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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VQ2J1

Calculation Name: 3VUQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VUQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLX6

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1859974.51541
FMO2-HF: Nuclear repulsion 1788193.583075
FMO2-HF: Total energy -71780.932335
FMO2-MP2: Total energy -71992.451796


3D Structure
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:8:ALA)


Summations of interaction energy for fragment #1(A:8:ALA)
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.
-3.433-1.907-0.022-0.625-0.8790.001
Interaction energy analysis for fragmet #1(A:8:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.001
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].
3A10VAL0-0.014-0.0123.7930.3461.769-0.021-0.619-0.7830.001
4A11LYS10.9180.9346.2940.4800.4800.0000.0000.0000.000
5A12ASP-1-0.838-0.9017.3300.2730.2730.0000.0000.0000.000
6A13LYS11.0251.0114.423-4.454-4.351-0.001-0.006-0.0960.000
7A14LYS10.8870.9439.256-0.137-0.1370.0000.0000.0000.000
8A15ARG10.8860.93311.556-0.315-0.3150.0000.0000.0000.000
9A16ALA00.0440.03012.355-0.039-0.0390.0000.0000.0000.000
10A17ILE00.0090.00111.747-0.059-0.0590.0000.0000.0000.000
11A18LEU0-0.0220.00715.160-0.043-0.0430.0000.0000.0000.000
12A19GLU-1-0.831-0.90917.1870.2270.2270.0000.0000.0000.000
13A20ALA00.0130.01217.851-0.025-0.0250.0000.0000.0000.000
14A21THR0-0.033-0.04618.911-0.028-0.0280.0000.0000.0000.000
15A22LEU00.0080.01021.259-0.020-0.0200.0000.0000.0000.000
16A23ALA00.0130.01022.672-0.016-0.0160.0000.0000.0000.000
17A24VAL00.003-0.00522.807-0.013-0.0130.0000.0000.0000.000
18A25LEU0-0.0130.02725.274-0.015-0.0150.0000.0000.0000.000
19A26ARG10.9060.95927.179-0.110-0.1100.0000.0000.0000.000
20A27GLH0-0.048-0.05326.717-0.004-0.0040.0000.0000.0000.000
21A28ARG10.8160.89527.629-0.169-0.1690.0000.0000.0000.000
22A29GLY00.0470.02830.418-0.008-0.0080.0000.0000.0000.000
23A30LEU00.005-0.02228.0760.0090.0090.0000.0000.0000.000
24A31SER00.0020.00429.7480.0040.0040.0000.0000.0000.000
25A32GLY00.0010.00930.6810.0000.0000.0000.0000.0000.000
26A33LEU0-0.029-0.00223.3920.0140.0140.0000.0000.0000.000
27A34LYS10.9770.98125.267-0.152-0.1520.0000.0000.0000.000
28A35MET00.0450.01419.1580.0060.0060.0000.0000.0000.000
29A36GLU-1-0.862-0.89520.0200.2890.2890.0000.0000.0000.000
30A37GLU-1-0.687-0.78620.8010.2280.2280.0000.0000.0000.000
31A38VAL0-0.0060.00217.7670.0190.0190.0000.0000.0000.000
32A39ALA0-0.009-0.01716.2350.0350.0350.0000.0000.0000.000
33A40ARG10.8600.91016.171-0.201-0.2010.0000.0000.0000.000
34A41ARG10.8380.89517.908-0.213-0.2130.0000.0000.0000.000
35A42ALA0-0.027-0.00914.0900.0060.0060.0000.0000.0000.000
36A43GLU-1-0.959-0.95413.1330.8270.8270.0000.0000.0000.000
37A44VAL0-0.057-0.03010.1960.2330.2330.0000.0000.0000.000
38A45GLY00.0650.03612.304-0.133-0.1330.0000.0000.0000.000
39A46LYS10.9900.96314.201-0.255-0.2550.0000.0000.0000.000
40A47GLY0-0.014-0.01215.525-0.028-0.0280.0000.0000.0000.000
41A48THR00.0400.0119.334-0.020-0.0200.0000.0000.0000.000
42A49ILE00.0450.03211.825-0.020-0.0200.0000.0000.0000.000
43A50TYR0-0.063-0.02814.031-0.037-0.0370.0000.0000.0000.000
44A51LEU0-0.030-0.0039.847-0.026-0.0260.0000.0000.0000.000
45A52TYR0-0.102-0.0496.1940.1060.1060.0000.0000.0000.000
46A53PHE00.0160.00612.528-0.050-0.0500.0000.0000.0000.000
47A54ARG10.9821.00216.321-0.035-0.0350.0000.0000.0000.000
48A55ASP-1-0.841-0.95818.9380.1070.1070.0000.0000.0000.000
49A56LYS10.9000.94620.474-0.141-0.1410.0000.0000.0000.000
50A57ARG10.8010.87722.303-0.053-0.0530.0000.0000.0000.000
51A58ASP-1-0.838-0.90619.1750.0600.0600.0000.0000.0000.000
52A59LEU0-0.020-0.01017.239-0.006-0.0060.0000.0000.0000.000
53A60LEU0-0.038-0.02620.038-0.001-0.0010.0000.0000.0000.000
54A61LYS10.8730.93223.250-0.026-0.0260.0000.0000.0000.000
55A62ALA00.0260.00918.865-0.010-0.0100.0000.0000.0000.000
56A63LEU0-0.008-0.00420.639-0.006-0.0060.0000.0000.0000.000
57A64VAL0-0.0020.00222.012-0.007-0.0070.0000.0000.0000.000
58A65GLU-1-0.843-0.90023.3420.0050.0050.0000.0000.0000.000
59A66GLU-1-0.849-0.92017.9630.0490.0490.0000.0000.0000.000
60A67ARG10.8150.87822.756-0.077-0.0770.0000.0000.0000.000
61A68THR00.009-0.02025.507-0.005-0.0050.0000.0000.0000.000
62A69TRP0-0.014-0.00322.207-0.005-0.0050.0000.0000.0000.000
63A70ALA0-0.020-0.01824.544-0.007-0.0070.0000.0000.0000.000
64A71PHE00.0300.02126.343-0.004-0.0040.0000.0000.0000.000
65A72TYR0-0.040-0.05729.657-0.001-0.0010.0000.0000.0000.000
66A73ARG10.9580.99723.0800.0190.0190.0000.0000.0000.000
67A74GLU-1-0.889-0.93629.0700.0270.0270.0000.0000.0000.000
68A75VAL0-0.026-0.01431.107-0.002-0.0020.0000.0000.0000.000
69A76GLU-1-0.882-0.93530.782-0.033-0.0330.0000.0000.0000.000
70A77GLU-1-0.838-0.88531.191-0.005-0.0050.0000.0000.0000.000
71A78VAL0-0.004-0.00233.325-0.001-0.0010.0000.0000.0000.000
72A79VAL0-0.049-0.03636.557-0.001-0.0010.0000.0000.0000.000
73A80ARG10.7460.83232.9240.0280.0280.0000.0000.0000.000
74A81ARG10.7390.86334.025-0.005-0.0050.0000.0000.0000.000
75A82LYS10.9390.97438.2320.0170.0170.0000.0000.0000.000
76A83ALA00.021-0.00141.2340.0020.0020.0000.0000.0000.000
77A84PRO00.0470.02243.364-0.001-0.0010.0000.0000.0000.000
78A85PHE00.0800.04745.3280.0010.0010.0000.0000.0000.000
79A86PHE00.032-0.01045.7680.0010.0010.0000.0000.0000.000
80A87VAL00.0210.02742.9960.0020.0020.0000.0000.0000.000
81A88ARG10.7980.87540.6180.0120.0120.0000.0000.0000.000
82A89LEU0-0.025-0.01241.7030.0010.0010.0000.0000.0000.000
83A90GLU-1-0.821-0.91443.4240.0160.0160.0000.0000.0000.000
84A91GLU-1-0.832-0.90638.2040.0120.0120.0000.0000.0000.000
85A92VAL0-0.023-0.01838.2730.0030.0030.0000.0000.0000.000
86A93LEU00.001-0.00439.3740.0030.0030.0000.0000.0000.000
87A94ARG10.8320.89239.827-0.020-0.0200.0000.0000.0000.000
88A95ARG10.8650.91633.569-0.016-0.0160.0000.0000.0000.000
89A96ARG10.9080.97036.557-0.012-0.0120.0000.0000.0000.000
90A97LEU00.0150.00738.3730.0020.0020.0000.0000.0000.000
91A98ALA00.0210.01636.1160.0030.0030.0000.0000.0000.000
92A99TRP0-0.005-0.00929.3780.0060.0060.0000.0000.0000.000
93A100VAL0-0.030-0.01635.2860.0030.0030.0000.0000.0000.000
94A101GLN0-0.019-0.00737.8330.0040.0040.0000.0000.0000.000
95A102GLU-1-0.760-0.82729.8880.0740.0740.0000.0000.0000.000
96A103TRP0-0.029-0.02930.4920.0050.0050.0000.0000.0000.000
97A104ARG10.8570.91534.514-0.030-0.0300.0000.0000.0000.000
98A105GLY00.0000.01436.0840.0010.0010.0000.0000.0000.000
99A106LEU0-0.056-0.02428.4130.0080.0080.0000.0000.0000.000
100A107TRP00.026-0.02825.2780.0040.0040.0000.0000.0000.000
101A108ALA00.0190.03831.213-0.002-0.0020.0000.0000.0000.000
102A109ALA00.0110.00233.165-0.002-0.0020.0000.0000.0000.000
103A110VAL00.016-0.01026.7340.0020.0020.0000.0000.0000.000
104A111ALA00.0010.00129.1000.0010.0010.0000.0000.0000.000
105A112ARG10.8310.91730.423-0.057-0.0570.0000.0000.0000.000
106A113GLU-1-0.839-0.91529.5740.0630.0630.0000.0000.0000.000
107A114ALA0-0.075-0.03126.0210.0020.0020.0000.0000.0000.000
108A115MET0-0.052-0.02227.255-0.006-0.0060.0000.0000.0000.000
109A116ASP-1-0.779-0.86729.6130.0390.0390.0000.0000.0000.000
110A117ASP-1-0.899-0.95932.1610.0090.0090.0000.0000.0000.000
111A118PRO0-0.0050.00232.256-0.004-0.0040.0000.0000.0000.000
112A119THR00.0340.01033.376-0.002-0.0020.0000.0000.0000.000
113A120PRO0-0.009-0.01334.223-0.002-0.0020.0000.0000.0000.000
114A121TRP00.0400.02327.7260.0000.0000.0000.0000.0000.000
115A122LEU00.004-0.00532.984-0.001-0.0010.0000.0000.0000.000
116A123LYS10.9340.97535.132-0.003-0.0030.0000.0000.0000.000
117A124GLY00.0530.03734.592-0.002-0.0020.0000.0000.0000.000
118A125LEU00.0050.00430.418-0.003-0.0030.0000.0000.0000.000
119A126HIS00.0130.01934.4960.0000.0000.0000.0000.0000.000
120A127GLU-1-0.905-0.95337.653-0.013-0.0130.0000.0000.0000.000
121A128HIS0-0.052-0.03231.833-0.004-0.0040.0000.0000.0000.000
122A129TYR0-0.0030.00436.214-0.001-0.0010.0000.0000.0000.000
123A130LEU00.0040.00637.715-0.001-0.0010.0000.0000.0000.000
124A131ARG10.9220.95134.9850.0170.0170.0000.0000.0000.000
125A132LEU00.0180.02234.022-0.001-0.0010.0000.0000.0000.000
126A133LEU00.0440.02038.6260.0000.0000.0000.0000.0000.000
127A134GLU-1-0.867-0.91942.018-0.013-0.0130.0000.0000.0000.000
128A135GLU-1-0.856-0.89037.819-0.024-0.0240.0000.0000.0000.000
129A136LEU00.0210.01441.4660.0000.0000.0000.0000.0000.000
130A137LEU0-0.025-0.02642.9520.0000.0000.0000.0000.0000.000
131A138ARG10.8740.92743.0360.0160.0160.0000.0000.0000.000
132A139SER00.0160.01943.661-0.001-0.0010.0000.0000.0000.000
133A140GLY00.0620.02645.8060.0000.0000.0000.0000.0000.000
134A141GLN0-0.101-0.05548.475-0.001-0.0010.0000.0000.0000.000
135A142SER0-0.097-0.04847.9310.0000.0000.0000.0000.0000.000
136A143GLU-1-0.823-0.90346.207-0.010-0.0100.0000.0000.0000.000
137A144GLY0-0.0030.01350.7040.0010.0010.0000.0000.0000.000
138A145ALA0-0.070-0.02850.4640.0010.0010.0000.0000.0000.000
139A146VAL0-0.020-0.00649.4090.0010.0010.0000.0000.0000.000
140A147ARG11.0070.99552.7300.0000.0000.0000.0000.0000.000
141A148THR00.0760.02454.1140.0000.0000.0000.0000.0000.000
142A149GLY0-0.0140.00355.0500.0000.0000.0000.0000.0000.000
143A150LEU0-0.043-0.00353.0250.0000.0000.0000.0000.0000.000
144A151SER00.0660.03351.478-0.001-0.0010.0000.0000.0000.000
145A152PRO00.0450.02047.1210.0010.0010.0000.0000.0000.000
146A153ARG10.9210.95742.3130.0100.0100.0000.0000.0000.000
147A154ALA00.002-0.00447.6100.0010.0010.0000.0000.0000.000
148A155THR00.028-0.01049.6450.0020.0020.0000.0000.0000.000
149A156ALA00.0110.00944.2210.0020.0020.0000.0000.0000.000
150A157ALA0-0.024-0.02245.6280.0020.0020.0000.0000.0000.000
151A158VAL0-0.0050.00346.9010.0020.0020.0000.0000.0000.000
152A159ILE00.0160.00544.8270.0020.0020.0000.0000.0000.000
153A160ALA0-0.050-0.03942.8050.0020.0020.0000.0000.0000.000
154A161ALA0-0.050-0.01343.8260.0020.0020.0000.0000.0000.000
155A162MET00.0010.02744.3140.0020.0020.0000.0000.0000.000
156A163GLY00.0420.00742.9290.0000.0000.0000.0000.0000.000
157A164CYS0-0.053-0.03743.3540.0020.0020.0000.0000.0000.000
158A165THR00.0090.00745.9270.0000.0000.0000.0000.0000.000
159A166PRO00.0110.01546.4860.0000.0000.0000.0000.0000.000
160A167SER0-0.0050.00147.4970.0010.0010.0000.0000.0000.000
161A168LEU0-0.001-0.01549.2200.0000.0000.0000.0000.0000.000
162A169GLU-1-0.851-0.93143.7410.0350.0350.0000.0000.0000.000
163A170VAL0-0.064-0.02345.5910.0000.0000.0000.0000.0000.000
164A171GLU-1-0.806-0.87344.2630.0250.0250.0000.0000.0000.000
165A172ALA00.0530.03247.767-0.002-0.0020.0000.0000.0000.000
166A173TYR0-0.014-0.01447.749-0.002-0.0020.0000.0000.0000.000
167A174LEU00.008-0.00644.415-0.002-0.0020.0000.0000.0000.000
168A175GLU-1-0.899-0.94948.5240.0150.0150.0000.0000.0000.000
169A176HIS0-0.001-0.00251.297-0.002-0.0020.0000.0000.0000.000
170A177LEU0-0.0200.00047.400-0.001-0.0010.0000.0000.0000.000
171A178MET0-0.021-0.01347.891-0.002-0.0020.0000.0000.0000.000
172A179GLU-1-0.903-0.94550.9790.0050.0050.0000.0000.0000.000
173A180VAL0-0.0020.00454.139-0.001-0.0010.0000.0000.0000.000
174A181LEU0-0.061-0.03648.485-0.001-0.0010.0000.0000.0000.000
175A182ARG10.8570.94551.881-0.006-0.0060.0000.0000.0000.000
176A183LYS10.8800.93554.203-0.004-0.0040.0000.0000.0000.000
177A184GLY0-0.0090.01556.7650.0000.0000.0000.0000.0000.000
178A185VAL0-0.005-0.03158.3580.0010.0010.0000.0000.0000.000
179A186GLU-1-0.986-0.96961.2030.0030.0030.0000.0000.0000.000
180A187PRO0-0.008-0.00263.9670.0000.0000.0000.0000.0000.000