# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:26:01 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (2~{S})-3-(2-bromophenyl)-2-[2-(4-methoxyphenyl)ethanoylamino]-~{N}-[(1~{S})-1-phenylethyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CC(=O)N[C@@H](Cc2ccccc2Br)C(=O)N[C@@H](C)c3ccccc3)cc1
#
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
 5RF  5RF  (2~{S})-3-(2-bromophenyl)-2-[2-(4-methoxyphenyl)ethanoylamino]-~{N}-[(1~{S})-1-phenylethyl]propanamide  ligand  59  32  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5RF
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
 5RF  C14   C   CH1   0  -0.210  -0.8973   0.7852   0.5494
 5RF  C10   C   C     0   0.569   1.4264   1.2990  -0.0493
 5RF  C01   C   CH3   0  -0.435   8.4663   0.5513  -2.0293
 5RF  O02   O   O2    0  -0.472   7.5788  -0.1104  -1.1512
 5RF  C03   C   CR6   0   0.367   6.4079   0.4863  -0.8519
 5RF  C04   C   CR16  0  -0.337   5.5797  -0.1923   0.0475
 5RF  C05   C   CR16  0  -0.261   4.3645   0.3475   0.4167
 5RF  C06   C   CR16  0  -0.370   5.9873   1.7061  -1.3704
 5RF  C07   C   CR16  0  -0.312   4.7561   2.2316  -0.9854
 5RF  C08   C   CR6   0   0.131   3.9286   1.5732  -0.0908
 5RF  C09   C   CH2   0  -0.688   2.6182   2.1555   0.3453
 5RF  O11   O   O     0  -0.470   1.4697   0.4879  -0.9573
 5RF  N12   N   NH1   0  -0.637   0.3174   1.5381   0.6802
 5RF  C15   C   CH2   0  -0.530  -1.0631  -0.2056   1.7224
 5RF  C16   C   CR6   0   0.211   0.1119  -1.1305   1.8424
 5RF  C17   C   CR6   0  -0.170   0.2890  -2.2670   1.0550
 5RF  BR1   BR  BR    0  -0.058  -1.0200  -2.7596  -0.2249
 5RF  C19   C   CR16  0  -0.213   1.4064  -3.0811   1.1752
 5RF  C20   C   CR16  0  -0.269   2.3877  -2.7614   2.1013
 5RF  C21   C   CR16  0  -0.245   2.2420  -1.6371   2.8999
 5RF  C22   C   CR16  0  -0.317   1.1178  -0.8382   2.7630
 5RF  C23   C   C     0   0.570  -2.0973   1.7269   0.5299
 5RF  O24   O   O     0  -0.488  -2.0860   2.7857   1.1387
 5RF  N25   N   NH1   0  -0.630  -3.1567   1.2595  -0.1431
 5RF  C27   C   CH1   0  -0.174  -4.4269   1.9665  -0.2332
 5RF  C28   C   CH3   0  -0.644  -4.4438   2.9373  -1.4110
 5RF  C29   C   CR6   0   0.152  -5.5565   0.9649  -0.2930
 5RF  C30   C   CR16  0  -0.312  -5.6790   0.0863  -1.3682
 5RF  C31   C   CR16  0  -0.237  -6.7165  -0.8340  -1.4150
 5RF  C32   C   CR16  0  -0.267  -7.6523  -0.8838  -0.3892
 5RF  C33   C   CR16  0  -0.237  -7.5404  -0.0107   0.6835
 5RF  C34   C   CR16  0  -0.322  -6.4960   0.9043   0.7308
 5RF  H141  H   HCH1  0   0.288  -0.8443   0.2342  -0.3900
 5RF  H012  H   HCH3  0   0.258   9.3455  -0.0822  -2.1172
 5RF  H013  H   HCH3  0   0.227   8.0334   0.6885  -3.0237
 5RF  H011  H   HCH3  0   0.227   8.7727   1.5264  -1.6418
 5RF  H051  H   HCR6  0   0.259   3.7396  -0.1974   1.1148
 5RF  H061  H   HCR6  0   0.276   6.5954   2.2642  -2.0690
 5RF  H071  H   HCR6  0   0.252   4.4497   3.1848  -1.3999
 5RF  H091  H   HCH2  0   0.300   2.4758   3.1454  -0.0990
 5RF  H092  H   HCH2  0   0.276   2.6109   2.3126   1.4276
 5RF  H13   H   HNH1  0   0.398   0.3599   2.2185   1.4230
 5RF  H152  H   HCH2  0   0.278  -1.1566   0.3679   2.6474
 5RF  H151  H   HCH2  0   0.273  -1.9974  -0.7582   1.6085
 5RF  H191  H   HCR6  0   0.278   1.5173  -3.9604   0.5549
 5RF  H201  H   HCR6  0   0.268   3.2585  -3.3964   2.1950
 5RF  H211  H   HCR6  0   0.268   3.0012  -1.3809   3.6269
 5RF  H221  H   HCR6  0   0.261   1.0083   0.0360   3.3933
 5RF  H26   H   HNH1  0   0.399  -3.0480   0.4186  -0.6890
 5RF  H271  H   HCH1  0   0.269  -4.5310   2.5443   0.6864
 5RF  H282  H   HCH3  0   0.238  -5.3853   3.4861  -1.4355
 5RF  H283  H   HCH3  0   0.242  -3.6319   3.6582  -1.3187
 5RF  H281  H   HCH3  0   0.230  -4.3313   2.4156  -2.3617
 5RF  H301  H   HCR6  0   0.259  -4.9656   0.1121  -2.1845
 5RF  H311  H   HCR6  0   0.258  -6.7963  -1.5105  -2.2560
 5RF  H321  H   HCR6  0   0.258  -8.4643  -1.5981  -0.4278
 5RF  H331  H   HCR6  0   0.258  -8.2637  -0.0423   1.4879
 5RF  H341  H   HCR6  0   0.255  -6.4139   1.5807   1.5732
 5RF  H041  H   HCR6  0   0.257   5.9003  -1.1438   0.4542

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
 5RF  C31  C30   aromatic  1.388  0.020  1.388
 5RF  C31  C32   aromatic  1.389  0.020  1.389
 5RF  C30  C29   aromatic  1.394  0.020  1.394
 5RF  C32  C33   aromatic  1.388  0.020  1.388
 5RF  C29  C27   single    1.511  0.020  1.511
 5RF  C29  C34   aromatic  1.391  0.020  1.391
 5RF  C28  C27   single    1.526  0.020  1.526
 5RF  C33  C34   aromatic  1.389  0.020  1.389
 5RF  C27  N25   single    1.456  0.020  1.456
 5RF  O24  C23   double    1.221  0.020  1.221
 5RF  N25  C23   single    1.339  0.020  1.339
 5RF  C23  C14   single    1.526  0.020  1.526
 5RF  BR1  C17   single    1.896  0.020  1.896
 5RF  O11  C10   double    1.218  0.020  1.218
 5RF  C14  C15   single    1.544  0.020  1.544
 5RF  C14  N12   single    1.435  0.020  1.435
 5RF  C15  C16   single    1.500  0.020  1.500
 5RF  C10  N12   single    1.349  0.020  1.349
 5RF  C10  C09   single    1.520  0.020  1.520
 5RF  C07  C06   aromatic  1.393  0.020  1.393
 5RF  C07  C08   aromatic  1.385  0.020  1.385
 5RF  C06  C03   aromatic  1.391  0.020  1.391
 5RF  C17  C16   aromatic  1.394  0.020  1.394
 5RF  C17  C19   aromatic  1.388  0.020  1.388
 5RF  C16  C22   aromatic  1.395  0.020  1.395
 5RF  C09  C08   single    1.499  0.020  1.499
 5RF  C08  C05   aromatic  1.396  0.020  1.396
 5RF  C03  O02   single    1.348  0.020  1.348
 5RF  C03  C04   aromatic  1.398  0.020  1.398
 5RF  O02  C01   single    1.413  0.020  1.413
 5RF  C19  C20   aromatic  1.387  0.020  1.387
 5RF  C22  C21   aromatic  1.386  0.020  1.386
 5RF  C05  C04   aromatic  1.380  0.020  1.380
 5RF  C20  C21   aromatic  1.387  0.020  1.387
 5RF  C14  H141  single    0.970  0.020  1.090
 5RF  C01  H012  single    0.970  0.020  1.090
 5RF  C01  H013  single    0.970  0.020  1.090
 5RF  C01  H011  single    0.970  0.020  1.090
 5RF  C04  H041  single    0.930  0.020  1.080
 5RF  C05  H051  single    0.930  0.020  1.080
 5RF  C06  H061  single    0.930  0.020  1.080
 5RF  C07  H071  single    0.930  0.020  1.080
 5RF  C09  H091  single    0.970  0.020  1.090
 5RF  C09  H092  single    0.970  0.020  1.090
 5RF  N12  H13   single    0.860  0.020  1.020
 5RF  C15  H152  single    0.970  0.020  1.090
 5RF  C15  H151  single    0.970  0.020  1.090
 5RF  C19  H191  single    0.930  0.020  1.080
 5RF  C20  H201  single    0.930  0.020  1.080
 5RF  C21  H211  single    0.930  0.020  1.080
 5RF  C22  H221  single    0.930  0.020  1.080
 5RF  N25  H26   single    0.860  0.020  1.020
 5RF  C27  H271  single    0.970  0.020  1.090
 5RF  C28  H282  single    0.970  0.020  1.090
 5RF  C28  H283  single    0.970  0.020  1.090
 5RF  C28  H281  single    0.970  0.020  1.090
 5RF  C30  H301  single    0.930  0.020  1.080
 5RF  C31  H311  single    0.930  0.020  1.080
 5RF  C32  H321  single    0.930  0.020  1.080
 5RF  C33  H331  single    0.930  0.020  1.080
 5RF  C34  H341  single    0.930  0.020  1.080

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
 5RF  H141  C14  C23   109.82  3.000
 5RF  H141  C14  C15   109.60  3.000
 5RF  C23   C14  C15   108.74  3.000
 5RF  H141  C14  N12   107.61  3.000
 5RF  C15   C14  N12   110.99  3.000
 5RF  C23   C14  N12   110.07  3.000
 5RF  N12   C10  O11   123.39  3.000
 5RF  N12   C10  C09   113.86  3.000
 5RF  O11   C10  C09   122.74  3.000
 5RF  H011  C01  H013  108.76  3.000
 5RF  H011  C01  H012  108.76  3.000
 5RF  H013  C01  H012  108.65  3.000
 5RF  H011  C01  O02   111.93  3.000
 5RF  H013  C01  O02   112.05  3.000
 5RF  H012  C01  O02   106.58  3.000
 5RF  C03   O02  C01   118.44  3.000
 5RF  C06   C03  C04   119.11  3.000
 5RF  C04   C03  O02   116.26  3.000
 5RF  C06   C03  O02   124.63  3.000
 5RF  H041  C04  C05   120.25  3.000
 5RF  H041  C04  C03   119.50  3.000
 5RF  C05   C04  C03   120.25  3.000
 5RF  H051  C05  C08   119.70  3.000
 5RF  H051  C05  C04   118.90  3.000
 5RF  C08   C05  C04   121.40  3.000
 5RF  H061  C06  C07   118.75  3.000
 5RF  H061  C06  C03   121.57  3.000
 5RF  C07   C06  C03   119.68  3.000
 5RF  H071  C07  C08   119.75  3.000
 5RF  H071  C07  C06   118.43  3.000
 5RF  C08   C07  C06   121.82  3.000
 5RF  C09   C08  C07   121.70  3.000
 5RF  C09   C08  C05   120.55  3.000
 5RF  C07   C08  C05   117.74  3.000
 5RF  H092  C09  H091  105.72  3.000
 5RF  H092  C09  C08   110.46  3.000
 5RF  H091  C09  C08   110.31  3.000
 5RF  H092  C09  C10   109.43  3.000
 5RF  H091  C09  C10   107.60  3.000
 5RF  C08   C09  C10   113.02  3.000
 5RF  H13   N12  C10   118.91  3.000
 5RF  H13   N12  C14   117.19  3.000
 5RF  C10   N12  C14   123.62  3.000
 5RF  H151  C15  H152  106.31  3.000
 5RF  H151  C15  C16   111.51  3.000
 5RF  H152  C15  C16   108.85  3.000
 5RF  H151  C15  C14   109.72  3.000
 5RF  H152  C15  C14   108.39  3.000
 5RF  C16   C15  C14   111.85  3.000
 5RF  C22   C16  C17   116.88  3.000
 5RF  C22   C16  C15   119.24  3.000
 5RF  C17   C16  C15   123.85  3.000
 5RF  C19   C17  BR1   117.51  3.000
 5RF  C19   C17  C16   122.13  3.000
 5RF  BR1   C17  C16   120.36  3.000
 5RF  H191  C19  C20   119.86  3.000
 5RF  H191  C19  C17   120.65  3.000
 5RF  C20   C19  C17   119.49  3.000
 5RF  H201  C20  C21   120.71  3.000
 5RF  H201  C20  C19   119.48  3.000
 5RF  C21   C20  C19   119.81  3.000
 5RF  H211  C21  C22   119.94  3.000
 5RF  H211  C21  C20   120.35  3.000
 5RF  C22   C21  C20   119.72  3.000
 5RF  H221  C22  C21   119.32  3.000
 5RF  H221  C22  C16   118.71  3.000
 5RF  C21   C22  C16   121.97  3.000
 5RF  N25   C23  O24   124.08  3.000
 5RF  N25   C23  C14   114.41  3.000
 5RF  O24   C23  C14   121.43  3.000
 5RF  H26   N25  C27   117.73  3.000
 5RF  H26   N25  C23   118.54  3.000
 5RF  C27   N25  C23   123.47  3.000
 5RF  H271  C27  C29   108.25  3.000
 5RF  H271  C27  C28   108.21  3.000
 5RF  C29   C27  C28   112.51  3.000
 5RF  H271  C27  N25   106.75  3.000
 5RF  C28   C27  N25   111.47  3.000
 5RF  C29   C27  N25   109.43  3.000
 5RF  H281  C28  H283  108.27  3.000
 5RF  H281  C28  H282  108.09  3.000
 5RF  H283  C28  H282  108.20  3.000
 5RF  H281  C28  C27   111.55  3.000
 5RF  H283  C28  C27   110.31  3.000
 5RF  H282  C28  C27   110.31  3.000
 5RF  C34   C29  C30   118.75  3.000
 5RF  C34   C29  C27   120.32  3.000
 5RF  C30   C29  C27   120.93  3.000
 5RF  H301  C30  C31   118.84  3.000
 5RF  H301  C30  C29   120.52  3.000
 5RF  C31   C30  C29   120.64  3.000
 5RF  H311  C31  C32   120.11  3.000
 5RF  H311  C31  C30   119.73  3.000
 5RF  C32   C31  C30   120.16  3.000
 5RF  H321  C32  C33   120.23  3.000
 5RF  H321  C32  C31   120.18  3.000
 5RF  C33   C32  C31   119.60  3.000
 5RF  H331  C33  C34   119.76  3.000
 5RF  H331  C33  C32   120.16  3.000
 5RF  C34   C33  C32   120.09  3.000
 5RF  H341  C34  C33   119.64  3.000
 5RF  H341  C34  C29   119.60  3.000
 5RF  C33   C34  C29   120.76  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
 5RF  CONST_01  C08   C07  C06  C03    0.00   0.0  0
 5RF  CONST_02  C08   C05  C04  C03    0.00   0.0  0
 5RF  CONST_03  C07   C06  C03  C04    0.00   0.0  0
 5RF  CONST_04  C07   C08  C05  C04    0.00   0.0  0
 5RF  CONST_05  C06   C07  C08  C05    0.00   0.0  0
 5RF  CONST_06  C06   C03  C04  C05    0.00   0.0  0
 5RF  CONST_07  C20   C19  C17  C16    0.00   0.0  0
 5RF  CONST_08  C20   C21  C22  C16    0.00   0.0  0
 5RF  CONST_09  C21   C22  C16  C17    0.00   0.0  0
 5RF  CONST_10  C21   C20  C19  C17    0.00   0.0  0
 5RF  CONST_11  C22   C16  C17  C19    0.00   0.0  0
 5RF  CONST_12  C22   C21  C20  C19    0.00   0.0  0
 5RF  CONST_13  C32   C31  C30  C29    0.00   0.0  0
 5RF  CONST_14  C32   C33  C34  C29    0.00   0.0  0
 5RF  CONST_15  C33   C32  C31  C30    0.00   0.0  0
 5RF  CONST_16  C33   C34  C29  C30    0.00   0.0  0
 5RF  CONST_17  C34   C29  C30  C31    0.00   0.0  0
 5RF  CONST_18  C34   C33  C32  C31    0.00   0.0  0
 5RF  CONST_19  C07   C06  C03  O02  180.00   0.0  0
 5RF  CONST_20  C05   C04  C03  O02  180.00   0.0  0
 5RF  CONST_21  C09   C08  C05  C04  180.00   0.0  0
 5RF  CONST_22  C09   C08  C07  C06  180.00   0.0  0
 5RF  CONST_23  C19   C17  C16  C15  180.00   0.0  0
 5RF  CONST_24  C21   C22  C16  C15  180.00   0.0  0
 5RF  CONST_25  C22   C16  C17  BR1  180.00   0.0  0
 5RF  CONST_26  C20   C19  C17  BR1  180.00   0.0  0
 5RF  CONST_27  C31   C30  C29  C27  180.00   0.0  0
 5RF  CONST_28  C33   C34  C29  C27  180.00   0.0  0
 5RF  CONST_29  H071  C07  C06  C03  180.00   0.0  0
 5RF  CONST_30  H051  C05  C04  C03  180.00   0.0  0
 5RF  CONST_31  H061  C06  C03  C04  180.00   0.0  0
 5RF  CONST_32  H041  C04  C03  C06  180.00   0.0  0
 5RF  CONST_33  H191  C19  C17  C16  180.00   0.0  0
 5RF  CONST_34  H211  C21  C22  C16  180.00   0.0  0
 5RF  CONST_35  H221  C22  C16  C17  180.00   0.0  0
 5RF  CONST_36  H201  C20  C19  C17  180.00   0.0  0
 5RF  CONST_37  H311  C31  C30  C29  180.00   0.0  0
 5RF  CONST_38  H331  C33  C34  C29  180.00   0.0  0
 5RF  CONST_39  H321  C32  C31  C30  180.00   0.0  0
 5RF  CONST_40  H341  C34  C29  C30  180.00   0.0  0
 5RF  CONST_41  H301  C30  C31  C32  180.00   0.0  0
 5RF  CONST_42  C27   N25  C23  C14  180.00   0.0  0
 5RF  CONST_43  O11   C10  N12  C14    0.00   0.0  0
 5RF  CONST_44  C09   C10  N12  C14  180.00   0.0  0
 5RF  CONST_45  C27   N25  C23  O24    0.00   0.0  0
 5RF  CONST_46  H26   N25  C23  C14    0.00   0.0  0
 5RF  CONST_47  H13   N12  C10  C09    0.00   0.0  0
 5RF  Var_01    C17   C16  C15  C14  -80.52  30.0  2
 5RF  Var_02    C07   C08  C09  C10  117.64  30.0  2
 5RF  Var_03    C06   C03  O02  C01    1.49  30.0  2
 5RF  Var_04    O11   C10  C09  C08  -21.93  30.0  1
 5RF  Var_05    H012  C01  O02  C03  178.79  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
 5RF  chir_01  C14  C23  C15  N12  positiv
 5RF  chir_02  C27  N25  C29  C28  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
 5RF  plan-1  O02   0.020
 5RF  plan-1  C03   0.020
 5RF  plan-1  C04   0.020
 5RF  plan-1  C05   0.020
 5RF  plan-1  C06   0.020
 5RF  plan-1  C07   0.020
 5RF  plan-1  C08   0.020
 5RF  plan-1  C09   0.020
 5RF  plan-1  H051  0.020
 5RF  plan-1  H061  0.020
 5RF  plan-1  H071  0.020
 5RF  plan-1  H041  0.020
 5RF  plan-2  C15   0.020
 5RF  plan-2  C16   0.020
 5RF  plan-2  C17   0.020
 5RF  plan-2  BR1   0.020
 5RF  plan-2  C19   0.020
 5RF  plan-2  C20   0.020
 5RF  plan-2  C21   0.020
 5RF  plan-2  C22   0.020
 5RF  plan-2  H191  0.020
 5RF  plan-2  H201  0.020
 5RF  plan-2  H211  0.020
 5RF  plan-2  H221  0.020
 5RF  plan-3  C27   0.020
 5RF  plan-3  C29   0.020
 5RF  plan-3  C30   0.020
 5RF  plan-3  C31   0.020
 5RF  plan-3  C32   0.020
 5RF  plan-3  C33   0.020
 5RF  plan-3  C34   0.020
 5RF  plan-3  H301  0.020
 5RF  plan-3  H311  0.020
 5RF  plan-3  H321  0.020
 5RF  plan-3  H331  0.020
 5RF  plan-3  H341  0.020
 5RF  plan-4  C14   0.020
 5RF  plan-4  C10   0.020
 5RF  plan-4  C09   0.020
 5RF  plan-4  O11   0.020
 5RF  plan-4  N12   0.020
 5RF  plan-4  H13   0.020
 5RF  plan-5  C14   0.020
 5RF  plan-5  C23   0.020
 5RF  plan-5  O24   0.020
 5RF  plan-5  N25   0.020
 5RF  plan-5  C27   0.020
 5RF  plan-5  H26   0.020

