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: K9N43

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 OptH
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 -2261387.21886
FMO2-HF: Nuclear repulsion 2183194.881406
FMO2-HF: Total energy -78192.337455
FMO2-MP2: Total energy -78419.378973


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.
-8.179-2.1678.69-3.926-10.775-0.003
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 : -0.036 / q_NPA : -0.046
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].
3X3PHE0-0.080-0.0442.496-4.067-1.3921.436-1.254-2.857-0.002
4X4SER00.0130.0025.7700.5080.5080.0000.0000.0000.000
5X5GLY0-0.036-0.0168.960-0.197-0.1970.0000.0000.0000.000
6X6LYS10.9020.9727.6490.7400.7400.0000.0000.0000.000
7X7ASN0-0.011-0.01510.7300.1630.1630.0000.0000.0000.000
8X8VAL0-0.007-0.0148.624-0.006-0.0060.0000.0000.0000.000
9X9TRP00.0210.00412.115-0.030-0.0300.0000.0000.0000.000
10X10VAL00.0100.00711.8700.0720.0720.0000.0000.0000.000
11X11THR00.0360.01814.897-0.049-0.0490.0000.0000.0000.000
12X12GLY0-0.008-0.01717.5490.0410.0410.0000.0000.0000.000
13X13ALA0-0.021-0.00216.4130.0210.0210.0000.0000.0000.000
14X14GLY00.0400.02417.6170.0070.0070.0000.0000.0000.000
15X15LYS10.8540.91219.758-0.349-0.3490.0000.0000.0000.000
16X16GLY00.008-0.00418.3300.0280.0280.0000.0000.0000.000
17X17ILE00.0290.00213.4840.0250.0250.0000.0000.0000.000
18X18GLY00.0610.04513.6660.1060.1060.0000.0000.0000.000
19X19TYR0-0.0060.01514.1220.0640.0640.0000.0000.0000.000
20X20ALA00.009-0.00212.0470.0370.0370.0000.0000.0000.000
21X21THR0-0.016-0.0319.2860.1550.1550.0000.0000.0000.000
22X22ALA0-0.019-0.0039.2360.1870.1870.0000.0000.0000.000
23X23LEU00.0240.00110.4670.0480.0480.0000.0000.0000.000
24X24ALA00.0070.0166.1950.0630.0630.0000.0000.0000.000
25X25PHE0-0.007-0.0215.8350.7690.7690.0000.0000.0000.000
26X26VAL0-0.0210.0026.8840.0680.0680.0000.0000.0000.000
27X27GLU-1-0.898-0.9546.2960.7050.7050.0000.0000.0000.000
28X28ALA0-0.086-0.0283.078-0.3430.6670.223-0.476-0.7570.003
29X29GLY00.0450.0224.553-1.506-1.4740.000-0.024-0.0070.000
30X30ALA0-0.036-0.0037.383-0.405-0.4050.0000.0000.0000.000
31X31LYS10.9440.9759.012-0.182-0.1820.0000.0000.0000.000
32X32VAL0-0.005-0.00510.2960.0020.0020.0000.0000.0000.000
33X33THR0-0.060-0.02613.067-0.084-0.0840.0000.0000.0000.000
34X34GLY00.001-0.00515.8430.0550.0550.0000.0000.0000.000
35X35PHE00.016-0.00717.219-0.044-0.0440.0000.0000.0000.000
36X36ASP-1-0.824-0.91520.2270.3640.3640.0000.0000.0000.000
37X37GLN0-0.032-0.01222.840-0.018-0.0180.0000.0000.0000.000
38X38ALA00.006-0.00225.742-0.021-0.0210.0000.0000.0000.000
39X39PHE0-0.047-0.02120.0830.0240.0240.0000.0000.0000.000
40X40THR0-0.045-0.01024.603-0.018-0.0180.0000.0000.0000.000
41X41GLN0-0.023-0.02220.8320.0010.0010.0000.0000.0000.000
42X42GLU-1-0.861-0.92825.6580.1380.1380.0000.0000.0000.000
43X43GLN0-0.055-0.02722.055-0.014-0.0140.0000.0000.0000.000
44X44TYR00.009-0.00318.4320.0070.0070.0000.0000.0000.000
45X45PRO0-0.0100.00614.580-0.032-0.0320.0000.0000.0000.000
46X46PHE00.0010.00414.0150.0370.0370.0000.0000.0000.000
47X47ALA00.0220.01815.908-0.043-0.0430.0000.0000.0000.000
48X48THR0-0.014-0.00618.1750.0370.0370.0000.0000.0000.000
49X49GLU-1-0.756-0.86920.7870.1510.1510.0000.0000.0000.000
50X50VAL0-0.036-0.02023.0170.0220.0220.0000.0000.0000.000
51X51MET0-0.036-0.02122.393-0.017-0.0170.0000.0000.0000.000
52X52ASP-1-0.820-0.90824.6000.2350.2350.0000.0000.0000.000
53X53VAL0-0.018-0.00422.327-0.009-0.0090.0000.0000.0000.000
54X54ALA00.0070.00225.665-0.008-0.0080.0000.0000.0000.000
55X55ASP-1-0.906-0.93929.0730.1310.1310.0000.0000.0000.000
56X56ALA00.029-0.00129.8980.0030.0030.0000.0000.0000.000
57X57ALA00.0030.00330.699-0.001-0.0010.0000.0000.0000.000
58X58GLN00.0480.03228.5800.0070.0070.0000.0000.0000.000
59X59VAL00.004-0.01225.1700.0030.0030.0000.0000.0000.000
60X60ALA0-0.032-0.02027.0040.0010.0010.0000.0000.0000.000
61X61GLN0-0.013-0.00829.023-0.008-0.0080.0000.0000.0000.000
62X62VAL0-0.0080.00724.160-0.006-0.0060.0000.0000.0000.000
63X63CYS0-0.005-0.01023.7940.0080.0080.0000.0000.0000.000
64X64GLN0-0.058-0.03224.955-0.015-0.0150.0000.0000.0000.000
65X65ARG10.8300.91625.309-0.150-0.1500.0000.0000.0000.000
66X66LEU00.011-0.00221.053-0.006-0.0060.0000.0000.0000.000
67X67LEU0-0.057-0.04821.245-0.006-0.0060.0000.0000.0000.000
68X68ALA0-0.057-0.01123.876-0.015-0.0150.0000.0000.0000.000
69X69GLU-1-0.951-0.97023.9710.0820.0820.0000.0000.0000.000
70X70THR0-0.088-0.02419.087-0.005-0.0050.0000.0000.0000.000
71X71GLU-1-0.933-0.95918.785-0.082-0.0820.0000.0000.0000.000
72X72ARG10.8410.90113.9670.0720.0720.0000.0000.0000.000
73X73LEU0-0.038-0.00315.1210.0150.0150.0000.0000.0000.000
74X74ASP-1-0.819-0.88610.856-0.063-0.0630.0000.0000.0000.000
75X75ALA00.011-0.0069.9730.0350.0350.0000.0000.0000.000
76X76LEU0-0.0030.02212.066-0.012-0.0120.0000.0000.0000.000
77X77VAL00.0150.00310.9340.0560.0560.0000.0000.0000.000
78X78ASN0-0.034-0.02314.208-0.087-0.0870.0000.0000.0000.000
79X79ALA00.027-0.00515.4910.0370.0370.0000.0000.0000.000
80X80ALA0-0.0210.01017.634-0.022-0.0220.0000.0000.0000.000
81X81GLY0-0.016-0.01921.2010.0060.0060.0000.0000.0000.000
82X82ILE0-0.041-0.00923.588-0.001-0.0010.0000.0000.0000.000
83X83LEU00.015-0.00526.2070.0020.0020.0000.0000.0000.000
84X84ARG10.9340.96828.027-0.201-0.2010.0000.0000.0000.000
85X85MET0-0.031-0.01330.4640.0040.0040.0000.0000.0000.000
86X86GLY00.0420.01533.396-0.008-0.0080.0000.0000.0000.000
87X87ALA00.0060.00836.6430.0050.0050.0000.0000.0000.000
88X88THR00.023-0.00438.1400.0030.0030.0000.0000.0000.000
89X89ASP-1-0.932-0.95039.3630.1050.1050.0000.0000.0000.000
90X90GLN0-0.041-0.02441.439-0.002-0.0020.0000.0000.0000.000
91X91LEU0-0.0290.01035.4270.0000.0000.0000.0000.0000.000
92X92SER00.0490.03338.991-0.005-0.0050.0000.0000.0000.000
93X93LYS10.9960.96139.011-0.092-0.0920.0000.0000.0000.000
94X94GLU-1-0.895-0.93837.3490.1330.1330.0000.0000.0000.000
95X95ASP-1-0.832-0.92735.2730.1600.1600.0000.0000.0000.000
96X96TRP0-0.037-0.01234.2430.0150.0150.0000.0000.0000.000
97X97GLN00.015-0.01134.4370.0140.0140.0000.0000.0000.000
98X98GLN00.0120.02032.4590.0180.0180.0000.0000.0000.000
99X99THR0-0.046-0.02529.6170.0180.0180.0000.0000.0000.000
100X100PHE0-0.015-0.02129.3410.0190.0190.0000.0000.0000.000
101X101ALA0-0.0010.01029.9360.0090.0090.0000.0000.0000.000
102X102VAL00.0090.00525.7540.0070.0070.0000.0000.0000.000
103X103ASN0-0.061-0.03925.1750.0300.0300.0000.0000.0000.000
104X104VAL0-0.013-0.00824.8800.0180.0180.0000.0000.0000.000
105X105GLY00.0170.00726.6680.0030.0030.0000.0000.0000.000
106X106GLY00.0480.02125.424-0.005-0.0050.0000.0000.0000.000
107X107ALA00.011-0.00222.0680.0020.0020.0000.0000.0000.000
108X108PHE0-0.0040.00723.480-0.005-0.0050.0000.0000.0000.000
109X109ASN0-0.006-0.01226.513-0.023-0.0230.0000.0000.0000.000
110X110LEU00.0360.00920.763-0.012-0.0120.0000.0000.0000.000
111X111PHE0-0.0050.00119.566-0.007-0.0070.0000.0000.0000.000
112X112GLN0-0.018-0.02024.007-0.025-0.0250.0000.0000.0000.000
113X113GLN0-0.0080.00724.971-0.024-0.0240.0000.0000.0000.000
114X114THR0-0.004-0.00220.432-0.005-0.0050.0000.0000.0000.000
115X115MET0-0.0190.00122.169-0.011-0.0110.0000.0000.0000.000
116X116ASN00.000-0.01323.519-0.016-0.0160.0000.0000.0000.000
117X117GLN00.0110.02220.146-0.015-0.0150.0000.0000.0000.000
118X118PHE00.0370.00315.597-0.027-0.0270.0000.0000.0000.000
119X119ARG10.9590.97720.426-0.123-0.1230.0000.0000.0000.000
120X120ARG10.8660.92023.228-0.066-0.0660.0000.0000.0000.000
121X121GLN0-0.0010.00216.564-0.031-0.0310.0000.0000.0000.000
122X122ARG10.8580.94719.647-0.018-0.0180.0000.0000.0000.000
123X123GLY00.0880.05316.052-0.040-0.0400.0000.0000.0000.000
124X124GLY00.0040.00312.8670.0230.0230.0000.0000.0000.000
125X125ALA0-0.020-0.00710.530-0.008-0.0080.0000.0000.0000.000
126X126ILE00.0290.01012.4630.0320.0320.0000.0000.0000.000
127X127VAL0-0.0150.0009.8770.0200.0200.0000.0000.0000.000
128X128THR00.0140.00413.362-0.058-0.0580.0000.0000.0000.000
129X129VAL00.0050.00914.5970.0260.0260.0000.0000.0000.000
130X130ALA00.0310.01217.000-0.070-0.0700.0000.0000.0000.000
131X131SER0-0.015-0.02520.063-0.009-0.0090.0000.0000.0000.000
132X132ASP-1-0.786-0.90321.3220.3170.3170.0000.0000.0000.000
133X133ALA0-0.005-0.01622.555-0.029-0.0290.0000.0000.0000.000
134X134ALA0-0.058-0.01323.491-0.021-0.0210.0000.0000.0000.000
135X135HIS10.7310.85020.506-0.372-0.3720.0000.0000.0000.000
136X136THR00.0170.01325.560-0.022-0.0220.0000.0000.0000.000
137X137PRO00.0110.02028.5420.0080.0080.0000.0000.0000.000
138X138ARG10.9330.96324.943-0.273-0.2730.0000.0000.0000.000
139X139ILE00.0490.01431.088-0.004-0.0040.0000.0000.0000.000
140X140GLY00.0000.00932.8920.0070.0070.0000.0000.0000.000
141X141MET0-0.006-0.00426.2330.0040.0040.0000.0000.0000.000
142X142SER00.0170.00130.9260.0120.0120.0000.0000.0000.000
143X143ALA00.0650.03232.4130.0050.0050.0000.0000.0000.000
144X144TYR00.0190.01123.1410.0090.0090.0000.0000.0000.000
145X145GLY00.0770.02927.3290.0170.0170.0000.0000.0000.000
146X146ALA00.0020.00627.7810.0090.0090.0000.0000.0000.000
147X147SER0-0.037-0.01828.0620.0080.0080.0000.0000.0000.000
148X148LYS10.8830.94421.155-0.379-0.3790.0000.0000.0000.000
149X149ALA00.0170.00824.0710.0210.0210.0000.0000.0000.000
150X150ALA0-0.019-0.00326.0690.0000.0000.0000.0000.0000.000
151X151LEU0-0.0240.00020.8880.0000.0000.0000.0000.0000.000
152X152LYS10.8760.92820.762-0.328-0.3280.0000.0000.0000.000
153X153SER0-0.036-0.01622.3700.0000.0000.0000.0000.0000.000
154X154LEU00.0250.00824.549-0.008-0.0080.0000.0000.0000.000
155X155ALA00.002-0.00319.227-0.008-0.0080.0000.0000.0000.000
156X156LEU0-0.020-0.01019.2960.0020.0020.0000.0000.0000.000
157X157SER0-0.0070.00221.558-0.026-0.0260.0000.0000.0000.000
158X158VAL00.0400.02420.822-0.017-0.0170.0000.0000.0000.000
159X159GLY00.009-0.03319.419-0.011-0.0110.0000.0000.0000.000
160X160LEU0-0.047-0.02020.141-0.023-0.0230.0000.0000.0000.000
161X161GLU-1-0.962-0.99023.0010.1260.1260.0000.0000.0000.000
162X162LEU0-0.050-0.03019.879-0.021-0.0210.0000.0000.0000.000
163X163ALA00.0530.03219.462-0.016-0.0160.0000.0000.0000.000
164X164GLY0-0.027-0.00920.322-0.021-0.0210.0000.0000.0000.000
165X165SER0-0.101-0.05220.858-0.019-0.0190.0000.0000.0000.000
166X166GLY00.0280.01417.764-0.016-0.0160.0000.0000.0000.000
167X167VAL0-0.059-0.01415.550-0.015-0.0150.0000.0000.0000.000
168X168ARG10.8590.9427.230-0.270-0.2700.0000.0000.0000.000
169X169CYS0-0.0050.02213.8120.0570.0570.0000.0000.0000.000
170X170ASN0-0.021-0.02111.603-0.086-0.0860.0000.0000.0000.000
171X171VAL00.000-0.00514.5680.0130.0130.0000.0000.0000.000
172X172VAL00.0360.03011.4360.0560.0560.0000.0000.0000.000
173X173SER0-0.031-0.05514.719-0.082-0.0820.0000.0000.0000.000
174X174PRO00.0000.01116.289-0.014-0.0140.0000.0000.0000.000
175X175GLY00.0710.03818.007-0.052-0.0520.0000.0000.0000.000
176X176SER0-0.066-0.04320.5760.0070.0070.0000.0000.0000.000
177X177THR0-0.0070.00718.6940.0070.0070.0000.0000.0000.000
178X214ARG10.9870.98515.662-0.404-0.4040.0000.0000.0000.000
179X215PRO00.026-0.00414.0890.0690.0690.0000.0000.0000.000
180X216GLN00.0820.0299.3910.0960.0960.0000.0000.0000.000
181X217GLU-1-0.876-0.9099.4210.9380.9380.0000.0000.0000.000
182X218ILE0-0.048-0.03710.0710.1800.1800.0000.0000.0000.000
183X219ALA00.0220.0198.5260.1880.1880.0000.0000.0000.000
184X220ASN00.008-0.0025.4570.4130.4130.0000.0000.0000.000
185X221THR0-0.027-0.0065.7100.9611.125-0.001-0.005-0.1580.000
186X222ILE0-0.031-0.0237.6000.1600.1600.0000.0000.0000.000
187X223LEU00.0240.0082.726-1.590-0.3300.410-0.326-1.3440.000
188X224PHE00.0260.0193.445-0.3041.1170.429-0.555-1.295-0.001
189X225LEU0-0.024-0.0134.350-1.655-1.7720.0030.176-0.0630.000
190X226ALA0-0.0010.0096.735-0.593-0.5930.0000.0000.0000.000
191X227SER0-0.020-0.0172.687-3.509-2.1891.192-0.831-1.680-0.005
192X228ASP-1-0.911-0.9604.515-1.051-0.957-0.001-0.016-0.0780.000
193X229LEU0-0.031-0.0202.1870.951-0.9455.000-0.612-2.4920.002
194X230ALA0-0.0210.0034.9010.2950.344-0.001-0.003-0.0440.000
195X231SER0-0.015-0.0097.3080.1360.1360.0000.0000.0000.000
196X232HIS00.0120.0069.7080.0530.0530.0000.0000.0000.000
197X233ILE0-0.036-0.0079.1220.0290.0290.0000.0000.0000.000
198X234THR00.0270.01112.2210.0720.0720.0000.0000.0000.000
199X235LEU0-0.017-0.00114.926-0.026-0.0260.0000.0000.0000.000
200X236GLN00.0120.02014.311-0.059-0.0590.0000.0000.0000.000
201X237ASP-1-0.741-0.86116.0590.5120.5120.0000.0000.0000.000
202X238ILE0-0.0070.01110.967-0.046-0.0460.0000.0000.0000.000
203X239VAL00.0060.01015.1210.0370.0370.0000.0000.0000.000
204X240VAL0-0.022-0.00413.0550.0020.0020.0000.0000.0000.000
205X241ASP-1-0.804-0.95016.3630.3630.3630.0000.0000.0000.000
206X242GLY0-0.032-0.02018.851-0.041-0.0410.0000.0000.0000.000
207X243GLY00.0330.02320.575-0.030-0.0300.0000.0000.0000.000
208X244SER0-0.0310.00122.353-0.037-0.0370.0000.0000.0000.000
209X245THR0-0.058-0.03923.115-0.020-0.0200.0000.0000.0000.000
210X246LEU0-0.038-0.02025.067-0.015-0.0150.0000.0000.0000.000
211X247GLY00.0130.01422.746-0.016-0.0160.0000.0000.0000.000
212X248ALA0-0.0070.03323.2610.0350.0350.0000.0000.0000.000