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: K2GQ3

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2085191.038709
FMO2-HF: Nuclear repulsion 1999298.849779
FMO2-HF: Total energy -85892.18893
FMO2-MP2: Total energy -86144.609823


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.
-14.427-12.5717.76-4.856-4.76-0.034
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 : -0.030 / q_NPA : -0.031
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-1-0.850-0.9043.8724.2715.496-0.011-0.529-0.6860.000
4A56LEU00.0230.0196.546-0.711-0.7110.0000.0000.0000.000
5A57PRO0-0.028-0.0109.7870.2500.2500.0000.0000.0000.000
6A58GLY00.0660.01613.207-0.076-0.0760.0000.0000.0000.000
7A59ARG10.8230.90914.382-0.276-0.2760.0000.0000.0000.000
8A60THR00.009-0.00317.287-0.023-0.0230.0000.0000.0000.000
9A61SER0-0.054-0.05118.601-0.048-0.0480.0000.0000.0000.000
10A62ALA00.011-0.00721.1830.0190.0190.0000.0000.0000.000
11A63TYR00.0060.02221.831-0.024-0.0240.0000.0000.0000.000
12A64ARG10.9170.94524.177-0.151-0.1510.0000.0000.0000.000
13A65ILE00.004-0.00527.4300.0180.0180.0000.0000.0000.000
14A66ALA00.0020.01130.507-0.013-0.0130.0000.0000.0000.000
15A67GLU-1-0.828-0.88434.3110.1010.1010.0000.0000.0000.000
16A68VAL0-0.019-0.00637.292-0.005-0.0050.0000.0000.0000.000
17A69ARG10.7950.85539.995-0.082-0.0820.0000.0000.0000.000
18A70PRO0-0.0020.01543.2210.0000.0000.0000.0000.0000.000
19A71GLN00.016-0.00345.0050.0000.0000.0000.0000.0000.000
20A72VAL0-0.014-0.00348.322-0.004-0.0040.0000.0000.0000.000
21A73SER00.0330.01251.2400.0030.0030.0000.0000.0000.000
22A74GLY00.0150.01553.618-0.002-0.0020.0000.0000.0000.000
23A75ILE00.0260.01953.7760.0010.0010.0000.0000.0000.000
24A76ILE0-0.021-0.00547.8290.0000.0000.0000.0000.0000.000
25A77LEU00.0030.01351.2550.0010.0010.0000.0000.0000.000
26A78LYS10.8580.91547.222-0.097-0.0970.0000.0000.0000.000
27A79ARG10.8380.91442.595-0.117-0.1170.0000.0000.0000.000
28A80ASN0-0.058-0.03644.117-0.001-0.0010.0000.0000.0000.000
29A81PHE00.0110.02038.6280.0030.0030.0000.0000.0000.000
30A82LYS10.9720.98938.056-0.155-0.1550.0000.0000.0000.000
31A83GLU-1-0.783-0.87437.1900.1410.1410.0000.0000.0000.000
32A84GLY00.0160.02132.9360.0050.0050.0000.0000.0000.000
33A85SER0-0.064-0.04232.3590.0130.0130.0000.0000.0000.000
34A86ASP-1-0.813-0.90129.4000.2540.2540.0000.0000.0000.000
35A87ILE0-0.041-0.02532.512-0.012-0.0120.0000.0000.0000.000
36A88GLU-1-0.815-0.88533.6090.1610.1610.0000.0000.0000.000
37A89ALA0-0.0030.00335.436-0.006-0.0060.0000.0000.0000.000
38A90GLY0-0.0030.00237.056-0.003-0.0030.0000.0000.0000.000
39A91VAL0-0.008-0.01439.493-0.007-0.0070.0000.0000.0000.000
40A92SER0-0.011-0.00741.7180.0000.0000.0000.0000.0000.000
41A93LEU00.0080.00538.5810.0030.0030.0000.0000.0000.000
42A94TYR00.012-0.03442.0890.0040.0040.0000.0000.0000.000
43A95GLN0-0.073-0.02546.0960.0000.0000.0000.0000.0000.000
44A96ILE0-0.0020.00249.3880.0000.0000.0000.0000.0000.000
45A97ASP-1-0.856-0.93451.9040.0560.0560.0000.0000.0000.000
46A98PRO0-0.0010.00454.885-0.002-0.0020.0000.0000.0000.000
47A99ALA00.0140.01256.675-0.003-0.0030.0000.0000.0000.000
48A100THR00.0280.00359.688-0.002-0.0020.0000.0000.0000.000
49A101TYR00.011-0.00355.942-0.003-0.0030.0000.0000.0000.000
50A102GLN0-0.033-0.03359.5220.0000.0000.0000.0000.0000.000
51A103ALA00.0450.02460.937-0.002-0.0020.0000.0000.0000.000
52A104THR0-0.027-0.01261.662-0.002-0.0020.0000.0000.0000.000
53A105TYR00.007-0.01160.367-0.002-0.0020.0000.0000.0000.000
54A106ASP-1-0.818-0.89162.5830.0390.0390.0000.0000.0000.000
55A107SER0-0.026-0.01865.701-0.002-0.0020.0000.0000.0000.000
56A108ALA00.0170.01464.446-0.002-0.0020.0000.0000.0000.000
57A109LYS10.8430.90663.289-0.040-0.0400.0000.0000.0000.000
58A110GLY00.0320.02267.132-0.001-0.0010.0000.0000.0000.000
59A111ASP-1-0.875-0.93969.6830.0260.0260.0000.0000.0000.000
60A112LEU0-0.017-0.00766.154-0.001-0.0010.0000.0000.0000.000
61A113ALA0-0.027-0.01169.910-0.001-0.0010.0000.0000.0000.000
62A114LYS10.8770.92672.317-0.027-0.0270.0000.0000.0000.000
63A115ALA00.0070.01372.156-0.001-0.0010.0000.0000.0000.000
64A116GLN00.039-0.00269.458-0.001-0.0010.0000.0000.0000.000
65A117ALA0-0.0070.01074.075-0.001-0.0010.0000.0000.0000.000
66A118ALA00.0080.00177.362-0.001-0.0010.0000.0000.0000.000
67A119ALA00.0320.00875.544-0.001-0.0010.0000.0000.0000.000
68A120ASN0-0.011-0.00277.419-0.001-0.0010.0000.0000.0000.000
69A121ILE0-0.018-0.01278.879-0.001-0.0010.0000.0000.0000.000
70A122ALA00.0270.01880.489-0.001-0.0010.0000.0000.0000.000
71A123GLN00.0130.00378.900-0.001-0.0010.0000.0000.0000.000
72A124LEU00.0060.00081.293-0.001-0.0010.0000.0000.0000.000
73A125THR0-0.045-0.00384.0660.0000.0000.0000.0000.0000.000
74A126VAL00.0730.05182.888-0.001-0.0010.0000.0000.0000.000
75A127ASN0-0.008-0.00881.705-0.001-0.0010.0000.0000.0000.000
76A128ARG10.8290.89485.764-0.014-0.0140.0000.0000.0000.000
77A129TYR00.0620.02189.0100.0000.0000.0000.0000.0000.000
78A130GLN00.0690.03584.3450.0000.0000.0000.0000.0000.000
79A131LYS10.8700.94088.516-0.011-0.0110.0000.0000.0000.000
80A132LEU00.0160.01991.4400.0000.0000.0000.0000.0000.000
81A133LEU00.0160.03389.4060.0000.0000.0000.0000.0000.000
82A134GLY0-0.0160.00093.8720.0000.0000.0000.0000.0000.000
83A135THR0-0.058-0.04496.8580.0000.0000.0000.0000.0000.000
84A136GLN0-0.011-0.01699.1490.0000.0000.0000.0000.0000.000
85A137TYR0-0.036-0.02898.2050.0000.0000.0000.0000.0000.000
86A138ILE0-0.0250.00892.9160.0000.0000.0000.0000.0000.000
87A139SER0-0.027-0.03495.508-0.001-0.0010.0000.0000.0000.000
88A140LYS10.8540.87889.129-0.007-0.0070.0000.0000.0000.000
89A141GLN00.0260.01690.9610.0000.0000.0000.0000.0000.000
90A142GLU-1-0.786-0.85290.7070.0100.0100.0000.0000.0000.000
91A143TYR0-0.030-0.02885.2730.0000.0000.0000.0000.0000.000
92A144ASP-1-0.816-0.89886.7140.0080.0080.0000.0000.0000.000
93A145GLN0-0.049-0.02285.7750.0000.0000.0000.0000.0000.000
94A146ALA00.0190.01085.4770.0010.0010.0000.0000.0000.000
95A147LEU0-0.012-0.01982.4820.0010.0010.0000.0000.0000.000
96A148ALA0-0.0120.00881.2920.0000.0000.0000.0000.0000.000
97A149ASP-1-0.869-0.92680.8100.0140.0140.0000.0000.0000.000
98A150ALA0-0.002-0.01079.8510.0010.0010.0000.0000.0000.000
99A151GLN0-0.0140.00074.5330.0010.0010.0000.0000.0000.000
100A152GLN00.0280.01575.9590.0010.0010.0000.0000.0000.000
101A153ALA0-0.0020.00075.9480.0010.0010.0000.0000.0000.000
102A154ASN0-0.020-0.03473.4460.0020.0020.0000.0000.0000.000
103A155ALA0-0.0050.02071.7030.0010.0010.0000.0000.0000.000
104A156ALA00.0140.01270.8460.0010.0010.0000.0000.0000.000
105A157VAL0-0.021-0.02169.7290.0010.0010.0000.0000.0000.000
106A158THR0-0.051-0.03166.6390.0010.0010.0000.0000.0000.000
107A159ALA00.0110.00466.2330.0010.0010.0000.0000.0000.000
108A160ALA00.0150.00666.0310.0010.0010.0000.0000.0000.000
109A161LYS10.9010.95164.082-0.021-0.0210.0000.0000.0000.000
110A162ALA00.0380.03161.6970.0020.0020.0000.0000.0000.000
111A163ALA00.0090.01861.2650.0020.0020.0000.0000.0000.000
112A164VAL0-0.004-0.01061.8220.0020.0020.0000.0000.0000.000
113A165GLU-1-0.808-0.85255.7580.0390.0390.0000.0000.0000.000
114A166THR0-0.008-0.01657.4850.0020.0020.0000.0000.0000.000
115A167ALA00.0010.00757.4820.0020.0020.0000.0000.0000.000
116A168ARG10.8070.86554.155-0.039-0.0390.0000.0000.0000.000
117A169ILE0-0.004-0.00251.1080.0030.0030.0000.0000.0000.000
118A170ASN0-0.037-0.03052.7720.0040.0040.0000.0000.0000.000
119A171LEU00.0220.01153.7950.0030.0030.0000.0000.0000.000
120A172ALA0-0.041-0.00651.0900.0030.0030.0000.0000.0000.000
121A173TYR00.002-0.01546.1350.0030.0030.0000.0000.0000.000
122A174THR0-0.045-0.01949.3170.0030.0030.0000.0000.0000.000
123A175LYS10.8690.96544.740-0.077-0.0770.0000.0000.0000.000
124A176VAL00.0360.01743.5470.0000.0000.0000.0000.0000.000
125A177THR0-0.045-0.02541.5540.0040.0040.0000.0000.0000.000
126A178SER00.0430.00435.407-0.003-0.0030.0000.0000.0000.000
127A179PRO0-0.006-0.01436.348-0.001-0.0010.0000.0000.0000.000
128A180ILE0-0.023-0.00630.737-0.003-0.0030.0000.0000.0000.000
129A181SER00.0470.00431.499-0.004-0.0040.0000.0000.0000.000
130A182GLY0-0.031-0.02129.6240.0050.0050.0000.0000.0000.000
131A183ARG10.8010.89727.244-0.272-0.2720.0000.0000.0000.000
132A184ILE0-0.0200.00130.672-0.006-0.0060.0000.0000.0000.000
133A185GLY00.0170.00533.4310.0110.0110.0000.0000.0000.000
134A186LYS10.9460.94734.200-0.171-0.1710.0000.0000.0000.000
135A187SER0-0.045-0.01737.374-0.004-0.0040.0000.0000.0000.000
136A188ASN0-0.073-0.04239.2280.0050.0050.0000.0000.0000.000
137A189VAL0-0.024-0.01542.490-0.006-0.0060.0000.0000.0000.000
138A190THR00.0020.01045.5050.0030.0030.0000.0000.0000.000
139A191GLU-1-0.799-0.90347.6940.0960.0960.0000.0000.0000.000
140A192GLY0-0.002-0.00350.0910.0000.0000.0000.0000.0000.000
141A193ALA0-0.0150.00950.113-0.003-0.0030.0000.0000.0000.000
142A194LEU0-0.020-0.01352.1950.0000.0000.0000.0000.0000.000
143A195VAL0-0.011-0.00648.4330.0020.0020.0000.0000.0000.000
144A196GLN00.009-0.00250.292-0.004-0.0040.0000.0000.0000.000
145A197ASN00.0080.00049.6710.0040.0040.0000.0000.0000.000
146A198GLY00.0390.02247.438-0.003-0.0030.0000.0000.0000.000
147A199GLN0-0.032-0.00945.771-0.003-0.0030.0000.0000.0000.000
148A200ALA00.0430.01545.1470.0030.0030.0000.0000.0000.000
149A201THR00.0150.01542.3870.0020.0020.0000.0000.0000.000
150A202ALA00.0280.02039.571-0.003-0.0030.0000.0000.0000.000
151A203LEU00.0230.01441.6940.0020.0020.0000.0000.0000.000
152A204ALA00.0460.03038.0950.0040.0040.0000.0000.0000.000
153A205THR00.0030.00633.085-0.007-0.0070.0000.0000.0000.000
154A206VAL0-0.0010.00332.4570.0080.0080.0000.0000.0000.000
155A207GLN00.004-0.01027.4220.0060.0060.0000.0000.0000.000
156A208GLN00.008-0.00625.773-0.008-0.0080.0000.0000.0000.000
157A209LEU0-0.038-0.01624.1920.0050.0050.0000.0000.0000.000
158A210ASP-1-0.798-0.87622.5260.3600.3600.0000.0000.0000.000
159A211PRO00.0350.01820.196-0.034-0.0340.0000.0000.0000.000
160A212ILE0-0.079-0.02917.746-0.024-0.0240.0000.0000.0000.000
161A213TYR0-0.044-0.04617.4970.0250.0250.0000.0000.0000.000
162A214VAL0-0.022-0.02813.0590.0520.0520.0000.0000.0000.000
163A215ASP-1-0.796-0.83914.4940.2080.2080.0000.0000.0000.000
164A216VAL0-0.001-0.01210.0630.0970.0970.0000.0000.0000.000
165A217THR0-0.070-0.04113.173-0.101-0.1010.0000.0000.0000.000
166A218GLN00.011-0.01910.3860.0360.0360.0000.0000.0000.000
167A219SER0-0.005-0.03313.6820.0060.0060.0000.0000.0000.000
168A220SER00.009-0.04115.561-0.072-0.0720.0000.0000.0000.000
169A221ASN0-0.068-0.02315.615-0.042-0.0420.0000.0000.0000.000
170A222ASP-1-0.833-0.87812.072-0.436-0.4360.0000.0000.0000.000
171A223MET0-0.0760.00512.002-0.135-0.1350.0000.0000.0000.000
172A241LYS10.9690.95612.9820.2750.2750.0000.0000.0000.000
173A242ALA00.0020.0178.6340.0030.0030.0000.0000.0000.000
174A243LYS10.8360.9056.535-0.448-0.4480.0000.0000.0000.000
175A244VAL00.0150.0106.515-0.179-0.1790.0000.0000.0000.000
176A245SER0-0.0050.0046.2290.2440.2440.0000.0000.0000.000
177A246LEU00.0050.0057.9960.3030.3030.0000.0000.0000.000
178A247ILE0-0.036-0.0148.527-0.047-0.0470.0000.0000.0000.000
179A248THR00.001-0.01711.492-0.108-0.1080.0000.0000.0000.000
180A249SER00.023-0.00215.135-0.138-0.1380.0000.0000.0000.000
181A250ASP-1-0.897-0.92714.1810.8680.8680.0000.0000.0000.000
182A251GLY00.0710.04113.831-0.085-0.0850.0000.0000.0000.000
183A252ILE0-0.029-0.01013.7090.1590.1590.0000.0000.0000.000
184A253LYS10.9140.94610.666-1.515-1.5150.0000.0000.0000.000
185A254PHE00.0130.01512.637-0.175-0.1750.0000.0000.0000.000
186A255PRO0-0.0020.00812.7910.1470.1470.0000.0000.0000.000
187A256GLN0-0.058-0.04213.824-0.196-0.1960.0000.0000.0000.000
188A257ASP-1-0.867-0.9349.2321.6091.6090.0000.0000.0000.000
189A258GLY00.011-0.00910.769-0.165-0.1650.0000.0000.0000.000
190A259THR0-0.058-0.02610.8070.0290.0290.0000.0000.0000.000
191A260LEU00.0370.00711.1070.0620.0620.0000.0000.0000.000
192A261GLU-1-0.827-0.89313.5210.1240.1240.0000.0000.0000.000
193A262PHE00.003-0.00617.306-0.015-0.0150.0000.0000.0000.000
194A263SER0-0.062-0.03317.121-0.030-0.0300.0000.0000.0000.000
195A264ASP-1-0.885-0.93218.237-0.128-0.1280.0000.0000.0000.000
196A265VAL0-0.055-0.02716.2670.0070.0070.0000.0000.0000.000
197A266THR0-0.036-0.02118.7220.0340.0340.0000.0000.0000.000
198A267VAL0-0.0020.00119.512-0.018-0.0180.0000.0000.0000.000
199A268ASP-1-0.800-0.86621.852-0.033-0.0330.0000.0000.0000.000
200A269GLN0-0.040-0.02023.940-0.016-0.0160.0000.0000.0000.000
201A270THR0-0.062-0.02826.915-0.006-0.0060.0000.0000.0000.000
202A271THR0-0.062-0.04623.164-0.010-0.0100.0000.0000.0000.000
203A272GLY00.0710.04122.1480.0020.0020.0000.0000.0000.000
204A273SER0-0.041-0.02118.703-0.042-0.0420.0000.0000.0000.000
205A274ILE00.0280.01115.3890.0110.0110.0000.0000.0000.000
206A275THR0-0.020-0.00115.7350.0170.0170.0000.0000.0000.000
207A276LEU00.002-0.00810.756-0.041-0.0410.0000.0000.0000.000
208A277ARG10.8750.92314.583-0.088-0.0880.0000.0000.0000.000
209A278ALA00.0070.00911.745-0.045-0.0450.0000.0000.0000.000
210A279ILE0-0.028-0.01713.730-0.008-0.0080.0000.0000.0000.000
211A280PHE00.0170.01010.3500.0420.0420.0000.0000.0000.000
212A281PRO00.0120.02315.903-0.065-0.0650.0000.0000.0000.000
213A282ASN0-0.029-0.04718.0820.1030.1030.0000.0000.0000.000
214A283PRO00.0620.05520.230-0.039-0.0390.0000.0000.0000.000
215A284ASP-1-0.937-0.97621.5270.4190.4190.0000.0000.0000.000
216A285HIS10.7610.87623.756-0.305-0.3050.0000.0000.0000.000
217A286THR00.0440.02521.321-0.007-0.0070.0000.0000.0000.000
218A287MET0-0.0340.00115.611-0.016-0.0160.0000.0000.0000.000
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