FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 98JN2

Calculation Name: 3LXU-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LXU

Chain ID: X

ChEMBL ID:

UniProt ID: Q9V6K1

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 1217
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -38760542.054726
FMO2-HF: Nuclear repulsion 38283800.877763
FMO2-HF: Total energy -476741.176963
FMO2-MP2: Total energy -478130.318444


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:18:LYS)


Summations of interaction energy for fragment #1(X:18:LYS)
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.
-204.238-196.6999.016-6.59-9.966-0.063
Interaction energy analysis for fragmet #1(X:18:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.043 / q_NPA : 1.000
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].
3X20GLU-1-0.863-0.9182.058-57.433-53.2617.044-4.976-6.240-0.047
4X21THR0-0.008-0.0104.7683.7903.925-0.001-0.019-0.1160.000
5X22GLY0-0.059-0.0227.4212.3992.3990.0000.0000.0000.000
6X23VAL00.0140.0148.0011.6821.6820.0000.0000.0000.000
7X24LEU0-0.076-0.0189.2072.1942.1940.0000.0000.0000.000
8X25ASN00.0460.0196.820-4.023-4.0230.0000.0000.0000.000
9X26PHE00.042-0.0079.5510.1270.1270.0000.0000.0000.000
10X27LEU00.1620.08313.2740.6680.6680.0000.0000.0000.000
11X28GLN00.0590.0239.6831.7531.7530.0000.0000.0000.000
12X29LYS10.7740.89411.84319.31219.3120.0000.0000.0000.000
13X30TYR00.0110.01615.9230.8590.8590.0000.0000.0000.000
14X31PRO0-0.032-0.02214.929-0.401-0.4010.0000.0000.0000.000
15X32GLU-1-0.880-0.92915.726-14.504-14.5040.0000.0000.0000.000
16X33TYR0-0.090-0.02415.9370.7390.7390.0000.0000.0000.000
17X34ASP-1-0.728-0.85112.860-17.606-17.6060.0000.0000.0000.000
18X35GLY00.046-0.00412.598-1.473-1.4730.0000.0000.0000.000
19X36ARG10.8020.86914.95115.11615.1160.0000.0000.0000.000
20X37ASP-1-0.961-0.97018.380-11.980-11.9800.0000.0000.0000.000
21X38VAL00.0310.01216.8110.2430.2430.0000.0000.0000.000
22X39THR0-0.051-0.02518.106-0.624-0.6240.0000.0000.0000.000
23X40ILE00.0150.00313.1360.3370.3370.0000.0000.0000.000
24X41ALA00.004-0.01017.2590.2130.2130.0000.0000.0000.000
25X42ILE0-0.027-0.02114.423-0.351-0.3510.0000.0000.0000.000
26X43PHE00.0060.00117.5960.5270.5270.0000.0000.0000.000
27X44ASP-1-0.739-0.85315.994-19.694-19.6940.0000.0000.0000.000
28X45SER0-0.049-0.03816.9670.7670.7670.0000.0000.0000.000
29X46GLY00.0540.02418.9020.2470.2470.0000.0000.0000.000
30X47VAL0-0.0310.00113.934-0.972-0.9720.0000.0000.0000.000
31X48ASP-1-0.828-0.95814.092-17.559-17.5590.0000.0000.0000.000
32X49PRO00.0250.00514.286-1.335-1.3350.0000.0000.0000.000
33X50ARG10.8650.92815.33316.36316.3630.0000.0000.0000.000
34X51ALA0-0.0270.00811.165-0.182-0.1820.0000.0000.0000.000
35X52THR00.0070.0018.897-0.316-0.3160.0000.0000.0000.000
36X53GLY00.0600.0339.063-3.670-3.6700.0000.0000.0000.000
37X54LEU0-0.108-0.09910.3300.7340.7340.0000.0000.0000.000
38X55GLU-1-0.858-0.90913.109-19.972-19.9720.0000.0000.0000.000
39X56THR0-0.006-0.00615.1870.9750.9750.0000.0000.0000.000
40X57LEU00.0110.01914.503-1.458-1.4580.0000.0000.0000.000
41X58CYS00.0250.00113.4620.3330.3330.0000.0000.0000.000
42X59ASP-1-0.837-0.89415.059-13.267-13.2670.0000.0000.0000.000
43X60GLY0-0.031-0.01017.4500.6690.6690.0000.0000.0000.000
44X61LYS10.7770.88218.64713.64713.6470.0000.0000.0000.000
45X62THR0-0.043-0.02720.2880.4150.4150.0000.0000.0000.000
46X63VAL00.0690.04319.335-1.071-1.0710.0000.0000.0000.000
47X64LYS10.8700.96211.51424.82924.8290.0000.0000.0000.000
48X65VAL0-0.063-0.01416.5140.1610.1610.0000.0000.0000.000
49X66ILE00.0260.00519.0180.6390.6390.0000.0000.0000.000
50X67GLU-1-0.807-0.92222.001-11.083-11.0830.0000.0000.0000.000
51X68ARG10.8270.89619.40114.06814.0680.0000.0000.0000.000
52X69TYR00.0130.00923.2610.6890.6890.0000.0000.0000.000
53X70ASP-1-0.839-0.91624.187-12.401-12.4010.0000.0000.0000.000
54X71CYS0-0.032-0.01426.3840.3820.3820.0000.0000.0000.000
55X72SER00.001-0.01427.6550.5450.5450.0000.0000.0000.000
56X73GLY0-0.0090.00129.4640.3780.3780.0000.0000.0000.000
57X74CYS0-0.110-0.03128.8160.3280.3280.0000.0000.0000.000
58X75GLY00.0480.01429.6700.1180.1180.0000.0000.0000.000
59X76ASP-1-0.851-0.90030.528-9.347-9.3470.0000.0000.0000.000
60X77VAL0-0.035-0.00934.0060.0950.0950.0000.0000.0000.000
61X78ASP-1-0.821-0.92036.617-7.462-7.4620.0000.0000.0000.000
62X79MET0-0.0050.03637.2720.2650.2650.0000.0000.0000.000
63X80LYS10.8610.91341.3217.4957.4950.0000.0000.0000.000
64X81LYS10.9440.97444.7986.6696.6690.0000.0000.0000.000
65X82LYS10.9270.95846.1716.7596.7590.0000.0000.0000.000
66X83VAL0-0.011-0.01547.4200.1480.1480.0000.0000.0000.000
67X84THR00.0060.00748.900-0.135-0.1350.0000.0000.0000.000
68X85PRO00.0250.02248.1180.0340.0340.0000.0000.0000.000
69X86ASP-1-0.911-0.95650.421-5.784-5.7840.0000.0000.0000.000
70X87GLU-1-1.005-1.00949.381-6.207-6.2070.0000.0000.0000.000
71X88ASN00.017-0.01452.3980.1690.1690.0000.0000.0000.000
72X89GLY0-0.0710.00154.944-0.012-0.0120.0000.0000.0000.000
73X113GLU-1-0.889-0.95043.585-6.781-6.7810.0000.0000.0000.000
74X114LYS10.7150.86343.9287.1627.1620.0000.0000.0000.000
75X115ALA0-0.0140.00744.7940.1780.1780.0000.0000.0000.000
76X116VAL00.0070.01646.3450.0600.0600.0000.0000.0000.000
77X117ARG10.9350.96046.0676.5576.5570.0000.0000.0000.000
78X118VAL0-0.073-0.04845.7440.1550.1550.0000.0000.0000.000
79X119GLY00.1120.05744.612-0.150-0.1500.0000.0000.0000.000
80X120LEU0-0.0060.00145.5410.0360.0360.0000.0000.0000.000
81X121LYS10.9300.96846.4726.4496.4490.0000.0000.0000.000
82X122SER00.0200.00242.619-0.054-0.0540.0000.0000.0000.000
83X123PHE0-0.008-0.00144.361-0.075-0.0750.0000.0000.0000.000
84X124SER0-0.042-0.03242.4580.0780.0780.0000.0000.0000.000
85X125ASP-1-0.813-0.89943.596-7.425-7.4250.0000.0000.0000.000
86X126LEU0-0.0410.02743.682-0.012-0.0120.0000.0000.0000.000
87X127LEU0-0.0410.01045.8800.2010.2010.0000.0000.0000.000
88X128PRO0-0.069-0.09047.262-0.101-0.1010.0000.0000.0000.000
89X129SER00.027-0.00549.7040.1020.1020.0000.0000.0000.000
90X130LYS10.9050.97048.7106.2966.2960.0000.0000.0000.000
91X131VAL00.0920.04343.989-0.103-0.1030.0000.0000.0000.000
92X132ARG10.7950.93342.3677.5487.5480.0000.0000.0000.000
93X133ASN00.1120.02241.977-0.244-0.2440.0000.0000.0000.000
94X134ASN0-0.077-0.01739.634-0.039-0.0390.0000.0000.0000.000
95X135ILE00.0710.03739.117-0.063-0.0630.0000.0000.0000.000
96X136VAL00.008-0.00233.415-0.011-0.0110.0000.0000.0000.000
97X137ALA0-0.0180.00733.980-0.096-0.0960.0000.0000.0000.000
98X138GLN00.039-0.00428.738-0.107-0.1070.0000.0000.0000.000
99X139ALA0-0.070-0.03328.321-0.366-0.3660.0000.0000.0000.000
100X140LYS10.9030.95728.3519.4219.4210.0000.0000.0000.000
101X141LEU00.0150.02525.952-0.255-0.2550.0000.0000.0000.000
102X142LYS10.9020.96223.38911.99911.9990.0000.0000.0000.000
103X143HIS00.029-0.00319.3310.1070.1070.0000.0000.0000.000
104X144TRP00.024-0.01922.8420.2820.2820.0000.0000.0000.000
105X145ASP-1-0.826-0.89420.350-14.446-14.4460.0000.0000.0000.000
106X146LYS10.7950.90319.32614.53414.5340.0000.0000.0000.000
107X147PRO00.0660.01623.6520.2520.2520.0000.0000.0000.000
108X148HIS00.0620.04320.9250.0260.0260.0000.0000.0000.000
109X149LYS10.8950.96425.04811.17311.1730.0000.0000.0000.000
110X150THR0-0.052-0.02726.3300.2040.2040.0000.0000.0000.000
111X151ALA00.0490.03628.3690.0720.0720.0000.0000.0000.000
112X152THR00.008-0.02430.3330.2040.2040.0000.0000.0000.000
113X153ALA00.0130.02832.3470.1230.1230.0000.0000.0000.000
114X154ASN0-0.018-0.02834.1700.1150.1150.0000.0000.0000.000
115X155ALA00.0320.02936.1900.1550.1550.0000.0000.0000.000
116X156SER0-0.008-0.01037.3520.2170.2170.0000.0000.0000.000
117X157ARG10.9180.94237.9837.9917.9910.0000.0000.0000.000
118X158LYS10.9340.97139.9557.9037.9030.0000.0000.0000.000
119X159ILE00.0380.03440.7940.1350.1350.0000.0000.0000.000
120X160VAL0-0.059-0.00643.9550.0970.0970.0000.0000.0000.000
121X161GLU-1-0.926-0.95845.632-6.812-6.8120.0000.0000.0000.000
122X162PHE0-0.032-0.02949.2270.0410.0410.0000.0000.0000.000
123X163GLU-1-0.900-0.93952.671-5.913-5.9130.0000.0000.0000.000
124X164SER0-0.045-0.02954.3310.0620.0620.0000.0000.0000.000
125X165GLN00.0270.02455.872-0.048-0.0480.0000.0000.0000.000
126X166ASN0-0.045-0.04659.5620.0950.0950.0000.0000.0000.000
127X167PRO00.0090.02362.9110.0330.0330.0000.0000.0000.000
128X168GLY0-0.050-0.03965.7680.0880.0880.0000.0000.0000.000
129X169GLU-1-0.973-0.98267.197-4.549-4.5490.0000.0000.0000.000
130X170ALA00.0410.02467.114-0.042-0.0420.0000.0000.0000.000
131X171SER0-0.009-0.00966.130-0.076-0.0760.0000.0000.0000.000
132X172LYS10.9520.96561.2785.2075.2070.0000.0000.0000.000
133X173LEU0-0.021-0.02566.9150.0180.0180.0000.0000.0000.000
134X174PRO00.0440.06067.6940.0510.0510.0000.0000.0000.000
135X175TRP0-0.0160.00770.484-0.067-0.0670.0000.0000.0000.000
136X176ASP-1-0.816-0.93671.014-4.490-4.4900.0000.0000.0000.000
137X177LYS10.9400.94167.7124.5034.5030.0000.0000.0000.000
138X178LYS10.9200.98365.8244.6764.6760.0000.0000.0000.000
139X179ILE00.1020.04464.619-0.089-0.0890.0000.0000.0000.000
140X180LEU0-0.0220.00063.358-0.074-0.0740.0000.0000.0000.000
141X181LYS10.9490.96361.5654.9134.9130.0000.0000.0000.000
142X182GLU-1-0.882-0.91059.990-5.173-5.1730.0000.0000.0000.000
143X183ASN00.0150.00758.769-0.177-0.1770.0000.0000.0000.000
144X184LEU0-0.006-0.01057.579-0.074-0.0740.0000.0000.0000.000
145X185ASP-1-0.892-0.94755.805-5.665-5.6650.0000.0000.0000.000
146X186PHE0-0.039-0.04854.338-0.131-0.1310.0000.0000.0000.000
147X187GLU-1-0.925-0.95253.232-5.869-5.8690.0000.0000.0000.000
148X188LEU00.0280.02949.432-0.151-0.1510.0000.0000.0000.000
149X189GLU-1-0.915-0.96549.455-6.179-6.1790.0000.0000.0000.000
150X190MET0-0.048-0.01948.689-0.136-0.1360.0000.0000.0000.000
151X191LEU0-0.013-0.00847.038-0.185-0.1850.0000.0000.0000.000
152X192ASN00.0780.02844.907-0.280-0.2800.0000.0000.0000.000
153X193SER0-0.126-0.05443.957-0.260-0.2600.0000.0000.0000.000
154X194TYR00.029-0.01243.465-0.106-0.1060.0000.0000.0000.000
155X195GLU-1-0.941-0.96738.820-8.253-8.2530.0000.0000.0000.000
156X196LYS10.8480.92239.2026.8796.8790.0000.0000.0000.000
157X197VAL00.0420.03339.183-0.134-0.1340.0000.0000.0000.000
158X198TYR00.0080.00634.365-0.194-0.1940.0000.0000.0000.000
159X199GLY0-0.018-0.02233.926-0.101-0.1010.0000.0000.0000.000
160X200ASP-1-0.892-0.93133.725-8.812-8.8120.0000.0000.0000.000
161X201ILE0-0.129-0.06536.2400.0940.0940.0000.0000.0000.000
162X202LYS10.9310.96833.8228.7548.7540.0000.0000.0000.000
163X203THR00.002-0.01734.0200.2420.2420.0000.0000.0000.000
164X204SER0-0.064-0.04934.553-0.281-0.2810.0000.0000.0000.000
165X205TYR00.0210.02831.432-0.016-0.0160.0000.0000.0000.000
166X206ASP-1-0.809-0.90836.803-7.564-7.5640.0000.0000.0000.000
167X207CYS0-0.075-0.03535.414-0.264-0.2640.0000.0000.0000.000
168X208ILE00.0550.01838.0410.2590.2590.0000.0000.0000.000
169X209LEU00.0180.00837.462-0.223-0.2230.0000.0000.0000.000
170X210PHE0-0.044-0.02739.7960.2500.2500.0000.0000.0000.000
171X211PRO0-0.017-0.01540.838-0.167-0.1670.0000.0000.0000.000
172X212THR00.0410.00739.5730.1560.1560.0000.0000.0000.000
173X213ALA00.0390.01942.1970.0310.0310.0000.0000.0000.000
174X214ASP-1-0.979-0.98437.003-8.365-8.3650.0000.0000.0000.000
175X215GLY0-0.041-0.04036.638-0.310-0.3100.0000.0000.0000.000
176X216TRP0-0.041-0.00236.3400.3010.3010.0000.0000.0000.000
177X217LEU0-0.0260.00035.677-0.280-0.2800.0000.0000.0000.000
178X218THR0-0.041-0.03433.0580.2780.2780.0000.0000.0000.000
179X219ILE00.028-0.00534.944-0.170-0.1700.0000.0000.0000.000
180X220VAL0-0.007-0.00632.2670.1210.1210.0000.0000.0000.000
181X221ASP-1-0.815-0.92035.060-8.173-8.1730.0000.0000.0000.000
182X222THR0-0.042-0.03532.181-0.083-0.0830.0000.0000.0000.000
183X223THR0-0.071-0.04334.692-0.076-0.0760.0000.0000.0000.000
184X224GLU-1-0.890-0.94937.284-8.126-8.1260.0000.0000.0000.000
185X225GLN0-0.081-0.02439.7040.0570.0570.0000.0000.0000.000
186X226GLY0-0.001-0.01142.3790.1130.1130.0000.0000.0000.000
187X227ASP-1-0.786-0.87641.423-7.441-7.4410.0000.0000.0000.000
188X228LEU0-0.0180.00942.079-0.008-0.0080.0000.0000.0000.000
189X229ASP-1-0.865-0.91940.348-7.618-7.6180.0000.0000.0000.000
190X230GLN0-0.157-0.09937.5200.0020.0020.0000.0000.0000.000
191X231ALA00.0270.01734.840-0.084-0.0840.0000.0000.0000.000
192X232LEU0-0.035-0.01528.761-0.094-0.0940.0000.0000.0000.000
193X233ARG10.9540.98432.6518.8318.8310.0000.0000.0000.000
194X234ILE0-0.0280.00227.566-0.132-0.1320.0000.0000.0000.000
195X235GLY00.0370.01130.7560.4000.4000.0000.0000.0000.000
196X236GLU-1-0.937-0.99130.314-9.454-9.4540.0000.0000.0000.000
197X237TYR0-0.0100.00021.306-0.258-0.2580.0000.0000.0000.000
198X238SER00.0840.04027.630-0.098-0.0980.0000.0000.0000.000
199X239ARG10.8980.98529.1278.6758.6750.0000.0000.0000.000
200X240THR0-0.003-0.03428.1680.2950.2950.0000.0000.0000.000
201X241HIS00.0240.03428.633-0.109-0.1090.0000.0000.0000.000
202X242GLU-1-0.914-0.94224.166-12.941-12.9410.0000.0000.0000.000
203X243THR0-0.065-0.04723.468-0.702-0.7020.0000.0000.0000.000
204X244ARG10.9180.98619.96814.50014.5000.0000.0000.0000.000
205X245ASN0-0.025-0.02823.5440.4430.4430.0000.0000.0000.000
206X246VAL0-0.031-0.03423.068-0.302-0.3020.0000.0000.0000.000
207X247ASP-1-0.840-0.89425.817-10.722-10.7220.0000.0000.0000.000
208X248ASP-1-0.876-0.98025.299-11.796-11.7960.0000.0000.0000.000
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