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

tag_button

FMODB ID: RYY88

Calculation Name: 3Q9S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q9S

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RRR8

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2427856.940079
FMO2-HF: Nuclear repulsion 2345500.730819
FMO2-HF: Total energy -82356.209261
FMO2-MP2: Total energy -82599.470668


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:3:GLU)


Summations of interaction energy for fragment #1(A:3:GLU)
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.
91.58497.1851.411-2.748-4.2630.002
Interaction energy analysis for fragmet #1(A:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.976 / q_NPA : -1.000
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].
3A5ARG10.9510.9613.797-30.424-28.613-0.018-0.826-0.9670.004
4A6ILE0-0.007-0.0035.892-3.409-3.4090.0000.0000.0000.000
5A7LEU0-0.0260.0008.9360.3660.3660.0000.0000.0000.000
6A8VAL00.006-0.00812.188-1.025-1.0250.0000.0000.0000.000
7A9ILE0-0.032-0.01414.554-0.398-0.3980.0000.0000.0000.000
8A10GLH0-0.040-0.07318.153-0.674-0.6740.0000.0000.0000.000
9A11ASP-1-0.868-0.93520.29512.26612.2660.0000.0000.0000.000
10A12ASP-1-0.869-0.92223.41512.14512.1450.0000.0000.0000.000
11A13HIS00.012-0.03021.2921.0071.0070.0000.0000.0000.000
12A14ASP-1-0.923-0.94120.76313.37113.3710.0000.0000.0000.000
13A15ILE0-0.043-0.02319.7520.6850.6850.0000.0000.0000.000
14A16ALA0-0.018-0.00717.4260.8480.8480.0000.0000.0000.000
15A17ASN0-0.002-0.00816.0442.3122.3120.0000.0000.0000.000
16A18VAL0-0.0020.00916.0481.0731.0730.0000.0000.0000.000
17A19LEU00.0040.00214.6780.8630.8630.0000.0000.0000.000
18A20ARG10.9230.96911.364-21.387-21.3870.0000.0000.0000.000
19A21MET0-0.049-0.01411.3382.0712.0710.0000.0000.0000.000
20A22ASP-1-0.814-0.90611.89520.40020.4000.0000.0000.0000.000
21A23LEU0-0.064-0.0429.2890.9560.9560.0000.0000.0000.000
22A24THR0-0.021-0.0236.9603.6203.6200.0000.0000.0000.000
23A25ASP-1-0.948-0.9617.28129.65529.6550.0000.0000.0000.000
24A26ALA0-0.112-0.0538.234-0.344-0.3440.0000.0000.0000.000
25A27GLY0-0.046-0.0254.3560.2010.379-0.001-0.017-0.1610.000
26A28TYR0-0.068-0.0262.7903.1714.7930.363-0.805-1.179-0.010
27A29VAL00.0270.0152.301-2.742-0.7391.068-1.095-1.9750.008
28A30VAL00.005-0.0054.776-5.541-5.554-0.001-0.0050.0190.000
29A31ASP-1-0.843-0.9138.45321.72421.7240.0000.0000.0000.000
30A32HIS0-0.093-0.05811.392-0.343-0.3430.0000.0000.0000.000
31A33ALA0-0.033-0.01614.955-0.320-0.3200.0000.0000.0000.000
32A34ASP-1-0.841-0.91418.13713.26113.2610.0000.0000.0000.000
33A35SER00.0500.02221.366-0.700-0.7000.0000.0000.0000.000
34A36ALA00.0800.02821.9910.4660.4660.0000.0000.0000.000
35A37MET0-0.048-0.02823.0320.1120.1120.0000.0000.0000.000
36A38ASN00.017-0.00720.3820.0390.0390.0000.0000.0000.000
37A39GLY00.0540.02318.5730.6430.6430.0000.0000.0000.000
38A40LEU0-0.057-0.03418.7600.4040.4040.0000.0000.0000.000
39A41ILE0-0.041-0.02520.3920.0640.0640.0000.0000.0000.000
40A42LYS10.9210.96214.822-18.859-18.8590.0000.0000.0000.000
41A43ALA0-0.023-0.00715.7110.8030.8030.0000.0000.0000.000
42A44ARG10.8190.90816.472-12.483-12.4830.0000.0000.0000.000
43A45GLU-1-0.971-0.97517.19214.16814.1680.0000.0000.0000.000
44A46ASP-1-0.889-0.95312.07020.49120.4910.0000.0000.0000.000
45A47HIS0-0.101-0.04111.1031.6351.6350.0000.0000.0000.000
46A48PRO0-0.028-0.0059.7531.9351.9350.0000.0000.0000.000
47A49ASP-1-0.812-0.8966.33029.05529.0550.0000.0000.0000.000
48A50LEU0-0.043-0.0379.666-1.611-1.6110.0000.0000.0000.000
49A51ILE0-0.0230.00411.7280.6390.6390.0000.0000.0000.000
50A52LEU00.0020.00213.395-0.761-0.7610.0000.0000.0000.000
51A53LEU00.000-0.00215.885-0.074-0.0740.0000.0000.0000.000
52A54ASP-1-0.784-0.84219.42812.53112.5310.0000.0000.0000.000
53A55LEU0-0.051-0.01821.871-0.255-0.2550.0000.0000.0000.000
54A56GLY00.0790.04025.508-0.038-0.0380.0000.0000.0000.000
55A57LEU0-0.077-0.02927.212-0.262-0.2620.0000.0000.0000.000
56A58PRO00.0240.01630.030-0.079-0.0790.0000.0000.0000.000
57A59ASP-1-0.776-0.89431.4119.6659.6650.0000.0000.0000.000
58A60PHE0-0.081-0.01832.2030.0910.0910.0000.0000.0000.000
59A61ASP-1-0.820-0.91730.6069.2579.2570.0000.0000.0000.000
60A62GLY00.005-0.00127.8200.3110.3110.0000.0000.0000.000
61A63GLY0-0.015-0.02427.2720.3800.3800.0000.0000.0000.000
62A64ASP-1-0.807-0.89828.46910.10510.1050.0000.0000.0000.000
63A65VAL0-0.027-0.01823.4430.3040.3040.0000.0000.0000.000
64A66VAL00.0130.01323.6070.4420.4420.0000.0000.0000.000
65A67GLN00.0310.00724.2100.2200.2200.0000.0000.0000.000
66A68ARG10.8220.88125.439-10.060-10.0600.0000.0000.0000.000
67A69LEU0-0.029-0.00618.9900.1470.1470.0000.0000.0000.000
68A70ARG10.8070.91819.152-13.269-13.2690.0000.0000.0000.000
69A71LYS10.8670.93822.996-11.168-11.1680.0000.0000.0000.000
70A72ASN0-0.089-0.03623.4450.2010.2010.0000.0000.0000.000
71A73SER00.0600.04818.4580.3630.3630.0000.0000.0000.000
72A74ALA00.0440.00916.863-0.364-0.3640.0000.0000.0000.000
73A75LEU0-0.0050.00113.2500.2150.2150.0000.0000.0000.000
74A76PRO00.0250.00913.208-1.155-1.1550.0000.0000.0000.000
75A77ILE0-0.028-0.01315.4910.5700.5700.0000.0000.0000.000
76A78ILE0-0.012-0.01215.124-0.612-0.6120.0000.0000.0000.000
77A79VAL0-0.005-0.00518.4290.2040.2040.0000.0000.0000.000
78A80LEU0-0.015-0.00918.663-0.308-0.3080.0000.0000.0000.000
79A81THR00.019-0.00722.376-0.425-0.4250.0000.0000.0000.000
80A82ALA00.0390.02626.1640.1340.1340.0000.0000.0000.000
81A83ARG10.8180.89228.923-9.786-9.7860.0000.0000.0000.000
82A84ASP-1-0.880-0.93630.44110.04810.0480.0000.0000.0000.000
83A85THR00.0070.00131.540-0.198-0.1980.0000.0000.0000.000
84A86VAL00.0250.00831.9940.3090.3090.0000.0000.0000.000
85A87GLU-1-0.888-0.97032.8408.3068.3060.0000.0000.0000.000
86A88GLU-1-0.797-0.88929.11610.04210.0420.0000.0000.0000.000
87A89LYS10.9190.96527.912-9.763-9.7630.0000.0000.0000.000
88A90VAL00.000-0.01028.5300.2140.2140.0000.0000.0000.000
89A91ARG10.8540.93429.470-9.748-9.7480.0000.0000.0000.000
90A92LEU00.003-0.00425.4590.1070.1070.0000.0000.0000.000
91A93LEU0-0.0170.00624.0990.2230.2230.0000.0000.0000.000
92A94GLY0-0.029-0.01226.5410.0290.0290.0000.0000.0000.000
93A95LEU0-0.078-0.03227.810-0.122-0.1220.0000.0000.0000.000
94A96GLY00.0050.00625.0020.1210.1210.0000.0000.0000.000
95A97ALA00.0130.01921.8370.5530.5530.0000.0000.0000.000
96A98ASP-1-0.802-0.90218.55413.90513.9050.0000.0000.0000.000
97A99ASP-1-0.802-0.89719.09813.34413.3440.0000.0000.0000.000
98A100TYR0-0.034-0.02821.0230.1200.1200.0000.0000.0000.000
99A101LEU0-0.016-0.01419.0710.1250.1250.0000.0000.0000.000
100A102ILE0-0.025-0.01122.374-0.067-0.0670.0000.0000.0000.000
101A103LYS10.8480.94323.170-11.893-11.8930.0000.0000.0000.000
102A104PRO0-0.011-0.03925.719-0.406-0.4060.0000.0000.0000.000
103A105PHE00.037-0.00118.920-0.196-0.1960.0000.0000.0000.000
104A106HIS0-0.005-0.00120.0510.2670.2670.0000.0000.0000.000
105A107PRO00.0670.01816.9440.1260.1260.0000.0000.0000.000
106A108ASP-1-0.836-0.93416.60517.42317.4230.0000.0000.0000.000
107A109GLU-1-0.934-0.95317.62012.92512.9250.0000.0000.0000.000
108A110LEU0-0.018-0.00914.884-0.030-0.0300.0000.0000.0000.000
109A111LEU00.0410.01911.1870.6740.6740.0000.0000.0000.000
110A112ALA0-0.035-0.00613.2430.6320.6320.0000.0000.0000.000
111A113ARG10.8330.89515.448-14.306-14.3060.0000.0000.0000.000
112A114VAL00.0570.02710.193-0.189-0.1890.0000.0000.0000.000
113A115LYS10.9690.98210.492-20.307-20.3070.0000.0000.0000.000
114A116VAL0-0.093-0.03711.998-0.090-0.0900.0000.0000.0000.000
115A117GLN0-0.049-0.03613.173-0.283-0.2830.0000.0000.0000.000
116A118LEU0-0.0020.0207.340-0.117-0.1170.0000.0000.0000.000
117A119ARG10.8760.9699.388-14.393-14.3930.0000.0000.0000.000
118A120GLN00.019-0.0079.384-1.651-1.6510.0000.0000.0000.000
119A121ARG10.9551.00111.912-16.835-16.8350.0000.0000.0000.000
120A122THR0-0.026-0.02814.965-0.454-0.4540.0000.0000.0000.000
121A123SER0-0.043-0.01718.388-0.051-0.0510.0000.0000.0000.000
122A124GLU-1-0.891-0.93319.90813.61213.6120.0000.0000.0000.000
123A125SER0-0.020-0.03721.9480.1090.1090.0000.0000.0000.000
124A126LEU0-0.024-0.00223.106-0.417-0.4170.0000.0000.0000.000
125A127SER0-0.003-0.02026.0480.0510.0510.0000.0000.0000.000
126A128MET0-0.031-0.00929.115-0.257-0.2570.0000.0000.0000.000
127A129GLY00.0100.01732.423-0.090-0.0900.0000.0000.0000.000
128A130ASP-1-0.900-0.95932.1628.6468.6460.0000.0000.0000.000
129A131LEU0-0.0070.01028.2270.1770.1770.0000.0000.0000.000
130A132THR0-0.032-0.02325.7160.1400.1400.0000.0000.0000.000
131A133LEU00.009-0.01623.1250.1880.1880.0000.0000.0000.000
132A134ASP-1-0.806-0.90418.56914.11714.1170.0000.0000.0000.000
133A135PRO0-0.071-0.04218.6260.5020.5020.0000.0000.0000.000
134A136GLN00.040-0.00613.408-0.021-0.0210.0000.0000.0000.000
135A137LYS10.9100.96513.654-14.025-14.0250.0000.0000.0000.000
136A138ARG10.8750.98314.906-15.007-15.0070.0000.0000.0000.000
137A139LEU00.0290.02517.234-0.155-0.1550.0000.0000.0000.000
138A140VAL0-0.001-0.00419.544-0.220-0.2200.0000.0000.0000.000
139A141THR0-0.037-0.00423.329-0.108-0.1080.0000.0000.0000.000
140A142TYR0-0.011-0.02526.212-0.105-0.1050.0000.0000.0000.000
141A143LYS10.9080.97929.933-8.082-8.0820.0000.0000.0000.000
142A144GLY0-0.066-0.02630.077-0.134-0.1340.0000.0000.0000.000
143A145GLU-1-0.941-0.96128.7469.7069.7060.0000.0000.0000.000
144A146GLU-1-0.968-0.98721.31912.65012.6500.0000.0000.0000.000
145A147LEU0-0.019-0.01524.530-0.214-0.2140.0000.0000.0000.000
146A148ARG10.9510.97322.320-10.737-10.7370.0000.0000.0000.000
147A149LEU0-0.035-0.01022.475-0.406-0.4060.0000.0000.0000.000
148A150SER00.0460.02121.2720.6260.6260.0000.0000.0000.000
149A151PRO00.005-0.02717.627-0.311-0.3110.0000.0000.0000.000
150A152LYS10.9340.96319.861-13.472-13.4720.0000.0000.0000.000
151A153GLU-1-0.822-0.89223.05710.56310.5630.0000.0000.0000.000
152A154PHE0-0.0090.00220.501-0.248-0.2480.0000.0000.0000.000
153A155ASP-1-0.862-0.94420.44713.21513.2150.0000.0000.0000.000
154A156ILE0-0.019-0.01023.334-0.383-0.3830.0000.0000.0000.000
155A157LEU00.0000.00626.332-0.346-0.3460.0000.0000.0000.000
156A158ALA00.0300.00024.176-0.253-0.2530.0000.0000.0000.000
157A159LEU0-0.069-0.02226.255-0.189-0.1890.0000.0000.0000.000
158A160LEU0-0.034-0.02828.121-0.305-0.3050.0000.0000.0000.000
159A161ILE00.0040.00228.289-0.258-0.2580.0000.0000.0000.000
160A162ARG10.9250.96922.676-11.588-11.5880.0000.0000.0000.000
161A163GLN0-0.032-0.01530.192-0.401-0.4010.0000.0000.0000.000
162A164PRO00.0640.04233.588-0.142-0.1420.0000.0000.0000.000
163A165GLY0-0.028-0.01035.683-0.135-0.1350.0000.0000.0000.000
164A166ARG10.8410.93734.047-8.592-8.5920.0000.0000.0000.000
165A167VAL00.0010.00336.7620.1010.1010.0000.0000.0000.000
166A168TYR00.0020.00131.631-0.062-0.0620.0000.0000.0000.000
167A169SER0-0.016-0.01135.859-0.065-0.0650.0000.0000.0000.000
168A170ARG10.9280.93834.924-7.544-7.5440.0000.0000.0000.000
169A171GLN0-0.012-0.01033.6270.2180.2180.0000.0000.0000.000
170A172GLU-1-0.798-0.89832.8228.3798.3790.0000.0000.0000.000
171A173ILE00.0000.00329.5440.3010.3010.0000.0000.0000.000
172A174GLY0-0.005-0.00828.8580.3660.3660.0000.0000.0000.000
173A175GLN0-0.001-0.00328.2750.1740.1740.0000.0000.0000.000
174A176GLU-1-0.948-0.97825.47611.23011.2300.0000.0000.0000.000
175A177ILE0-0.033-0.01224.0760.4510.4510.0000.0000.0000.000
176A178TRP0-0.006-0.02323.3060.4110.4110.0000.0000.0000.000
177A179GLN0-0.020-0.00220.4020.5470.5470.0000.0000.0000.000
178A180GLY00.0170.01124.8830.1870.1870.0000.0000.0000.000
179A181ARG10.8040.90622.407-12.732-12.7320.0000.0000.0000.000
180A182LEU00.0050.02126.125-0.090-0.0900.0000.0000.0000.000
181A183PRO0-0.0180.00028.812-0.214-0.2140.0000.0000.0000.000
182A184GLU-1-0.879-0.94932.2838.3208.3200.0000.0000.0000.000
183A185GLY0-0.012-0.00834.962-0.101-0.1010.0000.0000.0000.000
184A186SER0-0.0040.01233.129-0.113-0.1130.0000.0000.0000.000
185A187ASN00.0490.00635.495-0.120-0.1200.0000.0000.0000.000
186A188VAL00.0130.01928.779-0.015-0.0150.0000.0000.0000.000
187A189VAL00.0450.03030.8130.1550.1550.0000.0000.0000.000
188A190ASP-1-0.838-0.91632.0938.0908.0900.0000.0000.0000.000
189A191VAL00.0090.00031.165-0.075-0.0750.0000.0000.0000.000
190A192HIS0-0.027-0.01826.6530.3370.3370.0000.0000.0000.000
191A193MET00.0080.00430.4960.1070.1070.0000.0000.0000.000
192A194ALA0-0.084-0.05133.007-0.149-0.1490.0000.0000.0000.000
193A195ASN00.0130.00329.918-0.179-0.1790.0000.0000.0000.000
194A196LEU00.0070.01327.8950.0290.0290.0000.0000.0000.000
195A197ARG10.9240.95331.118-8.077-8.0770.0000.0000.0000.000
196A198ALA0-0.0120.00033.396-0.131-0.1310.0000.0000.0000.000
197A199LYS10.8260.90925.895-10.822-10.8220.0000.0000.0000.000
198A200LEU0-0.0220.00228.9660.0890.0890.0000.0000.0000.000
199A201ARG10.9160.95432.867-7.521-7.5210.0000.0000.0000.000
200A202ASP-1-0.808-0.87236.5877.8897.8890.0000.0000.0000.000
201A203LEU0-0.038-0.02838.781-0.126-0.1260.0000.0000.0000.000
202A204ASP-1-0.883-0.92941.5536.3806.3800.0000.0000.0000.000
203A205GLY0-0.045-0.02044.8260.0110.0110.0000.0000.0000.000
204A206TYR0-0.051-0.04740.3710.0810.0810.0000.0000.0000.000
205A207GLY00.015-0.00245.701-0.171-0.1710.0000.0000.0000.000
206A208LEU0-0.042-0.03145.7480.1300.1300.0000.0000.0000.000
207A209LEU0-0.017-0.02945.5690.0960.0960.0000.0000.0000.000
208A210ARG10.9320.97739.485-7.149-7.1490.0000.0000.0000.000
209A211THR00.0760.04642.5410.0410.0410.0000.0000.0000.000
210A212VAL0-0.0070.02036.9450.1120.1120.0000.0000.0000.000