FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 395QL

Calculation Name: 2V78-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V78

Chain ID: A

ChEMBL ID:

UniProt ID: Q97U29

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 OptAll
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 311
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4787311.76755
FMO2-HF: Nuclear repulsion 4667598.147467
FMO2-HF: Total energy -119713.620083
FMO2-MP2: Total energy -120069.881879


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:2:VAL)


Summations of interaction energy for fragment #1(A:2:VAL)
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.
-9.0181.36110.738-6.752-14.364-0.041
Interaction energy analysis for fragmet #1(A:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.014
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].
3A4VAL00.0140.0002.150-1.4121.2161.356-1.636-2.348-0.001
4A5ILE00.0020.0082.448-1.3070.1762.097-0.927-2.653-0.007
5A6ALA00.0020.0004.570-0.080-0.0290.000-0.019-0.0320.000
6A7LEU0-0.0010.0078.1780.1280.1280.0000.0000.0000.000
7A8GLY00.0640.03010.756-0.035-0.0350.0000.0000.0000.000
8A9GLU-1-0.773-0.83513.9230.0460.0460.0000.0000.0000.000
9A10PRO0-0.0100.00913.522-0.022-0.0220.0000.0000.0000.000
10A11LEU0-0.055-0.02915.7310.0130.0130.0000.0000.0000.000
11A12ILE0-0.040-0.00519.2180.0010.0010.0000.0000.0000.000
12A13GLN0-0.013-0.01321.878-0.011-0.0110.0000.0000.0000.000
13A14PHE0-0.003-0.00724.1300.0070.0070.0000.0000.0000.000
14A15ASN00.0500.01425.8180.0020.0020.0000.0000.0000.000
15A16SER00.003-0.00929.1800.0050.0050.0000.0000.0000.000
16A17PHE00.007-0.00632.496-0.004-0.0040.0000.0000.0000.000
17A18ASN0-0.016-0.00134.120-0.001-0.0010.0000.0000.0000.000
18A19PRO00.0000.00136.0870.0000.0000.0000.0000.0000.000
19A20GLY00.0060.01137.3650.0030.0030.0000.0000.0000.000
20A21PRO0-0.021-0.01837.673-0.001-0.0010.0000.0000.0000.000
21A22LEU00.0510.01133.4320.0030.0030.0000.0000.0000.000
22A23ARG10.8960.96037.5740.0160.0160.0000.0000.0000.000
23A24PHE00.001-0.01240.5670.0010.0010.0000.0000.0000.000
24A25VAL0-0.0290.00935.0180.0000.0000.0000.0000.0000.000
25A26ASN0-0.038-0.02438.1150.0030.0030.0000.0000.0000.000
26A27TYR00.0010.00935.7430.0040.0040.0000.0000.0000.000
27A28PHE00.013-0.01230.987-0.004-0.0040.0000.0000.0000.000
28A29GLU-1-0.787-0.84627.902-0.009-0.0090.0000.0000.0000.000
29A30LYS10.8800.94224.089-0.060-0.0600.0000.0000.0000.000
30A31HIS10.7840.85522.0120.0180.0180.0000.0000.0000.000
31A32VAL00.0150.00916.4610.0070.0070.0000.0000.0000.000
32A33ALA00.0220.02217.712-0.013-0.0130.0000.0000.0000.000
33A34GLY00.0550.02716.9690.0170.0170.0000.0000.0000.000
34A35SER0-0.068-0.04715.654-0.018-0.0180.0000.0000.0000.000
35A36GLU-1-0.721-0.84811.275-0.198-0.1980.0000.0000.0000.000
36A37LEU00.0130.02710.870-0.037-0.0370.0000.0000.0000.000
37A38ASN0-0.061-0.05312.1380.0040.0040.0000.0000.0000.000
38A39PHE00.0020.0138.382-0.009-0.0090.0000.0000.0000.000
39A40CYS0-0.021-0.0297.883-0.084-0.0840.0000.0000.0000.000
40A41ILE0-0.017-0.0038.997-0.027-0.0270.0000.0000.0000.000
41A42ALA00.0040.00111.696-0.005-0.0050.0000.0000.0000.000
42A43VAL0-0.013-0.0045.791-0.044-0.0440.0000.0000.0000.000
43A44VAL0-0.035-0.0096.312-0.050-0.0500.0000.0000.0000.000
44A45ARG10.7630.8688.7940.1350.1350.0000.0000.0000.000
45A46ASN0-0.031-0.02911.3800.0600.0600.0000.0000.0000.000
46A47HIS0-0.036-0.03210.180-0.101-0.1010.0000.0000.0000.000
47A48LEU0-0.0440.0055.985-0.088-0.0880.0000.0000.0000.000
48A49SER00.001-0.0252.500-2.619-0.8072.244-1.807-2.249-0.014
49A50CYS00.0270.0072.670-2.506-1.7512.163-1.038-1.881-0.012
50A51SER0-0.070-0.0412.210-0.0810.1652.025-0.357-1.914-0.002
51A52LEU00.0400.0123.558-0.265-0.2500.0130.093-0.1210.000
52A53ILE0-0.042-0.0215.9220.1430.1430.0000.0000.0000.000
53A54ALA00.010-0.0048.714-0.083-0.0830.0000.0000.0000.000
54A55ARG10.7590.85312.351-0.081-0.0810.0000.0000.0000.000
55A56VAL0-0.0130.00415.573-0.029-0.0290.0000.0000.0000.000
56A57GLY00.0820.03218.0490.0120.0120.0000.0000.0000.000
57A58ASN0-0.027-0.02420.9520.0170.0170.0000.0000.0000.000
58A59ASP-1-0.787-0.86322.7950.0870.0870.0000.0000.0000.000
59A60GLU-1-0.800-0.91222.7370.1330.1330.0000.0000.0000.000
60A61PHE0-0.029-0.01422.4140.0010.0010.0000.0000.0000.000
61A62GLY00.0570.02018.927-0.001-0.0010.0000.0000.0000.000
62A63LYS10.8350.89617.784-0.123-0.1230.0000.0000.0000.000
63A64ASN0-0.025-0.01118.2080.0030.0030.0000.0000.0000.000
64A65ILE00.0280.02414.340-0.001-0.0010.0000.0000.0000.000
65A66ILE00.0060.02113.4790.0050.0050.0000.0000.0000.000
66A67GLU-1-0.815-0.87913.9180.2760.2760.0000.0000.0000.000
67A68TYR0-0.033-0.03715.0770.0190.0190.0000.0000.0000.000
68A69SER0-0.001-0.02410.418-0.026-0.0260.0000.0000.0000.000
69A70ARG10.8300.87511.032-0.334-0.3340.0000.0000.0000.000
70A71ALA0-0.057-0.02212.2520.0140.0140.0000.0000.0000.000
71A72GLN0-0.017-0.00412.577-0.070-0.0700.0000.0000.0000.000
72A73GLY00.0210.0239.456-0.060-0.0600.0000.0000.0000.000
73A74ILE0-0.027-0.0046.2660.0380.0380.0000.0000.0000.000
74A75ASP-1-0.748-0.8163.8581.4111.5620.001-0.028-0.1230.000
75A76THR00.033-0.0025.900-0.170-0.1700.0000.0000.0000.000
76A77SER0-0.131-0.0887.144-0.077-0.0770.0000.0000.0000.000
77A78HIS10.8450.9095.976-1.344-1.3440.0000.0000.0000.000
78A79ILE00.0190.0308.952-0.112-0.1120.0000.0000.0000.000
79A80LYS10.8110.90711.605-0.196-0.1960.0000.0000.0000.000
80A81VAL00.0150.00414.370-0.043-0.0430.0000.0000.0000.000
81A82ASP-1-0.806-0.87217.8990.1290.1290.0000.0000.0000.000
82A83ASN0-0.013-0.03020.5710.0030.0030.0000.0000.0000.000
83A84GLU-1-0.844-0.88924.1520.0850.0850.0000.0000.0000.000
84A85SER0-0.061-0.04823.897-0.012-0.0120.0000.0000.0000.000
85A86PHE0-0.0260.00124.2560.0110.0110.0000.0000.0000.000
86A87THR00.018-0.02019.6810.0000.0000.0000.0000.0000.000
87A88GLY0-0.0130.01021.432-0.006-0.0060.0000.0000.0000.000
88A89ILE0-0.009-0.00922.0600.0020.0020.0000.0000.0000.000
89A90TYR0-0.053-0.05321.318-0.006-0.0060.0000.0000.0000.000
90A91PHE00.0180.02226.3530.0030.0030.0000.0000.0000.000
91A92ILE0-0.012-0.00725.754-0.005-0.0050.0000.0000.0000.000
92A93GLN0-0.0220.00230.1420.0070.0070.0000.0000.0000.000
93A94ARG10.8800.93032.1830.0330.0330.0000.0000.0000.000
94A95GLY0-0.041-0.02334.1330.0030.0030.0000.0000.0000.000
95A96TYR0-0.0040.01036.5760.0020.0020.0000.0000.0000.000
96A97PRO00.0320.01237.2220.0000.0000.0000.0000.0000.000
97A98ILE00.0140.00136.7370.0000.0000.0000.0000.0000.000
98A99PRO00.0610.02136.781-0.001-0.0010.0000.0000.0000.000
99A100MET00.004-0.00233.895-0.005-0.0050.0000.0000.0000.000
100A101LYS10.8610.94832.0060.0600.0600.0000.0000.0000.000
101A102SER00.047-0.00728.9730.0070.0070.0000.0000.0000.000
102A103GLU-1-0.918-0.94730.251-0.044-0.0440.0000.0000.0000.000
103A104LEU00.0050.01324.6460.0060.0060.0000.0000.0000.000
104A105VAL0-0.039-0.02328.7050.0000.0000.0000.0000.0000.000
105A106TYR00.0510.00723.4570.0040.0040.0000.0000.0000.000
106A107TYR0-0.012-0.00326.9170.0020.0020.0000.0000.0000.000
107A108ARG10.9010.92219.8120.0420.0420.0000.0000.0000.000
108A109LYS10.9450.97825.118-0.001-0.0010.0000.0000.0000.000
109A110GLY00.0490.02825.9620.0030.0030.0000.0000.0000.000
110A111SER0-0.040-0.01121.7150.0080.0080.0000.0000.0000.000
111A112ALA00.0410.02019.960-0.001-0.0010.0000.0000.0000.000
112A113GLY00.0430.01417.6500.0070.0070.0000.0000.0000.000
113A114SER0-0.076-0.04518.144-0.007-0.0070.0000.0000.0000.000
114A115ARG10.8150.87520.158-0.100-0.1000.0000.0000.0000.000
115A116LEU0-0.0220.01712.4450.0150.0150.0000.0000.0000.000
116A117SER00.009-0.00415.701-0.020-0.0200.0000.0000.0000.000
117A118PRO00.025-0.00115.1240.0240.0240.0000.0000.0000.000
118A119GLU-1-0.849-0.89415.1340.1620.1620.0000.0000.0000.000
119A120ASP-1-0.753-0.85812.1790.2070.2070.0000.0000.0000.000
120A121ILE0-0.040-0.00310.1850.0670.0670.0000.0000.0000.000
121A122ASN00.009-0.0119.2290.0020.0020.0000.0000.0000.000
122A123GLU-1-0.769-0.8979.0550.0400.0400.0000.0000.0000.000
123A124ASN00.0020.0009.470-0.162-0.1620.0000.0000.0000.000
124A125TYR0-0.038-0.0232.843-1.4810.1720.507-0.603-1.557-0.006
125A126VAL00.0350.0134.474-0.251-0.165-0.001-0.007-0.0780.000
126A127ARG10.9100.9666.250-0.265-0.2650.0000.0000.0000.000
127A128ASN0-0.052-0.0324.136-0.376-0.245-0.001-0.010-0.1200.000
128A129SER0-0.042-0.0042.907-1.931-0.9160.323-0.421-0.9180.001
129A130ARG10.8100.8853.7833.0263.3580.0120.009-0.3520.000
130A131LEU0-0.0340.0114.9880.7030.7030.0000.0000.0000.000
131A132VAL00.0030.0095.178-0.278-0.257-0.001-0.001-0.0180.000
132A133HIS00.0570.0437.5970.0370.0370.0000.0000.0000.000
133A134SER0-0.007-0.03110.2190.0760.0760.0000.0000.0000.000
134A135THR0-0.043-0.04313.226-0.013-0.0130.0000.0000.0000.000
135A136GLY00.0650.03116.9560.0200.0200.0000.0000.0000.000
136A137ILE0-0.074-0.03719.0110.0240.0240.0000.0000.0000.000
137A138THR0-0.032-0.03714.6980.0340.0340.0000.0000.0000.000
138A139LEU0-0.030-0.01717.9580.0170.0170.0000.0000.0000.000
139A140ALA0-0.0220.00420.0090.0100.0100.0000.0000.0000.000
140A141ILE0-0.074-0.03618.0810.0120.0120.0000.0000.0000.000
141A142SER0-0.006-0.02320.9840.0090.0090.0000.0000.0000.000
142A143ASP-1-0.854-0.90721.521-0.051-0.0510.0000.0000.0000.000
143A144ASN0-0.022-0.03419.462-0.009-0.0090.0000.0000.0000.000
144A145ALA00.0590.03317.1810.0030.0030.0000.0000.0000.000
145A146LYS10.7760.86816.8040.0380.0380.0000.0000.0000.000
146A147GLU-1-0.827-0.92018.078-0.075-0.0750.0000.0000.0000.000
147A148ALA0-0.067-0.01813.933-0.002-0.0020.0000.0000.0000.000
148A149VAL00.0230.00013.481-0.017-0.0170.0000.0000.0000.000
149A150ILE00.0060.01314.230-0.040-0.0400.0000.0000.0000.000
150A151LYS10.8680.94513.467-0.100-0.1000.0000.0000.0000.000
151A152ALA0-0.005-0.0189.919-0.013-0.0130.0000.0000.0000.000
152A153PHE0-0.019-0.01710.778-0.091-0.0910.0000.0000.0000.000
153A154GLU-1-0.847-0.89913.071-0.214-0.2140.0000.0000.0000.000
154A155LEU0-0.091-0.03810.2440.0160.0160.0000.0000.0000.000
155A156ALA0-0.034-0.0078.753-0.069-0.0690.0000.0000.0000.000
156A157LYS10.8270.9156.1471.6491.6490.0000.0000.0000.000
157A158SER0-0.027-0.0249.2230.1000.1000.0000.0000.0000.000
158A159ARG10.8130.8789.5410.3180.3180.0000.0000.0000.000
159A160SER00.002-0.01611.333-0.019-0.0190.0000.0000.0000.000
160A161LEU00.0230.00612.9730.0210.0210.0000.0000.0000.000
161A162ASP-1-0.833-0.89915.465-0.228-0.2280.0000.0000.0000.000
162A163THR0-0.009-0.04217.8540.0110.0110.0000.0000.0000.000
163A164ASN00.0330.02218.5390.0390.0390.0000.0000.0000.000
164A165ILE00.0290.02521.7920.0150.0150.0000.0000.0000.000
165A166ARG10.8570.92322.1670.1170.1170.0000.0000.0000.000
166A167PRO00.0340.00326.5300.0070.0070.0000.0000.0000.000
167A168LYS10.8550.91829.5240.0440.0440.0000.0000.0000.000
168A169LEU0-0.032-0.00523.4110.0070.0070.0000.0000.0000.000
169A170TRP00.0380.03123.3210.0050.0050.0000.0000.0000.000
170A171SER0-0.015-0.00728.8150.0010.0010.0000.0000.0000.000
171A172SER00.008-0.00431.1700.0010.0010.0000.0000.0000.000
172A173LEU00.0640.02030.735-0.003-0.0030.0000.0000.0000.000
173A174GLU-1-0.793-0.87030.406-0.083-0.0830.0000.0000.0000.000
174A175LYS10.8740.94426.0280.0650.0650.0000.0000.0000.000
175A176ALA00.0230.02326.173-0.005-0.0050.0000.0000.0000.000
176A177LYS10.8290.89925.7640.0720.0720.0000.0000.0000.000
177A178GLU-1-0.849-0.92526.764-0.094-0.0940.0000.0000.0000.000
178A179THR0-0.009-0.02422.138-0.005-0.0050.0000.0000.0000.000
179A180ILE00.0290.01021.546-0.012-0.0120.0000.0000.0000.000
180A181LEU0-0.024-0.00822.524-0.016-0.0160.0000.0000.0000.000
181A182SER0-0.056-0.01324.251-0.007-0.0070.0000.0000.0000.000
182A183ILE00.0020.00017.652-0.002-0.0020.0000.0000.0000.000
183A184LEU00.019-0.00119.801-0.013-0.0130.0000.0000.0000.000
184A185LYS10.9090.95421.5720.1170.1170.0000.0000.0000.000
185A186LYS10.8310.92520.7670.1410.1410.0000.0000.0000.000
186A187TYR0-0.058-0.05016.530-0.007-0.0070.0000.0000.0000.000
187A188ASP-1-0.800-0.87517.311-0.321-0.3210.0000.0000.0000.000
188A189ILE0-0.048-0.01615.665-0.047-0.0470.0000.0000.0000.000
189A190GLU-1-0.829-0.87813.659-0.498-0.4980.0000.0000.0000.000
190A191VAL0-0.003-0.02314.5130.0240.0240.0000.0000.0000.000
191A192LEU0-0.0020.01615.756-0.012-0.0120.0000.0000.0000.000
192A193ILE0-0.032-0.02115.1040.0080.0080.0000.0000.0000.000
193A194THR00.017-0.01319.3200.0170.0170.0000.0000.0000.000
194A195ASP-1-0.809-0.92122.771-0.158-0.1580.0000.0000.0000.000
195A196PRO00.0160.01626.2200.0020.0020.0000.0000.0000.000
196A197ASP-1-0.897-0.93429.178-0.095-0.0950.0000.0000.0000.000
197A198ASP-1-0.739-0.85424.269-0.137-0.1370.0000.0000.0000.000
198A199THR0-0.024-0.02627.290-0.004-0.0040.0000.0000.0000.000
199A200LYS10.7800.89828.7720.0900.0900.0000.0000.0000.000
200A201ILE0-0.047-0.02929.2890.0070.0070.0000.0000.0000.000
201A202LEU0-0.046-0.03024.7380.0040.0040.0000.0000.0000.000
202A203LEU0-0.024-0.02227.4710.0010.0010.0000.0000.0000.000
203A204ASP-1-0.873-0.89731.253-0.080-0.0800.0000.0000.0000.000
204A205VAL00.0210.00732.0640.0040.0040.0000.0000.0000.000
205A206THR00.0380.00632.3660.0000.0000.0000.0000.0000.000
206A207ASP-1-0.856-0.91132.446-0.124-0.1240.0000.0000.0000.000
207A208PRO00.0230.00329.554-0.006-0.0060.0000.0000.0000.000
208A209ASP-1-0.776-0.82929.658-0.155-0.1550.0000.0000.0000.000
209A210GLU-1-0.943-0.98231.575-0.115-0.1150.0000.0000.0000.000
210A211ALA00.0220.01728.253-0.004-0.0040.0000.0000.0000.000
211A212TYR00.000-0.00724.086-0.003-0.0030.0000.0000.0000.000
212A213ARG10.8440.92727.4430.1490.1490.0000.0000.0000.000
213A214LYS10.8390.90329.3600.1190.1190.0000.0000.0000.000
214A215TYR00.048-0.00823.926-0.003-0.0030.0000.0000.0000.000
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