  CG   C  CH2   0  -0.424  -0.6652   0.0159  -0.0438
 5MW  CD   C  CH2   0  -0.292   0.3462  -0.7190   0.8244
 5MW  N1   N  N     0  -0.317   3.3611  -0.9159  -0.9095
 5MW  C1   C  CR5   0   0.152   3.6807   0.1388  -0.1282
 5MW  C2   C  CR15  0  -0.084   2.6060   0.3856   0.6893
 5MW  N2   N  NR5   0  -0.249   1.7038  -0.5474   0.3445
 5MW  N3   N  N     0  -0.111   2.1702  -1.3177  -0.6209
 5MW  N5   N  NH2   0  -0.793   5.9647   0.1243   0.6942
 5MW  H1   H  HNH2  0   0.355  -3.5990   2.2015  -1.2436
 5MW  H2   H  HNH2  0   0.343  -3.1631   2.2487   0.3160
 5MW  H4   H  HCH1  0   0.271  -3.0163  -0.0455  -1.4784
 5MW  H6   H  HCH2  0   0.239  -2.2122   0.1251   1.4563
 5MW  H7   H  HCH2  0   0.249  -2.2474  -1.3330   0.4856
 5MW  H8   H  HCH2  0   0.237  -0.5570  -0.3194  -1.0790
 5MW  H9   H  HCH2  0   0.246  -0.4578   1.0867  -0.0303
 5MW  H10  H  HCH2  0   0.270   0.3122  -0.3641   1.8540
 5MW  H11  H  HCH2  0   0.272   0.1426  -1.7896   0.8398
 5MW  H12  H  HCR5  0   0.305   2.4305   1.1206   1.4568
 5MW  H13  H  HCH2  0   0.218   5.3364   0.8511  -1.2293
 5MW  H14  H  HCH2  0   0.240   4.9091   1.8334   0.1594
 5MW  H15  H  HNH2  0   0.342   6.1632  -0.7941   0.3161
 5MW  H16  H  HNH2  0   0.352   6.8453   0.6239   0.6713
 5MW  OXT  O  OH1   0  -0.593  -4.7652  -1.3181  -0.1650
 5MW  H3   H  HOH1  0   0.481  -5.6440  -1.5493   0.1724
 5MW  C8   C  CH2   0  -0.367   5.0142   0.8026  -0.1814

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    1.460  0.020  1.460
 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    1.450  0.020  1.450
 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    double    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  single    1.328  0.020  1.328
 5MW  OXT  H3   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
 5MW  H2   N    H1   106.30  3.000
 5MW  H2   N    CA   110.40  3.000
 5MW  H1   N    CA   110.36  3.000
 5MW  H4   CA   CB   107.75  3.000
 5MW  H4   CA   C    106.99  3.000
 5MW  CB   CA   C    110.10  1.900
 5MW  H4   CA   N    107.99  3.000
 5MW  C    CA   N    111.00  2.800
 5MW  CB   CA   N    110.50  1.700
 5MW  OXT  C    O    123.31  3.000
 5MW  OXT  C    CA   112.13  3.000
 5MW  O    C    CA   120.80  1.700
 5MW  H7   CB   H6   106.42  3.000
 5MW  H7   CB   CG   109.21  3.000
 5MW  H6   CB   CG   109.97  3.000
 5MW  H7   CB   CA   109.34  3.000
 5MW  H6   CB   CA   109.27  3.000
 5MW  CG   CB   CA   112.45  3.000
 5MW  H9   CG   H8   107.09  3.000
 5MW  H9   CG   CD   109.91  3.000
 5MW  H8   CG   CD   109.04  3.000
 5MW  H9   CG   CB   110.34  3.000
 5MW  H8   CG   CB   109.67  3.000
 5MW  CD   CG   CB   110.71  3.000
 5MW  H11  CD   H10  107.50  3.000
 5MW  H11  CD   N2   107.21  3.000
 5MW  H10  CD   N2   107.66  3.000
 5MW  H11  CD   CG   110.99  3.000
 5MW  H10  CD   CG   111.16  3.000
 5MW  N2   CD   CG   112.10  3.000
 5MW  N3   N1   C1   109.40  3.000
 5MW  C8   C1   C2   129.91  3.000
 5MW  C2   C1   N1   107.44  3.000
 5MW  C8   C1   N1   122.59  3.000
 5MW  H12  C2   N2   123.20  3.000
 5MW  H12  C2   C1   132.43  3.000
 5MW  N2   C2   C1   104.37  3.000
 5MW  N3   N2   C2   110.84  3.000
 5MW  N3   N2   CD   120.25  3.000
 5MW  C2   N2   CD   128.77  3.000
 5MW  N2   N3   N1   107.95  3.000
 5MW  H16  N5   H15  105.58  3.000
 5MW  H16  N5   C8   108.87  3.000
 5MW  H15  N5   C8   108.97  3.000
 5MW  H3   OXT  C    110.34  3.000
 5MW  H14  C8   H13  106.55  3.000
 5MW  H14  C8   N5   108.33  3.000
 5MW  H13  C8   N5   113.72  3.000
 5MW  H14  C8   C1   108.88  3.000
 5MW  H13  C8   C1   108.45  3.000
 5MW  N5   C8   C1   110.75  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  CONST_11  H3   OXT  C   CA   180.00   0.0  0
 5MW  Var_01    C2   N2   CD  CG    91.74  30.0  2
 5MW  Var_02    N5   C8   C1  N1   -86.17  30.0  1
 5MW  Var_03    N2   CD   CG  CB   176.54  30.0  3
 5MW  Var_04    H15  N5   C8  C1    68.07  30.0  3
 5MW  Var_05    CD   CG   CB  CA  -175.55  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
 5MW  plan-2  H3   0.020

