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: K9NV3

Calculation Name: 1VBF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VBF

Chain ID: A

ChEMBL ID:

UniProt ID: Q972K9

Base Structure: X-ray

Registration Date: 2023-09-20

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2736966.1866
FMO2-HF: Nuclear repulsion 2649110.643601
FMO2-HF: Total energy -87855.542999
FMO2-MP2: Total energy -88115.405021


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(A:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-9.57-5.1590.948-2.032-3.3290.002
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.004
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].
3A3GLU-1-0.669-0.8143.781-3.349-0.984-0.001-1.188-1.1770.006
4A4LYS10.9520.9745.9791.3021.3020.0000.0000.0000.000
5A5GLU-1-0.894-0.9652.6310.2700.8670.313-0.204-0.707-0.001
6A6GLU-1-0.960-0.9892.636-5.901-5.0630.586-0.462-0.963-0.004
7A7ILE0-0.020-0.0144.5590.4390.509-0.001-0.011-0.0580.000
8A8LEU00.0120.0017.4330.1770.1770.0000.0000.0000.000
9A9ARG10.8290.9163.134-2.707-2.1660.051-0.167-0.4240.001
10A10LYS10.9050.9578.1490.7230.7230.0000.0000.0000.000
11A11ILE0-0.0490.01210.6820.0200.0200.0000.0000.0000.000
12A12LYS10.9320.97013.313-0.023-0.0230.0000.0000.0000.000
13A13THR0-0.053-0.02616.2020.0380.0380.0000.0000.0000.000
14A14GLN00.0170.00915.970-0.001-0.0010.0000.0000.0000.000
15A15GLU-1-0.831-0.94117.412-0.016-0.0160.0000.0000.0000.000
16A16LEU0-0.0060.00116.162-0.017-0.0170.0000.0000.0000.000
17A17ALA00.0040.00913.316-0.041-0.0410.0000.0000.0000.000
18A18GLU-1-0.978-0.99614.2250.0080.0080.0000.0000.0000.000
19A19ALA0-0.005-0.00216.672-0.015-0.0150.0000.0000.0000.000
20A20PHE0-0.037-0.0309.755-0.043-0.0430.0000.0000.0000.000
21A21ASN0-0.068-0.03011.713-0.027-0.0270.0000.0000.0000.000
22A22LYS10.8830.93913.9430.0640.0640.0000.0000.0000.000
23A23VAL0-0.0110.01617.3100.0020.0020.0000.0000.0000.000
24A24ASP-1-0.818-0.89916.893-0.379-0.3790.0000.0000.0000.000
25A25ARG10.8650.92015.5130.6010.6010.0000.0000.0000.000
26A26SER0-0.057-0.05417.8490.0080.0080.0000.0000.0000.000
27A27LEU0-0.0230.00519.3700.0180.0180.0000.0000.0000.000
28A28PHE00.022-0.00420.9500.0140.0140.0000.0000.0000.000
29A29LEU0-0.0300.02318.5650.0100.0100.0000.0000.0000.000
30A30PRO00.0370.01522.8900.0140.0140.0000.0000.0000.000
31A31GLU-1-0.899-0.94923.977-0.291-0.2910.0000.0000.0000.000
32A32ASN0-0.010-0.02323.970-0.016-0.0160.0000.0000.0000.000
33A33LEU0-0.022-0.02021.433-0.019-0.0190.0000.0000.0000.000
34A34LYS10.9350.98319.9120.2280.2280.0000.0000.0000.000
35A35ASP-1-0.889-0.92617.108-0.552-0.5520.0000.0000.0000.000
36A36TYR0-0.018-0.02115.498-0.091-0.0910.0000.0000.0000.000
37A37ALA0-0.068-0.01615.301-0.052-0.0520.0000.0000.0000.000
38A38TYR0-0.009-0.02610.2570.0370.0370.0000.0000.0000.000
39A39ALA00.0010.01210.307-0.337-0.3370.0000.0000.0000.000
40A40HIS00.0350.02011.2750.1390.1390.0000.0000.0000.000
41A41THR0-0.092-0.0709.4390.2500.2500.0000.0000.0000.000
42A42HIS0-0.040-0.0269.5450.2640.2640.0000.0000.0000.000
43A43GLU-1-0.919-0.95414.111-0.568-0.5680.0000.0000.0000.000
44A44ALA0-0.053-0.01917.3060.0070.0070.0000.0000.0000.000
45A45LEU00.008-0.00218.2130.0050.0050.0000.0000.0000.000
46A46PRO00.0270.01721.8380.0330.0330.0000.0000.0000.000
47A47ILE0-0.038-0.01324.251-0.001-0.0010.0000.0000.0000.000
48A48LEU0-0.015-0.01627.6110.0170.0170.0000.0000.0000.000
49A49PRO0-0.013-0.00530.667-0.008-0.0080.0000.0000.0000.000
50A50GLY0-0.006-0.00331.7030.0090.0090.0000.0000.0000.000
51A51ILE0-0.027-0.00728.2940.0040.0040.0000.0000.0000.000
52A52ASN00.0650.02524.0460.0010.0010.0000.0000.0000.000
53A53THR0-0.045-0.01121.1450.0140.0140.0000.0000.0000.000
54A54THR00.043-0.00119.104-0.023-0.0230.0000.0000.0000.000
55A55ALA00.0220.04216.053-0.014-0.0140.0000.0000.0000.000
56A56LEU00.0740.02312.2850.0300.0300.0000.0000.0000.000
57A57ASN00.0230.01911.7240.0920.0920.0000.0000.0000.000
58A58LEU0-0.001-0.00813.0550.0730.0730.0000.0000.0000.000
59A59GLY00.0290.00116.6370.0580.0580.0000.0000.0000.000
60A60ILE00.019-0.00713.0770.0500.0500.0000.0000.0000.000
61A61PHE0-0.0040.00515.1080.0530.0530.0000.0000.0000.000
62A62MET00.0020.00116.3600.0390.0390.0000.0000.0000.000
63A63LEU0-0.035-0.01118.8760.0290.0290.0000.0000.0000.000
64A64ASP-1-0.781-0.90816.369-0.086-0.0860.0000.0000.0000.000
65A65GLU-1-0.930-0.96418.832-0.078-0.0780.0000.0000.0000.000
66A66LEU0-0.053-0.02721.1090.0180.0180.0000.0000.0000.000
67A67ASP-1-0.864-0.93622.450-0.022-0.0220.0000.0000.0000.000
68A68LEU00.0050.02221.7020.0090.0090.0000.0000.0000.000
69A69HIS10.8360.91423.7850.0400.0400.0000.0000.0000.000
70A70LYS11.0451.01424.901-0.005-0.0050.0000.0000.0000.000
71A71GLY0-0.009-0.03728.1200.0040.0040.0000.0000.0000.000
72A72GLN00.0110.00627.819-0.006-0.0060.0000.0000.0000.000
73A73LYS10.8960.94931.3630.0520.0520.0000.0000.0000.000
74A74VAL0-0.007-0.01527.6120.0010.0010.0000.0000.0000.000
75A75LEU0-0.030-0.00330.864-0.001-0.0010.0000.0000.0000.000
76A76GLU-1-0.766-0.83226.017-0.179-0.1790.0000.0000.0000.000
77A77ILE0-0.038-0.02429.9020.0050.0050.0000.0000.0000.000
78A78GLY00.000-0.01129.620-0.009-0.0090.0000.0000.0000.000
79A79THR0-0.032-0.03428.009-0.012-0.0120.0000.0000.0000.000
80A80GLY00.0160.01226.979-0.017-0.0170.0000.0000.0000.000
81A81ILE0-0.018-0.03521.6600.0080.0080.0000.0000.0000.000
82A82GLY00.0420.01925.8710.0040.0040.0000.0000.0000.000
83A83TYR00.0290.01315.777-0.006-0.0060.0000.0000.0000.000
84A84TYR00.000-0.00917.733-0.011-0.0110.0000.0000.0000.000
85A85THR00.025-0.01221.8910.0120.0120.0000.0000.0000.000
86A86ALA0-0.010-0.00122.3150.0180.0180.0000.0000.0000.000
87A87LEU0-0.037-0.02217.0920.0150.0150.0000.0000.0000.000
88A88ILE00.0110.00621.2010.0200.0200.0000.0000.0000.000
89A89ALA0-0.025-0.00324.0380.0170.0170.0000.0000.0000.000
90A90GLU-1-0.911-0.95521.610-0.084-0.0840.0000.0000.0000.000
91A91ILE0-0.091-0.03120.2240.0150.0150.0000.0000.0000.000
92A92VAL0-0.056-0.03524.1850.0150.0150.0000.0000.0000.000
93A93ASP-1-0.985-0.92827.644-0.044-0.0440.0000.0000.0000.000
94A94LYS10.8870.95731.2500.0600.0600.0000.0000.0000.000
95A95VAL00.0160.00527.900-0.001-0.0010.0000.0000.0000.000
96A96VAL0-0.043-0.00231.2910.0010.0010.0000.0000.0000.000
97A97SER0-0.004-0.00229.391-0.005-0.0050.0000.0000.0000.000
98A98VAL0-0.048-0.00232.2070.0050.0050.0000.0000.0000.000
99A99GLU-1-0.779-0.90931.520-0.172-0.1720.0000.0000.0000.000
100A100ILE00.0070.00234.0680.0070.0070.0000.0000.0000.000
101A101ASN0-0.029-0.01134.2180.0080.0080.0000.0000.0000.000
102A102GLU-1-0.858-0.94135.624-0.105-0.1050.0000.0000.0000.000
103A103LYS10.9220.95635.4190.1250.1250.0000.0000.0000.000
104A104MET0-0.0020.01728.174-0.007-0.0070.0000.0000.0000.000
105A105TYR00.0080.01432.182-0.003-0.0030.0000.0000.0000.000
106A106ASN00.005-0.01133.8260.0030.0030.0000.0000.0000.000
107A107TYR0-0.110-0.07125.8990.0070.0070.0000.0000.0000.000
108A108ALA00.0520.01329.343-0.003-0.0030.0000.0000.0000.000
109A109SER00.0110.00030.2650.0050.0050.0000.0000.0000.000
110A110LYS10.8910.94732.0460.1410.1410.0000.0000.0000.000
111A111LEU0-0.027-0.00826.2600.0060.0060.0000.0000.0000.000
112A112LEU00.0110.00326.8740.0000.0000.0000.0000.0000.000
113A113SER0-0.048-0.01429.7170.0100.0100.0000.0000.0000.000
114A114TYR0-0.064-0.01526.5930.0090.0090.0000.0000.0000.000
115A115TYR00.0100.00623.4980.0010.0010.0000.0000.0000.000
116A116ASN0-0.009-0.00329.9240.0020.0020.0000.0000.0000.000
117A117ASN0-0.038-0.03028.657-0.001-0.0010.0000.0000.0000.000
118A118ILE00.0340.01027.588-0.002-0.0020.0000.0000.0000.000
119A119LYS10.8610.93632.0970.0720.0720.0000.0000.0000.000
120A120LEU00.0270.01031.044-0.003-0.0030.0000.0000.0000.000
121A121ILE0-0.020-0.01334.9540.0060.0060.0000.0000.0000.000
122A122LEU00.0230.02536.426-0.007-0.0070.0000.0000.0000.000
123A123GLY00.008-0.02337.7540.0070.0070.0000.0000.0000.000
124A124ASP-1-0.770-0.90637.773-0.102-0.1020.0000.0000.0000.000
125A125GLY00.0530.01835.3650.0040.0040.0000.0000.0000.000
126A126THR00.0050.02136.2960.0010.0010.0000.0000.0000.000
127A127LEU0-0.037-0.03337.9310.0050.0050.0000.0000.0000.000
128A128GLY0-0.039-0.01136.7980.0050.0050.0000.0000.0000.000
129A129TYR0-0.032-0.03337.8670.0000.0000.0000.0000.0000.000
130A130GLU-1-0.759-0.90839.556-0.051-0.0510.0000.0000.0000.000
131A131GLU-1-0.834-0.91842.164-0.059-0.0590.0000.0000.0000.000
132A132GLU-1-0.960-0.97438.560-0.057-0.0570.0000.0000.0000.000
133A133LYS10.8140.93039.4240.0530.0530.0000.0000.0000.000
134A134PRO0-0.048-0.02739.091-0.002-0.0020.0000.0000.0000.000
135A135TYR00.0530.02633.911-0.002-0.0020.0000.0000.0000.000
136A136ASP-1-0.876-0.93831.566-0.044-0.0440.0000.0000.0000.000
137A137ARG10.7720.87626.9300.0640.0640.0000.0000.0000.000
138A138VAL00.0190.01629.8820.0000.0000.0000.0000.0000.000
139A139VAL00.0230.02024.369-0.002-0.0020.0000.0000.0000.000
140A140VAL0-0.028-0.01327.5310.0040.0040.0000.0000.0000.000
141A141TRP0-0.027-0.02021.173-0.021-0.0210.0000.0000.0000.000
142A142ALA00.022-0.00326.722-0.011-0.0110.0000.0000.0000.000
143A143THR0-0.036-0.00629.1090.0110.0110.0000.0000.0000.000
144A144ALA00.0460.01230.6190.0050.0050.0000.0000.0000.000
145A145PRO00.004-0.00134.123-0.001-0.0010.0000.0000.0000.000
146A146THR00.005-0.01037.0990.0040.0040.0000.0000.0000.000
147A147LEU0-0.0080.00234.478-0.005-0.0050.0000.0000.0000.000
148A148LEU00.0410.02233.5400.0040.0040.0000.0000.0000.000
149A149CYS00.005-0.00536.9220.0030.0030.0000.0000.0000.000
150A150LYS10.9611.01039.8470.0650.0650.0000.0000.0000.000
151A151PRO00.0510.01034.8610.0040.0040.0000.0000.0000.000
152A152TYR00.0250.00135.8130.0020.0020.0000.0000.0000.000
153A153GLU-1-0.901-0.96737.305-0.052-0.0520.0000.0000.0000.000
154A154GLN0-0.059-0.03138.2110.0030.0030.0000.0000.0000.000
155A155LEU00.0130.04132.8440.0000.0000.0000.0000.0000.000
156A156LYS10.9570.96935.9370.0380.0380.0000.0000.0000.000
157A157GLU-1-0.879-0.97437.153-0.040-0.0400.0000.0000.0000.000
158A158GLY00.0250.03435.6650.0010.0010.0000.0000.0000.000
159A159GLY0-0.061-0.02833.005-0.001-0.0010.0000.0000.0000.000
160A160ILE00.0300.01227.1380.0010.0010.0000.0000.0000.000
161A161MET0-0.022-0.01129.899-0.003-0.0030.0000.0000.0000.000
162A162ILE0-0.0110.00923.4510.0040.0040.0000.0000.0000.000
163A163LEU00.003-0.00527.278-0.005-0.0050.0000.0000.0000.000
164A164PRO00.0340.03226.3170.0050.0050.0000.0000.0000.000
165A165ILE0-0.0130.00728.4100.0070.0070.0000.0000.0000.000
166A166GLY00.008-0.00631.520-0.002-0.0020.0000.0000.0000.000
167A167VAL00.0510.02333.209-0.006-0.0060.0000.0000.0000.000
168A168GLY00.002-0.01033.6450.0010.0010.0000.0000.0000.000
169A169ARG10.9280.95327.4940.2060.2060.0000.0000.0000.000
170A170VAL00.0040.00926.213-0.015-0.0150.0000.0000.0000.000
171A171GLN0-0.0130.02527.4650.0030.0030.0000.0000.0000.000
172A172LYS10.9660.99326.8350.1050.1050.0000.0000.0000.000
173A173LEU00.0240.01021.8650.0040.0040.0000.0000.0000.000
174A174TYR0-0.022-0.02125.6810.0120.0120.0000.0000.0000.000
175A175LYS10.9751.01024.7570.0680.0680.0000.0000.0000.000
176A176VAL0-0.034-0.03027.6420.0100.0100.0000.0000.0000.000
177A177ILE0-0.026-0.00729.9860.0000.0000.0000.0000.0000.000
178A178LYS10.7550.89332.9730.0540.0540.0000.0000.0000.000
179A179LYS10.9770.98935.1300.0400.0400.0000.0000.0000.000
180A180GLY00.0330.03139.2750.0010.0010.0000.0000.0000.000
181A181ASN0-0.023-0.00141.391-0.006-0.0060.0000.0000.0000.000
182A182SER0-0.065-0.03640.8240.0000.0000.0000.0000.0000.000
183A183PRO00.0160.02836.1680.0030.0030.0000.0000.0000.000
184A184SER0-0.035-0.01032.7550.0030.0030.0000.0000.0000.000
185A185LEU0-0.004-0.01831.645-0.004-0.0040.0000.0000.0000.000
186A186GLU-1-0.892-0.94025.521-0.070-0.0700.0000.0000.0000.000
187A187ASN0-0.030-0.02026.453-0.019-0.0190.0000.0000.0000.000
188A188LEU00.0200.00121.8870.0030.0030.0000.0000.0000.000
189A189GLY00.0130.00921.652-0.018-0.0180.0000.0000.0000.000
190A190GLU-1-0.975-0.99223.053-0.173-0.1730.0000.0000.0000.000
191A191VAL0-0.0220.00121.551-0.030-0.0300.0000.0000.0000.000
192A192MET0-0.024-0.02723.0580.0180.0180.0000.0000.0000.000
193A193PHE0-0.022-0.00822.495-0.018-0.0180.0000.0000.0000.000
194A194GLY00.0150.00526.6720.0100.0100.0000.0000.0000.000
195A195ARG10.8620.93729.7110.1330.1330.0000.0000.0000.000
196A196ILE00.0110.02732.911-0.002-0.0020.0000.0000.0000.000
197A197GLY00.0260.00234.0670.0060.0060.0000.0000.0000.000
198A198GLY00.030-0.00437.3880.0000.0000.0000.0000.0000.000
199A199LEU00.0010.00240.2540.0010.0010.0000.0000.0000.000
200A200TYR0-0.080-0.03340.1230.0030.0030.0000.0000.0000.000
201A201GLY00.0250.02238.138-0.003-0.0030.0000.0000.0000.000
202A202PHE0-0.076-0.05034.5950.0040.0040.0000.0000.0000.000
203A203TYR0-0.052-0.04339.6130.0020.0020.0000.0000.0000.000
204A204ASP-1-0.897-0.93641.633-0.091-0.0910.0000.0000.0000.000
205A205ASP-1-0.930-0.97139.296-0.120-0.1200.0000.0000.0000.000
206A206TYR0-0.085-0.05334.7570.0010.0010.0000.0000.0000.000
207A207ASP-1-0.881-0.94337.562-0.098-0.0980.0000.0000.0000.000
208A208ASP-1-0.850-0.90236.906-0.138-0.1380.0000.0000.0000.000
209A209ILE00.033-0.02139.0650.0040.0040.0000.0000.0000.000
210A210GLU-1-0.881-0.93238.915-0.109-0.1090.0000.0000.0000.000
211A211PHE00.000-0.02337.2000.0050.0050.0000.0000.0000.000
212A212ARG10.8430.92941.7800.0970.0970.0000.0000.0000.000
213A213VAL00.0400.02144.5440.0060.0060.0000.0000.0000.000
214A214ASN00.0770.04841.2820.0060.0060.0000.0000.0000.000
215A215LYS10.8410.92845.4390.0890.0890.0000.0000.0000.000
216A216LEU0-0.035-0.01147.1400.0040.0040.0000.0000.0000.000
217A217GLU-1-0.872-0.93748.072-0.084-0.0840.0000.0000.0000.000
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