# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:37:26 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2~{S})-2-[2-chloranylethanoyl-(3-chloranyl-4-methoxy-phenyl)amino]-~{N}-(2-phenylethyl)-2-thiophen-2-yl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1Cl)N([C@@H](C(=O)NCCc2ccccc2)c3sccc3)C(=O)CCl
#
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
 G9N  G9N  (2~{S})-2-[2-chloranylethanoyl-(3-chloranyl-4-methoxy-phenyl)amino]-~{N}-(2-phenylethyl)-2-thiophen-2-yl-ethanamide  ligand  53  31  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G9N
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
 G9N  C4   C   CR16  0  -0.310  -5.6327   0.2677   1.3542
 G9N  C5   C   CR16  0  -0.240  -6.9735   0.2890   1.7161
 G9N  C6   C   CR16  0  -0.272  -7.9337  -0.2427   0.8655
 G9N  C8   C   CH2   0  -0.286  -3.1691  -1.6989   0.1266
 G9N  C10  C   C     0   0.563  -0.7736  -1.4072   0.5463
 G9N  C17  C   CR15  0  -0.183   1.2828  -0.6322  -3.6843
 G9N  C20  C   CH2   0  -0.617   1.7089  -3.1951   1.9567
 G9N  C24  C   CR16  0  -0.215   3.1076   0.6748  -0.1222
 G9N  C26  C   CR6   0   0.461   2.7595   3.0123   0.3606
 G9N  C28  C   CR16  0  -0.211   1.3398   1.3199   1.3617
 G9N  C31  C   CH3   0  -0.440   4.0836   4.7304  -0.5854
 G9N  O30  O   O2    0  -0.452   3.0223   4.3183   0.2576
 G9N  C27  C   CR6   0  -0.150   1.6974   2.6424   1.1932
 G9N  CL   CL  CL    0  -0.109   0.8178   3.8803   2.0201
 G9N  C25  C   CR16  0  -0.398   3.4636   2.0035  -0.2921
 G9N  C23  C   CR6   0   0.246   2.0458   0.3278   0.6941
 G9N  N13  N   NT    0  -0.538   1.6585  -1.0367   0.8083
 G9N  C19  C   C     0   0.558   2.1512  -1.7419   1.8627
 G9N  O22  O   O     0  -0.447   2.9228  -1.2537   2.6588
 G9N  C11  C   CH1   0  -0.310   0.6285  -1.5442  -0.0889
 G9N  C14  C   CR5   0  -0.175   0.7123  -0.9357  -1.4553
 G9N  C18  C   CR15  0  -0.213   1.3392  -1.4716  -2.5413
 G9N  C16  C   CR15  0  -0.454   0.6087   0.5260  -3.4425
 G9N  S15  S   S2    0   0.253   0.0455   0.6087  -1.8314
 G9N  O12  O   O     0  -0.470  -0.9136  -1.0270   1.6956
 G9N  N9   N   NH1   0  -0.616  -1.7760  -1.7951  -0.2475
 G9N  C3   C   CR6   0   0.127  -5.2302  -0.2806   0.1387
 G9N  C2   C   CR16  0  -0.304  -6.2029  -0.8128  -0.7058
 G9N  C1   C   CR16  0  -0.240  -7.5440  -0.7947  -0.3484
 G9N  H1   H   HCR6  0   0.247  -4.8905   0.6886   2.0229
 G9N  H2   H   HCR6  0   0.254  -7.2685   0.7246   2.6620
 G9N  H3   H   HCR6  0   0.254  -8.9792  -0.2234   1.1449
 G9N  H4   H   HCH2  0   0.253  -3.2221   0.4487   0.2737
 G9N  H5   H   HCH2  0   0.250  -3.6567  -0.1742  -1.3105
 G9N  H6   H   HCH2  0   0.256  -3.2639  -1.8795   1.1970
 G9N  H7   H   HCH2  0   0.262  -3.7061  -2.4984  -0.3842
 G9N  H8   H   HCR5  0   0.271   1.7183  -0.8813  -4.6409
 G9N  H9   H   HCH2  0   0.320   0.6277  -3.2802   2.0482
 G9N  H10  H   HCH2  0   0.323   2.0221  -3.7515   1.0729
 G9N  H12  H   HCR6  0   0.269   3.6572  -0.0941  -0.6485
 G9N  H13  H   HCR6  0   0.284   0.5062   1.0609   1.9990
 G9N  H14  H   HCH3  0   0.235   5.0426   4.3208  -0.2607
 G9N  H15  H   HCH3  0   0.235   3.9086   4.4457  -1.6254
 G9N  H16  H   HCH3  0   0.265   4.1230   5.8141  -0.5182
 G9N  H17  H   HCR6  0   0.292   4.2965   2.2394  -0.9399
 G9N  H18  H   HCH1  0   0.329   0.7938  -2.6143  -0.2430
 G9N  H19  H   HCR5  0   0.272   1.8240  -2.4385  -2.5227
 G9N  H20  H   HCR5  0   0.300   0.4106   1.3355  -4.1281
 G9N  H21  H   HNH1  0   0.411  -1.5682  -2.0587  -1.1985
 G9N  H22  H   HCR6  0   0.248  -5.9067  -1.2409  -1.6568
 G9N  H23  H   HCR6  0   0.254  -8.2860  -1.2069  -1.0205
 G9N  CL1  CL  CL    0  -0.119   2.4288  -3.9852   3.3708
 G9N  C7   C   CH2   0  -0.523  -3.7771  -0.3410  -0.2372

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
 G9N  C31  O30  single    1.417  0.020  1.417
 G9N  O30  C26  single    1.336  0.020  1.336
 G9N  C6   C5   aromatic  1.389  0.020  1.389
 G9N  C6   C1   aromatic  1.389  0.020  1.389
 G9N  C5   C4   aromatic  1.389  0.020  1.389
 G9N  C26  C25  aromatic  1.393  0.020  1.393
 G9N  C26  C27  aromatic  1.399  0.020  1.399
 G9N  C25  C24  aromatic  1.386  0.020  1.386
 G9N  C1   C2   aromatic  1.388  0.020  1.388
 G9N  C4   C3   aromatic  1.393  0.020  1.393
 G9N  CL   C27  single    1.729  0.020  1.729
 G9N  C27  C28  aromatic  1.380  0.020  1.380
 G9N  C24  C23  aromatic  1.384  0.020  1.384
 G9N  C2   C3   aromatic  1.394  0.020  1.394
 G9N  C3   C7   single    1.502  0.020  1.502
 G9N  C28  C23  aromatic  1.389  0.020  1.389
 G9N  C23  N13  single    1.423  0.020  1.423
 G9N  C20  C19  single    1.522  0.020  1.522
 G9N  C7   C8   single    1.532  0.020  1.532
 G9N  O12  C10  double    1.219  0.020  1.219
 G9N  N13  C19  single    1.361  0.020  1.361
 G9N  N13  C11  single    1.457  0.020  1.457
 G9N  S15  C16  aromatic  1.709  0.020  1.709
 G9N  S15  C14  aromatic  1.724  0.020  1.724
 G9N  C19  O22  double    1.211  0.020  1.211
 G9N  C10  C11  single    1.545  0.020  1.545
 G9N  C10  N9   single    1.336  0.020  1.336
 G9N  C8   N9   single    1.446  0.020  1.446
 G9N  C11  C14  single    1.498  0.020  1.498
 G9N  C16  C17  aromatic  1.362  0.020  1.362
 G9N  C14  C18  aromatic  1.364  0.020  1.364
 G9N  C17  C18  aromatic  1.419  0.020  1.419
 G9N  C4   H1   single    0.930  0.020  1.080
 G9N  C5   H2   single    0.930  0.020  1.080
 G9N  C6   H3   single    0.930  0.020  1.080
 G9N  C7   H4   single    0.970  0.020  1.090
 G9N  C7   H5   single    0.970  0.020  1.090
 G9N  C8   H6   single    0.970  0.020  1.090
 G9N  C8   H7   single    0.970  0.020  1.090
 G9N  C17  H8   single    0.930  0.020  1.080
 G9N  C20  H9   single    0.970  0.020  1.090
 G9N  C20  H10  single    0.970  0.020  1.090
 G9N  C24  H12  single    0.930  0.020  1.080
 G9N  C28  H13  single    0.930  0.020  1.080
 G9N  C31  H14  single    0.970  0.020  1.090
 G9N  C31  H15  single    0.970  0.020  1.090
 G9N  C31  H16  single    0.970  0.020  1.090
 G9N  C25  H17  single    0.930  0.020  1.080
 G9N  C11  H18  single    0.970  0.020  1.090
 G9N  C18  H19  single    0.930  0.020  1.080
 G9N  C16  H20  single    0.930  0.020  1.080
 G9N  N9   H21  single    0.860  0.020  1.020
 G9N  C2   H22  single    0.930  0.020  1.080
 G9N  C1   H23  single    0.930  0.020  1.080
 G9N  C20  CL1  single    1.773  0.020  1.773

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
 G9N  H1   C4   C3   119.56  3.000
 G9N  H1   C4   C5   119.62  3.000
 G9N  C3   C4   C5   120.82  3.000
 G9N  H2   C5   C6   120.06  3.000
 G9N  H2   C5   C4   119.80  3.000
 G9N  C6   C5   C4   120.14  3.000
 G9N  H3   C6   C1   120.24  3.000
 G9N  H3   C6   C5   120.20  3.000
 G9N  C1   C6   C5   119.56  3.000
 G9N  H7   C8   H6   107.21  3.000
 G9N  H7   C8   N9   107.73  3.000
 G9N  H6   C8   N9   109.09  3.000
 G9N  H7   C8   C7   110.08  3.000
 G9N  H6   C8   C7   110.23  3.000
 G9N  N9   C8   C7   112.34  3.000
 G9N  N9   C10  O12  124.38  3.000
 G9N  N9   C10  C11  114.25  3.000
 G9N  O12  C10  C11  121.30  3.000
 G9N  H8   C17  C16  123.58  3.000
 G9N  H8   C17  C18  124.11  3.000
 G9N  C16  C17  C18  112.31  3.000
 G9N  CL1  C20  H10  107.61  3.000
 G9N  CL1  C20  H9   107.55  3.000
 G9N  H10  C20  H9   108.27  3.000
 G9N  CL1  C20  C19  110.91  3.000
 G9N  H10  C20  C19  110.71  3.000
 G9N  H9   C20  C19  111.63  3.000
 G9N  H12  C24  C23  119.91  3.000
 G9N  H12  C24  C25  119.42  3.000
 G9N  C23  C24  C25  120.66  3.000
 G9N  C25  C26  C27  118.11  3.000
 G9N  C27  C26  O30  116.97  3.000
 G9N  C25  C26  O30  124.92  3.000
 G9N  H13  C28  C23  120.29  3.000
 G9N  H13  C28  C27  120.09  3.000
 G9N  C23  C28  C27  119.61  3.000
 G9N  H16  C31  H15  108.94  3.000
 G9N  H16  C31  H14  108.89  3.000
 G9N  H15  C31  H14  109.02  3.000
 G9N  H16  C31  O30  106.29  3.000
 G9N  H15  C31  O30  111.77  3.000
 G9N  H14  C31  O30  111.82  3.000
 G9N  C31  O30  C26  118.53  3.000
 G9N  CL   C27  C28  119.72  3.000
 G9N  C28  C27  C26  121.50  3.000
 G9N  CL   C27  C26  118.78  3.000
 G9N  H17  C25  C26  120.81  3.000
 G9N  H17  C25  C24  118.72  3.000
 G9N  C26  C25  C24  120.47  3.000
 G9N  N13  C23  C28  120.54  3.000
 G9N  N13  C23  C24  119.79  3.000
 G9N  C28  C23  C24  119.64  3.000
 G9N  C11  N13  C19  123.54  3.000
 G9N  C11  N13  C23  118.48  3.000
 G9N  C19  N13  C23  117.42  3.000
 G9N  O22  C19  N13  122.07  3.000
 G9N  O22  C19  C20  121.96  3.000
 G9N  N13  C19  C20  115.94  3.000
 G9N  H18  C11  C14  105.10  3.000
 G9N  H18  C11  N13  108.70  3.000
 G9N  C14  C11  N13  112.37  3.000
 G9N  H18  C11  C10  106.37  3.000
 G9N  C14  C11  C10  112.93  3.000
 G9N  N13  C11  C10  110.94  3.000
 G9N  S15  C14  C18  110.87  3.000
 G9N  C18  C14  C11  126.33  3.000
 G9N  S15  C14  C11  122.77  3.000
 G9N  H19  C18  C14  122.93  3.000
 G9N  H19  C18  C17  124.07  3.000
 G9N  C14  C18  C17  113.00  3.000
 G9N  H20  C16  S15  120.15  3.000
 G9N  H20  C16  C17  128.03  3.000
 G9N  S15  C16  C17  111.83  3.000
 G9N  C16  S15  C14   92.00  3.000
 G9N  H21  N9   C10  118.78  3.000
 G9N  H21  N9   C8   117.39  3.000
 G9N  C10  N9   C8   123.36  3.000
 G9N  C2   C3   C7   120.54  3.000
 G9N  C7   C3   C4   120.92  3.000
 G9N  C2   C3   C4   118.51  3.000
 G9N  H22  C2   C1   119.67  3.000
 G9N  H22  C2   C3   119.45  3.000
 G9N  C1   C2   C3   120.88  3.000
 G9N  H23  C1   C2   119.83  3.000
 G9N  H23  C1   C6   120.09  3.000
 G9N  C2   C1   C6   120.08  3.000
 G9N  H5   C7   H4   107.05  3.000
 G9N  H5   C7   C3   110.26  3.000
 G9N  H4   C7   C3   110.21  3.000
 G9N  H5   C7   C8   108.96  3.000
 G9N  H4   C7   C8   109.16  3.000
 G9N  C3   C7   C8   111.11  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
 G9N  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 G9N  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 G9N  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 G9N  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 G9N  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 G9N  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 G9N  CONST_07  C14  S15  C16  C17    0.00   0.0  0
 G9N  CONST_08  S15  C14  C18  C17    0.00   0.0  0
 G9N  CONST_09  C27  C26  C25  C24    0.00   0.0  0
 G9N  CONST_10  C27  C28  C23  C24    0.00   0.0  0
 G9N  CONST_11  C23  C24  C25  C26    0.00   0.0  0
 G9N  CONST_12  C23  C28  C27  C26    0.00   0.0  0
 G9N  CONST_13  C25  C26  C27  C28    0.00   0.0  0
 G9N  CONST_14  C25  C24  C23  C28    0.00   0.0  0
 G9N  CONST_15  C16  C17  C18  C14    0.00   0.0  0
 G9N  CONST_16  C16  S15  C14  C18    0.00   0.0  0
 G9N  CONST_17  S15  C16  C17  C18    0.00   0.0  0
 G9N  CONST_18  C7   C3   C4   C5   180.00   0.0  0
 G9N  CONST_19  C1   C2   C3   C7   180.00   0.0  0
 G9N  CONST_20  C11  C14  C18  C17  180.00   0.0  0
 G9N  CONST_21  O30  C26  C25  C24  180.00   0.0  0
 G9N  CONST_22  O30  C26  C27  C28  180.00   0.0  0
 G9N  CONST_23  N13  C23  C28  C27  180.00   0.0  0
 G9N  CONST_24  C25  C26  C27  CL   180.00   0.0  0
 G9N  CONST_25  C23  C28  C27  CL   180.00   0.0  0
 G9N  CONST_26  N13  C23  C24  C25  180.00   0.0  0
 G9N  CONST_27  C16  S15  C14  C11  180.00   0.0  0
 G9N  CONST_28  H3   C6   C5   C4   180.00   0.0  0
 G9N  CONST_29  H22  C2   C3   C4   180.00   0.0  0
 G9N  CONST_30  H23  C1   C6   C5   180.00   0.0  0
 G9N  CONST_31  H1   C4   C5   C6   180.00   0.0  0
 G9N  CONST_32  H13  C28  C23  C24  180.00   0.0  0
 G9N  CONST_33  H12  C24  C25  C26  180.00   0.0  0
 G9N  CONST_34  H17  C25  C26  C27  180.00   0.0  0
 G9N  CONST_35  H20  C16  S15  C14  180.00   0.0  0
 G9N  CONST_36  H8   C17  C18  C14  180.00   0.0  0
 G9N  CONST_37  H19  C18  C17  C16  180.00   0.0  0
 G9N  CONST_38  H2   C5   C4   C3   180.00   0.0  0
 G9N  CONST_43  C23  N13  C19  C20  180.00   0.0  0
 G9N  CONST_44  O22  C19  N13  C23    0.00   0.0  0
 G9N  CONST_45  O12  C10  N9   C8     0.00   0.0  0
 G9N  CONST_46  C11  C10  N9   C8   180.00   0.0  0
 G9N  CONST_47  C11  N13  C19  C20    0.00   0.0  0
 G9N  CONST_48  C11  N13  C19  O22  180.00   0.0  0
 G9N  CONST_49  H21  N9   C10  C11    0.00   0.0  0
 G9N  Var_01    C8   C7   C3   C4    95.11  30.0  2
 G9N  Var_02    C25  C26  O30  C31    0.74  30.0  2
 G9N  Var_03    C3   C7   C8   N9   178.89  30.0  1
 G9N  Var_04    H14  C31  O30  C26  -61.09  30.0  3
 G9N  Var_05    C10  N9   C8   C7    87.97  30.0  3
 G9N  Var_06    CL1  C20  C19  N13  179.87  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
 G9N  chir_01  C11  N13  C10  C14  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
 G9N  plan-1  C17  0.020
 G9N  plan-1  C11  0.020
 G9N  plan-1  C14  0.020
 G9N  plan-1  C18  0.020
 G9N  plan-1  C16  0.020
 G9N  plan-1  S15  0.020
 G9N  plan-1  H8   0.020
 G9N  plan-1  H19  0.020
 G9N  plan-1  H20  0.020
 G9N  plan-2  C4   0.020
 G9N  plan-2  C5   0.020
 G9N  plan-2  C6   0.020
 G9N  plan-2  C3   0.020
 G9N  plan-2  C2   0.020
 G9N  plan-2  C1   0.020
 G9N  plan-2  H1   0.020
 G9N  plan-2  H2   0.020
 G9N  plan-2  H3   0.020
 G9N  plan-2  H22  0.020
 G9N  plan-2  H23  0.020
 G9N  plan-2  C7   0.020
 G9N  plan-3  C24  0.020
 G9N  plan-3  C26  0.020
 G9N  plan-3  C28  0.020
 G9N  plan-3  O30  0.020
 G9N  plan-3  C27  0.020
 G9N  plan-3  CL   0.020
 G9N  plan-3  C25  0.020
 G9N  plan-3  C23  0.020
 G9N  plan-3  N13  0.020
 G9N  plan-3  H12  0.020
 G9N  plan-3  H13  0.020
 G9N  plan-3  H17  0.020
 G9N  plan-4  C8   0.020
 G9N  plan-4  C10  0.020
 G9N  plan-4  C11  0.020
 G9N  plan-4  O12  0.020
 G9N  plan-4  N9   0.020
 G9N  plan-4  H21  0.020
 G9N  plan-5  C20  0.020
 G9N  plan-5  C23  0.020
 G9N  plan-5  N13  0.020
 G9N  plan-5  C19  0.020
 G9N  plan-5  O22  0.020
 G9N  plan-5  C11  0.020

