FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: K93L3

Calculation Name: 3MQ9-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MQ9

Chain ID: D

ChEMBL ID:

UniProt ID: Q10589

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 454
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7323697.368984
FMO2-HF: Nuclear repulsion 7150091.498182
FMO2-HF: Total energy -173605.870801
FMO2-MP2: Total energy -174118.236963


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(D:4:GLU)


Summations of interaction energy for fragment #1(D:4:GLU)
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.
4.5232.625999999999925.133-12.225-11.010.121
Interaction energy analysis for fragmet #1(D:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.862 / q_NPA : -0.935
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].
3D6LYS10.7680.8661.814-137.994-141.64224.759-11.476-9.6350.121
4D7LEU00.0060.0164.8172.9823.096-0.001-0.010-0.1030.000
5D8VAL00.0190.0267.138-2.961-2.9610.0000.0000.0000.000
6D9ILE00.001-0.0079.519-0.953-0.9530.0000.0000.0000.000
7D10TRP0-0.043-0.04212.908-1.134-1.1340.0000.0000.0000.000
8D11ILE00.0350.00515.781-0.532-0.5320.0000.0000.0000.000
9D12ASN00.002-0.00819.3220.2950.2950.0000.0000.0000.000
10D13GLY00.0680.03322.6180.0140.0140.0000.0000.0000.000
11D14ASP-1-0.847-0.91924.42011.07011.0700.0000.0000.0000.000
12D15LYS10.8810.93423.500-11.382-11.3820.0000.0000.0000.000
13D16GLY00.0390.03625.038-0.052-0.0520.0000.0000.0000.000
14D17TYR00.024-0.00720.2520.4400.4400.0000.0000.0000.000
15D18ASN0-0.031-0.02820.4641.1881.1880.0000.0000.0000.000
16D19GLY00.0420.01322.5010.1320.1320.0000.0000.0000.000
17D20LEU0-0.0040.00617.3740.3360.3360.0000.0000.0000.000
18D21ALA0-0.017-0.01217.6900.7300.7300.0000.0000.0000.000
19D22GLU-1-0.877-0.92418.43314.66714.6670.0000.0000.0000.000
20D23VAL0-0.019-0.00418.7050.1390.1390.0000.0000.0000.000
21D24GLY00.017-0.00315.4930.4000.4000.0000.0000.0000.000
22D25LYS10.8830.93415.167-14.286-14.2860.0000.0000.0000.000
23D26LYS10.7500.84817.657-14.025-14.0250.0000.0000.0000.000
24D27PHE00.0560.03310.900-0.219-0.2190.0000.0000.0000.000
25D28GLU-1-0.827-0.89813.15823.85023.8500.0000.0000.0000.000
26D29LYS10.8640.93514.547-13.662-13.6620.0000.0000.0000.000
27D30ASP-1-0.791-0.86517.22314.70614.7060.0000.0000.0000.000
28D31THR0-0.0010.00912.3680.5280.5280.0000.0000.0000.000
29D32GLY00.0170.01112.816-0.255-0.2550.0000.0000.0000.000
30D33ILE0-0.083-0.0286.9012.6612.6610.0000.0000.0000.000
31D34LYS10.8590.9089.227-27.468-27.4680.0000.0000.0000.000
32D35VAL00.0020.0109.0162.7392.7390.0000.0000.0000.000
33D36THR0-0.056-0.01711.007-1.442-1.4420.0000.0000.0000.000
34D37VAL0-0.011-0.00412.4940.6220.6220.0000.0000.0000.000
35D38GLU-1-0.909-0.94612.81422.64922.6490.0000.0000.0000.000
36D39HIS00.004-0.01116.706-0.461-0.4610.0000.0000.0000.000
37D40PRO0-0.025-0.00316.731-0.824-0.8240.0000.0000.0000.000
38D41ASP-1-0.797-0.91319.87911.69711.6970.0000.0000.0000.000
39D42LYS10.7540.88022.186-11.092-11.0920.0000.0000.0000.000
40D43LEU00.0480.02618.5470.2330.2330.0000.0000.0000.000
41D44GLU-1-0.783-0.88819.52512.75612.7560.0000.0000.0000.000
42D45GLU-1-0.913-0.95721.49711.51711.5170.0000.0000.0000.000
43D46LYS10.8710.92218.227-14.455-14.4550.0000.0000.0000.000
44D47PHE00.0270.02013.3230.4360.4360.0000.0000.0000.000
45D48PRO0-0.020-0.01916.2430.6550.6550.0000.0000.0000.000
46D49GLN0-0.062-0.02618.059-0.156-0.1560.0000.0000.0000.000
47D50VAL0-0.0050.00613.3280.2410.2410.0000.0000.0000.000
48D51ALA00.0350.02912.2951.2251.2250.0000.0000.0000.000
49D52ALA0-0.057-0.02512.8150.6800.6800.0000.0000.0000.000
50D53THR0-0.097-0.07213.138-1.224-1.2240.0000.0000.0000.000
51D54GLY0-0.039-0.0089.6111.0271.0270.0000.0000.0000.000
52D55ASP-1-0.883-0.8997.98930.78330.7830.0000.0000.0000.000
53D56GLY0-0.018-0.0319.930-1.722-1.7220.0000.0000.0000.000
54D57PRO0-0.044-0.0078.8592.3392.3390.0000.0000.0000.000
55D58ASP-1-0.752-0.8656.19236.65636.6560.0000.0000.0000.000
56D59ILE0-0.031-0.0269.123-1.832-1.8320.0000.0000.0000.000
57D60ILE0-0.0150.00112.7820.2560.2560.0000.0000.0000.000
58D61PHE00.029-0.00115.885-0.749-0.7490.0000.0000.0000.000
59D62TRP0-0.034-0.03819.299-0.049-0.0490.0000.0000.0000.000
60D63ALA00.0170.02322.415-0.055-0.0550.0000.0000.0000.000
61D64HIS00.0450.00924.6280.3300.3300.0000.0000.0000.000
62D65ASP-1-0.896-0.94725.67710.57410.5740.0000.0000.0000.000
63D66ARG10.9620.97423.391-11.935-11.9350.0000.0000.0000.000
64D67PHE0-0.026-0.02119.7690.3060.3060.0000.0000.0000.000
65D68GLY00.0190.02022.8500.2070.2070.0000.0000.0000.000
66D69GLY0-0.034-0.01624.945-0.003-0.0030.0000.0000.0000.000
67D70TYR0-0.029-0.04219.2080.0410.0410.0000.0000.0000.000
68D71ALA00.0670.03220.6480.2890.2890.0000.0000.0000.000
69D72GLN0-0.0390.01621.703-0.020-0.0200.0000.0000.0000.000
70D73SER0-0.059-0.03120.859-0.325-0.3250.0000.0000.0000.000
71D74GLY0-0.044-0.02419.7370.3360.3360.0000.0000.0000.000
72D75LEU0-0.007-0.00716.1260.6110.6110.0000.0000.0000.000
73D76LEU0-0.056-0.01615.0571.0311.0310.0000.0000.0000.000
74D77ALA0-0.014-0.01413.597-0.509-0.5090.0000.0000.0000.000
75D78GLU-1-0.920-0.96915.74811.90811.9080.0000.0000.0000.000
76D79ILE0-0.0340.00117.0720.4500.4500.0000.0000.0000.000
77D80THR00.000-0.01418.093-0.559-0.5590.0000.0000.0000.000
78D81PRO00.0020.02920.0480.1750.1750.0000.0000.0000.000
79D82ASP-1-0.803-0.90621.78511.17111.1710.0000.0000.0000.000
80D83LYS10.8160.86024.647-8.981-8.9810.0000.0000.0000.000
81D84ALA00.0010.00327.139-0.328-0.3280.0000.0000.0000.000
82D85PHE00.0060.00422.598-0.167-0.1670.0000.0000.0000.000
83D86GLN0-0.047-0.02625.461-0.474-0.4740.0000.0000.0000.000
84D87ASP-1-0.787-0.86027.4518.8338.8330.0000.0000.0000.000
85D88LYS10.9350.97724.176-11.833-11.8330.0000.0000.0000.000
86D89LEU00.0180.02225.421-0.016-0.0160.0000.0000.0000.000
87D90TYR00.0360.02029.531-0.356-0.3560.0000.0000.0000.000
88D91PRO0-0.018-0.00731.6540.1830.1830.0000.0000.0000.000
89D92PHE00.0510.02032.0170.2080.2080.0000.0000.0000.000
90D93THR0-0.029-0.02728.7680.2370.2370.0000.0000.0000.000
91D94TRP00.022-0.01523.5660.5440.5440.0000.0000.0000.000
92D95ASP-1-0.807-0.88528.3299.1439.1430.0000.0000.0000.000
93D96ALA0-0.0060.01528.849-0.071-0.0710.0000.0000.0000.000
94D97VAL0-0.058-0.01423.8410.2660.2660.0000.0000.0000.000
95D98ARG10.9080.95224.848-9.458-9.4580.0000.0000.0000.000
96D99TYR00.023-0.00924.928-0.359-0.3590.0000.0000.0000.000
97D100ASN0-0.004-0.01026.278-0.011-0.0110.0000.0000.0000.000
98D101GLY0-0.010-0.00328.0950.1060.1060.0000.0000.0000.000
99D102LYS10.9350.99223.129-11.326-11.3260.0000.0000.0000.000
100D103LEU00.0020.01323.383-0.147-0.1470.0000.0000.0000.000
101D104ILE0-0.016-0.02620.4300.4340.4340.0000.0000.0000.000
102D105ALA0-0.027-0.01319.2190.7350.7350.0000.0000.0000.000
103D106TYR0-0.015-0.03716.858-0.408-0.4080.0000.0000.0000.000
104D107PRO00.0130.01821.6320.2170.2170.0000.0000.0000.000
105D108ILE0-0.024-0.01320.9020.2070.2070.0000.0000.0000.000
106D109ALA0-0.0080.00625.054-0.249-0.2490.0000.0000.0000.000
107D110VAL0-0.048-0.02828.2130.0920.0920.0000.0000.0000.000
108D111GLU-1-0.888-0.94131.3389.3419.3410.0000.0000.0000.000
109D112ALA00.0430.00733.698-0.034-0.0340.0000.0000.0000.000
110D113LEU0-0.0280.01437.144-0.076-0.0760.0000.0000.0000.000
111D114SER00.019-0.00240.3130.0030.0030.0000.0000.0000.000
112D115LEU00.0150.01142.868-0.014-0.0140.0000.0000.0000.000
113D116ILE0-0.041-0.00842.744-0.030-0.0300.0000.0000.0000.000
114D117TYR0-0.011-0.01947.165-0.121-0.1210.0000.0000.0000.000
115D118ASN00.0640.03350.4780.0400.0400.0000.0000.0000.000
116D119LYS10.9010.93449.430-6.424-6.4240.0000.0000.0000.000
117D120ASP-1-0.858-0.92354.6855.6215.6210.0000.0000.0000.000
118D121LEU0-0.100-0.04256.366-0.119-0.1190.0000.0000.0000.000
119D122LEU0-0.036-0.02754.982-0.090-0.0900.0000.0000.0000.000
120D123PRO00.0140.02955.4770.1160.1160.0000.0000.0000.000
121D124ASN0-0.067-0.04155.5170.0290.0290.0000.0000.0000.000
122D125PRO00.0130.02251.703-0.073-0.0730.0000.0000.0000.000
123D126PRO00.0230.01953.945-0.031-0.0310.0000.0000.0000.000
124D127LYS10.9540.96653.034-5.510-5.5100.0000.0000.0000.000
125D128THR0-0.090-0.04653.5080.0380.0380.0000.0000.0000.000
126D129TRP00.066-0.00848.504-0.071-0.0710.0000.0000.0000.000
127D130GLU-1-0.800-0.90454.6915.5185.5180.0000.0000.0000.000
128D131GLU-1-0.864-0.91257.4485.3425.3420.0000.0000.0000.000
129D132ILE00.0180.00453.716-0.053-0.0530.0000.0000.0000.000
130D133PRO00.0180.01558.263-0.053-0.0530.0000.0000.0000.000
131D134ALA0-0.054-0.03661.068-0.058-0.0580.0000.0000.0000.000
132D135LEU00.0640.03357.692-0.062-0.0620.0000.0000.0000.000
133D136ASP-1-0.747-0.84859.5635.2635.2630.0000.0000.0000.000
134D137LYS10.8990.95661.156-4.887-4.8870.0000.0000.0000.000
135D138GLU-1-0.864-0.92563.8434.8834.8830.0000.0000.0000.000
136D139LEU0-0.011-0.00158.769-0.041-0.0410.0000.0000.0000.000
137D140LYS10.8300.90659.770-5.259-5.2590.0000.0000.0000.000
138D141ALA0-0.043-0.00764.161-0.048-0.0480.0000.0000.0000.000
139D142LYS10.8150.90663.402-5.003-5.0030.0000.0000.0000.000
140D143GLY0-0.016-0.00464.2480.0520.0520.0000.0000.0000.000
141D144LYS10.8550.93258.715-5.309-5.3090.0000.0000.0000.000
142D145SER00.017-0.00256.337-0.051-0.0510.0000.0000.0000.000
143D146ALA00.0170.00957.0330.0470.0470.0000.0000.0000.000
144D147LEU0-0.046-0.02050.0830.0720.0720.0000.0000.0000.000
145D148MET0-0.027-0.00551.550-0.096-0.0960.0000.0000.0000.000
146D149PHE00.0620.01246.3220.0940.0940.0000.0000.0000.000
147D150ASN00.0060.00142.390-0.202-0.2020.0000.0000.0000.000
148D151LEU00.0080.00245.8950.0640.0640.0000.0000.0000.000
149D152GLN00.0050.00345.428-0.026-0.0260.0000.0000.0000.000
150D153GLU-1-0.844-0.91139.9307.6837.6830.0000.0000.0000.000
151D154PRO00.0320.00841.517-0.058-0.0580.0000.0000.0000.000
152D155TYR0-0.035-0.00835.675-0.127-0.1270.0000.0000.0000.000
153D156PHE00.0330.00639.9730.0450.0450.0000.0000.0000.000
154D157THR00.0140.01543.144-0.094-0.0940.0000.0000.0000.000
155D158TRP0-0.044-0.03241.144-0.228-0.2280.0000.0000.0000.000
156D159PRO00.0330.00842.290-0.106-0.1060.0000.0000.0000.000
157D160LEU0-0.0130.01244.696-0.079-0.0790.0000.0000.0000.000
158D161ILE0-0.059-0.02146.773-0.110-0.1100.0000.0000.0000.000
159D162ALA00.0230.00444.441-0.109-0.1090.0000.0000.0000.000
160D163ALA00.0340.03246.3730.0030.0030.0000.0000.0000.000
161D164ASP-1-0.864-0.92547.9205.8015.8010.0000.0000.0000.000
162D165GLY00.0120.00647.839-0.087-0.0870.0000.0000.0000.000
163D166GLY0-0.067-0.01646.784-0.002-0.0020.0000.0000.0000.000
164D167TYR0-0.047-0.05141.6110.0170.0170.0000.0000.0000.000
165D168ALA0-0.006-0.00538.696-0.094-0.0940.0000.0000.0000.000
166D169PHE0-0.014-0.02237.346-0.107-0.1070.0000.0000.0000.000
167D170LYS10.8360.90838.636-6.804-6.8040.0000.0000.0000.000
168D171TYR0-0.054-0.05232.0910.1910.1910.0000.0000.0000.000
169D172GLU-1-0.968-0.98336.1517.9507.9500.0000.0000.0000.000
170D173ASN0-0.069-0.04734.8860.0380.0380.0000.0000.0000.000
171D174GLY00.0700.03531.1180.1410.1410.0000.0000.0000.000
172D175LYS10.7780.90930.014-9.287-9.2870.0000.0000.0000.000
173D176TYR00.0850.03331.686-0.068-0.0680.0000.0000.0000.000
174D177ASP-1-0.796-0.88435.6257.5197.5190.0000.0000.0000.000
175D178ILE0-0.065-0.05735.094-0.087-0.0870.0000.0000.0000.000
176D179LYS10.8770.92338.083-7.038-7.0380.0000.0000.0000.000
177D180ASP-1-0.776-0.81641.4186.7226.7220.0000.0000.0000.000
178D181VAL00.018-0.01541.5220.1760.1760.0000.0000.0000.000
179D182GLY0-0.0440.00443.573-0.179-0.1790.0000.0000.0000.000
180D183VAL00.027-0.00743.838-0.028-0.0280.0000.0000.0000.000
181D184ASP-1-0.823-0.90546.6265.9275.9270.0000.0000.0000.000
182D185ASN0-0.0040.01348.199-0.159-0.1590.0000.0000.0000.000
183D186ALA0-0.010-0.02451.029-0.033-0.0330.0000.0000.0000.000
184D187GLY00.0360.02750.592-0.066-0.0660.0000.0000.0000.000
185D188ALA00.0500.02448.274-0.035-0.0350.0000.0000.0000.000
186D189LYS10.8250.90750.162-5.769-5.7690.0000.0000.0000.000
187D190ALA0-0.0100.01053.587-0.071-0.0710.0000.0000.0000.000
188D191GLY00.0700.03751.564-0.064-0.0640.0000.0000.0000.000
189D192LEU00.007-0.00550.384-0.030-0.0300.0000.0000.0000.000
190D193THR0-0.037-0.04252.529-0.075-0.0750.0000.0000.0000.000
191D194PHE00.0160.01754.475-0.090-0.0900.0000.0000.0000.000
192D195LEU0-0.002-0.00249.865-0.038-0.0380.0000.0000.0000.000
193D196VAL00.010-0.00353.972-0.040-0.0400.0000.0000.0000.000
194D197ASP-1-0.860-0.93156.3745.1145.1140.0000.0000.0000.000
195D198LEU0-0.024-0.00354.541-0.101-0.1010.0000.0000.0000.000
196D199ILE0-0.0070.00553.469-0.049-0.0490.0000.0000.0000.000
197D200LYS10.9150.96757.926-5.270-5.2700.0000.0000.0000.000
198D201ASN0-0.146-0.08661.215-0.171-0.1710.0000.0000.0000.000
199D202LYS10.9310.96361.118-4.847-4.8470.0000.0000.0000.000
200D203HIS0-0.073-0.05958.737-0.055-0.0550.0000.0000.0000.000
201D204MET0-0.0230.00051.1890.0700.0700.0000.0000.0000.000
202D205ASN0-0.022-0.01655.111-0.174-0.1740.0000.0000.0000.000
203D206ALA00.013-0.00553.9010.1030.1030.0000.0000.0000.000
204D207ASP-1-0.900-0.93151.6915.8915.8910.0000.0000.0000.000
205D208THR0-0.0130.00349.802-0.006-0.0060.0000.0000.0000.000
206D209ASP-1-0.825-0.92045.9786.8266.8260.0000.0000.0000.000
207D210TYR0-0.077-0.06340.690-0.019-0.0190.0000.0000.0000.000
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