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: R5RK8

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2400682.452736
FMO2-HF: Nuclear repulsion 2318536.65967
FMO2-HF: Total energy -82145.793066
FMO2-MP2: Total energy -82385.52961


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.
-16.773-8.6966.375-3.897-10.5580.002
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 : 0.040 / 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].
3A23LYS10.8980.9212.870-8.856-5.8670.772-1.412-2.3480.009
4A24LEU00.0350.0252.467-2.179-0.7670.612-0.467-1.5580.000
5A25PHE0-0.002-0.0042.610-0.987-0.0810.215-0.199-0.9220.001
6A26GLU-1-0.869-0.9156.7550.9330.9330.0000.0000.0000.000
7A27ILE00.0350.0167.122-0.191-0.1910.0000.0000.0000.000
8A28LEU00.0060.0158.877-0.103-0.1030.0000.0000.0000.000
9A29ALA0-0.013-0.01410.652-0.034-0.0340.0000.0000.0000.000
10A30ARG10.7920.87111.138-0.708-0.7080.0000.0000.0000.000
11A31GLU-1-0.751-0.86513.5210.3120.3120.0000.0000.0000.000
12A32MET00.0280.01914.551-0.042-0.0420.0000.0000.0000.000
13A33THR0-0.044-0.02116.342-0.034-0.0340.0000.0000.0000.000
14A34ILE0-0.0020.00617.586-0.015-0.0150.0000.0000.0000.000
15A35ILE00.0350.00817.393-0.019-0.0190.0000.0000.0000.000
16A36LYS10.9320.96820.426-0.042-0.0420.0000.0000.0000.000
17A37LYS10.8280.89722.202-0.130-0.1300.0000.0000.0000.000
18A38GLU-1-0.781-0.85823.0840.1110.1110.0000.0000.0000.000
19A39LYS10.8120.90921.201-0.027-0.0270.0000.0000.0000.000
20A40LEU0-0.031-0.00825.900-0.007-0.0070.0000.0000.0000.000
21A41GLN0-0.0020.03028.749-0.004-0.0040.0000.0000.0000.000
22A42THR00.0000.00030.747-0.002-0.0020.0000.0000.0000.000
23A43GLU-1-0.754-0.82634.0060.0310.0310.0000.0000.0000.000
24A44ILE00.0100.02035.363-0.003-0.0030.0000.0000.0000.000
25A45PRO00.0620.02138.8130.0000.0000.0000.0000.0000.000
26A46SER00.002-0.00541.525-0.002-0.0020.0000.0000.0000.000
27A47GLN0-0.004-0.02037.7500.0010.0010.0000.0000.0000.000
28A48PHE00.0270.00034.5290.0020.0020.0000.0000.0000.000
29A49GLY00.0400.02938.7030.0020.0020.0000.0000.0000.000
30A50LEU00.0360.02135.535-0.001-0.0010.0000.0000.0000.000
31A51LYS10.8620.94939.696-0.023-0.0230.0000.0000.0000.000
32A52ASN0-0.032-0.03741.331-0.001-0.0010.0000.0000.0000.000
33A53SER00.0340.00141.575-0.002-0.0020.0000.0000.0000.000
34A54MET0-0.0040.01534.546-0.002-0.0020.0000.0000.0000.000
35A55PHE0-0.032-0.03734.150-0.002-0.0020.0000.0000.0000.000
36A56GLU-1-0.809-0.87838.8620.0140.0140.0000.0000.0000.000
37A57LEU0-0.026-0.00539.924-0.003-0.0030.0000.0000.0000.000
38A58LEU0-0.036-0.01634.679-0.002-0.0020.0000.0000.0000.000
39A59ASN00.014-0.00138.235-0.001-0.0010.0000.0000.0000.000
40A60VAL0-0.0150.01033.5930.0000.0000.0000.0000.0000.000
41A61TYR00.013-0.02234.917-0.002-0.0020.0000.0000.0000.000
42A62LYS10.8530.92831.8390.0210.0210.0000.0000.0000.000
43A71LEU00.012-0.00438.9400.0000.0000.0000.0000.0000.000
44A72GLN00.0140.00038.9060.0020.0020.0000.0000.0000.000
45A73GLU-1-0.890-0.93639.5160.0000.0000.0000.0000.0000.000
46A74LYS10.8740.94239.727-0.012-0.0120.0000.0000.0000.000
47A75MET0-0.0180.00733.3270.0000.0000.0000.0000.0000.000
48A76ASN0-0.051-0.03037.193-0.001-0.0010.0000.0000.0000.000
49A77SER00.0130.02539.2800.0000.0000.0000.0000.0000.000
50A78SER00.0380.00539.0700.0020.0020.0000.0000.0000.000
51A79LEU00.0190.04036.154-0.001-0.0010.0000.0000.0000.000
52A80ALA00.0240.01533.3140.0030.0030.0000.0000.0000.000
53A81GLU-1-0.809-0.91331.293-0.013-0.0130.0000.0000.0000.000
54A82SER0-0.026-0.01631.9730.0040.0040.0000.0000.0000.000
55A83GLN0-0.005-0.00633.7330.0060.0060.0000.0000.0000.000
56A84LYS10.9000.95726.6100.0110.0110.0000.0000.0000.000
57A85MET00.0420.02328.9720.0060.0060.0000.0000.0000.000
58A86ARG10.7860.86430.266-0.014-0.0140.0000.0000.0000.000
59A87ARG10.7820.87323.763-0.040-0.0400.0000.0000.0000.000
60A88GLN0-0.039-0.03424.2050.0070.0070.0000.0000.0000.000
61A89PHE00.0580.02126.6380.0100.0100.0000.0000.0000.000
62A90TYR0-0.022-0.04128.6680.0090.0090.0000.0000.0000.000
63A91SER0-0.014-0.04023.7820.0030.0030.0000.0000.0000.000
64A92SER0-0.037-0.00324.1990.0170.0170.0000.0000.0000.000
65A93LEU00.0220.00924.9060.0140.0140.0000.0000.0000.000
66A94SER0-0.024-0.01923.2730.0070.0070.0000.0000.0000.000
67A95TYR0-0.082-0.06424.9730.0000.0000.0000.0000.0000.000
68A96ASN00.0320.02828.347-0.012-0.0120.0000.0000.0000.000
69A97THR00.005-0.01530.209-0.003-0.0030.0000.0000.0000.000
70A98THR0-0.053-0.02133.655-0.007-0.0070.0000.0000.0000.000
71A99ASP-1-0.765-0.87330.3400.1020.1020.0000.0000.0000.000
72A100ILE0-0.047-0.01430.576-0.005-0.0050.0000.0000.0000.000
73A101PHE00.010-0.00334.186-0.006-0.0060.0000.0000.0000.000
74A102ASN0-0.033-0.02236.647-0.001-0.0010.0000.0000.0000.000
75A103LEU00.0580.02932.875-0.003-0.0030.0000.0000.0000.000
76A104ALA0-0.018-0.00636.725-0.004-0.0040.0000.0000.0000.000
77A105GLU-1-0.864-0.90939.1910.0470.0470.0000.0000.0000.000
78A106ILE00.0450.03238.018-0.003-0.0030.0000.0000.0000.000
79A107VAL0-0.002-0.01037.192-0.003-0.0030.0000.0000.0000.000
80A108ASN0-0.007-0.01240.445-0.004-0.0040.0000.0000.0000.000
81A109LYS10.7680.89743.775-0.050-0.0500.0000.0000.0000.000
82A110LEU00.0220.01339.869-0.002-0.0020.0000.0000.0000.000
83A111TYR0-0.030-0.02243.442-0.002-0.0020.0000.0000.0000.000
84A112LYS10.8820.96245.028-0.036-0.0360.0000.0000.0000.000
85A113ASP-1-0.832-0.91747.2540.0260.0260.0000.0000.0000.000
86A114PRO00.006-0.00746.4940.0010.0010.0000.0000.0000.000
87A115LYS10.8800.94346.005-0.024-0.0240.0000.0000.0000.000
88A116ALA00.0710.04843.4720.0010.0010.0000.0000.0000.000
89A117HIS0-0.048-0.02441.9150.0010.0010.0000.0000.0000.000
90A118ASP-1-0.803-0.90238.9900.0340.0340.0000.0000.0000.000
91A119THR00.0390.00437.9850.0020.0020.0000.0000.0000.000
92A120ILE00.0200.02436.8210.0040.0040.0000.0000.0000.000
93A121LYS10.9210.96136.007-0.022-0.0220.0000.0000.0000.000
94A122LYS10.8100.92233.307-0.037-0.0370.0000.0000.0000.000
95A123ILE00.0860.03731.9960.0050.0050.0000.0000.0000.000
96A124SER0-0.077-0.05931.7510.0030.0030.0000.0000.0000.000
97A125GLY00.0450.02229.369-0.002-0.0020.0000.0000.0000.000
98A126GLY00.0550.02226.3240.0010.0010.0000.0000.0000.000
99A127ILE0-0.038-0.02525.7320.0030.0030.0000.0000.0000.000
100A128ARG10.8180.89725.950-0.028-0.0280.0000.0000.0000.000
101A129ILE00.0580.04121.551-0.005-0.0050.0000.0000.0000.000
102A130GLN0-0.0040.00120.6480.0140.0140.0000.0000.0000.000
103A131GLN0-0.061-0.03721.385-0.010-0.0100.0000.0000.0000.000
104A132GLY00.0500.02320.533-0.013-0.0130.0000.0000.0000.000
105A133PHE00.029-0.00114.695-0.015-0.0150.0000.0000.0000.000
106A134GLU-1-0.772-0.88016.6220.0270.0270.0000.0000.0000.000
107A135VAL00.0400.02317.245-0.015-0.0150.0000.0000.0000.000
108A136ALA00.0250.02214.229-0.032-0.0320.0000.0000.0000.000
109A137LEU0-0.032-0.02312.570-0.031-0.0310.0000.0000.0000.000
110A138GLU-1-1.002-0.99312.847-0.116-0.1160.0000.0000.0000.000
111A139ASP-1-0.841-0.94114.006-0.270-0.2700.0000.0000.0000.000
112A140LEU0-0.016-0.0036.643-0.079-0.0790.0000.0000.0000.000
113A141ALA0-0.046-0.0349.120-0.147-0.1470.0000.0000.0000.000
114A142ILE0-0.058-0.01910.660-0.062-0.0620.0000.0000.0000.000
115A143ASN0-0.0050.0009.794-0.036-0.0360.0000.0000.0000.000
116A144MET0-0.0070.0124.964-0.562-0.3860.000-0.023-0.1530.000
117A145ASP-1-0.844-0.9315.017-1.047-0.988-0.0010.000-0.0580.000
118A146LYS10.8210.9076.7520.4080.4080.0000.0000.0000.000
119A147LEU00.0110.0093.036-0.818-0.1320.120-0.167-0.640-0.002
120A148LYS10.8780.9392.213-2.813-1.3383.201-1.856-2.821-0.001
121A149ALA0-0.0020.0163.1921.0520.508-0.0030.710-0.1630.000
122A150ASN0-0.002-0.0135.713-0.213-0.2130.0000.0000.0000.000
123A151ASP-1-0.928-0.9586.691-0.569-0.5690.0000.0000.0000.000
124A152PHE00.0640.0355.9690.0550.0550.0000.0000.0000.000
125A153ASN00.0260.0137.368-0.160-0.1600.0000.0000.0000.000
126A154LYS10.8700.9166.7180.9020.9020.0000.0000.0000.000
127A155ASN0-0.007-0.0137.778-0.050-0.0500.0000.0000.0000.000
128A156THR00.0220.0159.5300.1050.1050.0000.0000.0000.000
129A157LEU0-0.038-0.0142.313-1.265-0.3471.459-0.483-1.895-0.005
130A158GLU-1-0.935-0.9586.5550.4620.4620.0000.0000.0000.000
131A159GLU-1-0.797-0.8887.8130.0370.0370.0000.0000.0000.000
132A160ILE00.0180.0087.3100.1020.1020.0000.0000.0000.000
133A161TYR0-0.029-0.0184.9590.7330.7330.0000.0000.0000.000
134A162ASN0-0.026-0.0287.1380.2530.2530.0000.0000.0000.000
135A163LEU0-0.0100.00310.6080.0010.0010.0000.0000.0000.000
136A164ILE0-0.005-0.0048.705-0.001-0.0010.0000.0000.0000.000
137A165VAL0-0.0110.0008.9520.0020.0020.0000.0000.0000.000
138A166ASP-1-0.763-0.87611.5480.1930.1930.0000.0000.0000.000
139A167LEU00.0010.01214.078-0.039-0.0390.0000.0000.0000.000
140A168THR0-0.117-0.07912.1550.0040.0040.0000.0000.0000.000
141A169LEU0-0.019-0.01115.033-0.023-0.0230.0000.0000.0000.000
142A170ILE00.0440.02217.321-0.033-0.0330.0000.0000.0000.000
143A171LYS10.8340.93018.748-0.178-0.1780.0000.0000.0000.000
144A172LYS10.8210.89116.495-0.343-0.3430.0000.0000.0000.000
145A173GLU-1-0.859-0.92621.3190.1840.1840.0000.0000.0000.000
146A174TRP0-0.0150.00823.256-0.021-0.0210.0000.0000.0000.000
147A175LEU0-0.024-0.00224.461-0.012-0.0120.0000.0000.0000.000
148A176SER00.0420.03025.441-0.011-0.0110.0000.0000.0000.000
149A177THR0-0.028-0.02127.117-0.012-0.0120.0000.0000.0000.000
150A178ILE00.002-0.00429.057-0.011-0.0110.0000.0000.0000.000
151A179GLU-1-0.901-0.95627.8880.1390.1390.0000.0000.0000.000
152A180THR0-0.070-0.04430.681-0.007-0.0070.0000.0000.0000.000
153A181LEU0-0.0010.00633.188-0.007-0.0070.0000.0000.0000.000
154A182ILE0-0.0080.00233.415-0.008-0.0080.0000.0000.0000.000
155A183LYS10.8910.95435.818-0.083-0.0830.0000.0000.0000.000
156A184SER0-0.027-0.03237.511-0.002-0.0020.0000.0000.0000.000
157A185SER00.007-0.01038.619-0.006-0.0060.0000.0000.0000.000
158A186ASN0-0.057-0.05040.860-0.004-0.0040.0000.0000.0000.000
159A187ALA0-0.049-0.01241.8120.0000.0000.0000.0000.0000.000
160A188THR00.001-0.00843.617-0.002-0.0020.0000.0000.0000.000
161A189LEU00.0500.01847.2850.0000.0000.0000.0000.0000.000
162A190GLU-1-0.784-0.87849.3290.0370.0370.0000.0000.0000.000
163A191LEU0-0.0100.01043.346-0.002-0.0020.0000.0000.0000.000
164A192GLN0-0.015-0.00545.4460.0000.0000.0000.0000.0000.000
165A193TYR0-0.021-0.00446.838-0.002-0.0020.0000.0000.0000.000
166A194ASN0-0.075-0.06749.685-0.003-0.0030.0000.0000.0000.000
167A195THR0-0.009-0.03146.2860.0020.0020.0000.0000.0000.000
168A196GLU-1-0.817-0.87546.6010.0360.0360.0000.0000.0000.000
169A197LYS10.8610.90146.953-0.036-0.0360.0000.0000.0000.000
170A198LEU0-0.0160.00841.8680.0030.0030.0000.0000.0000.000
171A199ASN00.001-0.01942.4030.0040.0040.0000.0000.0000.000
172A200ASP-1-0.893-0.91642.0260.0460.0460.0000.0000.0000.000
173A201HIS00.0680.05639.1710.0040.0040.0000.0000.0000.000
174A202ILE00.0200.00936.8800.0040.0040.0000.0000.0000.000
175A203GLU-1-0.866-0.92637.5170.0440.0440.0000.0000.0000.000
176A204GLN0-0.065-0.05338.1800.0030.0030.0000.0000.0000.000
177A205THR0-0.074-0.03735.9420.0020.0020.0000.0000.0000.000
178A206TYR0-0.011-0.03232.9780.0080.0080.0000.0000.0000.000
179A207LYS10.8000.90132.871-0.039-0.0390.0000.0000.0000.000
180A208ASP-1-0.826-0.91833.1150.0580.0580.0000.0000.0000.000
181A209THR00.0100.02128.3840.0000.0000.0000.0000.0000.000
182A210MET0-0.033-0.00728.4200.0050.0050.0000.0000.0000.000
183A211ILE0-0.025-0.01228.833-0.002-0.0020.0000.0000.0000.000
184A212SER0-0.015-0.02727.2560.0010.0010.0000.0000.0000.000
185A213LEU00.0160.01523.4430.0030.0030.0000.0000.0000.000
186A214CYS0-0.077-0.04023.7780.0010.0010.0000.0000.0000.000
187A215LEU00.005-0.00224.630-0.005-0.0050.0000.0000.0000.000
188A216LYS10.8480.93119.495-0.214-0.2140.0000.0000.0000.000
189A217SER00.0110.01619.9870.0060.0060.0000.0000.0000.000
190A218GLU-1-0.820-0.89720.2150.0180.0180.0000.0000.0000.000
191A219GLN0-0.013-0.01421.248-0.012-0.0120.0000.0000.0000.000
192A220THR0-0.008-0.01315.737-0.013-0.0130.0000.0000.0000.000
193A221LEU0-0.015-0.00316.781-0.015-0.0150.0000.0000.0000.000
194A222LEU0-0.0120.00117.780-0.028-0.0280.0000.0000.0000.000
195A223HIS0-0.040-0.00315.5600.0000.0000.0000.0000.0000.000
196A224LEU00.004-0.00711.058-0.034-0.0340.0000.0000.0000.000
197A225ASP-1-0.835-0.89714.026-0.186-0.1860.0000.0000.0000.000
198A226THR0-0.028-0.03116.576-0.027-0.0270.0000.0000.0000.000
199A227LEU0-0.032-0.01911.946-0.028-0.0280.0000.0000.0000.000
200A228PHE0-0.050-0.0138.862-0.103-0.1030.0000.0000.0000.000
201A229LYS10.7470.87012.8980.1500.1500.0000.0000.0000.000