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

tag_button

FMODB ID: 4J9KN

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1837721.786036
FMO2-HF: Nuclear repulsion 1761636.524481
FMO2-HF: Total energy -76085.261555
FMO2-MP2: Total energy -76308.566919


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.
5.0367.034-0.021-0.978-10
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 : -0.002 / 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].
3C54GLN00.0170.0273.8401.0223.020-0.021-0.978-1.0000.000
4C55SER00.0230.0056.353-0.537-0.5370.0000.0000.0000.000
5C56PRO0-0.049-0.00810.1040.1140.1140.0000.0000.0000.000
6C57ARG10.9120.95411.7330.5550.5550.0000.0000.0000.000
7C58ILE0-0.060-0.03614.050-0.048-0.0480.0000.0000.0000.000
8C59ILE0-0.015-0.01314.5620.0560.0560.0000.0000.0000.000
9C60GLU-1-0.845-0.91817.506-0.288-0.2880.0000.0000.0000.000
10C61HIS00.000-0.00520.588-0.014-0.0140.0000.0000.0000.000
11C62PRO00.0190.03523.7950.0120.0120.0000.0000.0000.000
12C63THR0-0.004-0.01526.8850.0080.0080.0000.0000.0000.000
13C64ASP-1-0.846-0.89530.032-0.174-0.1740.0000.0000.0000.000
14C65LEU0-0.040-0.01633.5520.0030.0030.0000.0000.0000.000
15C66VAL00.0100.00435.7360.0020.0020.0000.0000.0000.000
16C67VAL00.0070.00137.5710.0000.0000.0000.0000.0000.000
17C68LYS10.9010.96940.7260.1070.1070.0000.0000.0000.000
18C69LYS10.9780.96443.3080.1080.1080.0000.0000.0000.000
19C70ASN0-0.060-0.03243.5280.0020.0020.0000.0000.0000.000
20C71GLU-1-0.855-0.90141.319-0.129-0.1290.0000.0000.0000.000
21C72PRO0-0.030-0.00236.781-0.006-0.0060.0000.0000.0000.000
22C73ALA00.0040.00035.4690.0050.0050.0000.0000.0000.000
23C74THR0-0.056-0.03029.089-0.009-0.0090.0000.0000.0000.000
24C75LEU00.0250.03828.9910.0080.0080.0000.0000.0000.000
25C76ASN0-0.010-0.03024.440-0.021-0.0210.0000.0000.0000.000
26C77CYS00.001-0.00821.437-0.011-0.0110.0000.0000.0000.000
27C78LYS10.8960.97717.9050.3670.3670.0000.0000.0000.000
28C79VAL00.0270.01114.7830.0070.0070.0000.0000.0000.000
29C80GLU-1-0.812-0.89110.254-0.721-0.7210.0000.0000.0000.000
30C81GLY00.011-0.0159.2120.1030.1030.0000.0000.0000.000
31C82LYS10.8360.8995.0832.4882.4880.0000.0000.0000.000
32C83PRO00.015-0.0275.938-0.787-0.7870.0000.0000.0000.000
33C84GLU-1-0.836-0.8847.874-1.380-1.3800.0000.0000.0000.000
34C85PRO0-0.062-0.01611.2950.0610.0610.0000.0000.0000.000
35C86THR0-0.0170.00513.6280.0800.0800.0000.0000.0000.000
36C87ILE0-0.003-0.01516.8730.0100.0100.0000.0000.0000.000
37C88GLU-1-0.880-0.91820.016-0.424-0.4240.0000.0000.0000.000
38C89TRP0-0.005-0.02523.1700.0190.0190.0000.0000.0000.000
39C90PHE0-0.0070.00024.4640.0060.0060.0000.0000.0000.000
40C91LYS10.8140.89129.2850.1830.1830.0000.0000.0000.000
41C92ASP-1-0.813-0.90032.977-0.172-0.1720.0000.0000.0000.000
42C93GLY0-0.032-0.02131.9640.0080.0080.0000.0000.0000.000
43C94GLU-1-0.895-0.93131.799-0.216-0.2160.0000.0000.0000.000
44C95PRO0-0.0170.00628.205-0.010-0.0100.0000.0000.0000.000
45C96VAL0-0.024-0.03029.2940.0180.0180.0000.0000.0000.000
46C97SER0-0.020-0.00229.361-0.014-0.0140.0000.0000.0000.000
47C98THR0-0.006-0.02127.7820.0160.0160.0000.0000.0000.000
48C99ASN0-0.019-0.01828.264-0.014-0.0140.0000.0000.0000.000
49C100GLU-1-0.822-0.88731.292-0.237-0.2370.0000.0000.0000.000
50C101LYS10.8560.89931.4280.2380.2380.0000.0000.0000.000
51C102LYS10.9020.98834.2090.2320.2320.0000.0000.0000.000
52C103SER00.016-0.02233.299-0.015-0.0150.0000.0000.0000.000
53C104HIS0-0.100-0.03934.9760.0100.0100.0000.0000.0000.000
54C105ARG10.8500.91532.6980.2060.2060.0000.0000.0000.000
55C106VAL00.021-0.00229.896-0.016-0.0160.0000.0000.0000.000
56C107GLN00.0260.01123.762-0.026-0.0260.0000.0000.0000.000
57C108PHE0-0.011-0.00525.774-0.007-0.0070.0000.0000.0000.000
58C109LYS11.0020.98720.3790.5120.5120.0000.0000.0000.000
59C110ASP-1-0.904-0.95220.305-0.475-0.4750.0000.0000.0000.000
60C111GLY00.023-0.00220.682-0.026-0.0260.0000.0000.0000.000
61C112ALA0-0.0280.01222.3150.0240.0240.0000.0000.0000.000
62C113LEU0-0.0100.00525.4780.0010.0010.0000.0000.0000.000
63C114PHE0-0.006-0.00728.5610.0200.0200.0000.0000.0000.000
64C115PHE0-0.002-0.00731.5140.0020.0020.0000.0000.0000.000
65C116TYR00.010-0.01035.1840.0110.0110.0000.0000.0000.000
66C117ARG10.8670.91037.2930.1500.1500.0000.0000.0000.000
67C118THR00.0040.00538.059-0.001-0.0010.0000.0000.0000.000
68C119MET0-0.030-0.00139.8850.0150.0150.0000.0000.0000.000
69C120GLN00.0640.02042.021-0.008-0.0080.0000.0000.0000.000
70C121GLY0-0.078-0.04644.7680.0080.0080.0000.0000.0000.000
71C122LYS10.9870.98147.0810.0900.0900.0000.0000.0000.000
72C123LYS10.9580.98845.5040.1260.1260.0000.0000.0000.000
73C124GLU-1-0.775-0.86039.283-0.178-0.1780.0000.0000.0000.000
74C125GLN0-0.026-0.01941.5400.0130.0130.0000.0000.0000.000
75C126ASP-1-0.725-0.85737.532-0.186-0.1860.0000.0000.0000.000
76C127GLY00.0200.03137.497-0.008-0.0080.0000.0000.0000.000
77C128GLY0-0.007-0.00537.2020.0020.0020.0000.0000.0000.000
78C129GLU-1-0.895-0.95233.420-0.183-0.1830.0000.0000.0000.000
79C130TYR0-0.044-0.05530.125-0.012-0.0120.0000.0000.0000.000
80C131TRP0-0.021-0.00825.5730.0140.0140.0000.0000.0000.000
81C133VAL0-0.010-0.01120.0350.0040.0040.0000.0000.0000.000
82C134ALA00.0190.02616.048-0.027-0.0270.0000.0000.0000.000
83C135LYS10.9040.93115.0930.5810.5810.0000.0000.0000.000
84C136ASN00.0160.0029.1900.0370.0370.0000.0000.0000.000
85C137ARG10.9380.9445.5703.0463.0460.0000.0000.0000.000
86C138VAL0-0.034-0.0036.7990.0650.0650.0000.0000.0000.000
87C139GLY00.0260.01710.1210.2430.2430.0000.0000.0000.000
88C140GLN00.017-0.01113.431-0.097-0.0970.0000.0000.0000.000
89C141ALA0-0.0140.01616.0420.0730.0730.0000.0000.0000.000
90C142VAL0-0.002-0.00417.819-0.016-0.0160.0000.0000.0000.000
91C143SER00.0040.01221.3350.0100.0100.0000.0000.0000.000
92C144ARG10.9370.96023.0060.2460.2460.0000.0000.0000.000
93C145HIS10.8550.93526.3120.2280.2280.0000.0000.0000.000
94C146ALA00.0480.04529.3950.0110.0110.0000.0000.0000.000
95C147SER0-0.005-0.02331.185-0.001-0.0010.0000.0000.0000.000
96C148LEU0-0.0130.00334.4040.0020.0020.0000.0000.0000.000
97C149GLN0-0.014-0.02036.1770.0090.0090.0000.0000.0000.000
98C150ILE0-0.019-0.02039.9550.0010.0010.0000.0000.0000.000
99C151ALA0-0.0020.00142.6880.0050.0050.0000.0000.0000.000
100C152VAL0-0.067-0.05745.0630.0010.0010.0000.0000.0000.000
101C153LEU00.003-0.01148.6490.0010.0010.0000.0000.0000.000
102C154ARG10.9370.97951.2930.0870.0870.0000.0000.0000.000
103C155ASP-1-0.858-0.94554.953-0.078-0.0780.0000.0000.0000.000
104C156ASP-1-0.884-0.91058.075-0.065-0.0650.0000.0000.0000.000
105C157PHE0-0.009-0.02859.880-0.002-0.0020.0000.0000.0000.000
106C158ARG10.8950.96660.2530.0580.0580.0000.0000.0000.000
107C159VAL00.026-0.00562.2050.0010.0010.0000.0000.0000.000
108C160GLU-1-0.808-0.87064.605-0.054-0.0540.0000.0000.0000.000
109C161PRO00.0390.03766.6230.0010.0010.0000.0000.0000.000
110C162LYS10.8600.91769.5430.0470.0470.0000.0000.0000.000
111C163ASP-1-0.841-0.91373.210-0.040-0.0400.0000.0000.0000.000
112C164THR0-0.032-0.01375.0230.0000.0000.0000.0000.0000.000
113C165ARG10.9180.96177.4080.0340.0340.0000.0000.0000.000
114C166VAL00.0080.01378.0450.0000.0000.0000.0000.0000.000
115C167ALA00.0470.03681.0960.0000.0000.0000.0000.0000.000
116C168LYS10.9120.92580.8140.0290.0290.0000.0000.0000.000
117C169GLY0-0.124-0.06580.4210.0010.0010.0000.0000.0000.000
118C170GLU-1-0.872-0.92079.500-0.031-0.0310.0000.0000.0000.000
119C171THR0-0.041-0.03973.9780.0000.0000.0000.0000.0000.000
120C172ALA0-0.0080.00674.7950.0000.0000.0000.0000.0000.000
121C173LEU0-0.024-0.03068.384-0.001-0.0010.0000.0000.0000.000
122C174LEU0-0.0130.01369.2990.0000.0000.0000.0000.0000.000
123C175GLU-1-0.905-0.96567.204-0.048-0.0480.0000.0000.0000.000
124C176CYS0-0.050-0.02762.420-0.001-0.0010.0000.0000.0000.000
125C177GLY0-0.0210.00161.372-0.001-0.0010.0000.0000.0000.000
126C178PRO00.0260.00656.998-0.001-0.0010.0000.0000.0000.000
127C179PRO0-0.0060.01956.410-0.001-0.0010.0000.0000.0000.000
128C180LYS10.9570.96052.7050.0760.0760.0000.0000.0000.000
129C181GLY0-0.006-0.01850.8400.0000.0000.0000.0000.0000.000
130C182ILE00.0140.00943.6460.0010.0010.0000.0000.0000.000
131C183PRO00.022-0.02743.791-0.004-0.0040.0000.0000.0000.000
132C184GLU-1-0.899-0.91046.192-0.079-0.0790.0000.0000.0000.000
133C185PRO0-0.079-0.02049.1900.0000.0000.0000.0000.0000.000
134C186THR0-0.023-0.00451.4090.0020.0020.0000.0000.0000.000
135C187LEU0-0.007-0.00853.7040.0000.0000.0000.0000.0000.000
136C188ILE0-0.0070.00957.4480.0010.0010.0000.0000.0000.000
137C189TRP00.010-0.00659.7960.0000.0000.0000.0000.0000.000
138C190ILE0-0.010-0.00662.2250.0000.0000.0000.0000.0000.000
139C191LYS10.8710.95465.8080.0380.0380.0000.0000.0000.000
140C192ASP-1-0.810-0.90469.532-0.039-0.0390.0000.0000.0000.000
141C193GLY0-0.037-0.02067.7650.0010.0010.0000.0000.0000.000
142C194VAL0-0.004-0.00266.731-0.001-0.0010.0000.0000.0000.000
143C195PRO0-0.036-0.01962.1250.0000.0000.0000.0000.0000.000
144C196LEU0-0.022-0.00664.2530.0010.0010.0000.0000.0000.000
145C197ASP-1-0.902-0.94659.825-0.053-0.0530.0000.0000.0000.000
146C198ASP-1-0.921-0.94762.271-0.042-0.0420.0000.0000.0000.000
147C199LEU0-0.025-0.01659.163-0.002-0.0020.0000.0000.0000.000
148C200LYS10.8830.93157.2570.0530.0530.0000.0000.0000.000
149C208SER00.0130.00266.339-0.001-0.0010.0000.0000.0000.000
150C209ARG10.7440.83468.3980.0340.0340.0000.0000.0000.000
151C210VAL00.0450.02467.9440.0000.0000.0000.0000.0000.000
152C211ARG10.9080.94663.8950.0410.0410.0000.0000.0000.000
153C212ILE00.0310.01860.5320.0000.0000.0000.0000.0000.000
154C213VAL0-0.060-0.04562.6870.0000.0000.0000.0000.0000.000
155C214ASP-1-0.941-0.97461.546-0.052-0.0520.0000.0000.0000.000
156C215GLY0-0.034-0.01158.589-0.001-0.0010.0000.0000.0000.000
157C216GLY00.0500.01459.342-0.001-0.0010.0000.0000.0000.000
158C217ASN00.0450.03061.2360.0000.0000.0000.0000.0000.000
159C218LEU00.0080.02264.8720.0000.0000.0000.0000.0000.000
160C219LEU00.0030.00166.9400.0010.0010.0000.0000.0000.000
161C220ILE00.0150.00869.3560.0000.0000.0000.0000.0000.000
162C221SER00.0250.00872.2470.0010.0010.0000.0000.0000.000
163C222ASN00.0520.03174.0520.0010.0010.0000.0000.0000.000
164C223VAL00.0540.03776.1580.0000.0000.0000.0000.0000.000
165C224GLU-1-0.922-0.93777.458-0.029-0.0290.0000.0000.0000.000
166C225PRO00.0550.01079.598-0.001-0.0010.0000.0000.0000.000
167C226ILE00.0330.01776.2020.0000.0000.0000.0000.0000.000
168C227ASP-1-0.740-0.84474.908-0.035-0.0350.0000.0000.0000.000
169C228GLU-1-0.801-0.88175.584-0.033-0.0330.0000.0000.0000.000
170C229GLY0-0.014-0.00975.2270.0000.0000.0000.0000.0000.000
171C230ASN0-0.074-0.04773.1890.0000.0000.0000.0000.0000.000
172C231TYR0-0.033-0.04169.186-0.001-0.0010.0000.0000.0000.000
173C232LYS10.8550.92464.6900.0530.0530.0000.0000.0000.000
174C234ILE0-0.003-0.01158.363-0.001-0.0010.0000.0000.0000.000
175C235ALA00.0300.01156.1240.0000.0000.0000.0000.0000.000
176C236GLN0-0.039-0.03053.348-0.001-0.0010.0000.0000.0000.000
177C237ASN00.0460.01548.447-0.001-0.0010.0000.0000.0000.000
178C238LEU00.0520.02243.1620.0010.0010.0000.0000.0000.000
179C239VAL0-0.0410.00347.5060.0000.0000.0000.0000.0000.000
180C240GLY00.0050.00749.4930.0010.0010.0000.0000.0000.000
181C241THR0-0.011-0.01152.6150.0010.0010.0000.0000.0000.000
182C242ARG10.7960.90154.7140.0770.0770.0000.0000.0000.000
183C243GLU-1-0.809-0.89858.715-0.056-0.0560.0000.0000.0000.000
184C244SER00.0300.04562.2630.0000.0000.0000.0000.0000.000
185C245SER0-0.066-0.05465.0620.0010.0010.0000.0000.0000.000
186C246TYR0-0.017-0.03368.5660.0000.0000.0000.0000.0000.000
187C247ALA0-0.0100.01470.8330.0010.0010.0000.0000.0000.000
188C248LYS10.8000.88573.0590.0350.0350.0000.0000.0000.000
189C249LEU0-0.013-0.00274.1090.0000.0000.0000.0000.0000.000
190C250ILE0-0.060-0.04876.8210.0010.0010.0000.0000.0000.000
191C251VAL00.0090.00979.6060.0000.0000.0000.0000.0000.000
192C252GLN0-0.043-0.02082.0930.0010.0010.0000.0000.0000.000