Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 72L5K

Calculation Name: 2B9U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B9U

Chain ID: A

ChEMBL ID:

UniProt ID: Q96Z62

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1978051.240805
FMO2-HF: Nuclear repulsion 1906440.317273
FMO2-HF: Total energy -71610.923532
FMO2-MP2: Total energy -71820.216329


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.
-5.4730.327000000000013.055-3.498-5.356-0.015
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 : 0.032 / q_NPA : 0.013
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].
3A3PHE0-0.024-0.0042.962-0.1241.5730.076-0.747-1.0250.001
4A4GLU-1-0.809-0.8782.763-12.668-9.2290.669-2.010-2.098-0.020
5A5PHE00.001-0.0175.4330.4470.4470.0000.0000.0000.000
6A6GLU-1-0.804-0.8888.316-1.082-1.0820.0000.0000.0000.000
7A7ASN0-0.030-0.02411.7460.0140.0140.0000.0000.0000.000
8A8LEU00.0310.02414.8220.0440.0440.0000.0000.0000.000
9A9GLY00.0400.03117.7270.0530.0530.0000.0000.0000.000
10A10MET0-0.031-0.01120.166-0.001-0.0010.0000.0000.0000.000
11A11GLY00.0210.00619.1930.0310.0310.0000.0000.0000.000
12A12ILE0-0.0210.00917.783-0.032-0.0320.0000.0000.0000.000
13A13ILE0-0.054-0.02911.669-0.008-0.0080.0000.0000.0000.000
14A14LEU00.0150.02112.6340.0170.0170.0000.0000.0000.000
15A15ILE0-0.034-0.0238.281-0.120-0.1200.0000.0000.0000.000
16A16LYS10.8340.9108.2381.4791.4790.0000.0000.0000.000
17A17PRO00.0110.0147.141-0.773-0.7730.0000.0000.0000.000
18A18LYS10.7960.8812.0587.9428.5532.311-0.737-2.1850.004
19A19VAL0-0.002-0.0087.9140.2930.2930.0000.0000.0000.000
20A20PHE0-0.038-0.0226.5310.0570.0570.0000.0000.0000.000
21A21PRO00.0300.00912.0550.0690.0690.0000.0000.0000.000
22A22ASP-1-0.821-0.89215.264-0.070-0.0700.0000.0000.0000.000
23A23LYS10.9670.97718.0330.0030.0030.0000.0000.0000.000
24A24ARG10.8140.87917.0050.1040.1040.0000.0000.0000.000
25A25GLY00.0140.01720.582-0.003-0.0030.0000.0000.0000.000
26A26PHE0-0.030-0.01215.449-0.004-0.0040.0000.0000.0000.000
27A27PHE00.0000.01111.8570.0290.0290.0000.0000.0000.000
28A28LEU00.0440.01611.447-0.077-0.0770.0000.0000.0000.000
29A29GLU-1-0.825-0.8838.380-0.335-0.3350.0000.0000.0000.000
30A30VAL00.0190.00710.112-0.248-0.2480.0000.0000.0000.000
31A31PHE00.024-0.00511.287-0.075-0.0750.0000.0000.0000.000
32A32LYS10.8090.9006.2330.4880.4880.0000.0000.0000.000
33A33SER00.0060.0069.893-0.070-0.0700.0000.0000.0000.000
34A34GLU-1-0.825-0.8888.2730.1250.1250.0000.0000.0000.000
35A35ASP-1-0.812-0.9194.816-1.165-1.112-0.001-0.004-0.0480.000
36A36PHE00.042-0.0027.348-0.063-0.0630.0000.0000.0000.000
37A37THR00.0130.00410.4740.0690.0690.0000.0000.0000.000
38A38LYS10.7660.8705.6190.3160.3160.0000.0000.0000.000
39A39MET0-0.049-0.0217.0480.1490.1490.0000.0000.0000.000
40A40ARG10.8450.92111.2730.5570.5570.0000.0000.0000.000
41A41ILE0-0.0090.01611.9590.0420.0420.0000.0000.0000.000
42A42PRO0-0.019-0.00814.6260.0000.0000.0000.0000.0000.000
43A43ASN00.024-0.00216.780-0.059-0.0590.0000.0000.0000.000
44A44VAL0-0.014-0.00216.9220.0110.0110.0000.0000.0000.000
45A45ILE0-0.059-0.02219.5140.0250.0250.0000.0000.0000.000
46A46GLN00.0320.01623.0740.0280.0280.0000.0000.0000.000
47A47THR0-0.032-0.03021.523-0.041-0.0410.0000.0000.0000.000
48A48ASN00.0020.03223.7180.0340.0340.0000.0000.0000.000
49A49MET00.0300.00924.272-0.030-0.0300.0000.0000.0000.000
50A50SER0-0.032-0.00626.3580.0210.0210.0000.0000.0000.000
51A51PHE00.0110.02227.721-0.014-0.0140.0000.0000.0000.000
52A52SER0-0.012-0.00529.1160.0140.0140.0000.0000.0000.000
53A53ARG10.9941.00830.6070.1400.1400.0000.0000.0000.000
54A54LYS10.9020.93231.9700.2010.2010.0000.0000.0000.000
55A55GLY00.0240.01632.6230.0120.0120.0000.0000.0000.000
56A56VAL0-0.053-0.02132.3010.0040.0040.0000.0000.0000.000
57A57VAL0-0.017-0.00231.629-0.017-0.0170.0000.0000.0000.000
58A58ARG10.8480.92129.4540.2230.2230.0000.0000.0000.000
59A59GLY00.0080.00630.048-0.020-0.0200.0000.0000.0000.000
60A60LEU0-0.057-0.00629.1080.0100.0100.0000.0000.0000.000
61A61HIS00.021-0.01230.004-0.002-0.0020.0000.0000.0000.000
62A62TYR0-0.071-0.06128.832-0.022-0.0220.0000.0000.0000.000
63A63GLN0-0.017-0.01129.5770.0140.0140.0000.0000.0000.000
64A64ARG10.9080.96030.4330.1130.1130.0000.0000.0000.000
65A65THR00.0540.00931.2310.0010.0010.0000.0000.0000.000
66A66PRO0-0.114-0.05832.4630.0070.0070.0000.0000.0000.000
67A67LYS10.8370.89830.6700.1440.1440.0000.0000.0000.000
68A68GLU-1-0.792-0.86927.564-0.171-0.1710.0000.0000.0000.000
69A69GLN0-0.047-0.04325.258-0.005-0.0050.0000.0000.0000.000
70A70GLY00.0130.02021.315-0.002-0.0020.0000.0000.0000.000
71A71LYS10.8430.91920.6990.2980.2980.0000.0000.0000.000
72A72ILE00.0080.00114.506-0.035-0.0350.0000.0000.0000.000
73A73ILE0-0.030-0.00217.5680.0260.0260.0000.0000.0000.000
74A74PHE00.0450.00515.487-0.062-0.0620.0000.0000.0000.000
75A75VAL00.0060.00618.1620.0640.0640.0000.0000.0000.000
76A76PRO0-0.0190.01019.572-0.013-0.0130.0000.0000.0000.000
77A77LYS10.8360.88220.5040.2990.2990.0000.0000.0000.000
78A78GLY00.0340.02723.6600.0090.0090.0000.0000.0000.000
79A79ARG10.7960.84523.2150.2860.2860.0000.0000.0000.000
80A80ILE0-0.044-0.01122.3190.0360.0360.0000.0000.0000.000
81A81LEU00.0070.01223.221-0.033-0.0330.0000.0000.0000.000
82A82ASP-1-0.751-0.89621.501-0.372-0.3720.0000.0000.0000.000
83A83VAL0-0.010-0.01323.580-0.008-0.0080.0000.0000.0000.000
84A84ALA00.0100.00822.7330.0080.0080.0000.0000.0000.000
85A85VAL00.017-0.00224.675-0.003-0.0030.0000.0000.0000.000
86A86ASP-1-0.731-0.80526.435-0.225-0.2250.0000.0000.0000.000
87A87VAL0-0.004-0.01527.8230.0160.0160.0000.0000.0000.000
88A88ARG10.8360.89223.8140.2610.2610.0000.0000.0000.000
89A89LYS10.9770.97031.0860.1240.1240.0000.0000.0000.000
90A90SER0-0.0170.02332.4680.0050.0050.0000.0000.0000.000
91A91SER0-0.049-0.02928.1500.0030.0030.0000.0000.0000.000
92A92PRO00.0060.00228.6190.0050.0050.0000.0000.0000.000
93A93THR0-0.099-0.08326.396-0.001-0.0010.0000.0000.0000.000
94A94PHE00.0420.03329.229-0.010-0.0100.0000.0000.0000.000
95A95GLY00.0210.01131.4100.0070.0070.0000.0000.0000.000
96A96LYS10.8870.96127.9670.1820.1820.0000.0000.0000.000
97A97TYR00.010-0.01326.285-0.006-0.0060.0000.0000.0000.000
98A98VAL0-0.0020.01020.052-0.002-0.0020.0000.0000.0000.000
99A99LYS10.8690.93023.4200.2600.2600.0000.0000.0000.000
100A100ALA00.002-0.00118.974-0.022-0.0220.0000.0000.0000.000
101A101GLU-1-0.778-0.85020.622-0.356-0.3560.0000.0000.0000.000
102A102LEU0-0.039-0.00616.674-0.061-0.0610.0000.0000.0000.000
103A103ASN0-0.020-0.04918.5480.0230.0230.0000.0000.0000.000
104A104GLU-1-0.739-0.83518.484-0.373-0.3730.0000.0000.0000.000
105A105GLU-1-0.917-0.94317.836-0.489-0.4890.0000.0000.0000.000
106A106ASN0-0.007-0.00515.024-0.074-0.0740.0000.0000.0000.000
107A107HIS0-0.035-0.02013.711-0.173-0.1730.0000.0000.0000.000
108A108TYR00.007-0.01011.578-0.098-0.0980.0000.0000.0000.000
109A109MET0-0.043-0.02110.9930.1490.1490.0000.0000.0000.000
110A110LEU0-0.0070.00814.233-0.072-0.0720.0000.0000.0000.000
111A111TRP00.0160.00814.6070.0510.0510.0000.0000.0000.000
112A112ILE0-0.016-0.01416.3560.0180.0180.0000.0000.0000.000
113A113PRO0-0.0020.01519.1960.0210.0210.0000.0000.0000.000
114A114PRO00.0380.00121.2770.0130.0130.0000.0000.0000.000
115A115GLY0-0.026-0.01624.928-0.003-0.0030.0000.0000.0000.000
116A116PHE00.005-0.00923.0790.0050.0050.0000.0000.0000.000
117A117ALA0-0.0210.00626.5430.0030.0030.0000.0000.0000.000
118A118HIS0-0.048-0.04723.6530.0080.0080.0000.0000.0000.000
119A119GLY00.0370.00026.4370.0220.0220.0000.0000.0000.000
120A120PHE0-0.020-0.00825.454-0.019-0.0190.0000.0000.0000.000
121A121GLN00.002-0.01127.4700.0160.0160.0000.0000.0000.000
122A122ALA0-0.0040.00527.882-0.023-0.0230.0000.0000.0000.000
123A123LEU00.0290.00825.7880.0240.0240.0000.0000.0000.000
124A124GLU-1-0.876-0.93727.618-0.254-0.2540.0000.0000.0000.000
125A125ASP-1-0.837-0.90929.427-0.194-0.1940.0000.0000.0000.000
126A126SER0-0.012-0.02225.828-0.017-0.0170.0000.0000.0000.000
127A127ILE0-0.076-0.04124.6570.0240.0240.0000.0000.0000.000
128A128VAL00.0290.02622.652-0.028-0.0280.0000.0000.0000.000
129A129ILE0-0.019-0.02019.9870.0380.0380.0000.0000.0000.000
130A130TYR00.005-0.02021.051-0.033-0.0330.0000.0000.0000.000
131A131PHE00.0280.01716.5040.0370.0370.0000.0000.0000.000
132A132ILE0-0.030-0.00820.171-0.019-0.0190.0000.0000.0000.000
133A133THR00.0750.00818.3180.0010.0010.0000.0000.0000.000
134A134HIS0-0.0060.00921.0110.0010.0010.0000.0000.0000.000
135A135ASN0-0.001-0.00824.2630.0310.0310.0000.0000.0000.000
136A136GLU-1-0.790-0.88926.998-0.165-0.1650.0000.0000.0000.000
137A137TYR0-0.094-0.05828.9340.0030.0030.0000.0000.0000.000
138A138SER00.007-0.01031.4020.0140.0140.0000.0000.0000.000
139A139PRO00.0570.02334.4110.0000.0000.0000.0000.0000.000
140A140PRO0-0.016-0.00537.2650.0000.0000.0000.0000.0000.000
141A141HIS0-0.020-0.00134.3380.0030.0030.0000.0000.0000.000
142A142GLU-1-0.771-0.83333.791-0.162-0.1620.0000.0000.0000.000
143A143ARG10.7440.86533.9470.1360.1360.0000.0000.0000.000
144A144CYS0-0.052-0.01033.531-0.007-0.0070.0000.0000.0000.000
145A145ILE00.0190.02532.1130.0090.0090.0000.0000.0000.000
146A146SER00.0000.00434.649-0.008-0.0080.0000.0000.0000.000
147A147TYR00.0600.01633.684-0.006-0.0060.0000.0000.0000.000
148A148SER0-0.019-0.00934.494-0.006-0.0060.0000.0000.0000.000
149A149TYR0-0.067-0.04232.0720.0070.0070.0000.0000.0000.000
150A150ILE0-0.037-0.01529.819-0.008-0.0080.0000.0000.0000.000
151A151ASP-1-0.901-0.94032.560-0.199-0.1990.0000.0000.0000.000
152A152TRP0-0.012-0.02128.443-0.023-0.0230.0000.0000.0000.000
153A153PRO00.0080.01329.7570.0110.0110.0000.0000.0000.000
154A154ILE0-0.074-0.02432.0800.0100.0100.0000.0000.0000.000
155A155LYS10.8910.92335.0060.1400.1400.0000.0000.0000.000
156A156GLU-1-0.826-0.89038.190-0.138-0.1380.0000.0000.0000.000
157A157VAL0-0.003-0.00536.101-0.007-0.0070.0000.0000.0000.000
158A158ILE0-0.032-0.00536.5310.0100.0100.0000.0000.0000.000
159A159ILE00.0160.00236.039-0.011-0.0110.0000.0000.0000.000
160A160SER0-0.034-0.02136.8040.0110.0110.0000.0000.0000.000
161A161ASP-1-0.828-0.93038.738-0.118-0.1180.0000.0000.0000.000
162A162LYS10.8270.89036.1850.1510.1510.0000.0000.0000.000
163A163ASP-1-0.762-0.88634.306-0.178-0.1780.0000.0000.0000.000
164A164LEU0-0.041-0.02337.488-0.001-0.0010.0000.0000.0000.000
165A165GLN0-0.027-0.00540.7550.0070.0070.0000.0000.0000.000
166A167PRO00.0270.02238.8740.0000.0000.0000.0000.0000.000
167A168SER0-0.002-0.02638.426-0.007-0.0070.0000.0000.0000.000
168A169LEU00.0570.02933.9650.0020.0020.0000.0000.0000.000
169A170GLU-1-0.896-0.94137.292-0.134-0.1340.0000.0000.0000.000
170A171LYS10.8650.92440.4340.1080.1080.0000.0000.0000.000
171A172ALA00.0040.02937.2230.0040.0040.0000.0000.0000.000
172A173GLU-1-0.840-0.89438.550-0.110-0.1100.0000.0000.0000.000
173A174VAL0-0.047-0.00934.049-0.008-0.0080.0000.0000.0000.000
174A175PHE00.0310.01729.0820.0040.0040.0000.0000.0000.000
175A176ASP-1-0.928-0.97032.355-0.132-0.1320.0000.0000.0000.000