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: 52M1Z

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2269526.894696
FMO2-HF: Nuclear repulsion 2191333.616627
FMO2-HF: Total energy -78193.278069
FMO2-MP2: Total energy -78420.238803


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.
-7.248-0.8298.93-4.053-11.298-0.01
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 : -0.049 / q_NPA : -0.047
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].
3X3PHE0-0.032-0.0312.301-3.143-1.1451.713-1.097-2.6150.000
4X4SER0-0.002-0.0205.7690.3130.3130.0000.0000.0000.000
5X5GLY0-0.040-0.0159.072-0.155-0.1550.0000.0000.0000.000
6X6LYS10.8460.9327.5220.4320.4320.0000.0000.0000.000
7X7ASN0-0.021-0.01610.7610.1540.1540.0000.0000.0000.000
8X8VAL0-0.012-0.0158.713-0.002-0.0020.0000.0000.0000.000
9X9TRP00.0280.00912.188-0.046-0.0460.0000.0000.0000.000
10X10VAL00.006-0.00212.0780.0830.0830.0000.0000.0000.000
11X11THR00.0320.01615.077-0.063-0.0630.0000.0000.0000.000
12X12GLY0-0.013-0.01717.6370.0510.0510.0000.0000.0000.000
13X13ALA0-0.031-0.00616.9320.0220.0220.0000.0000.0000.000
14X14GLY00.0410.02017.9820.0050.0050.0000.0000.0000.000
15X15LYS10.8190.89419.834-0.431-0.4310.0000.0000.0000.000
16X16GLY00.0120.00318.3880.0410.0410.0000.0000.0000.000
17X17ILE00.0310.00713.5970.0430.0430.0000.0000.0000.000
18X18GLY00.0640.04913.7910.1510.1510.0000.0000.0000.000
19X19TYR0-0.0130.00714.4080.0950.0950.0000.0000.0000.000
20X20ALA00.0200.00312.2370.0490.0490.0000.0000.0000.000
21X21THR0-0.029-0.0409.3900.2320.2320.0000.0000.0000.000
22X22ALA0-0.019-0.0059.6550.2310.2310.0000.0000.0000.000
23X23LEU00.0350.01311.0720.0220.0220.0000.0000.0000.000
24X24ALA0-0.019-0.0046.2750.0790.0790.0000.0000.0000.000
25X25PHE00.001-0.0135.7710.7400.7400.0000.0000.0000.000
26X26VAL0-0.0070.0107.159-0.015-0.0150.0000.0000.0000.000
27X27GLU-1-0.927-0.9687.0990.8430.8430.0000.0000.0000.000
28X28ALA0-0.057-0.0173.5480.0510.5730.032-0.200-0.3540.001
29X29GLY00.0180.0015.224-0.941-0.957-0.001-0.0050.0220.000
30X30ALA0-0.020-0.0037.537-0.325-0.3250.0000.0000.0000.000
31X31LYS10.9250.9579.231-0.310-0.3100.0000.0000.0000.000
32X32VAL0-0.019-0.00510.354-0.008-0.0080.0000.0000.0000.000
33X33THR0-0.055-0.02012.930-0.110-0.1100.0000.0000.0000.000
34X34GLY00.002-0.00615.8280.0710.0710.0000.0000.0000.000
35X35PHE00.014-0.00217.329-0.055-0.0550.0000.0000.0000.000
36X36ASP-1-0.792-0.90220.3810.4530.4530.0000.0000.0000.000
37X37GLN0-0.043-0.02923.075-0.017-0.0170.0000.0000.0000.000
38X38ALA00.0010.00126.029-0.024-0.0240.0000.0000.0000.000
39X39PHE0-0.036-0.01620.2460.0310.0310.0000.0000.0000.000
40X40THR0-0.012-0.02025.138-0.024-0.0240.0000.0000.0000.000
41X41GLN0-0.067-0.01720.757-0.004-0.0040.0000.0000.0000.000
42X42GLU-1-0.873-0.93925.8440.1930.1930.0000.0000.0000.000
43X43GLN0-0.040-0.02221.943-0.015-0.0150.0000.0000.0000.000
44X44TYR00.0200.00518.8590.0040.0040.0000.0000.0000.000
45X45PRO0-0.0040.00514.756-0.036-0.0360.0000.0000.0000.000
46X46PHE00.0260.00814.2090.0410.0410.0000.0000.0000.000
47X47ALA00.0170.01216.141-0.052-0.0520.0000.0000.0000.000
48X48THR0-0.014-0.00118.6780.0350.0350.0000.0000.0000.000
49X49GLU-1-0.793-0.87921.0240.2130.2130.0000.0000.0000.000
50X50VAL0-0.037-0.02623.0620.0230.0230.0000.0000.0000.000
51X51MET00.0020.00622.289-0.022-0.0220.0000.0000.0000.000
52X52ASP-1-0.838-0.90624.8840.2760.2760.0000.0000.0000.000
53X53VAL0-0.0100.00522.531-0.012-0.0120.0000.0000.0000.000
54X54ALA00.0100.00825.903-0.010-0.0100.0000.0000.0000.000
55X55ASP-1-0.836-0.90229.1790.1600.1600.0000.0000.0000.000
56X56ALA00.0340.00329.9840.0070.0070.0000.0000.0000.000
57X57ALA00.0080.01030.825-0.002-0.0020.0000.0000.0000.000
58X58GLN0-0.019-0.00728.8070.0100.0100.0000.0000.0000.000
59X59VAL0-0.004-0.02225.2020.0070.0070.0000.0000.0000.000
60X60ALA0-0.0050.00226.8690.0050.0050.0000.0000.0000.000
61X61GLN0-0.047-0.02628.738-0.007-0.0070.0000.0000.0000.000
62X62VAL00.0130.01623.996-0.004-0.0040.0000.0000.0000.000
63X63CYS0-0.021-0.01623.8020.0140.0140.0000.0000.0000.000
64X64GLN0-0.054-0.04524.805-0.013-0.0130.0000.0000.0000.000
65X65ARG10.7950.89424.737-0.214-0.2140.0000.0000.0000.000
66X66LEU00.0170.00921.052-0.004-0.0040.0000.0000.0000.000
67X67LEU0-0.080-0.04921.561-0.002-0.0020.0000.0000.0000.000
68X68ALA0-0.067-0.01923.960-0.018-0.0180.0000.0000.0000.000
69X69GLU-1-0.881-0.94523.7340.1580.1580.0000.0000.0000.000
70X70THR0-0.074-0.04218.3280.0060.0060.0000.0000.0000.000
71X71GLU-1-0.944-0.96019.2250.0120.0120.0000.0000.0000.000
72X72ARG10.8330.89113.935-0.036-0.0360.0000.0000.0000.000
73X73LEU0-0.0160.00014.6900.0260.0260.0000.0000.0000.000
74X74ASP-1-0.795-0.86410.9810.0790.0790.0000.0000.0000.000
75X75ALA00.0150.0049.8920.0240.0240.0000.0000.0000.000
76X76LEU00.0080.02011.910-0.007-0.0070.0000.0000.0000.000
77X77VAL00.010-0.00110.9920.0380.0380.0000.0000.0000.000
78X78ASN0-0.023-0.01314.079-0.072-0.0720.0000.0000.0000.000
79X79ALA00.0280.00314.7830.0070.0070.0000.0000.0000.000
80X80ALA0-0.0170.01016.893-0.032-0.0320.0000.0000.0000.000
81X81GLY0-0.002-0.02220.6430.0040.0040.0000.0000.0000.000
82X82ILE0-0.043-0.01023.2970.0010.0010.0000.0000.0000.000
83X83LEU00.0040.00325.970-0.001-0.0010.0000.0000.0000.000
84X84ARG10.8640.92627.658-0.227-0.2270.0000.0000.0000.000
85X85MET0-0.025-0.01930.2820.0080.0080.0000.0000.0000.000
86X86GLY00.0450.02333.259-0.007-0.0070.0000.0000.0000.000
87X87ALA00.0270.02336.1600.0050.0050.0000.0000.0000.000
88X88THR00.008-0.01237.4730.0050.0050.0000.0000.0000.000
89X89ASP-1-0.915-0.95238.7120.1100.1100.0000.0000.0000.000
90X90GLN0-0.047-0.02440.7710.0000.0000.0000.0000.0000.000
91X91LEU0-0.0360.00234.4850.0020.0020.0000.0000.0000.000
92X92SER00.004-0.02638.323-0.007-0.0070.0000.0000.0000.000
93X93LYS10.9940.96338.322-0.098-0.0980.0000.0000.0000.000
94X94GLU-1-0.852-0.90537.3490.1510.1510.0000.0000.0000.000
95X95ASP-1-0.774-0.86134.6890.1780.1780.0000.0000.0000.000
96X96TRP0-0.0030.01633.5950.0150.0150.0000.0000.0000.000
97X97GLN00.008-0.00433.5550.0130.0130.0000.0000.0000.000
98X98GLN00.0060.00032.0640.0210.0210.0000.0000.0000.000
99X99THR0-0.044-0.04228.9590.0200.0200.0000.0000.0000.000
100X100PHE00.004-0.01428.5990.0200.0200.0000.0000.0000.000
101X101ALA00.0060.01929.2040.0090.0090.0000.0000.0000.000
102X102VAL00.0210.00725.0330.0110.0110.0000.0000.0000.000
103X103ASN0-0.063-0.03524.3280.0480.0480.0000.0000.0000.000
104X104VAL0-0.020-0.01024.2480.0150.0150.0000.0000.0000.000
105X105GLY00.0210.01026.2380.0010.0010.0000.0000.0000.000
106X106GLY00.0410.01224.969-0.003-0.0030.0000.0000.0000.000
107X107ALA00.0090.00421.6870.0080.0080.0000.0000.0000.000
108X108PHE00.000-0.00323.009-0.006-0.0060.0000.0000.0000.000
109X109ASN0-0.035-0.02626.087-0.025-0.0250.0000.0000.0000.000
110X110LEU00.0420.01220.576-0.010-0.0100.0000.0000.0000.000
111X111PHE0-0.0110.00418.963-0.003-0.0030.0000.0000.0000.000
112X112GLN0-0.008-0.00423.500-0.028-0.0280.0000.0000.0000.000
113X113GLN00.0000.01724.730-0.026-0.0260.0000.0000.0000.000
114X114THR0-0.010-0.01720.161-0.005-0.0050.0000.0000.0000.000
115X115MET0-0.0250.00122.219-0.008-0.0080.0000.0000.0000.000
116X116ASN00.0420.01623.398-0.020-0.0200.0000.0000.0000.000
117X117GLN00.0240.03420.102-0.032-0.0320.0000.0000.0000.000
118X118PHE00.021-0.00515.800-0.025-0.0250.0000.0000.0000.000
119X119ARG10.8790.91620.751-0.140-0.1400.0000.0000.0000.000
120X120ARG10.8190.91323.653-0.119-0.1190.0000.0000.0000.000
121X121GLN0-0.023-0.02416.640-0.026-0.0260.0000.0000.0000.000
122X122ARG10.8520.94019.694-0.034-0.0340.0000.0000.0000.000
123X123GLY00.0920.05516.297-0.043-0.0430.0000.0000.0000.000
124X124GLY00.0060.00713.0310.0310.0310.0000.0000.0000.000
125X125ALA0-0.025-0.00910.293-0.034-0.0340.0000.0000.0000.000
126X126ILE00.0290.01112.2540.0400.0400.0000.0000.0000.000
127X127VAL0-0.0160.0069.583-0.013-0.0130.0000.0000.0000.000
128X128THR00.0170.00313.047-0.041-0.0410.0000.0000.0000.000
129X129VAL00.0050.01014.3390.0050.0050.0000.0000.0000.000
130X130ALA00.0590.03016.720-0.067-0.0670.0000.0000.0000.000
131X131SER0-0.024-0.03019.6580.0020.0020.0000.0000.0000.000
132X132ASP-1-0.757-0.87020.7850.2950.2950.0000.0000.0000.000
133X133ALA00.004-0.00122.292-0.031-0.0310.0000.0000.0000.000
134X134ALA0-0.060-0.01422.729-0.021-0.0210.0000.0000.0000.000
135X135HIS10.7330.85219.322-0.324-0.3240.0000.0000.0000.000
136X136THR00.0190.01224.608-0.023-0.0230.0000.0000.0000.000
137X137PRO00.0190.01427.7180.0130.0130.0000.0000.0000.000
138X138ARG10.8420.89824.264-0.282-0.2820.0000.0000.0000.000
139X139ILE00.0620.02030.214-0.001-0.0010.0000.0000.0000.000
140X140GLY0-0.0040.00932.3640.0080.0080.0000.0000.0000.000
141X141MET0-0.012-0.00725.9060.0040.0040.0000.0000.0000.000
142X142SER00.0110.00330.1130.0140.0140.0000.0000.0000.000
143X143ALA00.0480.02331.3960.0050.0050.0000.0000.0000.000
144X144TYR00.0080.01522.2920.0090.0090.0000.0000.0000.000
145X145GLY00.0700.03226.4620.0170.0170.0000.0000.0000.000
146X146ALA00.0030.00126.9010.0070.0070.0000.0000.0000.000
147X147SER0-0.042-0.02127.3720.0070.0070.0000.0000.0000.000
148X148LYS10.8740.93220.488-0.420-0.4200.0000.0000.0000.000
149X149ALA00.0100.00723.1120.0180.0180.0000.0000.0000.000
150X150ALA0-0.024-0.00925.066-0.004-0.0040.0000.0000.0000.000
151X151LEU0-0.034-0.00620.310-0.004-0.0040.0000.0000.0000.000
152X152LYS10.8850.93519.853-0.274-0.2740.0000.0000.0000.000
153X153SER0-0.015-0.00821.637-0.007-0.0070.0000.0000.0000.000
154X154LEU00.0200.02524.046-0.013-0.0130.0000.0000.0000.000
155X155ALA00.0160.00118.577-0.009-0.0090.0000.0000.0000.000
156X156LEU0-0.0100.00218.209-0.002-0.0020.0000.0000.0000.000
157X157SER0-0.035-0.02320.827-0.029-0.0290.0000.0000.0000.000
158X158VAL00.005-0.01020.503-0.018-0.0180.0000.0000.0000.000
159X159GLY00.030-0.01819.102-0.008-0.0080.0000.0000.0000.000
160X160LEU0-0.036-0.01519.750-0.025-0.0250.0000.0000.0000.000
161X161GLU-1-0.892-0.94422.6500.1140.1140.0000.0000.0000.000
162X162LEU0-0.030-0.02119.571-0.017-0.0170.0000.0000.0000.000
163X163ALA00.0350.03019.022-0.015-0.0150.0000.0000.0000.000
164X164GLY0-0.020-0.00920.091-0.025-0.0250.0000.0000.0000.000
165X165SER0-0.088-0.04321.095-0.013-0.0130.0000.0000.0000.000
166X166GLY00.0260.01218.008-0.002-0.0020.0000.0000.0000.000
167X167VAL0-0.045-0.01415.414-0.012-0.0120.0000.0000.0000.000
168X168ARG10.8090.9147.627-0.130-0.1300.0000.0000.0000.000
169X169CYS0-0.0380.00813.0020.1030.1030.0000.0000.0000.000
170X170ASN0-0.009-0.02310.961-0.107-0.1070.0000.0000.0000.000
171X171VAL0-0.037-0.02413.8310.0310.0310.0000.0000.0000.000
172X172VAL00.0380.02211.0400.0430.0430.0000.0000.0000.000
173X173SER0-0.022-0.05114.203-0.062-0.0620.0000.0000.0000.000
174X174PRO0-0.0060.00515.473-0.028-0.0280.0000.0000.0000.000
175X175GLY00.0610.03817.496-0.061-0.0610.0000.0000.0000.000
176X176SER0-0.012-0.00619.9710.0220.0220.0000.0000.0000.000
177X177THR00.0310.02618.772-0.001-0.0010.0000.0000.0000.000
178X214ARG10.9450.95816.087-0.453-0.4530.0000.0000.0000.000
179X215PRO00.004-0.00914.2550.0850.0850.0000.0000.0000.000
180X216GLN00.0780.0319.4710.0290.0290.0000.0000.0000.000
181X217GLU-1-0.836-0.8879.4151.3071.3070.0000.0000.0000.000
182X218ILE0-0.051-0.0229.8960.1820.1820.0000.0000.0000.000
183X219ALA00.0260.0268.7640.1590.1590.0000.0000.0000.000
184X220ASN0-0.004-0.0205.5530.6590.758-0.001-0.007-0.0910.000
185X221THR0-0.040-0.0255.1071.1531.3720.000-0.021-0.1990.000
186X222ILE0-0.023-0.0207.245-0.150-0.1500.0000.0000.0000.000
187X223LEU00.0070.0062.772-1.795-0.9361.953-0.704-2.1090.001
188X224PHE00.0140.0052.411-1.2750.5291.275-0.892-2.187-0.002
189X225LEU0-0.0150.0013.490-1.230-1.4060.0040.327-0.1550.000
190X226ALA00.0290.0146.359-0.548-0.5480.0000.0000.0000.000
191X227SER0-0.005-0.0092.483-3.296-2.5762.789-1.206-2.302-0.009
192X228ASP-1-0.828-0.9074.373-0.878-0.746-0.001-0.026-0.1050.000
193X229LEU0-0.0010.0002.514-0.340-0.0821.167-0.222-1.203-0.001
194X230ALA0-0.0210.0025.3620.2620.2620.0000.0000.0000.000
195X231SER0-0.022-0.0246.9830.2430.2430.0000.0000.0000.000
196X232HIS0-0.010-0.0059.9030.1220.1220.0000.0000.0000.000
197X233ILE0-0.045-0.0108.0620.0380.0380.0000.0000.0000.000
198X234THR00.0320.01511.5250.0870.0870.0000.0000.0000.000
199X235LEU0-0.016-0.00514.234-0.026-0.0260.0000.0000.0000.000
200X236GLN00.0320.02413.278-0.003-0.0030.0000.0000.0000.000
201X237ASP-1-0.773-0.87014.6450.4710.4710.0000.0000.0000.000
202X238ILE00.0140.0249.440-0.054-0.0540.0000.0000.0000.000
203X239VAL0-0.006-0.00113.6730.0660.0660.0000.0000.0000.000
204X240VAL0-0.012-0.00712.5170.0020.0020.0000.0000.0000.000
205X241ASP-1-0.777-0.91215.7760.3400.3400.0000.0000.0000.000
206X242GLY0-0.0240.00318.428-0.035-0.0350.0000.0000.0000.000
207X243GLY00.0280.01720.043-0.032-0.0320.0000.0000.0000.000
208X244SER0-0.031-0.01821.500-0.035-0.0350.0000.0000.0000.000
209X245THR0-0.071-0.04321.800-0.019-0.0190.0000.0000.0000.000
210X246LEU0-0.028-0.01124.355-0.016-0.0160.0000.0000.0000.000
211X247GLY00.0270.02921.519-0.017-0.0170.0000.0000.0000.000
212X248ALA0-0.0280.00222.2680.0330.0330.0000.0000.0000.000