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: 4J6QN

Calculation Name: 1B8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZF99

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 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 327
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4751004.703351
FMO2-HF: Nuclear repulsion 4626978.443697
FMO2-HF: Total energy -124026.259654
FMO2-MP2: Total energy -124384.681859


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:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-203.608-192.7559.706-8.365-12.195-0.1
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.903 / q_NPA : 0.953
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].
3A5PRO00.0040.0113.770-7.413-5.838-0.006-0.737-0.8330.000
4A6MET0-0.0040.0205.3340.2380.2380.0000.0000.0000.000
5A7ARG10.8850.9317.51221.74521.7450.0000.0000.0000.000
6A8VAL0-0.006-0.00410.3440.1390.1390.0000.0000.0000.000
7A9ALA00.0170.01812.9771.1031.1030.0000.0000.0000.000
8A10VAL0-0.004-0.00816.428-0.193-0.1930.0000.0000.0000.000
9A11THR00.0410.02118.8950.5750.5750.0000.0000.0000.000
10A12GLY00.016-0.00322.674-0.134-0.1340.0000.0000.0000.000
11A13ALA0-0.015-0.02921.8080.0260.0260.0000.0000.0000.000
12A14ALA00.0140.01923.401-0.162-0.1620.0000.0000.0000.000
13A15GLY0-0.017-0.00426.0140.4850.4850.0000.0000.0000.000
14A16GLN0-0.001-0.02825.866-0.483-0.4830.0000.0000.0000.000
15A17ILE0-0.027-0.01322.223-0.173-0.1730.0000.0000.0000.000
16A18CYS00.0280.01721.292-0.807-0.8070.0000.0000.0000.000
17A19TYR0-0.043-0.01321.206-0.735-0.7350.0000.0000.0000.000
18A20SER0-0.049-0.02822.2450.0350.0350.0000.0000.0000.000
19A21LEU0-0.065-0.03316.809-0.463-0.4630.0000.0000.0000.000
20A22LEU00.016-0.00316.859-1.217-1.2170.0000.0000.0000.000
21A23PHE00.0640.04115.974-1.342-1.3420.0000.0000.0000.000
22A24ARG10.8450.88815.62717.95117.9510.0000.0000.0000.000
23A25ILE0-0.034-0.01511.385-1.694-1.6940.0000.0000.0000.000
24A26ALA00.0130.00911.095-2.536-2.5360.0000.0000.0000.000
25A27ASN0-0.025-0.00212.111-0.941-0.9410.0000.0000.0000.000
26A28GLY00.0410.0078.925-0.863-0.8630.0000.0000.0000.000
27A29ASP-1-0.926-0.9469.016-24.649-24.6490.0000.0000.0000.000
28A30MET0-0.064-0.02810.3510.7360.7360.0000.0000.0000.000
29A31LEU00.009-0.0115.5150.7430.7430.0000.0000.0000.000
30A32GLY00.0640.0484.399-10.662-10.562-0.001-0.011-0.0880.000
31A33LYS10.8870.9295.60627.55427.5540.0000.0000.0000.000
32A34ASP-1-0.874-0.9332.416-99.234-95.5223.107-3.298-3.521-0.041
33A35GLN0-0.074-0.0592.218-35.914-31.4796.422-4.164-6.693-0.058
34A36PRO00.0020.0182.9158.5419.5220.185-0.153-1.013-0.001
35A37VAL00.0080.0095.705-2.568-2.5680.0000.0000.0000.000
36A38ILE00.0110.0148.4472.2152.2150.0000.0000.0000.000
37A39LEU0-0.002-0.00411.491-0.121-0.1210.0000.0000.0000.000
38A40GLN0-0.0070.01414.5940.2780.2780.0000.0000.0000.000
39A41LEU00.018-0.00217.3860.0160.0160.0000.0000.0000.000
40A42LEU0-0.003-0.00320.3340.5640.5640.0000.0000.0000.000
41A43GLU-1-0.840-0.92623.577-11.504-11.5040.0000.0000.0000.000
42A44ILE0-0.040-0.01527.0060.1080.1080.0000.0000.0000.000
43A45PRO00.0450.00930.483-0.050-0.0500.0000.0000.0000.000
44A46ASN0-0.022-0.00832.136-0.033-0.0330.0000.0000.0000.000
45A47GLU-1-0.844-0.92533.168-8.541-8.5410.0000.0000.0000.000
46A48LYS10.9470.96733.7218.5118.5110.0000.0000.0000.000
47A49ALA0-0.003-0.00130.651-0.113-0.1130.0000.0000.0000.000
48A50GLN00.0200.00327.436-0.479-0.4790.0000.0000.0000.000
49A51LYS10.9600.98728.9698.5418.5410.0000.0000.0000.000
50A52ALA0-0.024-0.01929.983-0.145-0.1450.0000.0000.0000.000
51A53LEU00.0200.00822.981-0.258-0.2580.0000.0000.0000.000
52A54GLN0-0.005-0.00425.090-0.597-0.5970.0000.0000.0000.000
53A55GLY00.013-0.00225.997-0.185-0.1850.0000.0000.0000.000
54A56VAL00.005-0.00122.378-0.145-0.1450.0000.0000.0000.000
55A57MET0-0.006-0.01220.528-0.346-0.3460.0000.0000.0000.000
56A58MET0-0.0030.01621.648-0.174-0.1740.0000.0000.0000.000
57A59GLU-1-0.816-0.88323.150-12.209-12.2090.0000.0000.0000.000
58A60ILE0-0.055-0.03217.474-0.466-0.4660.0000.0000.0000.000
59A61ASP-1-0.912-0.94918.630-15.541-15.5410.0000.0000.0000.000
60A62ASP-1-0.970-0.98019.594-12.488-12.4880.0000.0000.0000.000
61A63CYS0-0.131-0.05918.6520.2590.2590.0000.0000.0000.000
62A64ALA0-0.044-0.01517.135-0.458-0.4580.0000.0000.0000.000
63A65PHE00.004-0.00913.166-0.524-0.5240.0000.0000.0000.000
64A66PRO00.004-0.00710.111-0.472-0.4720.0000.0000.0000.000
65A67LEU0-0.040-0.0046.366-0.849-0.8490.0000.0000.0000.000
66A68LEU0-0.0080.0028.595-2.048-2.0480.0000.0000.0000.000
67A69ALA00.0020.0078.0291.2301.2300.0000.0000.0000.000
68A70GLY0-0.009-0.01210.1671.2651.2650.0000.0000.0000.000
69A71MET0-0.0070.00113.592-1.061-1.0610.0000.0000.0000.000
70A72THR0-0.032-0.01116.6050.6000.6000.0000.0000.0000.000
71A73ALA00.0390.01419.557-0.316-0.3160.0000.0000.0000.000
72A74HIS0-0.016-0.00520.315-0.266-0.2660.0000.0000.0000.000
73A75ALA00.0390.00824.4440.0920.0920.0000.0000.0000.000
74A76ASP-1-0.872-0.94826.356-10.707-10.7070.0000.0000.0000.000
75A77PRO00.013-0.00424.511-0.523-0.5230.0000.0000.0000.000
76A78MET00.0150.02723.566-0.719-0.7190.0000.0000.0000.000
77A79THR0-0.038-0.01422.963-0.416-0.4160.0000.0000.0000.000
78A80ALA0-0.0020.00620.706-0.622-0.6220.0000.0000.0000.000
79A81PHE00.012-0.01718.968-0.876-0.8760.0000.0000.0000.000
80A82LYS10.9410.97418.57314.03814.0380.0000.0000.0000.000
81A83ASP-1-0.922-0.95814.615-17.484-17.4840.0000.0000.0000.000
82A84ALA0-0.033-0.00813.938-1.448-1.4480.0000.0000.0000.000
83A85ASP-1-0.797-0.91310.143-27.061-27.0610.0000.0000.0000.000
84A86VAL0-0.032-0.02110.429-0.260-0.2600.0000.0000.0000.000
85A87ALA00.0120.01113.2610.6210.6210.0000.0000.0000.000
86A88LEU0-0.027-0.01014.3710.1250.1250.0000.0000.0000.000
87A89LEU00.020-0.00418.2810.4910.4910.0000.0000.0000.000
88A90VAL00.016-0.00420.8470.4120.4120.0000.0000.0000.000
89A91GLY0-0.043-0.01423.5470.5510.5510.0000.0000.0000.000
90A92ALA00.0230.01026.574-0.078-0.0780.0000.0000.0000.000
91A93ARG10.8980.96229.7138.7778.7770.0000.0000.0000.000
92A94PRO0-0.010-0.00733.0180.1080.1080.0000.0000.0000.000
93A95ARG10.9850.96734.8478.0658.0650.0000.0000.0000.000
94A96GLY0-0.014-0.01138.2020.0310.0310.0000.0000.0000.000
95A97PRO00.024-0.01740.7920.0520.0520.0000.0000.0000.000
96A98GLY00.0090.01244.5950.0130.0130.0000.0000.0000.000
97A99MET0-0.0440.02838.575-0.031-0.0310.0000.0000.0000.000
98A100GLU-1-0.902-0.95043.884-6.803-6.8030.0000.0000.0000.000
99A101ARG10.8140.87638.5297.9587.9580.0000.0000.0000.000
100A102LYS11.0051.00140.4486.6076.6070.0000.0000.0000.000
101A103ASP-1-0.764-0.87541.215-7.429-7.4290.0000.0000.0000.000
102A104LEU0-0.084-0.04735.457-0.157-0.1570.0000.0000.0000.000
103A105LEU00.007-0.00535.764-0.293-0.2930.0000.0000.0000.000
104A106GLU-1-0.858-0.92636.287-7.961-7.9610.0000.0000.0000.000
105A107ALA0-0.052-0.02336.813-0.166-0.1660.0000.0000.0000.000
106A108ASN00.017-0.00832.052-0.534-0.5340.0000.0000.0000.000
107A109ALA00.0730.03932.120-0.356-0.3560.0000.0000.0000.000
108A110GLN00.0090.00333.137-0.365-0.3650.0000.0000.0000.000
109A111ILE0-0.064-0.01128.823-0.122-0.1220.0000.0000.0000.000
110A112PHE0-0.009-0.03725.287-0.374-0.3740.0000.0000.0000.000
111A113THR00.0100.02328.533-0.304-0.3040.0000.0000.0000.000
112A114VAL0-0.031-0.00729.286-0.226-0.2260.0000.0000.0000.000
113A115GLN00.009-0.01624.936-0.585-0.5850.0000.0000.0000.000
114A116GLY00.0340.02724.976-0.530-0.5300.0000.0000.0000.000
115A117LYS10.9820.98625.7509.3539.3530.0000.0000.0000.000
116A118ALA0-0.010-0.00625.055-0.104-0.1040.0000.0000.0000.000
117A119ILE0-0.025-0.01020.269-0.399-0.3990.0000.0000.0000.000
118A120ASP-1-0.813-0.87422.128-12.562-12.5620.0000.0000.0000.000
119A121ALA0-0.0050.01224.165-0.150-0.1500.0000.0000.0000.000
120A122VAL0-0.058-0.02921.449-0.086-0.0860.0000.0000.0000.000
121A123ALA0-0.0100.02718.004-0.556-0.5560.0000.0000.0000.000
122A124SER00.0450.02413.5420.9580.9580.0000.0000.0000.000
123A125ARG10.8230.88616.31415.03615.0360.0000.0000.0000.000
124A126ASN0-0.051-0.02914.4181.2581.2580.0000.0000.0000.000
125A127ILE0-0.0110.01514.419-1.288-1.2880.0000.0000.0000.000
126A128LYS10.8970.97510.92926.65426.6540.0000.0000.0000.000
127A129VAL00.0420.01615.201-0.309-0.3090.0000.0000.0000.000
128A130LEU0-0.0270.00517.3080.1950.1950.0000.0000.0000.000
129A131VAL0-0.0230.00219.2300.1070.1070.0000.0000.0000.000
130A132VAL0-0.022-0.03320.8000.0780.0780.0000.0000.0000.000
131A133GLY00.0040.00923.6530.4850.4850.0000.0000.0000.000
132A134ASN0-0.043-0.02726.827-0.129-0.1290.0000.0000.0000.000
133A135PRO00.0060.00030.0560.1200.1200.0000.0000.0000.000
134A136ALA00.0740.01925.763-0.035-0.0350.0000.0000.0000.000
135A137ASN0-0.016-0.01127.143-0.423-0.4230.0000.0000.0000.000
136A138THR00.043-0.01628.467-0.132-0.1320.0000.0000.0000.000
137A139ASN0-0.020-0.00527.8820.3290.3290.0000.0000.0000.000
138A140ALA00.000-0.01124.726-0.141-0.1410.0000.0000.0000.000
139A141TYR00.0540.02126.280-0.089-0.0890.0000.0000.0000.000
140A142ILE00.0020.01028.8660.0830.0830.0000.0000.0000.000
141A143ALA0-0.009-0.01225.0960.0720.0720.0000.0000.0000.000
142A144MET0-0.039-0.00425.235-0.126-0.1260.0000.0000.0000.000
143A145LYS10.8830.95026.37210.25310.2530.0000.0000.0000.000
144A146SER0-0.036-0.01928.7950.4000.4000.0000.0000.0000.000
145A147ALA0-0.058-0.01724.7980.0660.0660.0000.0000.0000.000
146A148PRO00.0050.00125.863-0.338-0.3380.0000.0000.0000.000
147A149SER0-0.081-0.07125.351-0.122-0.1220.0000.0000.0000.000
148A150LEU0-0.039-0.00820.206-0.545-0.5450.0000.0000.0000.000
149A151PRO00.0110.00319.3520.5220.5220.0000.0000.0000.000
150A152ALA00.0800.02121.530-0.427-0.4270.0000.0000.0000.000
151A153LYS10.9100.96617.91116.76816.7680.0000.0000.0000.000
152A154ASN00.0000.00116.705-0.770-0.7700.0000.0000.0000.000
153A155PHE00.0160.01818.804-0.590-0.5900.0000.0000.0000.000
154A156THR0-0.008-0.00318.8830.2530.2530.0000.0000.0000.000
155A157ALA00.0030.00121.3750.1220.1220.0000.0000.0000.000
156A158MET0-0.032-0.00821.058-0.397-0.3970.0000.0000.0000.000
157A159LEU00.0560.02322.6230.4990.4990.0000.0000.0000.000
158A160ARG10.8100.90116.71318.17818.1780.0000.0000.0000.000
159A161LEU0-0.007-0.00922.0890.1940.1940.0000.0000.0000.000
160A162ASP-1-0.816-0.89824.463-11.004-11.0040.0000.0000.0000.000
161A163HIS00.0650.05022.6510.4350.4350.0000.0000.0000.000
162A164ASN00.001-0.01320.2910.2710.2710.0000.0000.0000.000
163A165ARG10.8880.94924.54711.34411.3440.0000.0000.0000.000
164A166ALA00.0400.02328.1420.4050.4050.0000.0000.0000.000
165A167LEU00.0420.00222.8840.3170.3170.0000.0000.0000.000
166A168SER0-0.074-0.03427.4160.3080.3080.0000.0000.0000.000
167A169GLN0-0.013-0.00628.9870.5150.5150.0000.0000.0000.000
168A170ILE00.0350.03030.2910.3520.3520.0000.0000.0000.000
169A171ALA00.0040.01528.9150.2220.2220.0000.0000.0000.000
170A172ALA0-0.032-0.01331.0420.2250.2250.0000.0000.0000.000
171A173LYS10.8920.96533.9298.2358.2350.0000.0000.0000.000
172A174THR0-0.030-0.03533.1080.1650.1650.0000.0000.0000.000
173A175GLY00.0160.02834.8090.1370.1370.0000.0000.0000.000
174A176LYS10.8960.96530.9819.7099.7090.0000.0000.0000.000
175A177PRO00.0350.01526.789-0.120-0.1200.0000.0000.0000.000
176A178VAL00.0540.01123.932-0.104-0.1040.0000.0000.0000.000
177A179SER0-0.061-0.03322.091-0.007-0.0070.0000.0000.0000.000
178A180SER0-0.004-0.00623.272-0.198-0.1980.0000.0000.0000.000
179A181ILE0-0.029-0.00525.8630.2840.2840.0000.0000.0000.000
180A182GLU-1-0.948-0.97823.875-13.272-13.2720.0000.0000.0000.000
181A183LYS10.8900.94824.68212.43912.4390.0000.0000.0000.000
182A184LEU00.0270.03725.7790.4360.4360.0000.0000.0000.000
183A185PHE0-0.025-0.03525.246-0.678-0.6780.0000.0000.0000.000
184A186VAL0-0.021-0.01726.3980.5040.5040.0000.0000.0000.000
185A187TRP0-0.056-0.02027.565-0.443-0.4430.0000.0000.0000.000
186A188GLY0-0.011-0.01330.0130.1980.1980.0000.0000.0000.000
187A189ASN00.0540.01129.355-0.894-0.8940.0000.0000.0000.000
188A190HIS10.8270.91727.46011.59911.5990.0000.0000.0000.000
189A191SER0-0.069-0.07229.5210.0850.0850.0000.0000.0000.000
190A192PRO0-0.005-0.00933.060-0.090-0.0900.0000.0000.0000.000
191A193THR0-0.040-0.03235.4900.0880.0880.0000.0000.0000.000
192A194MET0-0.0560.01430.945-0.083-0.0830.0000.0000.0000.000
193A195TYR00.008-0.03432.3570.3580.3580.0000.0000.0000.000
194A196ALA00.0290.00830.717-0.299-0.2990.0000.0000.0000.000
195A197ASP-1-0.782-0.87030.779-9.231-9.2310.0000.0000.0000.000
196A198TYR00.031-0.01030.975-0.237-0.2370.0000.0000.0000.000
197A199ARG10.7510.83432.8309.0759.0750.0000.0000.0000.000
198A200TYR00.0520.03130.4540.1760.1760.0000.0000.0000.000
199A201ALA0-0.0220.00029.324-0.205-0.2050.0000.0000.0000.000
200A202GLN00.003-0.01429.0520.0250.0250.0000.0000.0000.000
201A203ILE00.0240.01128.700-0.402-0.4020.0000.0000.0000.000
202A204ASP-1-0.901-0.95128.846-10.438-10.4380.0000.0000.0000.000
203A205GLY0-0.0010.00430.0300.2630.2630.0000.0000.0000.000
204A206ALA0-0.026-0.00131.6630.3100.3100.0000.0000.0000.000
205A207SER00.0250.00733.327-0.337-0.3370.0000.0000.0000.000
206A208VAL00.0620.02231.4380.2040.2040.0000.0000.0000.000
207A209LYS10.9300.97034.6898.3958.3950.0000.0000.0000.000
208A210ASP-1-0.881-0.95837.394-7.899-7.8990.0000.0000.0000.000
209A211MET0-0.093-0.02734.1770.1460.1460.0000.0000.0000.000
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