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: 4971N

Calculation Name: 2FWM-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FWM

Chain ID: X

ChEMBL ID:

UniProt ID: P15047

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2262395.766901
FMO2-HF: Nuclear repulsion 2184202.679522
FMO2-HF: Total energy -78193.087379
FMO2-MP2: Total energy -78420.074807


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(X:1:MET)


Summations of interaction energy for fragment #1(X:1:MET)
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.
-9.04-1.5788.296-4.154-11.604-0.008
Interaction energy analysis for fragmet #1(X:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.045
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].
3X3PHE0-0.075-0.0452.643-4.089-1.3461.347-1.228-2.862-0.001
4X4SER00.005-0.0245.7520.4350.4350.0000.0000.0000.000
5X5GLY0-0.040-0.0178.924-0.198-0.1980.0000.0000.0000.000
6X6LYS10.8650.9557.3070.6960.6960.0000.0000.0000.000
7X7ASN0-0.041-0.02510.7560.1750.1750.0000.0000.0000.000
8X8VAL00.001-0.0098.521-0.014-0.0140.0000.0000.0000.000
9X9TRP00.0200.00512.005-0.045-0.0450.0000.0000.0000.000
10X10VAL00.0110.00611.7580.0790.0790.0000.0000.0000.000
11X11THR00.0450.02314.835-0.061-0.0610.0000.0000.0000.000
12X12GLY0-0.019-0.02117.5130.0490.0490.0000.0000.0000.000
13X13ALA0-0.019-0.00216.4550.0270.0270.0000.0000.0000.000
14X14GLY00.0430.02217.5930.0120.0120.0000.0000.0000.000
15X15LYS10.8420.90119.756-0.421-0.4210.0000.0000.0000.000
16X16GLY00.0110.00018.3650.0330.0330.0000.0000.0000.000
17X17ILE00.0290.00113.6450.0380.0380.0000.0000.0000.000
18X18GLY00.0650.04913.7340.1380.1380.0000.0000.0000.000
19X19TYR0-0.0080.01514.1110.0860.0860.0000.0000.0000.000
20X20ALA00.0110.00012.0830.0510.0510.0000.0000.0000.000
21X21THR0-0.031-0.0409.3490.2060.2060.0000.0000.0000.000
22X22ALA0-0.014-0.0019.2220.2440.2440.0000.0000.0000.000
23X23LEU00.0330.00610.4430.0560.0560.0000.0000.0000.000
24X24ALA0-0.0070.0086.2090.0580.0580.0000.0000.0000.000
25X25PHE00.001-0.0195.7840.8230.8230.0000.0000.0000.000
26X26VAL0-0.0120.0036.8400.0460.0460.0000.0000.0000.000
27X27GLU-1-0.918-0.9586.4610.8360.8360.0000.0000.0000.000
28X28ALA0-0.084-0.0293.030-0.3130.6710.197-0.455-0.7280.002
29X29GLY00.0450.0224.553-1.476-1.4460.000-0.024-0.0060.000
30X30ALA0-0.035-0.0027.259-0.422-0.4220.0000.0000.0000.000
31X31LYS10.9370.9668.913-0.295-0.2950.0000.0000.0000.000
32X32VAL0-0.010-0.01210.2070.0040.0040.0000.0000.0000.000
33X33THR0-0.048-0.01712.984-0.103-0.1030.0000.0000.0000.000
34X34GLY00.000-0.00615.7680.0660.0660.0000.0000.0000.000
35X35PHE00.010-0.01117.162-0.055-0.0550.0000.0000.0000.000
36X36ASP-1-0.811-0.90320.1820.4430.4430.0000.0000.0000.000
37X37GLN0-0.042-0.02622.799-0.020-0.0200.0000.0000.0000.000
38X38ALA00.0070.00025.719-0.024-0.0240.0000.0000.0000.000
39X39PHE0-0.035-0.01519.9990.0290.0290.0000.0000.0000.000
40X40THR0-0.049-0.01024.866-0.018-0.0180.0000.0000.0000.000
41X41GLN0-0.009-0.01320.663-0.005-0.0050.0000.0000.0000.000
42X42GLU-1-0.854-0.92825.6580.1780.1780.0000.0000.0000.000
43X43GLN0-0.062-0.03221.742-0.016-0.0160.0000.0000.0000.000
44X44TYR0-0.004-0.01018.4510.0090.0090.0000.0000.0000.000
45X45PRO0-0.0090.00314.596-0.036-0.0360.0000.0000.0000.000
46X46PHE00.0080.00513.8970.0450.0450.0000.0000.0000.000
47X47ALA00.0210.01915.864-0.054-0.0540.0000.0000.0000.000
48X48THR0-0.0070.00018.1130.0470.0470.0000.0000.0000.000
49X49GLU-1-0.799-0.87720.7300.1940.1940.0000.0000.0000.000
50X50VAL0-0.026-0.01722.9550.0250.0250.0000.0000.0000.000
51X51MET0-0.006-0.00522.208-0.019-0.0190.0000.0000.0000.000
52X52ASP-1-0.842-0.90024.5430.2770.2770.0000.0000.0000.000
53X53VAL0-0.005-0.00222.298-0.012-0.0120.0000.0000.0000.000
54X54ALA00.0090.00425.604-0.011-0.0110.0000.0000.0000.000
55X55ASP-1-0.878-0.91429.0180.1560.1560.0000.0000.0000.000
56X56ALA00.0380.00229.8240.0050.0050.0000.0000.0000.000
57X57ALA00.0040.00530.6130.0000.0000.0000.0000.0000.000
58X58GLN00.005-0.00528.6930.0100.0100.0000.0000.0000.000
59X59VAL00.002-0.01425.0320.0060.0060.0000.0000.0000.000
60X60ALA0-0.024-0.01326.9100.0040.0040.0000.0000.0000.000
61X61GLN0-0.014-0.00828.921-0.006-0.0060.0000.0000.0000.000
62X62VAL00.0000.00924.073-0.005-0.0050.0000.0000.0000.000
63X63CYS0-0.012-0.01423.8360.0110.0110.0000.0000.0000.000
64X64GLN0-0.054-0.03324.851-0.014-0.0140.0000.0000.0000.000
65X65ARG10.8270.89825.043-0.197-0.1970.0000.0000.0000.000
66X66LEU00.0160.00421.229-0.004-0.0040.0000.0000.0000.000
67X67LEU0-0.065-0.04721.321-0.006-0.0060.0000.0000.0000.000
68X68ALA0-0.067-0.02023.754-0.016-0.0160.0000.0000.0000.000
69X69GLU-1-0.933-0.96123.6920.1340.1340.0000.0000.0000.000
70X70THR0-0.081-0.03018.6120.0020.0020.0000.0000.0000.000
71X71GLU-1-0.934-0.96018.932-0.028-0.0280.0000.0000.0000.000
72X72ARG10.8260.88513.8790.0130.0130.0000.0000.0000.000
73X73LEU0-0.0310.00514.8900.0250.0250.0000.0000.0000.000
74X74ASP-1-0.784-0.86910.9000.0230.0230.0000.0000.0000.000
75X75ALA00.000-0.01110.0860.0250.0250.0000.0000.0000.000
76X76LEU0-0.0010.02112.104-0.002-0.0020.0000.0000.0000.000
77X77VAL00.0200.00410.8940.0470.0470.0000.0000.0000.000
78X78ASN0-0.036-0.02314.042-0.081-0.0810.0000.0000.0000.000
79X79ALA00.025-0.00615.2360.0340.0340.0000.0000.0000.000
80X80ALA0-0.0200.01317.370-0.024-0.0240.0000.0000.0000.000
81X81GLY0-0.010-0.01821.0670.0020.0020.0000.0000.0000.000
82X82ILE0-0.041-0.01123.3890.0010.0010.0000.0000.0000.000
83X83LEU00.008-0.00626.074-0.001-0.0010.0000.0000.0000.000
84X84ARG10.9010.95627.933-0.225-0.2250.0000.0000.0000.000
85X85MET0-0.032-0.01630.3710.0030.0030.0000.0000.0000.000
86X86GLY00.0410.01433.239-0.008-0.0080.0000.0000.0000.000
87X87ALA00.0010.00636.2850.0050.0050.0000.0000.0000.000
88X88THR00.016-0.01237.9120.0040.0040.0000.0000.0000.000
89X89ASP-1-0.936-0.95438.9350.1130.1130.0000.0000.0000.000
90X90GLN0-0.032-0.02041.110-0.001-0.0010.0000.0000.0000.000
91X91LEU0-0.0400.00534.9680.0010.0010.0000.0000.0000.000
92X92SER00.007-0.01438.749-0.007-0.0070.0000.0000.0000.000
93X93LYS10.9930.95838.683-0.099-0.0990.0000.0000.0000.000
94X94GLU-1-0.861-0.92037.3780.1510.1510.0000.0000.0000.000
95X95ASP-1-0.793-0.87835.0360.1760.1760.0000.0000.0000.000
96X96TRP0-0.0220.00233.9180.0160.0160.0000.0000.0000.000
97X97GLN00.007-0.01634.0010.0130.0130.0000.0000.0000.000
98X98GLN00.0280.02832.2430.0200.0200.0000.0000.0000.000
99X99THR0-0.037-0.03429.2580.0200.0200.0000.0000.0000.000
100X100PHE0-0.003-0.01128.9040.0200.0200.0000.0000.0000.000
101X101ALA0-0.0040.00829.5310.0090.0090.0000.0000.0000.000
102X102VAL00.0140.00325.4420.0090.0090.0000.0000.0000.000
103X103ASN0-0.073-0.04124.7450.0410.0410.0000.0000.0000.000
104X104VAL0-0.016-0.01024.4820.0180.0180.0000.0000.0000.000
105X105GLY00.0210.00826.3100.0030.0030.0000.0000.0000.000
106X106GLY00.0500.02125.155-0.005-0.0050.0000.0000.0000.000
107X107ALA00.005-0.00421.7550.0050.0050.0000.0000.0000.000
108X108PHE00.0040.00723.131-0.006-0.0060.0000.0000.0000.000
109X109ASN0-0.009-0.01226.203-0.027-0.0270.0000.0000.0000.000
110X110LEU00.0340.01220.629-0.012-0.0120.0000.0000.0000.000
111X111PHE0-0.015-0.00219.170-0.006-0.0060.0000.0000.0000.000
112X112GLN0-0.010-0.01323.743-0.030-0.0300.0000.0000.0000.000
113X113GLN0-0.0170.00724.895-0.026-0.0260.0000.0000.0000.000
114X114THR0-0.006-0.01520.309-0.003-0.0030.0000.0000.0000.000
115X115MET0-0.0350.00122.179-0.007-0.0070.0000.0000.0000.000
116X116ASN00.0310.00123.366-0.017-0.0170.0000.0000.0000.000
117X117GLN00.0200.03220.147-0.027-0.0270.0000.0000.0000.000
118X118PHE00.0340.00115.485-0.025-0.0250.0000.0000.0000.000
119X119ARG10.9110.95420.301-0.138-0.1380.0000.0000.0000.000
120X120ARG10.8470.91923.146-0.101-0.1010.0000.0000.0000.000
121X121GLN0-0.024-0.01916.610-0.024-0.0240.0000.0000.0000.000
122X122ARG10.8570.95019.701-0.024-0.0240.0000.0000.0000.000
123X123GLY00.0930.05616.024-0.043-0.0430.0000.0000.0000.000
124X124GLY00.0120.01012.7880.0350.0350.0000.0000.0000.000
125X125ALA0-0.027-0.01210.356-0.029-0.0290.0000.0000.0000.000
126X126ILE00.0280.01112.2210.0650.0650.0000.0000.0000.000
127X127VAL0-0.024-0.0069.591-0.006-0.0060.0000.0000.0000.000
128X128THR00.0180.00513.068-0.040-0.0400.0000.0000.0000.000
129X129VAL00.0110.01214.1360.0150.0150.0000.0000.0000.000
130X130ALA00.0320.01416.583-0.073-0.0730.0000.0000.0000.000
131X131SER0-0.003-0.01619.666-0.003-0.0030.0000.0000.0000.000
132X132ASP-1-0.760-0.87320.9610.3170.3170.0000.0000.0000.000
133X133ALA0-0.006-0.01222.182-0.033-0.0330.0000.0000.0000.000
134X134ALA0-0.058-0.01323.133-0.022-0.0220.0000.0000.0000.000
135X135HIS10.7330.86119.948-0.364-0.3640.0000.0000.0000.000
136X136THR00.0220.01225.214-0.024-0.0240.0000.0000.0000.000
137X137PRO00.0040.01828.2190.0110.0110.0000.0000.0000.000
138X138ARG10.9030.92724.392-0.286-0.2860.0000.0000.0000.000
139X139ILE00.0450.01030.692-0.003-0.0030.0000.0000.0000.000
140X140GLY00.0060.01232.5770.0080.0080.0000.0000.0000.000
141X141MET0-0.012-0.01026.1670.0060.0060.0000.0000.0000.000
142X142SER00.0280.01130.5040.0130.0130.0000.0000.0000.000
143X143ALA00.0510.02632.0100.0040.0040.0000.0000.0000.000
144X144TYR00.0240.01222.7090.0080.0080.0000.0000.0000.000
145X145GLY00.0800.03326.9270.0180.0180.0000.0000.0000.000
146X146ALA0-0.0040.00327.4050.0080.0080.0000.0000.0000.000
147X147SER0-0.043-0.02227.6610.0080.0080.0000.0000.0000.000
148X148LYS10.8820.93720.669-0.420-0.4200.0000.0000.0000.000
149X149ALA00.0140.00823.7180.0190.0190.0000.0000.0000.000
150X150ALA0-0.022-0.00525.642-0.002-0.0020.0000.0000.0000.000
151X151LEU0-0.0230.00020.509-0.001-0.0010.0000.0000.0000.000
152X152LYS10.8850.93320.197-0.303-0.3030.0000.0000.0000.000
153X153SER0-0.020-0.01021.776-0.005-0.0050.0000.0000.0000.000
154X154LEU00.0190.01324.110-0.011-0.0110.0000.0000.0000.000
155X155ALA00.009-0.00118.705-0.009-0.0090.0000.0000.0000.000
156X156LEU0-0.0150.00318.586-0.003-0.0030.0000.0000.0000.000
157X157SER0-0.021-0.01320.905-0.030-0.0300.0000.0000.0000.000
158X158VAL00.0180.00620.323-0.020-0.0200.0000.0000.0000.000
159X159GLY00.033-0.01818.969-0.011-0.0110.0000.0000.0000.000
160X160LEU0-0.043-0.02019.670-0.027-0.0270.0000.0000.0000.000
161X161GLU-1-0.917-0.97122.5780.1160.1160.0000.0000.0000.000
162X162LEU0-0.056-0.02919.537-0.018-0.0180.0000.0000.0000.000
163X163ALA00.0450.02819.239-0.016-0.0160.0000.0000.0000.000
164X164GLY0-0.025-0.01020.211-0.024-0.0240.0000.0000.0000.000
165X165SER0-0.089-0.04520.907-0.017-0.0170.0000.0000.0000.000
166X166GLY00.0240.01317.817-0.011-0.0110.0000.0000.0000.000
167X167VAL0-0.056-0.01415.455-0.016-0.0160.0000.0000.0000.000
168X168ARG10.8480.9497.375-0.103-0.1030.0000.0000.0000.000
169X169CYS0-0.0060.02213.4240.0780.0780.0000.0000.0000.000
170X170ASN0-0.013-0.01610.716-0.104-0.1040.0000.0000.0000.000
171X171VAL0-0.005-0.01013.8520.0380.0380.0000.0000.0000.000
172X172VAL00.0370.02911.0260.0360.0360.0000.0000.0000.000
173X173SER0-0.028-0.05514.367-0.067-0.0670.0000.0000.0000.000
174X174PRO0-0.0020.01015.481-0.023-0.0230.0000.0000.0000.000
175X175GLY00.0560.03217.579-0.058-0.0580.0000.0000.0000.000
176X176SER0-0.042-0.03020.4470.0130.0130.0000.0000.0000.000
177X177THR0-0.0080.00518.7200.0070.0070.0000.0000.0000.000
178X214ARG10.9930.98515.744-0.459-0.4590.0000.0000.0000.000
179X215PRO00.0220.00014.1430.0850.0850.0000.0000.0000.000
180X216GLN00.0680.0239.5460.0740.0740.0000.0000.0000.000
181X217GLU-1-0.871-0.9069.4451.1481.1480.0000.0000.0000.000
182X218ILE0-0.041-0.03310.1460.2000.2000.0000.0000.0000.000
183X219ALA00.0230.0208.6220.1990.1990.0000.0000.0000.000
184X220ASN00.002-0.0105.5640.6700.6700.0000.0000.0000.000
185X221THR0-0.027-0.0075.2821.1351.348-0.001-0.013-0.1990.000
186X222ILE0-0.031-0.0237.2660.0050.0050.0000.0000.0000.000
187X223LEU00.0260.0122.810-1.933-0.8651.513-0.588-1.9930.002
188X224PHE00.0260.0142.764-1.2420.5340.803-0.739-1.839-0.002
189X225LEU0-0.018-0.0033.854-1.762-1.9190.0080.263-0.1140.000
190X226ALA00.0100.0136.340-0.615-0.6150.0000.0000.0000.000
191X227SER0-0.023-0.0192.611-3.441-2.4131.988-1.045-1.971-0.009
192X228ASP-1-0.866-0.9524.491-0.904-0.793-0.001-0.017-0.0930.000
193X229LEU0-0.013-0.0062.3370.133-0.2532.443-0.308-1.7490.000
194X230ALA0-0.0230.0025.0690.3150.367-0.0010.000-0.0500.000
195X231SER0-0.014-0.0147.0100.2340.2340.0000.0000.0000.000
196X232HIS00.000-0.0029.7080.1050.1050.0000.0000.0000.000
197X233ILE0-0.044-0.0098.6440.0430.0430.0000.0000.0000.000
198X234THR00.0270.00711.7630.0760.0760.0000.0000.0000.000
199X235LEU0-0.013-0.00414.427-0.024-0.0240.0000.0000.0000.000
200X236GLN00.0090.01613.635-0.032-0.0320.0000.0000.0000.000
201X237ASP-1-0.753-0.86515.2490.4980.4980.0000.0000.0000.000
202X238ILE00.0000.01410.346-0.052-0.0520.0000.0000.0000.000
203X239VAL00.0050.00714.5900.0590.0590.0000.0000.0000.000
204X240VAL0-0.024-0.00512.616-0.011-0.0110.0000.0000.0000.000
205X241ASP-1-0.814-0.94416.0080.3700.3700.0000.0000.0000.000
206X242GLY0-0.020-0.00918.522-0.042-0.0420.0000.0000.0000.000
207X243GLY00.0340.02220.262-0.034-0.0340.0000.0000.0000.000
208X244SER0-0.039-0.01522.085-0.036-0.0360.0000.0000.0000.000
209X245THR0-0.052-0.03022.661-0.020-0.0200.0000.0000.0000.000
210X246LEU0-0.037-0.02024.789-0.017-0.0170.0000.0000.0000.000
211X247GLY00.0120.01422.133-0.018-0.0180.0000.0000.0000.000
212X248ALA0-0.0020.02522.7740.0340.0340.0000.0000.0000.000