# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 10:26:39 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2S)-2-amino-4-[([1~2~,2~2~:2~6~,3~2~-terpyridine]-2~4~-carbonyl)amino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCNC(=O)c1cc(nc(c1)c2ccccn2)c3ccccn3)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
 7WJ  7WJ  '(2S)-2-amino-4-[([1~2~,2~2~:2~6~,3~2~-terpyridine]-2~4~-carbonyl)amino]butanoic acid'  ligand  46  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7WJ
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
 7WJ  C    C  C      0   0.387   6.8218   0.1830  -0.4095
 7WJ  CA   C  CH1    0  -0.219   5.8408  -0.9832  -0.1202
 7WJ  CB   C  CH2    0  -0.466   4.4088  -0.4480  -0.1176
 7WJ  CE   C  C      0   0.534   0.9464  -1.5900   0.3995
 7WJ  O    O  O      0  -0.604   7.6313   0.4951   0.4848
 7WJ  N    N  NH2    0  -0.786   6.0916  -1.7335   1.1000
 7WJ  OE   O  O      0  -0.483   0.9622  -2.6820   0.9496
 7WJ  CG   C  CH2    0  -0.237   3.3672  -1.5507  -0.0285
 7WJ  ND   N  NH1    0  -0.650   2.0327  -0.9869  -0.0957
 7WJ  CQ   C  CR6    0   0.089  -0.3412  -0.8319   0.2479
 7WJ  CR1  C  CR16   0  -0.354  -0.3909   0.5538   0.2271
 7WJ  CR2  C  CR16   0  -0.335  -1.5277  -1.5461   0.1710
 7WJ  CS1  C  CR6    0   0.215  -1.6337   1.1751   0.1223
 7WJ  CS2  C  CR6    0   0.218  -2.7223  -0.8424   0.0487
 7WJ  CT1  C  CR6    0   0.199  -1.7458   2.6540   0.1145
 7WJ  CT3  C  CR6    0   0.194  -4.0201  -1.5515  -0.0636
 7WJ  CU2  C  CR16   0  -0.307  -2.9868   3.2813   0.0342
 7WJ  CU4  C  CR16   0  -0.306  -5.2178  -0.8476  -0.1667
 7WJ  CV1  C  CR16   0  -0.070  -0.6574   4.6614   0.1861
 7WJ  CV2  C  CR16   0  -0.151  -3.0312   4.6658   0.0326
 7WJ  CV3  C  CR16   0  -0.072  -5.1117  -3.5562  -0.1616
 7WJ  CV4  C  CR16   0  -0.151  -6.4005  -1.5608  -0.2713
 7WJ  CW1  C  CR16   0  -0.320  -1.8440   5.3774   0.1098
 7WJ  CW2  C  CR16   0  -0.319  -6.3536  -2.9463  -0.2697
 7WJ  NT2  N  N      0  -0.468  -2.7599   0.4838   0.0300
 7WJ  NU1  N  N      0  -0.434  -0.6071   3.3382   0.1889
 7WJ  NU3  N  N      0  -0.432  -3.9767  -2.8815  -0.0614
 7WJ  H2   H  HCH1   0   0.216   5.9250  -1.6867  -0.9581
 7WJ  H3   H  HCH2   0   0.224   4.2761   0.2449   0.7213
 7WJ  H4   H  HCH2   0   0.233   4.2539   0.1305  -1.0312
 7WJ  H5   H  HNH2   0   0.337   7.0134  -2.1490   1.0410
 7WJ  H6   H  HNH2   0   0.324   6.1636  -1.0741   1.8672
 7WJ  H8   H  HCH2   0   0.228   3.5161  -2.2697  -0.8416
 7WJ  H9   H  HCH2   0   0.243   3.4711  -2.0989   0.9058
 7WJ  H10  H  HNH1   0   0.406   1.9120  -0.1666  -0.6691
 7WJ  H11  H  HCR6   0   0.274   0.4972   1.1638   0.3149
 7WJ  H12  H  HCR6   0   0.272  -1.5322  -2.6259   0.1955
 7WJ  H13  H  HCR6   0   0.281  -3.8911   2.6931  -0.0255
 7WJ  H14  H  HCR6   0   0.280  -5.2187   0.2326  -0.1648
 7WJ  H15  H  HCR6   0   0.266   0.2921   5.1812   0.2481
 7WJ  H16  H  HCR6   0   0.276  -3.9806   5.1810  -0.0290
 7WJ  H17  H  HCR6   0   0.265  -5.0322  -4.6375  -0.1574
 7WJ  H18  H  HCR6   0   0.276  -7.3452  -1.0397  -0.3545
 7WJ  H19  H  HCR6   0   0.275  -1.8315   6.4582   0.1115
 7WJ  H20  H  HCR6   0   0.275  -7.2507  -3.5440  -0.3515
 7WJ  OXT  O  OC    -1  -0.622   6.7051   0.7239  -1.5293

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
 7WJ  CG   CB   single    1.519  0.020  1.519
 7WJ  CG   ND   single    1.450  0.020  1.450
 7WJ  N    CA   single    1.454  0.020  1.454
 7WJ  OE   CE   double    1.223  0.020  1.223
 7WJ  CB   CA   single    1.529  0.020  1.529
 7WJ  ND   CE   single    1.337  0.020  1.337
 7WJ  CE   CQ   single    1.502  0.020  1.502
 7WJ  CA   C    single    1.551  0.020  1.551
 7WJ  CQ   CR2  aromatic  1.387  0.020  1.387
 7WJ  CQ   CR1  aromatic  1.387  0.020  1.387
 7WJ  CR2  CS2  aromatic  1.392  0.020  1.392
 7WJ  CU4  CV4  aromatic  1.385  0.020  1.385
 7WJ  CU4  CT3  aromatic  1.393  0.020  1.393
 7WJ  C    O    deloc     1.246  0.020  1.246
 7WJ  CV4  CW2  aromatic  1.386  0.020  1.386
 7WJ  CR1  CS1  aromatic  1.393  0.020  1.393
 7WJ  CS2  CT3  single    1.483  0.020  1.483
 7WJ  CS2  NT2  aromatic  1.327  0.020  1.327
 7WJ  CT3  NU3  aromatic  1.331  0.020  1.331
 7WJ  CW2  CV3  aromatic  1.388  0.020  1.388
 7WJ  CS1  NT2  aromatic  1.325  0.020  1.325
 7WJ  CS1  CT1  single    1.483  0.020  1.483
 7WJ  NU3  CV3  aromatic  1.324  0.020  1.324
 7WJ  CT1  CU2  aromatic  1.393  0.020  1.393
 7WJ  CT1  NU1  aromatic  1.331  0.020  1.331
 7WJ  CU2  CV2  aromatic  1.385  0.020  1.385
 7WJ  NU1  CV1  aromatic  1.324  0.020  1.324
 7WJ  CV2  CW1  aromatic  1.386  0.020  1.386
 7WJ  CV1  CW1  aromatic  1.388  0.020  1.388
 7WJ  CA   H2   single    0.970  0.020  1.090
 7WJ  CB   H3   single    0.970  0.020  1.090
 7WJ  CB   H4   single    0.970  0.020  1.090
 7WJ  N    H5   single    0.890  0.020  1.040
 7WJ  N    H6   single    0.890  0.020  1.040
 7WJ  CG   H8   single    0.970  0.020  1.090
 7WJ  CG   H9   single    0.970  0.020  1.090
 7WJ  ND   H10  single    0.860  0.020  1.020
 7WJ  CR1  H11  single    0.930  0.020  1.080
 7WJ  CR2  H12  single    0.930  0.020  1.080
 7WJ  CU2  H13  single    0.930  0.020  1.080
 7WJ  CU4  H14  single    0.930  0.020  1.080
 7WJ  CV1  H15  single    0.930  0.020  1.080
 7WJ  CV2  H16  single    0.930  0.020  1.080
 7WJ  CV3  H17  single    0.930  0.020  1.080
 7WJ  CV4  H18  single    0.930  0.020  1.080
 7WJ  CW1  H19  single    0.930  0.020  1.080
 7WJ  CW2  H20  single    0.930  0.020  1.080
 7WJ  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
 7WJ  OXT  C    O    126.56  3.000
 7WJ  OXT  C    CA   115.70  3.000
 7WJ  O    C    CA   117.74  3.000
 7WJ  H2   CA   N    107.26  3.000
 7WJ  H2   CA   CB   107.32  3.000
 7WJ  N    CA   CB   109.92  3.000
 7WJ  H2   CA   C    106.92  3.000
 7WJ  CB   CA   C    109.24  3.000
 7WJ  N    CA   C    115.80  3.000
 7WJ  H4   CB   H3   106.75  3.000
 7WJ  H4   CB   CG   109.64  3.000
 7WJ  H3   CB   CG   109.32  3.000
 7WJ  H4   CB   CA   108.46  3.000
 7WJ  H3   CB   CA   109.64  3.000
 7WJ  CG   CB   CA   112.84  3.000
 7WJ  CQ   CE   ND   115.55  3.000
 7WJ  CQ   CE   OE   120.48  3.000
 7WJ  ND   CE   OE   123.97  3.000
 7WJ  H6   N    H5   104.25  3.000
 7WJ  H6   N    CA   108.15  3.000
 7WJ  H5   N    CA   108.64  3.000
 7WJ  H9   CG   H8   107.08  3.000
 7WJ  H9   CG   ND   108.87  3.000
 7WJ  H8   CG   ND   110.23  3.000
 7WJ  H9   CG   CB   110.52  3.000
 7WJ  H8   CG   CB   109.85  3.000
 7WJ  ND   CG   CB   110.24  3.000
 7WJ  H10  ND   CG   116.93  3.000
 7WJ  H10  ND   CE   118.70  3.000
 7WJ  CG   ND   CE   123.70  3.000
 7WJ  CR2  CQ   CR1  118.89  3.000
 7WJ  CR1  CQ   CE   122.45  3.000
 7WJ  CR2  CQ   CE   118.62  3.000
 7WJ  H11  CR1  CS1  119.17  3.000
 7WJ  H11  CR1  CQ   122.22  3.000
 7WJ  CS1  CR1  CQ   118.59  3.000
 7WJ  H12  CR2  CS2  120.26  3.000
 7WJ  H12  CR2  CQ   121.14  3.000
 7WJ  CS2  CR2  CQ   118.60  3.000
 7WJ  NT2  CS1  CT1  117.11  3.000
 7WJ  CT1  CS1  CR1  120.83  3.000
 7WJ  NT2  CS1  CR1  122.07  3.000
 7WJ  NT2  CS2  CT3  116.87  3.000
 7WJ  NT2  CS2  CR2  122.07  3.000
 7WJ  CT3  CS2  CR2  121.06  3.000
 7WJ  NU1  CT1  CU2  122.28  3.000
 7WJ  NU1  CT1  CS1  116.60  3.000
 7WJ  CU2  CT1  CS1  121.12  3.000
 7WJ  NU3  CT3  CU4  122.22  3.000
 7WJ  NU3  CT3  CS2  116.69  3.000
 7WJ  CU4  CT3  CS2  121.09  3.000
 7WJ  H13  CU2  CV2  121.15  3.000
 7WJ  H13  CU2  CT1  120.24  3.000
 7WJ  CV2  CU2  CT1  118.61  3.000
 7WJ  H14  CU4  CV4  120.95  3.000
 7WJ  H14  CU4  CT3  120.39  3.000
 7WJ  CV4  CU4  CT3  118.65  3.000
 7WJ  H15  CV1  NU1  116.46  3.000
 7WJ  H15  CV1  CW1  120.30  3.000
 7WJ  NU1  CV1  CW1  123.24  3.000
 7WJ  H16  CV2  CW1  120.68  3.000
 7WJ  H16  CV2  CU2  120.27  3.000
 7WJ  CW1  CV2  CU2  119.05  3.000
 7WJ  H17  CV3  NU3  116.43  3.000
 7WJ  H17  CV3  CW2  120.28  3.000
 7WJ  NU3  CV3  CW2  123.29  3.000
 7WJ  H18  CV4  CW2  120.72  3.000
 7WJ  H18  CV4  CU4  120.22  3.000
 7WJ  CW2  CV4  CU4  119.06  3.000
 7WJ  H19  CW1  CV2  121.55  3.000
 7WJ  H19  CW1  CV1  120.39  3.000
 7WJ  CV2  CW1  CV1  118.06  3.000
 7WJ  H20  CW2  CV4  121.63  3.000
 7WJ  H20  CW2  CV3  120.36  3.000
 7WJ  CV4  CW2  CV3  118.01  3.000
 7WJ  CS2  NT2  CS1  119.76  3.000
 7WJ  CV1  NU1  CT1  118.77  3.000
 7WJ  CV3  NU3  CT3  118.77  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
 7WJ  CONST_01  CT3  CS2  CR2  CQ    180.00   0.0  0
 7WJ  CONST_02  NT2  CS2  CR2  CQ      0.00   0.0  0
 7WJ  CONST_03  NT2  CS1  CR1  CQ      0.00   0.0  0
 7WJ  CONST_04  CT1  CS1  CR1  CQ    180.00   0.0  0
 7WJ  CONST_05  CS2  CR2  CQ   CR1     0.00   0.0  0
 7WJ  CONST_06  CS2  NT2  CS1  CR1     0.00   0.0  0
 7WJ  CONST_07  CU2  CT1  CS1  CR1   180.00   0.0  0
 7WJ  CONST_08  NU1  CT1  CS1  CR1     0.00   0.0  0
 7WJ  CONST_09  CS1  CR1  CQ   CR2     0.00   0.0  0
 7WJ  CONST_10  CU4  CT3  CS2  CR2   180.00   0.0  0
 7WJ  CONST_11  NU3  CT3  CS2  CR2     0.00   0.0  0
 7WJ  CONST_12  CS1  NT2  CS2  CR2     0.00   0.0  0
 7WJ  CONST_13  CT3  CS2  NT2  CS1   180.00   0.0  0
 7WJ  CONST_14  CV2  CU2  CT1  CS1   180.00   0.0  0
 7WJ  CONST_15  CV1  NU1  CT1  CS1   180.00   0.0  0
 7WJ  CONST_16  CV4  CU4  CT3  CS2   180.00   0.0  0
 7WJ  CONST_17  CV3  NU3  CT3  CS2   180.00   0.0  0
 7WJ  CONST_18  CT1  CS1  NT2  CS2   180.00   0.0  0
 7WJ  CONST_19  CW1  CV2  CU2  CT1     0.00   0.0  0
 7WJ  CONST_20  CW1  CV1  NU1  CT1     0.00   0.0  0
 7WJ  CONST_21  CW2  CV4  CU4  CT3     0.00   0.0  0
 7WJ  CONST_22  CW2  CV3  NU3  CT3     0.00   0.0  0
 7WJ  CONST_23  NT2  CS1  CT1  CU2     0.00   0.0  0
 7WJ  CONST_24  CV1  NU1  CT1  CU2     0.00   0.0  0
 7WJ  CONST_25  CV1  CW1  CV2  CU2     0.00   0.0  0
 7WJ  CONST_26  CV3  CW2  CV4  CU4     0.00   0.0  0
 7WJ  CONST_27  NT2  CS2  CT3  CU4     0.00   0.0  0
 7WJ  CONST_28  CV3  NU3  CT3  CU4     0.00   0.0  0
 7WJ  CONST_29  NU1  CT1  CU2  CV2     0.00   0.0  0
 7WJ  CONST_30  NU1  CV1  CW1  CV2     0.00   0.0  0
 7WJ  CONST_31  NU3  CT3  CU4  CV4     0.00   0.0  0
 7WJ  CONST_32  NU3  CV3  CW2  CV4     0.00   0.0  0
 7WJ  CONST_33  NU3  CT3  CS2  NT2   180.00   0.0  0
 7WJ  CONST_34  NU1  CT1  CS1  NT2   180.00   0.0  0
 7WJ  CONST_35  CS2  CR2  CQ   CE    180.00   0.0  0
 7WJ  CONST_36  CS1  CR1  CQ   CE    180.00   0.0  0
 7WJ  CONST_37  H12  CR2  CQ   CR1   180.00   0.0  0
 7WJ  CONST_38  H11  CR1  CQ   CR2   180.00   0.0  0
 7WJ  CONST_39  H13  CU2  CT1  CS1     0.00   0.0  0
 7WJ  CONST_40  H14  CU4  CT3  CS2     0.00   0.0  0
 7WJ  CONST_41  H16  CV2  CU2  CT1   180.00   0.0  0
 7WJ  CONST_42  H15  CV1  NU1  CT1   180.00   0.0  0
 7WJ  CONST_43  H18  CV4  CU4  CT3   180.00   0.0  0
 7WJ  CONST_44  H17  CV3  NU3  CT3   180.00   0.0  0
 7WJ  CONST_45  H19  CW1  CV2  CU2   180.00   0.0  0
 7WJ  CONST_46  H20  CW2  CV4  CU4   180.00   0.0  0
 7WJ  CONST_47  CQ   CE   ND   CG    180.00   0.0  0
 7WJ  CONST_48  H10  ND   CE   CQ      0.00   0.0  0
 7WJ  CONST_49  CG   ND   CE   OE      0.00   0.0  0
 7WJ  Var_01    CR2  CQ   CE   OE    -28.18  30.0  2
 7WJ  Var_02    ND   CG   CB   CA   -177.23  30.0  1
 7WJ  Var_03    CE   ND   CG   CB   -156.12  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
 7WJ  chir_01  CA  N  CB  C  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
 7WJ  plan-1  CE   0.020
 7WJ  plan-1  CQ   0.020
 7WJ  plan-1  CR1  0.020
 7WJ  plan-1  CR2  0.020
 7WJ  plan-1  CS1  0.020
 7WJ  plan-1  CS2  0.020
 7WJ  plan-1  CT1  0.020
 7WJ  plan-1  CT3  0.020
 7WJ  plan-1  NT2  0.020
 7WJ  plan-1  H11  0.020
 7WJ  plan-1  H12  0.020
 7WJ  plan-2  CS1  0.020
 7WJ  plan-2  CT1  0.020
 7WJ  plan-2  CU2  0.020
 7WJ  plan-2  CV1  0.020
 7WJ  plan-2  CV2  0.020
 7WJ  plan-2  CW1  0.020
 7WJ  plan-2  NU1  0.020
 7WJ  plan-2  H13  0.020
 7WJ  plan-2  H15  0.020
 7WJ  plan-2  H16  0.020
 7WJ  plan-2  H19  0.020
 7WJ  plan-3  CS2  0.020
 7WJ  plan-3  CT3  0.020
 7WJ  plan-3  CU4  0.020
 7WJ  plan-3  CV3  0.020
 7WJ  plan-3  CV4  0.020
 7WJ  plan-3  CW2  0.020
 7WJ  plan-3  NU3  0.020
 7WJ  plan-3  H14  0.020
 7WJ  plan-3  H17  0.020
 7WJ  plan-3  H18  0.020
 7WJ  plan-3  H20  0.020
 7WJ  plan-4  CE   0.020
 7WJ  plan-4  OE   0.020
 7WJ  plan-4  CG   0.020
 7WJ  plan-4  ND   0.020
 7WJ  plan-4  CQ   0.020
 7WJ  plan-4  H10  0.020
 7WJ  plan-5  C    0.020
 7WJ  plan-5  CA   0.020
 7WJ  plan-5  O    0.020
 7WJ  plan-5  OXT  0.020

