# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:43:59 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 5-[(2S)-2-{[(4-aminobenzoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](CNC(=O)c1ccc(N)cc1)Cc2ccc3OCOc3c2C(O)=O
#
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
 4VW  4VW  '5-[(2S)-2-{[(4-aminobenzoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  55  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4VW
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
 4VW  C1    C  CR16  0  -0.263  -5.0270  -1.2981   0.9247
 4VW  C2    C  CR16  0  -0.290  -3.8704  -0.3224  -0.9245
 4VW  C3    C  CR16  0  -0.343   3.1348  -0.6679   1.9968
 4VW  C4    C  CR16  0  -0.319  -6.1304  -1.5206   0.1275
 4VW  C5    C  CR16  0  -0.316  -4.9723  -0.5269  -1.7315
 4VW  C6    C  CR16  0  -0.324   3.9909  -1.7317   1.6849
 4VW  C7    C  CR6   0  -0.061  -3.8679  -0.7080   0.4177
 4VW  C8    C  CR6   0  -0.198   3.2317   0.1971  -0.2592
 4VW  C9    C  CR6   0   0.127   2.7530   0.2929   1.0736
 4VW  C10   C  CR6   0   0.324  -6.1293  -1.1357  -1.2227
 4VW  C11   C  CR56  0   0.297   4.4360  -1.8042   0.3941
 4VW  C12   C  CR56  0   0.338   4.0550  -0.8706  -0.5593
 4VW  C13   C  C     0   0.507  -2.7232  -0.4719   1.3360
 4VW  C15   C  CH2   0   0.070   5.3417  -2.3963  -1.5467
 4VW  C16   C  CH3   0  -0.648  -2.1887   4.2091   0.6583
 4VW  C17   C  CH3   0  -0.664  -1.3611   2.7695  -1.2159
 4VW  C18   C  CH2   0  -0.521   1.7940   1.3736   1.4981
 4VW  C19   C  CH2   0  -0.395  -0.3744   2.5645   1.1136
 4VW  C20   C  CH2   0  -0.248  -0.3017   0.0190   1.4470
 4VW  C21   C  CH1   0  -0.242  -1.6328   2.8383   0.2829
 4VW  C22   C  CH1   0  -0.271   0.3891   1.2581   0.8748
 4VW  N23   N  NH2   0  -0.856  -7.2391  -1.2984  -2.0012
 4VW  N24   N  NH1   0  -0.649  -1.5176  -0.3346   0.7527
 4VW  O25   O  OH1   0  -0.583   2.7372   0.6770  -2.4887
 4VW  O26   O  O     0  -0.498  -2.8870  -0.4038   2.5504
 4VW  O27   O  O     0  -0.424   2.8695   2.4059  -1.0905
 4VW  O28   O  O     0  -0.483   5.2893  -2.6965  -0.1608
 4VW  O29   O  O     0  -0.471   4.6672  -1.1556  -1.7262
 4VW  H1    H  HCR6  0   0.253  -5.0627  -1.5988   1.9638
 4VW  H4    H  HCR6  0   0.260  -7.0104  -1.9931   0.5473
 4VW  H2    H  HCR6  0   0.248  -3.0126   0.1739  -1.3631
 4VW  H5    H  HCR6  0   0.262  -4.9465  -0.2042  -2.7653
 4VW  H3    H  HCR6  0   0.261   2.7529  -0.5975   3.0072
 4VW  H6    H  HCR6  0   0.280   4.2840  -2.4544   2.4341
 4VW  H181  H  HCH2  0   0.249   1.6965   1.3428   2.5869
 4VW  H182  H  HCH2  0   0.262   2.2044   2.3532   1.2571
 4VW  H231  H  HNH2  0   0.387  -7.9299  -1.9615  -1.6915
 4VW  H232  H  HNH2  0   0.387  -7.1125  -1.2882  -2.9995
 4VW  H24   H  HNH1  0   0.397  -1.4298  -0.5508  -0.2263
 4VW  H25   H  HOH1  0   0.486   2.5942   1.3739  -3.1475
 4VW  H151  H  HCH2  0   0.248   6.3789  -2.2994  -1.8683
 4VW  H152  H  HCH2  0   0.240   4.8326  -3.1773  -2.1197
 4VW  H161  H  HCH3  0   0.225  -3.1015   4.4353   0.1043
 4VW  H162  H  HCH3  0   0.223  -2.4242   4.2648   1.7227
 4VW  H163  H  HCH3  0   0.211  -1.4649   4.9982   0.4383
 4VW  H21   H  HCH1  0   0.225  -2.3995   2.0975   0.5212
 4VW  H171  H  HCH3  0   0.218  -1.0703   1.7697  -1.5413
 4VW  H172  H  HCH3  0   0.228  -2.2492   3.0489  -1.7855
 4VW  H173  H  HCH3  0   0.218  -0.5553   3.4514  -1.5003
 4VW  H22   H  HCH1  0   0.231   0.5058   1.1103  -0.2040
 4VW  H191  H  HCH2  0   0.215   0.3194   3.3918   0.9211
 4VW  H192  H  HCH2  0   0.220  -0.6271   2.6348   2.1783
 4VW  H201  H  HCH2  0   0.247   0.3870  -0.8301   1.4087
 4VW  H202  H  HCH2  0   0.242  -0.5404   0.1815   2.4982
 4VW  C14   C  C     0   0.483   2.9280   1.2186  -1.2940

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
 4VW  C1   C4    aromatic  1.379  0.020  1.379
 4VW  C1   C7    aromatic  1.396  0.020  1.396
 4VW  C2   C5    aromatic  1.381  0.020  1.381
 4VW  C2   C7    aromatic  1.396  0.020  1.396
 4VW  C3   C6    aromatic  1.401  0.020  1.401
 4VW  C3   C9    aromatic  1.386  0.020  1.386
 4VW  C4   C10   aromatic  1.404  0.020  1.404
 4VW  C5   C10   aromatic  1.403  0.020  1.403
 4VW  C6   C11   aromatic  1.367  0.020  1.367
 4VW  C7   C13   single    1.486  0.020  1.486
 4VW  C8   C9    aromatic  1.419  0.020  1.419
 4VW  C8   C12   aromatic  1.381  0.020  1.381
 4VW  C8   C14   single    1.485  0.020  1.485
 4VW  C9   C18   single    1.506  0.020  1.506
 4VW  C10  N23   single    1.365  0.020  1.365
 4VW  C11  C12   aromatic  1.388  0.020  1.388
 4VW  C11  O28   single    1.354  0.020  1.354
 4VW  C12  O29   single    1.348  0.020  1.348
 4VW  C13  N24   single    1.346  0.020  1.346
 4VW  C13  O26   double    1.227  0.020  1.227
 4VW  C14  O25   single    1.326  0.020  1.326
 4VW  C14  O27   double    1.206  0.020  1.206
 4VW  C15  O28   single    1.419  0.020  1.419
 4VW  C15  O29   single    1.424  0.020  1.424
 4VW  C16  C21   single    1.526  0.020  1.526
 4VW  C17  C21   single    1.525  0.020  1.525
 4VW  C18  C22   single    1.541  0.020  1.541
 4VW  C19  C21   single    1.532  0.020  1.532
 4VW  C19  C22   single    1.532  0.020  1.532
 4VW  C20  C22   single    1.530  0.020  1.530
 4VW  C20  N24   single    1.444  0.020  1.444
 4VW  C1   H1    single    0.930  0.020  1.080
 4VW  C4   H4    single    0.930  0.020  1.080
 4VW  C2   H2    single    0.930  0.020  1.080
 4VW  C5   H5    single    0.930  0.020  1.080
 4VW  C3   H3    single    0.930  0.020  1.080
 4VW  C6   H6    single    0.930  0.020  1.080
 4VW  C18  H181  single    0.970  0.020  1.090
 4VW  C18  H182  single    0.970  0.020  1.090
 4VW  N23  H231  single    0.890  0.020  1.040
 4VW  N23  H232  single    0.890  0.020  1.040
 4VW  N24  H24   single    0.860  0.020  1.020
 4VW  O25  H25   single    0.850  0.020  0.980
 4VW  C15  H151  single    0.970  0.020  1.090
 4VW  C15  H152  single    0.970  0.020  1.090
 4VW  C16  H161  single    0.970  0.020  1.090
 4VW  C16  H162  single    0.970  0.020  1.090
 4VW  C16  H163  single    0.970  0.020  1.090
 4VW  C21  H21   single    0.970  0.020  1.090
 4VW  C17  H171  single    0.970  0.020  1.090
 4VW  C17  H172  single    0.970  0.020  1.090
 4VW  C17  H173  single    0.970  0.020  1.090
 4VW  C22  H22   single    0.970  0.020  1.090
 4VW  C19  H191  single    0.970  0.020  1.090
 4VW  C19  H192  single    0.970  0.020  1.090
 4VW  C20  H201  single    0.970  0.020  1.090
 4VW  C20  H202  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
 4VW  H1    C1   C7    119.58  3.000
 4VW  H1    C1   C4    118.92  3.000
 4VW  C7    C1   C4    121.50  3.000
 4VW  H2    C2   C7    120.93  3.000
 4VW  H2    C2   C5    117.57  3.000
 4VW  C7    C2   C5    121.48  3.000
 4VW  H3    C3   C9    118.65  3.000
 4VW  H3    C3   C6    118.23  3.000
 4VW  C9    C3   C6    123.13  3.000
 4VW  H4    C4   C10   119.53  3.000
 4VW  H4    C4   C1    119.75  3.000
 4VW  C10   C4   C1    120.73  3.000
 4VW  H5    C5   C10   119.67  3.000
 4VW  H5    C5   C2    119.64  3.000
 4VW  C10   C5   C2    120.69  3.000
 4VW  H6    C6   C11   122.04  3.000
 4VW  H6    C6   C3    121.25  3.000
 4VW  C11   C6   C3    116.71  3.000
 4VW  C13   C7   C2    123.46  3.000
 4VW  C13   C7   C1    118.83  3.000
 4VW  C2    C7   C1    117.66  3.000
 4VW  C14   C8   C12   120.14  3.000
 4VW  C14   C8   C9    122.60  3.000
 4VW  C12   C8   C9    117.20  3.000
 4VW  C18   C9   C8    121.86  3.000
 4VW  C18   C9   C3    119.02  3.000
 4VW  C8    C9   C3    119.06  3.000
 4VW  N23   C10  C5    121.02  3.000
 4VW  N23   C10  C4    121.00  3.000
 4VW  C5    C10  C4    117.93  3.000
 4VW  O28   C11  C12   109.57  3.000
 4VW  O28   C11  C6    128.84  3.000
 4VW  C12   C11  C6    121.57  3.000
 4VW  O29   C12  C11   109.13  3.000
 4VW  O29   C12  C8    128.47  3.000
 4VW  C11   C12  C8    122.31  3.000
 4VW  O26   C13  N24   122.85  3.000
 4VW  O26   C13  C7    121.16  3.000
 4VW  N24   C13  C7    115.99  3.000
 4VW  H152  C15  H151  110.59  3.000
 4VW  H152  C15  O29   109.61  3.000
 4VW  H151  C15  O29   109.64  3.000
 4VW  H152  C15  O28   110.07  3.000
 4VW  H151  C15  O28   110.00  3.000
 4VW  O29   C15  O28   106.86  3.000
 4VW  H163  C16  H162  107.59  3.000
 4VW  H163  C16  H161  107.58  3.000
 4VW  H162  C16  H161  107.70  3.000
 4VW  H163  C16  C21   110.96  3.000
 4VW  H162  C16  C21   111.36  3.000
 4VW  H161  C16  C21   111.47  3.000
 4VW  H173  C17  H172  107.72  3.000
 4VW  H173  C17  H171  107.31  3.000
 4VW  H172  C17  H171  107.21  3.000
 4VW  H173  C17  C21   111.03  3.000
 4VW  H172  C17  C21   110.88  3.000
 4VW  H171  C17  C21   112.46  3.000
 4VW  H182  C18  H181  106.21  3.000
 4VW  H182  C18  C22   108.75  3.000
 4VW  H181  C18  C22   108.62  3.000
 4VW  H182  C18  C9    110.07  3.000
 4VW  H181  C18  C9    108.49  3.000
 4VW  C22   C18  C9    114.38  3.000
 4VW  H192  C19  H191  105.53  3.000
 4VW  H192  C19  C22   108.72  3.000
 4VW  H191  C19  C22   107.50  3.000
 4VW  H192  C19  C21   109.00  3.000
 4VW  H191  C19  C21   106.83  3.000
 4VW  C22   C19  C21   118.50  3.000
 4VW  H202  C20  H201  106.70  3.000
 4VW  H202  C20  N24   108.40  3.000
 4VW  H201  C20  N24   108.85  3.000
 4VW  H202  C20  C22   109.81  3.000
 4VW  H201  C20  C22   109.35  3.000
 4VW  N24   C20  C22   113.50  3.000
 4VW  H21   C21  C19   109.69  3.000
 4VW  H21   C21  C17   107.99  3.000
 4VW  C19   C21  C17   112.24  3.000
 4VW  H21   C21  C16   107.44  3.000
 4VW  C19   C21  C16   109.05  3.000
 4VW  C17   C21  C16   110.32  3.000
 4VW  H22   C22  C20   107.90  3.000
 4VW  H22   C22  C19   108.77  3.000
 4VW  C20   C22  C19   114.04  3.000
 4VW  H22   C22  C18   108.14  3.000
 4VW  C20   C22  C18   108.72  3.000
 4VW  C19   C22  C18   109.11  3.000
 4VW  H232  N23  H231  113.47  3.000
 4VW  H232  N23  C10   117.53  3.000
 4VW  H231  N23  C10   117.45  3.000
 4VW  H24   N24  C20   116.54  3.000
 4VW  H24   N24  C13   118.53  3.000
 4VW  C20   N24  C13   124.80  3.000
 4VW  H25   O25  C14   109.87  3.000
 4VW  C15   O28  C11   106.51  3.000
 4VW  C15   O29  C12   106.87  3.000
 4VW  O27   C14  O25   123.19  3.000
 4VW  O27   C14  C8    124.70  3.000
 4VW  O25   C14  C8    112.11  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
 4VW  CONST_01  C5    C10  C4   C1      0.00   0.0  0
 4VW  CONST_02  C5    C2   C7   C1      0.00   0.0  0
 4VW  CONST_03  C4    C10  C5   C2      0.00   0.0  0
 4VW  CONST_04  C4    C1   C7   C2      0.00   0.0  0
 4VW  CONST_05  C12   C11  C6   C3      0.00   0.0  0
 4VW  CONST_06  C12   C8   C9   C3      0.00   0.0  0
 4VW  CONST_07  C8    C9   C3   C6      0.00   0.0  0
 4VW  CONST_08  C8    C12  C11  C6      0.00   0.0  0
 4VW  CONST_09  C10   C4   C1   C7      0.00   0.0  0
 4VW  CONST_10  C10   C5   C2   C7      0.00   0.0  0
 4VW  CONST_11  C11   C6   C3   C9      0.00   0.0  0
 4VW  CONST_12  C11   C12  C8   C9      0.00   0.0  0
 4VW  CONST_13  N23   C10  C4   C1    180.00   0.0  0
 4VW  CONST_14  N23   C10  C5   C2    180.00   0.0  0
 4VW  CONST_15  C14   C8   C9   C3    180.00   0.0  0
 4VW  CONST_16  C13   C7   C1   C4    180.00   0.0  0
 4VW  CONST_17  C13   C7   C2   C5    180.00   0.0  0
 4VW  CONST_18  C18   C9   C3   C6    180.00   0.0  0
 4VW  CONST_19  C14   C8   C12  C11   180.00   0.0  0
 4VW  CONST_20  C18   C9   C8   C12   180.00   0.0  0
 4VW  CONST_21  O29   C12  C8   C14     0.00   0.0  0
 4VW  CONST_22  H2    C2   C7   C1    180.00   0.0  0
 4VW  CONST_23  H1    C1   C7   C2    180.00   0.0  0
 4VW  CONST_24  H5    C5   C10  C4    180.00   0.0  0
 4VW  CONST_25  H4    C4   C10  C5    180.00   0.0  0
 4VW  CONST_26  H3    C3   C9   C8    180.00   0.0  0
 4VW  CONST_27  H6    C6   C3   C9    180.00   0.0  0
 4VW  CONST_30  C20   N24  C13  C7    180.00   0.0  0
 4VW  CONST_31  H24   N24  C13  C7      0.00   0.0  0
 4VW  CONST_32  H25   O25  C14  C8    180.00   0.0  0
 4VW  CONST_33  O26   C13  N24  C20     0.00   0.0  0
 4VW  Var_01    O29   C15  O28  C11     9.88  30.0  1
 4VW  Var_02    O28   C15  O29  C12   -10.13  30.0  1
 4VW  Var_03    N24   C13  C7   C1    158.50  30.0  2
 4VW  Var_04    C22   C18  C9   C3   -109.68  30.0  2
 4VW  Var_05    O25   C14  C8   C9   -142.91  30.0  2
 4VW  Var_06    C22   C20  N24  C13  -124.04  30.0  2
 4VW  Var_07    C22   C19  C21  C16  -178.02  30.0  2
 4VW  Var_08    H171  C17  C21  C16  -173.47  30.0  3
 4VW  Var_09    H161  C16  C21  C17    57.60  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
 4VW  chir_01  C22  C18  C19  C20  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
 4VW  plan-1  C1    0.020
 4VW  plan-1  C2    0.020
 4VW  plan-1  C4    0.020
 4VW  plan-1  C5    0.020
 4VW  plan-1  C7    0.020
 4VW  plan-1  C10   0.020
 4VW  plan-1  C13   0.020
 4VW  plan-1  N23   0.020
 4VW  plan-1  H1    0.020
 4VW  plan-1  H4    0.020
 4VW  plan-1  H2    0.020
 4VW  plan-1  H5    0.020
 4VW  plan-2  C3    0.020
 4VW  plan-2  C6    0.020
 4VW  plan-2  C8    0.020
 4VW  plan-2  C9    0.020
 4VW  plan-2  C11   0.020
 4VW  plan-2  C12   0.020
 4VW  plan-2  C18   0.020
 4VW  plan-2  O28   0.020
 4VW  plan-2  O29   0.020
 4VW  plan-2  H3    0.020
 4VW  plan-2  H6    0.020
 4VW  plan-2  C14   0.020
 4VW  plan-3  C7    0.020
 4VW  plan-3  C13   0.020
 4VW  plan-3  C20   0.020
 4VW  plan-3  N24   0.020
 4VW  plan-3  O26   0.020
 4VW  plan-3  H24   0.020
 4VW  plan-4  C10   0.020
 4VW  plan-4  N23   0.020
 4VW  plan-4  H231  0.020
 4VW  plan-4  H232  0.020
 4VW  plan-5  C8    0.020
 4VW  plan-5  O25   0.020
 4VW  plan-5  O27   0.020
 4VW  plan-5  H25   0.020
 4VW  plan-5  C14   0.020

