FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: RY598

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 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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1966736.418446
FMO2-HF: Nuclear repulsion 1889706.488907
FMO2-HF: Total energy -77029.929539
FMO2-MP2: Total energy -77251.789645


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.
-1.2631.760.062-1.392-1.6940.001
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 : -0.025 / 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-1-0.921-0.9553.802-1.3640.772-0.029-1.076-1.0320.000
4A46ALA0-0.0040.0265.5570.0850.0850.0000.0000.0000.000
5A47PHE0-0.011-0.0294.8140.1650.1650.0000.0000.0000.000
6A48THR00.0250.0128.8480.0370.0370.0000.0000.0000.000
7A49LYS10.9520.97010.8820.1960.1960.0000.0000.0000.000
8A50ALA0-0.0110.00111.9230.0260.0260.0000.0000.0000.000
9A51ILE00.0210.01413.1600.0220.0220.0000.0000.0000.000
10A52GLU-1-1.008-1.00315.387-0.086-0.0860.0000.0000.0000.000
11A53GLU-1-0.992-1.00117.545-0.024-0.0240.0000.0000.0000.000
12A54ASN00.0090.01417.8340.0010.0010.0000.0000.0000.000
13A55LYN0-0.070-0.02219.7700.0090.0090.0000.0000.0000.000
14A56GLU-1-0.847-0.93920.952-0.003-0.0030.0000.0000.0000.000
15A57ASP-1-0.919-0.95418.9230.0800.0800.0000.0000.0000.000
16A58ALA00.0750.02719.002-0.003-0.0030.0000.0000.0000.000
17A59ILE0-0.005-0.00615.2210.0180.0180.0000.0000.0000.000
18A60PRO0-0.029-0.00913.3570.0480.0480.0000.0000.0000.000
19A61TYR00.001-0.01112.7610.0050.0050.0000.0000.0000.000
20A62ILE0-0.0090.00414.0960.0160.0160.0000.0000.0000.000
21A63ASN0-0.038-0.01610.1130.0950.0950.0000.0000.0000.000
22A64PHE0-0.011-0.0067.5770.1710.1710.0000.0000.0000.000
23A65ALA00.0420.0259.747-0.001-0.0010.0000.0000.0000.000
24A66ASN00.0180.00710.599-0.062-0.0620.0000.0000.0000.000
25A67LEU0-0.0390.0003.329-0.7460.0340.091-0.298-0.5730.001
26A68LEU0-0.007-0.0136.896-0.083-0.0830.0000.0000.0000.000
27A69SER0-0.004-0.0028.827-0.092-0.0920.0000.0000.0000.000
28A70SER0-0.126-0.0506.4310.1280.1280.0000.0000.0000.000
29A71VAL0-0.001-0.0104.031-0.133-0.0260.000-0.018-0.0890.000
30A72ASN0-0.045-0.0147.204-0.097-0.0970.0000.0000.0000.000
31A73GLU-1-0.908-0.9558.996-0.486-0.4860.0000.0000.0000.000
32A74LEU00.0550.01611.7470.0230.0230.0000.0000.0000.000
33A75GLU-1-0.866-0.93914.515-0.009-0.0090.0000.0000.0000.000
34A76ARG10.9240.96510.6650.3170.3170.0000.0000.0000.000
35A77ALA00.0320.01812.5630.0030.0030.0000.0000.0000.000
36A78LEU0-0.011-0.01114.0060.0150.0150.0000.0000.0000.000
37A79ALA0-0.0090.00717.3230.0010.0010.0000.0000.0000.000
38A80PHE0-0.046-0.02213.703-0.017-0.0170.0000.0000.0000.000
39A81TYR00.007-0.01914.1510.0030.0030.0000.0000.0000.000
40A82ASP-1-0.954-0.96818.3860.0160.0160.0000.0000.0000.000
41A83LYS10.9240.97119.0750.0050.0050.0000.0000.0000.000
42A84ALA00.003-0.01018.3670.0000.0000.0000.0000.0000.000
43A85LEU0-0.037-0.01620.4020.0000.0000.0000.0000.0000.000
44A86GLU-1-0.976-0.98623.6700.0020.0020.0000.0000.0000.000
45A87LEU0-0.070-0.01120.829-0.003-0.0030.0000.0000.0000.000
46A88ASP-1-0.847-0.93823.4420.0650.0650.0000.0000.0000.000
47A89SER0-0.042-0.00924.5220.0090.0090.0000.0000.0000.000
48A90SER0-0.011-0.02426.6410.0010.0010.0000.0000.0000.000
49A91ALA00.0250.02521.2040.0080.0080.0000.0000.0000.000
50A92ALA00.0210.00522.4950.0070.0070.0000.0000.0000.000
51A93THR0-0.004-0.01617.707-0.005-0.0050.0000.0000.0000.000
52A94ALA00.0360.02918.5280.0210.0210.0000.0000.0000.000
53A95TYR0-0.037-0.01919.605-0.005-0.0050.0000.0000.0000.000
54A96TYR00.023-0.00318.190-0.010-0.0100.0000.0000.0000.000
55A97GLY0-0.017-0.00916.8710.0070.0070.0000.0000.0000.000
56A98ALA00.0450.00617.337-0.003-0.0030.0000.0000.0000.000
57A99GLY00.0110.00519.265-0.013-0.0130.0000.0000.0000.000
58A100ASN00.0420.00517.251-0.025-0.0250.0000.0000.0000.000
59A101VAL0-0.0330.00615.413-0.007-0.0070.0000.0000.0000.000
60A102TYR0-0.010-0.02117.968-0.019-0.0190.0000.0000.0000.000
61A103VAL0-0.0060.00420.863-0.011-0.0110.0000.0000.0000.000
62A104VAL0-0.0260.00316.454-0.009-0.0090.0000.0000.0000.000
63A105LYS10.8310.91919.148-0.031-0.0310.0000.0000.0000.000
64A106GLU-1-0.968-0.98221.6760.0360.0360.0000.0000.0000.000
65A107MET0-0.079-0.01824.411-0.008-0.0080.0000.0000.0000.000
66A108TYR00.0920.01225.5680.0070.0070.0000.0000.0000.000
67A109LYS10.9600.98927.910-0.025-0.0250.0000.0000.0000.000
68A110GLU-1-0.855-0.94726.1520.0380.0380.0000.0000.0000.000
69A111ALA00.0370.01924.4700.0050.0050.0000.0000.0000.000
70A112LYS10.9170.97525.603-0.039-0.0390.0000.0000.0000.000
71A113ASP-1-0.968-0.97428.3930.0470.0470.0000.0000.0000.000
72A114MET0-0.012-0.00723.1210.0020.0020.0000.0000.0000.000
73A115PHE00.0440.01321.7580.0050.0050.0000.0000.0000.000
74A116GLU-1-0.899-0.95626.2330.0540.0540.0000.0000.0000.000
75A117LYS10.8210.92127.225-0.050-0.0500.0000.0000.0000.000
76A118ALA00.0270.01724.2690.0000.0000.0000.0000.0000.000
77A119LEU0-0.0020.00125.9520.0000.0000.0000.0000.0000.000
78A120ARG10.8750.92628.799-0.053-0.0530.0000.0000.0000.000
79A121ALA0-0.048-0.01426.618-0.004-0.0040.0000.0000.0000.000
80A122GLY00.0120.01428.2660.0010.0010.0000.0000.0000.000
81A123MET0-0.090-0.02221.2960.0040.0040.0000.0000.0000.000
82A124GLU-1-0.910-0.96626.0450.0670.0670.0000.0000.0000.000
83A125ASN0-0.040-0.03322.7030.0030.0030.0000.0000.0000.000
84A126GLY00.0520.01926.474-0.003-0.0030.0000.0000.0000.000
85A127ASP-1-0.841-0.91620.8410.1710.1710.0000.0000.0000.000
86A128LEU0-0.048-0.01623.988-0.003-0.0030.0000.0000.0000.000
87A129PHE0-0.029-0.02725.187-0.008-0.0080.0000.0000.0000.000
88A130TYR0-0.003-0.02824.579-0.005-0.0050.0000.0000.0000.000
89A131MET0-0.0260.00221.556-0.009-0.0090.0000.0000.0000.000
90A132LEU0-0.029-0.00825.596-0.008-0.0080.0000.0000.0000.000
91A133GLY00.0260.00328.474-0.007-0.0070.0000.0000.0000.000
92A134THR00.030-0.01327.543-0.007-0.0070.0000.0000.0000.000
93A135VAL0-0.045-0.02226.026-0.006-0.0060.0000.0000.0000.000
94A136LEU0-0.077-0.05329.079-0.006-0.0060.0000.0000.0000.000
95A137VAL00.0080.02232.223-0.004-0.0040.0000.0000.0000.000
96A138LYS10.8990.95328.182-0.063-0.0630.0000.0000.0000.000
97A139LEU0-0.079-0.02530.961-0.004-0.0040.0000.0000.0000.000
98A140GLU-1-0.908-0.95434.1500.0280.0280.0000.0000.0000.000
99A141GLN0-0.073-0.04736.1920.0040.0040.0000.0000.0000.000
100A142PRO00.2050.11637.4950.0020.0020.0000.0000.0000.000
101A143LYS10.8920.94838.446-0.029-0.0290.0000.0000.0000.000
102A144LEU0-0.116-0.06136.718-0.001-0.0010.0000.0000.0000.000
103A145ALA00.0370.02034.1870.0020.0020.0000.0000.0000.000
104A146LEU00.0040.00234.9860.0040.0040.0000.0000.0000.000
105A147PRO00.0050.00436.9430.0020.0020.0000.0000.0000.000
106A148TYR00.001-0.00431.8150.0020.0020.0000.0000.0000.000
107A149LEU00.0430.00931.2870.0050.0050.0000.0000.0000.000
108A150GLN0-0.037-0.00533.628-0.001-0.0010.0000.0000.0000.000
109A151ARG10.8600.92632.531-0.065-0.0650.0000.0000.0000.000
110A152ALA00.011-0.00729.4640.0020.0020.0000.0000.0000.000
111A153VAL0-0.0010.01730.7290.0030.0030.0000.0000.0000.000
112A154GLU-1-0.858-0.91333.2210.0560.0560.0000.0000.0000.000
113A155LEU0-0.124-0.07129.2820.0010.0010.0000.0000.0000.000
114A156ASN0-0.029-0.02126.3570.0010.0010.0000.0000.0000.000
115A157GLU-1-0.798-0.89430.2550.0580.0580.0000.0000.0000.000
116A158ASN0-0.020-0.00929.367-0.009-0.0090.0000.0000.0000.000
117A159ASP-1-0.880-0.91727.0830.1020.1020.0000.0000.0000.000
118A160THR00.018-0.00729.193-0.005-0.0050.0000.0000.0000.000
119A161GLU-1-0.852-0.88926.7610.0720.0720.0000.0000.0000.000
120A162ALA00.0250.00829.154-0.005-0.0050.0000.0000.0000.000
121A163ARG10.7670.86730.634-0.064-0.0640.0000.0000.0000.000
122A164PHE0-0.008-0.00932.639-0.006-0.0060.0000.0000.0000.000
123A165GLN00.0160.00230.391-0.007-0.0070.0000.0000.0000.000
124A166PHE00.006-0.00233.779-0.004-0.0040.0000.0000.0000.000
125A167GLY00.0310.01836.155-0.004-0.0040.0000.0000.0000.000
126A168MET0-0.032-0.01736.440-0.002-0.0020.0000.0000.0000.000
127A169CYS0-0.050-0.00436.763-0.003-0.0030.0000.0000.0000.000
128A170LEU0-0.016-0.01438.929-0.003-0.0030.0000.0000.0000.000
129A171ALA0-0.005-0.00841.816-0.002-0.0020.0000.0000.0000.000
130A172ASN0-0.103-0.04541.177-0.003-0.0030.0000.0000.0000.000
131A173GLU-1-0.854-0.93642.8170.0310.0310.0000.0000.0000.000
132A174GLY0-0.040-0.01044.648-0.001-0.0010.0000.0000.0000.000
133A175MET0-0.061-0.02044.423-0.001-0.0010.0000.0000.0000.000
134A176LEU00.0650.01945.3770.0020.0020.0000.0000.0000.000
135A177ASP-1-0.850-0.92146.7680.0270.0270.0000.0000.0000.000
136A178GLU-1-0.868-0.94543.9170.0330.0330.0000.0000.0000.000
137A179ALA00.0210.01942.1820.0020.0020.0000.0000.0000.000
138A180LEU0-0.033-0.01442.1560.0020.0020.0000.0000.0000.000
139A181SER0-0.071-0.03043.5650.0000.0000.0000.0000.0000.000
140A182GLN00.0380.02738.2920.0030.0030.0000.0000.0000.000
141A183PHE0-0.002-0.02038.4640.0020.0020.0000.0000.0000.000
142A184ALA0-0.0150.00039.9290.0010.0010.0000.0000.0000.000
143A185ALA00.0310.01438.0180.0000.0000.0000.0000.0000.000
144A186VAL0-0.023-0.01034.7540.0020.0020.0000.0000.0000.000
145A187THR0-0.040-0.01136.2440.0010.0010.0000.0000.0000.000
146A188GLU-1-1.014-1.00538.7800.0430.0430.0000.0000.0000.000
147A189GLN0-0.056-0.02432.9970.0040.0040.0000.0000.0000.000
148A190ASP-1-0.868-0.94532.3360.0590.0590.0000.0000.0000.000
149A191PRO0-0.011-0.00234.570-0.002-0.0020.0000.0000.0000.000
150A192GLY0-0.044-0.01935.360-0.003-0.0030.0000.0000.0000.000
151A193HIS00.0500.02732.276-0.004-0.0040.0000.0000.0000.000
152A194ALA00.019-0.00435.845-0.002-0.0020.0000.0000.0000.000
153A195ASP-1-0.856-0.93334.2710.0420.0420.0000.0000.0000.000
154A196ALA00.0240.03837.138-0.002-0.0020.0000.0000.0000.000
155A197PHE00.0300.00938.593-0.002-0.0020.0000.0000.0000.000
156A198TYR00.0040.00339.925-0.003-0.0030.0000.0000.0000.000
157A199ASN0-0.018-0.03738.012-0.003-0.0030.0000.0000.0000.000
158A200ALA00.0110.01841.727-0.001-0.0010.0000.0000.0000.000
159A201GLY0-0.021-0.02044.107-0.002-0.0020.0000.0000.0000.000
160A202VAL0-0.039-0.03043.900-0.002-0.0020.0000.0000.0000.000
161A203THR00.0210.01344.295-0.001-0.0010.0000.0000.0000.000
162A204TYR00.002-0.02946.880-0.002-0.0020.0000.0000.0000.000
163A205ALA0-0.018-0.00649.621-0.001-0.0010.0000.0000.0000.000
164A206TYR0-0.0090.00147.895-0.001-0.0010.0000.0000.0000.000
165A207LYS10.8050.91150.266-0.025-0.0250.0000.0000.0000.000
166A208GLU-1-0.985-0.97553.0970.0170.0170.0000.0000.0000.000
167A209ASN00.008-0.01553.512-0.002-0.0020.0000.0000.0000.000
168A210ARG10.9110.96453.964-0.015-0.0150.0000.0000.0000.000
169A211GLU-1-0.928-0.97355.5860.0180.0180.0000.0000.0000.000
170A212LYS10.9760.98351.130-0.023-0.0230.0000.0000.0000.000
171A213ALA00.0090.02549.7480.0010.0010.0000.0000.0000.000
172A214LEU0-0.010-0.01649.3040.0010.0010.0000.0000.0000.000
173A215GLU-1-0.906-0.93449.6730.0250.0250.0000.0000.0000.000
174A216MET0-0.043-0.03445.6500.0010.0010.0000.0000.0000.000
175A217LEU00.0070.00245.2820.0010.0010.0000.0000.0000.000
176A218ASP-1-0.912-0.96345.8680.0220.0220.0000.0000.0000.000
177A219LYS10.9350.97343.443-0.029-0.0290.0000.0000.0000.000
178A220ALA00.0400.02341.6340.0010.0010.0000.0000.0000.000
179A221ILE0-0.067-0.03541.5420.0000.0000.0000.0000.0000.000
180A222ASP-1-1.045-1.01643.3800.0260.0260.0000.0000.0000.000
181A223ILE0-0.0090.01737.9090.0000.0000.0000.0000.0000.000
182A224GLN0-0.032-0.01935.3010.0020.0020.0000.0000.0000.000
183A225PRO0-0.006-0.01439.638-0.001-0.0010.0000.0000.0000.000
184A226ASP-1-0.957-0.97638.0850.0260.0260.0000.0000.0000.000
185A227HIS00.0720.04437.868-0.002-0.0020.0000.0000.0000.000
186A228MET00.001-0.02940.663-0.002-0.0020.0000.0000.0000.000
187A229LEU00.0090.01739.121-0.001-0.0010.0000.0000.0000.000
188A230ALA00.0550.03642.392-0.001-0.0010.0000.0000.0000.000
189A231LEU0-0.046-0.02344.013-0.001-0.0010.0000.0000.0000.000
190A232HIS0-0.051-0.04444.630-0.001-0.0010.0000.0000.0000.000
191A233ALA0-0.0060.00446.143-0.001-0.0010.0000.0000.0000.000
192A234LYS10.9370.98048.004-0.021-0.0210.0000.0000.0000.000
193A235LYS10.8370.93250.283-0.016-0.0160.0000.0000.0000.000
194A236LEU0-0.0160.00450.327-0.001-0.0010.0000.0000.0000.000