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: 52M5Z

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 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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2742656.383517
FMO2-HF: Nuclear repulsion 2654798.061695
FMO2-HF: Total energy -87858.321822
FMO2-MP2: Total energy -88118.013505


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.
-4.273-0.340.432-1.786-2.5770.002
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 : 0.036 / q_NPA : 0.018
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-1-0.690-0.8243.292-3.221-0.6620.073-1.350-1.2820.003
4A4LYS10.9440.9875.7411.0701.0700.0000.0000.0000.000
5A5GLU-1-0.815-0.8942.7010.4220.9450.208-0.155-0.5750.000
6A6GLU-1-0.880-0.9312.911-1.786-1.0100.148-0.261-0.663-0.001
7A7ILE00.0010.0104.2490.2460.3210.003-0.020-0.0570.000
8A8LEU00.0140.0077.1610.1570.1570.0000.0000.0000.000
9A9ARG10.7600.8564.989-1.315-1.3150.0000.0000.0000.000
10A10LYS10.7800.8667.0440.5480.5480.0000.0000.0000.000
11A11ILE0-0.0350.01210.725-0.015-0.0150.0000.0000.0000.000
12A12LYS10.8970.94413.130-0.078-0.0780.0000.0000.0000.000
13A13THR0-0.063-0.04516.3690.0220.0220.0000.0000.0000.000
14A14GLN0-0.037-0.03217.0780.0050.0050.0000.0000.0000.000
15A15GLU-1-0.788-0.89517.5610.0090.0090.0000.0000.0000.000
16A16LEU00.0370.01715.430-0.017-0.0170.0000.0000.0000.000
17A17ALA00.0120.01613.324-0.034-0.0340.0000.0000.0000.000
18A18GLU-1-0.820-0.90014.4650.0130.0130.0000.0000.0000.000
19A19ALA0-0.0080.02117.082-0.012-0.0120.0000.0000.0000.000
20A20PHE00.013-0.0069.154-0.036-0.0360.0000.0000.0000.000
21A21ASN0-0.090-0.04512.312-0.013-0.0130.0000.0000.0000.000
22A22LYS10.7670.86413.5340.0530.0530.0000.0000.0000.000
23A23VAL00.0220.02716.901-0.004-0.0040.0000.0000.0000.000
24A24ASP-1-0.753-0.86416.414-0.377-0.3770.0000.0000.0000.000
25A25ARG10.8550.92315.2210.4940.4940.0000.0000.0000.000
26A26SER0-0.078-0.07117.6130.0100.0100.0000.0000.0000.000
27A27LEU0-0.004-0.00919.1010.0160.0160.0000.0000.0000.000
28A28PHE00.0140.00220.9090.0180.0180.0000.0000.0000.000
29A29LEU0-0.0210.01618.3640.0060.0060.0000.0000.0000.000
30A30PRO00.0320.01022.6310.0090.0090.0000.0000.0000.000
31A31GLU-1-0.801-0.89523.543-0.259-0.2590.0000.0000.0000.000
32A32ASN0-0.042-0.02323.455-0.008-0.0080.0000.0000.0000.000
33A33LEU0-0.020-0.01620.867-0.014-0.0140.0000.0000.0000.000
34A34LYS10.8400.92119.2450.2130.2130.0000.0000.0000.000
35A35ASP-1-0.890-0.93616.487-0.517-0.5170.0000.0000.0000.000
36A36TYR0-0.069-0.05214.930-0.095-0.0950.0000.0000.0000.000
37A37ALA0-0.027-0.00415.429-0.007-0.0070.0000.0000.0000.000
38A38TYR0-0.031-0.03810.1380.0490.0490.0000.0000.0000.000
39A39ALA00.0000.0139.719-0.286-0.2860.0000.0000.0000.000
40A40HIS00.0420.01411.0380.1200.1200.0000.0000.0000.000
41A41THR0-0.057-0.0609.4570.2200.2200.0000.0000.0000.000
42A42HIS0-0.039-0.0319.1830.2020.2020.0000.0000.0000.000
43A43GLU-1-0.861-0.91513.843-0.423-0.4230.0000.0000.0000.000
44A44ALA0-0.029-0.01417.0680.0000.0000.0000.0000.0000.000
45A45LEU00.0320.02117.5190.0290.0290.0000.0000.0000.000
46A46PRO00.0010.00121.3660.0260.0260.0000.0000.0000.000
47A47ILE0-0.027-0.01123.315-0.009-0.0090.0000.0000.0000.000
48A48LEU0-0.028-0.01527.0860.0140.0140.0000.0000.0000.000
49A49PRO0-0.019-0.02330.330-0.006-0.0060.0000.0000.0000.000
50A50GLY00.0090.01731.5790.0080.0080.0000.0000.0000.000
51A51ILE0-0.022-0.00828.1230.0050.0050.0000.0000.0000.000
52A52ASN00.016-0.00323.7140.0120.0120.0000.0000.0000.000
53A53THR0-0.0100.00020.5430.0200.0200.0000.0000.0000.000
54A54THR0-0.015-0.01219.111-0.016-0.0160.0000.0000.0000.000
55A55ALA00.0220.03815.781-0.013-0.0130.0000.0000.0000.000
56A56LEU00.0360.01911.7050.0320.0320.0000.0000.0000.000
57A57ASN00.0240.01011.3750.0770.0770.0000.0000.0000.000
58A58LEU0-0.004-0.00412.8660.0660.0660.0000.0000.0000.000
59A59GLY00.0250.00816.4930.0440.0440.0000.0000.0000.000
60A60ILE00.0280.00212.6340.0390.0390.0000.0000.0000.000
61A61PHE0-0.0070.00115.2490.0420.0420.0000.0000.0000.000
62A62MET0-0.013-0.00916.6600.0260.0260.0000.0000.0000.000
63A63LEU0-0.0040.00618.6680.0190.0190.0000.0000.0000.000
64A64ASP-1-0.772-0.87016.067-0.005-0.0050.0000.0000.0000.000
65A65GLU-1-0.826-0.90518.759-0.014-0.0140.0000.0000.0000.000
66A66LEU0-0.033-0.01121.2540.0100.0100.0000.0000.0000.000
67A67ASP-1-0.814-0.87522.4950.0090.0090.0000.0000.0000.000
68A68LEU00.0100.01821.4570.0050.0050.0000.0000.0000.000
69A69HIS10.7710.83423.0470.0010.0010.0000.0000.0000.000
70A70LYS10.9050.94422.631-0.016-0.0160.0000.0000.0000.000
71A71GLY0-0.017-0.00627.7030.0050.0050.0000.0000.0000.000
72A72GLN0-0.048-0.00627.255-0.006-0.0060.0000.0000.0000.000
73A73LYS10.8480.91030.9920.0340.0340.0000.0000.0000.000
74A74VAL0-0.020-0.01727.2950.0020.0020.0000.0000.0000.000
75A75LEU0-0.0070.01630.729-0.001-0.0010.0000.0000.0000.000
76A76GLU-1-0.755-0.82025.306-0.136-0.1360.0000.0000.0000.000
77A77ILE0-0.032-0.01329.4400.0030.0030.0000.0000.0000.000
78A78GLY00.0210.00529.345-0.005-0.0050.0000.0000.0000.000
79A79THR0-0.022-0.02527.662-0.010-0.0100.0000.0000.0000.000
80A80GLY00.0350.01826.408-0.013-0.0130.0000.0000.0000.000
81A81ILE0-0.027-0.03820.8110.0080.0080.0000.0000.0000.000
82A82GLY00.0390.01725.2140.0000.0000.0000.0000.0000.000
83A83TYR0-0.017-0.01115.742-0.009-0.0090.0000.0000.0000.000
84A84TYR0-0.029-0.03417.261-0.008-0.0080.0000.0000.0000.000
85A85THR00.044-0.01021.6690.0110.0110.0000.0000.0000.000
86A86ALA00.0040.00622.3300.0140.0140.0000.0000.0000.000
87A87LEU0-0.035-0.01916.7050.0130.0130.0000.0000.0000.000
88A88ILE00.004-0.00120.7750.0170.0170.0000.0000.0000.000
89A89ALA00.005-0.00123.7060.0140.0140.0000.0000.0000.000
90A90GLU-1-0.820-0.90021.052-0.076-0.0760.0000.0000.0000.000
91A91ILE0-0.089-0.03319.8880.0140.0140.0000.0000.0000.000
92A92VAL0-0.034-0.00924.0560.0110.0110.0000.0000.0000.000
93A93ASP-1-0.961-0.96927.615-0.030-0.0300.0000.0000.0000.000
94A94LYS10.8600.92031.2500.0390.0390.0000.0000.0000.000
95A95VAL00.0070.00827.4180.0010.0010.0000.0000.0000.000
96A96VAL0-0.022-0.00730.698-0.002-0.0020.0000.0000.0000.000
97A97SER0-0.024-0.03228.616-0.004-0.0040.0000.0000.0000.000
98A98VAL0-0.0260.00631.5250.0040.0040.0000.0000.0000.000
99A99GLU-1-0.806-0.90830.789-0.136-0.1360.0000.0000.0000.000
100A100ILE00.0310.02233.7180.0060.0060.0000.0000.0000.000
101A101ASN0-0.028-0.01633.6060.0050.0050.0000.0000.0000.000
102A102GLU-1-0.855-0.93734.869-0.089-0.0890.0000.0000.0000.000
103A103LYS10.9330.96535.2190.1060.1060.0000.0000.0000.000
104A104MET00.0110.02828.603-0.007-0.0070.0000.0000.0000.000
105A105TYR00.0250.00331.420-0.004-0.0040.0000.0000.0000.000
106A106ASN0-0.051-0.02433.4050.0040.0040.0000.0000.0000.000
107A107TYR0-0.097-0.06225.1220.0050.0050.0000.0000.0000.000
108A108ALA00.0500.01928.650-0.002-0.0020.0000.0000.0000.000
109A109SER00.008-0.01329.6780.0040.0040.0000.0000.0000.000
110A110LYS10.8860.95331.4840.1240.1240.0000.0000.0000.000
111A111LEU0-0.0300.01125.4680.0040.0040.0000.0000.0000.000
112A112LEU00.002-0.00825.8560.0030.0030.0000.0000.0000.000
113A113SER0-0.032-0.02228.9780.0100.0100.0000.0000.0000.000
114A114TYR0-0.069-0.01725.7850.0070.0070.0000.0000.0000.000
115A115TYR0-0.061-0.03823.118-0.001-0.0010.0000.0000.0000.000
116A116ASN0-0.016-0.01629.786-0.001-0.0010.0000.0000.0000.000
117A117ASN0-0.036-0.01128.364-0.002-0.0020.0000.0000.0000.000
118A118ILE00.0250.01327.4230.0000.0000.0000.0000.0000.000
119A119LYS10.8040.89631.7340.0530.0530.0000.0000.0000.000
120A120LEU00.0500.02830.442-0.002-0.0020.0000.0000.0000.000
121A121ILE0-0.032-0.01234.3960.0040.0040.0000.0000.0000.000
122A122LEU00.0200.02136.004-0.005-0.0050.0000.0000.0000.000
123A123GLY00.005-0.02137.5360.0060.0060.0000.0000.0000.000
124A124ASP-1-0.793-0.90537.526-0.078-0.0780.0000.0000.0000.000
125A125GLY00.0510.01535.1640.0040.0040.0000.0000.0000.000
126A126THR00.0240.01935.8920.0020.0020.0000.0000.0000.000
127A127LEU0-0.062-0.03437.4690.0050.0050.0000.0000.0000.000
128A128GLY0-0.006-0.00236.1410.0040.0040.0000.0000.0000.000
129A129TYR0-0.068-0.06437.192-0.002-0.0020.0000.0000.0000.000
130A130GLU-1-0.726-0.83238.875-0.037-0.0370.0000.0000.0000.000
131A131GLU-1-0.857-0.91742.003-0.044-0.0440.0000.0000.0000.000
132A132GLU-1-0.772-0.86738.317-0.040-0.0400.0000.0000.0000.000
133A133LYS10.7620.88139.4160.0380.0380.0000.0000.0000.000
134A134PRO00.0000.00538.640-0.002-0.0020.0000.0000.0000.000
135A135TYR00.0390.01433.2330.0000.0000.0000.0000.0000.000
136A136ASP-1-0.830-0.90331.247-0.018-0.0180.0000.0000.0000.000
137A137ARG10.7750.85926.7050.0270.0270.0000.0000.0000.000
138A138VAL00.005-0.00429.685-0.001-0.0010.0000.0000.0000.000
139A139VAL00.0270.01924.2200.0010.0010.0000.0000.0000.000
140A140VAL0-0.019-0.01227.2390.0020.0020.0000.0000.0000.000
141A141TRP0-0.043-0.03320.747-0.015-0.0150.0000.0000.0000.000
142A142ALA00.0180.00126.496-0.010-0.0100.0000.0000.0000.000
143A143THR0-0.036-0.00929.0050.0090.0090.0000.0000.0000.000
144A144ALA00.0660.02730.4040.0020.0020.0000.0000.0000.000
145A145PRO00.0180.00733.847-0.001-0.0010.0000.0000.0000.000
146A146THR0-0.060-0.04836.5910.0050.0050.0000.0000.0000.000
147A147LEU00.0110.00834.705-0.004-0.0040.0000.0000.0000.000
148A148LEU00.0440.02933.6310.0030.0030.0000.0000.0000.000
149A149CYS00.0190.00836.9470.0030.0030.0000.0000.0000.000
150A150LYS10.8260.92040.1400.0420.0420.0000.0000.0000.000
151A151PRO00.0830.02234.5800.0030.0030.0000.0000.0000.000
152A152TYR00.004-0.01035.8330.0020.0020.0000.0000.0000.000
153A153GLU-1-0.797-0.90037.409-0.034-0.0340.0000.0000.0000.000
154A154GLN0-0.038-0.03637.6770.0010.0010.0000.0000.0000.000
155A155LEU0-0.0270.03632.3430.0020.0020.0000.0000.0000.000
156A156LYS10.8590.90934.9390.0230.0230.0000.0000.0000.000
157A157GLU-1-0.849-0.95336.835-0.019-0.0190.0000.0000.0000.000
158A158GLY00.0070.02435.8500.0020.0020.0000.0000.0000.000
159A159GLY0-0.034-0.00232.7230.0020.0020.0000.0000.0000.000
160A160ILE0-0.011-0.01027.3410.0000.0000.0000.0000.0000.000
161A161MET0-0.005-0.00229.446-0.004-0.0040.0000.0000.0000.000
162A162ILE0-0.0160.00823.3270.0030.0030.0000.0000.0000.000
163A163LEU00.017-0.00127.017-0.006-0.0060.0000.0000.0000.000
164A164PRO00.0200.01826.0100.0050.0050.0000.0000.0000.000
165A165ILE0-0.026-0.00328.2200.0060.0060.0000.0000.0000.000
166A166GLY00.0290.00131.067-0.001-0.0010.0000.0000.0000.000
167A167VAL00.0280.01632.747-0.006-0.0060.0000.0000.0000.000
168A168GLY00.009-0.00433.0260.0030.0030.0000.0000.0000.000
169A169ARG10.8810.93526.4680.1590.1590.0000.0000.0000.000
170A170VAL0-0.002-0.00325.744-0.015-0.0150.0000.0000.0000.000
171A171GLN0-0.069-0.02926.9940.0060.0060.0000.0000.0000.000
172A172LYS10.8670.92826.5380.0740.0740.0000.0000.0000.000
173A173LEU00.0100.00522.5850.0010.0010.0000.0000.0000.000
174A174TYR0-0.004-0.01925.7860.0100.0100.0000.0000.0000.000
175A175LYS10.8220.89623.9410.0230.0230.0000.0000.0000.000
176A176VAL0-0.022-0.01127.4320.0090.0090.0000.0000.0000.000
177A177ILE0-0.001-0.00629.4200.0010.0010.0000.0000.0000.000
178A178LYS10.7560.87232.7550.0310.0310.0000.0000.0000.000
179A179LYS10.9360.95434.5750.0140.0140.0000.0000.0000.000
180A180GLY00.0710.04839.2240.0000.0000.0000.0000.0000.000
181A181ASN0-0.053-0.01741.275-0.004-0.0040.0000.0000.0000.000
182A182SER0-0.059-0.03840.9440.0000.0000.0000.0000.0000.000
183A183PRO00.0140.03335.6060.0030.0030.0000.0000.0000.000
184A184SER0-0.0070.00433.0230.0020.0020.0000.0000.0000.000
185A185LEU0-0.006-0.01331.895-0.003-0.0030.0000.0000.0000.000
186A186GLU-1-0.847-0.90725.696-0.021-0.0210.0000.0000.0000.000
187A187ASN0-0.026-0.02226.035-0.012-0.0120.0000.0000.0000.000
188A188LEU00.0020.00421.8830.0050.0050.0000.0000.0000.000
189A189GLY0-0.0040.00021.759-0.005-0.0050.0000.0000.0000.000
190A190GLU-1-0.895-0.91922.408-0.099-0.0990.0000.0000.0000.000
191A191VAL0-0.0130.00121.206-0.022-0.0220.0000.0000.0000.000
192A192MET00.0140.01523.0500.0120.0120.0000.0000.0000.000
193A193PHE00.0250.02422.134-0.016-0.0160.0000.0000.0000.000
194A194GLY00.0430.02226.3910.0080.0080.0000.0000.0000.000
195A195ARG10.8100.89129.6140.0960.0960.0000.0000.0000.000
196A196ILE00.0020.01932.851-0.002-0.0020.0000.0000.0000.000
197A197GLY00.0370.01234.0650.0040.0040.0000.0000.0000.000
198A198GLY00.0450.00037.4890.0000.0000.0000.0000.0000.000
199A199LEU0-0.024-0.01540.3160.0010.0010.0000.0000.0000.000
200A200TYR0-0.049-0.01739.9820.0040.0040.0000.0000.0000.000
201A201GLY00.0120.01537.738-0.002-0.0020.0000.0000.0000.000
202A202PHE0-0.083-0.05434.2210.0030.0030.0000.0000.0000.000
203A203TYR0-0.066-0.04339.3120.0010.0010.0000.0000.0000.000
204A204ASP-1-0.854-0.90640.187-0.074-0.0740.0000.0000.0000.000
205A205ASP-1-0.873-0.93538.873-0.095-0.0950.0000.0000.0000.000
206A206TYR0-0.063-0.04334.1500.0010.0010.0000.0000.0000.000
207A207ASP-1-0.824-0.89137.051-0.075-0.0750.0000.0000.0000.000
208A208ASP-1-0.847-0.92736.234-0.108-0.1080.0000.0000.0000.000
209A209ILE00.010-0.01338.5960.0030.0030.0000.0000.0000.000
210A210GLU-1-0.828-0.90639.166-0.086-0.0860.0000.0000.0000.000
211A211PHE0-0.003-0.00136.7690.0030.0030.0000.0000.0000.000
212A212ARG10.8040.88641.2290.0740.0740.0000.0000.0000.000
213A213VAL00.0340.01844.2730.0040.0040.0000.0000.0000.000
214A214ASN0-0.002-0.01142.3280.0020.0020.0000.0000.0000.000
215A215LYS10.8420.93344.9600.0700.0700.0000.0000.0000.000
216A216LEU0-0.018-0.00546.5820.0030.0030.0000.0000.0000.000
217A217GLU-1-0.853-0.92648.919-0.064-0.0640.0000.0000.0000.000
218A218ARG10.9220.94442.9040.0870.0870.0000.0000.0000.000
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