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: 5J2QZ

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1839009.862728
FMO2-HF: Nuclear repulsion 1762923.483914
FMO2-HF: Total energy -76086.378814
FMO2-MP2: Total energy -76309.529006


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.
5.537.165-0.016-0.805-0.8140.002
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 : -0.001 / q_NPA : -0.010
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].
3C54GLN0-0.015-0.0123.8751.9913.626-0.016-0.805-0.8140.002
4C55SER00.0360.0196.793-0.488-0.4880.0000.0000.0000.000
5C56PRO0-0.039-0.00910.5840.0120.0120.0000.0000.0000.000
6C57ARG10.8890.93511.8790.7140.7140.0000.0000.0000.000
7C58ILE0-0.018-0.01214.518-0.056-0.0560.0000.0000.0000.000
8C59ILE0-0.018-0.00315.0860.0610.0610.0000.0000.0000.000
9C60GLU-1-0.842-0.90418.041-0.327-0.3270.0000.0000.0000.000
10C61HIS00.0050.00020.559-0.009-0.0090.0000.0000.0000.000
11C62PRO00.0140.02124.1060.0110.0110.0000.0000.0000.000
12C63THR0-0.009-0.01327.5280.0060.0060.0000.0000.0000.000
13C64ASP-1-0.833-0.88830.695-0.186-0.1860.0000.0000.0000.000
14C65LEU0-0.036-0.01133.7810.0020.0020.0000.0000.0000.000
15C66VAL00.0260.00736.2390.0030.0030.0000.0000.0000.000
16C67VAL00.0100.01338.0170.0020.0020.0000.0000.0000.000
17C68LYS10.8830.94641.1970.1170.1170.0000.0000.0000.000
18C69LYS10.9380.95643.8760.1120.1120.0000.0000.0000.000
19C70ASN0-0.039-0.01944.0660.0040.0040.0000.0000.0000.000
20C71GLU-1-0.851-0.90841.713-0.142-0.1420.0000.0000.0000.000
21C72PRO0-0.0130.00937.336-0.005-0.0050.0000.0000.0000.000
22C73ALA00.0060.01035.8030.0040.0040.0000.0000.0000.000
23C74THR0-0.053-0.04329.404-0.010-0.0100.0000.0000.0000.000
24C75LEU00.0030.01929.4160.0110.0110.0000.0000.0000.000
25C76ASN0-0.020-0.03425.016-0.017-0.0170.0000.0000.0000.000
26C77CYS00.0190.00321.873-0.005-0.0050.0000.0000.0000.000
27C78LYS10.8610.94518.5290.4160.4160.0000.0000.0000.000
28C79VAL0-0.004-0.01414.9020.0180.0180.0000.0000.0000.000
29C80GLU-1-0.805-0.87310.424-0.895-0.8950.0000.0000.0000.000
30C81GLY00.0560.0179.6240.1800.1800.0000.0000.0000.000
31C82LYS10.7970.8884.8882.7482.7480.0000.0000.0000.000
32C83PRO00.017-0.0225.903-0.888-0.8880.0000.0000.0000.000
33C84GLU-1-0.823-0.8857.797-1.618-1.6180.0000.0000.0000.000
34C85PRO0-0.050-0.01311.2050.0970.0970.0000.0000.0000.000
35C86THR0-0.0230.00813.7100.0980.0980.0000.0000.0000.000
36C87ILE0-0.005-0.00216.8800.0100.0100.0000.0000.0000.000
37C88GLU-1-0.815-0.88919.890-0.427-0.4270.0000.0000.0000.000
38C89TRP00.005-0.02023.1360.0150.0150.0000.0000.0000.000
39C90PHE0-0.009-0.00124.9650.0080.0080.0000.0000.0000.000
40C91LYS10.8030.88129.5960.1810.1810.0000.0000.0000.000
41C92ASP-1-0.826-0.90933.301-0.174-0.1740.0000.0000.0000.000
42C93GLY0-0.027-0.01732.9050.0110.0110.0000.0000.0000.000
43C94GLU-1-0.909-0.93931.961-0.213-0.2130.0000.0000.0000.000
44C95PRO0-0.0160.00028.331-0.010-0.0100.0000.0000.0000.000
45C96VAL0-0.025-0.02029.5060.0160.0160.0000.0000.0000.000
46C97SER0-0.015-0.00329.338-0.016-0.0160.0000.0000.0000.000
47C98THR00.008-0.00227.5520.0120.0120.0000.0000.0000.000
48C99ASN0-0.018-0.01528.346-0.014-0.0140.0000.0000.0000.000
49C100GLU-1-0.786-0.85731.243-0.243-0.2430.0000.0000.0000.000
50C101LYS10.8150.88431.4980.2480.2480.0000.0000.0000.000
51C102LYS10.8940.93734.2810.2360.2360.0000.0000.0000.000
52C103SER00.0120.01333.245-0.004-0.0040.0000.0000.0000.000
53C104HIS0-0.058-0.01835.1180.0060.0060.0000.0000.0000.000
54C105ARG10.8010.86832.7360.2070.2070.0000.0000.0000.000
55C106VAL00.000-0.00829.663-0.009-0.0090.0000.0000.0000.000
56C107GLN00.0260.00123.766-0.027-0.0270.0000.0000.0000.000
57C108PHE0-0.0070.00025.879-0.008-0.0080.0000.0000.0000.000
58C109LYS10.9550.95419.8780.5790.5790.0000.0000.0000.000
59C110ASP-1-0.847-0.91420.318-0.528-0.5280.0000.0000.0000.000
60C111GLY00.0470.02220.582-0.040-0.0400.0000.0000.0000.000
61C112ALA0-0.0340.00122.3440.0300.0300.0000.0000.0000.000
62C113LEU0-0.0130.00625.8670.0030.0030.0000.0000.0000.000
63C114PHE00.000-0.00428.8270.0170.0170.0000.0000.0000.000
64C115PHE00.0070.00031.7610.0010.0010.0000.0000.0000.000
65C116TYR0-0.005-0.02235.4550.0110.0110.0000.0000.0000.000
66C117ARG10.8600.90337.6560.1580.1580.0000.0000.0000.000
67C118THR0-0.009-0.00238.923-0.003-0.0030.0000.0000.0000.000
68C119MET0-0.033-0.00240.5370.0150.0150.0000.0000.0000.000
69C120GLN00.0970.03542.359-0.008-0.0080.0000.0000.0000.000
70C121GLY0-0.052-0.03245.1040.0080.0080.0000.0000.0000.000
71C122LYS10.9860.98846.9810.0910.0910.0000.0000.0000.000
72C123LYS10.9440.96645.4660.1270.1270.0000.0000.0000.000
73C124GLU-1-0.743-0.82439.077-0.185-0.1850.0000.0000.0000.000
74C125GLN0-0.048-0.03041.3560.0130.0130.0000.0000.0000.000
75C126ASP-1-0.706-0.84537.794-0.196-0.1960.0000.0000.0000.000
76C127GLY00.0160.01838.085-0.007-0.0070.0000.0000.0000.000
77C128GLY0-0.013-0.00437.6780.0040.0040.0000.0000.0000.000
78C129GLU-1-0.865-0.94033.816-0.197-0.1970.0000.0000.0000.000
79C130TYR0-0.045-0.04530.649-0.009-0.0090.0000.0000.0000.000
80C131TRP0-0.031-0.01626.0350.0120.0120.0000.0000.0000.000
81C133VAL00.002-0.00520.3300.0120.0120.0000.0000.0000.000
82C134ALA00.0150.01616.718-0.027-0.0270.0000.0000.0000.000
83C135LYS10.8500.89715.6340.5350.5350.0000.0000.0000.000
84C136ASN00.0420.0009.6040.1180.1180.0000.0000.0000.000
85C137ARG10.9280.9505.8232.7052.7050.0000.0000.0000.000
86C138VAL0-0.061-0.0236.707-0.085-0.0850.0000.0000.0000.000
87C139GLY00.0220.0189.8440.2490.2490.0000.0000.0000.000
88C140GLN0-0.001-0.01413.329-0.126-0.1260.0000.0000.0000.000
89C141ALA0-0.0150.01216.3060.0710.0710.0000.0000.0000.000
90C142VAL00.007-0.00318.283-0.021-0.0210.0000.0000.0000.000
91C143SER0-0.025-0.01521.7970.0080.0080.0000.0000.0000.000
92C144ARG10.9510.96423.5260.2770.2770.0000.0000.0000.000
93C145HIS10.8470.95026.6340.2220.2220.0000.0000.0000.000
94C146ALA00.0330.03229.7410.0050.0050.0000.0000.0000.000
95C147SER00.023-0.01431.938-0.002-0.0020.0000.0000.0000.000
96C148LEU0-0.0160.01634.6650.0040.0040.0000.0000.0000.000
97C149GLN0-0.043-0.03736.4070.0130.0130.0000.0000.0000.000
98C150ILE0-0.023-0.01040.2380.0000.0000.0000.0000.0000.000
99C151ALA00.0000.00543.1040.0060.0060.0000.0000.0000.000
100C152VAL0-0.051-0.04145.4330.0020.0020.0000.0000.0000.000
101C153LEU00.0120.01149.0560.0000.0000.0000.0000.0000.000
102C154ARG10.9100.97352.0450.0890.0890.0000.0000.0000.000
103C155ASP-1-0.800-0.91155.553-0.083-0.0830.0000.0000.0000.000
104C156ASP-1-0.928-0.95058.868-0.069-0.0690.0000.0000.0000.000
105C157PHE0-0.007-0.02260.169-0.002-0.0020.0000.0000.0000.000
106C158ARG10.8190.93360.8530.0590.0590.0000.0000.0000.000
107C159VAL00.0080.00062.6690.0010.0010.0000.0000.0000.000
108C160GLU-1-0.776-0.84564.964-0.057-0.0570.0000.0000.0000.000
109C161PRO00.0290.02867.1330.0010.0010.0000.0000.0000.000
110C162LYS10.8410.88470.0500.0510.0510.0000.0000.0000.000
111C163ASP-1-0.855-0.91573.705-0.043-0.0430.0000.0000.0000.000
112C164THR0-0.041-0.01875.6520.0010.0010.0000.0000.0000.000
113C165ARG10.8980.94278.0870.0370.0370.0000.0000.0000.000
114C166VAL00.0270.02478.4350.0000.0000.0000.0000.0000.000
115C167ALA00.0310.01581.3740.0000.0000.0000.0000.0000.000
116C168LYS10.8510.90181.1660.0310.0310.0000.0000.0000.000
117C169GLY0-0.078-0.04580.9100.0010.0010.0000.0000.0000.000
118C170GLU-1-0.862-0.90879.948-0.033-0.0330.0000.0000.0000.000
119C171THR0-0.046-0.03774.2500.0000.0000.0000.0000.0000.000
120C172ALA0-0.0010.00775.0950.0000.0000.0000.0000.0000.000
121C173LEU0-0.018-0.02368.695-0.001-0.0010.0000.0000.0000.000
122C174LEU0-0.0120.00669.8700.0000.0000.0000.0000.0000.000
123C175GLU-1-0.842-0.93867.051-0.053-0.0530.0000.0000.0000.000
124C176CYS0-0.044-0.02562.807-0.001-0.0010.0000.0000.0000.000
125C177GLY00.0150.02261.520-0.001-0.0010.0000.0000.0000.000
126C178PRO00.0290.00457.2910.0000.0000.0000.0000.0000.000
127C179PRO0-0.0110.01756.824-0.001-0.0010.0000.0000.0000.000
128C180LYS10.9850.97253.0580.0790.0790.0000.0000.0000.000
129C181GLY00.007-0.01751.0110.0000.0000.0000.0000.0000.000
130C182ILE0-0.0360.01443.8550.0010.0010.0000.0000.0000.000
131C183PRO00.035-0.02044.123-0.004-0.0040.0000.0000.0000.000
132C184GLU-1-0.904-0.94246.552-0.085-0.0850.0000.0000.0000.000
133C185PRO0-0.080-0.01749.799-0.001-0.0010.0000.0000.0000.000
134C186THR00.0070.00151.5260.0020.0020.0000.0000.0000.000
135C187LEU0-0.026-0.00953.8210.0000.0000.0000.0000.0000.000
136C188ILE0-0.017-0.00457.6060.0010.0010.0000.0000.0000.000
137C189TRP0-0.001-0.01560.2400.0000.0000.0000.0000.0000.000
138C190ILE0-0.013-0.00763.1480.0000.0000.0000.0000.0000.000
139C191LYS10.8540.93866.3950.0420.0420.0000.0000.0000.000
140C192ASP-1-0.821-0.91270.141-0.043-0.0430.0000.0000.0000.000
141C193GLY0-0.013-0.00268.5090.0010.0010.0000.0000.0000.000
142C194VAL0-0.014-0.00667.227-0.002-0.0020.0000.0000.0000.000
143C195PRO0-0.005-0.00162.6140.0000.0000.0000.0000.0000.000
144C196LEU0-0.002-0.00664.5360.0020.0020.0000.0000.0000.000
145C197ASP-1-0.923-0.95560.044-0.060-0.0600.0000.0000.0000.000
146C198ASP-1-0.916-0.95262.583-0.048-0.0480.0000.0000.0000.000
147C199LEU0-0.009-0.00459.952-0.002-0.0020.0000.0000.0000.000
148C200LYS10.8700.92557.7680.0590.0590.0000.0000.0000.000
149C208SER0-0.007-0.00766.3270.0000.0000.0000.0000.0000.000
150C209ARG10.7690.84568.4750.0370.0370.0000.0000.0000.000
151C210VAL00.0140.02068.1110.0010.0010.0000.0000.0000.000
152C211ARG10.9070.94263.7790.0450.0450.0000.0000.0000.000
153C212ILE00.0360.03160.7640.0000.0000.0000.0000.0000.000
154C213VAL0-0.048-0.03462.9870.0010.0010.0000.0000.0000.000
155C214ASP-1-0.903-0.97262.073-0.056-0.0560.0000.0000.0000.000
156C215GLY0-0.021-0.00358.662-0.001-0.0010.0000.0000.0000.000
157C216GLY00.018-0.00559.083-0.003-0.0030.0000.0000.0000.000
158C217ASN00.0360.04061.4640.0000.0000.0000.0000.0000.000
159C218LEU00.0110.02064.9560.0000.0000.0000.0000.0000.000
160C219LEU0-0.011-0.00967.2480.0010.0010.0000.0000.0000.000
161C220ILE00.0220.00069.7260.0000.0000.0000.0000.0000.000
162C221SER00.0120.00672.6030.0010.0010.0000.0000.0000.000
163C222ASN00.0330.01774.3890.0010.0010.0000.0000.0000.000
164C223VAL00.0600.04576.4880.0000.0000.0000.0000.0000.000
165C224GLU-1-0.888-0.93978.150-0.033-0.0330.0000.0000.0000.000
166C225PRO00.0490.01679.655-0.001-0.0010.0000.0000.0000.000
167C226ILE00.0170.01776.2840.0000.0000.0000.0000.0000.000
168C227ASP-1-0.714-0.82675.136-0.039-0.0390.0000.0000.0000.000
169C228GLU-1-0.775-0.87176.415-0.037-0.0370.0000.0000.0000.000
170C229GLY0-0.015-0.00675.7950.0000.0000.0000.0000.0000.000
171C230ASN0-0.083-0.04973.9160.0010.0010.0000.0000.0000.000
172C231TYR0-0.028-0.03669.913-0.001-0.0010.0000.0000.0000.000
173C232LYS10.8340.91065.0190.0590.0590.0000.0000.0000.000
174C234ILE00.0090.00458.663-0.001-0.0010.0000.0000.0000.000
175C235ALA00.0370.01956.8000.0000.0000.0000.0000.0000.000
176C236GLN0-0.035-0.02653.835-0.001-0.0010.0000.0000.0000.000
177C237ASN00.0290.00448.934-0.001-0.0010.0000.0000.0000.000
178C238LEU00.0560.02443.5060.0010.0010.0000.0000.0000.000
179C239VAL0-0.029-0.00147.772-0.002-0.0020.0000.0000.0000.000
180C240GLY00.0120.00549.8410.0000.0000.0000.0000.0000.000
181C241THR0-0.012-0.00153.1300.0000.0000.0000.0000.0000.000
182C242ARG10.7790.88355.1760.0830.0830.0000.0000.0000.000
183C243GLU-1-0.806-0.90359.239-0.062-0.0620.0000.0000.0000.000
184C244SER00.0000.00562.6520.0000.0000.0000.0000.0000.000
185C245SER0-0.037-0.04265.5630.0010.0010.0000.0000.0000.000
186C246TYR0-0.020-0.01869.090-0.001-0.0010.0000.0000.0000.000
187C247ALA0-0.0050.01771.1960.0000.0000.0000.0000.0000.000
188C248LYS10.8030.89773.7390.0390.0390.0000.0000.0000.000
189C249LEU00.0020.01074.5920.0000.0000.0000.0000.0000.000
190C250ILE0-0.045-0.03177.2860.0000.0000.0000.0000.0000.000
191C251VAL0-0.014-0.01279.9970.0000.0000.0000.0000.0000.000
192C252GLN0-0.036-0.01282.5610.0010.0010.0000.0000.0000.000