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: 6GG3Z

Calculation Name: 3IC6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IC6

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F8U0

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2429046.352621
FMO2-HF: Nuclear repulsion 2344671.216519
FMO2-HF: Total energy -84375.136102
FMO2-MP2: Total energy -84616.999285


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:4:LEU)


Summations of interaction energy for fragment #1(A:4:LEU)
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.
-3.158-0.892-0.014-1.103-1.1480.003
Interaction energy analysis for fragmet #1(A:4:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.002
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].
3A6PRO00.0260.0293.836-1.1011.165-0.014-1.103-1.1480.003
4A7ALA0-0.021-0.0176.2230.3430.3430.0000.0000.0000.000
5A8LEU00.009-0.0068.893-0.088-0.0880.0000.0000.0000.000
6A9PRO00.0240.02011.9830.0590.0590.0000.0000.0000.000
7A10ASP-1-0.845-0.92313.807-0.361-0.3610.0000.0000.0000.000
8A11TYR00.0270.01215.0070.0360.0360.0000.0000.0000.000
9A12LEU00.0090.00216.0100.0310.0310.0000.0000.0000.000
10A13GLY0-0.026-0.01819.3600.0280.0280.0000.0000.0000.000
11A14ASN0-0.130-0.05721.6580.0410.0410.0000.0000.0000.000
12A15ILE00.0070.00321.1660.0130.0130.0000.0000.0000.000
13A16ARG10.8330.89324.5890.1600.1600.0000.0000.0000.000
14A17ILE0-0.015-0.01525.525-0.002-0.0020.0000.0000.0000.000
15A18ILE00.0290.00829.1100.0100.0100.0000.0000.0000.000
16A19LEU0-0.029-0.01632.443-0.001-0.0010.0000.0000.0000.000
17A20THR00.0430.02535.2480.0040.0040.0000.0000.0000.000
18A21ARG10.8630.93838.8210.0900.0900.0000.0000.0000.000
19A22THR0-0.0040.00737.5720.0010.0010.0000.0000.0000.000
20A23SER00.0300.01040.4000.0040.0040.0000.0000.0000.000
21A24HIS00.0310.01039.0490.0020.0020.0000.0000.0000.000
22A25PRO00.0900.05038.592-0.007-0.0070.0000.0000.0000.000
23A26ALA00.0350.03236.514-0.006-0.0060.0000.0000.0000.000
24A27ASN0-0.076-0.06634.535-0.011-0.0110.0000.0000.0000.000
25A28ILE00.0210.02933.377-0.010-0.0100.0000.0000.0000.000
26A29GLY00.0580.03332.096-0.009-0.0090.0000.0000.0000.000
27A30SER0-0.058-0.04630.281-0.009-0.0090.0000.0000.0000.000
28A31ALA0-0.0090.00628.656-0.015-0.0150.0000.0000.0000.000
29A32ALA00.0630.04027.533-0.018-0.0180.0000.0000.0000.000
30A33ARG10.9540.97525.5200.1370.1370.0000.0000.0000.000
31A34ALA0-0.048-0.02624.135-0.021-0.0210.0000.0000.0000.000
32A35MET00.0170.00523.077-0.023-0.0230.0000.0000.0000.000
33A36LYS10.8890.96420.8700.1590.1590.0000.0000.0000.000
34A37THR0-0.095-0.04419.413-0.028-0.0280.0000.0000.0000.000
35A38MET0-0.058-0.00918.129-0.065-0.0650.0000.0000.0000.000
36A39GLY00.0140.00317.332-0.032-0.0320.0000.0000.0000.000
37A40LEU0-0.011-0.00718.2670.0060.0060.0000.0000.0000.000
38A41HIS00.021-0.01019.9900.0330.0330.0000.0000.0000.000
39A42ARG10.9130.97023.7430.1980.1980.0000.0000.0000.000
40A43LEU00.0320.02126.786-0.006-0.0060.0000.0000.0000.000
41A44THR00.0220.01729.8830.0040.0040.0000.0000.0000.000
42A45ILE0-0.056-0.03233.392-0.003-0.0030.0000.0000.0000.000
43A46VAL00.0520.02436.4170.0050.0050.0000.0000.0000.000
44A47THR0-0.050-0.02339.4310.0020.0020.0000.0000.0000.000
45A48PRO0-0.0040.01040.4380.0000.0000.0000.0000.0000.000
46A49ASN0-0.030-0.03542.2680.0030.0030.0000.0000.0000.000
47A50LEU0-0.0110.00040.3820.0000.0000.0000.0000.0000.000
48A51MET0-0.041-0.02542.8760.0040.0040.0000.0000.0000.000
49A52ALA00.0210.00845.462-0.002-0.0020.0000.0000.0000.000
50A53THR0-0.088-0.07142.7300.0000.0000.0000.0000.0000.000
51A54PRO00.004-0.02044.8380.0020.0020.0000.0000.0000.000
52A55MET0-0.043-0.00938.5740.0020.0020.0000.0000.0000.000
53A56THR0-0.047-0.02742.6940.0000.0000.0000.0000.0000.000
54A57GLU-1-0.878-0.93745.392-0.047-0.0470.0000.0000.0000.000
55A58ASN0-0.085-0.05348.4030.0010.0010.0000.0000.0000.000
56A59PRO0-0.0040.01445.768-0.001-0.0010.0000.0000.0000.000
57A60PRO00.0000.01743.1880.0030.0030.0000.0000.0000.000
58A61VAL0-0.006-0.01446.309-0.002-0.0020.0000.0000.0000.000
59A62PHE00.000-0.00443.0090.0000.0000.0000.0000.0000.000
60A63ASN00.023-0.00546.6110.0010.0010.0000.0000.0000.000
61A64PRO0-0.037-0.02046.763-0.001-0.0010.0000.0000.0000.000
62A65ASP-1-0.885-0.93647.511-0.058-0.0580.0000.0000.0000.000
63A66ASP-1-0.949-0.97547.866-0.056-0.0560.0000.0000.0000.000
64A67VAL00.0170.00641.6130.0000.0000.0000.0000.0000.000
65A68GLN0-0.068-0.03742.927-0.005-0.0050.0000.0000.0000.000
66A69SER0-0.0100.00443.5930.0010.0010.0000.0000.0000.000
67A70PHE0-0.074-0.03640.2280.0010.0010.0000.0000.0000.000
68A71ALA00.0380.02840.679-0.003-0.0030.0000.0000.0000.000
69A72LEU0-0.011-0.01835.6420.0010.0010.0000.0000.0000.000
70A73PRO00.0310.01039.6120.0030.0030.0000.0000.0000.000
71A74GLU-1-0.817-0.92638.501-0.071-0.0710.0000.0000.0000.000
72A75GLU-1-0.802-0.87037.807-0.080-0.0800.0000.0000.0000.000
73A76SER0-0.058-0.05235.641-0.003-0.0030.0000.0000.0000.000
74A77PHE00.035-0.00133.263-0.009-0.0090.0000.0000.0000.000
75A78ILE0-0.046-0.00533.052-0.004-0.0040.0000.0000.0000.000
76A79LEU0-0.027-0.02432.793-0.005-0.0050.0000.0000.0000.000
77A80ALA0-0.0150.01029.627-0.010-0.0100.0000.0000.0000.000
78A81SER0-0.044-0.02227.416-0.013-0.0130.0000.0000.0000.000
79A82GLY0-0.028-0.01525.4100.0060.0060.0000.0000.0000.000
80A83ALA0-0.059-0.03625.059-0.012-0.0120.0000.0000.0000.000
81A84ALA00.0380.01826.265-0.001-0.0010.0000.0000.0000.000
82A85ASP-1-0.834-0.92224.502-0.164-0.1640.0000.0000.0000.000
83A86VAL00.0480.01524.9880.0010.0010.0000.0000.0000.000
84A87LEU0-0.051-0.02427.6770.0020.0020.0000.0000.0000.000
85A88HIS0-0.028-0.00930.9070.0060.0060.0000.0000.0000.000
86A89ASN0-0.093-0.04527.928-0.002-0.0020.0000.0000.0000.000
87A90ALA0-0.0240.00430.671-0.006-0.0060.0000.0000.0000.000
88A91GLU-1-0.941-0.95732.271-0.121-0.1210.0000.0000.0000.000
89A92ILE0-0.018-0.01134.623-0.004-0.0040.0000.0000.0000.000
90A93VAL00.0220.01137.7130.0040.0040.0000.0000.0000.000
91A94ALA00.0310.00540.0810.0000.0000.0000.0000.0000.000
92A95THR0-0.051-0.02742.4200.0000.0000.0000.0000.0000.000
93A96LEU00.023-0.00736.972-0.003-0.0030.0000.0000.0000.000
94A97ASP-1-0.817-0.91638.760-0.099-0.0990.0000.0000.0000.000
95A98GLU-1-0.817-0.90739.440-0.090-0.0900.0000.0000.0000.000
96A99ALA0-0.029-0.00735.692-0.004-0.0040.0000.0000.0000.000
97A100LEU0-0.031-0.02034.266-0.010-0.0100.0000.0000.0000.000
98A101ALA00.0290.04435.411-0.005-0.0050.0000.0000.0000.000
99A102ASP-1-0.806-0.88332.728-0.144-0.1440.0000.0000.0000.000
100A103THR0-0.086-0.05031.117-0.011-0.0110.0000.0000.0000.000
101A104THR00.020-0.02129.6450.0070.0070.0000.0000.0000.000
102A105ILE0-0.038-0.01127.9570.0030.0030.0000.0000.0000.000
103A106ALA00.0490.01830.961-0.005-0.0050.0000.0000.0000.000
104A107CYS0-0.047-0.01129.9740.0050.0050.0000.0000.0000.000
105A108ALA00.0540.01832.6240.0000.0000.0000.0000.0000.000
106A109LEU0-0.0070.00931.537-0.002-0.0020.0000.0000.0000.000
107A110THR0-0.0360.00434.8830.0090.0090.0000.0000.0000.000
108A111SER00.0310.01236.805-0.005-0.0050.0000.0000.0000.000
109A112ARG10.8740.91639.2390.1100.1100.0000.0000.0000.000
110A113ARG10.9070.96541.8310.1000.1000.0000.0000.0000.000
111A114ARG10.8571.11544.6770.0810.0810.0000.0000.0000.000
112A115GLH00.1080.06139.5210.0000.0000.0000.0000.0000.000
113A116ILE0-0.030-0.51443.4200.0010.0010.0000.0000.0000.000
114A117THR00.7390.71144.494-0.002-0.0020.0000.0000.0000.000
115A118ALA0-0.667-0.36940.5140.0050.0050.0000.0000.0000.000
116A119PRO0-0.014-0.03337.4780.0020.0020.0000.0000.0000.000
117A120LEU0-0.0030.00236.026-0.002-0.0020.0000.0000.0000.000
118A121GLN00.0410.01931.1530.0070.0070.0000.0000.0000.000
119A122THR00.0030.01028.692-0.004-0.0040.0000.0000.0000.000
120A123PRO00.0510.00225.981-0.005-0.0050.0000.0000.0000.000
121A124ARG10.7860.87322.3550.3040.3040.0000.0000.0000.000
122A125ASP-1-0.868-0.95224.512-0.236-0.2360.0000.0000.0000.000
123A126LEU0-0.047-0.01727.1850.0020.0020.0000.0000.0000.000
124A127VAL0-0.0030.00021.0790.0040.0040.0000.0000.0000.000
125A128PRO00.0280.02621.516-0.012-0.0120.0000.0000.0000.000
126A129GLU-1-0.836-0.89122.604-0.206-0.2060.0000.0000.0000.000
127A130LEU0-0.013-0.01624.1450.0060.0060.0000.0000.0000.000
128A131LEU00.0210.00717.8230.0050.0050.0000.0000.0000.000
129A132GLN0-0.015-0.01420.8880.0120.0120.0000.0000.0000.000
130A133ALA00.0150.01022.1430.0070.0070.0000.0000.0000.000
131A134ALA00.0180.01721.5550.0100.0100.0000.0000.0000.000
132A135ASN0-0.035-0.03518.345-0.013-0.0130.0000.0000.0000.000
133A136ARG10.8260.92520.6020.2320.2320.0000.0000.0000.000
134A137GLY0-0.019-0.00523.4290.0200.0200.0000.0000.0000.000
135A138GLU-1-0.846-0.89624.736-0.182-0.1820.0000.0000.0000.000
136A139LYS10.9410.97725.8630.1680.1680.0000.0000.0000.000
137A140VAL00.0060.01325.2050.0090.0090.0000.0000.0000.000
138A141ALA00.0240.00327.804-0.005-0.0050.0000.0000.0000.000
139A142LEU0-0.030-0.00425.942-0.001-0.0010.0000.0000.0000.000
140A143VAL00.0200.00530.1620.0040.0040.0000.0000.0000.000
141A144PHE00.009-0.00729.3010.0010.0010.0000.0000.0000.000
142A145GLY00.0300.00035.0770.0050.0050.0000.0000.0000.000
143A146ASN00.0210.02638.4690.0000.0000.0000.0000.0000.000
144A147GLU-1-0.753-0.85638.458-0.102-0.1020.0000.0000.0000.000
145A148THR0-0.0300.00040.4470.0010.0010.0000.0000.0000.000
146A149PHE0-0.036-0.04043.7830.0010.0010.0000.0000.0000.000
147A150GLY00.0040.01540.2530.0000.0000.0000.0000.0000.000
148A151LEU0-0.019-0.00836.9920.0040.0040.0000.0000.0000.000
149A152SER0-0.060-0.03641.5100.0030.0030.0000.0000.0000.000
150A153ILE0-0.011-0.02443.652-0.004-0.0040.0000.0000.0000.000
151A154GLU-1-0.890-0.96044.845-0.081-0.0810.0000.0000.0000.000
152A155GLU-1-0.805-0.90040.760-0.103-0.1030.0000.0000.0000.000
153A156VAL0-0.031-0.02439.910-0.005-0.0050.0000.0000.0000.000
154A157ARG10.9060.93940.2150.0800.0800.0000.0000.0000.000
155A158ALA00.0230.03440.3980.0000.0000.0000.0000.0000.000
156A159CYS0-0.0410.01336.032-0.006-0.0060.0000.0000.0000.000
157A160ASN00.0350.01334.218-0.002-0.0020.0000.0000.0000.000
158A161ARG10.8370.89131.5860.1670.1670.0000.0000.0000.000
159A162LEU0-0.0170.00334.7270.0040.0040.0000.0000.0000.000
160A163MET00.0440.03327.717-0.005-0.0050.0000.0000.0000.000
161A164THR0-0.063-0.04232.7990.0120.0120.0000.0000.0000.000
162A165ILE00.0370.01229.765-0.013-0.0130.0000.0000.0000.000
163A166ASN0-0.012-0.00531.5370.0180.0180.0000.0000.0000.000
164A167GLY00.028-0.01031.943-0.009-0.0090.0000.0000.0000.000
165A168ASN0-0.0220.00033.9970.0050.0050.0000.0000.0000.000
166A169PRO00.0090.00436.8560.0000.0000.0000.0000.0000.000
167A170ASP-1-0.894-0.94039.990-0.079-0.0790.0000.0000.0000.000
168A171TYR0-0.082-0.04937.8970.0030.0030.0000.0000.0000.000
169A172PHE0-0.024-0.00733.784-0.005-0.0050.0000.0000.0000.000
170A173SER0-0.006-0.00836.6990.0060.0060.0000.0000.0000.000
171A174LEU0-0.0170.01530.810-0.002-0.0020.0000.0000.0000.000
172A175ASN00.0290.01333.797-0.006-0.0060.0000.0000.0000.000
173A176LEU00.0870.03233.678-0.008-0.0080.0000.0000.0000.000
174A177ALA00.0440.02731.298-0.010-0.0100.0000.0000.0000.000
175A178GLN0-0.002-0.01029.516-0.009-0.0090.0000.0000.0000.000
176A179ALA00.0130.01128.801-0.016-0.0160.0000.0000.0000.000
177A180VAL00.0260.01227.583-0.013-0.0130.0000.0000.0000.000
178A181GLN00.001-0.00223.538-0.037-0.0370.0000.0000.0000.000
179A182VAL0-0.032-0.02224.330-0.024-0.0240.0000.0000.0000.000
180A183VAL00.0100.00124.339-0.022-0.0220.0000.0000.0000.000
181A184CYS0-0.020-0.00422.527-0.017-0.0170.0000.0000.0000.000
182A185TYR00.0080.00318.004-0.049-0.0490.0000.0000.0000.000
183A186GLU-1-0.778-0.83719.440-0.400-0.4000.0000.0000.0000.000
184A187ILE00.0160.01519.540-0.035-0.0350.0000.0000.0000.000
185A188PHE00.0060.00212.481-0.051-0.0510.0000.0000.0000.000
186A189SER0-0.132-0.07115.524-0.094-0.0940.0000.0000.0000.000
187A190GLN00.027-0.00915.862-0.030-0.0300.0000.0000.0000.000
188A191THR0-0.071-0.03413.437-0.043-0.0430.0000.0000.0000.000
189A192ASP-1-0.972-0.97410.964-1.021-1.0210.0000.0000.0000.000
190A193SER0-0.031-0.02211.8940.0250.0250.0000.0000.0000.000
191A194PRO0-0.048-0.02213.525-0.016-0.0160.0000.0000.0000.000
192A195MET0-0.015-0.00514.4370.0900.0900.0000.0000.0000.000
193A196THR0-0.056-0.02416.1190.0030.0030.0000.0000.0000.000
194A197HIS00.0160.01015.2750.0220.0220.0000.0000.0000.000
195A198LEU0-0.026-0.02719.5420.0180.0180.0000.0000.0000.000
196A199GLN0-0.042-0.03123.292-0.001-0.0010.0000.0000.0000.000
197A200GLN00.0980.07924.1200.0050.0050.0000.0000.0000.000
198A201GLU-1-0.969-1.08728.750-0.105-0.1050.0000.0000.0000.000
199A202ASP-1-0.899-0.94930.504-0.149-0.1490.0000.0000.0000.000
200A203HIS0-0.1290.01529.519-0.001-0.0010.0000.0000.0000.000
201A204ALA0-0.0190.00631.8300.0070.0070.0000.0000.0000.000
202A205ALA0-0.012-0.00433.5360.0010.0010.0000.0000.0000.000
203A206THR00.023-0.00533.609-0.004-0.0040.0000.0000.0000.000
204A207HIS0-0.018-0.01135.6880.0040.0040.0000.0000.0000.000
205A208GLU-1-0.941-0.97537.772-0.092-0.0920.0000.0000.0000.000
206A209GLN00.0010.00337.4120.0020.0020.0000.0000.0000.000
207A210ILE0-0.020-0.01037.3070.0050.0050.0000.0000.0000.000
208A211LYS10.8840.93341.2610.0910.0910.0000.0000.0000.000
209A212GLY00.0010.00643.7780.0040.0040.0000.0000.0000.000
210A213MET00.000-0.00140.6330.0040.0040.0000.0000.0000.000
211A214LEU0-0.073-0.02443.7360.0020.0020.0000.0000.0000.000
212A215ALA0-0.071-0.02947.2660.0030.0030.0000.0000.0000.000
213A216HIS0-0.036-0.00749.1820.0030.0030.0000.0000.0000.000
214A217MET0-0.064-0.03348.3920.0040.0040.0000.0000.0000.000
215A218GLU-1-0.897-0.94546.198-0.072-0.0720.0000.0000.0000.000
216A219SER0-0.022-0.02047.0550.0040.0040.0000.0000.0000.000
217A220VAL0-0.030-0.00847.245-0.002-0.0020.0000.0000.0000.000