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: MNG6Z

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 OptHSide
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 -38758666.352003
FMO2-HF: Nuclear repulsion 38281914.917616
FMO2-HF: Total energy -476751.434386
FMO2-MP2: Total energy -478139.898966


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.
-240.989-236.04922.187-12.391-14.735-0.13
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 : 0.935 / q_NPA : 0.956
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-1-0.852-0.9141.854-78.811-76.24812.471-7.948-7.085-0.070
4X21THR0-0.027-0.0264.7314.9405.090-0.001-0.018-0.1310.000
5X22GLY0-0.037-0.0107.4032.9582.9580.0000.0000.0000.000
6X23VAL00.0120.0167.7532.0622.0620.0000.0000.0000.000
7X24LEU0-0.0340.0018.9272.7372.7370.0000.0000.0000.000
8X25ASN00.0280.0086.659-0.264-0.2640.0000.0000.0000.000
9X26PHE00.011-0.0099.5180.2480.2480.0000.0000.0000.000
10X27LEU00.1290.08013.1530.9910.9910.0000.0000.0000.000
11X28GLN00.0160.0099.5432.1992.1990.0000.0000.0000.000
12X29LYS10.8090.89912.03121.82521.8250.0000.0000.0000.000
13X30TYR00.0130.01315.8371.3501.3500.0000.0000.0000.000
14X31PRO0-0.022-0.01114.878-0.559-0.5590.0000.0000.0000.000
15X32GLU-1-0.896-0.92715.692-16.049-16.0490.0000.0000.0000.000
16X33TYR0-0.094-0.07616.0640.8640.8640.0000.0000.0000.000
17X34ASP-1-0.715-0.86012.834-19.877-19.8770.0000.0000.0000.000
18X35GLY00.0320.00012.592-1.871-1.8710.0000.0000.0000.000
19X36ARG10.7880.87214.94316.86816.8680.0000.0000.0000.000
20X37ASP-1-0.921-0.95918.381-12.947-12.9470.0000.0000.0000.000
21X38VAL00.0510.03116.7800.2960.2960.0000.0000.0000.000
22X39THR0-0.028-0.01618.127-0.615-0.6150.0000.0000.0000.000
23X40ILE0-0.007-0.00413.0800.4280.4280.0000.0000.0000.000
24X41ALA00.0120.00017.3010.2970.2970.0000.0000.0000.000
25X42ILE0-0.027-0.02614.101-0.464-0.4640.0000.0000.0000.000
26X43PHE00.0100.00417.4440.6340.6340.0000.0000.0000.000
27X44ASP-1-0.736-0.85715.798-19.475-19.4750.0000.0000.0000.000
28X45SER00.003-0.01016.9900.6430.6430.0000.0000.0000.000
29X46GLY00.0250.02018.4400.3110.3110.0000.0000.0000.000
30X47VAL0-0.0220.00213.614-0.908-0.9080.0000.0000.0000.000
31X48ASP-1-0.783-0.90414.486-16.401-16.4010.0000.0000.0000.000
32X49PRO00.0380.01214.153-1.318-1.3180.0000.0000.0000.000
33X50ARG10.8180.88514.80816.36016.3600.0000.0000.0000.000
34X51ALA0-0.0360.00111.6610.0030.0030.0000.0000.0000.000
35X52THR00.0210.0039.352-0.088-0.0880.0000.0000.0000.000
36X53GLY00.0550.0348.332-3.491-3.4910.0000.0000.0000.000
37X54LEU0-0.102-0.0779.1910.0270.0270.0000.0000.0000.000
38X55GLU-1-0.839-0.90411.871-20.867-20.8670.0000.0000.0000.000
39X56THR00.002-0.00613.7561.2371.2370.0000.0000.0000.000
40X57LEU0-0.0110.00713.387-1.740-1.7400.0000.0000.0000.000
41X58CYS0-0.003-0.00413.5050.7840.7840.0000.0000.0000.000
42X59ASP-1-0.791-0.85914.816-14.048-14.0480.0000.0000.0000.000
43X60GLY0-0.033-0.01216.7610.8370.8370.0000.0000.0000.000
44X61LYS10.7780.87217.74314.70114.7010.0000.0000.0000.000
45X62THR0-0.054-0.03719.7650.4880.4880.0000.0000.0000.000
46X63VAL00.0670.04318.182-1.206-1.2060.0000.0000.0000.000
47X64LYS10.8340.93810.31227.38027.3800.0000.0000.0000.000
48X65VAL0-0.051-0.01415.2430.1220.1220.0000.0000.0000.000
49X66ILE00.0440.02317.6320.7450.7450.0000.0000.0000.000
50X67GLU-1-0.746-0.83620.771-11.194-11.1940.0000.0000.0000.000
51X68ARG10.8360.89419.33914.03414.0340.0000.0000.0000.000
52X69TYR0-0.033-0.03722.3380.6200.6200.0000.0000.0000.000
53X70ASP-1-0.818-0.89923.676-12.253-12.2530.0000.0000.0000.000
54X71CYS0-0.045-0.00925.7900.4970.4970.0000.0000.0000.000
55X72SER0-0.012-0.03527.0160.5530.5530.0000.0000.0000.000
56X73GLY00.0060.00428.8350.3740.3740.0000.0000.0000.000
57X74CYS0-0.113-0.03628.5930.3450.3450.0000.0000.0000.000
58X75GLY00.0400.01629.6330.1530.1530.0000.0000.0000.000
59X76ASP-1-0.849-0.90330.501-9.323-9.3230.0000.0000.0000.000
60X77VAL0-0.0140.00133.8960.1250.1250.0000.0000.0000.000
61X78ASP-1-0.769-0.88936.693-7.464-7.4640.0000.0000.0000.000
62X79MET0-0.0110.02937.4500.2690.2690.0000.0000.0000.000
63X80LYS10.8180.88841.3517.4607.4600.0000.0000.0000.000
64X81LYS10.8040.90844.7476.8456.8450.0000.0000.0000.000
65X82LYS10.9280.95845.6716.8426.8420.0000.0000.0000.000
66X83VAL0-0.001-0.01347.8080.1440.1440.0000.0000.0000.000
67X84THR00.001-0.02448.967-0.151-0.1510.0000.0000.0000.000
68X85PRO00.0170.02948.0080.0550.0550.0000.0000.0000.000
69X86ASP-1-0.852-0.88250.554-5.787-5.7870.0000.0000.0000.000
70X87GLU-1-0.962-0.99249.910-6.216-6.2160.0000.0000.0000.000
71X88ASN0-0.015-0.02552.8170.1640.1640.0000.0000.0000.000
72X89GLY0-0.065-0.03155.165-0.017-0.0170.0000.0000.0000.000
73X113GLU-1-0.840-0.92344.455-6.669-6.6690.0000.0000.0000.000
74X114LYS10.7660.88544.5007.0547.0540.0000.0000.0000.000
75X115ALA0-0.0090.01245.4020.1690.1690.0000.0000.0000.000
76X116VAL0-0.0050.00147.1230.0420.0420.0000.0000.0000.000
77X117ARG10.8970.94146.6676.4946.4940.0000.0000.0000.000
78X118VAL0-0.067-0.04746.3020.1610.1610.0000.0000.0000.000
79X119GLY00.0640.04145.001-0.156-0.1560.0000.0000.0000.000
80X120LEU00.0210.01545.9270.0150.0150.0000.0000.0000.000
81X121LYS10.9180.96046.6266.3636.3630.0000.0000.0000.000
82X122SER0-0.006-0.03042.622-0.028-0.0280.0000.0000.0000.000
83X123PHE0-0.0310.00444.126-0.075-0.0750.0000.0000.0000.000
84X124SER0-0.029-0.03241.9870.0720.0720.0000.0000.0000.000
85X125ASP-1-0.829-0.91242.905-7.426-7.4260.0000.0000.0000.000
86X126LEU0-0.0290.02643.127-0.024-0.0240.0000.0000.0000.000
87X127LEU0-0.051-0.00145.3690.2000.2000.0000.0000.0000.000
88X128PRO0-0.045-0.07646.627-0.100-0.1000.0000.0000.0000.000
89X129SER00.031-0.00249.2210.1050.1050.0000.0000.0000.000
90X130LYS10.8970.95948.6336.2726.2720.0000.0000.0000.000
91X131VAL00.0700.04143.769-0.101-0.1010.0000.0000.0000.000
92X132ARG10.7360.87542.0187.6717.6710.0000.0000.0000.000
93X133ASN00.0430.01942.252-0.111-0.1110.0000.0000.0000.000
94X134ASN0-0.072-0.04339.884-0.042-0.0420.0000.0000.0000.000
95X135ILE00.0520.03639.728-0.053-0.0530.0000.0000.0000.000
96X136VAL00.0080.00133.868-0.023-0.0230.0000.0000.0000.000
97X137ALA00.0050.01834.535-0.079-0.0790.0000.0000.0000.000
98X138GLN00.020-0.01329.406-0.215-0.2150.0000.0000.0000.000
99X139ALA0-0.051-0.02328.975-0.343-0.3430.0000.0000.0000.000
100X140LYS10.9430.98128.6709.3049.3040.0000.0000.0000.000
101X141LEU0-0.0050.01726.169-0.274-0.2740.0000.0000.0000.000
102X142LYS10.8410.92023.22212.00512.0050.0000.0000.0000.000
103X143HIS0-0.010-0.01819.9390.1810.1810.0000.0000.0000.000
104X144TRP00.045-0.00523.3240.2550.2550.0000.0000.0000.000
105X145ASP-1-0.862-0.90621.028-13.583-13.5830.0000.0000.0000.000
106X146LYS10.8160.90119.97713.85113.8510.0000.0000.0000.000
107X147PRO00.0580.02524.5800.2190.2190.0000.0000.0000.000
108X148HIS00.0840.05021.896-0.026-0.0260.0000.0000.0000.000
109X149LYS10.8230.91725.90210.77410.7740.0000.0000.0000.000
110X150THR0-0.038-0.02427.3120.1740.1740.0000.0000.0000.000
111X151ALA00.0350.03029.4170.0910.0910.0000.0000.0000.000
112X152THR0-0.009-0.02031.4010.1640.1640.0000.0000.0000.000
113X153ALA00.0090.02033.3830.1230.1230.0000.0000.0000.000
114X154ASN0-0.021-0.03335.2550.0770.0770.0000.0000.0000.000
115X155ALA00.0610.03837.3710.1340.1340.0000.0000.0000.000
116X156SER0-0.014-0.00838.4430.1940.1940.0000.0000.0000.000
117X157ARG10.9170.94539.0217.6517.6510.0000.0000.0000.000
118X158LYS10.8230.91240.6777.6437.6430.0000.0000.0000.000
119X159ILE00.0340.02141.9440.1200.1200.0000.0000.0000.000
120X160VAL0-0.059-0.00645.1020.0930.0930.0000.0000.0000.000
121X161GLU-1-0.885-0.94447.250-6.475-6.4750.0000.0000.0000.000
122X162PHE0-0.029-0.02850.3670.0370.0370.0000.0000.0000.000
123X163GLU-1-0.850-0.90253.713-5.687-5.6870.0000.0000.0000.000
124X164SER0-0.030-0.02155.4810.0610.0610.0000.0000.0000.000
125X165GLN0-0.013-0.01256.9630.0990.0990.0000.0000.0000.000
126X166ASN0-0.046-0.04760.7220.0220.0220.0000.0000.0000.000
127X167PRO00.0110.02364.0690.0290.0290.0000.0000.0000.000
128X168GLY0-0.012-0.01766.9400.0810.0810.0000.0000.0000.000
129X169GLU-1-0.906-0.95368.344-4.448-4.4480.0000.0000.0000.000
130X170ALA00.0470.02968.202-0.036-0.0360.0000.0000.0000.000
131X171SER0-0.014-0.01467.185-0.068-0.0680.0000.0000.0000.000
132X172LYS10.9610.97161.7545.0775.0770.0000.0000.0000.000
133X173LEU0-0.016-0.01467.9910.0220.0220.0000.0000.0000.000
134X174PRO00.0390.06468.8120.0550.0550.0000.0000.0000.000
135X175TRP0-0.011-0.00471.569-0.068-0.0680.0000.0000.0000.000
136X176ASP-1-0.827-0.94371.575-4.406-4.4060.0000.0000.0000.000
137X177LYS10.8970.92368.8984.3694.3690.0000.0000.0000.000
138X178LYS10.8670.95066.7864.4664.4660.0000.0000.0000.000
139X179ILE00.1010.05565.687-0.083-0.0830.0000.0000.0000.000
140X180LEU0-0.0110.00564.419-0.076-0.0760.0000.0000.0000.000
141X181LYS10.9190.94862.6544.8924.8920.0000.0000.0000.000
142X182GLU-1-0.896-0.91861.078-5.016-5.0160.0000.0000.0000.000
143X183ASN0-0.009-0.01059.832-0.115-0.1150.0000.0000.0000.000
144X184LEU0-0.023-0.02458.646-0.074-0.0740.0000.0000.0000.000
145X185ASP-1-0.896-0.95056.898-5.466-5.4660.0000.0000.0000.000
146X186PHE0-0.035-0.04455.414-0.115-0.1150.0000.0000.0000.000
147X187GLU-1-0.868-0.91954.279-5.632-5.6320.0000.0000.0000.000
148X188LEU00.0140.02750.853-0.146-0.1460.0000.0000.0000.000
149X189GLU-1-0.817-0.89850.540-5.969-5.9690.0000.0000.0000.000
150X190MET0-0.045-0.01049.735-0.129-0.1290.0000.0000.0000.000
151X191LEU0-0.020-0.00848.093-0.168-0.1680.0000.0000.0000.000
152X192ASN00.018-0.00945.979-0.294-0.2940.0000.0000.0000.000
153X193SER0-0.109-0.04345.012-0.245-0.2450.0000.0000.0000.000
154X194TYR00.0530.00444.461-0.107-0.1070.0000.0000.0000.000
155X195GLU-1-0.856-0.91740.190-7.860-7.8600.0000.0000.0000.000
156X196LYS10.8430.92440.2506.6616.6610.0000.0000.0000.000
157X197VAL00.0220.00940.175-0.142-0.1420.0000.0000.0000.000
158X198TYR00.0170.01735.372-0.086-0.0860.0000.0000.0000.000
159X199GLY00.000-0.01034.906-0.100-0.1000.0000.0000.0000.000
160X200ASP-1-0.862-0.92334.648-8.491-8.4910.0000.0000.0000.000
161X201ILE0-0.100-0.03737.1390.0650.0650.0000.0000.0000.000
162X202LYS10.8360.92234.3808.2848.2840.0000.0000.0000.000
163X203THR00.0240.00034.6950.2130.2130.0000.0000.0000.000
164X204SER0-0.067-0.05135.281-0.270-0.2700.0000.0000.0000.000
165X205TYR00.0170.02432.4020.0210.0210.0000.0000.0000.000
166X206ASP-1-0.767-0.90537.445-7.429-7.4290.0000.0000.0000.000
167X207CYS0-0.072-0.02036.244-0.297-0.2970.0000.0000.0000.000
168X208ILE00.0530.01638.4200.2380.2380.0000.0000.0000.000
169X209LEU00.0030.00936.987-0.226-0.2260.0000.0000.0000.000
170X210PHE0-0.019-0.02139.6640.2410.2410.0000.0000.0000.000
171X211PRO0-0.020-0.01140.324-0.177-0.1770.0000.0000.0000.000
172X212THR00.0300.01238.5970.1480.1480.0000.0000.0000.000
173X213ALA00.0670.03041.1800.0160.0160.0000.0000.0000.000
174X214ASP-1-0.972-0.98435.965-8.486-8.4860.0000.0000.0000.000
175X215GLY0-0.030-0.03035.521-0.312-0.3120.0000.0000.0000.000
176X216TRP0-0.032-0.01235.5200.3120.3120.0000.0000.0000.000
177X217LEU0-0.0220.00235.057-0.279-0.2790.0000.0000.0000.000
178X218THR0-0.017-0.02533.0510.3100.3100.0000.0000.0000.000
179X219ILE00.014-0.01034.985-0.177-0.1770.0000.0000.0000.000
180X220VAL0-0.009-0.00832.7500.1080.1080.0000.0000.0000.000
181X221ASP-1-0.823-0.91635.622-8.027-8.0270.0000.0000.0000.000
182X222THR0-0.024-0.02332.735-0.037-0.0370.0000.0000.0000.000
183X223THR0-0.064-0.04035.373-0.021-0.0210.0000.0000.0000.000
184X224GLU-1-0.813-0.88838.314-7.922-7.9220.0000.0000.0000.000
185X225GLN0-0.088-0.03740.4380.1820.1820.0000.0000.0000.000
186X226GLY00.006-0.00343.1870.1010.1010.0000.0000.0000.000
187X227ASP-1-0.797-0.88042.088-7.427-7.4270.0000.0000.0000.000
188X228LEU00.0120.01842.861-0.016-0.0160.0000.0000.0000.000
189X229ASP-1-0.763-0.84240.709-7.854-7.8540.0000.0000.0000.000
190X230GLN0-0.134-0.08038.0780.0050.0050.0000.0000.0000.000
191X231ALA00.0140.01135.436-0.059-0.0590.0000.0000.0000.000
192X232LEU0-0.022-0.00529.179-0.121-0.1210.0000.0000.0000.000
193X233ARG10.8470.92132.9238.5258.5250.0000.0000.0000.000
194X234ILE0-0.030-0.00528.170-0.159-0.1590.0000.0000.0000.000
195X235GLY00.0480.01830.3520.3900.3900.0000.0000.0000.000
196X236GLU-1-0.929-0.99129.743-9.570-9.5700.0000.0000.0000.000
197X237TYR0-0.026-0.01920.303-0.216-0.2160.0000.0000.0000.000
198X238SER00.0520.02326.447-0.145-0.1450.0000.0000.0000.000
199X239ARG10.8600.96227.8468.7768.7760.0000.0000.0000.000
200X240THR00.012-0.00526.8140.3400.3400.0000.0000.0000.000
201X241HIS00.0220.03927.460-0.167-0.1670.0000.0000.0000.000
202X242GLU-1-0.889-0.94322.507-13.425-13.4250.0000.0000.0000.000
203X243THR0-0.082-0.06022.675-0.690-0.6900.0000.0000.0000.000
204X244ARG10.9040.96220.59913.96613.9660.0000.0000.0000.000
205X245ASN0-0.022-0.01623.6310.3750.3750.0000.0000.0000.000
206X246VAL0-0.029-0.03523.589-0.258-0.2580.0000.0000.0000.000
207X247ASP-1-0.810-0.87826.439-10.165-10.1650.0000.0000.0000.000
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