# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 20:06:13 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-[[(2~{R})-1-[4-(3-chlorophenyl)phenyl]-4-oxidanyl-4-oxidanylidene-butan-2-yl]amino]-4-oxidanylidene-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)N[C@@H](CC(O)=O)Cc1ccc(cc1)c2cccc(Cl)c2
#
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
 N9Q  N9Q  '4-[[(2~{R})-1-[4-(3-chlorophenyl)phenyl]-4-oxidanyl-4-oxidanylidene-butan-2-yl]amino]-4-oxidanylidene-butanoic acid'  ligand  47  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N9Q
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
 N9Q  C2   C   CR6   0  -0.021  -4.9371   0.4898  -0.3507
 N9Q  C3   C   CR16  0  -0.273  -3.6342   0.1385  -0.0409
 N9Q  C41  C   CH2   0  -0.587   4.7008  -1.9112   0.5778
 N9Q  C44  C   C     0   0.554   5.6921  -1.0797  -0.1910
 N9Q  C12  C   CR6   0   0.077  -1.7835  -1.5273  -0.0085
 N9Q  C13  C   CR16  0  -0.296  -1.0530  -2.3757  -0.8418
 N9Q  C15  C   CR16  0  -0.277   0.2501  -2.7266  -0.5305
 N9Q  C17  C   CR6   0   0.135   0.8665  -2.2520   0.6237
 N9Q  C18  C   CR16  0  -0.295   0.1329  -1.4173   1.4615
 N9Q  C20  C   CR16  0  -0.295  -1.1687  -1.0570   1.1513
 N9Q  C22  C   CH2   0  -0.513   2.3017  -2.5740   0.9177
 N9Q  C25  C   CH1   0  -0.077   3.2572  -1.6047   0.2023
 N9Q  CL1  CL  CL    0  -0.130  -5.4895   2.0897   0.0301
 N9Q  C5   C   CR6   0   0.089  -3.1691  -1.1422  -0.3420
 N9Q  C6   C   CR16  0  -0.305  -4.0390  -2.0417  -0.9602
 N9Q  C8   C   CR16  0  -0.245  -5.3391  -1.6713  -1.2668
 N9Q  C10  C   CR16  0  -0.230  -5.8047  -0.3997  -0.9644
 N9Q  N27  N   NH1   0  -0.642   2.9441  -0.2319   0.5277
 N9Q  O30  O   O     0  -0.485   1.9362   0.3153  -1.4236
 N9Q  C31  C   CH2   0  -0.591   1.8373   1.8952   0.3855
 N9Q  C34  C   CH2   0  -0.578   1.3122   2.9088  -0.6118
 N9Q  C37  C   C     0   0.555   0.8791   4.1939   0.0365
 N9Q  O38  O   OH1   0  -0.597   0.4694   5.0811  -0.8644
 N9Q  O39  O   O     0  -0.444   0.8880   4.4161   1.2216
 N9Q  O45  O   OH1   0  -0.593   6.8217  -0.9020   0.4852
 N9Q  O46  O   O     0  -0.437   5.5120  -0.6438  -1.2999
 N9Q  H1   H   HCR6  0   0.274  -2.9769   0.8649   0.4191
 N9Q  H2   H   HCH2  0   0.300   4.9187  -2.9623   0.3621
 N9Q  H3   H   HCH2  0   0.274   4.8534  -1.7840   1.6521
 N9Q  H4   H   HCR6  0   0.252  -1.4965  -2.7488  -1.7568
 N9Q  H5   H   HCR6  0   0.246   0.8003  -3.3737  -1.2040
 N9Q  H6   H   HCR6  0   0.249   0.5799  -1.0465   2.3762
 N9Q  H7   H   HCR6  0   0.254  -1.7163  -0.4218   1.8366
 N9Q  H8   H   HCH2  0   0.250   2.4855  -2.5313   1.9952
 N9Q  H9   H   HCH2  0   0.258   2.5377  -3.5908   0.5949
 N9Q  H10  H   HCH1  0   0.271   3.1308  -1.7186  -0.8736
 N9Q  H11  H   HCR6  0   0.260  -3.7054  -3.0460  -1.1873
 N9Q  H12  H   HCR6  0   0.270  -6.0043  -2.3824  -1.7386
 N9Q  H13  H   HCR6  0   0.280  -6.8195  -0.1102  -1.2004
 N9Q  H14  H   HNH1  0   0.395   3.0964   0.0586   1.4825
 N9Q  H15  H   HCH2  0   0.277   1.0752   1.6709   1.1379
 N9Q  H16  H   HCH2  0   0.272   2.6899   2.3007   0.9348
 N9Q  H17  H   HCH2  0   0.286   2.0669   3.1411  -1.3674
 N9Q  H18  H   HCH2  0   0.285   0.4597   2.5064  -1.1648
 N9Q  H19  H   HOH1  0   0.479   0.1874   5.8958  -0.4227
 N9Q  H20  H   HOH1  0   0.479   7.4514  -0.3960  -0.0501
 N9Q  C29  C   C     0   0.591   2.2370   0.5904  -0.2739

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
 N9Q  C8   C10  aromatic  1.388  0.020  1.388
 N9Q  C8   C6   aromatic  1.386  0.020  1.386
 N9Q  C10  C2   aromatic  1.386  0.020  1.386
 N9Q  C6   C5   aromatic  1.396  0.020  1.396
 N9Q  C2   CL1  single    1.735  0.020  1.735
 N9Q  C2   C3   aromatic  1.385  0.020  1.385
 N9Q  C5   C3   aromatic  1.395  0.020  1.395
 N9Q  C5   C12  single    1.476  0.020  1.476
 N9Q  C12  C13  aromatic  1.396  0.020  1.396
 N9Q  C12  C20  aromatic  1.394  0.020  1.394
 N9Q  C13  C15  aromatic  1.385  0.020  1.385
 N9Q  C20  C18  aromatic  1.386  0.020  1.386
 N9Q  C15  C17  aromatic  1.392  0.020  1.392
 N9Q  C18  C17  aromatic  1.392  0.020  1.392
 N9Q  C17  C22  single    1.500  0.020  1.500
 N9Q  C22  C25  single    1.538  0.020  1.538
 N9Q  C25  N27  single    1.445  0.020  1.445
 N9Q  C25  C41  single    1.523  0.020  1.523
 N9Q  O30  C29  double    1.220  0.020  1.220
 N9Q  N27  C29  single    1.349  0.020  1.349
 N9Q  O46  C44  double    1.205  0.020  1.205
 N9Q  C29  C31  single    1.516  0.020  1.516
 N9Q  C41  C44  single    1.505  0.020  1.505
 N9Q  C31  C34  single    1.516  0.020  1.516
 N9Q  C44  O45  single    1.328  0.020  1.328
 N9Q  O39  C37  double    1.206  0.020  1.206
 N9Q  C34  C37  single    1.503  0.020  1.503
 N9Q  C37  O38  single    1.329  0.020  1.329
 N9Q  C3   H1   single    0.930  0.020  1.080
 N9Q  C41  H2   single    0.970  0.020  1.090
 N9Q  C41  H3   single    0.970  0.020  1.090
 N9Q  C13  H4   single    0.930  0.020  1.080
 N9Q  C15  H5   single    0.930  0.020  1.080
 N9Q  C18  H6   single    0.930  0.020  1.080
 N9Q  C20  H7   single    0.930  0.020  1.080
 N9Q  C22  H8   single    0.970  0.020  1.090
 N9Q  C22  H9   single    0.970  0.020  1.090
 N9Q  C25  H10  single    0.970  0.020  1.090
 N9Q  C6   H11  single    0.930  0.020  1.080
 N9Q  C8   H12  single    0.930  0.020  1.080
 N9Q  C10  H13  single    0.930  0.020  1.080
 N9Q  N27  H14  single    0.860  0.020  1.020
 N9Q  C31  H15  single    0.970  0.020  1.090
 N9Q  C31  H16  single    0.970  0.020  1.090
 N9Q  C34  H17  single    0.970  0.020  1.090
 N9Q  C34  H18  single    0.970  0.020  1.090
 N9Q  O38  H19  single    0.850  0.020  0.980
 N9Q  O45  H20  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
 N9Q  C10  C2   CL1  119.32  3.000
 N9Q  CL1  C2   C3   118.98  3.000
 N9Q  C10  C2   C3   121.69  3.000
 N9Q  H1   C3   C5   120.36  3.000
 N9Q  H1   C3   C2   119.75  3.000
 N9Q  C5   C3   C2   119.88  3.000
 N9Q  H3   C41  H2   106.12  3.000
 N9Q  H3   C41  C25  110.58  3.000
 N9Q  H2   C41  C25  109.47  3.000
 N9Q  H3   C41  C44  110.24  3.000
 N9Q  H2   C41  C44  107.38  3.000
 N9Q  C25  C41  C44  112.79  3.000
 N9Q  O46  C44  O45  123.17  3.000
 N9Q  O45  C44  C41  111.96  3.000
 N9Q  O46  C44  C41  124.85  3.000
 N9Q  C5   C12  C20  120.91  3.000
 N9Q  C20  C12  C13  118.09  3.000
 N9Q  C5   C12  C13  121.00  3.000
 N9Q  H4   C13  C15  119.21  3.000
 N9Q  H4   C13  C12  119.96  3.000
 N9Q  C15  C13  C12  120.81  3.000
 N9Q  H5   C15  C17  119.61  3.000
 N9Q  H5   C15  C13  119.28  3.000
 N9Q  C17  C15  C13  121.11  3.000
 N9Q  C22  C17  C18  121.01  3.000
 N9Q  C22  C17  C15  120.87  3.000
 N9Q  C18  C17  C15  118.05  3.000
 N9Q  H6   C18  C20  119.18  3.000
 N9Q  H6   C18  C17  119.73  3.000
 N9Q  C20  C18  C17  121.09  3.000
 N9Q  H7   C20  C18  119.06  3.000
 N9Q  H7   C20  C12  120.08  3.000
 N9Q  C18  C20  C12  120.84  3.000
 N9Q  H9   C22  H8   106.92  3.000
 N9Q  H9   C22  C25  108.35  3.000
 N9Q  H8   C22  C25  109.22  3.000
 N9Q  H9   C22  C17  110.40  3.000
 N9Q  H8   C22  C17  110.21  3.000
 N9Q  C25  C22  C17  111.60  3.000
 N9Q  H10  C25  N27  107.25  3.000
 N9Q  H10  C25  C22  108.76  3.000
 N9Q  N27  C25  C22  111.06  3.000
 N9Q  H10  C25  C41  109.42  3.000
 N9Q  N27  C25  C41  109.94  3.000
 N9Q  C22  C25  C41  110.34  3.000
 N9Q  C6   C5   C12  121.12  3.000
 N9Q  C12  C5   C3   120.23  3.000
 N9Q  C6   C5   C3   118.64  3.000
 N9Q  H11  C6   C8   119.38  3.000
 N9Q  H11  C6   C5   119.92  3.000
 N9Q  C8   C6   C5   120.68  3.000
 N9Q  H12  C8   C10  119.40  3.000
 N9Q  H12  C8   C6   119.83  3.000
 N9Q  C10  C8   C6   120.76  3.000
 N9Q  H13  C10  C8   120.84  3.000
 N9Q  H13  C10  C2   120.82  3.000
 N9Q  C8   C10  C2   118.33  3.000
 N9Q  H14  N27  C29  117.76  3.000
 N9Q  H14  N27  C25  116.98  3.000
 N9Q  C29  N27  C25  123.98  3.000
 N9Q  H16  C31  H15  105.90  3.000
 N9Q  H16  C31  C34  110.67  3.000
 N9Q  H15  C31  C34  110.38  3.000
 N9Q  H16  C31  C29  109.42  3.000
 N9Q  H15  C31  C29  107.84  3.000
 N9Q  C34  C31  C29  112.38  3.000
 N9Q  H18  C34  H17  105.49  3.000
 N9Q  H18  C34  C37  107.95  3.000
 N9Q  H17  C34  C37  108.39  3.000
 N9Q  H18  C34  C31  110.91  3.000
 N9Q  H17  C34  C31  110.97  3.000
 N9Q  C37  C34  C31  112.81  3.000
 N9Q  O39  C37  O38  123.05  3.000
 N9Q  O38  C37  C34  111.55  3.000
 N9Q  O39  C37  C34  125.40  3.000
 N9Q  H19  O38  C37  110.00  3.000
 N9Q  H20  O45  C44  109.96  3.000
 N9Q  C31  C29  O30  122.63  3.000
 N9Q  C31  C29  N27  113.87  3.000
 N9Q  O30  C29  N27  123.50  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
 N9Q  CONST_01  C6   C8   C10  C2     0.00   0.0  0
 N9Q  CONST_02  C6   C5   C3   C2     0.00   0.0  0
 N9Q  CONST_03  C12  C5   C3   C2   180.00   0.0  0
 N9Q  CONST_04  C8   C10  C2   C3     0.00   0.0  0
 N9Q  CONST_05  C8   C6   C5   C3     0.00   0.0  0
 N9Q  CONST_08  C8   C6   C5   C12  180.00   0.0  0
 N9Q  CONST_09  C17  C15  C13  C12    0.00   0.0  0
 N9Q  CONST_10  C17  C18  C20  C12    0.00   0.0  0
 N9Q  CONST_12  C18  C20  C12  C13    0.00   0.0  0
 N9Q  CONST_13  C18  C17  C15  C13    0.00   0.0  0
 N9Q  CONST_14  C5   C12  C13  C15  180.00   0.0  0
 N9Q  CONST_15  C20  C12  C13  C15    0.00   0.0  0
 N9Q  CONST_16  C20  C18  C17  C15    0.00   0.0  0
 N9Q  CONST_17  C5   C12  C20  C18  180.00   0.0  0
 N9Q  CONST_19  C10  C8   C6   C5     0.00   0.0  0
 N9Q  CONST_20  C10  C2   C3   C5     0.00   0.0  0
 N9Q  CONST_21  C22  C17  C15  C13  180.00   0.0  0
 N9Q  CONST_22  C22  C17  C18  C20  180.00   0.0  0
 N9Q  CONST_23  C8   C10  C2   CL1  180.00   0.0  0
 N9Q  CONST_24  C5   C3   C2   CL1  180.00   0.0  0
 N9Q  CONST_25  H12  C8   C10  C2   180.00   0.0  0
 N9Q  CONST_26  H13  C10  C2   C3   180.00   0.0  0
 N9Q  CONST_27  H11  C6   C5   C3   180.00   0.0  0
 N9Q  CONST_28  H1   C3   C5   C12    0.00   0.0  0
 N9Q  CONST_29  H5   C15  C13  C12  180.00   0.0  0
 N9Q  CONST_30  H6   C18  C20  C12  180.00   0.0  0
 N9Q  CONST_31  H7   C20  C12  C13  180.00   0.0  0
 N9Q  CONST_32  H4   C13  C15  C17  180.00   0.0  0
 N9Q  CONST_33  O30  C29  N27  C25    0.00   0.0  0
 N9Q  CONST_34  C31  C29  N27  C25  180.00   0.0  0
 N9Q  CONST_35  H14  N27  C29  O30  180.00   0.0  0
 N9Q  CONST_36  H20  O45  C44  C41  180.00   0.0  0
 N9Q  CONST_37  H19  O38  C37  C34  180.00   0.0  0
 N9Q  Var_01    C25  C22  C17  C15   83.92  30.0  2
 N9Q  Var_02    O46  C44  C41  C25  -28.85  30.0  3
 N9Q  Var_03    C37  C34  C31  C29  178.49  30.0  3
 N9Q  Var_04    C34  C31  C29  N27  167.75  30.0  3
 N9Q  Var_05    O39  C37  C34  C31   -2.51  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
 N9Q  chir_01  C25  C22  N27  C41  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
 N9Q  plan-1  C12  0.020
 N9Q  plan-1  C13  0.020
 N9Q  plan-1  C15  0.020
 N9Q  plan-1  C17  0.020
 N9Q  plan-1  C18  0.020
 N9Q  plan-1  C20  0.020
 N9Q  plan-1  C22  0.020
 N9Q  plan-1  C5   0.020
 N9Q  plan-1  H4   0.020
 N9Q  plan-1  H5   0.020
 N9Q  plan-1  H6   0.020
 N9Q  plan-1  H7   0.020
 N9Q  plan-2  C2   0.020
 N9Q  plan-2  C3   0.020
 N9Q  plan-2  C12  0.020
 N9Q  plan-2  CL1  0.020
 N9Q  plan-2  C5   0.020
 N9Q  plan-2  C6   0.020
 N9Q  plan-2  C8   0.020
 N9Q  plan-2  C10  0.020
 N9Q  plan-2  H1   0.020
 N9Q  plan-2  H11  0.020
 N9Q  plan-2  H12  0.020
 N9Q  plan-2  H13  0.020
 N9Q  plan-3  C25  0.020
 N9Q  plan-3  N27  0.020
 N9Q  plan-3  O30  0.020
 N9Q  plan-3  C31  0.020
 N9Q  plan-3  H14  0.020
 N9Q  plan-3  C29  0.020
 N9Q  plan-4  C41  0.020
 N9Q  plan-4  C44  0.020
 N9Q  plan-4  O45  0.020
 N9Q  plan-4  O46  0.020
 N9Q  plan-4  H20  0.020
 N9Q  plan-5  C34  0.020
 N9Q  plan-5  C37  0.020
 N9Q  plan-5  O38  0.020
 N9Q  plan-5  O39  0.020
 N9Q  plan-5  H19  0.020

