# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 22:44:29 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (2S)-4-amino-N-[(1R)-1-(4-chloro-2-fluoro-3-phenoxyphenyl)propyl]-4-oxobutan-2-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H]([NH2+][C@@H](C)CC(N)=O)c1ccc(Cl)c(Oc2ccccc2)c1F
#
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
 4VA  4VA  (2S)-4-amino-N-[(1R)-1-(4-chloro-2-fluoro-3-phenoxyphenyl)propyl]-4-oxobutan-2-aminium  ligand  48  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4VA
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
 4VA  F     F   F     0  -0.285  -0.5473   1.5275  -1.0313
 4VA  CL    CL  CL    0  -0.069  -2.2344  -2.8207   0.7712
 4VA  C1    C   CH3   0  -0.691   2.7369   3.6234   1.9232
 4VA  C2    C   CH2   0  -0.426   1.8766   2.3670   1.9454
 4VA  C3    C   CH1   0  -0.205   1.7687   1.6676   0.5913
 4VA  N5    N   NT2   1  -0.697   3.1239   1.1851   0.1747
 4VA  C8    C   CH1   0  -0.129   3.2372   0.4627  -1.1354
 4VA  C10   C   CH3   0  -0.667   2.9458   1.3845  -2.3002
 4VA  C11   C   CH2   0  -0.600   4.6363  -0.1399  -1.2249
 4VA  C12   C   C     0   0.585   4.9542  -1.1007  -0.0962
 4VA  O13   O   O     0  -0.510   4.4556  -0.9564   1.0242
 4VA  N14   N   NH2   0  -0.787   5.8073  -2.0754  -0.3830
 4VA  C15   C   CR6   0  -0.081   0.7952   0.5195   0.6218
 4VA  C16   C   CR16  0  -0.298   0.9584  -0.5551   1.4940
 4VA  C17   C   CR16  0  -0.224   0.0419  -1.5891   1.5491
 4VA  C18   C   CR6   0  -0.119  -1.0716  -1.5578   0.7240
 4VA  C20   C   CR6   0   0.247  -1.2642  -0.5069  -0.1623
 4VA  O21   O   O2    0  -0.492  -2.3090  -0.4834  -1.0213
 4VA  C22   C   CR6   0   0.368  -3.5189   0.0019  -0.5900
 4VA  C23   C   CR16  0  -0.322  -4.5864  -0.1789  -1.4602
 4VA  C24   C   CR16  0  -0.247  -5.8397   0.2936  -1.1053
 4VA  C25   C   CR16  0  -0.268  -6.0337   0.9403   0.1098
 4VA  C26   C   CR16  0  -0.247  -4.9579   1.1107   0.9675
 4VA  C27   C   CR16  0  -0.333  -3.6933   0.6437   0.6272
 4VA  C28   C   CR6   0   0.517  -0.3272   0.5175  -0.1877
 4VA  H3    H   HCH1  0   0.320   1.4682   2.4042  -0.1522
 4VA  HN5   H   HNT2  0   0.456   3.7625   1.9838   0.1654
 4VA  HN5A  H   HNT2  0   0.473   3.5204   0.5186   0.8726
 4VA  H8    H   HCH1  0   0.314   2.5026  -0.3433  -1.0998
 4VA  H1    H   HCH3  0   0.230   3.7938   3.4158   1.7465
 4VA  H1A   H   HCH3  0   0.241   2.3963   4.3246   1.1604
 4VA  H1B   H   HCH3  0   0.262   2.6785   4.1297   2.8855
 4VA  H2A   H   HCH2  0   0.276   0.8601   2.6294   2.2410
 4VA  H10   H   HCH3  0   0.251   3.6458   2.2207  -2.3304
 4VA  H10A  H   HCH3  0   0.273   3.0485   0.8260  -3.2290
 4VA  H10B  H   HCH3  0   0.258   1.9322   1.7800  -2.2763
 4VA  H11   H   HCH2  0   0.305   4.7249  -0.6391  -2.1902
 4VA  H11A  H   HCH2  0   0.307   5.3907   0.6547  -1.2212
 4VA  HN14  H   HNH2  0   0.421   6.2070  -2.1812  -1.3002
 4VA  HN1A  H   HNH2  0   0.415   6.1093  -2.7182   0.3324
 4VA  H16   H   HCR6  0   0.285   1.8146  -0.5947   2.1545
 4VA  H17   H   HCR6  0   0.299   0.1879  -2.4114   2.2349
 4VA  H23   H   HCR6  0   0.274  -4.4336  -0.6869  -2.4040
 4VA  H24   H   HCR6  0   0.264  -6.6708   0.1502  -1.7832
 4VA  H25   H   HCR6  0   0.259  -7.0139   1.3059   0.3842
 4VA  H26   H   HCR6  0   0.266  -5.0938   1.6134   1.9162
 4VA  H27   H   HCR6  0   0.277  -2.8710   0.7895   1.3161
 4VA  H2    H   HCH2  0   0.254   2.2470   1.6641   2.6962

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
 4VA  F    C28   single    1.334  0.020  1.334
 4VA  CL   C18   single    1.717  0.020  1.717
 4VA  C1   C2    single    1.523  0.020  1.523
 4VA  C1   H1    single    0.970  0.020  1.090
 4VA  C1   H1A   single    0.970  0.020  1.090
 4VA  C1   H1B   single    0.970  0.020  1.090
 4VA  C2   C3    single    1.528  0.020  1.528
 4VA  C2   H2    single    0.970  0.020  1.090
 4VA  C2   H2A   single    0.970  0.020  1.090
 4VA  C3   N5    single    1.498  0.020  1.498
 4VA  C3   C15   single    1.506  0.020  1.506
 4VA  C3   H3    single    0.970  0.020  1.090
 4VA  N5   C8    single    1.500  0.020  1.500
 4VA  N5   HN5   single    0.890  0.020  1.040
 4VA  N5   HN5A  single    0.890  0.020  1.040
 4VA  C8   C10   single    1.514  0.020  1.514
 4VA  C8   C11   single    1.526  0.020  1.526
 4VA  C8   H8    single    0.970  0.020  1.090
 4VA  C10  H10   single    0.970  0.020  1.090
 4VA  C10  H10A  single    0.970  0.020  1.090
 4VA  C10  H10B  single    0.970  0.020  1.090
 4VA  C11  C12   single    1.516  0.020  1.516
 4VA  C11  H11   single    0.970  0.020  1.090
 4VA  C11  H11A  single    0.970  0.020  1.090
 4VA  C12  O13   double    1.235  0.020  1.235
 4VA  C12  N14   single    1.327  0.020  1.327
 4VA  N14  HN14  single    0.860  0.020  1.020
 4VA  N14  HN1A  single    0.860  0.020  1.020
 4VA  C15  C16   aromatic  1.394  0.020  1.394
 4VA  C15  C28   aromatic  1.384  0.020  1.384
 4VA  C16  C17   aromatic  1.383  0.020  1.383
 4VA  C16  H16   single    0.930  0.020  1.080
 4VA  C17  C18   aromatic  1.386  0.020  1.386
 4VA  C17  H17   single    0.930  0.020  1.080
 4VA  C18  C20   aromatic  1.388  0.020  1.388
 4VA  C20  O21   single    1.353  0.020  1.353
 4VA  C20  C28   aromatic  1.389  0.020  1.389
 4VA  O21  C22   single    1.373  0.020  1.373
 4VA  C22  C23   aromatic  1.389  0.020  1.389
 4VA  C22  C27   aromatic  1.387  0.020  1.387
 4VA  C23  C24   aromatic  1.386  0.020  1.386
 4VA  C23  H23   single    0.930  0.020  1.080
 4VA  C24  C25   aromatic  1.390  0.020  1.390
 4VA  C24  H24   single    0.930  0.020  1.080
 4VA  C25  C26   aromatic  1.386  0.020  1.386
 4VA  C25  H25   single    0.930  0.020  1.080
 4VA  C26  C27   aromatic  1.390  0.020  1.390
 4VA  C26  H26   single    0.930  0.020  1.080
 4VA  C27  H27   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
 4VA  H1B   C1   H1A   107.60  3.000
 4VA  H1B   C1   H1    106.47  3.000
 4VA  H1A   C1   H1    108.15  3.000
 4VA  H1B   C1   C2    109.90  3.000
 4VA  H1A   C1   C2    111.36  3.000
 4VA  H1    C1   C2    113.11  3.000
 4VA  H2A   C2   H2    106.52  3.000
 4VA  H2A   C2   C3    106.53  3.000
 4VA  H2    C2   C3    109.77  3.000
 4VA  H2A   C2   C1    109.39  3.000
 4VA  H2    C2   C1    110.43  3.000
 4VA  C3    C2   C1    113.87  3.000
 4VA  H3    C3   C15   110.56  3.000
 4VA  H3    C3   N5    106.13  3.000
 4VA  C15   C3   N5    110.19  3.000
 4VA  H3    C3   C2    108.36  3.000
 4VA  C15   C3   C2    112.13  3.000
 4VA  N5    C3   C2    109.27  3.000
 4VA  HN5A  N5   HN5   105.53  3.000
 4VA  HN5A  N5   C8    104.35  3.000
 4VA  HN5   N5   C8    108.72  3.000
 4VA  HN5A  N5   C3    111.33  3.000
 4VA  HN5   N5   C3    108.41  3.000
 4VA  C8    N5   C3    117.80  3.000
 4VA  H8    C8   C11   109.11  3.000
 4VA  H8    C8   C10   110.20  3.000
 4VA  C11   C8   C10   111.83  3.000
 4VA  H8    C8   N5    106.04  3.000
 4VA  C11   C8   N5    108.09  3.000
 4VA  C10   C8   N5    111.36  3.000
 4VA  H10B  C10  H10A  107.04  3.000
 4VA  H10B  C10  H10   108.65  3.000
 4VA  H10A  C10  H10   108.00  3.000
 4VA  H10B  C10  C8    112.56  3.000
 4VA  H10A  C10  C8    109.02  3.000
 4VA  H10   C10  C8    111.38  3.000
 4VA  H11A  C11  H11   106.20  3.000
 4VA  H11A  C11  C12   108.23  3.000
 4VA  H11   C11  C12   110.60  3.000
 4VA  H11A  C11  C8    110.16  3.000
 4VA  H11   C11  C8    107.89  3.000
 4VA  C12   C11  C8    113.51  3.000
 4VA  N14   C12  O13   122.79  3.000
 4VA  N14   C12  C11   116.08  3.000
 4VA  O13   C12  C11   121.12  3.000
 4VA  HN1A  N14  HN14  117.45  3.000
 4VA  HN1A  N14  C12   120.51  3.000
 4VA  HN14  N14  C12   121.99  3.000
 4VA  C28   C15  C16   117.39  3.000
 4VA  C28   C15  C3    120.91  3.000
 4VA  C16   C15  C3    121.66  3.000
 4VA  H16   C16  C17   118.21  3.000
 4VA  H16   C16  C15   120.19  3.000
 4VA  C17   C16  C15   121.59  3.000
 4VA  H17   C17  C18   120.23  3.000
 4VA  H17   C17  C16   120.32  3.000
 4VA  C18   C17  C16   119.46  3.000
 4VA  C20   C18  C17   120.57  3.000
 4VA  C20   C18  CL    118.71  3.000
 4VA  C17   C18  CL    120.72  3.000
 4VA  C28   C20  O21   119.78  3.000
 4VA  C28   C20  C18   118.46  3.000
 4VA  O21   C20  C18   121.72  3.000
 4VA  C22   O21  C20   119.16  3.000
 4VA  C27   C22  C23   120.89  3.000
 4VA  C27   C22  O21   123.37  3.000
 4VA  C23   C22  O21   115.75  3.000
 4VA  H23   C23  C24   120.73  3.000
 4VA  H23   C23  C22   119.91  3.000
 4VA  C24   C23  C22   119.36  3.000
 4VA  H24   C24  C25   120.14  3.000
 4VA  H24   C24  C23   119.28  3.000
 4VA  C25   C24  C23   120.58  3.000
 4VA  H25   C25  C26   120.31  3.000
 4VA  H25   C25  C24   120.37  3.000
 4VA  C26   C25  C24   119.32  3.000
 4VA  H26   C26  C27   119.00  3.000
 4VA  H26   C26  C25   120.13  3.000
 4VA  C27   C26  C25   120.87  3.000
 4VA  H27   C27  C26   119.33  3.000
 4VA  H27   C27  C22   121.68  3.000
 4VA  C26   C27  C22   118.99  3.000
 4VA  C20   C28  C15   122.53  3.000
 4VA  C20   C28  F     117.30  3.000
 4VA  C15   C28  F     120.17  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
 4VA  CONST_01  C18   C17  C16  C15     0.00   0.0  0
 4VA  CONST_02  C18   C20  C28  C15     0.00   0.0  0
 4VA  CONST_03  C20   C28  C15  C16     0.00   0.0  0
 4VA  CONST_04  C20   C18  C17  C16     0.00   0.0  0
 4VA  CONST_05  C28   C15  C16  C17     0.00   0.0  0
 4VA  CONST_06  C28   C20  C18  C17     0.00   0.0  0
 4VA  CONST_07  C25   C24  C23  C22     0.00   0.0  0
 4VA  CONST_08  C25   C26  C27  C22     0.00   0.0  0
 4VA  CONST_09  C26   C27  C22  C23     0.00   0.0  0
 4VA  CONST_10  C26   C25  C24  C23     0.00   0.0  0
 4VA  CONST_11  C27   C22  C23  C24     0.00   0.0  0
 4VA  CONST_12  C27   C26  C25  C24     0.00   0.0  0
 4VA  CONST_13  C16   C15  C28  F     180.00   0.0  0
 4VA  CONST_14  C18   C20  C28  F     180.00   0.0  0
 4VA  CONST_15  C16   C17  C18  CL    180.00   0.0  0
 4VA  CONST_16  C28   C20  C18  CL    180.00   0.0  0
 4VA  CONST_17  C17   C16  C15  C3    180.00   0.0  0
 4VA  CONST_18  C20   C28  C15  C3    180.00   0.0  0
 4VA  CONST_19  O21   C20  C28  C15   180.00   0.0  0
 4VA  CONST_20  O21   C20  C18  C17   180.00   0.0  0
 4VA  CONST_21  C24   C23  C22  O21   180.00   0.0  0
 4VA  CONST_22  C26   C27  C22  O21   180.00   0.0  0
 4VA  CONST_23  H17   C17  C16  C15   180.00   0.0  0
 4VA  CONST_24  H16   C16  C17  C18   180.00   0.0  0
 4VA  CONST_25  H24   C24  C23  C22   180.00   0.0  0
 4VA  CONST_26  H26   C26  C27  C22   180.00   0.0  0
 4VA  CONST_27  H27   C27  C22  C23   180.00   0.0  0
 4VA  CONST_28  H25   C25  C24  C23   180.00   0.0  0
 4VA  CONST_29  H23   C23  C24  C25   180.00   0.0  0
 4VA  CONST_30  HN14  N14  C12  C11     0.00   0.0  0
 4VA  CONST_31  HN1A  N14  C12  C11   180.00   0.0  0
 4VA  Var_01    C23   C22  O21  C20  -171.25  30.0  2
 4VA  Var_02    C28   C20  O21  C22   -97.40  30.0  2
 4VA  Var_03    O13   C12  C11  C8    -30.60  30.0  3
 4VA  Var_04    H1    C1   C2   C3    -67.57  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
 4VA  chir_01  C3  C2  N5   C15  negativ
 4VA  chir_02  C8  N5  C10  C11  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
 4VA  plan-1  F     0.020
 4VA  plan-1  CL    0.020
 4VA  plan-1  C3    0.020
 4VA  plan-1  C15   0.020
 4VA  plan-1  C16   0.020
 4VA  plan-1  C17   0.020
 4VA  plan-1  C18   0.020
 4VA  plan-1  C20   0.020
 4VA  plan-1  O21   0.020
 4VA  plan-1  C28   0.020
 4VA  plan-1  H16   0.020
 4VA  plan-1  H17   0.020
 4VA  plan-2  O21   0.020
 4VA  plan-2  C22   0.020
 4VA  plan-2  C23   0.020
 4VA  plan-2  C24   0.020
 4VA  plan-2  C25   0.020
 4VA  plan-2  C26   0.020
 4VA  plan-2  C27   0.020
 4VA  plan-2  H23   0.020
 4VA  plan-2  H24   0.020
 4VA  plan-2  H25   0.020
 4VA  plan-2  H26   0.020
 4VA  plan-2  H27   0.020
 4VA  plan-3  C11   0.020
 4VA  plan-3  C12   0.020
 4VA  plan-3  O13   0.020
 4VA  plan-3  N14   0.020
 4VA  plan-3  HN14  0.020
 4VA  plan-3  HN1A  0.020

