FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: Z78MN

Calculation Name: 1VLA-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VLA

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X021

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 144
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1280759.287084
FMO2-HF: Nuclear repulsion 1220121.595213
FMO2-HF: Total energy -60637.691871
FMO2-MP2: Total energy -60808.529797


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:-5:HIS)


Summations of interaction energy for fragment #1(A:-5:HIS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
2.1233.495-0.02-0.461-0.8920
Interaction energy analysis for fragmet #1(A:-5:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.839 / q_NPA : 0.906
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A-3HIS00.0440.0273.7951.8413.213-0.020-0.461-0.8920.000
4A-2HIS0-0.038-0.0195.6215.0195.0190.0000.0000.0000.000
5A-1HIS00.0230.0158.7102.2012.2010.0000.0000.0000.000
6A0HIS0-0.003-0.01412.270-0.233-0.2330.0000.0000.0000.000
7A1MET0-0.008-0.00715.3990.3680.3680.0000.0000.0000.000
8A2GLN00.0170.01819.156-0.494-0.4940.0000.0000.0000.000
9A3ALA00.0080.00822.3280.2220.2220.0000.0000.0000.000
10A4ARG10.8720.92825.97210.14610.1460.0000.0000.0000.000
11A5TRP0-0.006-0.00228.6700.1680.1680.0000.0000.0000.000
12A6ILE0-0.067-0.04832.032-0.047-0.0470.0000.0000.0000.000
13A7GLY00.0500.04234.9450.2530.2530.0000.0000.0000.000
14A8ASN0-0.032-0.02537.7580.0630.0630.0000.0000.0000.000
15A9MET00.0170.02036.824-0.174-0.1740.0000.0000.0000.000
16A10MET0-0.0200.01234.933-0.225-0.2250.0000.0000.0000.000
17A11PHE0-0.027-0.02729.407-0.136-0.1360.0000.0000.0000.000
18A12HIS00.0050.00128.5750.0850.0850.0000.0000.0000.000
19A13VAL0-0.008-0.00223.865-0.272-0.2720.0000.0000.0000.000
20A14ARG10.8550.93124.06811.73511.7350.0000.0000.0000.000
21A15THR0-0.018-0.03221.568-0.357-0.3570.0000.0000.0000.000
22A16ASP-1-0.867-0.92616.120-17.873-17.8730.0000.0000.0000.000
23A17SER0-0.008-0.00618.9130.2750.2750.0000.0000.0000.000
24A18ASN0-0.020-0.00620.6961.1241.1240.0000.0000.0000.000
25A19HIS0-0.018-0.00323.4950.9080.9080.0000.0000.0000.000
26A20ASP-1-0.836-0.90125.845-10.806-10.8060.0000.0000.0000.000
27A21VAL0-0.009-0.00326.5700.1210.1210.0000.0000.0000.000
28A22LEU00.0120.00129.158-0.082-0.0820.0000.0000.0000.000
29A23MET0-0.020-0.00627.660-0.139-0.1390.0000.0000.0000.000
30A24ASP-1-0.751-0.86532.969-8.052-8.0520.0000.0000.0000.000
31A25THR0-0.065-0.05036.417-0.064-0.0640.0000.0000.0000.000
32A26LYS10.9670.98039.0897.1227.1220.0000.0000.0000.000
33A27GLU-1-0.822-0.89142.750-6.892-6.8920.0000.0000.0000.000
34A28GLU-1-0.871-0.94045.090-6.860-6.8600.0000.0000.0000.000
35A29VAL0-0.073-0.03940.8200.0180.0180.0000.0000.0000.000
36A30GLY00.0200.01241.322-0.190-0.1900.0000.0000.0000.000
37A31GLY0-0.034-0.02440.285-0.137-0.1370.0000.0000.0000.000
38A32LYS10.7920.86140.7557.2627.2620.0000.0000.0000.000
39A33ASP-1-0.843-0.88541.224-7.462-7.4620.0000.0000.0000.000
40A34ALA00.0170.01440.1400.0320.0320.0000.0000.0000.000
41A35ALA0-0.049-0.03035.054-0.164-0.1640.0000.0000.0000.000
42A36PRO00.0380.02233.9280.1090.1090.0000.0000.0000.000
43A37ARG10.8220.89134.6487.9277.9270.0000.0000.0000.000
44A38PRO00.044-0.00229.809-0.192-0.1920.0000.0000.0000.000
45A39LEU0-0.021-0.01030.116-0.307-0.3070.0000.0000.0000.000
46A40GLU-1-0.796-0.88931.689-8.740-8.7400.0000.0000.0000.000
47A41LEU00.0090.01928.847-0.149-0.1490.0000.0000.0000.000
48A42VAL0-0.022-0.00326.327-0.355-0.3550.0000.0000.0000.000
49A43LEU0-0.007-0.00727.846-0.266-0.2660.0000.0000.0000.000
50A44THR00.003-0.01630.3150.0360.0360.0000.0000.0000.000
51A45GLY00.0180.01226.145-0.115-0.1150.0000.0000.0000.000
52A46LEU0-0.029-0.00824.586-0.372-0.3720.0000.0000.0000.000
53A47MET00.0140.00726.833-0.025-0.0250.0000.0000.0000.000
54A48GLY00.0190.01527.3350.0430.0430.0000.0000.0000.000
55A49CYS0-0.070-0.04123.080-0.319-0.3190.0000.0000.0000.000
56A50THR00.0170.00824.7160.1010.1010.0000.0000.0000.000
57A51GLY00.0690.02726.9500.2480.2480.0000.0000.0000.000
58A52MET0-0.031-0.02124.8150.2350.2350.0000.0000.0000.000
59A53ASP-1-0.791-0.84523.138-13.541-13.5410.0000.0000.0000.000
60A54VAL00.0100.00525.7730.1190.1190.0000.0000.0000.000
61A55VAL00.0220.01829.2140.2160.2160.0000.0000.0000.000
62A56SER0-0.057-0.02724.0400.2430.2430.0000.0000.0000.000
63A57ILE0-0.029-0.02225.6470.1120.1120.0000.0000.0000.000
64A58LEU00.0740.02828.4200.1780.1780.0000.0000.0000.000
65A59ARG10.9730.99628.54910.75110.7510.0000.0000.0000.000
66A60LYS10.9270.96524.44612.22112.2210.0000.0000.0000.000
67A61MET0-0.076-0.04029.3050.1640.1640.0000.0000.0000.000
68A62LYS10.8770.94632.2919.5149.5140.0000.0000.0000.000
69A63VAL00.0650.02534.6720.1970.1970.0000.0000.0000.000
70A64ILE0-0.0260.00232.6040.0880.0880.0000.0000.0000.000
71A65ASP-1-0.888-0.93835.981-8.287-8.2870.0000.0000.0000.000
72A66GLN0-0.002-0.00138.6930.1930.1930.0000.0000.0000.000
73A67MET0-0.070-0.02134.7410.0250.0250.0000.0000.0000.000
74A68LYS0-0.0340.00239.741-0.047-0.0470.0000.0000.0000.000
75A69ASP-1-0.838-0.91139.984-7.540-7.5400.0000.0000.0000.000
76A70PHE0-0.084-0.05931.882-0.150-0.1500.0000.0000.0000.000
77A71ARG10.7540.86236.5477.5197.5190.0000.0000.0000.000
78A72ILE0-0.014-0.00231.295-0.055-0.0550.0000.0000.0000.000
79A73GLU-1-0.806-0.88935.554-7.639-7.6390.0000.0000.0000.000
80A74ILE0-0.024-0.02331.501-0.147-0.1470.0000.0000.0000.000
81A75GLU-1-0.830-0.89735.602-7.644-7.6440.0000.0000.0000.000
82A76TYR0-0.029-0.03834.825-0.245-0.2450.0000.0000.0000.000
83A77GLU-1-0.890-0.94336.556-7.494-7.4940.0000.0000.0000.000
84A78ARG10.8910.93932.3879.0429.0420.0000.0000.0000.000
85A79THR00.0250.02636.4550.1600.1600.0000.0000.0000.000
86A80GLU-1-0.836-0.92537.888-7.673-7.6730.0000.0000.0000.000
87A81GLU-1-0.945-0.96839.740-7.589-7.5890.0000.0000.0000.000
88A82HIS0-0.025-0.00835.812-0.403-0.4030.0000.0000.0000.000
89A83PRO00.0150.00232.0480.0750.0750.0000.0000.0000.000
90A84ARG10.8490.92734.0498.1618.1610.0000.0000.0000.000
91A85ILE0-0.0100.00030.860-0.378-0.3780.0000.0000.0000.000
92A86PHE00.0350.00730.6240.2720.2720.0000.0000.0000.000
93A87THR00.0140.00532.970-0.159-0.1590.0000.0000.0000.000
94A88LYS10.9490.98835.3047.8337.8330.0000.0000.0000.000
95A89VAL00.0580.01830.812-0.024-0.0240.0000.0000.0000.000
96A90HIS10.7670.87033.8338.3098.3090.0000.0000.0000.000
97A91LEU00.0120.00130.285-0.035-0.0350.0000.0000.0000.000
98A92LYS10.8760.93534.6507.6437.6430.0000.0000.0000.000
99A93TYR0-0.022-0.03729.483-0.097-0.0970.0000.0000.0000.000
100A94ILE0-0.0060.00436.1170.1510.1510.0000.0000.0000.000
101A95PHE00.002-0.01834.370-0.207-0.2070.0000.0000.0000.000
102A96LYS10.8600.95040.0247.3367.3360.0000.0000.0000.000
103A97PHE00.002-0.03037.353-0.233-0.2330.0000.0000.0000.000
104A98ASP-1-0.889-0.93343.200-6.639-6.6390.0000.0000.0000.000
105A99GLY00.0010.00045.389-0.060-0.0600.0000.0000.0000.000
106A100GLU-1-0.868-0.92745.441-6.894-6.8940.0000.0000.0000.000
107A101PRO0-0.009-0.00141.898-0.164-0.1640.0000.0000.0000.000
108A102PRO00.0180.02538.3520.0140.0140.0000.0000.0000.000
109A103LYS10.8730.91938.2146.8696.8690.0000.0000.0000.000
110A104ASP-1-0.834-0.91037.426-8.272-8.2720.0000.0000.0000.000
111A105LYS10.8050.88934.2678.4648.4640.0000.0000.0000.000
112A106VAL00.0180.01733.337-0.409-0.4090.0000.0000.0000.000
113A107GLU-1-0.889-0.94433.705-8.551-8.5510.0000.0000.0000.000
114A108LYS10.9270.97028.30610.51610.5160.0000.0000.0000.000
115A109ALA00.003-0.00929.284-0.464-0.4640.0000.0000.0000.000
116A110VAL00.0210.01628.717-0.454-0.4540.0000.0000.0000.000
117A111GLN0-0.0080.00029.323-0.310-0.3100.0000.0000.0000.000
118A112LEU0-0.082-0.03424.699-0.350-0.3500.0000.0000.0000.000
119A113SER00.0090.00124.731-0.420-0.4200.0000.0000.0000.000
120A114GLN00.004-0.00824.852-0.613-0.6130.0000.0000.0000.000
121A115GLU-1-0.766-0.86826.083-11.008-11.0080.0000.0000.0000.000
122A116LYS10.7670.86720.90713.89213.8920.0000.0000.0000.000
123A117TYR0-0.023-0.00420.356-0.739-0.7390.0000.0000.0000.000
124A118CYS0-0.0340.00220.412-0.566-0.5660.0000.0000.0000.000
125A119SER0-0.015-0.03421.824-0.324-0.3240.0000.0000.0000.000
126A120VAL00.0110.01622.8850.0760.0760.0000.0000.0000.000
127A121SER00.038-0.00124.576-0.042-0.0420.0000.0000.0000.000
128A122ALA0-0.033-0.00219.1950.0010.0010.0000.0000.0000.000
129A123ILE0-0.054-0.01619.969-0.660-0.6600.0000.0000.0000.000
130A124LEU0-0.029-0.01621.9660.1140.1140.0000.0000.0000.000
131A125LYS10.9470.97123.04213.00813.0080.0000.0000.0000.000
132A126CYS0-0.0210.00026.6510.3970.3970.0000.0000.0000.000
133A127SER0-0.035-0.01430.026-0.128-0.1280.0000.0000.0000.000
134A128SER0-0.033-0.04332.1710.2580.2580.0000.0000.0000.000
135A129LYS10.8380.90529.55910.10210.1020.0000.0000.0000.000
136A130VAL00.0270.02128.1690.2980.2980.0000.0000.0000.000
137A131THR0-0.033-0.00631.1380.1020.1020.0000.0000.0000.000
138A132TYR0-0.046-0.05431.261-0.158-0.1580.0000.0000.0000.000
139A133GLU-1-0.835-0.89535.196-7.610-7.6100.0000.0000.0000.000
140A134ILE0-0.014-0.01034.995-0.245-0.2450.0000.0000.0000.000
141A135VAL00.0010.01038.5500.1930.1930.0000.0000.0000.000
142A136TYR00.012-0.01839.464-0.208-0.2080.0000.0000.0000.000
143A137GLU-1-0.850-0.90943.544-7.130-7.1300.0000.0000.0000.000
144A138ASN-1-0.861-0.94045.737-6.861-6.8610.0000.0000.0000.000