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: QV75Y

Calculation Name: 2FD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HZ91

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1695131.095152
FMO2-HF: Nuclear repulsion 1627772.33476
FMO2-HF: Total energy -67358.760391
FMO2-MP2: Total energy -67554.859469


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-3.326-1.161-0.036-1.073-1.0560.004
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.010
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].
3A3ASP-1-0.755-0.8353.753-2.784-0.619-0.036-1.073-1.0560.004
4A4LYS10.9940.9776.643-0.442-0.4420.0000.0000.0000.000
5A5LYS10.9811.0169.8150.4700.4700.0000.0000.0000.000
6A6THR0-0.012-0.0588.2000.1590.1590.0000.0000.0000.000
7A7GLN0-0.022-0.0126.606-0.166-0.1660.0000.0000.0000.000
8A8THR0-0.033-0.0319.6670.0730.0730.0000.0000.0000.000
9A9ARG10.8200.88913.2570.1760.1760.0000.0000.0000.000
10A10ALA00.0190.01011.2160.0070.0070.0000.0000.0000.000
11A11ARG10.8670.92812.489-0.446-0.4460.0000.0000.0000.000
12A12ILE0-0.0160.00314.920-0.017-0.0170.0000.0000.0000.000
13A13LEU00.0200.00716.004-0.005-0.0050.0000.0000.0000.000
14A14GLY00.0200.01416.452-0.012-0.0120.0000.0000.0000.000
15A15ALA00.0050.00317.396-0.008-0.0080.0000.0000.0000.000
16A16ALA0-0.015-0.01520.504-0.017-0.0170.0000.0000.0000.000
17A17THR0-0.021-0.01318.970-0.007-0.0070.0000.0000.0000.000
18A18GLN00.0180.01420.683-0.012-0.0120.0000.0000.0000.000
19A19ALA00.0130.00623.059-0.010-0.0100.0000.0000.0000.000
20A20LEU0-0.0340.00324.588-0.010-0.0100.0000.0000.0000.000
21A21LEU0-0.060-0.03822.987-0.012-0.0120.0000.0000.0000.000
22A22GLU-1-1.009-0.99826.3790.1310.1310.0000.0000.0000.000
23A23ARG10.8470.90628.051-0.093-0.0930.0000.0000.0000.000
24A24GLY00.0480.04930.053-0.006-0.0060.0000.0000.0000.000
25A25ALA0-0.012-0.03629.5080.0060.0060.0000.0000.0000.000
26A26VAL0-0.067-0.02930.507-0.002-0.0020.0000.0000.0000.000
27A27GLU-1-0.955-0.97432.9900.0540.0540.0000.0000.0000.000
28A28PRO0-0.0040.01628.2390.0040.0040.0000.0000.0000.000
29A29SER00.0280.02030.195-0.009-0.0090.0000.0000.0000.000
30A30VAL00.026-0.00725.6440.0090.0090.0000.0000.0000.000
31A31GLY0-0.015-0.01025.9760.0130.0130.0000.0000.0000.000
32A32GLU-1-0.771-0.88926.8270.0960.0960.0000.0000.0000.000
33A33VAL00.0130.02322.1590.0180.0180.0000.0000.0000.000
34A34MET0-0.049-0.02420.1670.0220.0220.0000.0000.0000.000
35A35GLY00.0280.01222.0150.0280.0280.0000.0000.0000.000
36A36ALA0-0.004-0.00222.9760.0230.0230.0000.0000.0000.000
37A37ALA0-0.0110.01118.0210.0330.0330.0000.0000.0000.000
38A38GLY0-0.0070.00418.0370.0580.0580.0000.0000.0000.000
39A39LEU0-0.105-0.04916.0630.0230.0230.0000.0000.0000.000
40A40THR00.0390.00420.121-0.019-0.0190.0000.0000.0000.000
41A41VAL00.0610.01822.202-0.006-0.0060.0000.0000.0000.000
42A42GLY00.001-0.00124.883-0.014-0.0140.0000.0000.0000.000
43A43GLY0-0.012-0.00520.958-0.015-0.0150.0000.0000.0000.000
44A44PHE00.0250.00921.123-0.018-0.0180.0000.0000.0000.000
45A45TYR00.0360.00122.205-0.013-0.0130.0000.0000.0000.000
46A46ALA0-0.052-0.00120.171-0.018-0.0180.0000.0000.0000.000
47A47HIS0-0.091-0.04415.177-0.059-0.0590.0000.0000.0000.000
48A48PHE00.0100.00418.207-0.025-0.0250.0000.0000.0000.000
49A49GLN00.0390.01022.8230.0030.0030.0000.0000.0000.000
50A50SER00.0230.00226.3310.0090.0090.0000.0000.0000.000
51A51LYS10.9100.95626.394-0.028-0.0280.0000.0000.0000.000
52A52ASP-1-0.851-0.92327.210-0.012-0.0120.0000.0000.0000.000
53A53ALA0-0.035-0.00925.511-0.003-0.0030.0000.0000.0000.000
54A54LEU0-0.032-0.00421.120-0.007-0.0070.0000.0000.0000.000
55A55MET0-0.022-0.01623.2860.0040.0040.0000.0000.0000.000
56A56LEU00.0130.02425.5030.0040.0040.0000.0000.0000.000
57A57GLU-1-0.717-0.83118.246-0.149-0.1490.0000.0000.0000.000
58A58ALA0-0.027-0.02621.015-0.002-0.0020.0000.0000.0000.000
59A59PHE0-0.020-0.02122.0820.0050.0050.0000.0000.0000.000
60A60GLU-1-0.911-0.97123.084-0.113-0.1130.0000.0000.0000.000
61A61GLN0-0.027-0.00815.7700.0290.0290.0000.0000.0000.000
62A62LEU0-0.011-0.00620.4760.0000.0000.0000.0000.0000.000
63A63LEU0-0.027-0.01822.1240.0010.0010.0000.0000.0000.000
64A64GLY0-0.005-0.00821.763-0.004-0.0040.0000.0000.0000.000
65A65LYS11.0141.01116.119-0.027-0.0270.0000.0000.0000.000
66A66ARG10.8530.91320.795-0.016-0.0160.0000.0000.0000.000
67A67ARG10.9090.93824.3350.0980.0980.0000.0000.0000.000
68A68GLU-1-0.953-0.96517.538-0.146-0.1460.0000.0000.0000.000
69A69LEU0-0.022-0.01720.7560.0050.0050.0000.0000.0000.000
70A70LEU0-0.046-0.01923.3340.0040.0040.0000.0000.0000.000
71A71GLY0-0.011-0.00424.9630.0000.0000.0000.0000.0000.000
72A72GLU-1-0.967-0.98120.226-0.052-0.0520.0000.0000.0000.000
73A73LEU0-0.109-0.04824.6700.0100.0100.0000.0000.0000.000
74A74ASP-1-0.861-0.92828.342-0.056-0.0560.0000.0000.0000.000
75A75PRO00.001-0.01828.8150.0020.0020.0000.0000.0000.000
76A76GLY0-0.034-0.01031.6090.0000.0000.0000.0000.0000.000
77A77LEU0-0.051-0.01232.3470.0050.0050.0000.0000.0000.000
78A78SER00.0400.01435.777-0.003-0.0030.0000.0000.0000.000
79A79GLY00.1100.03837.3040.0010.0010.0000.0000.0000.000
80A80LYS10.9180.95037.8990.0130.0130.0000.0000.0000.000
81A81GLU-1-0.890-0.93736.828-0.019-0.0190.0000.0000.0000.000
82A82ARG10.8480.93131.9070.0550.0550.0000.0000.0000.000
83A83ARG10.7840.87533.9750.0300.0300.0000.0000.0000.000
84A84ALA0-0.027-0.00735.9150.0050.0050.0000.0000.0000.000
85A85LEU00.005-0.00231.3830.0070.0070.0000.0000.0000.000
86A86ALA00.0230.02231.0620.0070.0070.0000.0000.0000.000
87A87ALA00.0170.00132.0100.0070.0070.0000.0000.0000.000
88A88ALA0-0.052-0.04033.7150.0070.0070.0000.0000.0000.000
89A89PHE0-0.010-0.00327.5090.0100.0100.0000.0000.0000.000
90A90TYR0-0.043-0.02929.6930.0110.0110.0000.0000.0000.000
91A91LEU0-0.0080.01231.2170.0080.0080.0000.0000.0000.000
92A92SER00.0060.00130.1800.0050.0050.0000.0000.0000.000
93A93ARG10.9790.97432.657-0.063-0.0630.0000.0000.0000.000
94A94LYS10.9650.99526.425-0.141-0.1410.0000.0000.0000.000
95A95HIS0-0.0020.00327.5610.0090.0090.0000.0000.0000.000
96A96ARG10.7770.85929.259-0.066-0.0660.0000.0000.0000.000
97A97ASP-1-0.812-0.89030.9880.0840.0840.0000.0000.0000.000
98A98ALA00.0080.01626.8930.0090.0090.0000.0000.0000.000
99A99GLN0-0.046-0.02525.3710.0120.0120.0000.0000.0000.000
100A100VAL0-0.040-0.03223.8100.0000.0000.0000.0000.0000.000
101A101ASP-1-0.856-0.92418.3830.2370.2370.0000.0000.0000.000
102A102ALA0-0.023-0.00719.5300.0020.0020.0000.0000.0000.000
103A103GLY00.0190.01921.259-0.019-0.0190.0000.0000.0000.000
104A104CYS0-0.0480.01224.421-0.012-0.0120.0000.0000.0000.000
105A105PRO00.0750.02825.7200.0070.0070.0000.0000.0000.000
106A106LEU00.018-0.00528.0470.0000.0000.0000.0000.0000.000
107A107PRO0-0.034-0.01930.821-0.001-0.0010.0000.0000.0000.000
108A108ALA00.0020.01530.510-0.001-0.0010.0000.0000.0000.000
109A109THR00.0230.00129.460-0.004-0.0040.0000.0000.0000.000
110A110LEU00.0060.00632.887-0.005-0.0050.0000.0000.0000.000
111A111ALA0-0.009-0.00535.593-0.004-0.0040.0000.0000.0000.000
112A112GLU-1-0.853-0.95433.6460.0190.0190.0000.0000.0000.000
113A113VAL00.0170.01633.470-0.004-0.0040.0000.0000.0000.000
114A114ALA0-0.055-0.03135.887-0.004-0.0040.0000.0000.0000.000
115A115ARG10.8670.94138.393-0.004-0.0040.0000.0000.0000.000
116A116LEU0-0.0180.01432.0880.0020.0020.0000.0000.0000.000
117A117PRO00.0170.00132.286-0.004-0.0040.0000.0000.0000.000
118A118GLU-1-0.839-0.93033.751-0.047-0.0470.0000.0000.0000.000
119A119GLY00.0370.02730.723-0.002-0.0020.0000.0000.0000.000
120A120PHE00.016-0.00328.768-0.003-0.0030.0000.0000.0000.000
121A121ARG11.0040.99831.5610.0340.0340.0000.0000.0000.000
122A122GLU-1-0.945-0.95632.244-0.083-0.0830.0000.0000.0000.000
123A123VAL0-0.037-0.01927.115-0.004-0.0040.0000.0000.0000.000
124A124LEU0-0.022-0.01630.0880.0000.0000.0000.0000.0000.000
125A125SER0-0.009-0.02132.1580.0030.0030.0000.0000.0000.000
126A126ARG11.0191.02328.5560.1040.1040.0000.0000.0000.000
127A127HIS0-0.0170.00827.179-0.010-0.0100.0000.0000.0000.000
128A128VAL0-0.006-0.01430.4780.0020.0020.0000.0000.0000.000
129A129GLU-1-0.898-0.94433.877-0.069-0.0690.0000.0000.0000.000
130A130ILE0-0.026-0.01428.430-0.002-0.0020.0000.0000.0000.000
131A131MET0-0.035-0.01828.7180.0030.0030.0000.0000.0000.000
132A132VAL00.0370.02232.0620.0020.0020.0000.0000.0000.000
133A133THR0-0.032-0.02134.2960.0020.0020.0000.0000.0000.000
134A134SER0-0.075-0.03531.3740.0000.0000.0000.0000.0000.000
135A135LEU0-0.019-0.01432.7800.0030.0030.0000.0000.0000.000
136A136ALA0-0.034-0.00135.3940.0060.0060.0000.0000.0000.000
137A137GLU-1-0.847-0.93537.235-0.058-0.0580.0000.0000.0000.000
138A138SER0-0.055-0.04040.064-0.002-0.0020.0000.0000.0000.000
139A139PRO00.0110.00243.0360.0010.0010.0000.0000.0000.000
140A140GLU-1-0.871-0.93044.737-0.035-0.0350.0000.0000.0000.000
141A141GLU-1-0.839-0.90641.375-0.031-0.0310.0000.0000.0000.000
142A142THR00.0060.00840.6980.0000.0000.0000.0000.0000.000
143A143ASP-1-0.889-0.95241.396-0.027-0.0270.0000.0000.0000.000
144A144VAL0-0.056-0.02242.0830.0030.0030.0000.0000.0000.000
145A145ALA00.0360.01737.6110.0030.0030.0000.0000.0000.000
146A146LEU0-0.0050.00338.3720.0020.0020.0000.0000.0000.000
147A147ALA00.010-0.00239.7400.0030.0030.0000.0000.0000.000
148A148ASP-1-0.712-0.86838.098-0.008-0.0080.0000.0000.0000.000
149A149LEU0-0.015-0.01433.1360.0050.0050.0000.0000.0000.000
150A150VAL0-0.032-0.00236.5460.0050.0050.0000.0000.0000.000
151A151LEU0-0.017-0.00639.0990.0050.0050.0000.0000.0000.000
152A152MET0-0.032-0.01533.9110.0070.0070.0000.0000.0000.000
153A153ILE00.0050.00233.3060.0070.0070.0000.0000.0000.000
154A154GLY00.0220.00535.3600.0050.0050.0000.0000.0000.000
155A155GLY00.0220.01338.4590.0040.0040.0000.0000.0000.000
156A156LEU0-0.046-0.02931.1470.0050.0050.0000.0000.0000.000
157A157ALA0-0.0090.00535.6990.0060.0060.0000.0000.0000.000
158A158LEU00.0000.00536.9590.0040.0040.0000.0000.0000.000
159A159ALA00.010-0.00637.3000.0030.0030.0000.0000.0000.000
160A160ARG10.8980.94829.934-0.058-0.0580.0000.0000.0000.000
161A161ALA0-0.033-0.00536.6580.0040.0040.0000.0000.0000.000
162A162LEU0-0.060-0.03339.5580.0010.0010.0000.0000.0000.000
163A163GLY00.0310.04438.2060.0020.0020.0000.0000.0000.000
164A164PRO0-0.050-0.04036.184-0.004-0.0040.0000.0000.0000.000
165A165GLY00.0740.03138.872-0.001-0.0010.0000.0000.0000.000
166A166GLU-1-0.918-0.96441.8860.0430.0430.0000.0000.0000.000
167A167LEU0-0.0110.00244.383-0.002-0.0020.0000.0000.0000.000
168A168SER00.0410.00939.149-0.003-0.0030.0000.0000.0000.000
169A169ASP-1-0.859-0.94439.1880.0560.0560.0000.0000.0000.000
170A170ARG10.8750.93440.832-0.029-0.0290.0000.0000.0000.000
171A171VAL00.0080.01340.623-0.004-0.0040.0000.0000.0000.000
172A172LEU00.0070.01135.920-0.003-0.0030.0000.0000.0000.000
173A173ARG10.9150.94939.343-0.039-0.0390.0000.0000.0000.000
174A174ALA0-0.033-0.00941.466-0.003-0.0030.0000.0000.0000.000
175A175ALA00.0360.02239.880-0.003-0.0030.0000.0000.0000.000
176A176LYS10.9470.96535.929-0.037-0.0370.0000.0000.0000.000
177A177GLN0-0.082-0.05139.8390.0000.0000.0000.0000.0000.000
178A178ALA0-0.0240.00843.188-0.002-0.0020.0000.0000.0000.000
179A179VAL0-0.0410.00338.493-0.003-0.0030.0000.0000.0000.000
180A180ASN0-0.062-0.02041.063-0.002-0.0020.0000.0000.0000.000