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: QNV5Y

Calculation Name: 2F1M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F1M

Chain ID: A

ChEMBL ID:

UniProt ID: P0AE06

Base Structure: X-ray

Registration Date: 2023-09-27

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2081814.184547
FMO2-HF: Nuclear repulsion 1995922.713083
FMO2-HF: Total energy -85891.471463
FMO2-MP2: Total energy -86143.901067


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:53:THR)


Summations of interaction energy for fragment #1(A:53:THR)
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.
-7.4-10.41714.664-5.595-6.054-0.028
Interaction energy analysis for fragmet #1(A:53:THR)
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 : -0.029
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].
3A55GLU-1-0.905-0.9543.8582.5213.912-0.019-0.629-0.7430.000
4A56LEU00.0250.0216.339-0.467-0.4670.0000.0000.0000.000
5A57PRO0-0.032-0.0119.9510.2600.2600.0000.0000.0000.000
6A58GLY00.0610.02213.256-0.060-0.0600.0000.0000.0000.000
7A59ARG10.9000.96114.780-0.141-0.1410.0000.0000.0000.000
8A60THR00.0370.02217.424-0.015-0.0150.0000.0000.0000.000
9A61SER0-0.037-0.02119.253-0.033-0.0330.0000.0000.0000.000
10A62ALA00.021-0.00521.9670.0160.0160.0000.0000.0000.000
11A63TYR00.0400.03722.132-0.021-0.0210.0000.0000.0000.000
12A64ARG10.9120.94124.630-0.109-0.1090.0000.0000.0000.000
13A65ILE00.0080.00628.0890.0150.0150.0000.0000.0000.000
14A66ALA00.0010.01031.020-0.011-0.0110.0000.0000.0000.000
15A67GLU-1-0.829-0.89134.7590.0620.0620.0000.0000.0000.000
16A68VAL0-0.026-0.01437.703-0.003-0.0030.0000.0000.0000.000
17A69ARG10.7970.85740.474-0.048-0.0480.0000.0000.0000.000
18A70PRO00.0080.02243.8050.0000.0000.0000.0000.0000.000
19A71GLN00.014-0.00145.754-0.001-0.0010.0000.0000.0000.000
20A72VAL0-0.017-0.01249.078-0.003-0.0030.0000.0000.0000.000
21A73SER00.0330.02351.7650.0020.0020.0000.0000.0000.000
22A74GLY00.0280.02454.151-0.001-0.0010.0000.0000.0000.000
23A75ILE00.0260.01954.1910.0010.0010.0000.0000.0000.000
24A76ILE0-0.0320.00148.4020.0000.0000.0000.0000.0000.000
25A77LEU0-0.003-0.00151.9880.0000.0000.0000.0000.0000.000
26A78LYS10.8810.93447.652-0.078-0.0780.0000.0000.0000.000
27A79ARG10.8240.91042.700-0.093-0.0930.0000.0000.0000.000
28A80ASN0-0.050-0.03844.8870.0010.0010.0000.0000.0000.000
29A81PHE00.0100.02439.4370.0030.0030.0000.0000.0000.000
30A82LYS10.9810.98538.870-0.129-0.1290.0000.0000.0000.000
31A83GLU-1-0.809-0.87838.0260.1070.1070.0000.0000.0000.000
32A84GLY00.0140.01433.6480.0050.0050.0000.0000.0000.000
33A85SER0-0.078-0.04533.0240.0130.0130.0000.0000.0000.000
34A86ASP-1-0.811-0.91430.3410.2030.2030.0000.0000.0000.000
35A87ILE0-0.044-0.02833.442-0.008-0.0080.0000.0000.0000.000
36A88GLU-1-0.816-0.89134.4460.1320.1320.0000.0000.0000.000
37A89ALA0-0.009-0.00935.925-0.006-0.0060.0000.0000.0000.000
38A90GLY00.0010.00637.654-0.002-0.0020.0000.0000.0000.000
39A91VAL0-0.024-0.01340.303-0.006-0.0060.0000.0000.0000.000
40A92SER0-0.040-0.02542.345-0.001-0.0010.0000.0000.0000.000
41A93LEU00.0050.00839.4090.0040.0040.0000.0000.0000.000
42A94TYR00.038-0.02042.8050.0030.0030.0000.0000.0000.000
43A95GLN0-0.065-0.01546.6760.0000.0000.0000.0000.0000.000
44A96ILE00.0120.00749.8710.0010.0010.0000.0000.0000.000
45A97ASP-1-0.869-0.94652.4790.0430.0430.0000.0000.0000.000
46A98PRO00.0120.00655.518-0.002-0.0020.0000.0000.0000.000
47A99ALA00.0100.02057.322-0.002-0.0020.0000.0000.0000.000
48A100THR00.036-0.00160.659-0.001-0.0010.0000.0000.0000.000
49A101TYR0-0.020-0.03056.227-0.003-0.0030.0000.0000.0000.000
50A102GLN0-0.018-0.03560.0230.0000.0000.0000.0000.0000.000
51A103ALA00.0330.02361.280-0.001-0.0010.0000.0000.0000.000
52A104THR0-0.0150.00162.102-0.002-0.0020.0000.0000.0000.000
53A105TYR00.0150.00260.814-0.001-0.0010.0000.0000.0000.000
54A106ASP-1-0.816-0.89063.0460.0290.0290.0000.0000.0000.000
55A107SER0-0.044-0.03166.171-0.001-0.0010.0000.0000.0000.000
56A108ALA00.0400.02164.709-0.001-0.0010.0000.0000.0000.000
57A109LYS10.8320.90263.520-0.030-0.0300.0000.0000.0000.000
58A110GLY00.0050.00967.325-0.001-0.0010.0000.0000.0000.000
59A111ASP-1-0.914-0.96569.8120.0170.0170.0000.0000.0000.000
60A112LEU0-0.037-0.01366.495-0.001-0.0010.0000.0000.0000.000
61A113ALA0-0.012-0.00570.191-0.001-0.0010.0000.0000.0000.000
62A114LYS10.9410.97672.588-0.017-0.0170.0000.0000.0000.000
63A115ALA00.0450.03372.388-0.001-0.0010.0000.0000.0000.000
64A116GLN00.025-0.00669.854-0.001-0.0010.0000.0000.0000.000
65A117ALA0-0.0070.01474.287-0.001-0.0010.0000.0000.0000.000
66A118ALA0-0.005-0.00977.644-0.001-0.0010.0000.0000.0000.000
67A119ALA00.024-0.00675.660-0.001-0.0010.0000.0000.0000.000
68A120ASN0-0.016-0.01077.533-0.001-0.0010.0000.0000.0000.000
69A121ILE0-0.023-0.02279.012-0.001-0.0010.0000.0000.0000.000
70A122ALA00.0270.01780.7580.0000.0000.0000.0000.0000.000
71A123GLN00.0000.00878.861-0.001-0.0010.0000.0000.0000.000
72A124LEU00.007-0.00981.388-0.001-0.0010.0000.0000.0000.000
73A125THR0-0.059-0.02484.2280.0000.0000.0000.0000.0000.000
74A126VAL00.0730.05782.8680.0000.0000.0000.0000.0000.000
75A127ASN00.005-0.00282.055-0.001-0.0010.0000.0000.0000.000
76A128ARG10.8690.91786.028-0.009-0.0090.0000.0000.0000.000
77A129TYR00.0560.02288.9990.0000.0000.0000.0000.0000.000
78A130GLN00.0500.02584.6810.0000.0000.0000.0000.0000.000
79A131LYS10.8770.94089.056-0.007-0.0070.0000.0000.0000.000
80A132LEU00.0090.01391.3450.0000.0000.0000.0000.0000.000
81A133LEU00.0070.02389.5320.0000.0000.0000.0000.0000.000
82A134GLY0-0.015-0.00393.9290.0000.0000.0000.0000.0000.000
83A135THR0-0.043-0.02796.9770.0000.0000.0000.0000.0000.000
84A136GLN0-0.008-0.02799.2260.0000.0000.0000.0000.0000.000
85A137TYR0-0.049-0.02898.3940.0000.0000.0000.0000.0000.000
86A138ILE0-0.0220.02493.2890.0000.0000.0000.0000.0000.000
87A139SER0-0.015-0.03795.6530.0000.0000.0000.0000.0000.000
88A140LYS10.8490.88089.351-0.001-0.0010.0000.0000.0000.000
89A141GLN00.0190.01691.1250.0000.0000.0000.0000.0000.000
90A142GLU-1-0.784-0.85590.9410.0050.0050.0000.0000.0000.000
91A143TYR0-0.027-0.01985.4940.0000.0000.0000.0000.0000.000
92A144ASP-1-0.805-0.89286.9270.0020.0020.0000.0000.0000.000
93A145GLN0-0.048-0.01786.1500.0000.0000.0000.0000.0000.000
94A146ALA00.0080.00485.9870.0000.0000.0000.0000.0000.000
95A147LEU0-0.025-0.03482.7010.0000.0000.0000.0000.0000.000
96A148ALA0-0.0110.01181.6280.0000.0000.0000.0000.0000.000
97A149ASP-1-0.859-0.91581.1670.0070.0070.0000.0000.0000.000
98A150ALA00.0140.00679.9670.0010.0010.0000.0000.0000.000
99A151GLN0-0.018-0.00274.7710.0010.0010.0000.0000.0000.000
100A152GLN00.0410.02376.2440.0000.0000.0000.0000.0000.000
101A153ALA0-0.015-0.01476.3280.0010.0010.0000.0000.0000.000
102A154ASN0-0.036-0.04473.8310.0010.0010.0000.0000.0000.000
103A155ALA00.0020.02071.9460.0000.0000.0000.0000.0000.000
104A156ALA00.0010.01471.1160.0010.0010.0000.0000.0000.000
105A157VAL0-0.013-0.01769.9390.0010.0010.0000.0000.0000.000
106A158THR0-0.047-0.02766.8580.0010.0010.0000.0000.0000.000
107A159ALA00.002-0.00166.7880.0010.0010.0000.0000.0000.000
108A160ALA00.0250.00366.4640.0010.0010.0000.0000.0000.000
109A161LYS10.8970.95564.404-0.013-0.0130.0000.0000.0000.000
110A162ALA00.0340.01862.1140.0010.0010.0000.0000.0000.000
111A163ALA00.0000.02161.7160.0010.0010.0000.0000.0000.000
112A164VAL0-0.005-0.00862.0270.0020.0020.0000.0000.0000.000
113A165GLU-1-0.792-0.84856.1380.0260.0260.0000.0000.0000.000
114A166THR0-0.024-0.02457.8370.0010.0010.0000.0000.0000.000
115A167ALA00.004-0.00457.5560.0020.0020.0000.0000.0000.000
116A168ARG10.7990.86354.256-0.027-0.0270.0000.0000.0000.000
117A169ILE0-0.027-0.01451.9450.0030.0030.0000.0000.0000.000
118A170ASN00.005-0.00153.2140.0020.0020.0000.0000.0000.000
119A171LEU00.0190.02454.4550.0020.0020.0000.0000.0000.000
120A172ALA0-0.019-0.00551.4230.0030.0030.0000.0000.0000.000
121A173TYR0-0.020-0.01146.4620.0020.0020.0000.0000.0000.000
122A174THR0-0.045-0.02050.0990.0020.0020.0000.0000.0000.000
123A175LYS10.8760.96245.433-0.059-0.0590.0000.0000.0000.000
124A176VAL00.0340.01244.172-0.001-0.0010.0000.0000.0000.000
125A177THR0-0.047-0.02842.1800.0050.0050.0000.0000.0000.000
126A178SER00.0330.00636.189-0.004-0.0040.0000.0000.0000.000
127A179PRO00.009-0.00636.8400.0010.0010.0000.0000.0000.000
128A180ILE0-0.0110.00131.162-0.001-0.0010.0000.0000.0000.000
129A181SER00.0400.00632.290-0.005-0.0050.0000.0000.0000.000
130A182GLY0-0.033-0.02130.5010.0050.0050.0000.0000.0000.000
131A183ARG10.8300.93428.075-0.216-0.2160.0000.0000.0000.000
132A184ILE0-0.0040.00331.613-0.006-0.0060.0000.0000.0000.000
133A185GLY00.0120.00934.2640.0090.0090.0000.0000.0000.000
134A186LYS10.9530.95335.024-0.127-0.1270.0000.0000.0000.000
135A187SER0-0.042-0.00838.124-0.003-0.0030.0000.0000.0000.000
136A188ASN0-0.089-0.05839.6500.0040.0040.0000.0000.0000.000
137A189VAL0-0.012-0.00242.955-0.005-0.0050.0000.0000.0000.000
138A190THR00.0270.02246.1150.0040.0040.0000.0000.0000.000
139A191GLU-1-0.802-0.92248.2230.0750.0750.0000.0000.0000.000
140A192GLY00.0120.00150.592-0.001-0.0010.0000.0000.0000.000
141A193ALA0-0.0360.00250.478-0.003-0.0030.0000.0000.0000.000
142A194LEU0-0.014-0.00852.5570.0000.0000.0000.0000.0000.000
143A195VAL00.0010.00248.7520.0010.0010.0000.0000.0000.000
144A196GLN00.008-0.01150.941-0.002-0.0020.0000.0000.0000.000
145A197ASN0-0.010-0.01250.2060.0020.0020.0000.0000.0000.000
146A198GLY00.0510.02548.314-0.002-0.0020.0000.0000.0000.000
147A199GLN0-0.040-0.00146.376-0.003-0.0030.0000.0000.0000.000
148A200ALA00.0470.00845.6050.0010.0010.0000.0000.0000.000
149A201THR00.0070.01643.0620.0010.0010.0000.0000.0000.000
150A202ALA00.0380.02739.946-0.001-0.0010.0000.0000.0000.000
151A203LEU00.0050.00542.0250.0020.0020.0000.0000.0000.000
152A204ALA00.0370.02638.6960.0040.0040.0000.0000.0000.000
153A205THR00.0040.00433.325-0.006-0.0060.0000.0000.0000.000
154A206VAL0-0.004-0.00332.8920.0080.0080.0000.0000.0000.000
155A207GLN0-0.001-0.00828.1580.0040.0040.0000.0000.0000.000
156A208GLN00.0240.01825.802-0.006-0.0060.0000.0000.0000.000
157A209LEU0-0.026-0.01125.1440.0040.0040.0000.0000.0000.000
158A210ASP-1-0.794-0.91523.1120.3040.3040.0000.0000.0000.000
159A211PRO0-0.0040.01121.252-0.006-0.0060.0000.0000.0000.000
160A212ILE0-0.056-0.01618.261-0.025-0.0250.0000.0000.0000.000
161A213TYR0-0.041-0.04218.1300.0280.0280.0000.0000.0000.000
162A214VAL0-0.016-0.02713.7000.0340.0340.0000.0000.0000.000
163A215ASP-1-0.854-0.89214.9150.0870.0870.0000.0000.0000.000
164A216VAL00.009-0.00810.1450.0670.0670.0000.0000.0000.000
165A217THR0-0.037-0.01913.455-0.092-0.0920.0000.0000.0000.000
166A218GLN00.0330.01210.010-0.104-0.1040.0000.0000.0000.000
167A219SER0-0.019-0.03913.5110.0430.0430.0000.0000.0000.000
168A220SER00.032-0.01015.167-0.060-0.0600.0000.0000.0000.000
169A221ASN0-0.046-0.02515.801-0.037-0.0370.0000.0000.0000.000
170A222ASP-1-0.805-0.85611.613-0.777-0.7770.0000.0000.0000.000
171A223MET0-0.112-0.02411.897-0.137-0.1370.0000.0000.0000.000
172A241LYS10.9750.96112.3340.2900.2900.0000.0000.0000.000
173A242ALA0-0.0100.0088.290-0.052-0.0520.0000.0000.0000.000
174A243LYS10.8480.9136.195-0.465-0.4650.0000.0000.0000.000
175A244VAL00.0340.0186.3650.1650.1650.0000.0000.0000.000
176A245SER00.0000.0046.7780.0000.0000.0000.0000.0000.000
177A246LEU00.0030.0068.5600.1630.1630.0000.0000.0000.000
178A247ILE0-0.043-0.0098.4420.0670.0670.0000.0000.0000.000
179A248THR0-0.023-0.03411.462-0.102-0.1020.0000.0000.0000.000
180A249SER00.005-0.01315.201-0.098-0.0980.0000.0000.0000.000
181A250ASP-1-0.928-0.94314.8160.4990.4990.0000.0000.0000.000
182A251GLY00.0370.00713.794-0.047-0.0470.0000.0000.0000.000
183A252ILE0-0.058-0.02912.9190.1980.1980.0000.0000.0000.000
184A253LYS10.9740.98910.851-1.400-1.4000.0000.0000.0000.000
185A254PHE00.0180.01312.939-0.112-0.1120.0000.0000.0000.000
186A255PRO00.0110.01613.6000.1310.1310.0000.0000.0000.000
187A256GLN0-0.073-0.04014.808-0.158-0.1580.0000.0000.0000.000
188A257ASP-1-0.852-0.93210.1271.5981.5980.0000.0000.0000.000
189A258GLY0-0.024-0.01511.166-0.190-0.1900.0000.0000.0000.000
190A259THR0-0.038-0.01910.8400.0890.0890.0000.0000.0000.000
191A260LEU00.0370.00710.2540.0460.0460.0000.0000.0000.000
192A261GLU-1-0.856-0.91013.3420.0360.0360.0000.0000.0000.000
193A262PHE00.005-0.00417.175-0.013-0.0130.0000.0000.0000.000
194A263SER0-0.061-0.01917.049-0.039-0.0390.0000.0000.0000.000
195A264ASP-1-0.906-0.96417.757-0.190-0.1900.0000.0000.0000.000
196A265VAL0-0.044-0.01415.858-0.005-0.0050.0000.0000.0000.000
197A266THR0-0.025-0.00818.3450.0420.0420.0000.0000.0000.000
198A267VAL0-0.004-0.00819.329-0.023-0.0230.0000.0000.0000.000
199A268ASP-1-0.850-0.91321.264-0.122-0.1220.0000.0000.0000.000
200A269GLN0-0.055-0.01723.212-0.011-0.0110.0000.0000.0000.000
201A270THR0-0.033-0.01526.663-0.004-0.0040.0000.0000.0000.000
202A271THR0-0.081-0.05122.868-0.011-0.0110.0000.0000.0000.000
203A272GLY00.0510.03121.6780.0040.0040.0000.0000.0000.000
204A273SER0-0.020-0.02118.155-0.037-0.0370.0000.0000.0000.000
205A274ILE00.001-0.00814.7290.0200.0200.0000.0000.0000.000
206A275THR0-0.011-0.01014.988-0.017-0.0170.0000.0000.0000.000
207A276LEU00.0080.00510.529-0.022-0.0220.0000.0000.0000.000
208A277ARG10.8890.93914.532-0.010-0.0100.0000.0000.0000.000
209A278ALA0-0.004-0.00611.945-0.033-0.0330.0000.0000.0000.000
210A279ILE0-0.030-0.02213.967-0.010-0.0100.0000.0000.0000.000
211A280PHE00.0180.00310.8530.0470.0470.0000.0000.0000.000
212A281PRO00.0120.02416.030-0.069-0.0690.0000.0000.0000.000
213A282ASN0-0.043-0.05018.5650.0900.0900.0000.0000.0000.000
214A283PRO00.0730.04820.726-0.034-0.0340.0000.0000.0000.000
215A284ASP-1-0.941-0.96722.5740.3730.3730.0000.0000.0000.000
216A285HIS10.7410.86224.353-0.265-0.2650.0000.0000.0000.000
217A286THR00.0350.01821.543-0.006-0.0060.0000.0000.0000.000
218A287MET0-0.0380.00816.008-0.018-0.0180.0000.0000.0000.000
219A288MET00.0490.01821.155-0.044-0.0440.0000.0000.0000.000
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