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: 2264R

Calculation Name: 3RIU-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RIU

Chain ID: C

ChEMBL ID:

UniProt ID: Q9VF77

Base Structure: X-ray

Registration Date: 2023-06-20

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2473140.460848
FMO2-HF: Nuclear repulsion 2385971.617854
FMO2-HF: Total energy -87168.842994
FMO2-MP2: Total energy -87419.265046


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:31:VAL)


Summations of interaction energy for fragment #1(C:31:VAL)
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.
-4.142-1.1353.303-2.339-3.9720.003
Interaction energy analysis for fragmet #1(C:31:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.015
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].
3C33GLN00.0350.0261.847-2.346-0.7273.244-1.984-2.8790.005
4C34PHE00.017-0.0083.640-2.013-0.7380.060-0.346-0.989-0.002
5C35ARG10.9420.9835.2400.0750.188-0.001-0.009-0.1040.000
6C36ILE00.0050.0107.563-0.025-0.0250.0000.0000.0000.000
7C37TYR00.0640.0346.4980.0200.0200.0000.0000.0000.000
8C38SER00.0210.0049.154-0.084-0.0840.0000.0000.0000.000
9C39ASN0-0.022-0.01510.877-0.031-0.0310.0000.0000.0000.000
10C40GLU-1-0.912-0.96012.7120.3710.3710.0000.0000.0000.000
11C41LEU0-0.036-0.01711.684-0.013-0.0130.0000.0000.0000.000
12C42ILE00.0340.02214.413-0.014-0.0140.0000.0000.0000.000
13C43MET0-0.037-0.02016.9550.0040.0040.0000.0000.0000.000
14C44LYS10.8660.93517.298-0.105-0.1050.0000.0000.0000.000
15C45HIS00.005-0.00816.261-0.011-0.0110.0000.0000.0000.000
16C46ASP-1-0.831-0.88920.866-0.005-0.0050.0000.0000.0000.000
17C47ARG10.8010.87922.821-0.060-0.0600.0000.0000.0000.000
18C48HIS00.0410.01823.9320.0060.0060.0000.0000.0000.000
19C49GLU-1-0.779-0.85225.173-0.017-0.0170.0000.0000.0000.000
20C50ARG10.8240.90025.253-0.016-0.0160.0000.0000.0000.000
21C51ILE00.0310.02127.9920.0000.0000.0000.0000.0000.000
22C52VAL0-0.005-0.00328.808-0.001-0.0010.0000.0000.0000.000
23C53LYS10.7800.86831.1630.0030.0030.0000.0000.0000.000
24C54LEU00.0140.02433.155-0.001-0.0010.0000.0000.0000.000
25C55SER0-0.006-0.00834.114-0.001-0.0010.0000.0000.0000.000
26C56ARG10.7900.85430.1940.0120.0120.0000.0000.0000.000
27C57ASP-1-0.819-0.90837.252-0.002-0.0020.0000.0000.0000.000
28C58ILE00.0130.00837.974-0.001-0.0010.0000.0000.0000.000
29C59THR0-0.012-0.01839.5270.0000.0000.0000.0000.0000.000
30C60ILE0-0.045-0.01840.373-0.001-0.0010.0000.0000.0000.000
31C61GLU-1-0.892-0.93143.3280.0040.0040.0000.0000.0000.000
32C62SER00.027-0.01644.4850.0000.0000.0000.0000.0000.000
33C63LYS10.8280.88743.7060.0000.0000.0000.0000.0000.000
34C64ARG10.9090.94145.9020.0030.0030.0000.0000.0000.000
35C65ILE0-0.0250.00348.6210.0000.0000.0000.0000.0000.000
36C66ILE00.0200.01548.9680.0000.0000.0000.0000.0000.000
37C67PHE0-0.001-0.00349.7260.0000.0000.0000.0000.0000.000
38C68LEU0-0.075-0.01453.5550.0000.0000.0000.0000.0000.000
39C69LEU0-0.017-0.00153.7600.0000.0000.0000.0000.0000.000
40C70HIS00.0000.00452.7910.0000.0000.0000.0000.0000.000
41C71SER0-0.087-0.04657.9000.0000.0000.0000.0000.0000.000
42C72ILE0-0.0140.00460.7250.0000.0000.0000.0000.0000.000
43C73ASP-1-0.743-0.84161.3490.0010.0010.0000.0000.0000.000
44C74SER0-0.120-0.09464.7190.0010.0010.0000.0000.0000.000
45C75ARG10.7730.86967.7010.0000.0000.0000.0000.0000.000
46C76LYS10.9600.98469.505-0.002-0.0020.0000.0000.0000.000
47C77GLN0-0.027-0.04469.1680.0000.0000.0000.0000.0000.000
48C78ASN0-0.070-0.02364.6210.0000.0000.0000.0000.0000.000
49C79LYS10.9680.97966.008-0.002-0.0020.0000.0000.0000.000
50C80GLU-1-0.786-0.89863.9680.0040.0040.0000.0000.0000.000
51C81LYS10.8800.94159.274-0.003-0.0030.0000.0000.0000.000
52C82VAL0-0.017-0.01758.8660.0000.0000.0000.0000.0000.000
53C83LEU00.0680.03957.9170.0000.0000.0000.0000.0000.000
54C84GLU-1-0.809-0.89757.7940.0090.0090.0000.0000.0000.000
55C85GLU-1-0.861-0.91055.3280.0030.0030.0000.0000.0000.000
56C86ALA00.0120.00954.0110.0000.0000.0000.0000.0000.000
57C87ARG10.9190.93652.955-0.009-0.0090.0000.0000.0000.000
58C88GLN0-0.044-0.01552.9700.0010.0010.0000.0000.0000.000
59C89ARG10.8720.92350.297-0.002-0.0020.0000.0000.0000.000
60C90LEU00.0360.01947.9680.0000.0000.0000.0000.0000.000
61C91ASN0-0.001-0.01647.8590.0020.0020.0000.0000.0000.000
62C92LYS10.8210.89545.842-0.004-0.0040.0000.0000.0000.000
63C93LEU00.007-0.00143.1850.0000.0000.0000.0000.0000.000
64C94ILE00.0420.04143.3040.0010.0010.0000.0000.0000.000
65C95ALA00.0150.01142.9850.0020.0020.0000.0000.0000.000
66C96VAL0-0.091-0.05639.5910.0000.0000.0000.0000.0000.000
67C97ASN00.0590.00538.9420.0010.0010.0000.0000.0000.000
68C98PHE00.0180.01738.2320.0020.0020.0000.0000.0000.000
69C99ARG10.8960.94636.764-0.009-0.0090.0000.0000.0000.000
70C100ALA0-0.039-0.02034.3900.0010.0010.0000.0000.0000.000
71C101VAL00.0260.01733.6940.0020.0020.0000.0000.0000.000
72C102ALA0-0.0150.00633.9390.0040.0040.0000.0000.0000.000
73C103LEU0-0.055-0.02028.6960.0010.0010.0000.0000.0000.000
74C104GLU-1-0.798-0.88028.2620.0650.0650.0000.0000.0000.000
75C105LEU0-0.006-0.01926.8850.0030.0030.0000.0000.0000.000
76C106ARG10.7880.85622.029-0.146-0.1460.0000.0000.0000.000
77C107ASP-1-0.836-0.87725.6750.1200.1200.0000.0000.0000.000
78C108GLN0-0.012-0.02728.775-0.001-0.0010.0000.0000.0000.000
79C109ASP-1-0.801-0.88731.6800.0530.0530.0000.0000.0000.000
80C110VAL00.0100.02126.144-0.004-0.0040.0000.0000.0000.000
81C111TYR00.045-0.00928.201-0.004-0.0040.0000.0000.0000.000
82C112GLN0-0.023-0.00121.176-0.001-0.0010.0000.0000.0000.000
83C113PHE00.0510.01922.769-0.003-0.0030.0000.0000.0000.000
84C114ARG10.8350.92827.528-0.051-0.0510.0000.0000.0000.000
85C115SER0-0.0130.00026.726-0.002-0.0020.0000.0000.0000.000
86C116SER00.0250.01429.070-0.007-0.0070.0000.0000.0000.000
87C117TYR0-0.0350.00231.628-0.002-0.0020.0000.0000.0000.000
88C118SER00.0260.00333.3320.0000.0000.0000.0000.0000.000
89C119PRO00.0000.00036.0480.0010.0010.0000.0000.0000.000
90C120GLY00.0340.02937.7350.0000.0000.0000.0000.0000.000
91C121LEU00.0230.01437.5000.0010.0010.0000.0000.0000.000
92C122GLN0-0.043-0.03839.2780.0000.0000.0000.0000.0000.000
93C123GLU-1-0.720-0.83041.9030.0010.0010.0000.0000.0000.000
94C124PHE00.0010.02342.661-0.001-0.0010.0000.0000.0000.000
95C125ILE0-0.0110.01242.0400.0000.0000.0000.0000.0000.000
96C126GLU-1-0.869-0.91245.7690.0050.0050.0000.0000.0000.000
97C127ALA00.0230.00147.6360.0000.0000.0000.0000.0000.000
98C128TYR0-0.030-0.00947.8170.0000.0000.0000.0000.0000.000
99C129THR00.008-0.02049.1310.0000.0000.0000.0000.0000.000
100C130TYR0-0.057-0.04851.6620.0000.0000.0000.0000.0000.000
101C131MET0-0.035-0.01553.1590.0000.0000.0000.0000.0000.000
102C132GLU-1-0.745-0.85653.1530.0140.0140.0000.0000.0000.000
103C133TYR00.016-0.02155.650-0.001-0.0010.0000.0000.0000.000
104C134LEU0-0.031-0.01457.536-0.001-0.0010.0000.0000.0000.000
105C135CYS0-0.084-0.03958.9390.0000.0000.0000.0000.0000.000
106C136HIS0-0.057-0.00360.6290.0000.0000.0000.0000.0000.000
107C137GLU-1-0.938-0.97662.7110.0080.0080.0000.0000.0000.000
108C145THR00.009-0.00960.4720.0000.0000.0000.0000.0000.000
109C146LYS10.8040.88954.294-0.017-0.0170.0000.0000.0000.000
110C147SER0-0.023-0.01355.9070.0000.0000.0000.0000.0000.000
111C148VAL00.0460.00954.3130.0000.0000.0000.0000.0000.000
112C149SER0-0.081-0.03950.4510.0010.0010.0000.0000.0000.000
113C150ASP-1-0.866-0.91150.3710.0190.0190.0000.0000.0000.000
114C151TRP00.016-0.00743.2640.0010.0010.0000.0000.0000.000
115C152GLN00.0170.00745.7770.0010.0010.0000.0000.0000.000
116C153ALA00.0020.00146.9190.0010.0010.0000.0000.0000.000
117C154ILE0-0.019-0.00444.5540.0000.0000.0000.0000.0000.000
118C155GLN00.0720.03342.0840.0020.0020.0000.0000.0000.000
119C156ALA0-0.041-0.01844.0800.0010.0010.0000.0000.0000.000
120C157VAL0-0.014-0.00446.6740.0000.0000.0000.0000.0000.000
121C158MET0-0.087-0.03741.357-0.001-0.0010.0000.0000.0000.000
122C159GLN0-0.049-0.03841.3320.0020.0020.0000.0000.0000.000
123C160TYR0-0.012-0.00743.0270.0000.0000.0000.0000.0000.000
124C161VAL0-0.096-0.02338.956-0.001-0.0010.0000.0000.0000.000
125C162GLU-1-0.928-0.94339.9550.0370.0370.0000.0000.0000.000
126C191PHE0-0.015-0.00837.446-0.001-0.0010.0000.0000.0000.000
127C192PHE0-0.003-0.01535.4170.0020.0020.0000.0000.0000.000
128C193VAL0-0.0020.01335.9000.0000.0000.0000.0000.0000.000
129C194ASP-1-0.759-0.89537.9110.0260.0260.0000.0000.0000.000
130C195PRO0-0.007-0.01137.841-0.001-0.0010.0000.0000.0000.000
131C196THR0-0.011-0.01337.957-0.002-0.0020.0000.0000.0000.000
132C197GLU-1-0.831-0.93536.1090.0300.0300.0000.0000.0000.000
133C198TYR00.026-0.00139.898-0.003-0.0030.0000.0000.0000.000
134C199ILE00.0130.01943.473-0.002-0.0020.0000.0000.0000.000
135C200LEU0-0.055-0.00739.794-0.002-0.0020.0000.0000.0000.000
136C201GLY00.0660.02443.615-0.002-0.0020.0000.0000.0000.000
137C202LEU00.0440.00744.931-0.001-0.0010.0000.0000.0000.000
138C203SER0-0.021-0.00646.630-0.001-0.0010.0000.0000.0000.000
139C204ASP-1-0.847-0.88244.2930.0070.0070.0000.0000.0000.000
140C205LEU00.0410.03547.829-0.001-0.0010.0000.0000.0000.000
141C206THR0-0.046-0.03550.822-0.001-0.0010.0000.0000.0000.000
142C207GLY00.007-0.00251.297-0.001-0.0010.0000.0000.0000.000
143C208GLU-1-0.735-0.83651.4060.0030.0030.0000.0000.0000.000
144C209LEU00.0050.00953.2610.0000.0000.0000.0000.0000.000
145C210MET0-0.042-0.01555.4790.0000.0000.0000.0000.0000.000
146C211ARG10.7140.81949.657-0.004-0.0040.0000.0000.0000.000
147C212ARG10.9040.91956.747-0.006-0.0060.0000.0000.0000.000
148C213CYS0-0.058-0.03259.2020.0000.0000.0000.0000.0000.000
149C214ILE0-0.097-0.04658.3390.0000.0000.0000.0000.0000.000
150C215ASN0-0.011-0.00558.4200.0000.0000.0000.0000.0000.000
151C216SER00.0310.02761.9890.0000.0000.0000.0000.0000.000
152C217LEU0-0.015-0.01165.4130.0000.0000.0000.0000.0000.000
153C218GLY00.0150.00466.7880.0000.0000.0000.0000.0000.000
154C219SER0-0.014-0.02567.3250.0000.0000.0000.0000.0000.000
155C220GLY0-0.054-0.02869.6160.0000.0000.0000.0000.0000.000
156C221ASP-1-0.766-0.84371.1330.0010.0010.0000.0000.0000.000
157C222THR0-0.019-0.01868.1050.0000.0000.0000.0000.0000.000
158C223ASP-1-0.879-0.92469.7380.0040.0040.0000.0000.0000.000
159C224THR00.0160.01066.3570.0000.0000.0000.0000.0000.000
160C225CYS00.0160.01464.8650.0000.0000.0000.0000.0000.000
161C226LEU00.035-0.00265.0600.0000.0000.0000.0000.0000.000
162C227ASP-1-0.759-0.84464.7910.0060.0060.0000.0000.0000.000
163C228THR0-0.008-0.00359.9640.0010.0010.0000.0000.0000.000
164C229CYS0-0.051-0.02860.9860.0000.0000.0000.0000.0000.000
165C230LYS10.8640.93262.244-0.008-0.0080.0000.0000.0000.000
166C231ALA00.0390.03158.9800.0010.0010.0000.0000.0000.000
167C232LEU00.001-0.00656.7090.0010.0010.0000.0000.0000.000
168C233GLN0-0.024-0.01957.8530.0010.0010.0000.0000.0000.000
169C234HIS0-0.042-0.00859.3500.0000.0000.0000.0000.0000.000
170C235PHE00.0600.02952.2930.0010.0010.0000.0000.0000.000
171C236TYR00.0360.00853.9590.0000.0000.0000.0000.0000.000
172C237SER0-0.022-0.02655.2970.0000.0000.0000.0000.0000.000
173C238GLY0-0.0080.02254.3850.0010.0010.0000.0000.0000.000
174C239TYR0-0.063-0.07047.4990.0010.0010.0000.0000.0000.000
175C240ILE0-0.088-0.04250.8370.0000.0000.0000.0000.0000.000
176C241SER0-0.043-0.02953.2020.0000.0000.0000.0000.0000.000
177C242LEU0-0.0040.01447.0210.0010.0010.0000.0000.0000.000
178C243ASN00.009-0.01144.384-0.002-0.0020.0000.0000.0000.000
179C244CYS0-0.001-0.00345.2050.0000.0000.0000.0000.0000.000
180C245GLN00.0220.00643.6330.0000.0000.0000.0000.0000.000
181C246ARG10.8230.92141.319-0.013-0.0130.0000.0000.0000.000
182C247ALA00.0850.07536.948-0.001-0.0010.0000.0000.0000.000
183C248ARG10.8670.89737.954-0.010-0.0100.0000.0000.0000.000
184C249GLU-1-0.727-0.85438.0230.0180.0180.0000.0000.0000.000
185C250LEU00.0770.02440.162-0.002-0.0020.0000.0000.0000.000
186C251TRP00.0530.03043.335-0.001-0.0010.0000.0000.0000.000
187C252ARG10.8790.94538.738-0.009-0.0090.0000.0000.0000.000
188C253LYS10.8190.90843.148-0.010-0.0100.0000.0000.0000.000
189C254ILE00.0510.03246.735-0.001-0.0010.0000.0000.0000.000
190C255THR0-0.037-0.03348.183-0.001-0.0010.0000.0000.0000.000
191C256THR0-0.006-0.00548.228-0.001-0.0010.0000.0000.0000.000
192C257MET00.0260.04350.1970.0000.0000.0000.0000.0000.000
193C258LYS10.9460.98752.465-0.007-0.0070.0000.0000.0000.000
194C259GLN00.012-0.00654.0630.0000.0000.0000.0000.0000.000
195C260SER0-0.095-0.05554.404-0.001-0.0010.0000.0000.0000.000
196C261VAL00.0380.01456.3290.0000.0000.0000.0000.0000.000
197C262LEU00.0180.00358.6810.0000.0000.0000.0000.0000.000
198C263LYS10.8970.96355.055-0.001-0.0010.0000.0000.0000.000
199C264ALA00.0550.02660.4110.0000.0000.0000.0000.0000.000
200C265GLU-1-0.844-0.92962.1800.0050.0050.0000.0000.0000.000
201C266ASN0-0.036-0.01364.0380.0000.0000.0000.0000.0000.000
202C267VAL00.0330.01864.1050.0000.0000.0000.0000.0000.000
203C269TYR0-0.056-0.01768.2140.0000.0000.0000.0000.0000.000
204C270ASN0-0.047-0.04168.3940.0000.0000.0000.0000.0000.000
205C271VAL00.0100.01469.9540.0000.0000.0000.0000.0000.000
206C272LYS10.8800.96072.440-0.004-0.0040.0000.0000.0000.000
207C273VAL0-0.0060.00074.9410.0000.0000.0000.0000.0000.000