# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 11:33:45 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[4-(2-ethyl-4-methoxy-phenyl)phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(OC)ccc1c2ccc(C[C@H](N)C(O)=O)cc2
#
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
 9DW  9DW  '(2~{S})-2-azanyl-3-[4-(2-ethyl-4-methoxy-phenyl)phenyl]propanoic acid'  ligand  42  22  .  2022-07-24  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_9DW
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
 9DW  C01  C  CH3    0  -0.655  -1.3317  -2.4483   1.4464
 9DW  C02  C  CH2    0  -0.522  -1.8376  -2.2310   0.0213
 9DW  C05  C  CR6    0   0.388  -4.8762   0.0359  -0.0707
 9DW  C07  C  CR16   0  -0.269  -2.9173   1.4093  -0.1870
 9DW  C08  C  CR6    0   0.003  -2.0841   0.2975  -0.1746
 9DW  C09  C  CR6    0   0.035  -0.6156   0.4920  -0.2382
 9DW  C11  C  CR16   0  -0.310   1.4414   1.3047   0.7426
 9DW  C12  C  CR6    0   0.117   2.1769   0.8938  -0.3655
 9DW  C13  C  CR16   0  -0.292   1.4877   0.2848  -1.4145
 9DW  C14  C  CR16   0  -0.283   0.1179   0.0887  -1.3545
 9DW  C15  C  CH2    0  -0.525   3.6688   1.0386  -0.4150
 9DW  C03  C  CR6    0   0.112  -2.6670  -0.9791  -0.0962
 9DW  C04  C  CR16   0  -0.398  -4.0491  -1.0876  -0.0458
 9DW  C06  C  CR16   0  -0.389  -4.3017   1.3002  -0.1382
 9DW  C10  C  CR16   0  -0.280   0.0670   1.1109   0.8049
 9DW  C16  C  CH1    0  -0.194   4.3983  -0.2816  -0.0680
 9DW  C88  C  C      0   0.403   5.9171  -0.0252  -0.1888
 9DW  CA7  C  CH3    0  -0.436  -7.0842   0.9033  -0.0589
 9DW  N17  N  NH2    0  -0.798   4.0649  -0.8291   1.2320
 9DW  O89  O  O      0  -0.604   6.5491   0.1622   0.8693
 9DW  H1   H  HCH3   0   0.231  -0.7525  -3.3700   1.5140
 9DW  H2   H  HCH3   0   0.229  -0.6890  -1.6273   1.7658
 9DW  H3   H  HCH3   0   0.224  -2.1607  -2.5204   2.1516
 9DW  H4   H  HCH2   0   0.246  -0.9849  -2.1987  -0.6582
 9DW  H5   H  HCH2   0   0.242  -2.4401  -3.0892  -0.2834
 9DW  H6   H  HCR6   0   0.249  -2.4779   2.3977  -0.2514
 9DW  H7   H  HCR6   0   0.247   1.9483   1.7871   1.5702
 9DW  H8   H  HCR6   0   0.244   2.0313  -0.0382  -2.2952
 9DW  H9   H  HCR6   0   0.248  -0.3926  -0.3715  -2.1921
 9DW  H10  H  HCH2   0   0.238   3.9766   1.3554  -1.4144
 9DW  H11  H  HCH2   0   0.234   3.9907   1.8163   0.2848
 9DW  H12  H  HCR6   0   0.251  -4.5043  -2.0696   0.0221
 9DW  H13  H  HCR6   0   0.276  -4.9027   2.1991  -0.1604
 9DW  H14  H  HCR6   0   0.245  -0.4787   1.4374   1.6822
 9DW  H15  H  HCH1   0   0.209   4.1191  -1.0139  -0.8341
 9DW  H17  H  HCH3   0   0.227  -6.9327   1.5769   0.7886
 9DW  H18  H  HCH3   0   0.227  -6.9863   1.4773  -0.9844
 9DW  H19  H  HCH3   0   0.258  -8.0910   0.4963  -0.0061
 9DW  H20  H  HNH2   0   0.328   4.5274  -0.2774   1.9434
 9DW  H21  H  HNH2   0   0.334   3.0687  -0.7622   1.4032
 9DW  OXT  O  OC    -1  -0.618   6.3743   0.0185  -1.3481
 9DW  OA6  O  O2     0  -0.473  -6.2020  -0.1999  -0.0241

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
 9DW  O89  C88  deloc     1.247  0.020  1.247
 9DW  C88  C16  single    1.545  0.020  1.545
 9DW  N17  C16  single    1.450  0.020  1.450
 9DW  C16  C15  single    1.548  0.020  1.548
 9DW  C11  C10  aromatic  1.389  0.020  1.389
 9DW  C11  C12  aromatic  1.392  0.020  1.392
 9DW  C15  C12  single    1.500  0.020  1.500
 9DW  C10  C09  aromatic  1.392  0.020  1.392
 9DW  C12  C13  aromatic  1.395  0.020  1.395
 9DW  C09  C08  single    1.483  0.020  1.483
 9DW  C09  C14  aromatic  1.395  0.020  1.395
 9DW  C13  C14  aromatic  1.385  0.020  1.385
 9DW  C08  C07  aromatic  1.389  0.020  1.389
 9DW  C08  C03  aromatic  1.406  0.020  1.406
 9DW  C07  C06  aromatic  1.389  0.020  1.389
 9DW  C02  C03  single    1.506  0.020  1.506
 9DW  C02  C01  single    1.528  0.020  1.528
 9DW  C03  C04  aromatic  1.387  0.020  1.387
 9DW  C06  C05  aromatic  1.390  0.020  1.390
 9DW  C04  C05  aromatic  1.395  0.020  1.395
 9DW  C05  OA6  single    1.347  0.020  1.347
 9DW  OA6  CA7  single    1.413  0.020  1.413
 9DW  C01  H1   single    0.970  0.020  1.090
 9DW  C01  H2   single    0.970  0.020  1.090
 9DW  C01  H3   single    0.970  0.020  1.090
 9DW  C02  H4   single    0.970  0.020  1.090
 9DW  C02  H5   single    0.970  0.020  1.090
 9DW  C07  H6   single    0.930  0.020  1.080
 9DW  C11  H7   single    0.930  0.020  1.080
 9DW  C13  H8   single    0.930  0.020  1.080
 9DW  C14  H9   single    0.930  0.020  1.080
 9DW  C15  H10  single    0.970  0.020  1.090
 9DW  C15  H11  single    0.970  0.020  1.090
 9DW  C04  H12  single    0.930  0.020  1.080
 9DW  C06  H13  single    0.930  0.020  1.080
 9DW  C10  H14  single    0.930  0.020  1.080
 9DW  C16  H15  single    0.970  0.020  1.090
 9DW  CA7  H17  single    0.970  0.020  1.090
 9DW  CA7  H18  single    0.970  0.020  1.090
 9DW  CA7  H19  single    0.970  0.020  1.090
 9DW  N17  H20  single    0.890  0.020  1.040
 9DW  N17  H21  single    0.890  0.020  1.040
 9DW  C88  OXT  deloc     1.247  0.020  1.247

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
 9DW  H3   C01  H2   107.96  3.000
 9DW  H3   C01  H1   107.92  3.000
 9DW  H2   C01  H1   107.76  3.000
 9DW  H3   C01  C02  111.15  3.000
 9DW  H2   C01  C02  111.18  3.000
 9DW  H1   C01  C02  110.73  3.000
 9DW  H5   C02  H4   106.31  3.000
 9DW  H5   C02  C03  109.12  3.000
 9DW  H4   C02  C03  110.93  3.000
 9DW  H5   C02  C01  109.34  3.000
 9DW  H4   C02  C01  109.05  3.000
 9DW  C03  C02  C01  111.92  3.000
 9DW  OA6  C05  C06  124.57  3.000
 9DW  OA6  C05  C04  116.21  3.000
 9DW  C06  C05  C04  119.22  3.000
 9DW  H6   C07  C06  118.53  3.000
 9DW  H6   C07  C08  119.16  3.000
 9DW  C06  C07  C08  122.30  3.000
 9DW  C03  C08  C09  122.16  3.000
 9DW  C03  C08  C07  118.59  3.000
 9DW  C09  C08  C07  119.25  3.000
 9DW  C10  C09  C14  118.06  3.000
 9DW  C14  C09  C08  121.13  3.000
 9DW  C10  C09  C08  120.79  3.000
 9DW  H7   C11  C10  119.37  3.000
 9DW  H7   C11  C12  119.48  3.000
 9DW  C10  C11  C12  121.14  3.000
 9DW  C15  C12  C13  120.58  3.000
 9DW  C13  C12  C11  117.80  3.000
 9DW  C15  C12  C11  121.56  3.000
 9DW  H8   C13  C14  119.27  3.000
 9DW  H8   C13  C12  119.55  3.000
 9DW  C14  C13  C12  121.18  3.000
 9DW  H9   C14  C13  119.51  3.000
 9DW  H9   C14  C09  119.58  3.000
 9DW  C13  C14  C09  120.90  3.000
 9DW  H11  C15  H10  107.22  3.000
 9DW  H11  C15  C16  108.91  3.000
 9DW  H10  C15  C16  108.64  3.000
 9DW  H11  C15  C12  109.88  3.000
 9DW  H10  C15  C12  109.78  3.000
 9DW  C16  C15  C12  112.28  3.000
 9DW  C04  C03  C08  119.09  3.000
 9DW  C04  C03  C02  118.74  3.000
 9DW  C08  C03  C02  122.06  3.000
 9DW  H12  C04  C03  119.42  3.000
 9DW  H12  C04  C05  118.78  3.000
 9DW  C03  C04  C05  121.80  3.000
 9DW  H13  C06  C07  119.19  3.000
 9DW  H13  C06  C05  121.81  3.000
 9DW  C07  C06  C05  119.00  3.000
 9DW  H14  C10  C11  119.50  3.000
 9DW  H14  C10  C09  119.59  3.000
 9DW  C11  C10  C09  120.90  3.000
 9DW  H15  C16  N17  108.42  3.000
 9DW  H15  C16  C88  107.86  3.000
 9DW  N17  C16  C88  111.03  3.000
 9DW  H15  C16  C15  107.05  3.000
 9DW  N17  C16  C15  114.51  3.000
 9DW  C88  C16  C15  107.71  3.000
 9DW  OXT  C88  O89  126.72  3.000
 9DW  OXT  C88  C16  116.03  3.000
 9DW  O89  C88  C16  117.19  3.000
 9DW  H19  CA7  H18  108.70  3.000
 9DW  H19  CA7  H17  108.75  3.000
 9DW  H18  CA7  H17  108.68  3.000
 9DW  H19  CA7  OA6  106.54  3.000
 9DW  H18  CA7  OA6  112.01  3.000
 9DW  H17  CA7  OA6  112.05  3.000
 9DW  H21  N17  H20  107.13  3.000
 9DW  H21  N17  C16  110.66  3.000
 9DW  H20  N17  C16  108.62  3.000
 9DW  CA7  OA6  C05  118.48  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
 9DW  CONST_01  C08  C07  C06  C05    0.00   0.0  0
 9DW  CONST_02  C08  C03  C04  C05    0.00   0.0  0
 9DW  CONST_05  C04  C03  C08  C07    0.00   0.0  0
 9DW  CONST_06  C04  C05  C06  C07    0.00   0.0  0
 9DW  CONST_07  C11  C10  C09  C08  180.00   0.0  0
 9DW  CONST_08  C13  C14  C09  C08  180.00   0.0  0
 9DW  CONST_09  C12  C11  C10  C09    0.00   0.0  0
 9DW  CONST_10  C06  C07  C08  C09  180.00   0.0  0
 9DW  CONST_11  C04  C03  C08  C09  180.00   0.0  0
 9DW  CONST_12  C12  C13  C14  C09    0.00   0.0  0
 9DW  CONST_13  C14  C09  C10  C11    0.00   0.0  0
 9DW  CONST_14  C14  C13  C12  C11    0.00   0.0  0
 9DW  CONST_15  C10  C11  C12  C13    0.00   0.0  0
 9DW  CONST_16  C10  C09  C14  C13    0.00   0.0  0
 9DW  CONST_19  C06  C07  C08  C03    0.00   0.0  0
 9DW  CONST_20  C06  C05  C04  C03    0.00   0.0  0
 9DW  CONST_21  C09  C08  C03  C02    0.00   0.0  0
 9DW  CONST_22  C07  C08  C03  C02  180.00   0.0  0
 9DW  CONST_23  C05  C04  C03  C02  180.00   0.0  0
 9DW  CONST_24  OA6  C05  C06  C07  180.00   0.0  0
 9DW  CONST_25  C15  C12  C13  C14  180.00   0.0  0
 9DW  CONST_26  C10  C11  C12  C15  180.00   0.0  0
 9DW  CONST_27  OA6  C05  C04  C03  180.00   0.0  0
 9DW  CONST_28  H6   C07  C06  C05  180.00   0.0  0
 9DW  CONST_29  H14  C10  C09  C08    0.00   0.0  0
 9DW  CONST_30  H9   C14  C09  C08    0.00   0.0  0
 9DW  CONST_31  H13  C06  C07  C08  180.00   0.0  0
 9DW  CONST_32  H12  C04  C03  C08  180.00   0.0  0
 9DW  CONST_33  H7   C11  C10  C09  180.00   0.0  0
 9DW  CONST_34  H8   C13  C14  C09  180.00   0.0  0
 9DW  Var_01    C08  C03  C02  C01   78.68  30.0  2
 9DW  Var_02    C16  C15  C12  C11   99.05  30.0  2
 9DW  Var_03    H17  CA7  OA6  C05  -60.88  30.0  3
 9DW  Var_04    H1   C01  C02  C03  178.77  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
 9DW  chir_01  C16  C88  N17  C15  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
 9DW  plan-1  C02  0.020
 9DW  plan-1  C05  0.020
 9DW  plan-1  C07  0.020
 9DW  plan-1  C08  0.020
 9DW  plan-1  C09  0.020
 9DW  plan-1  C03  0.020
 9DW  plan-1  C04  0.020
 9DW  plan-1  C06  0.020
 9DW  plan-1  H6   0.020
 9DW  plan-1  H12  0.020
 9DW  plan-1  H13  0.020
 9DW  plan-1  OA6  0.020
 9DW  plan-2  C08  0.020
 9DW  plan-2  C09  0.020
 9DW  plan-2  C11  0.020
 9DW  plan-2  C12  0.020
 9DW  plan-2  C13  0.020
 9DW  plan-2  C14  0.020
 9DW  plan-2  C15  0.020
 9DW  plan-2  C10  0.020
 9DW  plan-2  H7   0.020
 9DW  plan-2  H8   0.020
 9DW  plan-2  H9   0.020
 9DW  plan-2  H14  0.020
 9DW  plan-3  C16  0.020
 9DW  plan-3  C88  0.020
 9DW  plan-3  O89  0.020
 9DW  plan-3  OXT  0.020

