Manual

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: QY3YY

Calculation Name: 2VU8-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VU8

Chain ID: E

ChEMBL ID:

UniProt ID: P35049

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 OptH
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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2322294.637988
FMO2-HF: Nuclear repulsion 2243561.334673
FMO2-HF: Total energy -78733.303315
FMO2-MP2: Total energy -78961.008356


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(E:16:ILE)


Summations of interaction energy for fragment #1(E:16:ILE)
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.
-19.723-3.86327.209-13.987-29.08-0.084
Interaction energy analysis for fragmet #1(E:16:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : 0.018
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].
3E18GLY00.0400.0053.525-1.7781.6780.038-1.651-1.8430.009
4E19GLY0-0.055-0.0202.473-0.3070.2741.319-0.802-1.0970.003
5E20THR0-0.026-0.0193.258-0.274-0.902-0.0040.834-0.2020.000
6E21SER00.001-0.0094.8970.2220.294-0.001-0.002-0.0690.000
7E22ALA0-0.0010.0026.1560.0560.0560.0000.0000.0000.000
8E23SER00.0210.0097.902-0.115-0.1150.0000.0000.0000.000
9E24ALA0-0.001-0.01111.5440.0430.0430.0000.0000.0000.000
10E25GLY00.0360.01113.596-0.014-0.0140.0000.0000.0000.000
11E26ASP-1-0.868-0.93310.0710.5420.5420.0000.0000.0000.000
12E27PHE00.0010.0027.1880.0720.0720.0000.0000.0000.000
13E28PRO0-0.0080.00011.482-0.008-0.0080.0000.0000.0000.000
14E29PHE00.0450.02210.555-0.032-0.0320.0000.0000.0000.000
15E30ILE0-0.0350.0116.422-0.001-0.0010.0000.0000.0000.000
16E31VAL0-0.021-0.00710.834-0.071-0.0710.0000.0000.0000.000
17E32SER0-0.007-0.00510.1020.0670.0670.0000.0000.0000.000
18E33ILE0-0.017-0.01511.196-0.050-0.0500.0000.0000.0000.000
19E34SER00.0140.00912.8120.0040.0040.0000.0000.0000.000
20E35ARG10.9500.97615.0420.0100.0100.0000.0000.0000.000
21E37ASN0-0.043-0.03117.658-0.014-0.0140.0000.0000.0000.000
22E38GLY00.0120.01619.089-0.015-0.0150.0000.0000.0000.000
23E39GLY0-0.0050.00915.542-0.026-0.0260.0000.0000.0000.000
24E40PRO0-0.029-0.02510.1020.0590.0590.0000.0000.0000.000
25E41TRP0-0.031-0.03611.197-0.063-0.0630.0000.0000.0000.000
26E42CYS0-0.0710.0089.6240.0000.0000.0000.0000.0000.000
27E43GLY00.0440.0247.961-0.038-0.0380.0000.0000.0000.000
28E44GLY00.033-0.0018.989-0.054-0.0540.0000.0000.0000.000
29E45SER00.003-0.00210.3240.0720.0720.0000.0000.0000.000
30E46LEU0-0.0270.00212.653-0.039-0.0390.0000.0000.0000.000
31E47LEU00.003-0.00916.0510.0110.0110.0000.0000.0000.000
32E48ASN00.018-0.00318.548-0.018-0.0180.0000.0000.0000.000
33E49ALA00.0550.03021.0110.0050.0050.0000.0000.0000.000
34E50ASN0-0.0010.02223.013-0.001-0.0010.0000.0000.0000.000
35E51THR00.0310.01819.674-0.011-0.0110.0000.0000.0000.000
36E52VAL00.0330.02114.4290.0180.0180.0000.0000.0000.000
37E53LEU0-0.0290.00214.556-0.029-0.0290.0000.0000.0000.000
38E54THR00.018-0.00611.8260.0470.0470.0000.0000.0000.000
39E55ALA00.0570.03611.976-0.023-0.0230.0000.0000.0000.000
40E56ALA0-0.027-0.01313.829-0.031-0.0310.0000.0000.0000.000
41E57HIS0-0.0070.02312.1690.0020.0020.0000.0000.0000.000
42E59VAL00.009-0.00815.311-0.028-0.0280.0000.0000.0000.000
43E59SER0-0.027-0.00818.765-0.024-0.0240.0000.0000.0000.000
44E59GLY00.0160.01421.342-0.007-0.0070.0000.0000.0000.000
45E59TYR0-0.048-0.01017.640-0.030-0.0300.0000.0000.0000.000
46E59ALA00.0210.00623.1240.0070.0070.0000.0000.0000.000
47E60GLN00.047-0.00122.7930.0070.0070.0000.0000.0000.000
48E61SER0-0.013-0.01623.0380.0070.0070.0000.0000.0000.000
49E62GLY00.0210.02622.073-0.005-0.0050.0000.0000.0000.000
50E63PHE0-0.036-0.01217.012-0.007-0.0070.0000.0000.0000.000
51E64GLN0-0.035-0.01518.223-0.003-0.0030.0000.0000.0000.000
52E65ILE0-0.017-0.00515.0180.0160.0160.0000.0000.0000.000
53E65ARG10.9100.93014.276-0.112-0.1120.0000.0000.0000.000
54E66ALA00.0500.03214.1530.0510.0510.0000.0000.0000.000
55E69GLY00.0370.00515.144-0.034-0.0340.0000.0000.0000.000
56E70SER0-0.020-0.01913.904-0.026-0.0260.0000.0000.0000.000
57E71LEU00.0360.0179.7660.0380.0380.0000.0000.0000.000
58E72SER00.0290.0289.904-0.017-0.0170.0000.0000.0000.000
59E73ARG10.9230.9599.1390.3340.3340.0000.0000.0000.000
60E74THR0-0.069-0.04211.948-0.009-0.0090.0000.0000.0000.000
61E75SER0-0.026-0.00915.4250.0040.0040.0000.0000.0000.000
62E76GLY00.0630.02816.2670.0180.0180.0000.0000.0000.000
63E80GLY00.0020.02017.7210.0060.0060.0000.0000.0000.000
64E81ILE0-0.003-0.00118.595-0.019-0.0190.0000.0000.0000.000
65E82THR0-0.013-0.01118.4130.0170.0170.0000.0000.0000.000
66E83SER00.0290.00919.900-0.006-0.0060.0000.0000.0000.000
67E84SER00.0100.02720.4320.0090.0090.0000.0000.0000.000
68E85LEU00.0190.00419.2850.0110.0110.0000.0000.0000.000
69E86SER0-0.0070.00923.254-0.013-0.0130.0000.0000.0000.000
70E87SER0-0.028-0.01924.797-0.007-0.0070.0000.0000.0000.000
71E88VAL00.0590.02321.0920.0140.0140.0000.0000.0000.000
72E89ARG10.9050.96822.386-0.116-0.1160.0000.0000.0000.000
73E90VAL00.0460.01620.9030.0200.0200.0000.0000.0000.000
74E91HIS00.0320.02520.902-0.019-0.0190.0000.0000.0000.000
75E92PRO0-0.015-0.02322.807-0.008-0.0080.0000.0000.0000.000
76E93SER0-0.006-0.00325.066-0.010-0.0100.0000.0000.0000.000
77E94TYR0-0.0040.01118.507-0.003-0.0030.0000.0000.0000.000
78E95SER00.0000.00022.262-0.018-0.0180.0000.0000.0000.000
79E96GLY00.0160.01721.9320.0080.0080.0000.0000.0000.000
80E99ASN00.0420.01016.7290.0100.0100.0000.0000.0000.000
81E100ASN00.0560.05317.5260.0510.0510.0000.0000.0000.000
82E101ASN0-0.035-0.03419.7620.0020.0020.0000.0000.0000.000
83E102ASP-1-0.736-0.84014.6990.2570.2570.0000.0000.0000.000
84E103LEU0-0.009-0.01314.3130.0440.0440.0000.0000.0000.000
85E104ALA00.008-0.00416.595-0.039-0.0390.0000.0000.0000.000
86E105ILE0-0.037-0.00617.3290.0300.0300.0000.0000.0000.000
87E106LEU00.001-0.00216.184-0.024-0.0240.0000.0000.0000.000
88E107LYS10.8840.95420.257-0.135-0.1350.0000.0000.0000.000
89E108LEU0-0.019-0.01518.936-0.007-0.0070.0000.0000.0000.000
90E109SER0-0.024-0.02023.071-0.004-0.0040.0000.0000.0000.000
91E110THR0-0.044-0.01524.138-0.011-0.0110.0000.0000.0000.000
92E111SER0-0.014-0.01423.6660.0120.0120.0000.0000.0000.000
93E112ILE00.000-0.00719.385-0.008-0.0080.0000.0000.0000.000
94E113PRO00.0220.01922.4960.0140.0140.0000.0000.0000.000
95E114SER0-0.0130.00321.8000.0050.0050.0000.0000.0000.000
96E115GLY00.0460.01422.070-0.015-0.0150.0000.0000.0000.000
97E116GLY0-0.014-0.00922.0020.0020.0020.0000.0000.0000.000
98E117ASN0-0.024-0.02616.9180.0210.0210.0000.0000.0000.000
99E118ILE0-0.0080.03316.7420.0310.0310.0000.0000.0000.000
100E119GLY00.0150.00017.259-0.024-0.0240.0000.0000.0000.000
101E120TYR0-0.067-0.04417.2020.0130.0130.0000.0000.0000.000
102E121ALA00.0050.00514.5560.0030.0030.0000.0000.0000.000
103E122ARG10.9630.98416.417-0.292-0.2920.0000.0000.0000.000
104E123LEU0-0.014-0.00716.5180.0370.0370.0000.0000.0000.000
105E124ALA00.0260.01416.680-0.023-0.0230.0000.0000.0000.000
106E125ALA00.0150.00518.526-0.017-0.0170.0000.0000.0000.000
107E126SER00.0170.00921.8140.0120.0120.0000.0000.0000.000
108E127GLY00.0040.00523.030-0.011-0.0110.0000.0000.0000.000
109E128SER0-0.087-0.05320.3640.0030.0030.0000.0000.0000.000
110E129ASP-1-0.797-0.91719.3120.2360.2360.0000.0000.0000.000
111E130PRO0-0.028-0.00415.010-0.012-0.0120.0000.0000.0000.000
112E131VAL00.0610.03817.320-0.015-0.0150.0000.0000.0000.000
113E132ALA00.000-0.01217.5750.0230.0230.0000.0000.0000.000
114E133GLY0-0.016-0.00316.830-0.018-0.0180.0000.0000.0000.000
115E134SER0-0.059-0.01416.0700.0190.0190.0000.0000.0000.000
116E135SER00.032-0.00912.6480.0390.0390.0000.0000.0000.000
117E136ALA00.0220.0159.892-0.030-0.0300.0000.0000.0000.000
118E137THR0-0.0130.0126.2940.0280.0280.0000.0000.0000.000
119E138VAL0-0.0080.0172.280-0.965-0.5701.351-0.328-1.4180.003
120E139ALA00.012-0.0032.777-0.7540.5660.814-0.702-1.432-0.003
121E140GLY00.004-0.0042.640-1.159-0.6361.0470.061-1.631-0.005
122E141TRP0-0.070-0.0463.056-0.7940.1710.304-0.332-0.936-0.004
123E142GLY00.0400.0273.239-1.855-1.1230.082-0.294-0.5200.002
124E143ALA0-0.030-0.0172.683-4.931-3.5210.763-0.992-1.181-0.010
125E144THR00.015-0.0121.941-4.965-8.4629.623-3.161-2.965-0.022
126E145SER0-0.040-0.0324.1871.1571.2990.000-0.026-0.1160.000
127E146GLU-1-0.740-0.8626.205-0.767-0.7670.0000.0000.0000.000
128E147GLY00.0090.0097.9950.1570.1570.0000.0000.0000.000
129E148GLY0-0.032-0.0027.8320.1630.1630.0000.0000.0000.000
130E149SER00.004-0.0078.622-0.073-0.0730.0000.0000.0000.000
131E150SER0-0.0270.0006.492-0.114-0.1140.0000.0000.0000.000
132E151THR00.0310.0036.730-0.165-0.1650.0000.0000.0000.000
133E152PRO00.0320.0384.0570.3880.515-0.001-0.009-0.1170.000
134E153VAL00.0090.0117.2340.2210.2210.0000.0000.0000.000
135E154ASN0-0.001-0.0189.4360.1600.1600.0000.0000.0000.000
136E155LEU0-0.0260.0135.089-0.184-0.1840.0000.0000.0000.000
137E156LEU00.0000.0072.431-1.594-0.6021.810-0.738-2.0650.001
138E157LYS10.9230.9592.726-2.656-0.6011.249-0.989-2.315-0.013
139E158VAL00.0260.0212.448-1.709-0.4941.879-0.385-2.709-0.001
140E159THR0-0.014-0.0103.942-0.236-0.0620.006-0.005-0.1750.000
141E160VAL0-0.034-0.0236.380-0.157-0.1570.0000.0000.0000.000
142E161PRO00.0270.0148.9450.0160.0160.0000.0000.0000.000
143E162ILE00.0010.01011.9700.0180.0180.0000.0000.0000.000
144E163VAL0-0.0150.00013.723-0.053-0.0530.0000.0000.0000.000
145E164SER00.017-0.00215.7770.0040.0040.0000.0000.0000.000
146E165ARG10.8570.89519.038-0.212-0.2120.0000.0000.0000.000
147E166ALA0-0.012-0.00819.994-0.012-0.0120.0000.0000.0000.000
148E167THR00.0100.00618.431-0.016-0.0160.0000.0000.0000.000
149E168CYS00.0170.02012.4050.0070.0070.0000.0000.0000.000
150E169ARG10.8640.92818.325-0.126-0.1260.0000.0000.0000.000
151E170ALA0-0.0170.00921.520-0.013-0.0130.0000.0000.0000.000
152E171GLN00.0080.03216.2270.0050.0050.0000.0000.0000.000
153E172TYR0-0.021-0.07913.011-0.039-0.0390.0000.0000.0000.000
154E173GLY00.0390.03219.916-0.010-0.0100.0000.0000.0000.000
155E173THR0-0.016-0.04122.3010.0150.0150.0000.0000.0000.000
156E174SER0-0.020-0.01923.8420.0100.0100.0000.0000.0000.000
157E175ALA00.0100.02819.8130.0050.0050.0000.0000.0000.000
158E176ILE0-0.0060.01016.7910.0200.0200.0000.0000.0000.000
159E177THR00.016-0.04919.801-0.007-0.0070.0000.0000.0000.000
160E178ASN00.011-0.01820.2060.0190.0190.0000.0000.0000.000
161E179GLN0-0.0060.00019.8100.0030.0030.0000.0000.0000.000
162E180MET0-0.0310.02615.9340.0210.0210.0000.0000.0000.000
163E181PHE0-0.0030.00911.397-0.041-0.0410.0000.0000.0000.000
164E183ALA00.0350.0199.114-0.002-0.0020.0000.0000.0000.000
165E184GLY00.0610.0439.4010.0090.0090.0000.0000.0000.000
166E184VAL0-0.015-0.0109.8640.0180.0180.0000.0000.0000.000
167E185SER00.0240.01312.284-0.049-0.0490.0000.0000.0000.000
168E186SER00.0390.00814.233-0.008-0.0080.0000.0000.0000.000
169E187GLY00.0250.02111.377-0.046-0.0460.0000.0000.0000.000
170E188GLY0-0.047-0.0299.2380.0780.0780.0000.0000.0000.000
171E188LYS10.8120.9005.336-0.532-0.5320.0000.0000.0000.000
172E189ASP-1-0.772-0.8784.1010.2060.453-0.001-0.032-0.2130.000
173E190SER0-0.042-0.0062.132-3.429-0.7052.891-2.767-2.848-0.013
174E191CYS0-0.087-0.0412.750-1.142-1.1990.1260.761-0.8300.000
175E192GLN00.0810.0004.2870.6880.811-0.001-0.001-0.1210.000
176E193GLY00.0030.0045.185-0.534-0.512-0.001-0.001-0.0190.000
177E194ASP-1-0.756-0.8882.6827.90710.6023.917-2.421-4.192-0.031
178E195SER00.006-0.0405.498-0.176-0.1760.0000.0000.0000.000
179E196GLY0-0.025-0.0228.543-0.050-0.0500.0000.0000.0000.000
180E197GLY0-0.033-0.0076.186-0.094-0.0940.0000.0000.0000.000
181E198PRO0-0.024-0.0086.6320.0140.0140.0000.0000.0000.000
182E199ILE00.0100.0135.8250.2830.2830.0000.0000.0000.000
183E200VAL0-0.040-0.0237.722-0.177-0.1770.0000.0000.0000.000
184E201ASP-1-0.751-0.88510.6340.4360.4360.0000.0000.0000.000
185E201SER00.025-0.00813.0310.0280.0280.0000.0000.0000.000
186E202SER0-0.086-0.02814.862-0.039-0.0390.0000.0000.0000.000
187E203ASN0-0.040-0.04812.1070.0340.0340.0000.0000.0000.000
188E204THR0-0.073-0.01614.165-0.020-0.0200.0000.0000.0000.000
189E209LEU0-0.0040.00710.7050.0510.0510.0000.0000.0000.000
190E210ILE00.033-0.00511.804-0.067-0.0670.0000.0000.0000.000
191E211GLY0-0.003-0.02211.490-0.057-0.0570.0000.0000.0000.000
192E212ALA0-0.0070.0159.1060.0630.0630.0000.0000.0000.000
193E213VAL00.0140.0094.562-0.187-0.115-0.001-0.005-0.0660.000
194E214SER0-0.068-0.0627.963-0.131-0.1310.0000.0000.0000.000
195E215TRP00.004-0.01510.913-0.063-0.0630.0000.0000.0000.000
196E216GLY00.0700.02610.7650.0770.0770.0000.0000.0000.000
197E217ASN0-0.063-0.01312.004-0.078-0.0780.0000.0000.0000.000
198E219GLY0-0.0160.00410.937-0.018-0.0180.0000.0000.0000.000
199E221ALA0-0.033-0.0146.568-0.113-0.1130.0000.0000.0000.000
200E221ARG10.8800.9338.4240.3770.3770.0000.0000.0000.000
201E222PRO00.010-0.00412.1220.0720.0720.0000.0000.0000.000
202E223ASN0-0.086-0.04414.8610.0150.0150.0000.0000.0000.000
203E224TYR0-0.015-0.01013.745-0.001-0.0010.0000.0000.0000.000
204E225SER0-0.049-0.02011.913-0.013-0.0130.0000.0000.0000.000
205E226GLY00.1200.1208.563-0.067-0.0670.0000.0000.0000.000
206E227VAL0-0.028-0.0369.5730.0170.0170.0000.0000.0000.000
207E228TYR00.004-0.0085.390-0.030-0.0300.0000.0000.0000.000
208E229ALA00.0340.02411.641-0.086-0.0860.0000.0000.0000.000
209E230SER00.016-0.00913.3920.0540.0540.0000.0000.0000.000
210E231VAL00.0120.00814.113-0.035-0.0350.0000.0000.0000.000
211E232GLY00.0210.02016.660-0.029-0.0290.0000.0000.0000.000
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215E236SER00.0360.01621.769-0.006-0.0060.0000.0000.0000.000
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217E238ILE00.0210.00417.484-0.004-0.0040.0000.0000.0000.000
218E239ASP-1-0.831-0.92021.5670.1790.1790.0000.0000.0000.000
219E240THR0-0.077-0.02924.524-0.012-0.0120.0000.0000.0000.000
220E241TYR00.000-0.01023.639-0.014-0.0140.0000.0000.0000.000
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