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: M3GRZ

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 OptH
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 -2479586.321625
FMO2-HF: Nuclear repulsion 2392421.773258
FMO2-HF: Total energy -87164.548367
FMO2-MP2: Total energy -87415.676032


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.
-0.821-3.16510.197-2.205-5.6470.008
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 : 0.038 / q_NPA : 0.006
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].
3C33GLN00.0440.0341.9420.296-2.02510.111-2.902-4.8880.007
4C34PHE00.0580.0083.194-1.030-1.0530.0860.697-0.7590.001
5C35ARG10.9390.9845.868-0.049-0.0490.0000.0000.0000.000
6C36ILE0-0.008-0.0126.987-0.085-0.0850.0000.0000.0000.000
7C37TYR00.0600.0335.8110.0130.0130.0000.0000.0000.000
8C38SER00.0050.0009.410-0.088-0.0880.0000.0000.0000.000
9C39ASN00.0480.00411.294-0.049-0.0490.0000.0000.0000.000
10C40GLU-1-0.924-0.94811.8780.4880.4880.0000.0000.0000.000
11C41LEU0-0.040-0.02912.718-0.027-0.0270.0000.0000.0000.000
12C42ILE00.0260.03114.740-0.030-0.0300.0000.0000.0000.000
13C43MET0-0.027-0.00617.192-0.011-0.0110.0000.0000.0000.000
14C44LYS10.8790.93518.250-0.175-0.1750.0000.0000.0000.000
15C45HIS0-0.0030.00016.274-0.024-0.0240.0000.0000.0000.000
16C46ASP-1-0.842-0.92521.2230.0230.0230.0000.0000.0000.000
17C47ARG10.8490.92923.396-0.099-0.0990.0000.0000.0000.000
18C48HIS00.0740.03424.4420.0010.0010.0000.0000.0000.000
19C49GLU-1-0.874-0.93325.5000.0080.0080.0000.0000.0000.000
20C50ARG10.8780.93224.908-0.055-0.0550.0000.0000.0000.000
21C51ILE00.0260.02529.090-0.004-0.0040.0000.0000.0000.000
22C52VAL00.0160.01829.250-0.004-0.0040.0000.0000.0000.000
23C53LYS10.8570.93231.331-0.012-0.0120.0000.0000.0000.000
24C54LEU00.0400.02733.619-0.002-0.0020.0000.0000.0000.000
25C55SER0-0.017-0.00334.638-0.002-0.0020.0000.0000.0000.000
26C56ARG10.8740.92331.155-0.013-0.0130.0000.0000.0000.000
27C57ASP-1-0.919-0.96637.6470.0130.0130.0000.0000.0000.000
28C58ILE00.0170.01839.063-0.001-0.0010.0000.0000.0000.000
29C59THR0-0.034-0.00639.296-0.002-0.0020.0000.0000.0000.000
30C60ILE0-0.051-0.04140.734-0.002-0.0020.0000.0000.0000.000
31C61GLU-1-0.918-0.96643.3910.0150.0150.0000.0000.0000.000
32C62SER00.0480.02044.8190.0000.0000.0000.0000.0000.000
33C63LYS11.0081.01543.533-0.012-0.0120.0000.0000.0000.000
34C64ARG10.8740.91846.652-0.008-0.0080.0000.0000.0000.000
35C65ILE0-0.031-0.00549.228-0.001-0.0010.0000.0000.0000.000
36C66ILE00.0550.03049.586-0.001-0.0010.0000.0000.0000.000
37C67PHE0-0.047-0.03151.570-0.001-0.0010.0000.0000.0000.000
38C68LEU0-0.095-0.02653.629-0.001-0.0010.0000.0000.0000.000
39C69LEU0-0.067-0.02654.3890.0000.0000.0000.0000.0000.000
40C70HIS0-0.0040.00453.1490.0000.0000.0000.0000.0000.000
41C71SER0-0.121-0.04758.040-0.001-0.0010.0000.0000.0000.000
42C72ILE00.0050.01560.963-0.001-0.0010.0000.0000.0000.000
43C73ASP-1-0.733-0.84061.9280.0070.0070.0000.0000.0000.000
44C74SER0-0.102-0.06365.1520.0010.0010.0000.0000.0000.000
45C75ARG10.7550.87068.342-0.005-0.0050.0000.0000.0000.000
46C76LYS10.9570.98270.265-0.006-0.0060.0000.0000.0000.000
47C77GLN0-0.035-0.04469.5800.0000.0000.0000.0000.0000.000
48C78ASN0-0.0520.00164.870-0.001-0.0010.0000.0000.0000.000
49C79LYS10.9750.97667.001-0.007-0.0070.0000.0000.0000.000
50C80GLU-1-0.830-0.91564.2710.0090.0090.0000.0000.0000.000
51C81LYS10.9800.98960.910-0.008-0.0080.0000.0000.0000.000
52C82VAL0-0.021-0.02259.0640.0010.0010.0000.0000.0000.000
53C83LEU00.1020.05858.2040.0010.0010.0000.0000.0000.000
54C84GLU-1-0.925-0.99258.0680.0130.0130.0000.0000.0000.000
55C85GLU-1-0.962-0.98655.6740.0120.0120.0000.0000.0000.000
56C86ALA00.0680.04054.5920.0010.0010.0000.0000.0000.000
57C87ARG10.9760.99153.351-0.015-0.0150.0000.0000.0000.000
58C88GLN0-0.053-0.01252.9320.0010.0010.0000.0000.0000.000
59C89ARG10.9380.97848.917-0.011-0.0110.0000.0000.0000.000
60C90LEU00.0630.01848.9140.0010.0010.0000.0000.0000.000
61C91ASN0-0.020-0.02748.0220.0020.0020.0000.0000.0000.000
62C92LYS10.8890.96646.966-0.014-0.0140.0000.0000.0000.000
63C93LEU0-0.057-0.02143.5400.0010.0010.0000.0000.0000.000
64C94ILE00.0660.04243.5620.0020.0020.0000.0000.0000.000
65C95ALA00.016-0.00143.1110.0020.0020.0000.0000.0000.000
66C96VAL0-0.040-0.03639.8750.0020.0020.0000.0000.0000.000
67C97ASN00.0330.00039.0780.0040.0040.0000.0000.0000.000
68C98PHE00.0290.01738.2760.0030.0030.0000.0000.0000.000
69C99ARG10.8930.94636.897-0.020-0.0200.0000.0000.0000.000
70C100ALA0-0.059-0.05134.4040.0030.0030.0000.0000.0000.000
71C101VAL00.0510.04633.7690.0030.0030.0000.0000.0000.000
72C102ALA00.0010.00633.3900.0050.0050.0000.0000.0000.000
73C103LEU0-0.145-0.06928.4970.0030.0030.0000.0000.0000.000
74C104GLU-1-0.849-0.91629.0830.0810.0810.0000.0000.0000.000
75C105LEU0-0.002-0.02726.5490.0030.0030.0000.0000.0000.000
76C106ARG10.7630.84021.495-0.170-0.1700.0000.0000.0000.000
77C107ASP-1-0.832-0.87825.3580.1420.1420.0000.0000.0000.000
78C108GLN0-0.004-0.01728.397-0.002-0.0020.0000.0000.0000.000
79C109ASP-1-0.786-0.88231.1780.0720.0720.0000.0000.0000.000
80C110VAL00.0260.02826.188-0.003-0.0030.0000.0000.0000.000
81C111TYR00.053-0.03428.281-0.005-0.0050.0000.0000.0000.000
82C112GLN0-0.053-0.02322.432-0.009-0.0090.0000.0000.0000.000
83C113PHE00.0610.01023.1130.0020.0020.0000.0000.0000.000
84C114ARG10.8630.94127.710-0.081-0.0810.0000.0000.0000.000
85C115SER0-0.0150.00628.103-0.006-0.0060.0000.0000.0000.000
86C116SER00.0520.00630.041-0.004-0.0040.0000.0000.0000.000
87C117TYR0-0.0420.04332.155-0.002-0.0020.0000.0000.0000.000
88C118SER00.0780.00934.537-0.003-0.0030.0000.0000.0000.000
89C119PRO00.0040.01336.6980.0010.0010.0000.0000.0000.000
90C120GLY00.0210.02838.228-0.001-0.0010.0000.0000.0000.000
91C121LEU0-0.006-0.00737.483-0.001-0.0010.0000.0000.0000.000
92C122GLN0-0.008-0.01339.1810.0020.0020.0000.0000.0000.000
93C123GLU-1-0.938-0.98242.1540.0160.0160.0000.0000.0000.000
94C124PHE0-0.0310.00843.370-0.001-0.0010.0000.0000.0000.000
95C125ILE00.0030.02042.243-0.001-0.0010.0000.0000.0000.000
96C126GLU-1-0.815-0.90246.2720.0160.0160.0000.0000.0000.000
97C127ALA00.0260.00248.177-0.001-0.0010.0000.0000.0000.000
98C128TYR0-0.051-0.02948.293-0.001-0.0010.0000.0000.0000.000
99C129THR0-0.014-0.02349.4520.0000.0000.0000.0000.0000.000
100C130TYR0-0.008-0.01452.012-0.001-0.0010.0000.0000.0000.000
101C131MET0-0.064-0.02953.616-0.001-0.0010.0000.0000.0000.000
102C132GLU-1-0.830-0.94453.1690.0220.0220.0000.0000.0000.000
103C133TYR00.0070.00356.152-0.001-0.0010.0000.0000.0000.000
104C134LEU0-0.016-0.00357.728-0.001-0.0010.0000.0000.0000.000
105C135CYS0-0.121-0.05158.886-0.001-0.0010.0000.0000.0000.000
106C136HIS0-0.067-0.02160.6710.0000.0000.0000.0000.0000.000
107C137GLU-1-0.927-0.95462.9190.0130.0130.0000.0000.0000.000
108C145THR0-0.025-0.02561.0810.0000.0000.0000.0000.0000.000
109C146LYS10.8890.95855.619-0.023-0.0230.0000.0000.0000.000
110C147SER0-0.011-0.00456.4670.0000.0000.0000.0000.0000.000
111C148VAL00.098-0.00554.0380.0000.0000.0000.0000.0000.000
112C149SER0-0.063-0.01250.3950.0010.0010.0000.0000.0000.000
113C150ASP-1-0.843-0.90250.0790.0270.0270.0000.0000.0000.000
114C151TRP00.042-0.00344.0820.0010.0010.0000.0000.0000.000
115C152GLN0-0.045-0.00745.1450.0010.0010.0000.0000.0000.000
116C153ALA00.0370.00546.6580.0010.0010.0000.0000.0000.000
117C154ILE0-0.031-0.00544.3520.0000.0000.0000.0000.0000.000
118C155GLN00.0830.02941.2960.0020.0020.0000.0000.0000.000
119C156ALA0-0.043-0.02243.5890.0020.0020.0000.0000.0000.000
120C157VAL0-0.024-0.00846.2030.0000.0000.0000.0000.0000.000
121C158MET0-0.080-0.02641.325-0.001-0.0010.0000.0000.0000.000
122C159GLN0-0.046-0.03040.5250.0030.0030.0000.0000.0000.000
123C160TYR0-0.030-0.00642.6070.0000.0000.0000.0000.0000.000
124C161VAL0-0.074-0.00938.566-0.002-0.0020.0000.0000.0000.000
125C162GLU-1-0.960-0.96639.5250.0460.0460.0000.0000.0000.000
126C191PHE0-0.027-0.01336.826-0.001-0.0010.0000.0000.0000.000
127C192PHE0-0.008-0.01736.0650.0040.0040.0000.0000.0000.000
128C193VAL0-0.0060.00934.820-0.002-0.0020.0000.0000.0000.000
129C194ASP-1-0.759-0.88737.5630.0400.0400.0000.0000.0000.000
130C195PRO0-0.0090.00137.422-0.001-0.0010.0000.0000.0000.000
131C196THR00.024-0.01038.432-0.003-0.0030.0000.0000.0000.000
132C197GLU-1-0.886-0.96537.2250.0460.0460.0000.0000.0000.000
133C198TYR00.004-0.00640.611-0.004-0.0040.0000.0000.0000.000
134C199ILE0-0.016-0.00143.345-0.002-0.0020.0000.0000.0000.000
135C200LEU0-0.0400.00140.684-0.002-0.0020.0000.0000.0000.000
136C201GLY00.0960.04344.147-0.002-0.0020.0000.0000.0000.000
137C202LEU00.0340.01445.620-0.002-0.0020.0000.0000.0000.000
138C203SER0-0.056-0.03047.400-0.002-0.0020.0000.0000.0000.000
139C204ASP-1-0.853-0.90445.3800.0210.0210.0000.0000.0000.000
140C205LEU00.0380.05148.517-0.002-0.0020.0000.0000.0000.000
141C206THR0-0.065-0.04751.425-0.001-0.0010.0000.0000.0000.000
142C207GLY0-0.022-0.01651.777-0.001-0.0010.0000.0000.0000.000
143C208GLU-1-0.713-0.92252.1990.0130.0130.0000.0000.0000.000
144C209LEU0-0.0040.01853.863-0.001-0.0010.0000.0000.0000.000
145C210MET0-0.061-0.03356.125-0.001-0.0010.0000.0000.0000.000
146C211ARG10.7690.90550.077-0.014-0.0140.0000.0000.0000.000
147C212ARG11.0040.99657.322-0.012-0.0120.0000.0000.0000.000
148C213CYS0-0.086-0.02759.908-0.001-0.0010.0000.0000.0000.000
149C214ILE0-0.056-0.02158.777-0.001-0.0010.0000.0000.0000.000
150C215ASN0-0.0060.00159.2730.0000.0000.0000.0000.0000.000
151C216SER00.0050.01962.618-0.001-0.0010.0000.0000.0000.000
152C217LEU00.0150.02666.0620.0000.0000.0000.0000.0000.000
153C218GLY0-0.008-0.02167.6580.0000.0000.0000.0000.0000.000
154C219SER0-0.034-0.04767.736-0.001-0.0010.0000.0000.0000.000
155C220GLY0-0.037-0.01770.1810.0000.0000.0000.0000.0000.000
156C221ASP-1-0.802-0.86871.6530.0060.0060.0000.0000.0000.000
157C222THR00.038-0.02968.5890.0000.0000.0000.0000.0000.000
158C223ASP-1-0.955-0.96070.6610.0090.0090.0000.0000.0000.000
159C224THR0-0.0040.00766.9390.0000.0000.0000.0000.0000.000
160C225CYS00.0460.02065.3300.0000.0000.0000.0000.0000.000
161C226LEU00.018-0.00365.2840.0010.0010.0000.0000.0000.000
162C227ASP-1-0.861-0.92364.9630.0120.0120.0000.0000.0000.000
163C228THR0-0.0010.00160.2820.0010.0010.0000.0000.0000.000
164C229CYS0-0.064-0.03361.4260.0000.0000.0000.0000.0000.000
165C230LYS10.9560.98762.760-0.013-0.0130.0000.0000.0000.000
166C231ALA00.0320.03359.4230.0010.0010.0000.0000.0000.000
167C232LEU00.000-0.02057.1870.0010.0010.0000.0000.0000.000
168C233GLN0-0.0020.00258.4680.0010.0010.0000.0000.0000.000
169C234HIS0-0.035-0.00459.4060.0000.0000.0000.0000.0000.000
170C235PHE00.0370.01752.8120.0010.0010.0000.0000.0000.000
171C236TYR00.0130.00654.2860.0010.0010.0000.0000.0000.000
172C237SER0-0.018-0.02555.4300.0010.0010.0000.0000.0000.000
173C238GLY00.0330.01654.7660.0010.0010.0000.0000.0000.000
174C239TYR0-0.093-0.09548.0990.0010.0010.0000.0000.0000.000
175C240ILE0-0.099-0.05251.1520.0010.0010.0000.0000.0000.000
176C241SER0-0.079-0.02353.1200.0010.0010.0000.0000.0000.000
177C242LEU00.0350.03347.5360.0010.0010.0000.0000.0000.000
178C243ASN00.0130.00744.161-0.003-0.0030.0000.0000.0000.000
179C244CYS00.0000.00345.3630.0010.0010.0000.0000.0000.000
180C245GLN0-0.009-0.02943.7590.0000.0000.0000.0000.0000.000
181C246ARG10.8260.93041.883-0.026-0.0260.0000.0000.0000.000
182C247ALA00.0950.07337.273-0.001-0.0010.0000.0000.0000.000
183C248ARG10.8670.88738.902-0.028-0.0280.0000.0000.0000.000
184C249GLU-1-0.846-0.91239.1660.0390.0390.0000.0000.0000.000
185C250LEU00.1380.06441.151-0.002-0.0020.0000.0000.0000.000
186C251TRP00.0260.02744.310-0.001-0.0010.0000.0000.0000.000
187C252ARG10.9390.97638.482-0.028-0.0280.0000.0000.0000.000
188C253LYS10.8680.92444.106-0.024-0.0240.0000.0000.0000.000
189C254ILE00.0510.01947.175-0.001-0.0010.0000.0000.0000.000
190C255THR0-0.042-0.01948.828-0.001-0.0010.0000.0000.0000.000
191C256THR00.002-0.00249.035-0.001-0.0010.0000.0000.0000.000
192C257MET00.0080.03650.679-0.001-0.0010.0000.0000.0000.000
193C258LYS10.9801.01253.101-0.016-0.0160.0000.0000.0000.000
194C259GLN00.012-0.00554.8030.0000.0000.0000.0000.0000.000
195C260SER0-0.078-0.06955.130-0.001-0.0010.0000.0000.0000.000
196C261VAL00.0540.02256.943-0.001-0.0010.0000.0000.0000.000
197C262LEU00.0080.00459.2460.0000.0000.0000.0000.0000.000
198C263LYS10.8820.96355.086-0.011-0.0110.0000.0000.0000.000
199C264ALA00.0670.02060.9240.0000.0000.0000.0000.0000.000
200C265GLU-1-0.899-0.97362.7300.0120.0120.0000.0000.0000.000
201C266ASN0-0.053-0.02464.623-0.001-0.0010.0000.0000.0000.000
202C267VAL00.0390.01464.2530.0000.0000.0000.0000.0000.000
203C269TYR0-0.068-0.01668.7760.0000.0000.0000.0000.0000.000
204C270ASN00.007-0.00969.1190.0000.0000.0000.0000.0000.000
205C271VAL0-0.035-0.00170.4470.0000.0000.0000.0000.0000.000
206C272LYS10.9260.98273.002-0.009-0.0090.0000.0000.0000.000
207C273VAL0-0.015-0.00575.7050.0000.0000.0000.0000.0000.000