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: K2393

Calculation Name: 2Q7F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Q7F

Chain ID: A

ChEMBL ID:

UniProt ID: O34452

Base Structure: X-ray

Registration Date: 2023-09-26

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1974041.561616
FMO2-HF: Nuclear repulsion 1897009.365755
FMO2-HF: Total energy -77032.19586
FMO2-MP2: Total energy -77254.0034


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:43:ALA)


Summations of interaction energy for fragment #1(A:43: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.
-3.668-0.5930.067-1.405-1.735-0.004
Interaction energy analysis for fragmet #1(A:43:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.021
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].
3A45GLU-1-0.821-0.8903.863-0.9101.459-0.023-1.264-1.081-0.002
4A46ALA0-0.047-0.0065.6570.5300.5300.0000.0000.0000.000
5A47PHE0-0.015-0.0203.954-0.502-0.385-0.001-0.013-0.1030.000
6A48THR00.007-0.0248.447-0.193-0.1930.0000.0000.0000.000
7A49LYS10.7790.86410.557-0.332-0.3320.0000.0000.0000.000
8A50ALA0-0.016-0.00311.659-0.039-0.0390.0000.0000.0000.000
9A51ILE00.0450.02612.969-0.047-0.0470.0000.0000.0000.000
10A52GLU-1-0.837-0.89815.4630.1920.1920.0000.0000.0000.000
11A53GLU-1-1.000-1.01717.6610.1140.1140.0000.0000.0000.000
12A54ASN0-0.081-0.03216.879-0.009-0.0090.0000.0000.0000.000
13A55LYN00.0080.02319.372-0.011-0.0110.0000.0000.0000.000
14A56GLU-1-0.875-0.94120.665-0.019-0.0190.0000.0000.0000.000
15A57ASP-1-0.841-0.90518.072-0.020-0.0200.0000.0000.0000.000
16A58ALA00.0670.01818.309-0.008-0.0080.0000.0000.0000.000
17A59ILE0-0.030-0.01614.604-0.037-0.0370.0000.0000.0000.000
18A60PRO0-0.036-0.01012.575-0.047-0.0470.0000.0000.0000.000
19A61TYR0-0.032-0.03711.959-0.070-0.0700.0000.0000.0000.000
20A62ILE00.0150.01413.097-0.086-0.0860.0000.0000.0000.000
21A63ASN0-0.039-0.0199.350-0.128-0.1280.0000.0000.0000.000
22A64PHE0-0.007-0.0027.933-0.256-0.2560.0000.0000.0000.000
23A65ALA00.0360.0219.254-0.227-0.2270.0000.0000.0000.000
24A66ASN00.0210.0269.726-0.039-0.0390.0000.0000.0000.000
25A67LEU0-0.0250.0073.092-0.698-0.1960.092-0.114-0.479-0.002
26A68LEU00.0240.0096.894-0.187-0.1870.0000.0000.0000.000
27A69SER0-0.027-0.0238.9170.0930.0930.0000.0000.0000.000
28A70SER0-0.115-0.0656.330-0.056-0.0560.0000.0000.0000.000
29A71VAL0-0.027-0.0114.450-0.133-0.046-0.001-0.014-0.0720.000
30A72ASN0-0.032-0.0237.3980.2080.2080.0000.0000.0000.000
31A73GLU-1-0.842-0.9019.852-0.632-0.6320.0000.0000.0000.000
32A74LEU00.0320.01512.1900.0240.0240.0000.0000.0000.000
33A75GLU-1-0.841-0.91014.730-0.303-0.3030.0000.0000.0000.000
34A76ARG10.8340.90810.5030.5670.5670.0000.0000.0000.000
35A77ALA00.0120.00412.5010.0260.0260.0000.0000.0000.000
36A78LEU0-0.003-0.00114.1300.0450.0450.0000.0000.0000.000
37A79ALA0-0.0040.00517.7170.0310.0310.0000.0000.0000.000
38A80PHE0-0.036-0.01813.9970.0240.0240.0000.0000.0000.000
39A81TYR00.001-0.03313.4050.0160.0160.0000.0000.0000.000
40A82ASP-1-0.951-0.96417.815-0.118-0.1180.0000.0000.0000.000
41A83LYS10.8220.89918.9230.0870.0870.0000.0000.0000.000
42A84ALA0-0.005-0.01217.5270.0190.0190.0000.0000.0000.000
43A85LEU0-0.045-0.02019.6430.0160.0160.0000.0000.0000.000
44A86GLU-1-0.882-0.91722.957-0.057-0.0570.0000.0000.0000.000
45A87LEU0-0.054-0.00920.1480.0110.0110.0000.0000.0000.000
46A88ASP-1-0.822-0.90822.693-0.066-0.0660.0000.0000.0000.000
47A89SER00.0180.02423.760-0.011-0.0110.0000.0000.0000.000
48A90SER0-0.069-0.05425.905-0.002-0.0020.0000.0000.0000.000
49A91ALA00.0300.02520.312-0.003-0.0030.0000.0000.0000.000
50A92ALA00.003-0.00421.463-0.021-0.0210.0000.0000.0000.000
51A93THR00.006-0.00616.829-0.011-0.0110.0000.0000.0000.000
52A94ALA00.0300.02017.621-0.038-0.0380.0000.0000.0000.000
53A95TYR0-0.037-0.03418.664-0.021-0.0210.0000.0000.0000.000
54A96TYR00.0430.00817.510-0.005-0.0050.0000.0000.0000.000
55A97GLY00.0250.02216.277-0.016-0.0160.0000.0000.0000.000
56A98ALA00.0360.00416.921-0.019-0.0190.0000.0000.0000.000
57A99GLY00.0090.00019.3870.0040.0040.0000.0000.0000.000
58A100ASN0-0.030-0.03017.1280.0080.0080.0000.0000.0000.000
59A101VAL0-0.0050.00515.358-0.001-0.0010.0000.0000.0000.000
60A102TYR0-0.013-0.02517.9740.0100.0100.0000.0000.0000.000
61A103VAL00.0070.00621.1420.0160.0160.0000.0000.0000.000
62A104VAL0-0.032-0.00716.4260.0100.0100.0000.0000.0000.000
63A105LYS10.8260.89919.2370.2680.2680.0000.0000.0000.000
64A106GLU-1-0.805-0.87121.919-0.141-0.1410.0000.0000.0000.000
65A107MET0-0.045-0.00224.4320.0120.0120.0000.0000.0000.000
66A108TYR00.031-0.04425.987-0.003-0.0030.0000.0000.0000.000
67A109LYS10.8920.94527.8140.1110.1110.0000.0000.0000.000
68A110GLU-1-0.841-0.91926.232-0.124-0.1240.0000.0000.0000.000
69A111ALA00.0340.01424.427-0.004-0.0040.0000.0000.0000.000
70A112LYS10.9040.97425.3880.0940.0940.0000.0000.0000.000
71A113ASP-1-0.869-0.91628.543-0.113-0.1130.0000.0000.0000.000
72A114MET0-0.044-0.00623.0990.0020.0020.0000.0000.0000.000
73A115PHE00.0380.01121.0590.0040.0040.0000.0000.0000.000
74A116GLU-1-0.845-0.91825.565-0.084-0.0840.0000.0000.0000.000
75A117LYS10.7670.87626.9800.1260.1260.0000.0000.0000.000
76A118ALA00.0250.01023.5130.0050.0050.0000.0000.0000.000
77A119LEU00.0030.01225.2770.0070.0070.0000.0000.0000.000
78A120ARG10.7970.87228.2230.0970.0970.0000.0000.0000.000
79A121ALA0-0.0300.00226.0870.0070.0070.0000.0000.0000.000
80A122GLY0-0.023-0.00627.4300.0040.0040.0000.0000.0000.000
81A123MET0-0.095-0.02820.1260.0000.0000.0000.0000.0000.000
82A124GLU-1-0.828-0.92625.647-0.074-0.0740.0000.0000.0000.000
83A125ASN0-0.053-0.05121.7100.0070.0070.0000.0000.0000.000
84A126GLY00.0630.02825.709-0.002-0.0020.0000.0000.0000.000
85A127ASP-1-0.828-0.90020.818-0.173-0.1730.0000.0000.0000.000
86A128LEU0-0.033-0.00723.520-0.008-0.0080.0000.0000.0000.000
87A129PHE0-0.026-0.01624.5990.0030.0030.0000.0000.0000.000
88A130TYR00.002-0.02524.3770.0000.0000.0000.0000.0000.000
89A131MET0-0.038-0.01021.0140.0040.0040.0000.0000.0000.000
90A132LEU0-0.025-0.01325.4700.0020.0020.0000.0000.0000.000
91A133GLY00.0330.01228.1720.0060.0060.0000.0000.0000.000
92A134THR00.0440.00027.4570.0090.0090.0000.0000.0000.000
93A135VAL0-0.040-0.02125.7250.0000.0000.0000.0000.0000.000
94A136LEU0-0.083-0.04328.7220.0050.0050.0000.0000.0000.000
95A137VAL00.0490.02832.3090.0050.0050.0000.0000.0000.000
96A138LYS10.8070.92027.8170.1480.1480.0000.0000.0000.000
97A139LEU0-0.096-0.04130.7660.0000.0000.0000.0000.0000.000
98A140GLU-1-0.891-0.94034.158-0.072-0.0720.0000.0000.0000.000
99A141GLN0-0.075-0.04935.741-0.001-0.0010.0000.0000.0000.000
100A142PRO00.1230.06837.495-0.002-0.0020.0000.0000.0000.000
101A143LYS10.8370.89438.2080.0560.0560.0000.0000.0000.000
102A144LEU0-0.066-0.03336.4270.0020.0020.0000.0000.0000.000
103A145ALA00.0280.02334.028-0.003-0.0030.0000.0000.0000.000
104A146LEU00.0290.00534.665-0.002-0.0020.0000.0000.0000.000
105A147PRO0-0.0130.00236.3110.0000.0000.0000.0000.0000.000
106A148TYR0-0.011-0.01431.2070.0010.0010.0000.0000.0000.000
107A149LEU00.0320.00931.164-0.003-0.0030.0000.0000.0000.000
108A150GLN0-0.059-0.03033.3160.0010.0010.0000.0000.0000.000
109A151ARG10.8030.90031.5210.0700.0700.0000.0000.0000.000
110A152ALA00.001-0.01329.194-0.001-0.0010.0000.0000.0000.000
111A153VAL0-0.0020.01430.256-0.001-0.0010.0000.0000.0000.000
112A154GLU-1-0.882-0.93332.874-0.061-0.0610.0000.0000.0000.000
113A155LEU0-0.087-0.04028.6240.0030.0030.0000.0000.0000.000
114A156ASN0-0.036-0.02026.7410.0050.0050.0000.0000.0000.000
115A157GLU-1-0.784-0.84929.864-0.065-0.0650.0000.0000.0000.000
116A158ASN0-0.060-0.04329.2110.0070.0070.0000.0000.0000.000
117A159ASP-1-0.866-0.92526.860-0.128-0.1280.0000.0000.0000.000
118A160THR00.032-0.00529.6800.0010.0010.0000.0000.0000.000
119A161GLU-1-0.809-0.87027.210-0.120-0.1200.0000.0000.0000.000
120A162ALA00.0300.00528.8610.0030.0030.0000.0000.0000.000
121A163ARG10.7550.86330.5000.0740.0740.0000.0000.0000.000
122A164PHE0-0.015-0.00732.3650.0070.0070.0000.0000.0000.000
123A165GLN0-0.041-0.03630.2820.0070.0070.0000.0000.0000.000
124A166PHE00.0180.00333.6150.0050.0050.0000.0000.0000.000
125A167GLY00.0320.01335.9030.0040.0040.0000.0000.0000.000
126A168MET0-0.028-0.01536.1070.0030.0030.0000.0000.0000.000
127A169CYS0-0.049-0.00536.4650.0020.0020.0000.0000.0000.000
128A170LEU0-0.052-0.02038.5460.0030.0030.0000.0000.0000.000
129A171ALA00.003-0.00441.5360.0030.0030.0000.0000.0000.000
130A172ASN0-0.071-0.03241.0090.0030.0030.0000.0000.0000.000
131A173GLU-1-0.806-0.89542.305-0.059-0.0590.0000.0000.0000.000
132A174GLY0-0.012-0.00344.1770.0030.0030.0000.0000.0000.000
133A175MET0-0.079-0.02644.3070.0020.0020.0000.0000.0000.000
134A176LEU00.0650.01444.997-0.002-0.0020.0000.0000.0000.000
135A177ASP-1-0.809-0.88146.661-0.041-0.0410.0000.0000.0000.000
136A178GLU-1-0.848-0.92743.880-0.047-0.0470.0000.0000.0000.000
137A179ALA00.0240.02041.897-0.002-0.0020.0000.0000.0000.000
138A180LEU0-0.034-0.01842.070-0.002-0.0020.0000.0000.0000.000
139A181SER0-0.075-0.04143.6880.0010.0010.0000.0000.0000.000
140A182GLN00.0300.02438.272-0.002-0.0020.0000.0000.0000.000
141A183PHE00.018-0.00538.093-0.002-0.0020.0000.0000.0000.000
142A184ALA0-0.024-0.00339.965-0.001-0.0010.0000.0000.0000.000
143A185ALA00.0470.01638.5540.0000.0000.0000.0000.0000.000
144A186VAL0-0.030-0.01134.869-0.002-0.0020.0000.0000.0000.000
145A187THR0-0.049-0.02436.458-0.001-0.0010.0000.0000.0000.000
146A188GLU-1-1.013-1.00638.853-0.049-0.0490.0000.0000.0000.000
147A189GLN0-0.052-0.01533.480-0.003-0.0030.0000.0000.0000.000
148A190ASP-1-0.856-0.93632.782-0.084-0.0840.0000.0000.0000.000
149A191PRO0-0.021-0.00834.8410.0010.0010.0000.0000.0000.000
150A192GLY0-0.014-0.01135.4760.0030.0030.0000.0000.0000.000
151A193HIS00.0470.03732.3370.0020.0020.0000.0000.0000.000
152A194ALA0-0.007-0.01835.8210.0030.0030.0000.0000.0000.000
153A195ASP-1-0.829-0.91435.294-0.080-0.0800.0000.0000.0000.000
154A196ALA00.0410.02836.8000.0020.0020.0000.0000.0000.000
155A197PHE0-0.014-0.00138.4180.0040.0040.0000.0000.0000.000
156A198TYR00.015-0.00639.2670.0050.0050.0000.0000.0000.000
157A199ASN0-0.017-0.01838.0350.0040.0040.0000.0000.0000.000
158A200ALA00.0340.03941.6470.0020.0020.0000.0000.0000.000
159A201GLY0-0.0010.00443.9680.0030.0030.0000.0000.0000.000
160A202VAL0-0.012-0.01844.0500.0030.0030.0000.0000.0000.000
161A203THR00.009-0.01743.9890.0010.0010.0000.0000.0000.000
162A204TYR0-0.001-0.01546.5960.0030.0030.0000.0000.0000.000
163A205ALA0-0.042-0.01449.3850.0020.0020.0000.0000.0000.000
164A206TYR0-0.028-0.01347.5680.0020.0020.0000.0000.0000.000
165A207LYS10.7650.87749.7120.0410.0410.0000.0000.0000.000
166A208GLU-1-0.954-0.97252.944-0.032-0.0320.0000.0000.0000.000
167A209ASN0-0.026-0.01053.2320.0010.0010.0000.0000.0000.000
168A210ARG10.9560.94653.6540.0310.0310.0000.0000.0000.000
169A211GLU-1-0.927-0.93655.362-0.031-0.0310.0000.0000.0000.000
170A212LYS10.8220.87550.7880.0350.0350.0000.0000.0000.000
171A213ALA0-0.0010.00749.599-0.002-0.0020.0000.0000.0000.000
172A214LEU0-0.034-0.01849.224-0.002-0.0020.0000.0000.0000.000
173A215GLU-1-0.830-0.88849.600-0.038-0.0380.0000.0000.0000.000
174A216MET0-0.008-0.00745.173-0.001-0.0010.0000.0000.0000.000
175A217LEU00.0280.02744.708-0.002-0.0020.0000.0000.0000.000
176A218ASP-1-0.810-0.89645.677-0.042-0.0420.0000.0000.0000.000
177A219LYS10.7310.85843.6550.0460.0460.0000.0000.0000.000
178A220ALA00.0430.02941.482-0.002-0.0020.0000.0000.0000.000
179A221ILE0-0.034-0.02241.525-0.002-0.0020.0000.0000.0000.000
180A222ASP-1-0.856-0.91943.495-0.047-0.0470.0000.0000.0000.000
181A223ILE0-0.0330.01237.9330.0010.0010.0000.0000.0000.000
182A224GLN0-0.060-0.04435.789-0.003-0.0030.0000.0000.0000.000
183A225PRO0-0.001-0.00439.7210.0000.0000.0000.0000.0000.000
184A226ASP-1-0.892-0.93337.724-0.067-0.0670.0000.0000.0000.000
185A227HIS00.0260.01037.8350.0010.0010.0000.0000.0000.000
186A228MET0-0.017-0.03440.1270.0040.0040.0000.0000.0000.000
187A229LEU0-0.0190.00638.8760.0030.0030.0000.0000.0000.000
188A230ALA00.0650.03042.4380.0030.0030.0000.0000.0000.000
189A231LEU0-0.028-0.01044.2460.0030.0030.0000.0000.0000.000
190A232HIS0-0.032-0.02944.8660.0040.0040.0000.0000.0000.000
191A233ALA00.0280.02246.4230.0020.0020.0000.0000.0000.000
192A234LYS10.8230.89748.2260.0420.0420.0000.0000.0000.000
193A235LYS10.8510.94050.2890.0400.0400.0000.0000.0000.000
194A236LEU0-0.077-0.03650.4210.0030.0030.0000.0000.0000.000