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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: J3N89

Calculation Name: 3M7M-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M7M

Chain ID: X

ChEMBL ID:

UniProt ID: P0A6Y5

Base Structure: X-ray

Registration Date: 2023-06-19

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2869264.67998
FMO2-HF: Nuclear repulsion 2778686.733288
FMO2-HF: Total energy -90577.946692
FMO2-MP2: Total energy -90843.233875


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:2:ILE)


Summations of interaction energy for fragment #1(X:2: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.
-4.673-1.245-0.043-1.804-1.581-0.005
Interaction energy analysis for fragmet #1(X:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.043
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].
3X4PRO00.0280.0203.821-1.4561.972-0.043-1.804-1.581-0.005
4X5GLN0-0.020-0.0406.752-0.045-0.0450.0000.0000.0000.000
5X6HIS00.0040.0169.607-0.002-0.0020.0000.0000.0000.000
6X7ASP-1-0.767-0.82512.590-0.310-0.3100.0000.0000.0000.000
7X8GLN00.009-0.0149.328-0.111-0.1110.0000.0000.0000.000
8X9LEU0-0.041-0.01414.3410.0150.0150.0000.0000.0000.000
9X10HIS00.035-0.00711.0850.0430.0430.0000.0000.0000.000
10X11ARG10.8800.96615.5400.4100.4100.0000.0000.0000.000
11X12TYR00.0190.02416.815-0.052-0.0520.0000.0000.0000.000
12X13LEU0-0.013-0.01018.7280.0420.0420.0000.0000.0000.000
13X14PHE00.009-0.00120.950-0.024-0.0240.0000.0000.0000.000
14X15GLU-1-0.736-0.81821.621-0.256-0.2560.0000.0000.0000.000
15X16ASN0-0.102-0.05524.2870.0080.0080.0000.0000.0000.000
16X17PHE0-0.037-0.03226.2240.0100.0100.0000.0000.0000.000
17X18ALA0-0.072-0.00627.6200.0110.0110.0000.0000.0000.000
18X19VAL00.0520.01026.5170.0120.0120.0000.0000.0000.000
19X20ARG10.8930.95123.5160.2240.2240.0000.0000.0000.000
20X21GLY00.037-0.02022.2280.0250.0250.0000.0000.0000.000
21X22GLU-1-0.870-0.96319.457-0.304-0.3040.0000.0000.0000.000
22X23LEU00.0330.04815.0140.0290.0290.0000.0000.0000.000
23X24VAL0-0.025-0.03517.144-0.046-0.0460.0000.0000.0000.000
24X25THR00.0000.01615.5950.0290.0290.0000.0000.0000.000
25X26VAL00.006-0.00917.502-0.009-0.0090.0000.0000.0000.000
26X27SER00.0490.03818.9820.0340.0340.0000.0000.0000.000
27X28GLU-1-0.918-0.96415.264-0.013-0.0130.0000.0000.0000.000
28X29THR0-0.045-0.04519.2870.0350.0350.0000.0000.0000.000
29X30LEU0-0.016-0.01821.2690.0180.0180.0000.0000.0000.000
30X31GLN0-0.0140.00619.7560.0130.0130.0000.0000.0000.000
31X32GLN0-0.024-0.02719.9390.0120.0120.0000.0000.0000.000
32X33ILE0-0.047-0.01024.8590.0070.0070.0000.0000.0000.000
33X34LEU0-0.034-0.02427.4060.0040.0040.0000.0000.0000.000
34X35GLU-1-0.946-0.95725.9640.0300.0300.0000.0000.0000.000
35X36ASN0-0.063-0.03329.3480.0030.0030.0000.0000.0000.000
36X37HIS0-0.097-0.04632.1540.0020.0020.0000.0000.0000.000
37X38ASP-1-0.922-0.94234.1030.0000.0000.0000.0000.0000.000
38X39TYR0-0.006-0.00732.374-0.002-0.0020.0000.0000.0000.000
39X40PRO00.0850.03135.3620.0010.0010.0000.0000.0000.000
40X41GLN00.010-0.01631.675-0.008-0.0080.0000.0000.0000.000
41X42PRO00.1350.07434.442-0.004-0.0040.0000.0000.0000.000
42X43VAL00.006-0.01235.223-0.005-0.0050.0000.0000.0000.000
43X44LYS10.8160.92230.7770.0280.0280.0000.0000.0000.000
44X45ASN00.0160.00930.5750.0000.0000.0000.0000.0000.000
45X46VAL00.0850.04830.939-0.008-0.0080.0000.0000.0000.000
46X47LEU0-0.0110.00330.277-0.007-0.0070.0000.0000.0000.000
47X48ALA00.0230.02426.745-0.009-0.0090.0000.0000.0000.000
48X49GLU-1-0.919-0.97727.212-0.121-0.1210.0000.0000.0000.000
49X50LEU0-0.035-0.00528.764-0.009-0.0090.0000.0000.0000.000
50X51LEU0-0.040-0.00523.832-0.008-0.0080.0000.0000.0000.000
51X52VAL00.0150.01323.148-0.012-0.0120.0000.0000.0000.000
52X53ALA00.0530.01825.006-0.014-0.0140.0000.0000.0000.000
53X54THR0-0.053-0.05227.263-0.001-0.0010.0000.0000.0000.000
54X55SER0-0.0230.00021.881-0.012-0.0120.0000.0000.0000.000
55X56LEU00.0220.01622.025-0.015-0.0150.0000.0000.0000.000
56X57LEU00.0990.05724.4760.0010.0010.0000.0000.0000.000
57X58THR0-0.135-0.07324.5050.0090.0090.0000.0000.0000.000
58X59ALA0-0.084-0.01521.5110.0030.0030.0000.0000.0000.000
59X60THR0-0.086-0.07423.337-0.011-0.0110.0000.0000.0000.000
60X61LEU00.0090.01025.9950.0130.0130.0000.0000.0000.000
61X62LYS10.9020.95426.9410.1680.1680.0000.0000.0000.000
62X63PHE0-0.042-0.04327.7400.0130.0130.0000.0000.0000.000
63X64ASP-1-0.928-0.95526.818-0.145-0.1450.0000.0000.0000.000
64X65GLY0-0.041-0.01128.3860.0130.0130.0000.0000.0000.000
65X66ASP-1-0.916-0.96128.871-0.093-0.0930.0000.0000.0000.000
66X67ILE00.0140.00128.7140.0020.0020.0000.0000.0000.000
67X68THR0-0.062-0.01831.0400.0000.0000.0000.0000.0000.000
68X69VAL00.0900.05631.5380.0010.0010.0000.0000.0000.000
69X70GLN0-0.012-0.03333.5990.0010.0010.0000.0000.0000.000
70X71LEU00.0190.03535.711-0.002-0.0020.0000.0000.0000.000
71X72GLN0-0.007-0.02238.3470.0040.0040.0000.0000.0000.000
72X73GLY00.0610.00341.981-0.002-0.0020.0000.0000.0000.000
73X74ASP-1-0.938-0.89945.157-0.039-0.0390.0000.0000.0000.000
74X75GLY00.0640.06544.8240.0020.0020.0000.0000.0000.000
75X76PRO0-0.035-0.01943.7860.0020.0020.0000.0000.0000.000
76X77MET00.0030.01137.8860.0030.0030.0000.0000.0000.000
77X78ASN00.0080.02042.381-0.002-0.0020.0000.0000.0000.000
78X79LEU0-0.073-0.06038.822-0.002-0.0020.0000.0000.0000.000
79X80ALA00.0200.01335.4140.0030.0030.0000.0000.0000.000
80X81VAL0-0.0080.00533.921-0.003-0.0030.0000.0000.0000.000
81X82ILE00.0380.02727.6980.0060.0060.0000.0000.0000.000
82X83ASN0-0.088-0.06430.0670.0020.0020.0000.0000.0000.000
83X84GLY00.0760.01926.9580.0010.0010.0000.0000.0000.000
84X85ASN00.0150.01024.717-0.008-0.0080.0000.0000.0000.000
85X86ASN00.0550.02823.9620.0010.0010.0000.0000.0000.000
86X87ASN0-0.097-0.05621.426-0.035-0.0350.0000.0000.0000.000
87X88GLN00.0730.03919.7220.0040.0040.0000.0000.0000.000
88X89GLN00.0040.02721.2340.0120.0120.0000.0000.0000.000
89X90MET0-0.034-0.00723.1460.0110.0110.0000.0000.0000.000
90X91ARG10.9250.96425.0640.0610.0610.0000.0000.0000.000
91X92GLY00.0450.01827.879-0.007-0.0070.0000.0000.0000.000
92X93VAL0-0.071-0.02630.9920.0080.0080.0000.0000.0000.000
93X94ALA00.0640.03733.973-0.006-0.0060.0000.0000.0000.000
94X95ARG10.8400.93036.5030.0350.0350.0000.0000.0000.000
95X96VAL00.0320.01939.818-0.002-0.0020.0000.0000.0000.000
96X97GLN0-0.086-0.04442.0910.0050.0050.0000.0000.0000.000
97X98GLY0-0.023-0.02645.2450.0020.0020.0000.0000.0000.000
98X99GLU-1-0.944-0.96145.669-0.017-0.0170.0000.0000.0000.000
99X100ILE0-0.026-0.03840.772-0.003-0.0030.0000.0000.0000.000
100X101PRO0-0.025-0.01443.2310.0010.0010.0000.0000.0000.000
101X102GLU-1-0.887-0.94641.379-0.027-0.0270.0000.0000.0000.000
102X103ASN0-0.059-0.01539.562-0.001-0.0010.0000.0000.0000.000
103X104ALA0-0.051-0.02840.231-0.002-0.0020.0000.0000.0000.000
104X105ASP-1-0.751-0.86338.833-0.063-0.0630.0000.0000.0000.000
105X106LEU00.0640.03036.8790.0030.0030.0000.0000.0000.000
106X107LYS10.8920.94539.5740.0680.0680.0000.0000.0000.000
107X108THR0-0.085-0.04242.9410.0040.0040.0000.0000.0000.000
108X109LEU0-0.080-0.05337.5980.0030.0030.0000.0000.0000.000
109X110VAL0-0.034-0.01239.8150.0020.0020.0000.0000.0000.000
110X111GLY0-0.082-0.07342.7650.0010.0010.0000.0000.0000.000
111X112ASN0-0.001-0.03945.338-0.003-0.0030.0000.0000.0000.000
112X113GLY0-0.055-0.03944.306-0.001-0.0010.0000.0000.0000.000
113X114TYR00.0020.01042.1440.0000.0000.0000.0000.0000.000
114X115VAL00.0330.01535.6450.0010.0010.0000.0000.0000.000
115X116VAL0-0.119-0.04938.1710.0000.0000.0000.0000.0000.000
116X117ILE00.0320.01133.218-0.002-0.0020.0000.0000.0000.000
117X118THR0-0.041-0.00735.4940.0030.0030.0000.0000.0000.000
118X119ILE00.0370.01432.128-0.003-0.0030.0000.0000.0000.000
119X120THR0-0.112-0.09033.9750.0080.0080.0000.0000.0000.000
120X121PRO00.0280.03732.6300.0010.0010.0000.0000.0000.000
121X122SER00.032-0.03231.8650.0050.0050.0000.0000.0000.000
122X123GLU-1-1.028-0.98433.982-0.062-0.0620.0000.0000.0000.000
123X124GLY00.0660.03336.777-0.002-0.0020.0000.0000.0000.000
124X125GLU-1-1.007-0.99038.716-0.074-0.0740.0000.0000.0000.000
125X126ARG10.9170.95237.8920.0590.0590.0000.0000.0000.000
126X127TYR0-0.002-0.00935.808-0.001-0.0010.0000.0000.0000.000
127X128GLN00.0240.01137.482-0.004-0.0040.0000.0000.0000.000
128X129GLY00.0500.03237.8820.0000.0000.0000.0000.0000.000
129X130VAL0-0.068-0.03438.8750.0010.0010.0000.0000.0000.000
130X131VAL00.0450.03237.4360.0020.0020.0000.0000.0000.000
131X132GLY00.0380.00740.5490.0020.0020.0000.0000.0000.000
132X133LEU0-0.006-0.00339.421-0.004-0.0040.0000.0000.0000.000
133X134GLU-1-0.912-0.95542.075-0.060-0.0600.0000.0000.0000.000
134X135GLY00.0030.00439.7710.0020.0020.0000.0000.0000.000
135X136ASP-1-0.947-0.99738.439-0.081-0.0810.0000.0000.0000.000
136X137THR0-0.0020.02233.224-0.001-0.0010.0000.0000.0000.000
137X138LEU00.0430.06031.531-0.002-0.0020.0000.0000.0000.000
138X139ALA00.019-0.02530.350-0.003-0.0030.0000.0000.0000.000
139X140ALA00.0240.01632.231-0.003-0.0030.0000.0000.0000.000
140X141ASP-1-0.852-0.94735.303-0.087-0.0870.0000.0000.0000.000
141X142LEU00.0060.00731.4930.0000.0000.0000.0000.0000.000
142X143GLU-1-0.798-0.88332.142-0.142-0.1420.0000.0000.0000.000
143X144ASP-1-0.922-0.97534.453-0.086-0.0860.0000.0000.0000.000
144X145TYR0-0.039-0.02636.0470.0060.0060.0000.0000.0000.000
145X146PHE0-0.028-0.06132.1470.0010.0010.0000.0000.0000.000
146X147MET0-0.0210.01436.2890.0000.0000.0000.0000.0000.000
147X148ARG10.8370.91838.5800.0850.0850.0000.0000.0000.000
148X149SER0-0.035-0.02440.2880.0020.0020.0000.0000.0000.000
149X150GLU-1-0.944-0.96035.708-0.107-0.1070.0000.0000.0000.000
150X151GLU-1-1.011-0.97738.387-0.089-0.0890.0000.0000.0000.000
151X152LEU0-0.057-0.02031.662-0.003-0.0030.0000.0000.0000.000
152X153PRO0-0.011-0.00233.801-0.001-0.0010.0000.0000.0000.000
153X154THR00.019-0.01429.675-0.015-0.0150.0000.0000.0000.000
154X155ARG10.8400.90429.0750.1560.1560.0000.0000.0000.000
155X156LEU00.0130.01827.529-0.017-0.0170.0000.0000.0000.000
156X157PHE00.003-0.01224.7100.0140.0140.0000.0000.0000.000
157X158ILE00.0230.02424.691-0.021-0.0210.0000.0000.0000.000
158X159ARG10.8280.92323.3950.1910.1910.0000.0000.0000.000
159X160THR00.0290.00524.234-0.008-0.0080.0000.0000.0000.000
160X161GLY0-0.033-0.01725.0980.0060.0060.0000.0000.0000.000
161X162ASP-1-0.901-0.95324.764-0.050-0.0500.0000.0000.0000.000
162X163VAL00.0170.01118.258-0.005-0.0050.0000.0000.0000.000
163X164ASP-1-0.925-0.95618.6600.0530.0530.0000.0000.0000.000
164X165GLY0-0.094-0.04222.2100.0150.0150.0000.0000.0000.000
165X166LYS10.8880.94420.412-0.063-0.0630.0000.0000.0000.000
166X167PRO00.0470.02923.814-0.010-0.0100.0000.0000.0000.000
167X168ALA0-0.028-0.03720.867-0.001-0.0010.0000.0000.0000.000
168X169ALA00.029-0.01921.6160.0080.0080.0000.0000.0000.000
169X170GLY00.0660.02220.170-0.022-0.0220.0000.0000.0000.000
170X171GLY0-0.054-0.04020.4590.0320.0320.0000.0000.0000.000
171X172MET00.005-0.00220.201-0.042-0.0420.0000.0000.0000.000
172X173LEU0-0.0370.02622.4760.0300.0300.0000.0000.0000.000
173X174LEU00.0130.01423.817-0.024-0.0240.0000.0000.0000.000
174X175GLN0-0.007-0.01726.4420.0040.0040.0000.0000.0000.000
175X176VAL0-0.0130.01928.580-0.010-0.0100.0000.0000.0000.000
176X177MET0-0.0190.00327.101-0.006-0.0060.0000.0000.0000.000
177X178PRO00.0420.03530.0260.0100.0100.0000.0000.0000.000
178X179ALA0-0.045-0.05133.285-0.001-0.0010.0000.0000.0000.000
179X180GLN00.013-0.00128.9100.0010.0010.0000.0000.0000.000
180X181ASN0-0.087-0.04734.0970.0020.0020.0000.0000.0000.000
181X182ALA00.0560.04431.8260.0040.0040.0000.0000.0000.000
182X183GLN0-0.050-0.02633.7290.0110.0110.0000.0000.0000.000
183X184GLN00.0340.02834.068-0.009-0.0090.0000.0000.0000.000
184X185ASP-1-0.915-0.96534.330-0.123-0.1230.0000.0000.0000.000
185X186ASP-1-0.832-0.93130.363-0.157-0.1570.0000.0000.0000.000
186X187PHE0-0.0430.00029.736-0.013-0.0130.0000.0000.0000.000
187X188ASP-1-0.843-0.91830.447-0.136-0.1360.0000.0000.0000.000
188X189HIS0-0.0270.00430.294-0.004-0.0040.0000.0000.0000.000
189X190LEU00.0750.02624.726-0.009-0.0090.0000.0000.0000.000
190X191ALA0-0.030-0.03726.803-0.013-0.0130.0000.0000.0000.000
191X192THR0-0.077-0.05028.5350.0020.0020.0000.0000.0000.000
192X193LEU0-0.023-0.00423.7140.0020.0020.0000.0000.0000.000
193X194THR0-0.0320.01223.323-0.012-0.0120.0000.0000.0000.000
194X195GLU-1-0.925-0.94924.886-0.148-0.1480.0000.0000.0000.000
195X196THR0-0.172-0.12425.0210.0030.0030.0000.0000.0000.000
196X197ILE0-0.043-0.00319.6480.0010.0010.0000.0000.0000.000
197X198LYS10.9070.94222.2490.1920.1920.0000.0000.0000.000
198X199THR00.014-0.01621.484-0.015-0.0150.0000.0000.0000.000
199X200GLU-1-0.907-0.95619.978-0.174-0.1740.0000.0000.0000.000
200X201GLU-1-0.813-0.92518.017-0.275-0.2750.0000.0000.0000.000
201X202LEU00.003-0.00216.782-0.036-0.0360.0000.0000.0000.000
202X203LEU0-0.073-0.02516.994-0.031-0.0310.0000.0000.0000.000
203X204THR0-0.0260.00415.585-0.010-0.0100.0000.0000.0000.000
204X205LEU0-0.047-0.00913.168-0.019-0.0190.0000.0000.0000.000
205X206PRO00.0170.0198.437-0.030-0.0300.0000.0000.0000.000
206X207ALA00.0920.05310.4190.0000.0000.0000.0000.0000.000
207X208ASN00.0650.0138.086-0.049-0.0490.0000.0000.0000.000
208X209GLU-1-0.888-0.92510.754-0.457-0.4570.0000.0000.0000.000
209X210VAL0-0.0150.00012.0440.1080.1080.0000.0000.0000.000
210X211LEU0-0.002-0.01113.8470.0590.0590.0000.0000.0000.000
211X212TRP0-0.0250.00113.4000.0720.0720.0000.0000.0000.000
212X213ARG10.7990.86315.4170.4100.4100.0000.0000.0000.000
213X214LEU0-0.0420.00417.7570.0440.0440.0000.0000.0000.000
214X215TYR00.053-0.00318.7280.0240.0240.0000.0000.0000.000
215X216HIS10.8480.92717.6870.3030.3030.0000.0000.0000.000
216X217GLU-1-1.035-1.00418.618-0.216-0.2160.0000.0000.0000.000
217X218GLU-1-0.894-0.95320.588-0.229-0.2290.0000.0000.0000.000
218X219GLU-1-1.016-0.98220.039-0.341-0.3410.0000.0000.0000.000
219X220VAL0-0.004-0.02416.4850.0080.0080.0000.0000.0000.000
220X221THR0-0.077-0.07417.220-0.038-0.0380.0000.0000.0000.000
221X222VAL0-0.041-0.03312.2860.0150.0150.0000.0000.0000.000
222X223TYR0-0.055-0.02314.038-0.014-0.0140.0000.0000.0000.000
223X224ASP-1-0.923-0.97712.004-0.794-0.7940.0000.0000.0000.000
224X225PRO0-0.072-0.0209.5880.0810.0810.0000.0000.0000.000
225X226GLN00.0680.02212.8930.0490.0490.0000.0000.0000.000
226X227ASP-1-0.858-0.92213.296-0.455-0.4550.0000.0000.0000.000
227X228VAL0-0.046-0.01715.3290.0360.0360.0000.0000.0000.000
228X229GLU-1-0.877-0.93917.376-0.129-0.1290.0000.0000.0000.000
229X230PHE00.0110.02119.7800.0030.0030.0000.0000.0000.000
230X231LYS10.9640.99022.8060.0670.0670.0000.0000.0000.000
231X232CYS0-0.060-0.03425.4870.0050.0050.0000.0000.0000.000