# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:29:06 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (2~{S},3~{R})-2-azanyl-3-(1~{H}-indol-3-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@H](N)C(O)=O)c1c[nH]c2ccccc12
#
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
 JD3  JD3  "(2S,3R)-2-azanyl-3-(1H-indol-3-yl)butanoic acid"  ligand  29  16  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JD3
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
 JD3  C09  C  CR15   0  -0.086  4.9939  39.5137  149.6836
 JD3  C11  C  CR56   0   0.353  6.5038  38.1150  150.5366
 JD3  C13  C  CR16   0  -0.377  7.1976  39.2792  152.5452
 JD3  C15  C  CR16   0  -0.284  8.1327  37.1217  151.9486
 JD3  C02  C  C      0   0.399  2.7972  40.4447  152.0624
 JD3  C04  C  CH1    0  -0.172  3.4857  41.6300  151.3453
 JD3  C06  C  CH1    0  -0.311  5.0121  41.4583  151.3683
 JD3  C07  C  CH3    0  -0.636  5.7383  42.5821  150.6272
 JD3  C08  C  CR5    0   0.040  5.4258  40.1200  150.8300
 JD3  C12  C  CR56   0   0.004  6.4029  39.2357  151.3930
 JD3  C14  C  CR16   0  -0.267  8.0522  38.2274  152.8124
 JD3  C16  C  CR16   0  -0.306  7.3632  37.0497  150.8029
 JD3  N05  N  NH2    0  -0.795  3.1299  42.9180  151.9441
 JD3  N10  N  NR15   0  -0.691  5.6371  38.3184  149.5051
 JD3  H1   H  HCR5   0   0.272  4.2596  39.8452  148.9662
 JD3  H2   H  HCR6   0   0.236  7.1430  40.1266  153.2184
 JD3  H3   H  HCR6   0   0.243  8.8106  36.3116  152.1850
 JD3  H4   H  HCH1   0   0.192  3.1570  41.6581  150.3004
 JD3  H5   H  HCH1   0   0.212  5.3162  41.4980  152.4206
 JD3  H6   H  HCH3   0   0.220  5.5386  43.5534  151.0777
 JD3  H7   H  HCH3   0   0.218  6.8175  42.4214  150.6409
 JD3  H8   H  HCH3   0   0.206  5.4239  42.6237  149.5817
 JD3  H9   H  HCR6   0   0.239  8.6707  38.2507  153.7007
 JD3  H10  H  HCR6   0   0.253  7.4256  36.1970  150.1382
 JD3  H11  H  HNH2   0   0.336  2.1357  43.0740  151.8245
 JD3  H12  H  HNH2   0   0.323  3.2672  42.8380  152.9462
 JD3  H14  H  HNR5   0   0.403  5.4751  37.6841  148.7412
 JD3  O01  O  O      0  -0.608  2.0008  39.7472  151.4032
 JD3  O03  O  OC    -1  -0.615  3.0833  40.3071  153.2730

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
 JD3  N10  C09  aromatic  1.369  0.020  1.369
 JD3  N10  C11  aromatic  1.363  0.020  1.363
 JD3  C09  C08  aromatic  1.367  0.020  1.367
 JD3  C11  C16  aromatic  1.394  0.020  1.394
 JD3  C11  C12  aromatic  1.414  0.020  1.414
 JD3  C16  C15  aromatic  1.382  0.020  1.382
 JD3  C08  C12  aromatic  1.433  0.020  1.433
 JD3  C08  C06  single    1.501  0.020  1.501
 JD3  C07  C06  single    1.530  0.020  1.530
 JD3  C04  N05  single    1.464  0.020  1.464
 JD3  C04  C06  single    1.536  0.020  1.536
 JD3  C04  C02  single    1.547  0.020  1.547
 JD3  C12  C13  aromatic  1.400  0.020  1.400
 JD3  C15  C14  aromatic  1.405  0.020  1.405
 JD3  O01  C02  deloc     1.247  0.020  1.247
 JD3  C02  O03  deloc     1.251  0.020  1.251
 JD3  C13  C14  aromatic  1.381  0.020  1.381
 JD3  C09  H1   single    0.930  0.020  1.080
 JD3  C13  H2   single    0.930  0.020  1.080
 JD3  C15  H3   single    0.930  0.020  1.080
 JD3  C04  H4   single    0.970  0.020  1.090
 JD3  C06  H5   single    0.970  0.020  1.090
 JD3  C07  H6   single    0.970  0.020  1.090
 JD3  C07  H7   single    0.970  0.020  1.090
 JD3  C07  H8   single    0.970  0.020  1.090
 JD3  C14  H9   single    0.930  0.020  1.080
 JD3  C16  H10  single    0.930  0.020  1.080
 JD3  N05  H11  single    0.890  0.020  1.040
 JD3  N05  H12  single    0.890  0.020  1.040
 JD3  N10  H14  single    0.860  0.020  1.020

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
 JD3  H1   C09  N10  120.09  3.000
 JD3  H1   C09  C08  129.53  3.000
 JD3  N10  C09  C08  110.38  3.000
 JD3  N10  C11  C16  130.59  3.000
 JD3  C16  C11  C12  122.26  3.000
 JD3  N10  C11  C12  107.15  3.000
 JD3  H2   C13  C14  120.43  3.000
 JD3  H2   C13  C12  120.45  3.000
 JD3  C14  C13  C12  119.12  3.000
 JD3  H3   C15  C16  119.39  3.000
 JD3  H3   C15  C14  119.36  3.000
 JD3  C16  C15  C14  121.24  3.000
 JD3  O03  C02  O01  126.57  3.000
 JD3  O03  C02  C04  115.53  3.000
 JD3  O01  C02  C04  117.88  3.000
 JD3  H4   C04  N05  107.13  3.000
 JD3  H4   C04  C06  108.37  3.000
 JD3  N05  C04  C06  109.49  3.000
 JD3  H4   C04  C02  109.16  3.000
 JD3  C06  C04  C02  110.46  3.000
 JD3  N05  C04  C02  112.10  3.000
 JD3  H5   C06  C08  107.47  3.000
 JD3  H5   C06  C07  107.87  3.000
 JD3  C08  C06  C07  110.52  3.000
 JD3  H5   C06  C04  106.62  3.000
 JD3  C07  C06  C04  112.48  3.000
 JD3  C08  C06  C04  111.61  3.000
 JD3  H8   C07  H7   107.59  3.000
 JD3  H8   C07  H6   108.01  3.000
 JD3  H7   C07  H6   107.91  3.000
 JD3  H8   C07  C06  110.80  3.000
 JD3  H7   C07  C06  110.81  3.000
 JD3  H6   C07  C06  111.57  3.000
 JD3  C12  C08  C06  126.68  3.000
 JD3  C06  C08  C09  127.54  3.000
 JD3  C12  C08  C09  105.74  3.000
 JD3  C08  C12  C13  133.71  3.000
 JD3  C13  C12  C11  118.85  3.000
 JD3  C08  C12  C11  107.44  3.000
 JD3  H9   C14  C15  119.24  3.000
 JD3  H9   C14  C13  119.72  3.000
 JD3  C15  C14  C13  121.03  3.000
 JD3  H10  C16  C15  121.18  3.000
 JD3  H10  C16  C11  121.32  3.000
 JD3  C15  C16  C11  117.50  3.000
 JD3  H12  N05  H11  105.15  3.000
 JD3  H12  N05  C04  107.55  3.000
 JD3  H11  N05  C04  109.00  3.000
 JD3  H14  N10  C11  125.67  3.000
 JD3  H14  N10  C09  125.01  3.000
 JD3  C11  N10  C09  109.30  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
 JD3  CONST_01  C16  C11  N10  C09  180.00  0.0  0
 JD3  CONST_02  C12  C11  N10  C09    0.00  0.0  0
 JD3  CONST_03  C11  C12  C08  C09    0.00  0.0  0
 JD3  CONST_04  C13  C12  C08  C09  180.00  0.0  0
 JD3  CONST_05  C08  C09  N10  C11    0.00  0.0  0
 JD3  CONST_06  C14  C15  C16  C11    0.00  0.0  0
 JD3  CONST_07  C14  C13  C12  C11    0.00  0.0  0
 JD3  CONST_08  N10  C11  C12  C13  180.00  0.0  0
 JD3  CONST_09  C16  C11  C12  C13    0.00  0.0  0
 JD3  CONST_10  C16  C15  C14  C13    0.00  0.0  0
 JD3  CONST_11  N10  C11  C16  C15  180.00  0.0  0
 JD3  CONST_12  C12  C11  C16  C15    0.00  0.0  0
 JD3  CONST_13  C12  C13  C14  C15    0.00  0.0  0
 JD3  CONST_14  N10  C11  C12  C08    0.00  0.0  0
 JD3  CONST_15  C16  C11  C12  C08  180.00  0.0  0
 JD3  CONST_16  C14  C13  C12  C08  180.00  0.0  0
 JD3  CONST_17  N10  C09  C08  C12    0.00  0.0  0
 JD3  CONST_18  C06  C08  C12  C11  180.00  0.0  0
 JD3  CONST_19  C06  C08  C12  C13    0.00  0.0  0
 JD3  CONST_20  N10  C09  C08  C06  180.00  0.0  0
 JD3  CONST_21  H1   C09  N10  C11  180.00  0.0  0
 JD3  CONST_22  H3   C15  C16  C11  180.00  0.0  0
 JD3  CONST_23  H2   C13  C12  C11  180.00  0.0  0
 JD3  CONST_24  H3   C15  C14  C13  180.00  0.0  0
 JD3  CONST_25  H2   C13  C14  C15  180.00  0.0  0
 JD3  CONST_26  H14  N10  C09  C08  180.00  0.0  0
 JD3  CONST_27  H2   C13  C12  C08    0.00  0.0  0
 JD3  CONST_28  H14  N10  C11  C12  180.00  0.0  0
 JD3  CONST_29  H10  C16  C11  C12  180.00  0.0  0
 JD3  CONST_30  H1   C09  C08  C12  180.00  0.0  0
 JD3  CONST_31  H9   C14  C13  C12  180.00  0.0  0
 JD3  CONST_32  H10  C16  C15  C14  180.00  0.0  0
 JD3  CONST_33  H14  N10  C11  C16    0.00  0.0  0
 JD3  CONST_34  H9   C14  C15  C16  180.00  0.0  0
 JD3  CONST_35  H10  C16  C11  N10    0.00  0.0  0

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
 JD3  chir_01  C04  N05  C06  C02  negativ
 JD3  chir_02  C06  C04  C07  C08  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
 JD3  plan-1  C09  0.020
 JD3  plan-1  C11  0.020
 JD3  plan-1  C13  0.020
 JD3  plan-1  C15  0.020
 JD3  plan-1  C06  0.020
 JD3  plan-1  C08  0.020
 JD3  plan-1  C12  0.020
 JD3  plan-1  C14  0.020
 JD3  plan-1  C16  0.020
 JD3  plan-1  N10  0.020
 JD3  plan-1  H1   0.020
 JD3  plan-1  H2   0.020
 JD3  plan-1  H3   0.020
 JD3  plan-1  H9   0.020
 JD3  plan-1  H10  0.020
 JD3  plan-1  H14  0.020
 JD3  plan-2  C02  0.020
 JD3  plan-2  C04  0.020
 JD3  plan-2  O01  0.020
 JD3  plan-2  O03  0.020

