# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:56:32 2021
#   Inital geometry file: a 104 line input string
#   Ligand name: (2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](Cc1ccc(OCc2coc(CN)c2)cc1)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
 L6K  L6K  '(2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic acid'  ligand  42  22  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_L6K
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
 L6K  C1   C  CH2   0  -0.391  -6.1282  -32.3932  -54.7721
 L6K  O1   O  O     0  -0.410  -4.4967  -30.6418  -54.3125
 L6K  C2   C  CR5   0   0.382  -5.0257  -31.8331  -53.9480
 L6K  O2   O  O2    0  -0.471  -3.1935  -31.3245  -50.1671
 L6K  C3   C  CR15  0  -0.422  -4.3936  -32.2913  -52.8418
 L6K  C4   C  CR5   0   0.036  -3.4035  -31.3140  -52.5026
 L6K  C5   C  CR15  0  -0.043  -3.5242  -30.3377  -53.4318
 L6K  C6   C  CR6   0   0.136  -1.3601  -31.7150  -46.4496
 L6K  N2   N  NH1   0  -0.570   0.4001  -29.6396  -45.2230
 L6K  C15  C  CH1   0  -0.216  -0.5252  -30.4446  -44.4554
 L6K  C12  C  CH2   0  -0.531  -0.7474  -31.8235  -45.0832
 L6K  C11  C  CR16  0  -0.287  -0.5868  -31.6751  -47.6011
 L6K  C10  C  CR16  0  -0.373  -1.1549  -31.5490  -48.8649
 L6K  C7   C  CR16  0  -0.292  -2.7433  -31.6174  -46.6001
 L6K  C8   C  CR16  0  -0.335  -3.3303  -31.4875  -47.8455
 L6K  C9   C  CR6   0   0.369  -2.5377  -31.4519  -48.9934
 L6K  C13  C  CH2   0  -0.285  -2.4430  -31.3580  -51.3719
 L6K  N1   N  NH2   0  -0.794  -7.2649  -31.4858  -54.8290
 L6K  C35  C  C     0   0.540  -0.1344  -30.5686  -42.9825
 L6K  O36  O  O     0  -0.436   0.0411  -31.6010  -42.3854
 L6K  O37  O  OH1   0  -0.595   0.0001  -29.3736  -42.4166
 L6K  H1   H  HCH2  0   0.227  -6.3563  -33.3868  -54.3667
 L6K  H2   H  HCH2  0   0.247  -5.7732  -32.5561  -55.7938
 L6K  H3   H  HCR5  0   0.259  -4.6046  -33.2166  -52.3286
 L6K  H4   H  HCR5  0   0.282  -2.9995  -29.4067  -53.5814
 L6K  H5   H  HCH3  0   0.243   2.3823  -29.3497  -45.7680
 L6K  H6   H  HCH3  0   0.201   2.2259  -29.9228  -44.1092
 L6K  H7   H  HCH3  0   0.230   1.9589  -31.0226  -45.4639
 L6K  H10  H  HCH1  0   0.291  -1.4853  -29.9155  -44.4679
 L6K  H11  H  HCH2  0   0.257  -1.4067  -32.4021  -44.4336
 L6K  H12  H  HCH2  0   0.251   0.1941  -32.3762  -45.1306
 L6K  H13  H  HCR6  0   0.244   0.4910  -31.7487  -47.5247
 L6K  H14  H  HCR6  0   0.277  -0.5018  -31.5264  -49.7267
 L6K  H15  H  HCR6  0   0.246  -3.3809  -31.6491  -45.7238
 L6K  H16  H  HCR6  0   0.257  -4.4074  -31.4201  -47.9382
 L6K  H17  H  HCH2  0   0.238  -1.8434  -32.2739  -51.4158
 L6K  H18  H  HCH2  0   0.240  -1.7528  -30.5093  -51.4274
 L6K  H19  H  HNH2  0   0.355  -7.9599  -31.8695  -55.4566
 L6K  H20  H  HNH2  0   0.344  -7.7075  -31.4433  -53.9193
 L6K  H22  H  HOH1  0   0.479   0.2637  -29.4726  -41.4895
 L6K  H8   H  HNH1  0   0.359   0.2774  -28.6617  -45.0028
 L6K  C16  C  CH3   0  -0.537   1.7988  -30.0012  -45.1184

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
 L6K  N1   C1   single    1.456  0.020  1.456
 L6K  O1   C5   aromatic  1.347  0.020  1.347
 L6K  O1   C2   aromatic  1.354  0.020  1.354
 L6K  C1   C2   single    1.486  0.020  1.486
 L6K  C5   C4   aromatic  1.353  0.020  1.353
 L6K  C2   C3   aromatic  1.354  0.020  1.354
 L6K  C4   C3   aromatic  1.432  0.020  1.432
 L6K  C4   C13  single    1.484  0.020  1.484
 L6K  C13  O2   single    1.420  0.020  1.420
 L6K  O2   C9   single    1.351  0.020  1.351
 L6K  C9   C10  aromatic  1.392  0.020  1.392
 L6K  C9   C8   aromatic  1.395  0.020  1.395
 L6K  C10  C11  aromatic  1.391  0.020  1.391
 L6K  C8   C7   aromatic  1.383  0.020  1.383
 L6K  C11  C6   aromatic  1.388  0.020  1.388
 L6K  C7   C6   aromatic  1.395  0.020  1.395
 L6K  C6   C12  single    1.501  0.020  1.501
 L6K  C12  C15  single    1.531  0.020  1.531
 L6K  N2   C16  single    1.449  0.020  1.449
 L6K  N2   C15  single    1.447  0.020  1.447
 L6K  C15  C35  single    1.529  0.020  1.529
 L6K  C35  O36  double    1.206  0.020  1.206
 L6K  C35  O37  single    1.329  0.020  1.329
 L6K  C1   H1   single    0.970  0.020  1.090
 L6K  C1   H2   single    0.970  0.020  1.090
 L6K  C3   H3   single    0.930  0.020  1.080
 L6K  C5   H4   single    0.930  0.020  1.080
 L6K  C16  H5   single    0.970  0.020  1.090
 L6K  C16  H6   single    0.970  0.020  1.090
 L6K  C16  H7   single    0.970  0.020  1.090
 L6K  N2   H8   single    0.890  0.020  1.040
 L6K  C15  H10  single    0.970  0.020  1.090
 L6K  C12  H11  single    0.970  0.020  1.090
 L6K  C12  H12  single    0.970  0.020  1.090
 L6K  C11  H13  single    0.930  0.020  1.080
 L6K  C10  H14  single    0.930  0.020  1.080
 L6K  C7   H15  single    0.930  0.020  1.080
 L6K  C8   H16  single    0.930  0.020  1.080
 L6K  C13  H17  single    0.970  0.020  1.090
 L6K  C13  H18  single    0.970  0.020  1.090
 L6K  N1   H19  single    0.890  0.020  1.040
 L6K  N1   H20  single    0.890  0.020  1.040
 L6K  O37  H22  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
 L6K  H2   C1   H1   106.13  3.000
 L6K  H2   C1   N1   108.05  3.000
 L6K  H1   C1   N1   114.62  3.000
 L6K  H2   C1   C2   109.47  3.000
 L6K  H1   C1   C2   106.90  3.000
 L6K  N1   C1   C2   111.48  3.000
 L6K  C5   O1   C2   107.75  3.000
 L6K  C3   C2   O1   109.60  3.000
 L6K  C3   C2   C1   132.21  3.000
 L6K  O1   C2   C1   118.19  3.000
 L6K  C13  O2   C9   118.59  3.000
 L6K  H3   C3   C4   127.44  3.000
 L6K  H3   C3   C2   125.98  3.000
 L6K  C4   C3   C2   106.58  3.000
 L6K  C13  C4   C5   127.03  3.000
 L6K  C13  C4   C3   127.42  3.000
 L6K  C5   C4   C3   105.55  3.000
 L6K  H4   C5   C4   132.40  3.000
 L6K  H4   C5   O1   117.08  3.000
 L6K  C4   C5   O1   110.52  3.000
 L6K  C7   C6   C11  117.46  3.000
 L6K  C7   C6   C12  120.53  3.000
 L6K  C11  C6   C12  121.99  3.000
 L6K  H8   N2   C15  110.21  3.000
 L6K  H8   N2   C16  110.08  3.000
 L6K  C15  N2   C16  116.13  3.000
 L6K  H10  C15  C35  105.90  3.000
 L6K  H10  C15  C12  107.63  3.000
 L6K  C35  C15  C12  111.04  3.000
 L6K  H10  C15  N2   106.59  3.000
 L6K  C35  C15  N2   113.12  3.000
 L6K  C12  C15  N2   112.11  3.000
 L6K  H12  C12  H11  106.15  3.000
 L6K  H12  C12  C15  110.38  3.000
 L6K  H11  C12  C15  108.72  3.000
 L6K  H12  C12  C6   110.41  3.000
 L6K  H11  C12  C6   109.48  3.000
 L6K  C15  C12  C6   111.54  3.000
 L6K  H13  C11  C10  118.47  3.000
 L6K  H13  C11  C6   119.61  3.000
 L6K  C10  C11  C6   121.92  3.000
 L6K  H14  C10  C9   121.65  3.000
 L6K  H14  C10  C11  118.62  3.000
 L6K  C9   C10  C11  119.72  3.000
 L6K  H15  C7   C8   118.75  3.000
 L6K  H15  C7   C6   119.60  3.000
 L6K  C8   C7   C6   121.64  3.000
 L6K  H16  C8   C9   119.53  3.000
 L6K  H16  C8   C7   120.33  3.000
 L6K  C9   C8   C7   120.14  3.000
 L6K  C8   C9   C10  119.11  3.000
 L6K  C8   C9   O2   116.20  3.000
 L6K  C10  C9   O2   124.69  3.000
 L6K  H18  C13  H17  107.51  3.000
 L6K  H18  C13  C4   110.26  3.000
 L6K  H17  C13  C4   110.39  3.000
 L6K  H18  C13  O2   110.96  3.000
 L6K  H17  C13  O2   110.06  3.000
 L6K  C4   C13  O2   107.68  3.000
 L6K  H20  N1   H19  105.83  3.000
 L6K  H20  N1   C1   109.42  3.000
 L6K  H19  N1   C1   108.92  3.000
 L6K  O37  C35  O36  122.98  3.000
 L6K  O37  C35  C15  111.30  3.000
 L6K  O36  C35  C15  125.72  3.000
 L6K  H22  O37  C35  110.07  3.000
 L6K  H7   C16  H6   107.51  3.000
 L6K  H7   C16  H5   107.03  3.000
 L6K  H6   C16  H5   107.27  3.000
 L6K  H7   C16  N2   110.66  3.000
 L6K  H6   C16  N2   115.08  3.000
 L6K  H5   C16  N2   108.96  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
 L6K  CONST_01  C3   C4   C5   O1     0.00   0.0  0
 L6K  CONST_02  C4   C3   C2   O1     0.00   0.0  0
 L6K  CONST_03  C4   C5   O1   C2     0.00   0.0  0
 L6K  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 L6K  CONST_05  C5   O1   C2   C3     0.00   0.0  0
 L6K  CONST_06  C9   C10  C11  C6     0.00   0.0  0
 L6K  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 L6K  CONST_08  C8   C9   C10  C11    0.00   0.0  0
 L6K  CONST_09  C8   C7   C6   C11    0.00   0.0  0
 L6K  CONST_10  C7   C8   C9   C10    0.00   0.0  0
 L6K  CONST_11  C7   C6   C11  C10    0.00   0.0  0
 L6K  CONST_12  C5   O1   C2   C1   180.00   0.0  0
 L6K  CONST_13  C4   C3   C2   C1   180.00   0.0  0
 L6K  CONST_14  C13  C4   C5   O1   180.00   0.0  0
 L6K  CONST_15  C13  C4   C3   C2   180.00   0.0  0
 L6K  CONST_16  C11  C10  C9   O2   180.00   0.0  0
 L6K  CONST_17  C7   C8   C9   O2   180.00   0.0  0
 L6K  CONST_18  C10  C11  C6   C12  180.00   0.0  0
 L6K  CONST_19  C8   C7   C6   C12  180.00   0.0  0
 L6K  CONST_20  H3   C3   C2   O1   180.00   0.0  0
 L6K  CONST_21  H4   C5   O1   C2   180.00   0.0  0
 L6K  CONST_22  H14  C10  C11  C6   180.00   0.0  0
 L6K  CONST_23  H16  C8   C7   C6   180.00   0.0  0
 L6K  CONST_24  H15  C7   C6   C11  180.00   0.0  0
 L6K  CONST_25  H13  C11  C6   C7   180.00   0.0  0
 L6K  CONST_26  H22  O37  C35  C15  180.00   0.0  0
 L6K  Var_01    N1   C1   C2   O1   -58.63  30.0  1
 L6K  Var_02    C5   C4   C13  O2   116.19  30.0  2
 L6K  Var_03    C11  C6   C12  C15   92.83  30.0  1
 L6K  Var_04    H19  N1   C1   C2   175.53  30.0  3
 L6K  Var_05    H5   C16  N2   C15  177.83  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
 L6K  chir_01  C15  C12  N2  C35  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
 L6K  plan-1  C1   0.020
 L6K  plan-1  O1   0.020
 L6K  plan-1  C2   0.020
 L6K  plan-1  C3   0.020
 L6K  plan-1  C4   0.020
 L6K  plan-1  C5   0.020
 L6K  plan-1  C13  0.020
 L6K  plan-1  H3   0.020
 L6K  plan-1  H4   0.020
 L6K  plan-2  O2   0.020
 L6K  plan-2  C6   0.020
 L6K  plan-2  C12  0.020
 L6K  plan-2  C11  0.020
 L6K  plan-2  C10  0.020
 L6K  plan-2  C7   0.020
 L6K  plan-2  C8   0.020
 L6K  plan-2  C9   0.020
 L6K  plan-2  H13  0.020
 L6K  plan-2  H14  0.020
 L6K  plan-2  H15  0.020
 L6K  plan-2  H16  0.020
 L6K  plan-3  C15  0.020
 L6K  plan-3  C35  0.020
 L6K  plan-3  O36  0.020
 L6K  plan-3  O37  0.020
 L6K  plan-3  H22  0.020

