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: K9QQ3

Calculation Name: 2NN6-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN6

Chain ID: F

ChEMBL ID:

UniProt ID: Q9Y3B2

Base Structure: X-ray

Registration Date: 2023-06-26

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2375288.166374
FMO2-HF: Nuclear repulsion 2293537.435189
FMO2-HF: Total energy -81750.731185
FMO2-MP2: Total energy -81988.786799


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(F:29:GLY)


Summations of interaction energy for fragment #1(F:29:GLY)
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.
-1.0020.701-0.011-0.959-0.7330.003
Interaction energy analysis for fragmet #1(F:29:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.027
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].
3F31ARG10.8190.9053.8811.8103.513-0.011-0.959-0.7330.003
4F32ASP-1-0.796-0.9067.227-0.860-0.8600.0000.0000.0000.000
5F33PRO00.0100.00910.993-0.096-0.0960.0000.0000.0000.000
6F34THR00.0400.01912.9450.0220.0220.0000.0000.0000.000
7F35ARG10.7890.8888.4481.4461.4460.0000.0000.0000.000
8F36LEU0-0.006-0.00113.273-0.059-0.0590.0000.0000.0000.000
9F37ARG10.7270.84911.4450.5140.5140.0000.0000.0000.000
10F38PRO0-0.006-0.01214.0170.0240.0240.0000.0000.0000.000
11F39VAL00.0420.02816.8860.0110.0110.0000.0000.0000.000
12F40TYR0-0.066-0.02619.9100.0280.0280.0000.0000.0000.000
13F41ALA00.0630.02122.663-0.006-0.0060.0000.0000.0000.000
14F42ARG10.8740.93625.8620.0310.0310.0000.0000.0000.000
15F43ALA00.0640.04229.3500.0030.0030.0000.0000.0000.000
16F44GLY00.018-0.00632.0340.0070.0070.0000.0000.0000.000
17F45LEU0-0.124-0.05430.3730.0060.0060.0000.0000.0000.000
18F46LEU0-0.016-0.00633.0250.0060.0060.0000.0000.0000.000
19F47SER00.0590.01535.845-0.003-0.0030.0000.0000.0000.000
20F48GLN00.0210.02839.0500.0000.0000.0000.0000.0000.000
21F49ALA00.0040.02737.470-0.001-0.0010.0000.0000.0000.000
22F50LYS10.8300.88539.4640.0360.0360.0000.0000.0000.000
23F51GLY00.0390.04437.8500.0000.0000.0000.0000.0000.000
24F52SER0-0.063-0.04334.472-0.002-0.0020.0000.0000.0000.000
25F53ALA0-0.0040.00529.589-0.001-0.0010.0000.0000.0000.000
26F54TYR0-0.001-0.02223.5100.0070.0070.0000.0000.0000.000
27F55LEU00.0020.00221.906-0.003-0.0030.0000.0000.0000.000
28F56GLU-1-0.787-0.90718.228-0.048-0.0480.0000.0000.0000.000
29F57ALA0-0.002-0.00516.256-0.017-0.0170.0000.0000.0000.000
30F58GLY0-0.0070.00514.271-0.051-0.0510.0000.0000.0000.000
31F59GLY0-0.044-0.02013.4900.0170.0170.0000.0000.0000.000
32F60THR0-0.007-0.00315.465-0.033-0.0330.0000.0000.0000.000
33F61LYS10.7870.91118.4910.0170.0170.0000.0000.0000.000
34F62VAL00.000-0.00922.2150.0010.0010.0000.0000.0000.000
35F63LEU0-0.0130.01525.1040.0010.0010.0000.0000.0000.000
36F64CYS0-0.032-0.00728.740-0.011-0.0110.0000.0000.0000.000
37F65ALA0-0.011-0.00731.3530.0060.0060.0000.0000.0000.000
38F66VAL00.0210.02235.123-0.003-0.0030.0000.0000.0000.000
39F67SER0-0.028-0.03237.8860.0070.0070.0000.0000.0000.000
40F68GLY00.0310.00341.544-0.003-0.0030.0000.0000.0000.000
41F69PRO0-0.029-0.01344.3900.0000.0000.0000.0000.0000.000
42F70ARG10.8310.87543.4890.0480.0480.0000.0000.0000.000
43F71GLN00.0200.01948.465-0.003-0.0030.0000.0000.0000.000
44F72ALA0-0.0110.00347.7560.0010.0010.0000.0000.0000.000
45F92LEU00.015-0.00152.1580.0000.0000.0000.0000.0000.000
46F93ARG10.9410.95849.2570.0570.0570.0000.0000.0000.000
47F94GLY00.0640.04247.7390.0000.0000.0000.0000.0000.000
48F95ARG10.8440.91240.1630.0730.0730.0000.0000.0000.000
49F96LEU0-0.0170.00036.7740.0050.0050.0000.0000.0000.000
50F97LEU0-0.009-0.00138.848-0.002-0.0020.0000.0000.0000.000
51F98CYS0-0.042-0.02033.762-0.002-0.0020.0000.0000.0000.000
52F99ASP-1-0.877-0.93834.085-0.071-0.0710.0000.0000.0000.000
53F100PHE00.000-0.00224.279-0.004-0.0040.0000.0000.0000.000
54F101ARG10.9230.97329.2310.0550.0550.0000.0000.0000.000
55F102ARG10.8420.90420.8750.1430.1430.0000.0000.0000.000
56F103ALA00.0110.01324.8450.0090.0090.0000.0000.0000.000
57F104PRO0-0.028-0.01625.459-0.001-0.0010.0000.0000.0000.000
58F105PHE0-0.003-0.01224.1430.0060.0060.0000.0000.0000.000
59F106ALA00.0390.03821.5520.0140.0140.0000.0000.0000.000
60F107GLY0-0.020-0.01618.180-0.025-0.0250.0000.0000.0000.000
61F108ARG10.9480.96414.9710.0830.0830.0000.0000.0000.000
62F109ARG10.9500.97519.237-0.030-0.0300.0000.0000.0000.000
63F110ARG10.9830.99922.423-0.026-0.0260.0000.0000.0000.000
64F111ARG10.8210.89322.9050.1000.1000.0000.0000.0000.000
65F112ALA0-0.020-0.02326.982-0.002-0.0020.0000.0000.0000.000
66F113PRO00.0030.01630.3600.0010.0010.0000.0000.0000.000
67F114PRO00.0140.00230.674-0.005-0.0050.0000.0000.0000.000
68F115GLY00.1140.06129.3520.0020.0020.0000.0000.0000.000
69F116GLY0-0.014-0.02030.426-0.010-0.0100.0000.0000.0000.000
70F117CYS0-0.046-0.03829.6270.0030.0030.0000.0000.0000.000
71F118GLU-1-0.749-0.82723.522-0.144-0.1440.0000.0000.0000.000
72F119GLU-1-0.770-0.90126.281-0.116-0.1160.0000.0000.0000.000
73F120ARG10.8870.96929.1870.0850.0850.0000.0000.0000.000
74F121GLU-1-0.884-0.93726.976-0.177-0.1770.0000.0000.0000.000
75F122LEU00.002-0.00624.099-0.003-0.0030.0000.0000.0000.000
76F123ALA0-0.030-0.01427.989-0.001-0.0010.0000.0000.0000.000
77F124LEU0-0.036-0.00531.3910.0020.0020.0000.0000.0000.000
78F125ALA00.0900.03928.9880.0020.0020.0000.0000.0000.000
79F126LEU0-0.040-0.01127.856-0.005-0.0050.0000.0000.0000.000
80F127GLN0-0.027-0.05030.5060.0090.0090.0000.0000.0000.000
81F128GLU-1-0.892-0.95533.166-0.132-0.1320.0000.0000.0000.000
82F129ALA0-0.014-0.00230.0120.0000.0000.0000.0000.0000.000
83F130LEU0-0.051-0.04030.144-0.001-0.0010.0000.0000.0000.000
84F131GLU-1-0.868-0.92833.812-0.089-0.0890.0000.0000.0000.000
85F132PRO0-0.032-0.01835.2950.0070.0070.0000.0000.0000.000
86F133ALA00.0030.01535.0410.0030.0030.0000.0000.0000.000
87F134VAL0-0.028-0.00937.1540.0060.0060.0000.0000.0000.000
88F135ARG10.8800.93140.2400.0630.0630.0000.0000.0000.000
89F136LEU00.0320.00241.9620.0050.0050.0000.0000.0000.000
90F137GLY0-0.046-0.02445.4570.0040.0040.0000.0000.0000.000
91F138ARG10.8240.90546.7660.0570.0570.0000.0000.0000.000
92F139TYR00.0200.01144.1420.0030.0030.0000.0000.0000.000
93F140PRO0-0.012-0.00348.800-0.001-0.0010.0000.0000.0000.000
94F141ARG10.9220.94951.5940.0420.0420.0000.0000.0000.000
95F142ALA00.0030.00948.7040.0020.0020.0000.0000.0000.000
96F143GLN00.0280.01543.334-0.005-0.0050.0000.0000.0000.000
97F144LEU00.0110.02639.6940.0040.0040.0000.0000.0000.000
98F145GLU-1-0.776-0.84839.683-0.050-0.0500.0000.0000.0000.000
99F146VAL00.0310.01933.8910.0020.0020.0000.0000.0000.000
100F147SER0-0.0100.00433.9770.0010.0010.0000.0000.0000.000
101F148ALA00.0580.01128.658-0.001-0.0010.0000.0000.0000.000
102F149LEU0-0.047-0.02527.1940.0030.0030.0000.0000.0000.000
103F150LEU00.0450.01620.9000.0060.0060.0000.0000.0000.000
104F151LEU0-0.024-0.02324.3430.0070.0070.0000.0000.0000.000
105F152GLU-1-0.862-0.93317.8730.0190.0190.0000.0000.0000.000
106F153ASP-1-0.859-0.94217.243-0.255-0.2550.0000.0000.0000.000
107F154GLY00.0650.02714.4870.0150.0150.0000.0000.0000.000
108F155GLY00.004-0.00813.612-0.079-0.0790.0000.0000.0000.000
109F156SER00.0710.05214.5670.0590.0590.0000.0000.0000.000
110F157ALA0-0.030-0.03316.9100.0470.0470.0000.0000.0000.000
111F158LEU00.0430.02719.3830.0340.0340.0000.0000.0000.000
112F159ALA00.0560.03520.4090.0260.0260.0000.0000.0000.000
113F160ALA0-0.023-0.00820.5460.0250.0250.0000.0000.0000.000
114F161ALA0-0.002-0.01122.4970.0260.0260.0000.0000.0000.000
115F162LEU00.0330.02425.0730.0180.0180.0000.0000.0000.000
116F163THR00.0190.00324.3310.0110.0110.0000.0000.0000.000
117F164ALA0-0.019-0.01926.0740.0150.0150.0000.0000.0000.000
118F165ALA00.0490.00127.7280.0140.0140.0000.0000.0000.000
119F166ALA00.0170.01630.0290.0110.0110.0000.0000.0000.000
120F167LEU0-0.026-0.01227.7530.0100.0100.0000.0000.0000.000
121F168ALA0-0.019-0.00231.7940.0090.0090.0000.0000.0000.000
122F169LEU00.0200.01034.0790.0080.0080.0000.0000.0000.000
123F170ALA00.0470.00435.1970.0060.0060.0000.0000.0000.000
124F171ASP-1-0.836-0.90135.085-0.047-0.0470.0000.0000.0000.000
125F172ALA00.0010.00237.1150.0060.0060.0000.0000.0000.000
126F173GLY0-0.066-0.01239.6330.0030.0030.0000.0000.0000.000
127F174VAL0-0.047-0.02439.2890.0020.0020.0000.0000.0000.000
128F175GLU-1-0.786-0.86441.308-0.064-0.0640.0000.0000.0000.000
129F176MET0-0.0160.00637.048-0.003-0.0030.0000.0000.0000.000
130F177TYR0-0.036-0.01939.2870.0070.0070.0000.0000.0000.000
131F178ASP-1-0.756-0.88134.390-0.131-0.1310.0000.0000.0000.000
132F179LEU0-0.048-0.03331.7120.0030.0030.0000.0000.0000.000
133F180VAL00.0350.00728.737-0.009-0.0090.0000.0000.0000.000
134F181VAL0-0.020-0.00724.9530.0030.0030.0000.0000.0000.000
135F182GLY00.0310.01324.151-0.001-0.0010.0000.0000.0000.000
136F183CYS0-0.074-0.03219.0010.0040.0040.0000.0000.0000.000
137F184GLY00.0490.02917.0400.0190.0190.0000.0000.0000.000
138F185LEU0-0.046-0.03415.920-0.030-0.0300.0000.0000.0000.000
139F186SER0-0.0140.00612.6910.0030.0030.0000.0000.0000.000
140F187LEU00.0330.03313.504-0.104-0.1040.0000.0000.0000.000
141F188ALA00.0390.0158.501-0.047-0.0470.0000.0000.0000.000
142F189PRO00.0070.0098.0490.1380.1380.0000.0000.0000.000
143F190GLY0-0.043-0.01510.4870.0390.0390.0000.0000.0000.000
144F191PRO0-0.025-0.02111.1840.1190.1190.0000.0000.0000.000
145F192ALA00.0070.00814.2950.1090.1090.0000.0000.0000.000
146F193PRO00.0190.01114.618-0.112-0.1120.0000.0000.0000.000
147F194THR0-0.032-0.01610.184-0.016-0.0160.0000.0000.0000.000
148F195TRP00.0030.00612.493-0.148-0.1480.0000.0000.0000.000
149F196LEU0-0.028-0.0138.130-0.140-0.1400.0000.0000.0000.000
150F197LEU0-0.0020.01312.7420.1140.1140.0000.0000.0000.000
151F198ASP-1-0.783-0.87712.932-0.644-0.6440.0000.0000.0000.000
152F199PRO0-0.0160.04110.758-0.133-0.1330.0000.0000.0000.000
153F200THR00.027-0.0398.8970.3100.3100.0000.0000.0000.000
154F201ARG10.8380.91110.486-0.024-0.0240.0000.0000.0000.000
155F202LEU0-0.033-0.0326.5600.0630.0630.0000.0000.0000.000
156F203GLU-1-0.768-0.8376.062-2.314-2.3140.0000.0000.0000.000
157F204GLU-1-0.866-0.9497.774-0.571-0.5710.0000.0000.0000.000
158F205GLU-1-0.861-0.8989.653-0.183-0.1830.0000.0000.0000.000
159F206ARG10.8050.8845.6990.5970.5970.0000.0000.0000.000
160F207ALA0-0.0140.00710.106-0.162-0.1620.0000.0000.0000.000
161F208ALA00.0200.01512.1660.0900.0900.0000.0000.0000.000
162F209ALA00.017-0.00114.8280.0800.0800.0000.0000.0000.000
163F210GLY00.0100.02015.866-0.083-0.0830.0000.0000.0000.000
164F211LEU0-0.001-0.01517.6930.0620.0620.0000.0000.0000.000
165F212THR0-0.043-0.02518.428-0.043-0.0430.0000.0000.0000.000
166F213VAL0-0.0250.00320.9500.0340.0340.0000.0000.0000.000
167F214ALA00.030-0.00223.763-0.009-0.0090.0000.0000.0000.000
168F215LEU0-0.039-0.01726.5620.0060.0060.0000.0000.0000.000
169F216MET0-0.0310.00128.972-0.001-0.0010.0000.0000.0000.000
170F217PRO0-0.0030.00929.3290.0000.0000.0000.0000.0000.000
171F218VAL0-0.024-0.00631.2460.0010.0010.0000.0000.0000.000
172F219LEU0-0.019-0.01434.7670.0050.0050.0000.0000.0000.000
173F220ASN0-0.046-0.03332.4000.0010.0010.0000.0000.0000.000
174F221GLN0-0.0040.01033.3380.0010.0010.0000.0000.0000.000
175F222VAL00.005-0.00830.216-0.006-0.0060.0000.0000.0000.000
176F223ALA0-0.0230.00429.8700.0100.0100.0000.0000.0000.000
177F224GLY00.0480.00929.3300.0120.0120.0000.0000.0000.000
178F225LEU0-0.063-0.03326.271-0.018-0.0180.0000.0000.0000.000
179F226LEU00.0200.00924.3050.0140.0140.0000.0000.0000.000
180F227GLY00.0530.01122.224-0.031-0.0310.0000.0000.0000.000
181F228SER0-0.0460.00620.8680.0260.0260.0000.0000.0000.000
182F229GLY0-0.012-0.00721.547-0.034-0.0340.0000.0000.0000.000
183F230GLU-1-0.913-0.96717.621-0.469-0.4690.0000.0000.0000.000
184F231GLY00.0400.02418.9480.0120.0120.0000.0000.0000.000
185F232GLY0-0.024-0.01819.987-0.026-0.0260.0000.0000.0000.000
186F233LEU0-0.0130.00723.0280.0210.0210.0000.0000.0000.000
187F234THR00.033-0.00526.078-0.022-0.0220.0000.0000.0000.000
188F235GLU-1-0.874-0.94827.637-0.229-0.2290.0000.0000.0000.000
189F236SER0-0.038-0.01722.208-0.013-0.0130.0000.0000.0000.000
190F237TRP00.0350.01619.602-0.039-0.0390.0000.0000.0000.000
191F238ALA0-0.001-0.00524.036-0.005-0.0050.0000.0000.0000.000
192F239GLU-1-0.897-0.95818.288-0.607-0.6070.0000.0000.0000.000
193F240ALA00.0880.03620.3570.0000.0000.0000.0000.0000.000
194F241VAL0-0.038-0.01721.4610.0170.0170.0000.0000.0000.000
195F242ARG10.9100.95024.3590.2990.2990.0000.0000.0000.000
196F243LEU00.0060.01016.9650.0190.0190.0000.0000.0000.000
197F244GLY00.0480.01421.358-0.008-0.0080.0000.0000.0000.000
198F245LEU0-0.009-0.01522.8370.0200.0200.0000.0000.0000.000
199F246GLU-1-0.840-0.89119.348-0.389-0.3890.0000.0000.0000.000
200F247GLY00.0650.02721.0220.0210.0210.0000.0000.0000.000
201F248CYS0-0.0260.00121.6420.0200.0200.0000.0000.0000.000
202F249GLN00.015-0.01425.0580.0340.0340.0000.0000.0000.000
203F250ARG10.7600.86616.5420.4260.4260.0000.0000.0000.000
204F251LEU0-0.001-0.01020.3050.0190.0190.0000.0000.0000.000
205F252TYR00.0130.01124.3770.0200.0200.0000.0000.0000.000
206F253PRO0-0.0080.00126.7910.0160.0160.0000.0000.0000.000
207F254VAL00.0500.02323.3520.0140.0140.0000.0000.0000.000
208F255LEU00.0070.01425.8250.0160.0160.0000.0000.0000.000
209F256GLN00.0790.04727.9020.0160.0160.0000.0000.0000.000
210F257GLN0-0.019-0.01428.7940.0050.0050.0000.0000.0000.000
211F258SER0-0.108-0.06227.8750.0100.0100.0000.0000.0000.000
212F259LEU00.0330.02430.0230.0090.0090.0000.0000.0000.000
213F260VAL00.0350.00833.0570.0090.0090.0000.0000.0000.000
214F261ARG10.9000.95727.9600.0480.0480.0000.0000.0000.000
215F262ALA0-0.0040.00533.6070.0070.0070.0000.0000.0000.000
216F263ALA00.0520.02235.3670.0050.0050.0000.0000.0000.000
217F264ARG10.9570.98137.9060.0460.0460.0000.0000.0000.000
218F265ARG10.9010.95235.5890.0210.0210.0000.0000.0000.000
219F266ARG10.8590.90937.9830.0460.0460.0000.0000.0000.000
220F267GLY00.0160.01141.2750.0020.0020.0000.0000.0000.000
221F268ALA0-0.023-0.02442.5990.0020.0020.0000.0000.0000.000
222F269ALA0-0.048-0.01843.0840.0020.0020.0000.0000.0000.000
223F270ALA0-0.0430.00144.9830.0010.0010.0000.0000.0000.000