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: RYY18

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2436787.596262
FMO2-HF: Nuclear repulsion 2352409.231092
FMO2-HF: Total energy -84378.36517
FMO2-MP2: Total energy -84619.821722


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.
-3.283-0.95-0.004-1.136-1.1920.004
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 : 0.036 / q_NPA : 0.013
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].
3A6PRO00.0430.0333.798-1.4730.860-0.004-1.136-1.1920.004
4A7ALA0-0.026-0.0225.9310.3600.3600.0000.0000.0000.000
5A8LEU00.004-0.0058.737-0.063-0.0630.0000.0000.0000.000
6A9PRO00.0260.02012.0710.0650.0650.0000.0000.0000.000
7A10ASP-1-0.870-0.93513.692-0.348-0.3480.0000.0000.0000.000
8A11TYR00.0320.01014.5430.0380.0380.0000.0000.0000.000
9A12LEU00.004-0.00815.8700.0290.0290.0000.0000.0000.000
10A13GLY0-0.010-0.00519.3440.0230.0230.0000.0000.0000.000
11A14ASN0-0.102-0.04021.6720.0440.0440.0000.0000.0000.000
12A15ILE00.0130.00820.9110.0140.0140.0000.0000.0000.000
13A16ARG10.7680.85324.7640.1450.1450.0000.0000.0000.000
14A17ILE0-0.029-0.01825.422-0.004-0.0040.0000.0000.0000.000
15A18ILE00.016-0.00329.0700.0080.0080.0000.0000.0000.000
16A19LEU0-0.019-0.00632.1290.0010.0010.0000.0000.0000.000
17A20THR00.0210.01035.1110.0070.0070.0000.0000.0000.000
18A21ARG10.7180.80838.7100.0960.0960.0000.0000.0000.000
19A22THR00.0050.01037.3470.0020.0020.0000.0000.0000.000
20A23SER00.0380.00640.1390.0040.0040.0000.0000.0000.000
21A24HIS00.0170.00739.2170.0030.0030.0000.0000.0000.000
22A25PRO00.0750.03738.614-0.008-0.0080.0000.0000.0000.000
23A26ALA00.0430.03436.508-0.006-0.0060.0000.0000.0000.000
24A27ASN0-0.054-0.04234.496-0.015-0.0150.0000.0000.0000.000
25A28ILE00.0140.02133.269-0.011-0.0110.0000.0000.0000.000
26A29GLY00.0590.03032.146-0.008-0.0080.0000.0000.0000.000
27A30SER0-0.066-0.05930.295-0.012-0.0120.0000.0000.0000.000
28A31ALA0-0.0060.00228.764-0.016-0.0160.0000.0000.0000.000
29A32ALA00.0590.03727.449-0.018-0.0180.0000.0000.0000.000
30A33ARG10.9580.97925.7450.1670.1670.0000.0000.0000.000
31A34ALA0-0.051-0.00924.222-0.024-0.0240.0000.0000.0000.000
32A35MET00.012-0.00522.994-0.024-0.0240.0000.0000.0000.000
33A36LYS10.8390.91521.0640.1860.1860.0000.0000.0000.000
34A37THR0-0.126-0.07519.730-0.027-0.0270.0000.0000.0000.000
35A38MET0-0.047-0.00518.136-0.070-0.0700.0000.0000.0000.000
36A39GLY00.0100.00817.174-0.032-0.0320.0000.0000.0000.000
37A40LEU0-0.0090.00518.0700.0240.0240.0000.0000.0000.000
38A41HIS0-0.018-0.03019.9420.0350.0350.0000.0000.0000.000
39A42ARG10.8850.94723.6680.1940.1940.0000.0000.0000.000
40A43LEU00.0110.01526.600-0.005-0.0050.0000.0000.0000.000
41A44THR00.0200.01129.5550.0050.0050.0000.0000.0000.000
42A45ILE0-0.032-0.02033.064-0.004-0.0040.0000.0000.0000.000
43A46VAL00.0420.02436.3070.0050.0050.0000.0000.0000.000
44A47THR0-0.029-0.02639.4040.0010.0010.0000.0000.0000.000
45A48PRO0-0.0190.00240.0760.0000.0000.0000.0000.0000.000
46A49ASN0-0.055-0.03842.0580.0050.0050.0000.0000.0000.000
47A50LEU0-0.033-0.01140.0480.0000.0000.0000.0000.0000.000
48A51MET0-0.010-0.00443.0250.0040.0040.0000.0000.0000.000
49A52ALA00.0240.00945.591-0.002-0.0020.0000.0000.0000.000
50A53THR0-0.050-0.06342.7800.0000.0000.0000.0000.0000.000
51A54PRO00.028-0.00744.7320.0020.0020.0000.0000.0000.000
52A55MET0-0.066-0.02238.5810.0000.0000.0000.0000.0000.000
53A56THR0-0.041-0.03742.4520.0000.0000.0000.0000.0000.000
54A57GLU-1-0.889-0.93945.242-0.057-0.0570.0000.0000.0000.000
55A58ASN0-0.123-0.06248.1360.0030.0030.0000.0000.0000.000
56A59PRO00.0160.01945.642-0.001-0.0010.0000.0000.0000.000
57A60PRO0-0.0100.00842.7710.0030.0030.0000.0000.0000.000
58A61VAL00.001-0.01445.887-0.002-0.0020.0000.0000.0000.000
59A62PHE00.0040.00342.3780.0010.0010.0000.0000.0000.000
60A63ASN00.010-0.00746.2450.0030.0030.0000.0000.0000.000
61A64PRO0-0.016-0.01346.318-0.001-0.0010.0000.0000.0000.000
62A65ASP-1-0.920-0.95246.951-0.059-0.0590.0000.0000.0000.000
63A66ASP-1-0.885-0.92347.512-0.059-0.0590.0000.0000.0000.000
64A67VAL00.0100.01241.168-0.001-0.0010.0000.0000.0000.000
65A68GLN0-0.064-0.03842.808-0.005-0.0050.0000.0000.0000.000
66A69SER0-0.020-0.02543.4950.0000.0000.0000.0000.0000.000
67A70PHE0-0.069-0.03639.7780.0000.0000.0000.0000.0000.000
68A71ALA00.0070.01340.452-0.005-0.0050.0000.0000.0000.000
69A72LEU00.001-0.00835.5910.0000.0000.0000.0000.0000.000
70A73PRO00.010-0.00439.4950.0030.0030.0000.0000.0000.000
71A74GLU-1-0.863-0.93337.962-0.091-0.0910.0000.0000.0000.000
72A75GLU-1-0.813-0.87037.465-0.096-0.0960.0000.0000.0000.000
73A76SER0-0.044-0.03935.361-0.004-0.0040.0000.0000.0000.000
74A77PHE00.0480.01033.181-0.011-0.0110.0000.0000.0000.000
75A78ILE0-0.0020.00632.678-0.008-0.0080.0000.0000.0000.000
76A79LEU0-0.036-0.01732.477-0.007-0.0070.0000.0000.0000.000
77A80ALA00.0010.01329.572-0.012-0.0120.0000.0000.0000.000
78A81SER0-0.058-0.03128.006-0.018-0.0180.0000.0000.0000.000
79A82GLY0-0.026-0.01125.1420.0050.0050.0000.0000.0000.000
80A83ALA0-0.015-0.01224.739-0.014-0.0140.0000.0000.0000.000
81A84ALA00.0260.01026.2720.0020.0020.0000.0000.0000.000
82A85ASP-1-0.809-0.89224.763-0.181-0.1810.0000.0000.0000.000
83A86VAL00.0300.00724.7380.0030.0030.0000.0000.0000.000
84A87LEU0-0.048-0.01927.7150.0040.0040.0000.0000.0000.000
85A88HIS0-0.029-0.01031.0360.0080.0080.0000.0000.0000.000
86A89ASN0-0.095-0.04627.654-0.002-0.0020.0000.0000.0000.000
87A90ALA0-0.0080.01530.536-0.006-0.0060.0000.0000.0000.000
88A91GLU-1-0.801-0.88230.706-0.138-0.1380.0000.0000.0000.000
89A92ILE0-0.006-0.00334.169-0.002-0.0020.0000.0000.0000.000
90A93VAL00.004-0.00136.9460.0030.0030.0000.0000.0000.000
91A94ALA00.0400.02639.6810.0000.0000.0000.0000.0000.000
92A95THR0-0.073-0.06542.284-0.001-0.0010.0000.0000.0000.000
93A96LEU00.017-0.00636.566-0.003-0.0030.0000.0000.0000.000
94A97ASP-1-0.790-0.89038.461-0.094-0.0940.0000.0000.0000.000
95A98GLU-1-0.790-0.87039.108-0.089-0.0890.0000.0000.0000.000
96A99ALA0-0.035-0.01335.600-0.004-0.0040.0000.0000.0000.000
97A100LEU0-0.0030.00333.836-0.011-0.0110.0000.0000.0000.000
98A101ALA00.0300.04835.255-0.004-0.0040.0000.0000.0000.000
99A102ASP-1-0.774-0.86831.918-0.137-0.1370.0000.0000.0000.000
100A103THR0-0.085-0.06130.818-0.008-0.0080.0000.0000.0000.000
101A104THR00.026-0.01729.4960.0060.0060.0000.0000.0000.000
102A105ILE0-0.043-0.01027.6200.0040.0040.0000.0000.0000.000
103A106ALA00.0530.02930.450-0.008-0.0080.0000.0000.0000.000
104A107CYS0-0.030-0.00429.8980.0050.0050.0000.0000.0000.000
105A108ALA00.0520.01732.508-0.002-0.0020.0000.0000.0000.000
106A109LEU0-0.0260.00231.553-0.001-0.0010.0000.0000.0000.000
107A110THR0-0.055-0.03934.6350.0080.0080.0000.0000.0000.000
108A111SER00.0770.05336.383-0.005-0.0050.0000.0000.0000.000
109A112ARG10.8880.94438.8140.1080.1080.0000.0000.0000.000
110A113ARG10.8670.92741.5980.1040.1040.0000.0000.0000.000
111A114ARG10.9010.95044.3570.0800.0800.0000.0000.0000.000
112A115GLH00.0630.04639.174-0.001-0.0010.0000.0000.0000.000
113A116ILE0-0.038-0.04843.7560.0000.0000.0000.0000.0000.000
114A117THR00.0040.00644.5720.0000.0000.0000.0000.0000.000
115A118ALA00.0860.05340.258-0.001-0.0010.0000.0000.0000.000
116A119PRO0-0.005-0.00336.9310.0000.0000.0000.0000.0000.000
117A120LEU0-0.006-0.00535.7320.0000.0000.0000.0000.0000.000
118A121GLN00.0100.01129.9870.0090.0090.0000.0000.0000.000
119A122THR0-0.030-0.05128.243-0.004-0.0040.0000.0000.0000.000
120A123PRO00.037-0.00925.706-0.004-0.0040.0000.0000.0000.000
121A124ARG10.8230.88621.9170.3150.3150.0000.0000.0000.000
122A125ASP-1-0.848-0.89824.322-0.215-0.2150.0000.0000.0000.000
123A126LEU0-0.020-0.02126.2430.0140.0140.0000.0000.0000.000
124A127VAL00.0010.00720.8340.0050.0050.0000.0000.0000.000
125A128PRO00.0320.02421.237-0.010-0.0100.0000.0000.0000.000
126A129GLU-1-0.812-0.86622.318-0.181-0.1810.0000.0000.0000.000
127A130LEU0-0.005-0.01024.0630.0050.0050.0000.0000.0000.000
128A131LEU00.0240.00817.4830.0070.0070.0000.0000.0000.000
129A132GLN0-0.004-0.00720.5420.0190.0190.0000.0000.0000.000
130A133ALA0-0.019-0.01021.9880.0110.0110.0000.0000.0000.000
131A134ALA00.0160.01521.3900.0100.0100.0000.0000.0000.000
132A135ASN0-0.031-0.03517.576-0.033-0.0330.0000.0000.0000.000
133A136ARG10.8240.89920.4270.1980.1980.0000.0000.0000.000
134A137GLY0-0.0040.01123.3350.0190.0190.0000.0000.0000.000
135A138GLU-1-0.807-0.85624.568-0.157-0.1570.0000.0000.0000.000
136A139LYS10.8640.93625.8160.1600.1600.0000.0000.0000.000
137A140VAL0-0.0070.00125.1540.0080.0080.0000.0000.0000.000
138A141ALA00.0330.01227.972-0.005-0.0050.0000.0000.0000.000
139A142LEU0-0.021-0.00125.8890.0000.0000.0000.0000.0000.000
140A143VAL00.0150.01030.0110.0010.0010.0000.0000.0000.000
141A144PHE00.018-0.00328.8530.0010.0010.0000.0000.0000.000
142A145GLY00.0370.00534.9560.0050.0050.0000.0000.0000.000
143A146ASN00.0140.01038.380-0.002-0.0020.0000.0000.0000.000
144A147GLU-1-0.732-0.86438.743-0.112-0.1120.0000.0000.0000.000
145A148THR0-0.072-0.01940.7660.0020.0020.0000.0000.0000.000
146A149PHE0-0.008-0.01744.0380.0010.0010.0000.0000.0000.000
147A150GLY00.0060.03640.4960.0010.0010.0000.0000.0000.000
148A151LEU00.0340.02536.7930.0040.0040.0000.0000.0000.000
149A152SER0-0.051-0.04141.2010.0020.0020.0000.0000.0000.000
150A153ILE0-0.006-0.02143.188-0.003-0.0030.0000.0000.0000.000
151A154GLU-1-0.860-0.93244.590-0.080-0.0800.0000.0000.0000.000
152A155GLU-1-0.694-0.80840.487-0.102-0.1020.0000.0000.0000.000
153A156VAL0-0.027-0.01939.728-0.005-0.0050.0000.0000.0000.000
154A157ARG10.8720.93340.1690.0760.0760.0000.0000.0000.000
155A158ALA00.0140.02840.5550.0010.0010.0000.0000.0000.000
156A159CYS0-0.058-0.00335.997-0.007-0.0070.0000.0000.0000.000
157A160ASN00.000-0.01533.856-0.001-0.0010.0000.0000.0000.000
158A161ARG10.7940.86631.0630.1550.1550.0000.0000.0000.000
159A162LEU0-0.024-0.00834.2630.0040.0040.0000.0000.0000.000
160A163MET00.0210.02527.560-0.006-0.0060.0000.0000.0000.000
161A164THR0-0.043-0.04932.4510.0100.0100.0000.0000.0000.000
162A165ILE00.0220.00629.684-0.011-0.0110.0000.0000.0000.000
163A166ASN00.0060.00031.8890.0150.0150.0000.0000.0000.000
164A167GLY00.015-0.00731.958-0.011-0.0110.0000.0000.0000.000
165A168ASN0-0.054-0.02734.0700.0060.0060.0000.0000.0000.000
166A169PRO0-0.0040.00736.9540.0000.0000.0000.0000.0000.000
167A170ASP-1-0.912-0.95340.205-0.086-0.0860.0000.0000.0000.000
168A171TYR0-0.056-0.03638.6980.0020.0020.0000.0000.0000.000
169A172PHE00.0200.01933.850-0.005-0.0050.0000.0000.0000.000
170A173SER0-0.031-0.01936.9900.0050.0050.0000.0000.0000.000
171A174LEU0-0.0070.00531.150-0.006-0.0060.0000.0000.0000.000
172A175ASN00.0220.01534.240-0.002-0.0020.0000.0000.0000.000
173A176LEU00.0580.02633.917-0.009-0.0090.0000.0000.0000.000
174A177ALA00.0630.03631.493-0.010-0.0100.0000.0000.0000.000
175A178GLN0-0.010-0.00929.783-0.009-0.0090.0000.0000.0000.000
176A179ALA00.0110.00729.118-0.016-0.0160.0000.0000.0000.000
177A180VAL00.0400.01627.652-0.012-0.0120.0000.0000.0000.000
178A181GLN00.0430.02223.655-0.030-0.0300.0000.0000.0000.000
179A182VAL0-0.047-0.02024.465-0.027-0.0270.0000.0000.0000.000
180A183VAL00.0150.00324.454-0.021-0.0210.0000.0000.0000.000
181A184CYS0-0.033-0.01622.870-0.014-0.0140.0000.0000.0000.000
182A185TYR0-0.009-0.01318.134-0.051-0.0510.0000.0000.0000.000
183A186GLU-1-0.784-0.83719.498-0.398-0.3980.0000.0000.0000.000
184A187ILE00.0100.00619.456-0.032-0.0320.0000.0000.0000.000
185A188PHE00.0180.01012.705-0.055-0.0550.0000.0000.0000.000
186A189SER0-0.116-0.06215.285-0.088-0.0880.0000.0000.0000.000
187A190GLN00.0270.00715.9770.0000.0000.0000.0000.0000.000
188A191THR0-0.043-0.03313.024-0.035-0.0350.0000.0000.0000.000
189A192ASP-1-0.951-0.96810.522-0.954-0.9540.0000.0000.0000.000
190A193SER0-0.041-0.02411.5420.0410.0410.0000.0000.0000.000
191A194PRO0-0.056-0.02313.2710.0000.0000.0000.0000.0000.000
192A195MET0-0.003-0.00414.2140.0700.0700.0000.0000.0000.000
193A196THR0-0.045-0.02316.4670.0080.0080.0000.0000.0000.000
194A197HIS00.0090.01514.7880.0300.0300.0000.0000.0000.000
195A198LEU0-0.015-0.02119.3920.0190.0190.0000.0000.0000.000
196A199GLN0-0.065-0.02923.0580.0030.0030.0000.0000.0000.000
197A200GLN00.0290.02323.7980.0060.0060.0000.0000.0000.000
198A201GLU-1-0.940-0.96628.390-0.085-0.0850.0000.0000.0000.000
199A202ASP-1-0.899-0.96130.800-0.115-0.1150.0000.0000.0000.000
200A203HIS0-0.094-0.05229.938-0.003-0.0030.0000.0000.0000.000
201A204ALA0-0.0100.01131.4640.0050.0050.0000.0000.0000.000
202A205ALA00.0050.00533.360-0.002-0.0020.0000.0000.0000.000
203A206THR0-0.008-0.01533.613-0.003-0.0030.0000.0000.0000.000
204A207HIS0-0.044-0.02835.6660.0050.0050.0000.0000.0000.000
205A208GLU-1-0.952-0.97237.754-0.082-0.0820.0000.0000.0000.000
206A209GLN00.0350.02037.2210.0020.0020.0000.0000.0000.000
207A210ILE0-0.018-0.00637.0230.0050.0050.0000.0000.0000.000
208A211LYS10.8500.90941.1400.0870.0870.0000.0000.0000.000
209A212GLY00.0160.01343.4770.0040.0040.0000.0000.0000.000
210A213MET00.003-0.00440.6010.0040.0040.0000.0000.0000.000
211A214LEU0-0.073-0.03143.4980.0030.0030.0000.0000.0000.000
212A215ALA0-0.057-0.02146.9600.0030.0030.0000.0000.0000.000
213A216HIS0-0.071-0.02649.0390.0040.0040.0000.0000.0000.000
214A217MET0-0.072-0.03348.4170.0030.0030.0000.0000.0000.000
215A218GLU-1-0.885-0.94045.892-0.061-0.0610.0000.0000.0000.000
216A219SER0-0.020-0.02246.8600.0040.0040.0000.0000.0000.000
217A220VAL0-0.033-0.00547.325-0.001-0.0010.0000.0000.0000.000