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: GQ911

Calculation Name: 1TII-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TII

Chain ID: A

ChEMBL ID:

UniProt ID: P43528

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2032087.658802
FMO2-HF: Nuclear repulsion 1959084.584115
FMO2-HF: Total energy -73003.074687
FMO2-MP2: Total energy -73218.948272


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:1:ASN )


Summations of interaction energy for fragment #1(A:1:ASN )
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.
-14.058-9.343.782-2.974-5.525-0.026
Interaction energy analysis for fragmet #1(A:1:ASN )
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 : -0.036
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].
3A3TYR 0-0.022-0.0172.272-8.578-4.6302.892-2.482-4.358-0.025
4A4PHE 0-0.023-0.0215.5871.0861.0860.0000.0000.0000.000
5A5ARG 10.8410.8959.2411.1061.1060.0000.0000.0000.000
6A6ALA 0-0.0220.02112.5280.1630.1630.0000.0000.0000.000
7A7ASP -1-0.732-0.83415.976-0.861-0.8610.0000.0000.0000.000
8A8SER 00.035-0.00518.4420.0470.0470.0000.0000.0000.000
9A9ARG 10.7860.89718.7980.7820.7820.0000.0000.0000.000
10A10THR 00.0150.02320.891-0.027-0.0270.0000.0000.0000.000
11A11PRO 00.0370.00720.046-0.019-0.0190.0000.0000.0000.000
12A12ASP -1-0.901-0.95421.514-0.253-0.2530.0000.0000.0000.000
13A13GLU -1-0.896-0.94923.576-0.395-0.3950.0000.0000.0000.000
14A14VAL 00.0210.01917.840-0.017-0.0170.0000.0000.0000.000
15A15ARG 10.9170.95020.8930.2670.2670.0000.0000.0000.000
16A16ARG 10.9070.95822.2400.3030.3030.0000.0000.0000.000
17A17SER 00.0000.01622.1390.0110.0110.0000.0000.0000.000
18A18GLY 00.0050.01921.184-0.023-0.0230.0000.0000.0000.000
19A19GLY 00.009-0.00817.785-0.062-0.0620.0000.0000.0000.000
20A20LEU 0-0.082-0.02413.9950.0710.0710.0000.0000.0000.000
21A21ILE 00.0580.03817.006-0.133-0.1330.0000.0000.0000.000
22A22PRO 00.020-0.00518.6810.0080.0080.0000.0000.0000.000
23A23ARG 10.9380.96020.5630.5810.5810.0000.0000.0000.000
24A24GLY 0-0.019-0.00323.7480.0460.0460.0000.0000.0000.000
25A25GLN 0-0.034-0.00222.537-0.022-0.0220.0000.0000.0000.000
26A26ASP -1-0.890-0.95025.492-0.411-0.4110.0000.0000.0000.000
27A27GLU -1-0.978-0.98127.108-0.356-0.3560.0000.0000.0000.000
28A28ALA 00.019-0.01824.181-0.041-0.0410.0000.0000.0000.000
29A29TYR 0-0.003-0.01716.704-0.030-0.0300.0000.0000.0000.000
30A30GLU -1-0.942-0.99419.876-0.593-0.5930.0000.0000.0000.000
31A31ARG 10.7920.93122.7980.4020.4020.0000.0000.0000.000
32A32GLY 00.1120.06725.5530.0230.0230.0000.0000.0000.000
33A33THR 0-0.008-0.00823.717-0.031-0.0310.0000.0000.0000.000
34A34PRO 0-0.040-0.01321.2570.0260.0260.0000.0000.0000.000
35A35ILE 00.0040.00324.3800.0140.0140.0000.0000.0000.000
36A36ASN 0-0.018-0.01226.0310.0410.0410.0000.0000.0000.000
37A37ILE 0-0.035-0.01320.369-0.043-0.0430.0000.0000.0000.000
38A38ASN 00.0400.02521.876-0.012-0.0120.0000.0000.0000.000
39A39LEU 00.0230.01715.004-0.021-0.0210.0000.0000.0000.000
40A40TYR 00.0330.01619.030-0.014-0.0140.0000.0000.0000.000
41A41ASP -1-0.869-0.94021.086-0.568-0.5680.0000.0000.0000.000
42A42HIS 10.7300.84815.7571.1781.1780.0000.0000.0000.000
43A43ALA 0-0.032-0.01717.412-0.007-0.0070.0000.0000.0000.000
44A44ARG 10.8710.92818.8380.5960.5960.0000.0000.0000.000
45A45GLY 0-0.0010.01922.2110.0570.0570.0000.0000.0000.000
46A46THR 0-0.0040.00622.137-0.049-0.0490.0000.0000.0000.000
47A47ALA 0-0.070-0.02721.8040.0160.0160.0000.0000.0000.000
48A48THR 00.0250.00723.7390.0220.0220.0000.0000.0000.000
49A49GLY 00.0150.01625.9980.0010.0010.0000.0000.0000.000
50A50ASN 00.0470.00020.371-0.033-0.0330.0000.0000.0000.000
51A51THR 00.0290.00317.2750.0010.0010.0000.0000.0000.000
52A52ARG 10.8210.88017.6090.8590.8590.0000.0000.0000.000
53A53TYR 0-0.018-0.02117.363-0.112-0.1120.0000.0000.0000.000
54A54ASN 00.0420.02419.2390.0580.0580.0000.0000.0000.000
55A55ASP -1-0.828-0.90820.793-0.735-0.7350.0000.0000.0000.000
56A56GLY 00.0650.01720.943-0.042-0.0420.0000.0000.0000.000
57A57TYR 00.0150.02114.972-0.031-0.0310.0000.0000.0000.000
58A58VAL 0-0.044-0.01913.9040.1290.1290.0000.0000.0000.000
59A59SER 0-0.0090.01113.334-0.236-0.2360.0000.0000.0000.000
60A60THR 0-0.045-0.0118.560-0.143-0.1430.0000.0000.0000.000
61A61THR 00.0540.0199.2040.0050.0050.0000.0000.0000.000
62A62THR 00.0610.0154.985-0.222-0.2220.0000.0000.0000.000
63A63THR 0-0.0030.0116.6260.6740.6740.0000.0000.0000.000
64A64LEU 00.0530.0329.175-0.140-0.1400.0000.0000.0000.000
65A65ARG 11.0040.99411.6960.1680.1680.0000.0000.0000.000
66A66GLN 00.005-0.00411.732-0.064-0.0640.0000.0000.0000.000
67A67ALA 00.0610.02311.689-0.001-0.0010.0000.0000.0000.000
68A68HIS 0-0.038-0.02113.5530.0720.0720.0000.0000.0000.000
69A69LEU 0-0.065-0.02916.4110.0430.0430.0000.0000.0000.000
70A70LEU 00.019-0.00314.0150.0380.0380.0000.0000.0000.000
71A71GLY 00.0190.01117.6350.0250.0250.0000.0000.0000.000
72A72GLN 0-0.009-0.00219.2720.0270.0270.0000.0000.0000.000
73A73ASN 0-0.052-0.01020.9980.0590.0590.0000.0000.0000.000
74A74MET 0-0.013-0.01019.808-0.016-0.0160.0000.0000.0000.000
75A75LEU 0-0.037-0.00819.7700.0110.0110.0000.0000.0000.000
76A76GLY 00.0520.04923.4100.0380.0380.0000.0000.0000.000
77A77GLY 0-0.027-0.02225.804-0.006-0.0060.0000.0000.0000.000
78A78TYR 0-0.056-0.01225.3370.0190.0190.0000.0000.0000.000
79A79ASN 0-0.051-0.03727.0620.0160.0160.0000.0000.0000.000
80A80GLU -1-0.874-0.94324.636-0.193-0.1930.0000.0000.0000.000
81A81TYR 0-0.012-0.00118.463-0.048-0.0480.0000.0000.0000.000
82A82TYR 00.001-0.01118.2290.0640.0640.0000.0000.0000.000
83A83ILE 0-0.0020.00912.938-0.087-0.0870.0000.0000.0000.000
84A84TYR 0-0.036-0.06013.2180.1250.1250.0000.0000.0000.000
85A85VAL 0-0.0080.0027.927-0.204-0.2040.0000.0000.0000.000
86A86VAL 0-0.024-0.0177.5390.3900.3900.0000.0000.0000.000
87A87ALA 00.0530.0304.796-1.190-1.1660.000-0.011-0.0120.000
88A88ALA 00.0050.0012.4290.0830.5600.890-0.433-0.934-0.001
89A89ALA 00.0090.0004.5471.3721.5310.000-0.022-0.1370.000
90A90PRO 00.0430.0167.650-0.426-0.4260.0000.0000.0000.000
91A91ASN 00.0390.03610.093-0.126-0.1260.0000.0000.0000.000
92A92LEU 0-0.067-0.0155.9970.0710.0710.0000.0000.0000.000
93A93PHE 00.0610.0209.125-0.194-0.1940.0000.0000.0000.000
94A94ASP -1-0.838-0.9207.987-2.769-2.7690.0000.0000.0000.000
95A95VAL 00.019-0.0019.4190.4440.4440.0000.0000.0000.000
96A96ASN 0-0.018-0.00511.6570.3370.3370.0000.0000.0000.000
97A97GLY 0-0.0200.00811.6890.2260.2260.0000.0000.0000.000
98A98VAL 0-0.027-0.00412.7390.2050.2050.0000.0000.0000.000
99A99LEU 00.007-0.00814.9800.1730.1730.0000.0000.0000.000
100A100GLY 00.0590.04516.4120.1270.1270.0000.0000.0000.000
101A101ARG 10.9310.94817.9640.4010.4010.0000.0000.0000.000
102A102TYR 0-0.067-0.03920.3480.0530.0530.0000.0000.0000.000
103A103SER 0-0.037-0.02515.247-0.007-0.0070.0000.0000.0000.000
104A104PRO 00.0160.00718.3280.0550.0550.0000.0000.0000.000
105A105TYR 0-0.022-0.00817.3480.1030.1030.0000.0000.0000.000
106A106PRO 00.0340.02815.231-0.115-0.1150.0000.0000.0000.000
107A107SER 0-0.017-0.01314.253-0.121-0.1210.0000.0000.0000.000
108A108GLU -1-0.840-0.91814.061-1.004-1.0040.0000.0000.0000.000
109A109ASN 0-0.088-0.0278.983-0.222-0.2220.0000.0000.0000.000
110A110GLU -1-0.798-0.9019.205-1.989-1.9890.0000.0000.0000.000
111A111TYR 00.0140.0115.277-1.173-1.1730.0000.0000.0000.000
112A112ALA 0-0.0100.0019.0310.1110.1110.0000.0000.0000.000
113A113ALA 00.0120.00311.323-0.141-0.1410.0000.0000.0000.000
114A114LEU 00.011-0.00812.5430.2610.2610.0000.0000.0000.000
115A115GLY 00.0180.00415.6360.0170.0170.0000.0000.0000.000
116A116GLY 0-0.035-0.01615.8580.1090.1090.0000.0000.0000.000
117A117ILE 0-0.062-0.03211.308-0.154-0.1540.0000.0000.0000.000
118A118PRO 00.0650.05013.3350.1790.1790.0000.0000.0000.000
119A119LEU 00.044-0.00414.152-0.099-0.0990.0000.0000.0000.000
120A120SER 0-0.027-0.01214.281-0.043-0.0430.0000.0000.0000.000
121A121GLN 00.0180.0068.2280.5490.5490.0000.0000.0000.000
122A122ILE 0-0.049-0.0189.599-0.295-0.2950.0000.0000.0000.000
123A123ILE 00.0470.0336.2240.3420.3420.0000.0000.0000.000
124A124GLY 00.007-0.01510.8150.2870.2870.0000.0000.0000.000
125A125TRP 00.0050.01113.302-0.191-0.1910.0000.0000.0000.000
126A126TYR 00.0110.01511.9310.1760.1760.0000.0000.0000.000
127A127ARG 10.9300.96117.0460.0580.0580.0000.0000.0000.000
128A128VAL 0-0.0080.00319.0990.0450.0450.0000.0000.0000.000
129A129SER 00.0230.00521.806-0.023-0.0230.0000.0000.0000.000
130A130PHE 00.005-0.01525.5530.0210.0210.0000.0000.0000.000
131A131GLY 0-0.0100.01323.7990.0110.0110.0000.0000.0000.000
132A132ALA 00.0010.01122.961-0.001-0.0010.0000.0000.0000.000
133A133ILE 0-0.013-0.01716.466-0.027-0.0270.0000.0000.0000.000
134A134GLU -1-0.942-0.97120.5940.0030.0030.0000.0000.0000.000
135A135GLY 0-0.023-0.00221.639-0.005-0.0050.0000.0000.0000.000
136A136GLY 0-0.008-0.01417.8690.0170.0170.0000.0000.0000.000
137A137MET 0-0.054-0.01412.086-0.055-0.0550.0000.0000.0000.000
138A138HIS 0-0.021-0.01016.0020.0920.0920.0000.0000.0000.000
139A139ARG 10.9270.95113.152-0.616-0.6160.0000.0000.0000.000
140A140ASN 0-0.001-0.01014.2120.0970.0970.0000.0000.0000.000
141A141ARG 10.9240.94515.5430.0490.0490.0000.0000.0000.000
142A142ASP -1-0.899-0.95017.448-0.230-0.2300.0000.0000.0000.000
143A143TYR 0-0.0170.0137.2470.2460.2460.0000.0000.0000.000
144A144ARG 10.8740.93712.7090.3500.3500.0000.0000.0000.000
145A145ARG 10.9800.97510.010-0.480-0.4800.0000.0000.0000.000
146A146ASP -1-0.938-0.98210.298-0.023-0.0230.0000.0000.0000.000
147A147LEU 00.0120.01312.2000.0030.0030.0000.0000.0000.000
148A148PHE 00.0270.0057.014-0.125-0.1250.0000.0000.0000.000
149A149ARG 10.8860.9476.457-1.489-1.4890.0000.0000.0000.000
150A150GLY 0-0.011-0.0125.648-0.001-0.0010.0000.0000.0000.000
151A151LEU 00.0110.0495.8720.0200.0200.0000.0000.0000.000
152A152SER 0-0.026-0.0294.257-0.651-0.5410.000-0.026-0.0840.000
153A153ALA 00.000-0.0114.8610.2620.2620.0000.0000.0000.000
154A154ALA 0-0.0130.0036.6420.6170.6170.0000.0000.0000.000
155A155PRO 0-0.0220.0129.867-0.273-0.2730.0000.0000.0000.000
156A156ASN 00.049-0.00611.245-0.159-0.1590.0000.0000.0000.000
157A157GLU -1-0.907-0.95113.287-0.848-0.8480.0000.0000.0000.000
158A158ASP -1-0.905-0.95914.788-0.928-0.9280.0000.0000.0000.000
159A159GLY 0-0.018-0.01815.1670.0120.0120.0000.0000.0000.000
160A160TYR 0-0.057-0.03316.0300.0900.0900.0000.0000.0000.000
161A161ARG 10.9600.99218.8960.5690.5690.0000.0000.0000.000
162A162ILE 0-0.054-0.02516.8250.0620.0620.0000.0000.0000.000
163A163ALA 00.0130.01119.007-0.033-0.0330.0000.0000.0000.000
164A164GLY 0-0.012-0.01620.012-0.010-0.0100.0000.0000.0000.000
165A165PHE 00.0160.01420.7650.0130.0130.0000.0000.0000.000
166A166PRO 0-0.0110.00424.8810.0170.0170.0000.0000.0000.000
167A167ASP -1-0.865-0.95828.527-0.339-0.3390.0000.0000.0000.000
168A168GLY 00.0340.02331.2050.0120.0120.0000.0000.0000.000
169A169PHE 0-0.068-0.02024.8690.0100.0100.0000.0000.0000.000
170A170PRO 00.0480.00428.073-0.001-0.0010.0000.0000.0000.000
171A171ALA 00.0240.01623.9460.0090.0090.0000.0000.0000.000
172A172TRP 0-0.047-0.02423.528-0.023-0.0230.0000.0000.0000.000
173A173GLU -1-0.951-0.97827.747-0.260-0.2600.0000.0000.0000.000
174A174GLU -1-0.904-0.94525.934-0.391-0.3910.0000.0000.0000.000
175A175VAL 0-0.0170.02823.699-0.028-0.0280.0000.0000.0000.000
176A176PRO 0-0.017-0.03519.5090.0110.0110.0000.0000.0000.000
177A177TRP 0-0.001-0.02519.0550.0350.0350.0000.0000.0000.000
178A178ARG 10.9680.98523.2940.3040.3040.0000.0000.0000.000
179A179GLU -1-0.962-0.98224.406-0.308-0.3080.0000.0000.0000.000
180A180PHE 0-0.064-0.03720.907-0.008-0.0080.0000.0000.0000.000
181A181ALA 00.0050.01324.208-0.025-0.0250.0000.0000.0000.000
182A182PRO 0-0.034-0.00725.1760.0310.0310.0000.0000.0000.000
183A183ASN 00.059-0.00427.8420.0040.0040.0000.0000.0000.000
184A184SER 0-0.059-0.03231.3820.0070.0070.0000.0000.0000.000
185A185CYS 0-0.0260.01228.453-0.011-0.0110.0000.0000.0000.000
186A186LEU 0-0.039-0.00629.4480.0000.0000.0000.0000.0000.000
187A187PRO 00.0060.02531.7900.0100.0100.0000.0000.0000.000
188A188NME 0-0.032-0.02134.7310.0150.0150.0000.0000.0000.000