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: ZY3GN

Calculation Name: 4BG5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BG5

Chain ID: A

ChEMBL ID:

UniProt ID: O50954

Base Structure: X-ray

Registration Date: 2023-06-20

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2391102.599721
FMO2-HF: Nuclear repulsion 2308958.043786
FMO2-HF: Total energy -82144.555935
FMO2-MP2: Total energy -82384.414863


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:21:ILE)


Summations of interaction energy for fragment #1(A:21:ILE)
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.
-17.598-9.7296.721-4.017-10.5710.002
Interaction energy analysis for fragmet #1(A:21:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.001
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].
3A23LYS10.8920.9423.158-9.062-5.9700.269-1.377-1.9830.009
4A24LEU00.0520.0272.471-3.103-1.6771.034-0.602-1.858-0.001
5A25PHE00.0060.0042.751-1.406-0.2560.226-0.318-1.058-0.001
6A26GLU-1-0.866-0.9186.3680.9520.9520.0000.0000.0000.000
7A27ILE00.022-0.0026.703-0.149-0.1490.0000.0000.0000.000
8A28LEU0-0.0030.0138.544-0.091-0.0910.0000.0000.0000.000
9A29ALA0-0.032-0.02310.299-0.017-0.0170.0000.0000.0000.000
10A30ARG10.8000.88110.779-0.708-0.7080.0000.0000.0000.000
11A31GLU-1-0.786-0.90313.1180.3220.3220.0000.0000.0000.000
12A32MET00.0350.01914.109-0.039-0.0390.0000.0000.0000.000
13A33THR0-0.059-0.01715.893-0.032-0.0320.0000.0000.0000.000
14A34ILE00.0090.00217.102-0.017-0.0170.0000.0000.0000.000
15A35ILE00.0490.01517.457-0.011-0.0110.0000.0000.0000.000
16A36LYS10.9620.98320.326-0.001-0.0010.0000.0000.0000.000
17A37LYS10.8270.90322.080-0.119-0.1190.0000.0000.0000.000
18A38GLU-1-0.778-0.85923.0280.1000.1000.0000.0000.0000.000
19A39LYS10.7890.89321.123-0.001-0.0010.0000.0000.0000.000
20A40LEU0-0.028-0.00425.825-0.006-0.0060.0000.0000.0000.000
21A41GLN0-0.0040.02228.713-0.002-0.0020.0000.0000.0000.000
22A42THR00.0030.00830.739-0.004-0.0040.0000.0000.0000.000
23A43GLU-1-0.794-0.84033.9920.0260.0260.0000.0000.0000.000
24A44ILE00.0090.01535.283-0.003-0.0030.0000.0000.0000.000
25A45PRO00.0850.02738.7520.0000.0000.0000.0000.0000.000
26A46SER0-0.005-0.01241.213-0.001-0.0010.0000.0000.0000.000
27A47GLN00.017-0.00537.5840.0010.0010.0000.0000.0000.000
28A48PHE00.016-0.00234.4940.0010.0010.0000.0000.0000.000
29A49GLY00.0380.03038.4520.0030.0030.0000.0000.0000.000
30A50LEU00.0310.01735.426-0.001-0.0010.0000.0000.0000.000
31A51LYS10.8980.96139.483-0.018-0.0180.0000.0000.0000.000
32A52ASN0-0.053-0.05141.242-0.001-0.0010.0000.0000.0000.000
33A53SER00.024-0.00241.019-0.001-0.0010.0000.0000.0000.000
34A54MET00.0150.02234.121-0.002-0.0020.0000.0000.0000.000
35A55PHE0-0.034-0.03933.871-0.002-0.0020.0000.0000.0000.000
36A56GLU-1-0.823-0.88638.7090.0100.0100.0000.0000.0000.000
37A57LEU0-0.0200.00539.544-0.002-0.0020.0000.0000.0000.000
38A58LEU0-0.044-0.02434.651-0.003-0.0030.0000.0000.0000.000
39A59ASN00.011-0.00238.168-0.002-0.0020.0000.0000.0000.000
40A60VAL0-0.0080.01633.314-0.001-0.0010.0000.0000.0000.000
41A61TYR00.005-0.01334.856-0.002-0.0020.0000.0000.0000.000
42A62LYS10.8750.94231.5230.0330.0330.0000.0000.0000.000
43A71LEU00.005-0.01338.2550.0000.0000.0000.0000.0000.000
44A72GLN00.005-0.01338.6440.0030.0030.0000.0000.0000.000
45A73GLU-1-0.891-0.92639.244-0.006-0.0060.0000.0000.0000.000
46A74LYS10.8750.93439.669-0.008-0.0080.0000.0000.0000.000
47A75MET0-0.050-0.01433.306-0.001-0.0010.0000.0000.0000.000
48A76ASN0-0.021-0.02337.029-0.001-0.0010.0000.0000.0000.000
49A77SER0-0.0030.01139.219-0.001-0.0010.0000.0000.0000.000
50A78SER00.032-0.00638.7090.0020.0020.0000.0000.0000.000
51A79LEU00.0350.05236.218-0.002-0.0020.0000.0000.0000.000
52A80ALA00.0470.01133.0830.0020.0020.0000.0000.0000.000
53A81GLU-1-0.815-0.91831.178-0.024-0.0240.0000.0000.0000.000
54A82SER0-0.0320.00131.4410.0040.0040.0000.0000.0000.000
55A83GLN0-0.004-0.00532.7200.0060.0060.0000.0000.0000.000
56A84LYS10.8970.95025.9280.0270.0270.0000.0000.0000.000
57A85MET00.017-0.00128.6630.0060.0060.0000.0000.0000.000
58A86ARG10.8030.88530.214-0.008-0.0080.0000.0000.0000.000
59A87ARG10.7940.88223.299-0.026-0.0260.0000.0000.0000.000
60A88GLN0-0.048-0.02723.8980.0100.0100.0000.0000.0000.000
61A89PHE00.0730.03326.1340.0110.0110.0000.0000.0000.000
62A90TYR00.001-0.02128.4130.0100.0100.0000.0000.0000.000
63A91SER0-0.020-0.04723.4990.0020.0020.0000.0000.0000.000
64A92SER0-0.039-0.00523.8240.0180.0180.0000.0000.0000.000
65A93LEU00.008-0.00424.5890.0170.0170.0000.0000.0000.000
66A94SER0-0.021-0.02023.3650.0070.0070.0000.0000.0000.000
67A95TYR0-0.071-0.04925.076-0.002-0.0020.0000.0000.0000.000
68A96ASN00.0320.02828.368-0.013-0.0130.0000.0000.0000.000
69A97THR00.019-0.01030.064-0.003-0.0030.0000.0000.0000.000
70A98THR0-0.040-0.01133.444-0.007-0.0070.0000.0000.0000.000
71A99ASP-1-0.755-0.86630.2380.1010.1010.0000.0000.0000.000
72A100ILE0-0.043-0.01430.278-0.004-0.0040.0000.0000.0000.000
73A101PHE0-0.013-0.01834.079-0.006-0.0060.0000.0000.0000.000
74A102ASN0-0.056-0.04036.3120.0000.0000.0000.0000.0000.000
75A103LEU00.0570.03432.751-0.002-0.0020.0000.0000.0000.000
76A104ALA0-0.0300.00036.613-0.004-0.0040.0000.0000.0000.000
77A105GLU-1-0.846-0.90238.9820.0480.0480.0000.0000.0000.000
78A106ILE00.0620.03337.844-0.003-0.0030.0000.0000.0000.000
79A107VAL00.002-0.01637.051-0.004-0.0040.0000.0000.0000.000
80A108ASN0-0.041-0.01940.303-0.003-0.0030.0000.0000.0000.000
81A109LYS10.7910.89843.552-0.050-0.0500.0000.0000.0000.000
82A110LEU00.019-0.00539.832-0.002-0.0020.0000.0000.0000.000
83A111TYR0-0.017-0.01543.287-0.002-0.0020.0000.0000.0000.000
84A112LYS10.8860.96944.900-0.035-0.0350.0000.0000.0000.000
85A113ASP-1-0.855-0.92947.1260.0280.0280.0000.0000.0000.000
86A114PRO00.021-0.00646.3540.0010.0010.0000.0000.0000.000
87A115LYS10.8840.95545.796-0.024-0.0240.0000.0000.0000.000
88A116ALA00.0510.04243.4220.0010.0010.0000.0000.0000.000
89A117HIS0-0.026-0.02442.2380.0000.0000.0000.0000.0000.000
90A118ASP-1-0.819-0.89838.7590.0360.0360.0000.0000.0000.000
91A119THR00.032-0.00737.8110.0020.0020.0000.0000.0000.000
92A120ILE00.0070.01136.7350.0030.0030.0000.0000.0000.000
93A121LYS10.9150.96736.100-0.022-0.0220.0000.0000.0000.000
94A122LYS10.8280.90933.278-0.039-0.0390.0000.0000.0000.000
95A123ILE00.0510.02531.8110.0050.0050.0000.0000.0000.000
96A124SER0-0.032-0.01831.6140.0020.0020.0000.0000.0000.000
97A125GLY00.0240.00229.121-0.005-0.0050.0000.0000.0000.000
98A126GLY00.0810.03826.4310.0040.0040.0000.0000.0000.000
99A127ILE0-0.053-0.02825.5710.0040.0040.0000.0000.0000.000
100A128ARG10.8370.91625.361-0.024-0.0240.0000.0000.0000.000
101A129ILE00.0590.03021.510-0.004-0.0040.0000.0000.0000.000
102A130GLN00.0170.01520.5850.0100.0100.0000.0000.0000.000
103A131GLN0-0.063-0.03920.741-0.011-0.0110.0000.0000.0000.000
104A132GLY00.0900.03720.045-0.015-0.0150.0000.0000.0000.000
105A133PHE00.0320.01214.202-0.016-0.0160.0000.0000.0000.000
106A134GLU-1-0.781-0.89416.2230.0030.0030.0000.0000.0000.000
107A135VAL00.0290.02616.991-0.021-0.0210.0000.0000.0000.000
108A136ALA00.0260.01413.669-0.033-0.0330.0000.0000.0000.000
109A137LEU0-0.034-0.02912.219-0.049-0.0490.0000.0000.0000.000
110A138GLU-1-1.014-0.98512.769-0.158-0.1580.0000.0000.0000.000
111A139ASP-1-0.853-0.94113.066-0.273-0.2730.0000.0000.0000.000
112A140LEU0-0.095-0.0386.399-0.096-0.0960.0000.0000.0000.000
113A141ALA0-0.017-0.0258.819-0.181-0.1810.0000.0000.0000.000
114A142ILE0-0.0180.0019.997-0.070-0.0700.0000.0000.0000.000
115A143ASN00.0110.0049.431-0.047-0.0470.0000.0000.0000.000
116A144MET0-0.037-0.0054.504-0.819-0.4890.011-0.058-0.2830.000
117A145ASP-1-0.894-0.9664.649-1.259-1.182-0.001-0.003-0.0720.000
118A146LYS10.9020.9536.5010.4360.4360.0000.0000.0000.000
119A147LEU0-0.037-0.0163.201-0.4920.0110.045-0.112-0.436-0.001
120A148LYS10.9180.9472.180-2.382-1.2014.126-2.114-3.194-0.002
121A149ALA00.0080.0283.1471.0230.2910.0010.959-0.227-0.001
122A150ASN0-0.025-0.0175.752-0.212-0.2120.0000.0000.0000.000
123A151ASP-1-0.930-0.9717.030-0.526-0.5260.0000.0000.0000.000
124A152PHE00.0440.0225.5920.1120.1120.0000.0000.0000.000
125A153ASN00.0150.0077.205-0.182-0.1820.0000.0000.0000.000
126A154LYS10.9480.9557.0060.7850.7850.0000.0000.0000.000
127A155ASN0-0.056-0.0188.0580.0290.0290.0000.0000.0000.000
128A156THR00.0250.0179.3760.0950.0950.0000.0000.0000.000
129A157LEU0-0.0010.0112.260-1.014-0.1721.010-0.392-1.460-0.001
130A158GLU-1-0.937-0.9596.8230.5300.5300.0000.0000.0000.000
131A159GLU-1-0.836-0.9267.6870.0860.0860.0000.0000.0000.000
132A160ILE00.018-0.0047.5530.1050.1050.0000.0000.0000.000
133A161TYR0-0.037-0.0165.1250.7290.7290.0000.0000.0000.000
134A162ASN0-0.009-0.0207.2340.2920.2920.0000.0000.0000.000
135A163LEU00.0110.02310.628-0.003-0.0030.0000.0000.0000.000
136A164ILE0-0.002-0.0018.3530.0130.0130.0000.0000.0000.000
137A165VAL0-0.0050.0009.025-0.018-0.0180.0000.0000.0000.000
138A166ASP-1-0.744-0.85311.5810.2190.2190.0000.0000.0000.000
139A167LEU0-0.0190.00013.939-0.049-0.0490.0000.0000.0000.000
140A168THR0-0.101-0.07111.8550.0010.0010.0000.0000.0000.000
141A169LEU0-0.047-0.03314.824-0.015-0.0150.0000.0000.0000.000
142A170ILE00.0450.02217.167-0.033-0.0330.0000.0000.0000.000
143A171LYS10.8030.91418.712-0.173-0.1730.0000.0000.0000.000
144A172LYS10.8290.90416.121-0.367-0.3670.0000.0000.0000.000
145A173GLU-1-0.871-0.93321.0260.1920.1920.0000.0000.0000.000
146A174TRP00.0190.02323.233-0.021-0.0210.0000.0000.0000.000
147A175LEU0-0.033-0.00224.043-0.013-0.0130.0000.0000.0000.000
148A176SER00.0170.02025.135-0.009-0.0090.0000.0000.0000.000
149A177THR0-0.028-0.02526.856-0.013-0.0130.0000.0000.0000.000
150A178ILE00.008-0.00828.888-0.011-0.0110.0000.0000.0000.000
151A179GLU-1-0.927-0.95528.1670.1380.1380.0000.0000.0000.000
152A180THR0-0.056-0.03930.394-0.006-0.0060.0000.0000.0000.000
153A181LEU0-0.0050.00032.957-0.008-0.0080.0000.0000.0000.000
154A182ILE0-0.011-0.01833.358-0.006-0.0060.0000.0000.0000.000
155A183LYS10.9000.97135.754-0.086-0.0860.0000.0000.0000.000
156A184SER0-0.067-0.05837.432-0.003-0.0030.0000.0000.0000.000
157A185SER00.004-0.00538.586-0.006-0.0060.0000.0000.0000.000
158A186ASN0-0.036-0.02640.895-0.003-0.0030.0000.0000.0000.000
159A187ALA0-0.043-0.00841.9730.0000.0000.0000.0000.0000.000
160A188THR00.0210.00143.708-0.002-0.0020.0000.0000.0000.000
161A189LEU00.0490.01747.358-0.001-0.0010.0000.0000.0000.000
162A190GLU-1-0.774-0.88749.5910.0380.0380.0000.0000.0000.000
163A191LEU0-0.019-0.00443.420-0.002-0.0020.0000.0000.0000.000
164A192GLN0-0.0180.00245.2990.0010.0010.0000.0000.0000.000
165A193TYR0-0.064-0.02246.831-0.002-0.0020.0000.0000.0000.000
166A194ASN0-0.059-0.04949.960-0.003-0.0030.0000.0000.0000.000
167A195THR0-0.001-0.01446.0310.0020.0020.0000.0000.0000.000
168A196GLU-1-0.858-0.91246.5360.0380.0380.0000.0000.0000.000
169A197LYS10.8950.93647.135-0.039-0.0390.0000.0000.0000.000
170A198LEU0-0.0240.00241.6690.0030.0030.0000.0000.0000.000
171A199ASN00.015-0.00842.1730.0040.0040.0000.0000.0000.000
172A200ASP-1-0.866-0.91041.8040.0480.0480.0000.0000.0000.000
173A201HIS00.0550.04439.4050.0050.0050.0000.0000.0000.000
174A202ILE00.0320.02536.6870.0040.0040.0000.0000.0000.000
175A203GLU-1-0.870-0.92837.4370.0470.0470.0000.0000.0000.000
176A204GLN0-0.084-0.05038.1060.0050.0050.0000.0000.0000.000
177A205THR0-0.070-0.03735.9740.0030.0030.0000.0000.0000.000
178A206TYR0-0.013-0.03732.8840.0080.0080.0000.0000.0000.000
179A207LYS10.8070.89332.734-0.042-0.0420.0000.0000.0000.000
180A208ASP-1-0.833-0.91633.0270.0650.0650.0000.0000.0000.000
181A209THR00.0220.00728.255-0.001-0.0010.0000.0000.0000.000
182A210MET0-0.032-0.00828.3180.0060.0060.0000.0000.0000.000
183A211ILE0-0.018-0.00728.997-0.004-0.0040.0000.0000.0000.000
184A212SER0-0.020-0.01527.2720.0030.0030.0000.0000.0000.000
185A213LEU00.0080.01423.2900.0000.0000.0000.0000.0000.000
186A214CYS0-0.034-0.02423.953-0.001-0.0010.0000.0000.0000.000
187A215LEU0-0.007-0.00325.052-0.007-0.0070.0000.0000.0000.000
188A216LYS10.9040.95219.233-0.226-0.2260.0000.0000.0000.000
189A217SER00.0300.01620.1250.0050.0050.0000.0000.0000.000
190A218GLU-1-0.988-0.96820.4350.0130.0130.0000.0000.0000.000
191A219GLN00.042-0.00721.217-0.012-0.0120.0000.0000.0000.000
192A220THR0-0.0060.00715.636-0.005-0.0050.0000.0000.0000.000
193A221LEU00.0080.01916.964-0.020-0.0200.0000.0000.0000.000
194A222LEU00.0060.01717.492-0.030-0.0300.0000.0000.0000.000
195A223HIS00.0000.00615.783-0.009-0.0090.0000.0000.0000.000
196A224LEU0-0.002-0.01911.060-0.029-0.0290.0000.0000.0000.000
197A225ASP-1-0.858-0.90214.334-0.204-0.2040.0000.0000.0000.000
198A226THR0-0.045-0.03916.440-0.033-0.0330.0000.0000.0000.000
199A227LEU0-0.018-0.00912.233-0.036-0.0360.0000.0000.0000.000
200A228PHE0-0.061-0.0239.029-0.091-0.0910.0000.0000.0000.000
201A229LYS10.7260.85813.0990.1380.1380.0000.0000.0000.000