# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 14:04:47 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (4R)-6-phenyl-4-[(7-phenylheptanoyl)amino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@@H](CCc1ccccc1)NC(=O)CCCCCCc2ccccc2
#
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
 BR4  BR4  '(4R)-6-phenyl-4-[(7-phenylheptanoyl)amino]hexanoic acid'  ligand  61  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BR4
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
 BR4  C9    C  CH2    0  -0.418   0.1184   0.6697   3.9037
 BR4  C8    C  CH2    0  -0.411  -0.4333   0.0999   5.2031
 BR4  C7    C  CH2    0  -0.507   0.2146   0.7248   6.4399
 BR4  C6    C  CR6    0   0.139  -0.3443   0.1663   7.7180
 BR4  C1    C  CR16   0  -0.313   0.1879  -0.9909   8.2842
 BR4  C5    C  CR16   0  -0.315  -1.4387   0.7638   8.3405
 BR4  C2    C  CR16   0  -0.239  -0.3551  -1.5356   9.4404
 BR4  C4    C  CR16   0  -0.239  -1.9859   0.2237   9.4973
 BR4  C3    C  CR16   0  -0.275  -1.4456  -0.9295  10.0516
 BR4  C13   C  C      0   0.556  -0.1201   0.7274  -1.1409
 BR4  O1    O  O      0  -0.510  -0.1580   1.9457  -1.2704
 BR4  C12   C  CH2    0  -0.570  -0.6105   0.0572   0.1253
 BR4  C11   C  CH2    0  -0.417   0.0265   0.6631   1.3724
 BR4  C10   C  CH2    0  -0.416  -0.5179   0.0613   2.6607
 BR4  N1    N  NH1    0  -0.628   0.3500  -0.1028  -2.0854
 BR4  C23   C  CH2    0  -0.402   2.3175  -0.2328  -3.5400
 BR4  C14   C  CH1    0  -0.097   0.9001   0.3092  -3.3635
 BR4  C15   C  CH2    0  -0.400  -0.0104  -0.1168  -4.5147
 BR4  C16   C  CH2    0  -0.510  -1.4222   0.4635  -4.4248
 BR4  C17   C  CR6    0   0.143  -2.2495   0.1035  -5.6267
 BR4  C18   C  CR16   0  -0.317  -3.0899  -1.0074  -5.6124
 BR4  C22   C  CR16   0  -0.311  -2.1594   0.8499  -6.8009
 BR4  C19   C  CR16   0  -0.239  -3.8217  -1.3645  -6.7379
 BR4  C21   C  CR16   0  -0.240  -2.8883   0.4979  -7.9286
 BR4  C20   C  CR16   0  -0.275  -3.7236  -0.6121  -7.9010
 BR4  C24   C  CH2    0  -0.585   3.2922   0.2634  -2.4858
 BR4  C25   C  C      0   0.414   4.7562  -0.1718  -2.6781
 BR4  O2    O  O      0  -0.609   5.0238  -0.9115  -3.6455
 BR4  OT3   O  OC    -1  -0.633   5.5682   0.2592  -1.8319
 BR4  H91   H  HCH2   0   0.213   1.2024   0.5147   3.8697
 BR4  H92   H  HCH2   0   0.212  -0.0314   1.7550   3.8921
 BR4  H81   H  HCH2   0   0.220  -1.5158   0.2584   5.2449
 BR4  H82   H  HCH2   0   0.220  -0.2821  -0.9842   5.2255
 BR4  H71   H  HCH2   0   0.237   1.2946   0.5571   6.4011
 BR4  H72   H  HCH2   0   0.236   0.0658   1.8079   6.4125
 BR4  H11   H  HCR6   0   0.244   1.0395  -1.4711   7.8151
 BR4  H51   H  HCR6   0   0.244  -1.8663   1.6654   7.9162
 BR4  H21   H  HCR6   0   0.251   0.0756  -2.4330   9.8664
 BR4  H41   H  HCR6   0   0.251  -2.8326   0.7070   9.9683
 BR4  H31   H  HCR6   0   0.252  -1.8687  -1.3509  10.9544
 BR4  H121  H  HCH2   0   0.257  -1.6962   0.1902   0.1709
 BR4  H122  H  HCH2   0   0.243  -0.4303  -1.0203   0.0996
 BR4  H111  H  HCH2   0   0.222   1.1111   0.5189   1.3334
 BR4  H112  H  HCH2   0   0.224  -0.1410   1.7428   1.3774
 BR4  H101  H  HCH2   0   0.213  -1.6032   0.2057   2.6985
 BR4  H102  H  HCH2   0   0.213  -0.3559  -1.0219   2.6600
 BR4  HN11  H  HNH1   0   0.389   0.3420  -1.0920  -1.8897
 BR4  H231  H  HCH2   0   0.219   2.6678   0.0623  -4.5322
 BR4  H232  H  HCH2   0   0.208   2.2885  -1.3274  -3.5466
 BR4  H141  H  HCH1   0   0.238   0.9428   1.4002  -3.3455
 BR4  H151  H  HCH2   0   0.232   0.4523   0.2064  -5.4516
 BR4  H152  H  HCH2   0   0.224  -0.0641  -1.2100  -4.5599
 BR4  H161  H  HCH2   0   0.240  -1.9110   0.0977  -3.5192
 BR4  H162  H  HCH2   0   0.238  -1.3578   1.5509  -4.3296
 BR4  H181  H  HCR6   0   0.243  -3.1739  -1.5988  -4.7074
 BR4  H221  H  HCR6   0   0.244  -1.5111   1.7185  -6.8321
 BR4  H191  H  HCR6   0   0.252  -4.4713  -2.2300  -6.7052
 BR4  H211  H  HCR6   0   0.251  -2.8057   1.0926  -8.8297
 BR4  H201  H  HCR6   0   0.252  -4.2960  -0.8862  -8.7779
 BR4  H241  H  HCH2   0   0.222   2.9707  -0.0635  -1.4914
 BR4  H242  H  HCH2   0   0.219   3.2621   1.3585  -2.4455

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
 BR4  C9   C8    single    1.522  0.020  1.522
 BR4  C9   C10   single    1.523  0.020  1.523
 BR4  C9   H91   single    0.970  0.020  1.090
 BR4  C9   H92   single    0.970  0.020  1.090
 BR4  C8   C7    single    1.530  0.020  1.530
 BR4  C8   H81   single    0.970  0.020  1.090
 BR4  C8   H82   single    0.970  0.020  1.090
 BR4  C7   C6    single    1.503  0.020  1.503
 BR4  C7   H71   single    0.970  0.020  1.090
 BR4  C7   H72   single    0.970  0.020  1.090
 BR4  C6   C1    aromatic  1.394  0.020  1.394
 BR4  C6   C5    aromatic  1.394  0.020  1.394
 BR4  C1   C2    aromatic  1.389  0.020  1.389
 BR4  C1   H11   single    0.930  0.020  1.080
 BR4  C5   C4    aromatic  1.389  0.020  1.389
 BR4  C5   H51   single    0.930  0.020  1.080
 BR4  C2   C3    aromatic  1.389  0.020  1.389
 BR4  C2   H21   single    0.930  0.020  1.080
 BR4  C4   C3    aromatic  1.389  0.020  1.389
 BR4  C4   H41   single    0.930  0.020  1.080
 BR4  C3   H31   single    0.930  0.020  1.080
 BR4  C13  O1    double    1.226  0.020  1.226
 BR4  C13  C12   single    1.514  0.020  1.514
 BR4  C13  N1    single    1.343  0.020  1.343
 BR4  C12  C11   single    1.526  0.020  1.526
 BR4  C12  H121  single    0.970  0.020  1.090
 BR4  C12  H122  single    0.970  0.020  1.090
 BR4  C11  C10   single    1.523  0.020  1.523
 BR4  C11  H111  single    0.970  0.020  1.090
 BR4  C11  H112  single    0.970  0.020  1.090
 BR4  C10  H101  single    0.970  0.020  1.090
 BR4  C10  H102  single    0.970  0.020  1.090
 BR4  N1   C14   single    1.451  0.020  1.451
 BR4  N1   HN11  single    0.860  0.020  1.020
 BR4  C23  C14   single    1.528  0.020  1.528
 BR4  C23  C24   single    1.519  0.020  1.519
 BR4  C23  H231  single    0.970  0.020  1.090
 BR4  C23  H232  single    0.970  0.020  1.090
 BR4  C14  C15   single    1.528  0.020  1.528
 BR4  C14  H141  single    0.970  0.020  1.090
 BR4  C15  C16   single    1.529  0.020  1.529
 BR4  C15  H151  single    0.970  0.020  1.090
 BR4  C15  H152  single    0.970  0.020  1.090
 BR4  C16  C17   single    1.503  0.020  1.503
 BR4  C16  H161  single    0.970  0.020  1.090
 BR4  C16  H162  single    0.970  0.020  1.090
 BR4  C17  C18   aromatic  1.393  0.020  1.393
 BR4  C17  C22   aromatic  1.394  0.020  1.394
 BR4  C18  C19   aromatic  1.389  0.020  1.389
 BR4  C18  H181  single    0.930  0.020  1.080
 BR4  C22  C21   aromatic  1.388  0.020  1.388
 BR4  C22  H221  single    0.930  0.020  1.080
 BR4  C19  C20   aromatic  1.389  0.020  1.389
 BR4  C19  H191  single    0.930  0.020  1.080
 BR4  C21  C20   aromatic  1.389  0.020  1.389
 BR4  C21  H211  single    0.930  0.020  1.080
 BR4  C20  H201  single    0.930  0.020  1.080
 BR4  C24  C25   single    1.539  0.020  1.539
 BR4  C24  H241  single    0.970  0.020  1.090
 BR4  C24  H242  single    0.970  0.020  1.090
 BR4  C25  O2    deloc     1.247  0.020  1.247
 BR4  C25  OT3   deloc     1.249  0.020  1.249

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
 BR4  H92   C9   H91   105.97  3.000
 BR4  H92   C9   C10   109.26  3.000
 BR4  H91   C9   C10   109.36  3.000
 BR4  H92   C9   C8    109.28  3.000
 BR4  H91   C9   C8    109.39  3.000
 BR4  C10   C9   C8    113.31  3.000
 BR4  H82   C8   H81   106.20  3.000
 BR4  H82   C8   C7    109.24  3.000
 BR4  H81   C8   C7    109.20  3.000
 BR4  H82   C8   C9    109.76  3.000
 BR4  H81   C8   C9    109.68  3.000
 BR4  C7    C8   C9    112.57  3.000
 BR4  H72   C7   H71   106.59  3.000
 BR4  H72   C7   C6    109.81  3.000
 BR4  H71   C7   C6    109.91  3.000
 BR4  H72   C7   C8    109.07  3.000
 BR4  H71   C7   C8    109.08  3.000
 BR4  C6    C7   C8    112.23  3.000
 BR4  C5    C6   C1    118.32  3.000
 BR4  C5    C6   C7    120.84  3.000
 BR4  C1    C6   C7    120.80  3.000
 BR4  H11   C1   C2    119.58  3.000
 BR4  H11   C1   C6    119.46  3.000
 BR4  C2    C1   C6    120.97  3.000
 BR4  H51   C5   C4    119.59  3.000
 BR4  H51   C5   C6    119.43  3.000
 BR4  C4    C5   C6    120.97  3.000
 BR4  H21   C2   C3    120.05  3.000
 BR4  H21   C2   C1    119.81  3.000
 BR4  C3    C2   C1    120.14  3.000
 BR4  H41   C4   C3    120.07  3.000
 BR4  H41   C4   C5    119.79  3.000
 BR4  C3    C4   C5    120.13  3.000
 BR4  H31   C3   C4    120.27  3.000
 BR4  H31   C3   C2    120.26  3.000
 BR4  C4    C3   C2    119.47  3.000
 BR4  N1    C13  C12   115.34  3.000
 BR4  N1    C13  O1    123.45  3.000
 BR4  C12   C13  O1    121.21  3.000
 BR4  H122  C12  H121  106.52  3.000
 BR4  H122  C12  C11   109.99  3.000
 BR4  H121  C12  C11   109.37  3.000
 BR4  H122  C12  C13   111.31  3.000
 BR4  H121  C12  C13   107.60  3.000
 BR4  C11   C12  C13   111.87  3.000
 BR4  H112  C11  H111  106.39  3.000
 BR4  H112  C11  C10   109.39  3.000
 BR4  H111  C11  C10   109.40  3.000
 BR4  H112  C11  C12   109.40  3.000
 BR4  H111  C11  C12   109.40  3.000
 BR4  C10   C11  C12   112.67  3.000
 BR4  H102  C10  H101  106.08  3.000
 BR4  H102  C10  C11   109.73  3.000
 BR4  H101  C10  C11   109.34  3.000
 BR4  H102  C10  C9    109.50  3.000
 BR4  H101  C10  C9    109.45  3.000
 BR4  C11   C10  C9    112.53  3.000
 BR4  HN11  N1   C14   116.90  3.000
 BR4  HN11  N1   C13   117.87  3.000
 BR4  C14   N1   C13   125.22  3.000
 BR4  H232  C23  H231  105.84  3.000
 BR4  H232  C23  C24   110.35  3.000
 BR4  H231  C23  C24   109.64  3.000
 BR4  H232  C23  C14   109.32  3.000
 BR4  H231  C23  C14   107.84  3.000
 BR4  C24   C23  C14   113.53  3.000
 BR4  H141  C14  C15   108.32  3.000
 BR4  H141  C14  C23   108.67  3.000
 BR4  C15   C14  C23   111.52  3.000
 BR4  H141  C14  N1    106.50  3.000
 BR4  C15   C14  N1    111.01  3.000
 BR4  C23   C14  N1    110.65  3.000
 BR4  H152  C15  H151  106.28  3.000
 BR4  H152  C15  C16   109.63  3.000
 BR4  H151  C15  C16   109.20  3.000
 BR4  H152  C15  C14   109.78  3.000
 BR4  H151  C15  C14   108.11  3.000
 BR4  C16   C15  C14   113.57  3.000
 BR4  H162  C16  H161  106.69  3.000
 BR4  H162  C16  C17   109.89  3.000
 BR4  H161  C16  C17   109.66  3.000
 BR4  H162  C16  C15   109.16  3.000
 BR4  H161  C16  C15   109.56  3.000
 BR4  C17   C16  C15   111.74  3.000
 BR4  C22   C17  C18   118.33  3.000
 BR4  C22   C17  C16   120.64  3.000
 BR4  C18   C17  C16   120.99  3.000
 BR4  H181  C18  C19   119.68  3.000
 BR4  H181  C18  C17   119.36  3.000
 BR4  C19   C18  C17   120.96  3.000
 BR4  H221  C22  C21   119.58  3.000
 BR4  H221  C22  C17   119.45  3.000
 BR4  C21   C22  C17   120.97  3.000
 BR4  H191  C19  C20   120.06  3.000
 BR4  H191  C19  C18   119.80  3.000
 BR4  C20   C19  C18   120.14  3.000
 BR4  H211  C21  C20   120.08  3.000
 BR4  H211  C21  C22   119.79  3.000
 BR4  C20   C21  C22   120.13  3.000
 BR4  H201  C20  C21   120.27  3.000
 BR4  H201  C20  C19   120.26  3.000
 BR4  C21   C20  C19   119.47  3.000
 BR4  H242  C24  H241  104.87  3.000
 BR4  H242  C24  C25   108.25  3.000
 BR4  H241  C24  C25   107.95  3.000
 BR4  H242  C24  C23   109.52  3.000
 BR4  H241  C24  C23   110.14  3.000
 BR4  C25   C24  C23   115.55  3.000
 BR4  OT3   C25  O2    126.20  3.000
 BR4  OT3   C25  C24   115.85  3.000
 BR4  O2    C25  C24   117.95  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
 BR4  CONST_01  C3    C2   C1   C6      0.00   0.0  0
 BR4  CONST_02  C3    C4   C5   C6      0.00   0.0  0
 BR4  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 BR4  CONST_04  C4    C3   C2   C1      0.00   0.0  0
 BR4  CONST_05  C2    C1   C6   C5      0.00   0.0  0
 BR4  CONST_06  C2    C3   C4   C5      0.00   0.0  0
 BR4  CONST_07  C20   C19  C18  C17     0.00   0.0  0
 BR4  CONST_08  C20   C21  C22  C17     0.00   0.0  0
 BR4  CONST_09  C21   C22  C17  C18     0.00   0.0  0
 BR4  CONST_10  C21   C20  C19  C18     0.00   0.0  0
 BR4  CONST_11  C19   C18  C17  C22     0.00   0.0  0
 BR4  CONST_12  C19   C20  C21  C22     0.00   0.0  0
 BR4  CONST_13  C2    C1   C6   C7    180.00   0.0  0
 BR4  CONST_14  C4    C5   C6   C7    180.00   0.0  0
 BR4  CONST_15  C19   C18  C17  C16   180.00   0.0  0
 BR4  CONST_16  C21   C22  C17  C16   180.00   0.0  0
 BR4  CONST_17  H21   C2   C1   C6    180.00   0.0  0
 BR4  CONST_18  H41   C4   C5   C6    180.00   0.0  0
 BR4  CONST_19  H51   C5   C6   C1    180.00   0.0  0
 BR4  CONST_20  H31   C3   C2   C1    180.00   0.0  0
 BR4  CONST_21  H11   C1   C6   C5    180.00   0.0  0
 BR4  CONST_22  H191  C19  C18  C17   180.00   0.0  0
 BR4  CONST_23  H211  C21  C22  C17   180.00   0.0  0
 BR4  CONST_24  H221  C22  C17  C18   180.00   0.0  0
 BR4  CONST_25  H201  C20  C19  C18   180.00   0.0  0
 BR4  CONST_26  H181  C18  C17  C22   180.00   0.0  0
 BR4  CONST_27  C14   N1   C13  O1      0.00   0.0  0
 BR4  CONST_28  C14   N1   C13  C12   180.00   0.0  0
 BR4  CONST_29  HN11  N1   C13  O1    180.00   0.0  0
 BR4  Var_01    C1    C6   C7   C8     86.92  30.0  2
 BR4  Var_02    C18   C17  C16  C15    94.63  30.0  2
 BR4  Var_03    C6    C7   C8   C9    179.47  30.0  3
 BR4  Var_04    C17   C16  C15  C14   175.74  30.0  3
 BR4  Var_05    C12   C11  C10  C9   -179.91  30.0  1
 BR4  Var_06    C11   C10  C9   C8    178.86  30.0  3
 BR4  Var_07    C10   C9   C8   C7   -179.86  30.0  2
 BR4  Var_08    C10   C11  C12  C13   176.46  30.0  3
 BR4  Var_09    C11   C12  C13  O1    -52.02  30.0  3
 BR4  Var_10    O2    C25  C24  C23    -1.72  30.0  3
 BR4  Var_11    C25   C24  C23  C14  -175.73  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
 BR4  chir_01  C14  N1  C23  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
 BR4  plan-1  C7    0.020
 BR4  plan-1  C6    0.020
 BR4  plan-1  C1    0.020
 BR4  plan-1  C5    0.020
 BR4  plan-1  C2    0.020
 BR4  plan-1  C4    0.020
 BR4  plan-1  C3    0.020
 BR4  plan-1  H11   0.020
 BR4  plan-1  H51   0.020
 BR4  plan-1  H21   0.020
 BR4  plan-1  H41   0.020
 BR4  plan-1  H31   0.020
 BR4  plan-2  C16   0.020
 BR4  plan-2  C17   0.020
 BR4  plan-2  C18   0.020
 BR4  plan-2  C22   0.020
 BR4  plan-2  C19   0.020
 BR4  plan-2  C21   0.020
 BR4  plan-2  C20   0.020
 BR4  plan-2  H181  0.020
 BR4  plan-2  H221  0.020
 BR4  plan-2  H191  0.020
 BR4  plan-2  H211  0.020
 BR4  plan-2  H201  0.020
 BR4  plan-3  C13   0.020
 BR4  plan-3  O1    0.020
 BR4  plan-3  C12   0.020
 BR4  plan-3  N1    0.020
 BR4  plan-3  C14   0.020
 BR4  plan-3  HN11  0.020
 BR4  plan-4  C24   0.020
 BR4  plan-4  C25   0.020
 BR4  plan-4  O2    0.020
 BR4  plan-4  OT3   0.020

