# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 09:06:36 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 3,4,5-trimethoxy-~{N}-(2-thiophen-2-ylethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)C(=O)NCCc2sccc2
#
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
 RMR  RMR  3,4,5-trimethoxy-~{N}-(2-thiophen-2-ylethyl)benzamide  ligand  41  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RMR
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
 RMR  C1   C  CR16  0  -0.447  -2.3452   1.4625   0.0289
 RMR  C2   C  CR6   0  -0.001  -1.3382   0.5216   0.2028
 RMR  C3   C  CR16  0  -0.467  -1.6207  -0.8402   0.1852
 RMR  C4   C  CR6   0   0.354  -2.9302  -1.2671  -0.0212
 RMR  C5   C  CR6   0   0.182  -3.9463  -0.3289  -0.2213
 RMR  C6   C  CR6   0   0.352  -3.6519   1.0379  -0.1908
 RMR  C7   C  C     0   0.535   0.0487   1.0299   0.4398
 RMR  N8   N  NH1   0  -0.659   1.0476   0.2187   0.0527
 RMR  C9   C  CH2   0  -0.233   2.4416   0.5771   0.1972
 RMR  C10  C  CH2   0  -0.545   3.3193  -0.6593   0.0174
 RMR  C11  C  CR5   0  -0.148   4.7714  -0.3392   0.1520
 RMR  S12  S  S2    0   0.200   5.6234   0.5028  -1.0902
 RMR  C13  C  CR15  0  -0.471   7.0836   0.5003  -0.1904
 RMR  C14  C  CR15  0  -0.183   6.9238  -0.1202   1.0094
 RMR  C15  C  CR15  0  -0.236   5.5980  -0.5989   1.2044
 RMR  O16  O  O2    0  -0.462  -4.6953   1.8581  -0.3896
 RMR  C17  C  CH3   0  -0.440  -4.4667   3.2539  -0.3759
 RMR  O18  O  O2    0  -0.479  -5.2152  -0.7439  -0.4569
 RMR  C19  C  CH3   0  -0.410  -6.0057  -0.9031   0.7163
 RMR  O20  O  O2    0  -0.462  -3.3152  -2.5527  -0.0450
 RMR  C21  C  CH3   0  -0.442  -2.3271  -3.5560   0.0923
 RMR  O22  O  O     0  -0.489   0.2475   2.1210   0.9569
 RMR  H1   H  HCR6  0   0.282  -2.0973   2.5142   0.0618
 RMR  H2   H  HCR6  0   0.280  -0.8366  -1.5613   0.3694
 RMR  H3   H  HNH1  0   0.406   0.8321  -0.5672  -0.5398
 RMR  H4   H  HCH2  0   0.237   2.7202   1.3463  -0.5304
 RMR  H5   H  HCH2  0   0.251   2.6057   0.9992   1.1889
 RMR  H6   H  HCH2  0   0.270   3.0587  -1.4034   0.7728
 RMR  H7   H  HCH2  0   0.265   3.1194  -1.1122  -0.9580
 RMR  H9   H  HCR5  0   0.294   7.9764   0.9503  -0.5961
 RMR  H11  H  HCR5  0   0.265   7.7208  -0.2368   1.7297
 RMR  H13  H  HCR5  0   0.261   5.2681  -1.1194   2.0935
 RMR  H15  H  HCH3  0   0.231  -4.0887   3.5960   0.5907
 RMR  H16  H  HCH3  0   0.231  -3.7680   3.5611  -1.1580
 RMR  H17  H  HCH3  0   0.263  -5.4288   3.7243  -0.5627
 RMR  H18  H  HCH3  0   0.223  -5.5845  -1.6548   1.3876
 RMR  H19  H  HCH3  0   0.224  -6.1108   0.0375   1.2617
 RMR  H20  H  HCH3  0   0.239  -6.9916  -1.2338   0.3956
 RMR  H21  H  HCH3  0   0.264  -2.8411  -4.5088  -0.0046
 RMR  H22  H  HCH3  0   0.231  -1.5639  -3.4843  -0.6866
 RMR  H23  H  HCH3  0   0.232  -1.8396  -3.5192   1.0697

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
 RMR  C14  C13  aromatic  1.360  0.020  1.360
 RMR  C14  C15  aromatic  1.423  0.020  1.423
 RMR  C13  S12  aromatic  1.715  0.020  1.715
 RMR  C15  C11  aromatic  1.363  0.020  1.363
 RMR  C11  S12  aromatic  1.726  0.020  1.726
 RMR  C11  C10  single    1.493  0.020  1.493
 RMR  C10  C9   single    1.527  0.020  1.527
 RMR  C21  O20  single    1.415  0.020  1.415
 RMR  C9   N8   single    1.447  0.020  1.447
 RMR  N8   C7   single    1.344  0.020  1.344
 RMR  O20  C4   single    1.342  0.020  1.342
 RMR  C3   C4   aromatic  1.393  0.020  1.393
 RMR  C3   C2   aromatic  1.391  0.020  1.391
 RMR  C4   C5   aromatic  1.397  0.020  1.397
 RMR  C7   C2   single    1.496  0.020  1.496
 RMR  C7   O22  double    1.224  0.020  1.224
 RMR  C2   C1   aromatic  1.389  0.020  1.389
 RMR  C5   O18  single    1.356  0.020  1.356
 RMR  C5   C6   aromatic  1.398  0.020  1.398
 RMR  O18  C19  single    1.424  0.020  1.424
 RMR  C1   C6   aromatic  1.391  0.020  1.391
 RMR  C6   O16  single    1.342  0.020  1.342
 RMR  O16  C17  single    1.415  0.020  1.415
 RMR  C1   H1   single    0.930  0.020  1.080
 RMR  C3   H2   single    0.930  0.020  1.080
 RMR  N8   H3   single    0.860  0.020  1.020
 RMR  C9   H4   single    0.970  0.020  1.090
 RMR  C9   H5   single    0.970  0.020  1.090
 RMR  C10  H6   single    0.970  0.020  1.090
 RMR  C10  H7   single    0.970  0.020  1.090
 RMR  C13  H9   single    0.930  0.020  1.080
 RMR  C14  H11  single    0.930  0.020  1.080
 RMR  C15  H13  single    0.930  0.020  1.080
 RMR  C17  H15  single    0.970  0.020  1.090
 RMR  C17  H16  single    0.970  0.020  1.090
 RMR  C17  H17  single    0.970  0.020  1.090
 RMR  C19  H18  single    0.970  0.020  1.090
 RMR  C19  H19  single    0.970  0.020  1.090
 RMR  C19  H20  single    0.970  0.020  1.090
 RMR  C21  H21  single    0.970  0.020  1.090
 RMR  C21  H22  single    0.970  0.020  1.090
 RMR  C21  H23  single    0.970  0.020  1.090

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
 RMR  H1   C1   C6   121.14  3.000
 RMR  H1   C1   C2   119.27  3.000
 RMR  C6   C1   C2   119.59  3.000
 RMR  C7   C2   C3   121.53  3.000
 RMR  C7   C2   C1   117.50  3.000
 RMR  C3   C2   C1   120.96  3.000
 RMR  H2   C3   C4   120.18  3.000
 RMR  H2   C3   C2   120.24  3.000
 RMR  C4   C3   C2   119.54  3.000
 RMR  O20  C4   C5   115.60  3.000
 RMR  C5   C4   C3   119.94  3.000
 RMR  O20  C4   C3   124.47  3.000
 RMR  O18  C5   C6   120.00  3.000
 RMR  C6   C5   C4   120.00  3.000
 RMR  O18  C5   C4   119.99  3.000
 RMR  O16  C6   C5   115.49  3.000
 RMR  O16  C6   C1   124.54  3.000
 RMR  C5   C6   C1   119.96  3.000
 RMR  O22  C7   N8   122.63  3.000
 RMR  O22  C7   C2   121.37  3.000
 RMR  N8   C7   C2   116.00  3.000
 RMR  H3   N8   C9   117.26  3.000
 RMR  H3   N8   C7   118.77  3.000
 RMR  C9   N8   C7   122.55  3.000
 RMR  H5   C9   H4   107.11  3.000
 RMR  H5   C9   C10  109.52  3.000
 RMR  H4   C9   C10  110.14  3.000
 RMR  H5   C9   N8   109.39  3.000
 RMR  H4   C9   N8   110.66  3.000
 RMR  C10  C9   N8   109.97  3.000
 RMR  H7   C10  H6   106.92  3.000
 RMR  H7   C10  C11  110.30  3.000
 RMR  H6   C10  C11  108.41  3.000
 RMR  H7   C10  C9   109.59  3.000
 RMR  H6   C10  C9   109.46  3.000
 RMR  C11  C10  C9   112.02  3.000
 RMR  C15  C11  S12  110.45  3.000
 RMR  S12  C11  C10  121.32  3.000
 RMR  C15  C11  C10  128.21  3.000
 RMR  C13  S12  C11   92.40  3.000
 RMR  H9   C13  C14  128.25  3.000
 RMR  H9   C13  S12  120.44  3.000
 RMR  C14  C13  S12  111.31  3.000
 RMR  H11  C14  C15  124.02  3.000
 RMR  H11  C14  C13  123.41  3.000
 RMR  C15  C14  C13  112.57  3.000
 RMR  H13  C15  C14  123.96  3.000
 RMR  H13  C15  C11  122.77  3.000
 RMR  C14  C15  C11  113.27  3.000
 RMR  C17  O16  C6   118.43  3.000
 RMR  H17  C17  H16  108.74  3.000
 RMR  H17  C17  H15  108.83  3.000
 RMR  H16  C17  H15  108.90  3.000
 RMR  H17  C17  O16  106.40  3.000
 RMR  H16  C17  O16  111.94  3.000
 RMR  H15  C17  O16  111.93  3.000
 RMR  C19  O18  C5   114.25  3.000
 RMR  H20  C19  H19  108.76  3.000
 RMR  H20  C19  H18  108.74  3.000
 RMR  H19  C19  H18  108.84  3.000
 RMR  H20  C19  O18  107.11  3.000
 RMR  H19  C19  O18  111.63  3.000
 RMR  H18  C19  O18  111.67  3.000
 RMR  C21  O20  C4   118.50  3.000
 RMR  H23  C21  H22  108.89  3.000
 RMR  H23  C21  H21  108.67  3.000
 RMR  H22  C21  H21  108.92  3.000
 RMR  H23  C21  O20  111.98  3.000
 RMR  H22  C21  O20  111.84  3.000
 RMR  H21  C21  O20  106.42  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
 RMR  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 RMR  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 RMR  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 RMR  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 RMR  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 RMR  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 RMR  CONST_07  C13  C14  C15  C11     0.00   0.0  0
 RMR  CONST_08  C14  C13  S12  C11     0.00   0.0  0
 RMR  CONST_09  C15  C14  C13  S12     0.00   0.0  0
 RMR  CONST_10  C14  C15  C11  S12     0.00   0.0  0
 RMR  CONST_11  C15  C11  S12  C13     0.00   0.0  0
 RMR  CONST_12  O18  C5   C6   C1    180.00   0.0  0
 RMR  CONST_13  O20  C4   C3   C2    180.00   0.0  0
 RMR  CONST_14  O16  C6   C1   C2    180.00   0.0  0
 RMR  CONST_15  O18  C5   C4   C3    180.00   0.0  0
 RMR  CONST_16  C7   C2   C3   C4    180.00   0.0  0
 RMR  CONST_17  O16  C6   C5   C4    180.00   0.0  0
 RMR  CONST_18  O20  C4   C5   C6    180.00   0.0  0
 RMR  CONST_19  C7   C2   C1   C6    180.00   0.0  0
 RMR  CONST_20  C14  C15  C11  C10   180.00   0.0  0
 RMR  CONST_21  C13  S12  C11  C10   180.00   0.0  0
 RMR  CONST_22  H2   C3   C2   C1    180.00   0.0  0
 RMR  CONST_23  H1   C1   C2   C3    180.00   0.0  0
 RMR  CONST_24  H11  C14  C15  C11   180.00   0.0  0
 RMR  CONST_25  H9   C13  S12  C11   180.00   0.0  0
 RMR  CONST_26  H13  C15  C11  S12   180.00   0.0  0
 RMR  CONST_27  C9   N8   C7   C2    180.00   0.0  0
 RMR  CONST_28  H3   N8   C7   C2      0.00   0.0  0
 RMR  CONST_29  O22  C7   N8   C9      0.00   0.0  0
 RMR  Var_01    N8   C7   C2   C1   -152.84  30.0  2
 RMR  Var_02    C15  C11  C10  C9    104.31  30.0  2
 RMR  Var_03    C11  C10  C9   N8    179.75  30.0  1
 RMR  Var_04    H21  C21  O20  C4   -177.19  30.0  3
 RMR  Var_05    H18  C19  O18  C5    -61.16  30.0  3
 RMR  Var_06    H15  C17  O16  C6    -61.72  30.0  3
 RMR  Var_07    C10  C9   N8   C7    165.30  30.0  2

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
 RMR  plan-1  C10  0.020
 RMR  plan-1  C11  0.020
 RMR  plan-1  S12  0.020
 RMR  plan-1  C13  0.020
 RMR  plan-1  C14  0.020
 RMR  plan-1  C15  0.020
 RMR  plan-1  H9   0.020
 RMR  plan-1  H11  0.020
 RMR  plan-1  H13  0.020
 RMR  plan-2  C1   0.020
 RMR  plan-2  C2   0.020
 RMR  plan-2  C3   0.020
 RMR  plan-2  C4   0.020
 RMR  plan-2  C5   0.020
 RMR  plan-2  C6   0.020
 RMR  plan-2  C7   0.020
 RMR  plan-2  O16  0.020
 RMR  plan-2  O18  0.020
 RMR  plan-2  O20  0.020
 RMR  plan-2  H1   0.020
 RMR  plan-2  H2   0.020
 RMR  plan-3  C2   0.020
 RMR  plan-3  C7   0.020
 RMR  plan-3  N8   0.020
 RMR  plan-3  C9   0.020
 RMR  plan-3  O22  0.020
 RMR  plan-3  H3   0.020

