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: YV6R2

Calculation Name: 2FBQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FBQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HZJ9

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 OptHSide
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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2347829.284422
FMO2-HF: Nuclear repulsion 2264401.272902
FMO2-HF: Total energy -83428.01152
FMO2-MP2: Total energy -83669.333114


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-11.564-13.03314.077-6.386-6.2220.018
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.016
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].
3A4SER00.0890.0243.230-2.967-0.5220.370-1.257-1.5580.008
4A5GLU-1-0.886-0.9411.914-5.232-9.83113.654-5.089-3.9660.009
5A6THR0-0.046-0.0223.384-2.361-1.7620.054-0.035-0.6180.001
6A7VAL0-0.0090.0005.133-0.416-0.330-0.001-0.005-0.0800.000
7A8GLU-1-0.809-0.9066.6380.7950.7950.0000.0000.0000.000
8A9ARG10.8780.9435.553-0.049-0.0490.0000.0000.0000.000
9A10ILE0-0.041-0.0178.647-0.170-0.1700.0000.0000.0000.000
10A11LEU0-0.014-0.00410.833-0.138-0.1380.0000.0000.0000.000
11A12ASP-1-0.797-0.88111.5570.4350.4350.0000.0000.0000.000
12A13ALA0-0.064-0.03012.808-0.079-0.0790.0000.0000.0000.000
13A14ALA00.000-0.01514.716-0.039-0.0390.0000.0000.0000.000
14A15GLU-1-0.804-0.86116.1590.3340.3340.0000.0000.0000.000
15A16GLN0-0.010-0.00817.371-0.023-0.0230.0000.0000.0000.000
16A17LEU00.016-0.01218.083-0.024-0.0240.0000.0000.0000.000
17A18PHE0-0.048-0.03319.286-0.016-0.0160.0000.0000.0000.000
18A19ALA00.0140.00421.927-0.013-0.0130.0000.0000.0000.000
19A20GLU-1-0.921-0.94722.4090.0690.0690.0000.0000.0000.000
20A21LYS10.8340.90324.682-0.056-0.0560.0000.0000.0000.000
21A22GLY00.0310.02825.754-0.007-0.0070.0000.0000.0000.000
22A23PHE00.012-0.01222.9210.0000.0000.0000.0000.0000.000
23A24ALA0-0.022-0.01425.448-0.003-0.0030.0000.0000.0000.000
24A25GLU-1-0.806-0.89727.5560.0360.0360.0000.0000.0000.000
25A26THR00.0090.03220.944-0.010-0.0100.0000.0000.0000.000
26A27SER0-0.012-0.00922.6630.0070.0070.0000.0000.0000.000
27A28LEU00.1120.03418.0500.0040.0040.0000.0000.0000.000
28A29ARG10.9591.00817.9600.0080.0080.0000.0000.0000.000
29A30LEU0-0.0110.00218.641-0.017-0.0170.0000.0000.0000.000
30A31ILE00.0630.02214.735-0.011-0.0110.0000.0000.0000.000
31A32THR0-0.022-0.01714.0220.0020.0020.0000.0000.0000.000
32A33SER0-0.049-0.03113.942-0.029-0.0290.0000.0000.0000.000
33A34LYS10.8560.93015.236-0.101-0.1010.0000.0000.0000.000
34A35ALA00.0370.02910.653-0.002-0.0020.0000.0000.0000.000
35A36GLY00.0080.02210.144-0.054-0.0540.0000.0000.0000.000
36A37VAL0-0.010-0.0017.979-0.120-0.1200.0000.0000.0000.000
37A38ASN00.023-0.00210.6200.0720.0720.0000.0000.0000.000
38A39LEU00.0750.01512.8610.0210.0210.0000.0000.0000.000
39A40ALA00.0090.00814.0220.0390.0390.0000.0000.0000.000
40A41ALA00.0300.0309.5360.0280.0280.0000.0000.0000.000
41A42VAL00.006-0.00211.5850.0960.0960.0000.0000.0000.000
42A43ASN0-0.054-0.04713.7870.0580.0580.0000.0000.0000.000
43A44TYR0-0.017-0.00610.7410.0190.0190.0000.0000.0000.000
44A45HIS00.0060.0117.6510.1410.1410.0000.0000.0000.000
45A46PHE0-0.026-0.01711.6470.0360.0360.0000.0000.0000.000
46A47GLY00.0530.03916.023-0.013-0.0130.0000.0000.0000.000
47A48SER0-0.029-0.02518.704-0.025-0.0250.0000.0000.0000.000
48A49LYS10.8620.92719.744-0.065-0.0650.0000.0000.0000.000
49A50LYS10.9560.98121.225-0.088-0.0880.0000.0000.0000.000
50A51ALA00.0520.03719.2060.0110.0110.0000.0000.0000.000
51A52LEU00.0140.02014.9060.0280.0280.0000.0000.0000.000
52A53ILE0-0.025-0.01818.0120.0300.0300.0000.0000.0000.000
53A54GLN0-0.018-0.03020.6730.0220.0220.0000.0000.0000.000
54A55ALA00.0050.00315.2910.0100.0100.0000.0000.0000.000
55A56VAL00.0050.00916.4590.0450.0450.0000.0000.0000.000
56A57PHE0-0.011-0.01817.7340.0050.0050.0000.0000.0000.000
57A58SER00.0110.01018.193-0.017-0.0170.0000.0000.0000.000
58A59ARG10.7310.84011.276-0.690-0.6900.0000.0000.0000.000
59A60PHE0-0.016-0.01216.4200.0050.0050.0000.0000.0000.000
60A61LEU00.009-0.01119.575-0.016-0.0160.0000.0000.0000.000
61A62GLY00.0350.03618.983-0.021-0.0210.0000.0000.0000.000
62A63PRO0-0.004-0.01417.162-0.025-0.0250.0000.0000.0000.000
63A64PHE00.0260.01420.037-0.028-0.0280.0000.0000.0000.000
64A65CYS0-0.043-0.01523.353-0.028-0.0280.0000.0000.0000.000
65A66ALA00.0040.01421.939-0.018-0.0180.0000.0000.0000.000
66A67SER0-0.033-0.03823.506-0.019-0.0190.0000.0000.0000.000
67A68LEU0-0.008-0.00525.253-0.019-0.0190.0000.0000.0000.000
68A69GLU-1-0.855-0.93227.5220.1430.1430.0000.0000.0000.000
69A70LYS10.9740.99325.078-0.195-0.1950.0000.0000.0000.000
70A71GLU-1-0.755-0.83428.9960.1050.1050.0000.0000.0000.000
71A72LEU0-0.023-0.00731.162-0.012-0.0120.0000.0000.0000.000
72A73ASP-1-0.811-0.87831.3770.1230.1230.0000.0000.0000.000
73A74ARG10.7960.86531.921-0.119-0.1190.0000.0000.0000.000
74A75ARG10.8040.86733.670-0.112-0.1120.0000.0000.0000.000
75A76GLN00.0200.00936.932-0.002-0.0020.0000.0000.0000.000
76A77ALA00.0160.02737.108-0.004-0.0040.0000.0000.0000.000
77A78LYS10.8830.94937.981-0.084-0.0840.0000.0000.0000.000
78A79PRO00.0260.00540.964-0.001-0.0010.0000.0000.0000.000
79A80GLU-1-0.910-0.94644.4470.0510.0510.0000.0000.0000.000
80A81ALA0-0.061-0.02242.1090.0000.0000.0000.0000.0000.000
81A82GLN0-0.023-0.01143.945-0.002-0.0020.0000.0000.0000.000
82A83HIS0-0.020-0.01143.7370.0030.0030.0000.0000.0000.000
83A84ALA0-0.033-0.00340.380-0.001-0.0010.0000.0000.0000.000
84A85THR00.021-0.01842.340-0.002-0.0020.0000.0000.0000.000
85A86LEU00.006-0.01541.7300.0040.0040.0000.0000.0000.000
86A87GLU-1-0.744-0.84140.4660.0670.0670.0000.0000.0000.000
87A88ASP-1-0.838-0.87939.3400.0780.0780.0000.0000.0000.000
88A89LEU0-0.0020.00237.1400.0070.0070.0000.0000.0000.000
89A90LEU0-0.0180.00435.7470.0080.0080.0000.0000.0000.000
90A91HIS00.0770.01734.9720.0100.0100.0000.0000.0000.000
91A92LEU0-0.069-0.01431.7700.0070.0070.0000.0000.0000.000
92A93LEU0-0.0100.00330.9590.0110.0110.0000.0000.0000.000
93A94VAL00.0310.01729.8320.0120.0120.0000.0000.0000.000
94A95SER0-0.036-0.02229.5640.0080.0080.0000.0000.0000.000
95A96GLN00.0280.01726.9110.0210.0210.0000.0000.0000.000
96A97ALA0-0.022-0.01525.5730.0180.0180.0000.0000.0000.000
97A98MET0-0.063-0.03224.8420.0130.0130.0000.0000.0000.000
98A99ALA0-0.0250.00424.6030.0020.0020.0000.0000.0000.000
99A100VAL0-0.059-0.01419.6380.0230.0230.0000.0000.0000.000
100A101LYS10.9530.97113.826-0.380-0.3800.0000.0000.0000.000
101A102PRO0-0.0070.00317.5900.0340.0340.0000.0000.0000.000
102A103ARG10.8190.88613.211-0.417-0.4170.0000.0000.0000.000
103A104SER00.019-0.01615.681-0.041-0.0410.0000.0000.0000.000
104A105GLY0-0.0080.00217.670-0.035-0.0350.0000.0000.0000.000
105A106ASN0-0.078-0.05320.605-0.037-0.0370.0000.0000.0000.000
106A107ASP-1-0.704-0.82918.2890.2660.2660.0000.0000.0000.000
107A108LEU00.0680.03421.2370.0030.0030.0000.0000.0000.000
108A109SER0-0.022-0.03024.667-0.005-0.0050.0000.0000.0000.000
109A110ILE00.0300.01120.437-0.009-0.0090.0000.0000.0000.000
110A111PHE00.0060.00722.602-0.004-0.0040.0000.0000.0000.000
111A112MET00.0150.01723.807-0.009-0.0090.0000.0000.0000.000
112A113ARG10.8500.92925.780-0.109-0.1090.0000.0000.0000.000
113A114LEU0-0.033-0.02421.085-0.009-0.0090.0000.0000.0000.000
114A115LEU00.0150.00725.686-0.005-0.0050.0000.0000.0000.000
115A116GLY00.0320.01628.064-0.008-0.0080.0000.0000.0000.000
116A117LEU0-0.016-0.00126.604-0.008-0.0080.0000.0000.0000.000
117A118ALA0-0.042-0.02227.595-0.006-0.0060.0000.0000.0000.000
118A119PHE0-0.0030.00629.299-0.006-0.0060.0000.0000.0000.000
119A120SER00.0000.00232.526-0.006-0.0060.0000.0000.0000.000
120A121GLN00.0120.00329.133-0.002-0.0020.0000.0000.0000.000
121A122SER00.0270.02931.9130.0010.0010.0000.0000.0000.000
122A123GLN0-0.037-0.01627.3110.0070.0070.0000.0000.0000.000
123A124GLY00.0300.00729.8950.0090.0090.0000.0000.0000.000
124A125HIS0-0.053-0.04524.6440.0080.0080.0000.0000.0000.000
125A126LEU00.0340.03324.0400.0080.0080.0000.0000.0000.000
126A127ARG10.9790.99427.177-0.092-0.0920.0000.0000.0000.000
127A128LYS10.8480.90128.753-0.130-0.1300.0000.0000.0000.000
128A129TYR00.0550.03219.6590.0060.0060.0000.0000.0000.000
129A130LEU0-0.016-0.02023.8840.0100.0100.0000.0000.0000.000
130A131GLU-1-0.830-0.86926.7600.1280.1280.0000.0000.0000.000
131A132GLU-1-0.857-0.91627.3750.1430.1430.0000.0000.0000.000
132A133VAL0-0.0410.00222.1590.0030.0030.0000.0000.0000.000
133A134TYR0-0.003-0.03620.5000.0090.0090.0000.0000.0000.000
134A135GLY00.0480.03227.016-0.010-0.0100.0000.0000.0000.000
135A136LYS10.8910.94330.077-0.129-0.1290.0000.0000.0000.000
136A137VAL00.0730.04627.690-0.010-0.0100.0000.0000.0000.000
137A138PHE00.0130.00027.104-0.008-0.0080.0000.0000.0000.000
138A139ARG10.8150.86832.131-0.126-0.1260.0000.0000.0000.000
139A140ARG10.7750.85732.352-0.130-0.1300.0000.0000.0000.000
140A141TYR0-0.003-0.03133.474-0.006-0.0060.0000.0000.0000.000
141A142MET0-0.022-0.02035.483-0.007-0.0070.0000.0000.0000.000
142A143LEU0-0.023-0.00437.727-0.006-0.0060.0000.0000.0000.000
143A144LEU00.0380.02637.157-0.004-0.0040.0000.0000.0000.000
144A145VAL0-0.002-0.00438.123-0.004-0.0040.0000.0000.0000.000
145A146ASN0-0.111-0.06340.986-0.006-0.0060.0000.0000.0000.000
146A147GLU-1-0.908-0.96743.4540.0710.0710.0000.0000.0000.000
147A148ALA0-0.0230.00343.327-0.003-0.0030.0000.0000.0000.000
148A149ALA0-0.068-0.02445.142-0.002-0.0020.0000.0000.0000.000
149A150PRO00.0160.01046.920-0.001-0.0010.0000.0000.0000.000
150A151LYS10.9410.96449.314-0.045-0.0450.0000.0000.0000.000
151A152LEU00.0400.03347.200-0.001-0.0010.0000.0000.0000.000
152A153PRO00.0420.02849.7830.0010.0010.0000.0000.0000.000
153A154PRO00.0420.00746.2510.0020.0020.0000.0000.0000.000
154A155ILE0-0.0030.00145.2850.0030.0030.0000.0000.0000.000
155A156GLU-1-0.723-0.83445.7860.0520.0520.0000.0000.0000.000
156A157LEU00.0240.02142.7920.0020.0020.0000.0000.0000.000
157A158PHE0-0.011-0.00239.0320.0050.0050.0000.0000.0000.000
158A159TRP00.0130.00541.1600.0050.0050.0000.0000.0000.000
159A160ARG10.8100.89542.202-0.052-0.0520.0000.0000.0000.000
160A161VAL0-0.015-0.01437.3910.0030.0030.0000.0000.0000.000
161A162HIS0-0.068-0.04936.4830.0100.0100.0000.0000.0000.000
162A163PHE00.0010.00438.2910.0020.0020.0000.0000.0000.000
163A164MET0-0.0090.01737.8290.0000.0000.0000.0000.0000.000
164A165LEU00.0010.00131.5750.0040.0040.0000.0000.0000.000
165A166GLY00.0040.00134.2860.0040.0040.0000.0000.0000.000
166A167ALA00.0210.01335.9780.0000.0000.0000.0000.0000.000
167A168ALA00.0540.02232.8590.0000.0000.0000.0000.0000.000
168A169ALA00.003-0.01031.1800.0040.0040.0000.0000.0000.000
169A170PHE0-0.015-0.01031.7180.0030.0030.0000.0000.0000.000
170A171SER00.008-0.01633.737-0.003-0.0030.0000.0000.0000.000
171A172MET0-0.015-0.00328.8160.0020.0020.0000.0000.0000.000
172A173SER00.0130.02928.8240.0020.0020.0000.0000.0000.000
173A174GLY00.0010.00729.908-0.002-0.0020.0000.0000.0000.000
174A175ILE00.0180.01228.816-0.006-0.0060.0000.0000.0000.000
175A176LYS10.8860.93524.911-0.094-0.0940.0000.0000.0000.000
176A177ALA00.0370.02231.555-0.005-0.0050.0000.0000.0000.000
177A178LEU00.0200.01434.830-0.004-0.0040.0000.0000.0000.000
178A179ARG10.8670.92129.591-0.073-0.0730.0000.0000.0000.000
179A180ALA00.0060.01735.343-0.003-0.0030.0000.0000.0000.000
180A181MET00.0020.00136.938-0.002-0.0020.0000.0000.0000.000
181A182ALA00.0330.02738.858-0.002-0.0020.0000.0000.0000.000
182A183GLU-1-0.943-0.97338.1090.0350.0350.0000.0000.0000.000
183A184THR0-0.063-0.04640.233-0.004-0.0040.0000.0000.0000.000
184A185ASP-1-0.958-0.97242.7440.0330.0330.0000.0000.0000.000
185A186PHE0-0.111-0.07343.602-0.001-0.0010.0000.0000.0000.000
186A187GLY0-0.0050.03043.045-0.001-0.0010.0000.0000.0000.000
187A188VAL0-0.050-0.01840.5090.0000.0000.0000.0000.0000.000
188A189ASN00.0920.05233.2330.0050.0050.0000.0000.0000.000
189A190THR0-0.016-0.00236.5000.0000.0000.0000.0000.0000.000
190A191SER00.003-0.01931.9740.0040.0040.0000.0000.0000.000
191A192THR00.038-0.01428.413-0.003-0.0030.0000.0000.0000.000
192A193GLU-1-0.879-0.94430.3930.0970.0970.0000.0000.0000.000
193A194GLN00.0390.02631.901-0.002-0.0020.0000.0000.0000.000
194A195VAL00.0140.00534.040-0.002-0.0020.0000.0000.0000.000
195A196MET0-0.0050.00128.9070.0010.0010.0000.0000.0000.000
196A197HIS0-0.009-0.01534.4210.0000.0000.0000.0000.0000.000
197A198LEU0-0.0010.00237.009-0.003-0.0030.0000.0000.0000.000
198A199MET0-0.053-0.01433.8840.0000.0000.0000.0000.0000.000
199A200VAL0-0.0040.02037.452-0.002-0.0020.0000.0000.0000.000
200A201PRO00.0330.01539.885-0.001-0.0010.0000.0000.0000.000
201A202PHE0-0.0020.01141.560-0.002-0.0020.0000.0000.0000.000
202A203PHE00.006-0.02636.297-0.001-0.0010.0000.0000.0000.000
203A204ALA00.0100.01742.165-0.001-0.0010.0000.0000.0000.000
204A205ALA00.007-0.00844.032-0.002-0.0020.0000.0000.0000.000
205A206GLY00.0090.01045.680-0.002-0.0020.0000.0000.0000.000
206A207MET0-0.050-0.04042.352-0.001-0.0010.0000.0000.0000.000
207A208ARG10.8040.85845.699-0.059-0.0590.0000.0000.0000.000
208A209ALA0-0.0240.01349.053-0.002-0.0020.0000.0000.0000.000
209A210GLU-1-0.886-0.93851.1660.0400.0400.0000.0000.0000.000
210A211SER0-0.077-0.06952.3190.0010.0010.0000.0000.0000.000
211A212GLY00.0300.01552.333-0.002-0.0020.0000.0000.0000.000
212A213ILE0-0.111-0.05650.6920.0000.0000.0000.0000.0000.000
213A214ASP-1-0.948-0.96754.9730.0360.0360.0000.0000.0000.000