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: JQML9

Calculation Name: 3F5C-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5C

Chain ID: C

ChEMBL ID:

UniProt ID: Q61066

Base Structure: X-ray

Registration Date: 2023-09-20

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014263.330002
FMO2-HF: Nuclear repulsion 1938910.078775
FMO2-HF: Total energy -75353.251227
FMO2-MP2: Total energy -75565.267662


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(C:252:ASP)


Summations of interaction energy for fragment #1(C:252:ASP)
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.
-19.635-16.24311.617-6.9-8.1080.087
Interaction energy analysis for fragmet #1(C:252:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.825 / q_NPA : -0.920
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].
3C254GLN00.0700.0213.681-4.219-2.7370.031-0.529-0.9840.005
4C255VAL0-0.0060.0043.182-5.611-4.8740.094-0.215-0.6150.000
5C256VAL00.0250.0093.294-6.617-5.6670.040-0.320-0.6690.001
6C257CYS0-0.023-0.0045.848-5.460-5.4600.0000.0000.0000.000
7C258GLU-1-0.907-0.9388.25520.90120.9010.0000.0000.0000.000
8C259ALA0-0.012-0.0109.069-2.787-2.7870.0000.0000.0000.000
9C260ALA00.0250.0129.862-2.355-2.3550.0000.0000.0000.000
10C261SER00.008-0.01011.671-2.629-2.6290.0000.0000.0000.000
11C262ALA0-0.039-0.00913.778-1.804-1.8040.0000.0000.0000.000
12C263GLY00.0530.02514.379-1.399-1.3990.0000.0000.0000.000
13C264LEU00.0000.01515.873-1.378-1.3780.0000.0000.0000.000
14C265LEU0-0.010-0.01117.706-1.295-1.2950.0000.0000.0000.000
15C266LYS10.7490.85217.734-17.048-17.0480.0000.0000.0000.000
16C267THR00.010-0.01419.038-0.817-0.8170.0000.0000.0000.000
17C268LEU00.012-0.00821.579-0.798-0.7980.0000.0000.0000.000
18C269ARG10.9070.96522.878-13.360-13.3600.0000.0000.0000.000
19C270PHE0-0.008-0.00924.225-0.633-0.6330.0000.0000.0000.000
20C271VAL0-0.003-0.00325.287-0.470-0.4700.0000.0000.0000.000
21C272LYS10.8240.91527.599-10.475-10.4750.0000.0000.0000.000
22C273TYR0-0.009-0.02028.635-0.293-0.2930.0000.0000.0000.000
23C274LEU00.0110.02830.683-0.386-0.3860.0000.0000.0000.000
24C275PRO00.0300.00432.503-0.113-0.1130.0000.0000.0000.000
25C276CYS0-0.020-0.01234.778-0.105-0.1050.0000.0000.0000.000
26C277PHE00.0250.02329.566-0.105-0.1050.0000.0000.0000.000
27C278GLN00.0410.01534.1580.0480.0480.0000.0000.0000.000
28C279ILE0-0.082-0.01636.105-0.169-0.1690.0000.0000.0000.000
29C280LEU00.004-0.00734.112-0.069-0.0690.0000.0000.0000.000
30C281PRO00.0050.01137.3690.0870.0870.0000.0000.0000.000
31C282LEU00.0060.01132.1070.0020.0020.0000.0000.0000.000
32C283ASP-1-0.787-0.89933.4528.8638.8630.0000.0000.0000.000
33C284GLN0-0.003-0.02633.5080.2560.2560.0000.0000.0000.000
34C285GLN0-0.023-0.00931.1340.2880.2880.0000.0000.0000.000
35C286LEU00.0140.00327.7860.4230.4230.0000.0000.0000.000
36C287VAL0-0.019-0.00628.8170.4260.4260.0000.0000.0000.000
37C288LEU00.0020.00829.3830.2480.2480.0000.0000.0000.000
38C289VAL00.0170.00824.4140.4260.4260.0000.0000.0000.000
39C290ARG10.8260.88524.463-11.583-11.5830.0000.0000.0000.000
40C291SER00.0010.00724.3780.3750.3750.0000.0000.0000.000
41C292CYS0-0.051-0.02323.8110.3020.3020.0000.0000.0000.000
42C293TRP00.0090.00516.2310.6960.6960.0000.0000.0000.000
43C294ALA00.0570.04017.6810.5360.5360.0000.0000.0000.000
44C295PRO00.014-0.01217.8100.7120.7120.0000.0000.0000.000
45C296LEU0-0.014-0.00419.7300.1890.1890.0000.0000.0000.000
46C297LEU00.0000.01214.3330.0960.0960.0000.0000.0000.000
47C298MET0-0.015-0.00212.8011.2691.2690.0000.0000.0000.000
48C299LEU00.003-0.00416.2770.1150.1150.0000.0000.0000.000
49C300GLU-1-0.864-0.90317.14714.33014.3300.0000.0000.0000.000
50C301LEU0-0.002-0.00211.1330.1690.1690.0000.0000.0000.000
51C302ALA00.0040.01313.7590.6820.6820.0000.0000.0000.000
52C303GLN00.0110.01115.937-0.278-0.2780.0000.0000.0000.000
53C304ASP-1-0.859-0.91814.46216.72916.7290.0000.0000.0000.000
54C305HIS0-0.086-0.04014.108-0.017-0.0170.0000.0000.0000.000
55C306LEU00.0190.0097.5510.7030.7030.0000.0000.0000.000
56C307HIS0-0.047-0.0377.644-0.771-0.7710.0000.0000.0000.000
57C308PHE0-0.050-0.0244.8442.1712.1710.0000.0000.0000.000
58C309GLU-1-0.920-0.9414.46228.32128.412-0.001-0.012-0.0780.000
59C310MET0-0.041-0.0354.1887.8658.1810.001-0.043-0.2740.000
60C311MET00.0260.0334.138-4.841-4.645-0.001-0.030-0.1660.000
61C312GLU-1-0.969-0.9806.68927.99027.9900.0000.0000.0000.000
62C353HIS0-0.014-0.0301.884-41.218-41.59811.453-5.751-5.3220.081
63C354LEU0-0.033-0.0257.331-4.505-4.5050.0000.0000.0000.000
64C355LEU00.0290.02110.875-0.022-0.0220.0000.0000.0000.000
65C356PRO00.0170.00613.014-1.047-1.0470.0000.0000.0000.000
66C357ALA00.0460.01313.8990.2830.2830.0000.0000.0000.000
67C358ALA0-0.011-0.00414.9460.1820.1820.0000.0000.0000.000
68C359ALA00.0480.02515.303-0.241-0.2410.0000.0000.0000.000
69C360VAL00.0420.02710.2530.0510.0510.0000.0000.0000.000
70C361GLN00.0140.00312.6191.4511.4510.0000.0000.0000.000
71C362ALA0-0.0060.01714.988-0.688-0.6880.0000.0000.0000.000
72C363ILE00.0350.01211.772-0.682-0.6820.0000.0000.0000.000
73C364LYS10.9710.98910.721-27.579-27.5790.0000.0000.0000.000
74C365SER0-0.033-0.04513.563-0.888-0.8880.0000.0000.0000.000
75C366PHE0-0.018-0.01216.461-1.068-1.0680.0000.0000.0000.000
76C367PHE00.0220.01511.668-0.828-0.8280.0000.0000.0000.000
77C368PHE00.0200.00612.819-0.726-0.7260.0000.0000.0000.000
78C369LYS10.9070.96917.176-13.601-13.6010.0000.0000.0000.000
79C370CYS0-0.015-0.02018.476-0.916-0.9160.0000.0000.0000.000
80C371TRP0-0.049-0.03211.568-0.585-0.5850.0000.0000.0000.000
81C372SER0-0.057-0.02919.373-0.615-0.6150.0000.0000.0000.000
82C373LEU0-0.059-0.01822.039-0.632-0.6320.0000.0000.0000.000
83C374ASN0-0.049-0.01823.234-0.188-0.1880.0000.0000.0000.000
84C375ILE00.0010.02122.409-0.433-0.4330.0000.0000.0000.000
85C376ASP-1-0.723-0.84223.68410.87310.8730.0000.0000.0000.000
86C377THR00.000-0.03024.7810.3270.3270.0000.0000.0000.000
87C378LYS10.8830.95525.821-9.017-9.0170.0000.0000.0000.000
88C379GLU-1-0.778-0.87227.07910.69910.6990.0000.0000.0000.000
89C380TYR00.0760.02919.3970.0770.0770.0000.0000.0000.000
90C381ALA0-0.033-0.00324.7310.1430.1430.0000.0000.0000.000
91C382TYR00.018-0.01226.849-0.163-0.1630.0000.0000.0000.000
92C383LEU00.0140.02424.873-0.162-0.1620.0000.0000.0000.000
93C384LYS10.8400.91121.284-13.890-13.8900.0000.0000.0000.000
94C385GLY00.0050.00125.845-0.086-0.0860.0000.0000.0000.000
95C386THR0-0.047-0.04328.959-0.297-0.2970.0000.0000.0000.000
96C387VAL0-0.0070.00623.947-0.177-0.1770.0000.0000.0000.000
97C388LEU0-0.024-0.01127.266-0.042-0.0420.0000.0000.0000.000
98C389PHE0-0.011-0.01028.496-0.206-0.2060.0000.0000.0000.000
99C390ASN0-0.0020.00428.813-0.386-0.3860.0000.0000.0000.000
100C391PRO00.010-0.00832.3290.0340.0340.0000.0000.0000.000
101C392ASP-1-0.882-0.95132.6849.1529.1520.0000.0000.0000.000
102C393LEU0-0.0310.00029.119-0.013-0.0130.0000.0000.0000.000
103C394PRO00.009-0.01032.281-0.288-0.2880.0000.0000.0000.000
104C395GLY00.0160.01333.7710.2300.2300.0000.0000.0000.000
105C396LEU0-0.0230.00534.289-0.127-0.1270.0000.0000.0000.000
106C397GLN0-0.054-0.02737.078-0.383-0.3830.0000.0000.0000.000
107C398CYS0-0.031-0.01237.738-0.155-0.1550.0000.0000.0000.000
108C399VAL00.0390.02538.6580.0470.0470.0000.0000.0000.000
109C400LYS11.0050.98539.449-6.753-6.7530.0000.0000.0000.000
110C401TYR0-0.081-0.03437.860-0.141-0.1410.0000.0000.0000.000
111C402ILE00.0320.00534.2580.0330.0330.0000.0000.0000.000
112C403GLU-1-0.851-0.92836.8047.7987.7980.0000.0000.0000.000
113C404GLY0-0.0010.00439.0230.0050.0050.0000.0000.0000.000
114C405LEU0-0.055-0.03035.668-0.029-0.0290.0000.0000.0000.000
115C406GLN00.0020.00931.8760.1310.1310.0000.0000.0000.000
116C407TRP00.0150.00935.6490.0680.0680.0000.0000.0000.000
117C408ARG10.9370.95838.307-7.624-7.6240.0000.0000.0000.000
118C409THR0-0.021-0.01031.6500.0530.0530.0000.0000.0000.000
119C410GLN00.013-0.00633.901-0.031-0.0310.0000.0000.0000.000
120C411GLN0-0.0250.01835.617-0.081-0.0810.0000.0000.0000.000
121C412ILE0-0.016-0.02034.610-0.092-0.0920.0000.0000.0000.000
122C413LEU00.0180.01530.9510.0400.0400.0000.0000.0000.000
123C414THR0-0.049-0.03534.358-0.003-0.0030.0000.0000.0000.000
124C415GLU-1-0.936-0.97237.3587.3887.3880.0000.0000.0000.000
125C416HIS0-0.076-0.06831.224-0.347-0.3470.0000.0000.0000.000
126C417ILE00.0140.00932.826-0.018-0.0180.0000.0000.0000.000
127C418ARG10.9290.96235.843-7.661-7.6610.0000.0000.0000.000
128C419MET0-0.055-0.01737.943-0.216-0.2160.0000.0000.0000.000
129C420MET0-0.063-0.01733.4870.0910.0910.0000.0000.0000.000
130C421GLN0-0.041-0.01030.8200.0120.0120.0000.0000.0000.000
131C422ARG10.9610.96336.131-7.412-7.4120.0000.0000.0000.000
132C423GLU-1-0.875-0.93837.3267.8347.8340.0000.0000.0000.000
133C424TYR0-0.007-0.01836.6440.1940.1940.0000.0000.0000.000
134C425GLN00.0370.00136.3410.2510.2510.0000.0000.0000.000
135C426ILE00.0100.02133.5800.1820.1820.0000.0000.0000.000
136C427ARG10.8360.88927.589-10.394-10.3940.0000.0000.0000.000
137C428SER00.0140.01231.4340.4290.4290.0000.0000.0000.000
138C429ALA00.0210.01331.9500.2820.2820.0000.0000.0000.000
139C430GLU-1-0.868-0.91528.28710.82810.8280.0000.0000.0000.000
140C431LEU00.0200.00526.7810.5080.5080.0000.0000.0000.000
141C432ASN0-0.059-0.04727.0460.4920.4920.0000.0000.0000.000
142C433SER0-0.056-0.03326.7370.2120.2120.0000.0000.0000.000
143C434ALA00.0110.00722.6820.4550.4550.0000.0000.0000.000
144C435LEU00.0340.00022.9820.5250.5250.0000.0000.0000.000
145C436PHE0-0.055-0.02025.293-0.010-0.0100.0000.0000.0000.000
146C437LEU0-0.004-0.01219.8190.0930.0930.0000.0000.0000.000
147C438LEU0-0.0040.00319.5350.4810.4810.0000.0000.0000.000
148C439ARG10.8940.95821.559-10.973-10.9730.0000.0000.0000.000
149C440PHE0-0.050-0.01320.620-0.300-0.3000.0000.0000.0000.000
150C441ILE00.0540.02716.0860.7820.7820.0000.0000.0000.000
151C442ASN0-0.095-0.04417.4480.7420.7420.0000.0000.0000.000
152C443SER00.0330.01017.917-0.758-0.7580.0000.0000.0000.000
153C444ASP-1-0.847-0.92017.20816.10616.1060.0000.0000.0000.000
154C445VAL00.016-0.00512.7600.9890.9890.0000.0000.0000.000
155C446VAL00.0270.01612.4381.9521.9520.0000.0000.0000.000
156C447THR00.0150.01012.2151.3141.3140.0000.0000.0000.000
157C448GLU-1-0.842-0.91012.26321.81121.8110.0000.0000.0000.000
158C449LEU0-0.036-0.0177.2861.6411.6410.0000.0000.0000.000
159C450PHE0-0.022-0.0057.1754.5024.5020.0000.0000.0000.000
160C451PHE00.0270.0009.178-0.727-0.7270.0000.0000.0000.000
161C452ARG10.8400.90211.565-20.203-20.2030.0000.0000.0000.000
162C453PRO0-0.028-0.0207.472-1.444-1.4440.0000.0000.0000.000
163C454ILE0-0.019-0.0029.664-0.238-0.2380.0000.0000.0000.000
164C455ILE00.0090.00112.928-1.497-1.4970.0000.0000.0000.000
165C456GLY00.0350.02315.050-1.433-1.4330.0000.0000.0000.000
166C457ALA0-0.074-0.05916.7430.0210.0210.0000.0000.0000.000
167C458VAL0-0.0430.00319.611-0.645-0.6450.0000.0000.0000.000
168C459SER0-0.048-0.04920.564-0.114-0.1140.0000.0000.0000.000
169C460MET0-0.034-0.01316.0290.9380.9380.0000.0000.0000.000
170C461ASP-1-0.816-0.88319.99813.34013.3400.0000.0000.0000.000
171C462ASP-1-0.827-0.91123.79312.24512.2450.0000.0000.0000.000
172C463MET00.0080.00217.819-0.427-0.4270.0000.0000.0000.000
173C464MET0-0.020-0.00319.665-0.277-0.2770.0000.0000.0000.000
174C465LEU00.0060.00024.393-0.368-0.3680.0000.0000.0000.000
175C466GLU-1-0.835-0.90825.30311.02411.0240.0000.0000.0000.000
176C467MET0-0.055-0.02220.019-0.382-0.3820.0000.0000.0000.000
177C468LEU0-0.014-0.00325.309-0.159-0.1590.0000.0000.0000.000
178C469CYS0-0.044-0.02228.533-0.474-0.4740.0000.0000.0000.000
179C470ALA00.0420.02727.522-0.287-0.2870.0000.0000.0000.000
180C471LYS10.8180.91324.400-12.736-12.7360.0000.0000.0000.000
181C472LEU00.0150.02429.678-0.201-0.2010.0000.0000.0000.000