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: 22R7R

Calculation Name: 1TII-A-Xray372

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: 2023-03-13

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 OptHSide
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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2030323.621224
FMO2-HF: Nuclear repulsion 1957338.973571
FMO2-HF: Total energy -72984.647653
FMO2-MP2: Total energy -73200.438496


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.
-9.059-3.6973.352-3.144-5.569-0.018
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 : -0.013 / q_NPA : -0.007
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].
3A3TYR0-0.028-0.0172.304-8.051-3.4502.466-2.700-4.367-0.016
4A4PHE0-0.019-0.0225.6930.6980.6980.0000.0000.0000.000
5A5ARG10.8230.8869.3831.2211.2210.0000.0000.0000.000
6A6ALA0-0.0230.02012.6180.1070.1070.0000.0000.0000.000
7A7ASP-1-0.730-0.83316.106-0.911-0.9110.0000.0000.0000.000
8A8SER00.037-0.00418.5010.0250.0250.0000.0000.0000.000
9A9ARG10.7800.89718.7700.8660.8660.0000.0000.0000.000
10A10THR00.001-0.02020.893-0.052-0.0520.0000.0000.0000.000
11A11PRO00.0290.00420.059-0.015-0.0150.0000.0000.0000.000
12A12ASP-1-0.841-0.90621.468-0.427-0.4270.0000.0000.0000.000
13A13GLU-1-0.816-0.87823.671-0.490-0.4900.0000.0000.0000.000
14A14VAL00.0070.02117.702-0.012-0.0120.0000.0000.0000.000
15A15ARG10.8930.93120.9920.4960.4960.0000.0000.0000.000
16A16ARG10.8510.91522.3760.4270.4270.0000.0000.0000.000
17A17SER0-0.0230.00121.7510.0300.0300.0000.0000.0000.000
18A18GLY00.0080.01821.266-0.012-0.0120.0000.0000.0000.000
19A19GLY00.006-0.00817.646-0.083-0.0830.0000.0000.0000.000
20A20LEU0-0.069-0.01914.0280.0890.0890.0000.0000.0000.000
21A21ILE00.0610.04016.837-0.127-0.1270.0000.0000.0000.000
22A22PRO00.031-0.00118.4570.0130.0130.0000.0000.0000.000
23A23ARG10.8760.93120.4220.5710.5710.0000.0000.0000.000
24A24GLY0-0.016-0.00423.6440.0430.0430.0000.0000.0000.000
25A25GLN0-0.053-0.01022.424-0.009-0.0090.0000.0000.0000.000
26A26ASP-1-0.891-0.94725.301-0.449-0.4490.0000.0000.0000.000
27A27GLU-1-0.971-0.97926.903-0.400-0.4000.0000.0000.0000.000
28A28ALA00.017-0.01524.200-0.044-0.0440.0000.0000.0000.000
29A29TYR0-0.004-0.02116.403-0.027-0.0270.0000.0000.0000.000
30A30GLU-1-0.930-0.98319.726-0.705-0.7050.0000.0000.0000.000
31A31ARG10.7990.92822.8020.4990.4990.0000.0000.0000.000
32A32GLY00.0860.05425.2770.0320.0320.0000.0000.0000.000
33A33THR00.003-0.00623.453-0.030-0.0300.0000.0000.0000.000
34A34PRO0-0.039-0.00921.0910.0250.0250.0000.0000.0000.000
35A35ILE00.0120.00724.1650.0170.0170.0000.0000.0000.000
36A36ASN0-0.031-0.01625.8370.0370.0370.0000.0000.0000.000
37A37ILE0-0.029-0.01519.953-0.046-0.0460.0000.0000.0000.000
38A38ASN00.0340.01621.504-0.003-0.0030.0000.0000.0000.000
39A39LEU00.0130.01214.698-0.024-0.0240.0000.0000.0000.000
40A40TYR00.0440.02718.714-0.021-0.0210.0000.0000.0000.000
41A41ASP-1-0.842-0.91620.799-0.472-0.4720.0000.0000.0000.000
42A42HIS10.7430.86115.4061.0791.0790.0000.0000.0000.000
43A43ALA0-0.028-0.01717.183-0.012-0.0120.0000.0000.0000.000
44A44ARG10.8510.90618.5160.4970.4970.0000.0000.0000.000
45A45GLY0-0.0130.01221.8340.0480.0480.0000.0000.0000.000
46A46THR0-0.009-0.00221.777-0.042-0.0420.0000.0000.0000.000
47A47ALA0-0.049-0.01521.5820.0100.0100.0000.0000.0000.000
48A48THR00.022-0.00223.4460.0270.0270.0000.0000.0000.000
49A49GLY00.0300.03026.065-0.005-0.0050.0000.0000.0000.000
50A50ASN00.017-0.00320.051-0.062-0.0620.0000.0000.0000.000
51A51THR00.0500.01217.2250.0070.0070.0000.0000.0000.000
52A52ARG10.8270.87816.9830.7260.7260.0000.0000.0000.000
53A53TYR00.007-0.01417.175-0.115-0.1150.0000.0000.0000.000
54A54ASN00.0040.00219.1370.0540.0540.0000.0000.0000.000
55A55ASP-1-0.792-0.89020.396-0.651-0.6510.0000.0000.0000.000
56A56GLY00.0690.02020.735-0.027-0.0270.0000.0000.0000.000
57A57TYR00.0230.02614.494-0.027-0.0270.0000.0000.0000.000
58A58VAL0-0.056-0.02213.8550.1180.1180.0000.0000.0000.000
59A59SER0-0.022-0.01513.144-0.233-0.2330.0000.0000.0000.000
60A60THR0-0.064-0.0308.624-0.190-0.1900.0000.0000.0000.000
61A61THR00.0480.0138.8700.0930.0930.0000.0000.0000.000
62A62THR00.0710.0224.941-0.296-0.2960.0000.0000.0000.000
63A63THR0-0.0060.0086.3460.7590.7590.0000.0000.0000.000
64A64LEU00.0450.0319.064-0.207-0.2070.0000.0000.0000.000
65A65ARG11.0040.99411.723-0.024-0.0240.0000.0000.0000.000
66A66GLN0-0.014-0.01211.425-0.024-0.0240.0000.0000.0000.000
67A67ALA00.0570.02311.884-0.016-0.0160.0000.0000.0000.000
68A68HIS0-0.037-0.02613.6890.0530.0530.0000.0000.0000.000
69A69LEU0-0.060-0.02616.0550.0400.0400.0000.0000.0000.000
70A70LEU00.0270.00113.7170.0290.0290.0000.0000.0000.000
71A71GLY00.0200.01017.6460.0130.0130.0000.0000.0000.000
72A72GLN0-0.0050.00719.4430.0090.0090.0000.0000.0000.000
73A73ASN0-0.034-0.00420.5640.0690.0690.0000.0000.0000.000
74A74MET0-0.037-0.01219.659-0.021-0.0210.0000.0000.0000.000
75A75LEU0-0.031-0.01019.9380.0010.0010.0000.0000.0000.000
76A76GLY00.0440.04623.5730.0260.0260.0000.0000.0000.000
77A77GLY0-0.026-0.02225.945-0.003-0.0030.0000.0000.0000.000
78A78TYR0-0.071-0.03325.4640.0180.0180.0000.0000.0000.000
79A79ASN0-0.046-0.03527.2390.0140.0140.0000.0000.0000.000
80A80GLU-1-0.828-0.89324.501-0.321-0.3210.0000.0000.0000.000
81A81TYR0-0.017-0.01218.609-0.043-0.0430.0000.0000.0000.000
82A82TYR0-0.020-0.04318.3280.0320.0320.0000.0000.0000.000
83A83ILE0-0.0140.00312.999-0.055-0.0550.0000.0000.0000.000
84A84TYR0-0.016-0.04513.1600.0570.0570.0000.0000.0000.000
85A85VAL0-0.005-0.0017.951-0.107-0.1070.0000.0000.0000.000
86A86VAL0-0.046-0.0287.6490.3400.3400.0000.0000.0000.000
87A87ALA00.0610.0414.934-1.258-1.2580.0000.0000.0000.000
88A88ALA00.0040.0062.5390.5631.0720.888-0.391-1.005-0.002
89A89ALA00.0250.0044.5631.2141.373-0.001-0.023-0.1350.000
90A90PRO00.0500.0167.776-0.378-0.3780.0000.0000.0000.000
91A91ASN00.0330.03310.193-0.130-0.1300.0000.0000.0000.000
92A92LEU0-0.060-0.0135.8320.0760.0760.0000.0000.0000.000
93A93PHE00.0510.0158.845-0.094-0.0940.0000.0000.0000.000
94A94ASP-1-0.789-0.8607.818-2.211-2.2110.0000.0000.0000.000
95A95VAL00.029-0.0029.2100.3890.3890.0000.0000.0000.000
96A96ASN0-0.025-0.01011.5630.2640.2640.0000.0000.0000.000
97A97GLY0-0.0180.00711.5700.2060.2060.0000.0000.0000.000
98A98VAL0-0.017-0.00312.5430.1710.1710.0000.0000.0000.000
99A99LEU00.006-0.00814.8440.1310.1310.0000.0000.0000.000
100A100GLY00.0610.04216.3140.0970.0970.0000.0000.0000.000
101A101ARG10.9210.94817.8890.1990.1990.0000.0000.0000.000
102A102TYR0-0.070-0.06820.2530.0300.0300.0000.0000.0000.000
103A103SER0-0.049-0.02515.173-0.023-0.0230.0000.0000.0000.000
104A104PRO00.0190.00418.1480.0470.0470.0000.0000.0000.000
105A105TYR0-0.014-0.00717.2430.0860.0860.0000.0000.0000.000
106A106PRO00.0510.03715.070-0.094-0.0940.0000.0000.0000.000
107A107SER00.0100.00213.989-0.049-0.0490.0000.0000.0000.000
108A108GLU-1-0.870-0.91013.835-0.781-0.7810.0000.0000.0000.000
109A109ASN0-0.077-0.0288.811-0.140-0.1400.0000.0000.0000.000
110A110GLU-1-0.759-0.8518.945-1.725-1.7250.0000.0000.0000.000
111A111TYR0-0.021-0.0335.216-1.098-1.0980.0000.0000.0000.000
112A112ALA0-0.0190.0018.6730.0260.0260.0000.0000.0000.000
113A113ALA00.0200.01011.122-0.120-0.1200.0000.0000.0000.000
114A114LEU00.012-0.01712.3540.2320.2320.0000.0000.0000.000
115A115GLY00.0180.00615.397-0.008-0.0080.0000.0000.0000.000
116A116GLY0-0.035-0.01615.6680.0920.0920.0000.0000.0000.000
117A117ILE0-0.054-0.02911.192-0.149-0.1490.0000.0000.0000.000
118A118PRO00.0690.05213.1020.1580.1580.0000.0000.0000.000
119A119LEU00.036-0.00414.232-0.161-0.1610.0000.0000.0000.000
120A120SER0-0.017-0.00914.395-0.097-0.0970.0000.0000.0000.000
121A121GLN00.002-0.0027.9650.4940.4940.0000.0000.0000.000
122A122ILE0-0.057-0.0209.730-0.454-0.4540.0000.0000.0000.000
123A123ILE00.0280.0156.3070.4360.4360.0000.0000.0000.000
124A124GLY00.009-0.01410.9740.3320.3320.0000.0000.0000.000
125A125TRP00.0070.01313.302-0.185-0.1850.0000.0000.0000.000
126A126TYR00.0000.00611.5900.1810.1810.0000.0000.0000.000
127A127ARG10.8310.89817.0800.2210.2210.0000.0000.0000.000
128A128VAL0-0.013-0.00519.2540.0430.0430.0000.0000.0000.000
129A129SER00.0310.01821.839-0.016-0.0160.0000.0000.0000.000
130A130PHE00.013-0.01325.5860.0240.0240.0000.0000.0000.000
131A131GLY0-0.0070.00724.0360.0200.0200.0000.0000.0000.000
132A132ALA0-0.0070.01022.9960.0060.0060.0000.0000.0000.000
133A133ILE0-0.009-0.01816.444-0.036-0.0360.0000.0000.0000.000
134A134GLU-1-0.857-0.91420.625-0.140-0.1400.0000.0000.0000.000
135A135GLY0-0.028-0.00421.670-0.023-0.0230.0000.0000.0000.000
136A136GLY0-0.006-0.01217.8990.0100.0100.0000.0000.0000.000
137A137MET0-0.061-0.01911.592-0.069-0.0690.0000.0000.0000.000
138A138HIS0-0.025-0.00816.0340.0590.0590.0000.0000.0000.000
139A139ARG10.9370.95512.7820.1580.1580.0000.0000.0000.000
140A140ASN00.0220.00714.5190.2210.2210.0000.0000.0000.000
141A141ARG10.9330.95215.6490.3030.3030.0000.0000.0000.000
142A142ASP-1-0.885-0.93717.641-0.531-0.5310.0000.0000.0000.000
143A143TYR0-0.0110.0147.3910.1980.1980.0000.0000.0000.000
144A144ARG10.8400.91712.8800.8210.8210.0000.0000.0000.000
145A145ARG10.9850.98110.1960.2090.2090.0000.0000.0000.000
146A146ASP-1-0.943-0.98410.443-0.577-0.5770.0000.0000.0000.000
147A147LEU00.0160.01012.2690.0660.0660.0000.0000.0000.000
148A148PHE00.0320.0077.095-0.077-0.0770.0000.0000.0000.000
149A149ARG10.8800.9446.500-0.320-0.3200.0000.0000.0000.000
150A150GLY0-0.012-0.0155.7080.1890.1890.0000.0000.0000.000
151A151LEU00.0140.0535.8240.3430.3430.0000.0000.0000.000
152A152SER0-0.008-0.0214.2850.1380.231-0.001-0.030-0.0620.000
153A153ALA0-0.033-0.0204.914-0.020-0.0200.0000.0000.0000.000
154A154ALA00.0010.0066.7620.6850.6850.0000.0000.0000.000
155A155PRO0-0.0080.0169.752-0.182-0.1820.0000.0000.0000.000
156A156ASN00.041-0.00911.134-0.211-0.2110.0000.0000.0000.000
157A157GLU-1-0.909-0.95413.228-0.428-0.4280.0000.0000.0000.000
158A158ASP-1-0.909-0.95914.603-0.675-0.6750.0000.0000.0000.000
159A159GLY0-0.026-0.02314.990-0.022-0.0220.0000.0000.0000.000
160A160TYR0-0.080-0.04015.7440.0670.0670.0000.0000.0000.000
161A161ARG10.8790.94218.7590.4030.4030.0000.0000.0000.000
162A162ILE0-0.052-0.02916.5530.0400.0400.0000.0000.0000.000
163A163ALA00.0020.01018.774-0.040-0.0400.0000.0000.0000.000
164A164GLY00.002-0.01119.785-0.017-0.0170.0000.0000.0000.000
165A165PHE00.0020.01120.4920.0040.0040.0000.0000.0000.000
166A166PRO0-0.0020.00424.6470.0110.0110.0000.0000.0000.000
167A167ASP-1-0.865-0.95628.278-0.250-0.2500.0000.0000.0000.000
168A168GLY00.0280.02430.9790.0080.0080.0000.0000.0000.000
169A169PHE0-0.069-0.02224.6070.0090.0090.0000.0000.0000.000
170A170PRO00.0480.00228.0910.0010.0010.0000.0000.0000.000
171A171ALA00.0240.02423.7680.0110.0110.0000.0000.0000.000
172A172TRP0-0.060-0.03723.278-0.011-0.0110.0000.0000.0000.000
173A173GLU-1-0.937-0.96527.616-0.166-0.1660.0000.0000.0000.000
174A174GLU-1-0.891-0.91625.897-0.227-0.2270.0000.0000.0000.000
175A175VAL0-0.0380.01323.821-0.023-0.0230.0000.0000.0000.000
176A176PRO00.000-0.02319.4790.0130.0130.0000.0000.0000.000
177A177TRP0-0.002-0.03118.9420.0260.0260.0000.0000.0000.000
178A178ARG10.8770.93123.2090.1610.1610.0000.0000.0000.000
179A179GLU-1-0.870-0.92624.445-0.157-0.1570.0000.0000.0000.000
180A180PHE0-0.020-0.01420.584-0.003-0.0030.0000.0000.0000.000
181A181ALA00.0310.03724.114-0.031-0.0310.0000.0000.0000.000
182A182PRO0-0.0110.00424.9640.0240.0240.0000.0000.0000.000
183A183ASN00.037-0.01127.6590.0000.0000.0000.0000.0000.000
184A184SER0-0.032-0.02230.9370.0070.0070.0000.0000.0000.000
185A185CYS0-0.0420.00028.360-0.011-0.0110.0000.0000.0000.000
186A186LEU0-0.0370.00129.3060.0030.0030.0000.0000.0000.000
187A187PRO0-0.0130.00631.6400.0090.0090.0000.0000.0000.000