Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: KG9Z3

Calculation Name: 2VR9-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VR9

Chain ID: C

ChEMBL ID:

UniProt ID: O44924

Base Structure: X-ray

Registration Date: 2023-09-21

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1837188.57895
FMO2-HF: Nuclear repulsion 1761104.608449
FMO2-HF: Total energy -76083.970501
FMO2-MP2: Total energy -76307.443397


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:52:GLN)


Summations of interaction energy for fragment #1(C:52:GLN)
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.
5.4257.414-0.016-0.97-1.0030.001
Interaction energy analysis for fragmet #1(C:52:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / 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].
3C54GLN0-0.0080.0513.8291.2143.203-0.016-0.970-1.0030.001
4C55SER00.0420.0006.402-0.643-0.6430.0000.0000.0000.000
5C56PRO0-0.049-0.00310.1540.1390.1390.0000.0000.0000.000
6C57ARG10.9911.00111.9640.2170.2170.0000.0000.0000.000
7C58ILE0-0.059-0.03514.093-0.038-0.0380.0000.0000.0000.000
8C59ILE0-0.025-0.01014.3490.0550.0550.0000.0000.0000.000
9C60GLU-1-0.900-0.97217.537-0.192-0.1920.0000.0000.0000.000
10C61HIS00.0120.00621.039-0.028-0.0280.0000.0000.0000.000
11C62PRO00.0030.02823.8310.0130.0130.0000.0000.0000.000
12C63THR00.006-0.01226.9200.0080.0080.0000.0000.0000.000
13C64ASP-1-0.839-0.90130.067-0.139-0.1390.0000.0000.0000.000
14C65LEU0-0.041-0.01933.6220.0040.0040.0000.0000.0000.000
15C66VAL00.0110.00835.769-0.001-0.0010.0000.0000.0000.000
16C67VAL0-0.001-0.00537.6620.0010.0010.0000.0000.0000.000
17C68LYS10.9691.00840.7560.0880.0880.0000.0000.0000.000
18C69LYS11.0210.98543.3360.0970.0970.0000.0000.0000.000
19C70ASN0-0.082-0.04943.5500.0000.0000.0000.0000.0000.000
20C71GLU-1-0.865-0.90841.421-0.108-0.1080.0000.0000.0000.000
21C72PRO0-0.027-0.00536.847-0.006-0.0060.0000.0000.0000.000
22C73ALA00.0160.00335.4930.0060.0060.0000.0000.0000.000
23C74THR0-0.047-0.03029.211-0.011-0.0110.0000.0000.0000.000
24C75LEU00.0240.03829.0420.0100.0100.0000.0000.0000.000
25C76ASN00.0200.00124.413-0.030-0.0300.0000.0000.0000.000
26C77CYS00.0190.00021.425-0.013-0.0130.0000.0000.0000.000
27C78LYS10.9241.00017.8600.2520.2520.0000.0000.0000.000
28C79VAL00.0280.00614.5590.0180.0180.0000.0000.0000.000
29C80GLU-1-0.877-0.93510.284-0.400-0.4000.0000.0000.0000.000
30C81GLY00.053-0.0149.3270.0580.0580.0000.0000.0000.000
31C82LYS10.8000.8765.2011.9221.9220.0000.0000.0000.000
32C83PRO00.002-0.0316.070-0.787-0.7870.0000.0000.0000.000
33C84GLU-1-0.832-0.8918.149-0.984-0.9840.0000.0000.0000.000
34C85PRO0-0.073-0.01611.643-0.009-0.0090.0000.0000.0000.000
35C86THR00.0080.01913.9340.0650.0650.0000.0000.0000.000
36C87ILE00.002-0.02017.0820.0110.0110.0000.0000.0000.000
37C88GLU-1-0.937-0.95320.298-0.418-0.4180.0000.0000.0000.000
38C89TRP0-0.033-0.03723.3740.0240.0240.0000.0000.0000.000
39C90PHE0-0.0030.00424.6500.0010.0010.0000.0000.0000.000
40C91LYS10.8840.94729.5020.1770.1770.0000.0000.0000.000
41C92ASP-1-0.852-0.93533.026-0.161-0.1610.0000.0000.0000.000
42C93GLY0-0.045-0.02732.0010.0050.0050.0000.0000.0000.000
43C94GLU-1-0.894-0.93231.882-0.226-0.2260.0000.0000.0000.000
44C95PRO0-0.0140.00928.297-0.004-0.0040.0000.0000.0000.000
45C96VAL0-0.016-0.03229.4500.0190.0190.0000.0000.0000.000
46C97SER0-0.031-0.01929.529-0.013-0.0130.0000.0000.0000.000
47C98THR0-0.017-0.02728.0450.0200.0200.0000.0000.0000.000
48C99ASN0-0.015-0.00628.423-0.016-0.0160.0000.0000.0000.000
49C100GLU-1-0.824-0.89431.303-0.261-0.2610.0000.0000.0000.000
50C101LYS10.8660.91331.3080.2550.2550.0000.0000.0000.000
51C102LYS10.9060.99033.9870.2470.2470.0000.0000.0000.000
52C103SER00.000-0.03833.430-0.016-0.0160.0000.0000.0000.000
53C104HIS0-0.0450.00035.1880.0100.0100.0000.0000.0000.000
54C105ARG10.9670.99932.6950.2160.2160.0000.0000.0000.000
55C106VAL00.0280.00130.266-0.017-0.0170.0000.0000.0000.000
56C107GLN00.0170.01123.686-0.026-0.0260.0000.0000.0000.000
57C108PHE0-0.027-0.00425.868-0.007-0.0070.0000.0000.0000.000
58C109LYS10.9830.97721.0570.4520.4520.0000.0000.0000.000
59C110ASP-1-0.920-0.96320.323-0.395-0.3950.0000.0000.0000.000
60C111GLY00.032-0.00120.706-0.016-0.0160.0000.0000.0000.000
61C112ALA0-0.0120.02322.3410.0190.0190.0000.0000.0000.000
62C113LEU0-0.0140.00525.504-0.005-0.0050.0000.0000.0000.000
63C114PHE0-0.006-0.00728.5890.0210.0210.0000.0000.0000.000
64C115PHE00.0100.00031.539-0.003-0.0030.0000.0000.0000.000
65C116TYR00.005-0.00635.2100.0120.0120.0000.0000.0000.000
66C117ARG10.9050.93937.3150.1390.1390.0000.0000.0000.000
67C118THR00.0070.01538.296-0.003-0.0030.0000.0000.0000.000
68C119MET0-0.055-0.02739.9140.0140.0140.0000.0000.0000.000
69C120GLN00.0430.01642.054-0.006-0.0060.0000.0000.0000.000
70C121GLY0-0.096-0.06144.8020.0080.0080.0000.0000.0000.000
71C122LYS10.9820.97647.2320.0860.0860.0000.0000.0000.000
72C123LYS10.9520.98845.3970.1260.1260.0000.0000.0000.000
73C124GLU-1-0.859-0.91640.221-0.167-0.1670.0000.0000.0000.000
74C125GLN0-0.022-0.02441.7810.0130.0130.0000.0000.0000.000
75C126ASP-1-0.799-0.91037.531-0.169-0.1690.0000.0000.0000.000
76C127GLY00.0110.01437.533-0.006-0.0060.0000.0000.0000.000
77C128GLY00.002-0.00537.246-0.001-0.0010.0000.0000.0000.000
78C129GLU-1-0.902-0.94933.501-0.153-0.1530.0000.0000.0000.000
79C130TYR0-0.056-0.04630.154-0.016-0.0160.0000.0000.0000.000
80C131TRP0-0.039-0.02025.6280.0190.0190.0000.0000.0000.000
81C133VAL0-0.010-0.00920.1070.0080.0080.0000.0000.0000.000
82C134ALA00.0370.03016.068-0.030-0.0300.0000.0000.0000.000
83C135LYS10.9570.95815.2180.6300.6300.0000.0000.0000.000
84C136ASN00.0460.0469.706-0.040-0.0400.0000.0000.0000.000
85C137ARG10.9610.9805.6023.7303.7300.0000.0000.0000.000
86C138VAL0-0.033-0.0106.5890.0040.0040.0000.0000.0000.000
87C139GLY00.0220.0149.9390.2710.2710.0000.0000.0000.000
88C140GLN0-0.001-0.02613.237-0.110-0.1100.0000.0000.0000.000
89C141ALA0-0.0090.02116.0380.0770.0770.0000.0000.0000.000
90C142VAL00.001-0.00217.867-0.026-0.0260.0000.0000.0000.000
91C143SER0-0.0050.00821.3810.0170.0170.0000.0000.0000.000
92C144ARG10.9280.95423.0490.1680.1680.0000.0000.0000.000
93C145HIS10.8680.93626.3550.1940.1940.0000.0000.0000.000
94C146ALA00.0320.03729.4380.0110.0110.0000.0000.0000.000
95C147SER00.0040.00031.224-0.005-0.0050.0000.0000.0000.000
96C148LEU0-0.0090.00134.5010.0040.0040.0000.0000.0000.000
97C149GLN00.011-0.01136.2130.0030.0030.0000.0000.0000.000
98C150ILE0-0.022-0.01539.9910.0020.0020.0000.0000.0000.000
99C151ALA0-0.007-0.00242.7220.0040.0040.0000.0000.0000.000
100C152VAL0-0.077-0.05745.0960.0000.0000.0000.0000.0000.000
101C153LEU00.000-0.02248.6820.0010.0010.0000.0000.0000.000
102C154ARG10.9020.95451.7340.0750.0750.0000.0000.0000.000
103C155ASP-1-0.952-0.99654.988-0.064-0.0640.0000.0000.0000.000
104C156ASP-1-0.847-0.87358.108-0.057-0.0570.0000.0000.0000.000
105C157PHE0-0.020-0.03759.916-0.001-0.0010.0000.0000.0000.000
106C158ARG10.8840.96360.0590.0480.0480.0000.0000.0000.000
107C159VAL00.031-0.00462.2430.0010.0010.0000.0000.0000.000
108C160GLU-1-0.844-0.90464.641-0.045-0.0450.0000.0000.0000.000
109C161PRO00.0350.03966.6870.0010.0010.0000.0000.0000.000
110C162LYS10.8950.93469.5780.0390.0390.0000.0000.0000.000
111C163ASP-1-0.835-0.90873.246-0.031-0.0310.0000.0000.0000.000
112C164THR0-0.030-0.01575.0780.0000.0000.0000.0000.0000.000
113C165ARG10.9170.96177.4430.0270.0270.0000.0000.0000.000
114C166VAL00.0090.01678.1500.0000.0000.0000.0000.0000.000
115C167ALA00.0380.03281.1310.0000.0000.0000.0000.0000.000
116C168LYS10.9020.92280.9690.0200.0200.0000.0000.0000.000
117C169GLY0-0.109-0.06480.3950.0000.0000.0000.0000.0000.000
118C170GLU-1-0.876-0.92179.536-0.023-0.0230.0000.0000.0000.000
119C171THR0-0.029-0.02073.9960.0000.0000.0000.0000.0000.000
120C172ALA0-0.0120.00374.7630.0000.0000.0000.0000.0000.000
121C173LEU0-0.011-0.02768.5100.0000.0000.0000.0000.0000.000
122C174LEU0-0.0130.01269.2490.0000.0000.0000.0000.0000.000
123C175GLU-1-0.897-0.98167.427-0.039-0.0390.0000.0000.0000.000
124C176CYS0-0.065-0.02962.417-0.001-0.0010.0000.0000.0000.000
125C177GLY0-0.028-0.00761.4190.0000.0000.0000.0000.0000.000
126C178PRO00.0220.01057.098-0.001-0.0010.0000.0000.0000.000
127C179PRO0-0.0090.01656.510-0.001-0.0010.0000.0000.0000.000
128C180LYS10.9630.95852.7690.0650.0650.0000.0000.0000.000
129C181GLY00.002-0.01550.874-0.001-0.0010.0000.0000.0000.000
130C182ILE00.0060.00643.7520.0020.0020.0000.0000.0000.000
131C183PRO00.025-0.02843.918-0.004-0.0040.0000.0000.0000.000
132C184GLU-1-0.904-0.92246.227-0.063-0.0630.0000.0000.0000.000
133C185PRO0-0.092-0.02249.2260.0000.0000.0000.0000.0000.000
134C186THR00.0080.00751.6760.0020.0020.0000.0000.0000.000
135C187LEU0-0.004-0.01153.736-0.001-0.0010.0000.0000.0000.000
136C188ILE0-0.0160.01157.4810.0020.0020.0000.0000.0000.000
137C189TRP00.015-0.00459.8270.0000.0000.0000.0000.0000.000
138C190ILE0-0.005-0.00462.6310.0010.0010.0000.0000.0000.000
139C191LYS10.8920.95765.8370.0260.0260.0000.0000.0000.000
140C192ASP-1-0.843-0.93569.561-0.029-0.0290.0000.0000.0000.000
141C193GLY0-0.047-0.02667.7910.0010.0010.0000.0000.0000.000
142C194VAL0-0.010-0.00566.757-0.001-0.0010.0000.0000.0000.000
143C195PRO0-0.041-0.02162.1600.0000.0000.0000.0000.0000.000
144C196LEU0-0.012-0.00564.2810.0010.0010.0000.0000.0000.000
145C197ASP-1-0.901-0.93959.974-0.035-0.0350.0000.0000.0000.000
146C198ASP-1-0.923-0.95262.333-0.028-0.0280.0000.0000.0000.000
147C199LEU0-0.025-0.01759.131-0.002-0.0020.0000.0000.0000.000
148C200LYS10.8830.93257.0660.0360.0360.0000.0000.0000.000
149C208SER0-0.001-0.01666.390-0.001-0.0010.0000.0000.0000.000
150C209ARG10.8130.90168.4320.0230.0230.0000.0000.0000.000
151C210VAL00.0370.01968.0880.0000.0000.0000.0000.0000.000
152C211ARG10.9300.96863.8890.0280.0280.0000.0000.0000.000
153C212ILE00.0380.02360.2560.0000.0000.0000.0000.0000.000
154C213VAL0-0.051-0.04462.7290.0010.0010.0000.0000.0000.000
155C214ASP-1-0.929-0.97161.642-0.040-0.0400.0000.0000.0000.000
156C215GLY0-0.047-0.01658.627-0.001-0.0010.0000.0000.0000.000
157C216GLY00.0500.01859.379-0.001-0.0010.0000.0000.0000.000
158C217ASN00.0330.03561.2720.0000.0000.0000.0000.0000.000
159C218LEU00.0050.02564.9080.0010.0010.0000.0000.0000.000
160C219LEU00.003-0.00366.9750.0000.0000.0000.0000.0000.000
161C220ILE00.0190.01269.3910.0000.0000.0000.0000.0000.000
162C221SER00.0310.01172.2820.0000.0000.0000.0000.0000.000
163C222ASN00.0390.02174.0870.0000.0000.0000.0000.0000.000
164C223VAL00.0740.04276.4690.0000.0000.0000.0000.0000.000
165C224GLU-1-0.979-0.96977.314-0.019-0.0190.0000.0000.0000.000
166C225PRO00.0480.00879.630-0.001-0.0010.0000.0000.0000.000
167C226ILE00.0450.02876.109-0.001-0.0010.0000.0000.0000.000
168C227ASP-1-0.784-0.89175.268-0.025-0.0250.0000.0000.0000.000
169C228GLU-1-0.825-0.90875.615-0.025-0.0250.0000.0000.0000.000
170C229GLY00.0070.00175.2570.0000.0000.0000.0000.0000.000
171C230ASN0-0.064-0.02573.053-0.001-0.0010.0000.0000.0000.000
172C231TYR0-0.034-0.04069.2010.0000.0000.0000.0000.0000.000
173C232LYS10.9060.97164.9190.0400.0400.0000.0000.0000.000
174C234ILE00.0200.00258.293-0.001-0.0010.0000.0000.0000.000
175C235ALA00.0230.00856.0590.0000.0000.0000.0000.0000.000
176C236GLN0-0.052-0.03653.307-0.001-0.0010.0000.0000.0000.000
177C237ASN00.0580.03248.3840.0010.0010.0000.0000.0000.000
178C238LEU00.0290.00143.4280.0000.0000.0000.0000.0000.000
179C239VAL0-0.088-0.01147.535-0.001-0.0010.0000.0000.0000.000
180C240GLY0-0.0090.00149.5220.0000.0000.0000.0000.0000.000
181C241THR00.0220.00252.6430.0010.0010.0000.0000.0000.000
182C242ARG10.8820.94154.6400.0640.0640.0000.0000.0000.000
183C243GLU-1-0.901-0.95658.746-0.045-0.0450.0000.0000.0000.000
184C244SER00.0390.05562.2940.0000.0000.0000.0000.0000.000
185C245SER0-0.040-0.03065.0950.0010.0010.0000.0000.0000.000
186C246TYR0-0.024-0.03868.5980.0000.0000.0000.0000.0000.000
187C247ALA0-0.0110.01370.8640.0000.0000.0000.0000.0000.000
188C248LYS10.8200.89873.0920.0270.0270.0000.0000.0000.000
189C249LEU0-0.0050.00174.3640.0000.0000.0000.0000.0000.000
190C250ILE0-0.087-0.05376.8540.0010.0010.0000.0000.0000.000
191C251VAL00.0130.01679.7630.0000.0000.0000.0000.0000.000
192C252GLN0-0.047-0.02582.1260.0000.0000.0000.0000.0000.000