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: MM7VZ

Calculation Name: 3BU2-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BU2

Chain ID: A

ChEMBL ID:

UniProt ID: Q49YH3

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1869498.567808
FMO2-HF: Nuclear repulsion 1794157.626268
FMO2-HF: Total energy -75340.94154
FMO2-MP2: Total energy -75558.261469


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.
-8.439-1.7155.591-4.184-8.132-0.013
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 : 0.003 / q_NPA : 0.009
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].
3A3LEU 00.005-0.0073.682-0.4572.1190.000-1.287-1.2890.004
4A4PHE 0-0.0070.0135.4450.0410.0410.0000.0000.0000.000
5A5TYR 0-0.055-0.1129.2330.2990.2990.0000.0000.0000.000
6A6ASN 00.0230.00011.788-0.044-0.0440.0000.0000.0000.000
7A7LYS 10.9650.99815.547-0.078-0.0780.0000.0000.0000.000
8A8GLU -1-0.916-0.97617.936-0.035-0.0350.0000.0000.0000.000
9A9ALA 0-0.0250.00418.6910.0010.0010.0000.0000.0000.000
10A10VAL 00.0560.01715.5720.0070.0070.0000.0000.0000.000
11A11GLY 00.0850.03917.9140.0270.0270.0000.0000.0000.000
12A12ASP -1-0.972-0.91616.1140.2230.2230.0000.0000.0000.000
13A13VAL 0-0.005-0.01012.6130.0710.0710.0000.0000.0000.000
14A14ALA 0-0.0130.0058.507-0.100-0.1000.0000.0000.0000.000
15A15PHE 0-0.018-0.0168.4040.1800.1800.0000.0000.0000.000
16A16LEU 00.0160.0012.939-1.928-1.3682.319-0.599-2.2800.004
17A17GLN 0-0.012-0.0023.604-0.3130.0190.003-0.082-0.2540.000
18A18ILE 00.015-0.0112.309-5.440-2.4683.261-2.172-4.061-0.021
19A19ASN 00.0120.0133.559-1.243-0.9590.008-0.044-0.2480.000
20A20PRO 0-0.016-0.0135.5000.6030.6030.0000.0000.0000.000
21A21THR 0-0.025-0.0198.645-0.052-0.0520.0000.0000.0000.000
22A22GLU -1-0.912-0.94410.9240.0210.0210.0000.0000.0000.000
23A23GLY 00.0130.01813.3670.0090.0090.0000.0000.0000.000
24A24GLU -1-0.945-0.96616.4960.0990.0990.0000.0000.0000.000
25A25TYR 0-0.050-0.04013.533-0.034-0.0340.0000.0000.0000.000
26A26ASN 0-0.075-0.03919.8620.0030.0030.0000.0000.0000.000
27A27TYR 0-0.019-0.02219.694-0.008-0.0080.0000.0000.0000.000
28A28VAL 00.0280.02725.3950.0060.0060.0000.0000.0000.000
29A29THR 0-0.061-0.02828.387-0.010-0.0100.0000.0000.0000.000
30A30GLN 0-0.005-0.01130.4580.0100.0100.0000.0000.0000.000
31A31GLY 00.0050.00732.909-0.005-0.0050.0000.0000.0000.000
32A32ASP -1-0.798-0.88932.295-0.083-0.0830.0000.0000.0000.000
33A33VAL 0-0.041-0.00528.489-0.011-0.0110.0000.0000.0000.000
34A34VAL 0-0.013-0.01425.3350.0090.0090.0000.0000.0000.000
35A35GLU -1-0.806-0.89924.717-0.069-0.0690.0000.0000.0000.000
36A36ILE 0-0.026-0.00218.2820.0110.0110.0000.0000.0000.000
37A37GLN 00.022-0.00220.490-0.003-0.0030.0000.0000.0000.000
38A38ASN 00.0270.02215.8820.0080.0080.0000.0000.0000.000
39A39ASP -1-0.919-0.94718.1040.1230.1230.0000.0000.0000.000
40A40GLY 0-0.044-0.03020.801-0.010-0.0100.0000.0000.0000.000
41A41GLU -1-0.932-0.95118.666-0.023-0.0230.0000.0000.0000.000
42A42VAL 0-0.015-0.01420.377-0.001-0.0010.0000.0000.0000.000
43A43VAL 0-0.055-0.02916.200-0.008-0.0080.0000.0000.0000.000
44A44GLY 0-0.010-0.01117.340-0.042-0.0420.0000.0000.0000.000
45A45TYR 0-0.070-0.06319.9210.0210.0210.0000.0000.0000.000
46A46ASN 0-0.0040.02321.940-0.034-0.0340.0000.0000.0000.000
47A47ILE 00.0090.01724.4650.0150.0150.0000.0000.0000.000
48A48PHE 00.013-0.01626.732-0.012-0.0120.0000.0000.0000.000
49A49ASN 0-0.027-0.02129.9600.0020.0020.0000.0000.0000.000
50A50ALA 00.0640.01628.5980.0030.0030.0000.0000.0000.000
51A51SER 0-0.005-0.00230.6630.0020.0020.0000.0000.0000.000
52A52ASN 0-0.003-0.00432.9090.0000.0000.0000.0000.0000.000
53A53LYS 10.7250.84932.1800.1020.1020.0000.0000.0000.000
54A54ALA 00.0260.01230.5210.0000.0000.0000.0000.0000.000
55A55THR 0-0.018-0.00432.5980.0030.0030.0000.0000.0000.000
56A56LEU 00.005-0.00526.910-0.008-0.0080.0000.0000.0000.000
57A57THR 0-0.0360.00229.519-0.009-0.0090.0000.0000.0000.000
58A58GLY 00.0370.02430.646-0.009-0.0090.0000.0000.0000.000
59A59ASN 0-0.045-0.04630.5090.0000.0000.0000.0000.0000.000
60A60GLY 00.0380.01626.721-0.007-0.0070.0000.0000.0000.000
61A61HIS 0-0.033-0.01422.387-0.012-0.0120.0000.0000.0000.000
62A62ILE 00.0020.01022.163-0.015-0.0150.0000.0000.0000.000
63A63LYS 10.9930.99420.3700.3590.3590.0000.0000.0000.000
64A64LEU 00.0200.01220.2740.0260.0260.0000.0000.0000.000
65A65THR 00.0410.02223.7170.0020.0020.0000.0000.0000.000
66A66GLU -1-0.848-0.93426.749-0.120-0.1200.0000.0000.0000.000
67A67THR 0-0.007-0.01028.5220.0110.0110.0000.0000.0000.000
68A68LEU 0-0.029-0.01826.3160.0070.0070.0000.0000.0000.000
69A69VAL 00.0340.01724.6520.0050.0050.0000.0000.0000.000
70A70GLN 00.0050.00927.2460.0130.0130.0000.0000.0000.000
71A71ALA 0-0.034-0.00630.7900.0090.0090.0000.0000.0000.000
72A72PHE 00.016-0.01525.3540.0060.0060.0000.0000.0000.000
73A73GLN 00.0680.05328.4420.0010.0010.0000.0000.0000.000
74A74LYS 10.9730.97929.8030.0880.0880.0000.0000.0000.000
75A75ALA 0-0.053-0.02930.9590.0070.0070.0000.0000.0000.000
76A76ILE 00.0090.00227.4280.0050.0050.0000.0000.0000.000
77A77GLU -1-0.910-0.95630.724-0.063-0.0630.0000.0000.0000.000
78A78ALA 0-0.100-0.03433.4140.0070.0070.0000.0000.0000.000
79A79ALA 0-0.050-0.01432.4650.0040.0040.0000.0000.0000.000
80A80GLY 0-0.029-0.01834.6140.0050.0050.0000.0000.0000.000
81A81PHE 0-0.023-0.00529.3830.0030.0030.0000.0000.0000.000
82A82THR 0-0.003-0.01930.872-0.003-0.0030.0000.0000.0000.000
83A83TYR 00.0350.03221.352-0.006-0.0060.0000.0000.0000.000
84A84LYS 10.9270.94526.6800.0650.0650.0000.0000.0000.000
85A85LEU 0-0.022-0.01323.717-0.003-0.0030.0000.0000.0000.000
86A86ASP -1-0.913-0.93521.292-0.162-0.1620.0000.0000.0000.000
87A87ALA 0-0.014-0.02623.388-0.013-0.0130.0000.0000.0000.000
88A88ASP -1-0.819-0.86223.979-0.129-0.1290.0000.0000.0000.000
89A89PHE 0-0.038-0.02023.991-0.022-0.0220.0000.0000.0000.000
90A90THR 0-0.060-0.05426.0100.0020.0020.0000.0000.0000.000
91A91PRO 0-0.014-0.01225.083-0.018-0.0180.0000.0000.0000.000
92A92LYS 10.8900.95020.6720.1890.1890.0000.0000.0000.000
93A93PHE 0-0.0020.00418.8180.0060.0060.0000.0000.0000.000
94A94VAL 00.0100.00624.1730.0080.0080.0000.0000.0000.000
95A95VAL 0-0.0040.02027.331-0.001-0.0010.0000.0000.0000.000
96A96GLY 00.0210.00629.1480.0040.0040.0000.0000.0000.000
97A97TYR 0-0.024-0.00230.095-0.001-0.0010.0000.0000.0000.000
98A98VAL 0-0.0080.00829.0530.0030.0030.0000.0000.0000.000
99A99GLU -1-0.856-0.91331.457-0.018-0.0180.0000.0000.0000.000
100A100THR 0-0.005-0.00832.1540.0010.0010.0000.0000.0000.000
101A101LYS 10.8820.93828.557-0.007-0.0070.0000.0000.0000.000
102A102ASP -1-0.897-0.92929.6420.0260.0260.0000.0000.0000.000
103A103LYS 10.8890.93627.772-0.072-0.0720.0000.0000.0000.000
104A104HIS 0-0.038-0.02121.357-0.008-0.0080.0000.0000.0000.000
105A105PRO 0-0.020-0.01325.8050.0030.0030.0000.0000.0000.000
106A106ASP -1-0.932-0.97423.6010.1570.1570.0000.0000.0000.000
107A107ALA 00.0090.00421.8010.0210.0210.0000.0000.0000.000
108A108ASP -1-0.981-0.99723.2420.1060.1060.0000.0000.0000.000
109A109LYS 10.9300.96621.211-0.153-0.1530.0000.0000.0000.000
110A110LEU 0-0.0070.00819.236-0.007-0.0070.0000.0000.0000.000
111A111SER 0-0.032-0.02223.6630.0030.0030.0000.0000.0000.000
112A112VAL 00.0130.01124.286-0.001-0.0010.0000.0000.0000.000
113A113LEU 0-0.004-0.01525.596-0.003-0.0030.0000.0000.0000.000
114A114SER 00.0100.03126.9290.0000.0000.0000.0000.0000.000
115A115VAL 0-0.014-0.03526.564-0.003-0.0030.0000.0000.0000.000
116A116ASP -1-0.885-0.93229.263-0.046-0.0460.0000.0000.0000.000
117A117VAL 00.033-0.00227.325-0.008-0.0080.0000.0000.0000.000
118A118ALA 0-0.0220.00230.546-0.007-0.0070.0000.0000.0000.000
119A119THR 0-0.048-0.03629.9820.0020.0020.0000.0000.0000.000
120A120GLU -1-0.948-0.97827.265-0.059-0.0590.0000.0000.0000.000
121A121LYS 10.8500.92230.3500.0220.0220.0000.0000.0000.000
122A122LEU 00.0000.01124.1430.0030.0030.0000.0000.0000.000
123A123GLN 0-0.0010.01224.0860.0000.0000.0000.0000.0000.000
124A124ILE 0-0.037-0.00720.953-0.001-0.0010.0000.0000.0000.000
125A125VAL 00.009-0.00120.0310.0080.0080.0000.0000.0000.000
126A126CYS 0-0.070-0.02620.347-0.017-0.0170.0000.0000.0000.000
127A127GLY 00.0520.00021.0930.0150.0150.0000.0000.0000.000
128A128ALA 0-0.0240.00222.4100.0020.0020.0000.0000.0000.000
129A129PRO 0-0.065-0.03323.9150.0050.0050.0000.0000.0000.000
130A130ASN 0-0.011-0.01326.9130.0050.0050.0000.0000.0000.000
131A131VAL 0-0.0140.01726.402-0.004-0.0040.0000.0000.0000.000
132A132GLU -1-0.878-0.97128.8910.0080.0080.0000.0000.0000.000
133A133ALA 0-0.0030.01132.068-0.006-0.0060.0000.0000.0000.000
134A134GLY 0-0.002-0.01933.8620.0000.0000.0000.0000.0000.000
135A135GLN 0-0.0020.00030.683-0.009-0.0090.0000.0000.0000.000
136A136LYS 10.9140.97732.5060.0570.0570.0000.0000.0000.000
137A137VAL 00.016-0.00126.310-0.004-0.0040.0000.0000.0000.000
138A138VAL 00.0320.02024.5460.0010.0010.0000.0000.0000.000
139A139VAL 0-0.015-0.01123.431-0.007-0.0070.0000.0000.0000.000
140A140ALA 0-0.003-0.00419.079-0.009-0.0090.0000.0000.0000.000
141A141LYS 10.9840.97320.1030.1200.1200.0000.0000.0000.000
142A142VAL 00.0440.01617.833-0.038-0.0380.0000.0000.0000.000
143A143GLY 0-0.006-0.00417.1490.0160.0160.0000.0000.0000.000
144A144ALA 0-0.040-0.01717.352-0.037-0.0370.0000.0000.0000.000
145A145VAL 0-0.007-0.00114.486-0.036-0.0360.0000.0000.0000.000
146A146MET 0-0.0020.00213.7320.0690.0690.0000.0000.0000.000
147A147PRO 00.0220.01114.322-0.112-0.1120.0000.0000.0000.000
148A148SER 0-0.065-0.03611.909-0.067-0.0670.0000.0000.0000.000
149A149GLY 00.0020.00810.206-0.288-0.2880.0000.0000.0000.000
150A150MET 0-0.035-0.0089.3630.0620.0620.0000.0000.0000.000
151A151VAL 00.0350.02010.3090.1650.1650.0000.0000.0000.000
152A152ILE 0-0.032-0.00812.3110.0530.0530.0000.0000.0000.000
153A153LYS 10.9900.98012.8130.1140.1140.0000.0000.0000.000
154A154ASP -1-0.869-0.92315.200-0.025-0.0250.0000.0000.0000.000
155A155ALA 0-0.052-0.02014.5050.0330.0330.0000.0000.0000.000
156A156GLU -1-0.911-0.96515.5500.1770.1770.0000.0000.0000.000
157A157LEU 0-0.032-0.00915.0680.0450.0450.0000.0000.0000.000
158A158ARG 10.9110.95017.072-0.299-0.2990.0000.0000.0000.000
159A159GLY 00.0730.04219.104-0.017-0.0170.0000.0000.0000.000
160A160VAL 00.0010.02121.331-0.012-0.0120.0000.0000.0000.000
161A161ALA 00.0450.01520.2500.0060.0060.0000.0000.0000.000
162A162SER 00.017-0.00418.278-0.006-0.0060.0000.0000.0000.000
163A163SER 0-0.010-0.01318.733-0.003-0.0030.0000.0000.0000.000
164A164GLY 00.0200.00819.005-0.010-0.0100.0000.0000.0000.000
165A165MET 0-0.047-0.02314.3530.0100.0100.0000.0000.0000.000
166A166ILE 00.0030.01519.571-0.013-0.0130.0000.0000.0000.000
167A167CYS 0-0.0290.00221.159-0.022-0.0220.0000.0000.0000.000
168A168SER 00.046-0.02620.2540.0210.0210.0000.0000.0000.000
169A169MET 00.026-0.00422.665-0.019-0.0190.0000.0000.0000.000
170A170LYS 10.8640.93618.8320.1600.1600.0000.0000.0000.000
171A171GLU -1-0.804-0.86816.976-0.324-0.3240.0000.0000.0000.000
172A172LEU 0-0.026-0.00919.345-0.032-0.0320.0000.0000.0000.000
173A173GLY 00.0100.00920.669-0.001-0.0010.0000.0000.0000.000
174A174LEU 0-0.068-0.03021.6800.0090.0090.0000.0000.0000.000
175A175PRO 0-0.012-0.00522.087-0.013-0.0130.0000.0000.0000.000
176A176ASN 0-0.0030.00022.205-0.021-0.0210.0000.0000.0000.000
177A177ALA 00.009-0.00121.9520.0030.0030.0000.0000.0000.000
178A178PRO 00.0120.01023.5100.0170.0170.0000.0000.0000.000
179A179GLN 0-0.0090.00025.7470.0030.0030.0000.0000.0000.000
180A180GLU -1-0.896-0.94227.638-0.051-0.0510.0000.0000.0000.000
181A181LYS 10.8370.89721.6220.0970.0970.0000.0000.0000.000
182A182GLY 00.0680.05622.927-0.006-0.0060.0000.0000.0000.000
183A183ILE 0-0.051-0.03322.853-0.022-0.0220.0000.0000.0000.000
184A184MET 0-0.016-0.00525.0390.0090.0090.0000.0000.0000.000
185A185VAL 0-0.019-0.00327.6280.0010.0010.0000.0000.0000.000
186A186LEU 0-0.051-0.02130.134-0.003-0.0030.0000.0000.0000.000
187A187SER 00.0200.00733.0830.0060.0060.0000.0000.0000.000
188A188ASP -1-0.926-0.98536.545-0.050-0.0500.0000.0000.0000.000
189A189ASP -1-0.997-0.98638.473-0.072-0.0720.0000.0000.0000.000
190A190TYR 00.0310.01232.663-0.002-0.0020.0000.0000.0000.000
191A191THR 00.014-0.00135.7470.0080.0080.0000.0000.0000.000
192A192VAL 00.004-0.01032.645-0.007-0.0070.0000.0000.0000.000
193A193GLY 00.006-0.00331.6570.0040.0040.0000.0000.0000.000
194A194GLN 0-0.043-0.02131.6890.0000.0000.0000.0000.0000.000
195A195SER 0-0.037-0.03128.679-0.008-0.0080.0000.0000.0000.000
196A196PHE 0-0.008-0.01126.5180.0070.0070.0000.0000.0000.000
197A197PHE 0-0.039-0.02123.2770.0000.0000.0000.0000.0000.000
198A198GLU -1-0.922-0.94928.501-0.130-0.1300.0000.0000.0000.000
199A199NME 0-0.019-0.00528.3450.0060.0060.0000.0000.0000.000