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: RY848

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2080351.784232
FMO2-HF: Nuclear repulsion 1994461.556926
FMO2-HF: Total energy -85890.227306
FMO2-MP2: Total energy -86142.669363


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.
-14.962-20.51722.705-9.808-7.341-0.054
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 : -0.051 / q_NPA : -0.026
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-1-0.983-1.0033.858-0.8320.943-0.020-0.909-0.8450.002
4A56LEU00.0470.0296.3380.0400.0400.0000.0000.0000.000
5A57PRO0-0.036-0.0139.5570.2580.2580.0000.0000.0000.000
6A58GLY00.0650.02512.975-0.093-0.0930.0000.0000.0000.000
7A59ARG10.9080.96714.0950.3310.3310.0000.0000.0000.000
8A60THR00.0360.02316.870-0.037-0.0370.0000.0000.0000.000
9A61SER0-0.034-0.02718.4000.0130.0130.0000.0000.0000.000
10A62ALA00.0410.00721.1310.0080.0080.0000.0000.0000.000
11A63TYR00.0250.04721.749-0.004-0.0040.0000.0000.0000.000
12A64ARG10.9200.94423.8910.0710.0710.0000.0000.0000.000
13A65ILE00.0060.00627.6780.0110.0110.0000.0000.0000.000
14A66ALA0-0.0080.00230.230-0.003-0.0030.0000.0000.0000.000
15A67GLU-1-0.855-0.91533.971-0.067-0.0670.0000.0000.0000.000
16A68VAL0-0.021-0.01236.8820.0020.0020.0000.0000.0000.000
17A69ARG10.7970.86039.5950.0610.0610.0000.0000.0000.000
18A70PRO00.0110.02442.9860.0020.0020.0000.0000.0000.000
19A71GLN00.0350.01245.347-0.004-0.0040.0000.0000.0000.000
20A72VAL0-0.030-0.02048.3090.0000.0000.0000.0000.0000.000
21A73SER00.0480.03750.945-0.001-0.0010.0000.0000.0000.000
22A74GLY00.0370.05653.3230.0020.0020.0000.0000.0000.000
23A75ILE00.0320.02653.372-0.002-0.0020.0000.0000.0000.000
24A76ILE0-0.039-0.00648.0520.0010.0010.0000.0000.0000.000
25A77LEU00.0060.00451.2280.0010.0010.0000.0000.0000.000
26A78LYS10.9450.97347.532-0.011-0.0110.0000.0000.0000.000
27A79ARG10.9210.98442.060-0.005-0.0050.0000.0000.0000.000
28A80ASN0-0.085-0.05843.9690.0050.0050.0000.0000.0000.000
29A81PHE00.0330.02938.8300.0040.0040.0000.0000.0000.000
30A82LYS10.9680.97138.543-0.040-0.0400.0000.0000.0000.000
31A83GLU-1-0.873-0.92037.539-0.005-0.0050.0000.0000.0000.000
32A84GLY00.0020.00533.2040.0040.0040.0000.0000.0000.000
33A85SER0-0.086-0.06032.6420.0080.0080.0000.0000.0000.000
34A86ASP-1-0.840-0.94329.9480.0340.0340.0000.0000.0000.000
35A87ILE0-0.044-0.02732.8480.0020.0020.0000.0000.0000.000
36A88GLU-1-0.865-0.94133.8010.0250.0250.0000.0000.0000.000
37A89ALA0-0.008-0.01735.195-0.003-0.0030.0000.0000.0000.000
38A90GLY0-0.0100.00036.9570.0040.0040.0000.0000.0000.000
39A91VAL0-0.033-0.01339.8960.0020.0020.0000.0000.0000.000
40A92SER0-0.050-0.02641.683-0.005-0.0050.0000.0000.0000.000
41A93LEU00.0110.00938.7300.0030.0030.0000.0000.0000.000
42A94TYR00.033-0.01841.9280.0020.0020.0000.0000.0000.000
43A95GLN0-0.069-0.01945.9480.0010.0010.0000.0000.0000.000
44A96ILE00.0080.00549.0970.0000.0000.0000.0000.0000.000
45A97ASP-1-0.877-0.95451.715-0.005-0.0050.0000.0000.0000.000
46A98PRO00.0090.01254.894-0.002-0.0020.0000.0000.0000.000
47A99ALA00.0070.01956.5720.0000.0000.0000.0000.0000.000
48A100THR00.030-0.00159.9050.0000.0000.0000.0000.0000.000
49A101TYR0-0.013-0.05655.286-0.001-0.0010.0000.0000.0000.000
50A102GLN0-0.004-0.00959.2340.0000.0000.0000.0000.0000.000
51A103ALA00.0330.02360.5280.0000.0000.0000.0000.0000.000
52A104THR0-0.013-0.00961.4090.0000.0000.0000.0000.0000.000
53A105TYR0-0.012-0.00459.9930.0000.0000.0000.0000.0000.000
54A106ASP-1-0.891-0.95762.307-0.005-0.0050.0000.0000.0000.000
55A107SER0-0.049-0.02465.4260.0000.0000.0000.0000.0000.000
56A108ALA00.0450.02764.0060.0000.0000.0000.0000.0000.000
57A109LYS10.9030.94361.9420.0060.0060.0000.0000.0000.000
58A110GLY00.0000.00966.6340.0010.0010.0000.0000.0000.000
59A111ASP-1-0.918-0.96469.118-0.012-0.0120.0000.0000.0000.000
60A112LEU0-0.041-0.01965.8600.0000.0000.0000.0000.0000.000
61A113ALA0-0.011-0.00869.5420.0000.0000.0000.0000.0000.000
62A114LYS10.9600.98271.9340.0090.0090.0000.0000.0000.000
63A115ALA00.0420.03271.7770.0000.0000.0000.0000.0000.000
64A116GLN00.008-0.00769.016-0.001-0.0010.0000.0000.0000.000
65A117ALA0-0.0300.00473.6850.0000.0000.0000.0000.0000.000
66A118ALA0-0.012-0.01277.0350.0000.0000.0000.0000.0000.000
67A119ALA00.0330.00375.1040.0000.0000.0000.0000.0000.000
68A120ASN0-0.018-0.01376.9770.0000.0000.0000.0000.0000.000
69A121ILE0-0.006-0.01478.4480.0000.0000.0000.0000.0000.000
70A122ALA00.0260.01380.2220.0000.0000.0000.0000.0000.000
71A123GLN0-0.0190.00378.351-0.001-0.0010.0000.0000.0000.000
72A124LEU0-0.035-0.03380.8650.0000.0000.0000.0000.0000.000
73A125THR0-0.060-0.03783.7010.0000.0000.0000.0000.0000.000
74A126VAL00.0980.06982.3550.0000.0000.0000.0000.0000.000
75A127ASN00.0240.00181.5330.0000.0000.0000.0000.0000.000
76A128ARG10.8780.94085.5500.0070.0070.0000.0000.0000.000
77A129TYR00.0430.01888.4260.0000.0000.0000.0000.0000.000
78A130GLN00.0340.01984.6230.0000.0000.0000.0000.0000.000
79A131LYS10.8810.94388.2540.0060.0060.0000.0000.0000.000
80A132LEU00.0170.01290.9080.0000.0000.0000.0000.0000.000
81A133LEU00.0050.02689.1030.0000.0000.0000.0000.0000.000
82A134GLY0-0.017-0.00193.4990.0000.0000.0000.0000.0000.000
83A135THR0-0.046-0.03296.5680.0000.0000.0000.0000.0000.000
84A136GLN0-0.028-0.04498.7790.0000.0000.0000.0000.0000.000
85A137TYR0-0.028-0.01297.9520.0000.0000.0000.0000.0000.000
86A138ILE0-0.0200.02692.8050.0000.0000.0000.0000.0000.000
87A139SER0-0.0070.00195.1890.0000.0000.0000.0000.0000.000
88A140LYS10.9640.95889.7320.0140.0140.0000.0000.0000.000
89A141GLN00.0170.01590.6620.0000.0000.0000.0000.0000.000
90A142GLU-1-0.803-0.89690.444-0.010-0.0100.0000.0000.0000.000
91A143TYR0-0.030-0.02184.9100.0000.0000.0000.0000.0000.000
92A144ASP-1-0.864-0.94986.439-0.014-0.0140.0000.0000.0000.000
93A145GLN0-0.063-0.01685.655-0.001-0.0010.0000.0000.0000.000
94A146ALA00.003-0.00385.4570.0000.0000.0000.0000.0000.000
95A147LEU0-0.019-0.02982.2520.0000.0000.0000.0000.0000.000
96A148ALA0-0.0140.00881.125-0.001-0.0010.0000.0000.0000.000
97A149ASP-1-0.863-0.92080.630-0.013-0.0130.0000.0000.0000.000
98A150ALA00.0030.00179.3600.0000.0000.0000.0000.0000.000
99A151GLN0-0.031-0.01574.1740.0000.0000.0000.0000.0000.000
100A152GLN00.0420.02675.709-0.001-0.0010.0000.0000.0000.000
101A153ALA0-0.017-0.02075.7540.0000.0000.0000.0000.0000.000
102A154ASN0-0.003-0.02373.3020.0000.0000.0000.0000.0000.000
103A155ALA0-0.0220.00571.404-0.001-0.0010.0000.0000.0000.000
104A156ALA0-0.0040.01170.541-0.001-0.0010.0000.0000.0000.000
105A157VAL00.000-0.00769.3770.0000.0000.0000.0000.0000.000
106A158THR0-0.044-0.02166.2150.0000.0000.0000.0000.0000.000
107A159ALA00.007-0.00366.2020.0000.0000.0000.0000.0000.000
108A160ALA00.0300.00865.8400.0000.0000.0000.0000.0000.000
109A161LYS10.9330.96463.7280.0140.0140.0000.0000.0000.000
110A162ALA00.0220.01361.5080.0000.0000.0000.0000.0000.000
111A163ALA00.0010.01161.077-0.001-0.0010.0000.0000.0000.000
112A164VAL0-0.010-0.00661.1770.0000.0000.0000.0000.0000.000
113A165GLU-1-0.845-0.91355.258-0.018-0.0180.0000.0000.0000.000
114A166THR00.0010.00157.152-0.001-0.0010.0000.0000.0000.000
115A167ALA00.004-0.00456.8580.0000.0000.0000.0000.0000.000
116A168ARG10.8470.91453.2350.0150.0150.0000.0000.0000.000
117A169ILE0-0.023-0.01251.5980.0010.0010.0000.0000.0000.000
118A170ASN00.0100.00252.491-0.001-0.0010.0000.0000.0000.000
119A171LEU00.0120.01853.6880.0000.0000.0000.0000.0000.000
120A172ALA0-0.017-0.01650.6300.0010.0010.0000.0000.0000.000
121A173TYR0-0.021-0.01245.7230.0000.0000.0000.0000.0000.000
122A174THR0-0.042-0.00749.3060.0000.0000.0000.0000.0000.000
123A175LYS10.9370.97845.8150.0030.0030.0000.0000.0000.000
124A176VAL00.0290.01143.443-0.002-0.0020.0000.0000.0000.000
125A177THR0-0.019-0.01341.3920.0020.0020.0000.0000.0000.000
126A178SER00.009-0.01135.519-0.007-0.0070.0000.0000.0000.000
127A179PRO00.0240.00336.1510.0040.0040.0000.0000.0000.000
128A180ILE0-0.0070.00230.6260.0000.0000.0000.0000.0000.000
129A181SER00.0420.04031.7340.0000.0000.0000.0000.0000.000
130A182GLY0-0.029-0.02029.826-0.007-0.0070.0000.0000.0000.000
131A183ARG10.9050.99228.406-0.028-0.0280.0000.0000.0000.000
132A184ILE00.0000.00730.929-0.012-0.0120.0000.0000.0000.000
133A185GLY00.0130.00933.6970.0060.0060.0000.0000.0000.000
134A186LYS10.9530.95534.4030.0180.0180.0000.0000.0000.000
135A187SER0-0.045-0.00837.619-0.005-0.0050.0000.0000.0000.000
136A188ASN0-0.089-0.06438.8910.0020.0020.0000.0000.0000.000
137A189VAL0-0.014-0.00342.282-0.001-0.0010.0000.0000.0000.000
138A190THR00.0100.00745.4900.0020.0020.0000.0000.0000.000
139A191GLU-1-0.884-0.96847.9290.0020.0020.0000.0000.0000.000
140A192GLY00.0220.00949.9900.0000.0000.0000.0000.0000.000
141A193ALA0-0.0300.00549.779-0.001-0.0010.0000.0000.0000.000
142A194LEU00.003-0.00151.8140.0010.0010.0000.0000.0000.000
143A195VAL0-0.022-0.00548.081-0.002-0.0020.0000.0000.0000.000
144A196GLN00.010-0.02350.1350.0030.0030.0000.0000.0000.000
145A197ASN0-0.057-0.03249.411-0.005-0.0050.0000.0000.0000.000
146A198GLY00.0610.03047.5470.0000.0000.0000.0000.0000.000
147A199GLN0-0.0160.01645.903-0.001-0.0010.0000.0000.0000.000
148A200ALA00.0560.01444.735-0.002-0.0020.0000.0000.0000.000
149A201THR0-0.0100.01342.214-0.003-0.0030.0000.0000.0000.000
150A202ALA00.0430.03139.0740.0030.0030.0000.0000.0000.000
151A203LEU0-0.0010.00741.1620.0010.0010.0000.0000.0000.000
152A204ALA00.0380.02737.9260.0040.0040.0000.0000.0000.000
153A205THR00.0130.00932.447-0.004-0.0040.0000.0000.0000.000
154A206VAL0-0.008-0.00131.9020.0060.0060.0000.0000.0000.000
155A207GLN0-0.004-0.01127.364-0.004-0.0040.0000.0000.0000.000
156A208GLN00.0570.02525.8270.0080.0080.0000.0000.0000.000
157A209LEU0-0.027-0.01724.334-0.012-0.0120.0000.0000.0000.000
158A210ASP-1-0.849-0.94722.4100.0700.0700.0000.0000.0000.000
159A211PRO00.0110.01520.581-0.014-0.0140.0000.0000.0000.000
160A212ILE0-0.057-0.00917.629-0.021-0.0210.0000.0000.0000.000
161A213TYR0-0.040-0.05217.372-0.009-0.0090.0000.0000.0000.000
162A214VAL0-0.034-0.03412.7150.0400.0400.0000.0000.0000.000
163A215ASP-1-0.858-0.91214.174-0.500-0.5000.0000.0000.0000.000
164A216VAL0-0.026-0.0209.8790.0210.0210.0000.0000.0000.000
165A217THR0-0.019-0.01112.8070.0030.0030.0000.0000.0000.000
166A218GLN00.0990.05010.198-0.362-0.3620.0000.0000.0000.000
167A219SER00.0080.01013.2060.1610.1610.0000.0000.0000.000
168A220SER00.042-0.01115.139-0.095-0.0950.0000.0000.0000.000
169A221ASN0-0.083-0.04216.675-0.009-0.0090.0000.0000.0000.000
170A222ASP-1-0.902-0.93811.342-1.870-1.8700.0000.0000.0000.000
171A223MET0-0.086-0.01612.104-0.148-0.1480.0000.0000.0000.000
172A241LYS10.9770.96212.2800.0650.0650.0000.0000.0000.000
173A242ALA0-0.0030.0118.2550.1420.1420.0000.0000.0000.000
174A243LYS10.9600.9916.671-1.373-1.3730.0000.0000.0000.000
175A244VAL00.0490.0285.963-0.632-0.6320.0000.0000.0000.000
176A245SER0-0.014-0.0036.4650.4330.4330.0000.0000.0000.000
177A246LEU00.0150.0078.101-0.250-0.2500.0000.0000.0000.000
178A247ILE0-0.062-0.0157.8630.2540.2540.0000.0000.0000.000
179A248THR0-0.024-0.03211.474-0.125-0.1250.0000.0000.0000.000
180A249SER00.006-0.01115.215-0.081-0.0810.0000.0000.0000.000
181A250ASP-1-0.919-0.93914.8780.0450.0450.0000.0000.0000.000
182A251GLY00.0370.00713.7940.0200.0200.0000.0000.0000.000
183A252ILE0-0.080-0.03712.9240.1440.1440.0000.0000.0000.000
184A253LYS10.9900.99310.928-0.991-0.9910.0000.0000.0000.000
185A254PHE00.0260.01112.955-0.005-0.0050.0000.0000.0000.000
186A255PRO0-0.0040.01013.6260.0850.0850.0000.0000.0000.000
187A256GLN0-0.059-0.03014.682-0.045-0.0450.0000.0000.0000.000
188A257ASP-1-0.882-0.93710.9261.1491.1490.0000.0000.0000.000
189A258GLY0-0.019-0.01510.792-0.086-0.0860.0000.0000.0000.000
190A259THR0-0.054-0.02410.4020.0050.0050.0000.0000.0000.000
191A260LEU00.0380.00110.138-0.023-0.0230.0000.0000.0000.000
192A261GLU-1-0.866-0.90512.983-0.190-0.1900.0000.0000.0000.000
193A262PHE00.0160.00316.7910.0520.0520.0000.0000.0000.000
194A263SER0-0.076-0.05216.876-0.069-0.0690.0000.0000.0000.000
195A264ASP-1-0.925-0.95117.616-0.375-0.3750.0000.0000.0000.000
196A265VAL0-0.030-0.00315.819-0.068-0.0680.0000.0000.0000.000
197A266THR0-0.0150.00018.1510.0800.0800.0000.0000.0000.000
198A267VAL0-0.010-0.01419.059-0.063-0.0630.0000.0000.0000.000
199A268ASP-1-0.895-0.93821.047-0.367-0.3670.0000.0000.0000.000
200A269GLN0-0.0050.00622.950-0.010-0.0100.0000.0000.0000.000
201A270THR0-0.039-0.02226.4590.0130.0130.0000.0000.0000.000
202A271THR0-0.074-0.03622.4530.0000.0000.0000.0000.0000.000
203A272GLY00.0380.02321.636-0.005-0.0050.0000.0000.0000.000
204A273SER0-0.015-0.02117.982-0.069-0.0690.0000.0000.0000.000
205A274ILE00.012-0.00214.4780.0620.0620.0000.0000.0000.000
206A275THR0-0.017-0.00114.669-0.098-0.0980.0000.0000.0000.000
207A276LEU0-0.011-0.01510.2090.0220.0220.0000.0000.0000.000
208A277ARG10.9420.97814.1090.3790.3790.0000.0000.0000.000
209A278ALA0-0.024-0.01111.282-0.019-0.0190.0000.0000.0000.000
210A279ILE0-0.026-0.02313.3420.0600.0600.0000.0000.0000.000
211A280PHE00.003-0.00510.2470.0250.0250.0000.0000.0000.000
212A281PRO00.0190.02715.627-0.032-0.0320.0000.0000.0000.000
213A282ASN0-0.050-0.04418.1550.0640.0640.0000.0000.0000.000
214A283PRO00.0560.04020.625-0.017-0.0170.0000.0000.0000.000
215A284ASP-1-0.924-0.96422.7800.2010.2010.0000.0000.0000.000
216A285HIS10.8160.90923.996-0.071-0.0710.0000.0000.0000.000
217A286THR00.0010.00221.224-0.014-0.0140.0000.0000.0000.000
218A287MET0-0.0330.00815.989-0.029-0.0290.0000.0000.0000.000
219A288MET00.0370.00820.740-0.007-0.0070.0000.0000.0000.000
220A289PRO00.0060.01221.290-0.015-0.0150.0000.0000.0000.000
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