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

tag_button

FMODB ID: R8LG8

Calculation Name: 3D8H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D8H

Chain ID: A

ChEMBL ID:

UniProt ID: Q5CXZ9

Base Structure: X-ray

Registration Date: 2023-09-23

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2967110.991155
FMO2-HF: Nuclear repulsion 2875517.398774
FMO2-HF: Total energy -91593.592382
FMO2-MP2: Total energy -91860.45753


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:20:THR)


Summations of interaction energy for fragment #1(A:20:THR)
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.
-25.59-26.06621.375-10.097-10.803-0.083
Interaction energy analysis for fragmet #1(A:20:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.048
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].
3A22LYS10.9300.9553.780-2.180-0.274-0.010-1.061-0.8360.005
4A23LEU0-0.0190.0066.543-0.071-0.0710.0000.0000.0000.000
5A24THR0-0.004-0.0039.7790.0340.0340.0000.0000.0000.000
6A25LEU00.0080.00313.067-0.025-0.0250.0000.0000.0000.000
7A26ILE00.0270.01615.9980.0140.0140.0000.0000.0000.000
8A27ARG10.8970.95519.641-0.037-0.0370.0000.0000.0000.000
9A28HIS00.0330.00022.8220.0020.0020.0000.0000.0000.000
10A29GLY00.0750.03526.114-0.002-0.0020.0000.0000.0000.000
11A30GLU-1-0.839-0.85528.7340.0290.0290.0000.0000.0000.000
12A31SER00.026-0.00631.9070.0010.0010.0000.0000.0000.000
13A32GLU-1-0.783-0.88033.9990.0260.0260.0000.0000.0000.000
14A33TRP00.0380.01436.831-0.002-0.0020.0000.0000.0000.000
15A34ASN0-0.057-0.02132.0910.0000.0000.0000.0000.0000.000
16A35LYS10.8640.91335.693-0.032-0.0320.0000.0000.0000.000
17A36GLU-1-0.833-0.89638.6240.0160.0160.0000.0000.0000.000
18A37ASN0-0.071-0.03738.236-0.002-0.0020.0000.0000.0000.000
19A38ARG10.8350.90338.889-0.015-0.0150.0000.0000.0000.000
20A39PHE0-0.025-0.01535.8340.0010.0010.0000.0000.0000.000
21A40THR00.0080.01333.7160.0010.0010.0000.0000.0000.000
22A41GLY0-0.0010.00332.115-0.001-0.0010.0000.0000.0000.000
23A42TRP0-0.002-0.02229.4640.0040.0040.0000.0000.0000.000
24A43THR00.0220.02433.0940.0010.0010.0000.0000.0000.000
25A44ASP-1-0.732-0.83533.8630.0310.0310.0000.0000.0000.000
26A45VAL0-0.063-0.02634.5200.0010.0010.0000.0000.0000.000
27A46SER0-0.006-0.03334.1500.0030.0030.0000.0000.0000.000
28A47LEU0-0.071-0.02929.547-0.002-0.0020.0000.0000.0000.000
29A48SER0-0.028-0.04533.699-0.001-0.0010.0000.0000.0000.000
30A49GLU-1-0.882-0.95634.9650.0370.0370.0000.0000.0000.000
31A50GLN0-0.045-0.01732.5160.0020.0020.0000.0000.0000.000
32A51GLY00.0260.01831.2750.0040.0040.0000.0000.0000.000
33A52VAL00.000-0.01230.3180.0050.0050.0000.0000.0000.000
34A53SER0-0.040-0.03430.9250.0050.0050.0000.0000.0000.000
35A54GLU-1-0.777-0.88828.2520.0560.0560.0000.0000.0000.000
36A55ALA00.0140.00026.3890.0080.0080.0000.0000.0000.000
37A56ILE0-0.045-0.01826.4890.0080.0080.0000.0000.0000.000
38A57GLU-1-0.816-0.90827.3580.0930.0930.0000.0000.0000.000
39A58ALA0-0.0140.01022.9650.0100.0100.0000.0000.0000.000
40A59GLY00.008-0.00522.5330.0160.0160.0000.0000.0000.000
41A60ARG10.7710.86523.417-0.071-0.0710.0000.0000.0000.000
42A61MET00.0130.02220.6550.0170.0170.0000.0000.0000.000
43A62LEU0-0.023-0.02417.3020.0220.0220.0000.0000.0000.000
44A63LEU0-0.010-0.00119.5360.0230.0230.0000.0000.0000.000
45A64GLU-1-0.887-0.92321.7470.1750.1750.0000.0000.0000.000
46A65LYS10.7710.87117.001-0.190-0.1900.0000.0000.0000.000
47A66GLY00.0110.01416.9830.0440.0440.0000.0000.0000.000
48A67PHE0-0.063-0.03412.5490.0350.0350.0000.0000.0000.000
49A68LYS10.8630.92116.078-0.181-0.1810.0000.0000.0000.000
50A69PHE0-0.0080.00114.0580.0260.0260.0000.0000.0000.000
51A70ASP-1-0.784-0.88514.6940.1750.1750.0000.0000.0000.000
52A71VAL0-0.040-0.03115.938-0.016-0.0160.0000.0000.0000.000
53A72VAL0-0.013-0.00517.4500.0150.0150.0000.0000.0000.000
54A73TYR0-0.004-0.00215.337-0.009-0.0090.0000.0000.0000.000
55A74THR0-0.012-0.02519.9020.0000.0000.0000.0000.0000.000
56A75SER0-0.030-0.01922.935-0.003-0.0030.0000.0000.0000.000
57A76VAL0-0.012-0.01925.7260.0030.0030.0000.0000.0000.000
58A77LEU0-0.022-0.00128.892-0.002-0.0020.0000.0000.0000.000
59A78LYS10.8830.90729.692-0.024-0.0240.0000.0000.0000.000
60A79ARG10.7900.90129.627-0.024-0.0240.0000.0000.0000.000
61A80ALA00.0060.01225.3890.0040.0040.0000.0000.0000.000
62A81ILE00.0310.03026.1810.0070.0070.0000.0000.0000.000
63A82MET00.0290.02127.9140.0060.0060.0000.0000.0000.000
64A83THR00.014-0.00524.3670.0030.0030.0000.0000.0000.000
65A84THR00.0110.00623.0060.0090.0090.0000.0000.0000.000
66A85TRP0-0.018-0.01724.9050.0050.0050.0000.0000.0000.000
67A86THR0-0.030-0.01927.8110.0020.0020.0000.0000.0000.000
68A87VAL00.005-0.00321.3900.0040.0040.0000.0000.0000.000
69A88LEU0-0.005-0.01121.6330.0090.0090.0000.0000.0000.000
70A89LYS10.8460.92024.759-0.073-0.0730.0000.0000.0000.000
71A90GLU-1-0.786-0.86726.3300.0830.0830.0000.0000.0000.000
72A91LEU00.0050.01320.3190.0040.0040.0000.0000.0000.000
73A92GLY0-0.0060.00323.8490.0060.0060.0000.0000.0000.000
74A93ASN0-0.042-0.03320.3230.0050.0050.0000.0000.0000.000
75A94ILE00.0330.01224.2370.0000.0000.0000.0000.0000.000
76A95ASN0-0.038-0.01525.375-0.002-0.0020.0000.0000.0000.000
77A96CYS0-0.065-0.00519.9910.0000.0000.0000.0000.0000.000
78A97PRO00.0130.00721.212-0.007-0.0070.0000.0000.0000.000
79A98ILE00.0150.00721.8250.0080.0080.0000.0000.0000.000
80A99ILE0-0.022-0.00719.971-0.007-0.0070.0000.0000.0000.000
81A100ASN00.0290.00722.7880.0050.0050.0000.0000.0000.000
82A101HIS00.001-0.00523.595-0.004-0.0040.0000.0000.0000.000
83A102TRP00.0950.03525.421-0.001-0.0010.0000.0000.0000.000
84A103ARG10.8730.94622.955-0.008-0.0080.0000.0000.0000.000
85A104LEU00.0370.02919.262-0.006-0.0060.0000.0000.0000.000
86A105ASN00.0550.02023.3640.0060.0060.0000.0000.0000.000
87A106GLU-1-0.754-0.86126.0110.0100.0100.0000.0000.0000.000
88A107ARG10.8350.91427.8390.0070.0070.0000.0000.0000.000
89A108HIS00.0040.01029.1010.0020.0020.0000.0000.0000.000
90A109TYR00.004-0.03730.911-0.003-0.0030.0000.0000.0000.000
91A110GLY00.0620.02735.242-0.001-0.0010.0000.0000.0000.000
92A111ALA0-0.037-0.02338.0470.0020.0020.0000.0000.0000.000
93A112LEU0-0.0130.00137.5730.0010.0010.0000.0000.0000.000
94A113GLN00.0330.02335.0820.0020.0020.0000.0000.0000.000
95A114GLY00.0780.03539.2030.0000.0000.0000.0000.0000.000
96A115LEU0-0.066-0.00241.3180.0000.0000.0000.0000.0000.000
97A116ASN00.0520.00841.2780.0010.0010.0000.0000.0000.000
98A117LYS10.8740.93240.073-0.005-0.0050.0000.0000.0000.000
99A118SER00.008-0.00442.196-0.001-0.0010.0000.0000.0000.000
100A119GLU-1-0.784-0.87045.2970.0080.0080.0000.0000.0000.000
101A120THR0-0.019-0.02740.965-0.001-0.0010.0000.0000.0000.000
102A121ALA0-0.021-0.01544.295-0.001-0.0010.0000.0000.0000.000
103A122SER0-0.0040.00946.0070.0000.0000.0000.0000.0000.000
104A123LYS10.8340.92447.139-0.005-0.0050.0000.0000.0000.000
105A124PHE00.0040.00044.079-0.001-0.0010.0000.0000.0000.000
106A125GLY00.0620.03746.3360.0010.0010.0000.0000.0000.000
107A126GLU-1-0.838-0.92743.8910.0010.0010.0000.0000.0000.000
108A127ASP-1-0.839-0.92342.240-0.006-0.0060.0000.0000.0000.000
109A128GLN00.0250.01340.9460.0000.0000.0000.0000.0000.000
110A129VAL00.0080.00439.595-0.001-0.0010.0000.0000.0000.000
111A130LYS10.8330.91137.9690.0070.0070.0000.0000.0000.000
112A131ILE00.0370.01836.420-0.001-0.0010.0000.0000.0000.000
113A132TRP00.0170.02235.2000.0000.0000.0000.0000.0000.000
114A133ARG10.8920.95933.513-0.005-0.0050.0000.0000.0000.000
115A134ARG10.9150.95131.6350.0090.0090.0000.0000.0000.000
116A135SER00.0060.02331.433-0.003-0.0030.0000.0000.0000.000
117A136PHE00.0400.01523.8490.0020.0020.0000.0000.0000.000
118A137ASP-1-0.870-0.96429.081-0.030-0.0300.0000.0000.0000.000
119A138VAL00.0290.01731.5580.0020.0020.0000.0000.0000.000
120A139PRO0-0.016-0.00134.2150.0020.0020.0000.0000.0000.000
121A140PRO0-0.008-0.00834.8440.0000.0000.0000.0000.0000.000
122A141PRO0-0.0010.02137.942-0.001-0.0010.0000.0000.0000.000
123A142VAL00.0000.00039.4450.0010.0010.0000.0000.0000.000
124A143LEU0-0.0370.00339.0600.0000.0000.0000.0000.0000.000
125A144GLU-1-0.859-0.90742.0480.0000.0000.0000.0000.0000.000
126A145LYS10.9070.93641.1980.0010.0010.0000.0000.0000.000
127A146SER0-0.021-0.02344.7010.0010.0010.0000.0000.0000.000
128A147ASP-1-0.786-0.85944.2810.0060.0060.0000.0000.0000.000
129A148PRO00.0400.00044.3250.0000.0000.0000.0000.0000.000
130A149ARG10.7510.83540.514-0.004-0.0040.0000.0000.0000.000
131A150TRP0-0.022-0.00237.9430.0000.0000.0000.0000.0000.000
132A151PRO00.0480.01535.4920.0010.0010.0000.0000.0000.000
133A152GLY0-0.031-0.01737.7760.0010.0010.0000.0000.0000.000
134A153ASN0-0.055-0.01539.6320.0000.0000.0000.0000.0000.000
135A154GLU-1-0.913-0.95337.1190.0170.0170.0000.0000.0000.000
136A155LEU0-0.022-0.03238.7290.0000.0000.0000.0000.0000.000
137A156ILE00.0000.00433.2590.0010.0010.0000.0000.0000.000
138A157TYR00.022-0.00331.2530.0020.0020.0000.0000.0000.000
139A158LYS10.9490.97635.334-0.019-0.0190.0000.0000.0000.000
140A159GLY0-0.0090.00035.939-0.001-0.0010.0000.0000.0000.000
141A160ILE0-0.0300.00531.2940.0010.0010.0000.0000.0000.000
142A161CYS00.008-0.00232.916-0.002-0.0020.0000.0000.0000.000
143A162PRO00.0550.01134.302-0.001-0.0010.0000.0000.0000.000
144A163SER0-0.0090.00134.3380.0000.0000.0000.0000.0000.000
145A164CYS0-0.053-0.02230.513-0.002-0.0020.0000.0000.0000.000
146A165LEU0-0.0220.00831.4690.0010.0010.0000.0000.0000.000
147A166PRO00.0150.01431.388-0.001-0.0010.0000.0000.0000.000
148A167THR0-0.001-0.00734.3530.0010.0010.0000.0000.0000.000
149A168THR0-0.005-0.04235.5600.0010.0010.0000.0000.0000.000
150A169GLU-1-0.715-0.80729.017-0.002-0.0020.0000.0000.0000.000
151A170CYS0-0.103-0.01630.8890.0000.0000.0000.0000.0000.000
152A171LEU0-0.011-0.01523.7650.0010.0010.0000.0000.0000.000
153A172LYS10.8810.91225.6640.0290.0290.0000.0000.0000.000
154A173ASP-1-0.738-0.85225.834-0.021-0.0210.0000.0000.0000.000
155A174THR0-0.053-0.04424.1720.0020.0020.0000.0000.0000.000
156A175VAL00.006-0.00120.6150.0030.0030.0000.0000.0000.000
157A176GLU-1-0.848-0.90821.771-0.033-0.0330.0000.0000.0000.000
158A177ARG10.6480.78223.5680.0000.0000.0000.0000.0000.000
159A178VAL0-0.0010.00418.8320.0070.0070.0000.0000.0000.000
160A179LYS10.9020.96117.6950.0710.0710.0000.0000.0000.000
161A180PRO00.0430.02417.7780.0050.0050.0000.0000.0000.000
162A181TYR0-0.004-0.00819.0000.0120.0120.0000.0000.0000.000
163A182PHE00.0360.0069.7420.0100.0100.0000.0000.0000.000
164A183GLU-1-0.865-0.95214.373-0.013-0.0130.0000.0000.0000.000
165A184ASP-1-0.869-0.93315.1330.0430.0430.0000.0000.0000.000
166A185VAL0-0.080-0.04016.8900.0070.0070.0000.0000.0000.000
167A186ILE0-0.041-0.00312.7730.0120.0120.0000.0000.0000.000
168A187ALA00.0200.01310.8230.0350.0350.0000.0000.0000.000
169A188PRO00.0240.01010.6230.0870.0870.0000.0000.0000.000
170A189SER0-0.026-0.01612.3590.0140.0140.0000.0000.0000.000
171A190ILE00.0030.0156.810-0.014-0.0140.0000.0000.0000.000
172A191MET00.0350.0207.4280.0110.0110.0000.0000.0000.000
173A192SER0-0.096-0.0478.485-0.089-0.0890.0000.0000.0000.000
174A193GLY00.0160.0028.342-0.056-0.0560.0000.0000.0000.000
175A194LYS10.8590.9449.386-0.150-0.1500.0000.0000.0000.000
176A195SER0-0.014-0.01510.7990.0540.0540.0000.0000.0000.000
177A196VAL0-0.009-0.01411.919-0.040-0.0400.0000.0000.0000.000
178A197LEU0-0.0140.00113.1450.0170.0170.0000.0000.0000.000
179A198VAL0-0.015-0.01314.994-0.016-0.0160.0000.0000.0000.000
180A199SER0-0.008-0.00517.621-0.002-0.0020.0000.0000.0000.000
181A200ALA00.0290.00921.041-0.007-0.0070.0000.0000.0000.000
182A201HIS0-0.0190.01522.9500.0030.0030.0000.0000.0000.000
183A202GLY0-0.0100.00022.942-0.001-0.0010.0000.0000.0000.000
184A203ASN0-0.066-0.06923.265-0.010-0.0100.0000.0000.0000.000
185A204SER00.0230.00621.969-0.006-0.0060.0000.0000.0000.000
186A205LEU00.0120.01017.810-0.005-0.0050.0000.0000.0000.000
187A206ARG10.8530.91518.1850.0070.0070.0000.0000.0000.000
188A207ALA00.0180.01019.405-0.016-0.0160.0000.0000.0000.000
189A208LEU00.0140.00814.895-0.014-0.0140.0000.0000.0000.000
190A209LEU00.0110.00914.282-0.027-0.0270.0000.0000.0000.000
191A210TYR00.026-0.00215.321-0.035-0.0350.0000.0000.0000.000
192A211LEU0-0.0180.00015.097-0.022-0.0220.0000.0000.0000.000
193A212LEU00.0260.01410.067-0.028-0.0280.0000.0000.0000.000
194A213GLU-1-0.750-0.85610.718-0.262-0.2620.0000.0000.0000.000
195A214GLY0-0.039-0.02213.012-0.050-0.0500.0000.0000.0000.000
196A215MET0-0.098-0.01415.6320.0150.0150.0000.0000.0000.000
197A216THR00.0560.00418.8520.0120.0120.0000.0000.0000.000
198A217PRO0-0.029-0.04022.4190.0040.0040.0000.0000.0000.000
199A218GLU-1-0.909-0.94925.003-0.058-0.0580.0000.0000.0000.000
200A219GLN00.1120.07519.9920.0010.0010.0000.0000.0000.000
201A220ILE0-0.003-0.00219.6410.0080.0080.0000.0000.0000.000
202A221LEU0-0.101-0.04022.6840.0120.0120.0000.0000.0000.000
203A222GLU-1-0.932-0.95324.117-0.041-0.0410.0000.0000.0000.000
204A223VAL0-0.050-0.00719.4800.0080.0080.0000.0000.0000.000
205A224ASN0-0.016-0.02122.5540.0040.0040.0000.0000.0000.000
206A225ILE00.0040.00419.1510.0010.0010.0000.0000.0000.000
207A226PRO00.0100.01121.541-0.003-0.0030.0000.0000.0000.000
208A227THR0-0.010-0.01223.3860.0040.0040.0000.0000.0000.000
209A228ALA0-0.0100.00424.0600.0030.0030.0000.0000.0000.000
210A229CYS0-0.0290.00221.3660.0130.0130.0000.0000.0000.000
211A230PRO00.0130.00917.607-0.006-0.0060.0000.0000.0000.000
212A231LEU0-0.014-0.01014.2620.0070.0070.0000.0000.0000.000
213A232VAL0-0.0010.0039.503-0.014-0.0140.0000.0000.0000.000
214A233LEU00.000-0.0078.911-0.045-0.0450.0000.0000.0000.000
215A234GLU-1-0.782-0.8634.4091.6461.787-0.001-0.009-0.1300.000
216A235LEU0-0.010-0.0063.281-0.6640.3650.006-0.430-0.6060.000
217A236ASP-1-0.829-0.9131.857-19.571-26.90718.887-6.707-4.844-0.074
218A237ASP-1-0.884-0.9462.711-2.8600.4512.474-1.857-3.928-0.015
219A238TYR0-0.062-0.0403.833-0.745-0.5120.021-0.015-0.2390.001
220A239LEU0-0.050-0.0275.120-0.329-0.232-0.001-0.006-0.0890.000
221A240LYS10.8390.9276.3470.4000.4000.0000.0000.0000.000
222A241VAL0-0.025-0.0216.072-0.702-0.7020.0000.0000.0000.000
223A242THR00.0100.0194.0490.3480.491-0.001-0.012-0.1310.000
224A243LYS10.8270.8946.957-0.699-0.6990.0000.0000.0000.000
225A244LYS10.8160.8888.4500.1160.1160.0000.0000.0000.000
226A245TYR0-0.072-0.0599.391-0.089-0.0890.0000.0000.0000.000
227A246TYR00.0400.01414.0960.0120.0120.0000.0000.0000.000
228A247LEU0-0.040-0.00914.8760.0170.0170.0000.0000.0000.000
229A248ILE00.001-0.00218.273-0.014-0.0140.0000.0000.0000.000