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: 497YN

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 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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2739227.660434
FMO2-HF: Nuclear repulsion 2651370.229105
FMO2-HF: Total energy -87857.431329
FMO2-MP2: Total energy -88117.212222


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.
-5.09-1.2780.383-1.595-2.6030.003
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 : 0.026 / q_NPA : 0.012
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-1-0.666-0.7953.802-3.223-0.876-0.007-1.165-1.1760.006
4A4LYS10.9510.9796.0781.1531.1530.0000.0000.0000.000
5A5GLU-1-0.830-0.9182.7680.2290.7940.206-0.173-0.599-0.001
6A6GLU-1-0.895-0.9512.684-2.612-1.9600.185-0.216-0.622-0.002
7A7ILE0-0.034-0.0144.6200.3610.427-0.001-0.007-0.0580.000
8A8LEU00.0070.0027.4190.1660.1660.0000.0000.0000.000
9A9ARG10.7780.8763.944-1.616-1.4340.000-0.034-0.1480.000
10A10LYS10.8260.9087.1120.9640.9640.0000.0000.0000.000
11A11ILE0-0.0480.01310.7020.0190.0190.0000.0000.0000.000
12A12LYS10.9290.96313.321-0.027-0.0270.0000.0000.0000.000
13A13THR0-0.066-0.04916.1950.0330.0330.0000.0000.0000.000
14A14GLN0-0.032-0.02616.747-0.001-0.0010.0000.0000.0000.000
15A15GLU-1-0.813-0.92017.437-0.022-0.0220.0000.0000.0000.000
16A16LEU00.0250.01116.006-0.016-0.0160.0000.0000.0000.000
17A17ALA00.0190.01713.264-0.038-0.0380.0000.0000.0000.000
18A18GLU-1-0.900-0.94714.273-0.008-0.0080.0000.0000.0000.000
19A19ALA0-0.0110.00516.717-0.013-0.0130.0000.0000.0000.000
20A20PHE0-0.019-0.0269.669-0.036-0.0360.0000.0000.0000.000
21A21ASN0-0.080-0.04112.129-0.016-0.0160.0000.0000.0000.000
22A22LYS10.8420.92214.0120.0710.0710.0000.0000.0000.000
23A23VAL0-0.0100.01617.3850.0000.0000.0000.0000.0000.000
24A24ASP-1-0.782-0.87816.979-0.372-0.3720.0000.0000.0000.000
25A25ARG10.8530.91315.6930.5440.5440.0000.0000.0000.000
26A26SER0-0.101-0.08917.8580.0040.0040.0000.0000.0000.000
27A27LEU0-0.0100.01019.4680.0160.0160.0000.0000.0000.000
28A28PHE00.013-0.00721.2020.0140.0140.0000.0000.0000.000
29A29LEU0-0.0220.02018.6530.0080.0080.0000.0000.0000.000
30A30PRO00.0370.01822.9830.0110.0110.0000.0000.0000.000
31A31GLU-1-0.821-0.90223.977-0.262-0.2620.0000.0000.0000.000
32A32ASN0-0.033-0.02823.970-0.011-0.0110.0000.0000.0000.000
33A33LEU0-0.013-0.01721.597-0.017-0.0170.0000.0000.0000.000
34A34LYS10.8830.94619.9120.2110.2110.0000.0000.0000.000
35A35ASP-1-0.913-0.94217.163-0.506-0.5060.0000.0000.0000.000
36A36TYR0-0.026-0.02515.498-0.087-0.0870.0000.0000.0000.000
37A37ALA0-0.056-0.00815.401-0.048-0.0480.0000.0000.0000.000
38A38TYR00.010-0.01810.4280.0270.0270.0000.0000.0000.000
39A39ALA0-0.0150.00710.320-0.307-0.3070.0000.0000.0000.000
40A40HIS00.0240.00511.2590.1090.1090.0000.0000.0000.000
41A41THR0-0.079-0.0769.5900.2260.2260.0000.0000.0000.000
42A42HIS0-0.057-0.0379.4490.2230.2230.0000.0000.0000.000
43A43GLU-1-0.894-0.94114.178-0.499-0.4990.0000.0000.0000.000
44A44ALA0-0.048-0.02117.3800.0060.0060.0000.0000.0000.000
45A45LEU00.0260.00618.2040.0010.0010.0000.0000.0000.000
46A46PRO0-0.018-0.00321.9270.0290.0290.0000.0000.0000.000
47A47ILE0-0.018-0.00224.045-0.002-0.0020.0000.0000.0000.000
48A48LEU0-0.011-0.00827.7070.0160.0160.0000.0000.0000.000
49A49PRO0-0.007-0.00530.755-0.007-0.0070.0000.0000.0000.000
50A50GLY0-0.0040.00031.7930.0080.0080.0000.0000.0000.000
51A51ILE0-0.029-0.01128.4280.0040.0040.0000.0000.0000.000
52A52ASN00.0440.01424.1580.0040.0040.0000.0000.0000.000
53A53THR00.0000.00621.2320.0210.0210.0000.0000.0000.000
54A54THR00.001-0.01019.457-0.022-0.0220.0000.0000.0000.000
55A55ALA00.0290.04516.138-0.013-0.0130.0000.0000.0000.000
56A56LEU00.0610.01912.3620.0270.0270.0000.0000.0000.000
57A57ASN00.0080.00811.7800.0890.0890.0000.0000.0000.000
58A58LEU00.006-0.00313.1240.0670.0670.0000.0000.0000.000
59A59GLY00.0230.01216.6990.0520.0520.0000.0000.0000.000
60A60ILE00.029-0.00513.0340.0450.0450.0000.0000.0000.000
61A61PHE00.0010.00615.0460.0490.0490.0000.0000.0000.000
62A62MET00.0060.00716.4110.0350.0350.0000.0000.0000.000
63A63LEU0-0.034-0.01118.8710.0260.0260.0000.0000.0000.000
64A64ASP-1-0.767-0.88016.323-0.073-0.0730.0000.0000.0000.000
65A65GLU-1-0.839-0.90118.881-0.058-0.0580.0000.0000.0000.000
66A66LEU0-0.029-0.01721.1470.0160.0160.0000.0000.0000.000
67A67ASP-1-0.832-0.87222.490-0.017-0.0170.0000.0000.0000.000
68A68LEU00.0020.01221.6570.0070.0070.0000.0000.0000.000
69A69HIS10.7740.85123.7340.0340.0340.0000.0000.0000.000
70A70LYS11.0051.00223.5080.0060.0060.0000.0000.0000.000
71A71GLY0-0.014-0.02328.1520.0040.0040.0000.0000.0000.000
72A72GLN0-0.0180.00327.843-0.006-0.0060.0000.0000.0000.000
73A73LYS10.8850.95631.3980.0480.0480.0000.0000.0000.000
74A74VAL0-0.015-0.01727.5280.0010.0010.0000.0000.0000.000
75A75LEU0-0.0120.00530.908-0.001-0.0010.0000.0000.0000.000
76A76GLU-1-0.760-0.83525.894-0.163-0.1630.0000.0000.0000.000
77A77ILE0-0.031-0.02129.9800.0040.0040.0000.0000.0000.000
78A78GLY00.007-0.00829.702-0.007-0.0070.0000.0000.0000.000
79A79THR0-0.038-0.03028.096-0.011-0.0110.0000.0000.0000.000
80A80GLY00.0260.01727.060-0.015-0.0150.0000.0000.0000.000
81A81ILE0-0.017-0.03521.6930.0080.0080.0000.0000.0000.000
82A82GLY00.0440.01925.9500.0030.0030.0000.0000.0000.000
83A83TYR00.0220.01115.945-0.011-0.0110.0000.0000.0000.000
84A84TYR0-0.010-0.03017.660-0.011-0.0110.0000.0000.0000.000
85A85THR00.029-0.00521.9580.0120.0120.0000.0000.0000.000
86A86ALA0-0.008-0.00122.5570.0160.0160.0000.0000.0000.000
87A87LEU0-0.041-0.02017.3740.0130.0130.0000.0000.0000.000
88A88ILE00.0140.00521.2650.0180.0180.0000.0000.0000.000
89A89ALA0-0.0090.00524.0940.0160.0160.0000.0000.0000.000
90A90GLU-1-0.888-0.94121.629-0.087-0.0870.0000.0000.0000.000
91A91ILE0-0.095-0.03820.1530.0140.0140.0000.0000.0000.000
92A92VAL0-0.035-0.02624.2310.0140.0140.0000.0000.0000.000
93A93ASP-1-0.958-0.95127.689-0.044-0.0440.0000.0000.0000.000
94A94LYS10.8440.92731.2970.0530.0530.0000.0000.0000.000
95A95VAL00.005-0.00227.997-0.001-0.0010.0000.0000.0000.000
96A96VAL0-0.044-0.00131.3480.0000.0000.0000.0000.0000.000
97A97SER00.001-0.01529.311-0.004-0.0040.0000.0000.0000.000
98A98VAL0-0.048-0.00832.2700.0040.0040.0000.0000.0000.000
99A99GLU-1-0.784-0.90031.304-0.155-0.1550.0000.0000.0000.000
100A100ILE00.0070.00734.1580.0060.0060.0000.0000.0000.000
101A101ASN0-0.032-0.01534.2690.0060.0060.0000.0000.0000.000
102A102GLU-1-0.839-0.93335.719-0.097-0.0970.0000.0000.0000.000
103A103LYS10.9180.95235.8580.1140.1140.0000.0000.0000.000
104A104MET00.0060.01928.801-0.007-0.0070.0000.0000.0000.000
105A105TYR00.0180.00332.266-0.004-0.0040.0000.0000.0000.000
106A106ASN0-0.025-0.01033.9100.0020.0020.0000.0000.0000.000
107A107TYR0-0.096-0.05826.0420.0060.0060.0000.0000.0000.000
108A108ALA00.0500.01429.420-0.003-0.0030.0000.0000.0000.000
109A109SER0-0.007-0.01530.3500.0050.0050.0000.0000.0000.000
110A110LYS10.8810.93632.1280.1300.1300.0000.0000.0000.000
111A111LEU0-0.021-0.00226.3620.0060.0060.0000.0000.0000.000
112A112LEU0-0.005-0.00426.5990.0000.0000.0000.0000.0000.000
113A113SER0-0.044-0.01229.8010.0090.0090.0000.0000.0000.000
114A114TYR0-0.065-0.01426.4340.0080.0080.0000.0000.0000.000
115A115TYR00.0090.00323.4290.0000.0000.0000.0000.0000.000
116A116ASN0-0.004-0.00830.0010.0010.0010.0000.0000.0000.000
117A117ASN0-0.045-0.02528.619-0.001-0.0010.0000.0000.0000.000
118A118ILE00.0250.00627.839-0.002-0.0020.0000.0000.0000.000
119A119LYS10.8000.90232.1650.0640.0640.0000.0000.0000.000
120A120LEU00.0510.02131.068-0.003-0.0030.0000.0000.0000.000
121A121ILE0-0.030-0.00535.0260.0050.0050.0000.0000.0000.000
122A122LEU00.0290.02936.495-0.006-0.0060.0000.0000.0000.000
123A123GLY00.002-0.02437.8410.0060.0060.0000.0000.0000.000
124A124ASP-1-0.763-0.89637.859-0.093-0.0930.0000.0000.0000.000
125A125GLY00.0550.02435.4360.0040.0040.0000.0000.0000.000
126A126THR00.0070.01236.3690.0020.0020.0000.0000.0000.000
127A127LEU0-0.046-0.02838.0030.0050.0050.0000.0000.0000.000
128A128GLY0-0.026-0.00436.8720.0040.0040.0000.0000.0000.000
129A129TYR0-0.043-0.03937.940-0.001-0.0010.0000.0000.0000.000
130A130GLU-1-0.722-0.85639.621-0.048-0.0480.0000.0000.0000.000
131A131GLU-1-0.823-0.91041.990-0.056-0.0560.0000.0000.0000.000
132A132GLU-1-0.851-0.91138.592-0.052-0.0520.0000.0000.0000.000
133A133LYS10.8000.89139.4680.0490.0490.0000.0000.0000.000
134A134PRO0-0.031-0.01439.129-0.001-0.0010.0000.0000.0000.000
135A135TYR00.0680.03333.946-0.002-0.0020.0000.0000.0000.000
136A136ASP-1-0.847-0.91231.680-0.037-0.0370.0000.0000.0000.000
137A137ARG10.7880.86026.9270.0550.0550.0000.0000.0000.000
138A138VAL00.0240.01829.936-0.001-0.0010.0000.0000.0000.000
139A139VAL00.0230.02124.443-0.001-0.0010.0000.0000.0000.000
140A140VAL0-0.027-0.01427.5880.0030.0030.0000.0000.0000.000
141A141TRP0-0.033-0.02620.989-0.019-0.0190.0000.0000.0000.000
142A142ALA00.020-0.00226.796-0.010-0.0100.0000.0000.0000.000
143A143THR0-0.029-0.00329.1780.0090.0090.0000.0000.0000.000
144A144ALA00.0420.01030.6790.0040.0040.0000.0000.0000.000
145A145PRO00.0170.00834.180-0.001-0.0010.0000.0000.0000.000
146A146THR0-0.032-0.03237.0960.0050.0050.0000.0000.0000.000
147A147LEU00.0030.01535.074-0.005-0.0050.0000.0000.0000.000
148A148LEU00.0420.02033.5630.0040.0040.0000.0000.0000.000
149A149CYS00.001-0.01436.9790.0030.0030.0000.0000.0000.000
150A150LYS10.8440.93240.1430.0560.0560.0000.0000.0000.000
151A151PRO00.0750.02234.9740.0030.0030.0000.0000.0000.000
152A152TYR00.006-0.00735.7780.0020.0020.0000.0000.0000.000
153A153GLU-1-0.770-0.88837.359-0.047-0.0470.0000.0000.0000.000
154A154GLN0-0.099-0.05838.2950.0010.0010.0000.0000.0000.000
155A155LEU00.0220.04532.8590.0000.0000.0000.0000.0000.000
156A156LYS10.8560.90835.3640.0390.0390.0000.0000.0000.000
157A157GLU-1-0.851-0.95837.197-0.035-0.0350.0000.0000.0000.000
158A158GLY00.0190.02735.6970.0010.0010.0000.0000.0000.000
159A159GLY0-0.064-0.02733.0470.0000.0000.0000.0000.0000.000
160A160ILE00.0290.00927.3770.0010.0010.0000.0000.0000.000
161A161MET0-0.019-0.00629.895-0.004-0.0040.0000.0000.0000.000
162A162ILE0-0.0180.01023.6170.0030.0030.0000.0000.0000.000
163A163LEU00.004-0.00827.329-0.005-0.0050.0000.0000.0000.000
164A164PRO00.0350.03626.3480.0040.0040.0000.0000.0000.000
165A165ILE0-0.0100.00728.4600.0060.0060.0000.0000.0000.000
166A166GLY00.009-0.00731.560-0.001-0.0010.0000.0000.0000.000
167A167VAL00.0390.02533.252-0.005-0.0050.0000.0000.0000.000
168A168GLY00.006-0.00533.6810.0010.0010.0000.0000.0000.000
169A169ARG10.9170.94426.9710.1840.1840.0000.0000.0000.000
170A170VAL00.0030.00325.865-0.015-0.0150.0000.0000.0000.000
171A171GLN0-0.0240.01127.5290.0040.0040.0000.0000.0000.000
172A172LYS10.8850.94526.8690.1040.1040.0000.0000.0000.000
173A173LEU00.0150.00622.5350.0030.0030.0000.0000.0000.000
174A174TYR0-0.012-0.01925.7200.0110.0110.0000.0000.0000.000
175A175LYS10.8060.89224.0160.0640.0640.0000.0000.0000.000
176A176VAL0-0.031-0.02227.6760.0090.0090.0000.0000.0000.000
177A177ILE0-0.008-0.00629.7120.0000.0000.0000.0000.0000.000
178A178LYS10.7420.88033.0050.0470.0470.0000.0000.0000.000
179A179LYS10.9620.97234.7110.0340.0340.0000.0000.0000.000
180A180GLY00.0420.03439.3050.0010.0010.0000.0000.0000.000
181A181ASN0-0.042-0.01341.428-0.005-0.0050.0000.0000.0000.000
182A182SER0-0.051-0.03040.8340.0000.0000.0000.0000.0000.000
183A183PRO00.0220.02935.7090.0020.0020.0000.0000.0000.000
184A184SER0-0.0170.00532.9970.0030.0030.0000.0000.0000.000
185A185LEU0-0.010-0.01731.697-0.004-0.0040.0000.0000.0000.000
186A186GLU-1-0.860-0.90625.763-0.055-0.0550.0000.0000.0000.000
187A187ASN0-0.003-0.01626.761-0.017-0.0170.0000.0000.0000.000
188A188LEU0-0.002-0.00421.9400.0030.0030.0000.0000.0000.000
189A189GLY00.0100.01221.671-0.015-0.0150.0000.0000.0000.000
190A190GLU-1-0.924-0.95423.067-0.136-0.1360.0000.0000.0000.000
191A191VAL0-0.0040.00521.401-0.026-0.0260.0000.0000.0000.000
192A192MET0-0.025-0.02523.3090.0150.0150.0000.0000.0000.000
193A193PHE0-0.0090.00622.384-0.017-0.0170.0000.0000.0000.000
194A194GLY00.0300.01426.7350.0090.0090.0000.0000.0000.000
195A195ARG10.8400.91629.7800.1150.1150.0000.0000.0000.000
196A196ILE00.0090.02432.824-0.002-0.0020.0000.0000.0000.000
197A197GLY00.0230.00134.1380.0050.0050.0000.0000.0000.000
198A198GLY00.038-0.00437.4640.0000.0000.0000.0000.0000.000
199A199LEU0-0.024-0.00740.3300.0010.0010.0000.0000.0000.000
200A200TYR0-0.069-0.02840.3360.0030.0030.0000.0000.0000.000
201A201GLY00.0180.01838.203-0.003-0.0030.0000.0000.0000.000
202A202PHE0-0.058-0.04234.5450.0040.0040.0000.0000.0000.000
203A203TYR0-0.051-0.03939.6770.0020.0020.0000.0000.0000.000
204A204ASP-1-0.911-0.92840.684-0.086-0.0860.0000.0000.0000.000
205A205ASP-1-0.886-0.95439.351-0.108-0.1080.0000.0000.0000.000
206A206TYR0-0.081-0.05234.5670.0000.0000.0000.0000.0000.000
207A207ASP-1-0.838-0.90537.617-0.086-0.0860.0000.0000.0000.000
208A208ASP-1-0.850-0.91436.685-0.123-0.1230.0000.0000.0000.000
209A209ILE00.020-0.02339.1130.0030.0030.0000.0000.0000.000
210A210GLU-1-0.834-0.90839.015-0.097-0.0970.0000.0000.0000.000
211A211PHE00.0090.00637.1350.0050.0050.0000.0000.0000.000
212A212ARG10.8220.89741.7600.0860.0860.0000.0000.0000.000
213A213VAL00.0210.01444.5290.0050.0050.0000.0000.0000.000
214A214ASN0-0.001-0.01642.1040.0030.0030.0000.0000.0000.000
215A215LYS10.8370.92545.4160.0800.0800.0000.0000.0000.000
216A216LEU00.0000.00747.1180.0030.0030.0000.0000.0000.000
217A217GLU-1-0.880-0.93348.632-0.072-0.0720.0000.0000.0000.000
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