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: LJY59

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2861360.632513
FMO2-HF: Nuclear repulsion 2770775.801083
FMO2-HF: Total energy -90584.831431
FMO2-MP2: Total energy -90848.818811


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.
-2.932-0.772-0.016-1.016-1.128-0.002
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 : -0.041 / q_NPA : -0.041
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].
3X4PRO0-0.0020.0133.805-0.2241.936-0.016-1.016-1.128-0.002
4X5GLN00.005-0.0186.366-0.340-0.3400.0000.0000.0000.000
5X6HIS00.0010.0198.862-0.057-0.0570.0000.0000.0000.000
6X7ASP-1-0.748-0.84812.363-0.239-0.2390.0000.0000.0000.000
7X8GLN0-0.034-0.0228.336-0.106-0.1060.0000.0000.0000.000
8X9LEU00.0050.00914.1920.0360.0360.0000.0000.0000.000
9X10HIS00.004-0.01510.7980.0270.0270.0000.0000.0000.000
10X11ARG10.8670.94115.3820.3550.3550.0000.0000.0000.000
11X12TYR00.0260.00116.671-0.055-0.0550.0000.0000.0000.000
12X13LEU0-0.029-0.01018.7340.0370.0370.0000.0000.0000.000
13X14PHE00.0470.01821.069-0.020-0.0200.0000.0000.0000.000
14X15GLU-1-0.816-0.88721.779-0.233-0.2330.0000.0000.0000.000
15X16ASN0-0.120-0.07224.4590.0170.0170.0000.0000.0000.000
16X17PHE00.0070.00926.3530.0120.0120.0000.0000.0000.000
17X18ALA0-0.033-0.00327.7510.0090.0090.0000.0000.0000.000
18X19VAL00.0330.02625.7730.0100.0100.0000.0000.0000.000
19X20ARG10.7840.87823.2370.2010.2010.0000.0000.0000.000
20X21GLY00.027-0.00322.1220.0210.0210.0000.0000.0000.000
21X22GLU-1-0.812-0.90119.281-0.280-0.2800.0000.0000.0000.000
22X23LEU0-0.0280.00215.3430.0280.0280.0000.0000.0000.000
23X24VAL00.000-0.00517.415-0.034-0.0340.0000.0000.0000.000
24X25THR0-0.0080.00215.8140.0040.0040.0000.0000.0000.000
25X26VAL0-0.017-0.02118.031-0.006-0.0060.0000.0000.0000.000
26X27SER00.0700.02918.2390.0290.0290.0000.0000.0000.000
27X28GLU-1-0.922-0.96314.9640.0560.0560.0000.0000.0000.000
28X29THR0-0.038-0.03818.7740.0260.0260.0000.0000.0000.000
29X30LEU0-0.011-0.00221.0890.0120.0120.0000.0000.0000.000
30X31GLN0-0.022-0.01319.1890.0150.0150.0000.0000.0000.000
31X32GLN0-0.032-0.03119.0520.0120.0120.0000.0000.0000.000
32X33ILE0-0.047-0.01124.3200.0020.0020.0000.0000.0000.000
33X34LEU0-0.057-0.03526.8650.0020.0020.0000.0000.0000.000
34X35GLU-1-0.890-0.92125.3450.0540.0540.0000.0000.0000.000
35X36ASN0-0.105-0.06928.919-0.002-0.0020.0000.0000.0000.000
36X37HIS0-0.070-0.02031.300-0.004-0.0040.0000.0000.0000.000
37X38ASP-1-0.911-0.95633.8870.0150.0150.0000.0000.0000.000
38X39TYR0-0.003-0.01532.496-0.006-0.0060.0000.0000.0000.000
39X40PRO00.0350.03035.2050.0020.0020.0000.0000.0000.000
40X41GLN00.0680.02230.9240.0000.0000.0000.0000.0000.000
41X42PRO00.0730.04133.955-0.004-0.0040.0000.0000.0000.000
42X43VAL00.0190.00934.907-0.005-0.0050.0000.0000.0000.000
43X44LYS10.8570.92230.527-0.002-0.0020.0000.0000.0000.000
44X45ASN0-0.012-0.00130.2820.0000.0000.0000.0000.0000.000
45X46VAL00.0740.02930.846-0.008-0.0080.0000.0000.0000.000
46X47LEU0-0.037-0.01130.104-0.006-0.0060.0000.0000.0000.000
47X48ALA00.0090.00226.719-0.007-0.0070.0000.0000.0000.000
48X49GLU-1-0.859-0.94427.051-0.093-0.0930.0000.0000.0000.000
49X50LEU00.0160.00028.907-0.010-0.0100.0000.0000.0000.000
50X51LEU0-0.0410.01223.497-0.007-0.0070.0000.0000.0000.000
51X52VAL0-0.0030.00523.342-0.013-0.0130.0000.0000.0000.000
52X53ALA00.0170.01125.096-0.014-0.0140.0000.0000.0000.000
53X54THR0-0.020-0.04027.205-0.003-0.0030.0000.0000.0000.000
54X55SER0-0.035-0.00921.743-0.012-0.0120.0000.0000.0000.000
55X56LEU00.0400.01722.197-0.013-0.0130.0000.0000.0000.000
56X57LEU00.0270.00924.561-0.005-0.0050.0000.0000.0000.000
57X58THR0-0.052-0.03924.7180.0050.0050.0000.0000.0000.000
58X59ALA0-0.055-0.01721.680-0.003-0.0030.0000.0000.0000.000
59X60THR00.003-0.00923.571-0.007-0.0070.0000.0000.0000.000
60X61LEU00.0050.01726.2950.0040.0040.0000.0000.0000.000
61X62LYS10.9410.95926.8800.1580.1580.0000.0000.0000.000
62X63PHE0-0.037-0.01927.5880.0120.0120.0000.0000.0000.000
63X64ASP-1-0.823-0.90227.189-0.123-0.1230.0000.0000.0000.000
64X65GLY00.0300.03528.4270.0110.0110.0000.0000.0000.000
65X66ASP-1-0.925-0.97328.935-0.080-0.0800.0000.0000.0000.000
66X67ILE0-0.014-0.01128.5930.0020.0020.0000.0000.0000.000
67X68THR0-0.079-0.03431.1830.0020.0020.0000.0000.0000.000
68X69VAL00.0560.03530.870-0.002-0.0020.0000.0000.0000.000
69X70GLN0-0.040-0.02233.4120.0020.0020.0000.0000.0000.000
70X71LEU00.0690.05435.6810.0000.0000.0000.0000.0000.000
71X72GLN0-0.020-0.02638.2000.0020.0020.0000.0000.0000.000
72X73GLY00.0750.02841.794-0.002-0.0020.0000.0000.0000.000
73X74ASP-1-0.888-0.92445.081-0.028-0.0280.0000.0000.0000.000
74X75GLY00.0400.03044.8620.0010.0010.0000.0000.0000.000
75X76PRO0-0.046-0.00743.8110.0020.0020.0000.0000.0000.000
76X77MET00.0150.01437.3380.0030.0030.0000.0000.0000.000
77X78ASN0-0.0010.00641.677-0.002-0.0020.0000.0000.0000.000
78X79LEU0-0.040-0.02838.360-0.002-0.0020.0000.0000.0000.000
79X80ALA00.0070.00534.8830.0040.0040.0000.0000.0000.000
80X81VAL0-0.020-0.01034.196-0.004-0.0040.0000.0000.0000.000
81X82ILE00.0380.02927.6850.0060.0060.0000.0000.0000.000
82X83ASN0-0.051-0.03429.8440.0070.0070.0000.0000.0000.000
83X84GLY00.0930.03226.8980.0020.0020.0000.0000.0000.000
84X85ASN0-0.019-0.00824.700-0.004-0.0040.0000.0000.0000.000
85X86ASN00.0510.03724.834-0.003-0.0030.0000.0000.0000.000
86X87ASN0-0.067-0.04021.674-0.030-0.0300.0000.0000.0000.000
87X88GLN00.0430.03319.4090.0080.0080.0000.0000.0000.000
88X89GLN0-0.019-0.01421.3600.0100.0100.0000.0000.0000.000
89X90MET0-0.0150.00322.7770.0090.0090.0000.0000.0000.000
90X91ARG10.8650.92824.8900.0470.0470.0000.0000.0000.000
91X92GLY00.0340.01427.658-0.006-0.0060.0000.0000.0000.000
92X93VAL0-0.064-0.01930.4160.0080.0080.0000.0000.0000.000
93X94ALA00.0760.03733.433-0.006-0.0060.0000.0000.0000.000
94X95ARG10.8140.91036.2400.0220.0220.0000.0000.0000.000
95X96VAL00.0440.02039.454-0.002-0.0020.0000.0000.0000.000
96X97GLN0-0.089-0.04542.1490.0030.0030.0000.0000.0000.000
97X98GLY0-0.029-0.02345.3960.0010.0010.0000.0000.0000.000
98X99GLU-1-0.931-0.96045.407-0.007-0.0070.0000.0000.0000.000
99X100ILE0-0.011-0.01240.340-0.003-0.0030.0000.0000.0000.000
100X101PRO0-0.016-0.00843.1190.0020.0020.0000.0000.0000.000
101X102GLU-1-0.904-0.95240.941-0.011-0.0110.0000.0000.0000.000
102X103ASN0-0.069-0.04538.475-0.002-0.0020.0000.0000.0000.000
103X104ALA0-0.031-0.00840.415-0.002-0.0020.0000.0000.0000.000
104X105ASP-1-0.758-0.86439.217-0.042-0.0420.0000.0000.0000.000
105X106LEU00.0470.01936.7540.0030.0030.0000.0000.0000.000
106X107LYS10.8510.91939.4780.0510.0510.0000.0000.0000.000
107X108THR0-0.091-0.04642.8630.0040.0040.0000.0000.0000.000
108X109LEU0-0.050-0.03737.5570.0030.0030.0000.0000.0000.000
109X110VAL0-0.043-0.02139.5480.0030.0030.0000.0000.0000.000
110X111GLY00.0280.02042.7050.0000.0000.0000.0000.0000.000
111X112ASN0-0.087-0.06645.198-0.003-0.0030.0000.0000.0000.000
112X113GLY0-0.045-0.02044.9550.0000.0000.0000.0000.0000.000
113X114TYR0-0.023-0.01642.1080.0000.0000.0000.0000.0000.000
114X115VAL00.0220.01935.2430.0020.0020.0000.0000.0000.000
115X116VAL0-0.062-0.03138.0950.0000.0000.0000.0000.0000.000
116X117ILE00.0460.01233.284-0.002-0.0020.0000.0000.0000.000
117X118THR0-0.067-0.02635.6170.0020.0020.0000.0000.0000.000
118X119ILE00.0510.01832.203-0.004-0.0040.0000.0000.0000.000
119X120THR0-0.051-0.04034.0990.0070.0070.0000.0000.0000.000
120X121PRO00.0300.01332.7620.0000.0000.0000.0000.0000.000
121X122SER0-0.058-0.05331.0970.0070.0070.0000.0000.0000.000
122X123GLU-1-1.002-0.99733.776-0.054-0.0540.0000.0000.0000.000
123X124GLY00.0080.00636.335-0.005-0.0050.0000.0000.0000.000
124X125GLU-1-0.914-0.92238.596-0.065-0.0650.0000.0000.0000.000
125X126ARG10.8380.90538.1210.0560.0560.0000.0000.0000.000
126X127TYR0-0.056-0.04435.3980.0000.0000.0000.0000.0000.000
127X128GLN00.022-0.00237.928-0.001-0.0010.0000.0000.0000.000
128X129GLY00.0670.05937.8470.0020.0020.0000.0000.0000.000
129X130VAL0-0.075-0.05738.8430.0030.0030.0000.0000.0000.000
130X131VAL00.0300.02337.5590.0000.0000.0000.0000.0000.000
131X132GLY00.0180.01440.9980.0020.0020.0000.0000.0000.000
132X133LEU00.0070.01439.509-0.003-0.0030.0000.0000.0000.000
133X134GLU-1-0.915-0.97742.223-0.048-0.0480.0000.0000.0000.000
134X135GLY0-0.017-0.00240.0070.0020.0020.0000.0000.0000.000
135X136ASP-1-0.938-0.96337.966-0.064-0.0640.0000.0000.0000.000
136X137THR0-0.045-0.03233.2350.0020.0020.0000.0000.0000.000
137X138LEU00.0240.01231.969-0.001-0.0010.0000.0000.0000.000
138X139ALA00.009-0.00230.724-0.003-0.0030.0000.0000.0000.000
139X140ALA00.0400.02132.421-0.003-0.0030.0000.0000.0000.000
140X141ASP-1-0.850-0.92635.670-0.066-0.0660.0000.0000.0000.000
141X142LEU0-0.032-0.02231.6060.0000.0000.0000.0000.0000.000
142X143GLU-1-0.790-0.87131.797-0.120-0.1200.0000.0000.0000.000
143X144ASP-1-0.828-0.89134.679-0.071-0.0710.0000.0000.0000.000
144X145TYR0-0.055-0.05336.0510.0030.0030.0000.0000.0000.000
145X146PHE00.020-0.01232.4170.0000.0000.0000.0000.0000.000
146X147MET0-0.0320.00636.116-0.001-0.0010.0000.0000.0000.000
147X148ARG10.7230.83138.4540.0710.0710.0000.0000.0000.000
148X149SER0-0.067-0.04339.6590.0050.0050.0000.0000.0000.000
149X150GLU-1-0.877-0.90735.865-0.087-0.0870.0000.0000.0000.000
150X151GLU-1-1.004-0.98637.589-0.080-0.0800.0000.0000.0000.000
151X152LEU0-0.038-0.00531.209-0.003-0.0030.0000.0000.0000.000
152X153PRO00.011-0.00133.679-0.003-0.0030.0000.0000.0000.000
153X154THR00.017-0.01029.244-0.014-0.0140.0000.0000.0000.000
154X155ARG10.7570.85528.9780.1280.1280.0000.0000.0000.000
155X156LEU0-0.004-0.01227.591-0.015-0.0150.0000.0000.0000.000
156X157PHE00.0090.00324.7930.0130.0130.0000.0000.0000.000
157X158ILE0-0.003-0.00424.685-0.016-0.0160.0000.0000.0000.000
158X159ARG10.7810.88823.0480.1490.1490.0000.0000.0000.000
159X160THR00.0260.00124.323-0.003-0.0030.0000.0000.0000.000
160X161GLY0-0.029-0.01325.3370.0010.0010.0000.0000.0000.000
161X162ASP-1-0.914-0.95124.570-0.010-0.0100.0000.0000.0000.000
162X163VAL00.0300.01218.393-0.001-0.0010.0000.0000.0000.000
163X164ASP-1-0.931-0.96618.1070.1370.1370.0000.0000.0000.000
164X165GLY0-0.057-0.02921.6950.0150.0150.0000.0000.0000.000
165X166LYS10.8510.93319.837-0.104-0.1040.0000.0000.0000.000
166X167PRO00.0380.03123.510-0.009-0.0090.0000.0000.0000.000
167X168ALA0-0.025-0.01920.8650.0010.0010.0000.0000.0000.000
168X169ALA00.023-0.01821.4650.0030.0030.0000.0000.0000.000
169X170GLY00.0720.03120.380-0.016-0.0160.0000.0000.0000.000
170X171GLY0-0.004-0.01320.7580.0290.0290.0000.0000.0000.000
171X172MET0-0.0370.00419.832-0.042-0.0420.0000.0000.0000.000
172X173LEU0-0.0340.00222.4600.0270.0270.0000.0000.0000.000
173X174LEU00.0120.01423.556-0.021-0.0210.0000.0000.0000.000
174X175GLN0-0.005-0.02826.0970.0090.0090.0000.0000.0000.000
175X176VAL00.0380.02928.052-0.012-0.0120.0000.0000.0000.000
176X177MET0-0.0160.00326.875-0.002-0.0020.0000.0000.0000.000
177X178PRO00.0340.01630.0940.0090.0090.0000.0000.0000.000
178X179ALA0-0.044-0.04233.253-0.002-0.0020.0000.0000.0000.000
179X180GLN0-0.042-0.02228.908-0.001-0.0010.0000.0000.0000.000
180X181ASN0-0.064-0.03433.6440.0010.0010.0000.0000.0000.000
181X182ALA00.0710.05931.5450.0020.0020.0000.0000.0000.000
182X183GLN0-0.067-0.03433.2910.0120.0120.0000.0000.0000.000
183X184GLN0-0.040-0.03233.752-0.005-0.0050.0000.0000.0000.000
184X185ASP-1-0.904-0.94834.390-0.103-0.1030.0000.0000.0000.000
185X186ASP-1-0.864-0.94630.378-0.137-0.1370.0000.0000.0000.000
186X187PHE0-0.032-0.00429.139-0.011-0.0110.0000.0000.0000.000
187X188ASP-1-0.802-0.90130.232-0.117-0.1170.0000.0000.0000.000
188X189HIS0-0.056-0.01330.608-0.001-0.0010.0000.0000.0000.000
189X190LEU00.0170.01124.532-0.005-0.0050.0000.0000.0000.000
190X191ALA0-0.016-0.00526.635-0.011-0.0110.0000.0000.0000.000
191X192THR0-0.022-0.03028.4850.0010.0010.0000.0000.0000.000
192X193LEU0-0.050-0.00923.7440.0020.0020.0000.0000.0000.000
193X194THR00.0230.00723.408-0.013-0.0130.0000.0000.0000.000
194X195GLU-1-0.860-0.90924.813-0.125-0.1250.0000.0000.0000.000
195X196THR0-0.120-0.06425.1910.0050.0050.0000.0000.0000.000
196X197ILE0-0.0060.01719.3920.0020.0020.0000.0000.0000.000
197X198LYS10.8310.89422.4850.1850.1850.0000.0000.0000.000
198X199THR00.019-0.01521.961-0.017-0.0170.0000.0000.0000.000
199X200GLU-1-0.863-0.90519.375-0.091-0.0910.0000.0000.0000.000
200X201GLU-1-0.769-0.87517.935-0.205-0.2050.0000.0000.0000.000
201X202LEU0-0.0080.00316.744-0.037-0.0370.0000.0000.0000.000
202X203LEU0-0.050-0.00917.811-0.010-0.0100.0000.0000.0000.000
203X204THR0-0.071-0.05215.7660.0070.0070.0000.0000.0000.000
204X205LEU0-0.047-0.00112.8920.0120.0120.0000.0000.0000.000
205X206PRO00.0000.0098.433-0.033-0.0330.0000.0000.0000.000
206X207ALA00.0930.03610.3530.0200.0200.0000.0000.0000.000
207X208ASN00.0210.0047.785-0.021-0.0210.0000.0000.0000.000
208X209GLU-1-0.833-0.90510.972-0.312-0.3120.0000.0000.0000.000
209X210VAL0-0.0090.00112.4160.0870.0870.0000.0000.0000.000
210X211LEU00.0360.01113.6960.0500.0500.0000.0000.0000.000
211X212TRP0-0.0160.00813.4960.0550.0550.0000.0000.0000.000
212X213ARG10.7590.83315.5300.3210.3210.0000.0000.0000.000
213X214LEU0-0.054-0.00918.1340.0330.0330.0000.0000.0000.000
214X215TYR00.0620.00618.3310.0220.0220.0000.0000.0000.000
215X216HIS10.7410.86817.4950.2510.2510.0000.0000.0000.000
216X217GLU-1-0.894-0.94118.626-0.201-0.2010.0000.0000.0000.000
217X218GLU-1-0.932-0.95820.796-0.197-0.1970.0000.0000.0000.000
218X219GLU-1-0.980-0.97920.127-0.292-0.2920.0000.0000.0000.000
219X220VAL0-0.029-0.02817.1780.0110.0110.0000.0000.0000.000
220X221THR0-0.058-0.04417.105-0.045-0.0450.0000.0000.0000.000
221X222VAL0-0.040-0.03012.4600.0150.0150.0000.0000.0000.000
222X223TYR0-0.048-0.02914.234-0.010-0.0100.0000.0000.0000.000
223X224ASP-1-0.936-0.97212.393-0.657-0.6570.0000.0000.0000.000
224X225PRO0-0.049-0.0199.4150.0540.0540.0000.0000.0000.000
225X226GLN0-0.025-0.00412.7120.0450.0450.0000.0000.0000.000
226X227ASP-1-0.875-0.94012.270-0.428-0.4280.0000.0000.0000.000
227X228VAL0-0.003-0.00515.0130.0260.0260.0000.0000.0000.000
228X229GLU-1-0.855-0.90717.190-0.066-0.0660.0000.0000.0000.000
229X230PHE00.0360.01719.340-0.004-0.0040.0000.0000.0000.000
230X231LYS10.8790.95522.5720.0690.0690.0000.0000.0000.000
231X232CYS0-0.041-0.02525.1320.0040.0040.0000.0000.0000.000