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: QY1GY

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 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 454
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7314266.494592
FMO2-HF: Nuclear repulsion 7140665.162683
FMO2-HF: Total energy -173601.331909
FMO2-MP2: Total energy -174113.715326


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.
63.5369.541.782-3.008-4.7850.018
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 : -0.995 / q_NPA : -1.006
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].
3D6LYS10.8790.9292.265-69.360-65.4001.396-2.107-3.2500.015
4D7LEU00.0240.0214.8172.9323.056-0.001-0.010-0.1130.000
5D8VAL0-0.0060.0167.208-2.490-2.4900.0000.0000.0000.000
6D9ILE00.013-0.0059.519-0.607-0.6070.0000.0000.0000.000
7D10TRP0-0.031-0.02012.908-0.997-0.9970.0000.0000.0000.000
8D11ILE00.024-0.00215.806-0.384-0.3840.0000.0000.0000.000
9D12ASN0-0.012-0.01919.3220.1990.1990.0000.0000.0000.000
10D13GLY00.0600.02922.6320.0170.0170.0000.0000.0000.000
11D14ASP-1-0.950-0.96024.41510.40110.4010.0000.0000.0000.000
12D15LYS10.9490.97623.452-10.934-10.9340.0000.0000.0000.000
13D16GLY00.0380.03325.038-0.037-0.0370.0000.0000.0000.000
14D17TYR0-0.005-0.01720.2330.4460.4460.0000.0000.0000.000
15D18ASN00.0180.00120.4641.2091.2090.0000.0000.0000.000
16D19GLY00.0390.01722.5010.1370.1370.0000.0000.0000.000
17D20LEU00.0000.00617.0330.3040.3040.0000.0000.0000.000
18D21ALA0-0.031-0.01817.6910.6830.6830.0000.0000.0000.000
19D22GLU-1-0.966-0.98218.43313.32813.3280.0000.0000.0000.000
20D23VAL0-0.025-0.00218.2490.1580.1580.0000.0000.0000.000
21D24GLY00.001-0.01015.4890.4110.4110.0000.0000.0000.000
22D25LYS10.9920.99715.167-13.996-13.9960.0000.0000.0000.000
23D26LYS10.8880.93517.657-12.994-12.9940.0000.0000.0000.000
24D27PHE00.0380.02811.148-0.121-0.1210.0000.0000.0000.000
25D28GLU-1-0.933-0.96613.10520.79220.7920.0000.0000.0000.000
26D29LYS10.8500.93014.547-13.017-13.0170.0000.0000.0000.000
27D30ASP-1-0.915-0.96417.24714.35614.3560.0000.0000.0000.000
28D31THR0-0.0190.00212.2900.4770.4770.0000.0000.0000.000
29D32GLY00.0120.00912.816-0.010-0.0100.0000.0000.0000.000
30D33ILE0-0.075-0.0237.0312.5222.5220.0000.0000.0000.000
31D34LYS10.9470.9689.358-29.090-29.0900.0000.0000.0000.000
32D35VAL00.0230.0219.0162.1522.1520.0000.0000.0000.000
33D36THR0-0.090-0.03511.021-0.885-0.8850.0000.0000.0000.000
34D37VAL00.0160.01112.4780.5450.5450.0000.0000.0000.000
35D38GLU-1-0.942-0.97413.10920.28020.2800.0000.0000.0000.000
36D39HIS00.009-0.00716.699-0.401-0.4010.0000.0000.0000.000
37D40PRO0-0.019-0.00116.845-0.644-0.6440.0000.0000.0000.000
38D41ASP-1-0.843-0.93219.88411.28711.2870.0000.0000.0000.000
39D42LYS10.8660.92822.202-10.243-10.2430.0000.0000.0000.000
40D43LEU00.0370.02718.2560.2450.2450.0000.0000.0000.000
41D44GLU-1-0.821-0.92419.54512.21812.2180.0000.0000.0000.000
42D45GLU-1-0.977-0.99321.51610.98110.9810.0000.0000.0000.000
43D46LYS10.9320.96618.167-14.055-14.0550.0000.0000.0000.000
44D47PHE00.0210.01813.3250.4270.4270.0000.0000.0000.000
45D48PRO0-0.009-0.01516.2590.6320.6320.0000.0000.0000.000
46D49GLN0-0.057-0.02718.070-0.107-0.1070.0000.0000.0000.000
47D50VAL0-0.0250.00213.4080.2880.2880.0000.0000.0000.000
48D51ALA00.0410.03112.3101.1371.1370.0000.0000.0000.000
49D52ALA0-0.055-0.02112.8240.7380.7380.0000.0000.0000.000
50D53THR0-0.076-0.04213.110-0.913-0.9130.0000.0000.0000.000
51D54GLY0-0.043-0.0109.6111.0681.0680.0000.0000.0000.000
52D55ASP-1-0.905-0.9307.99328.79028.7900.0000.0000.0000.000
53D56GLY0-0.031-0.0389.936-1.403-1.4030.0000.0000.0000.000
54D57PRO0-0.048-0.0048.8771.9261.9260.0000.0000.0000.000
55D58ASP-1-0.778-0.9016.04933.10233.1020.0000.0000.0000.000
56D59ILE0-0.023-0.0149.151-1.434-1.4340.0000.0000.0000.000
57D60ILE0-0.013-0.00312.8110.1050.1050.0000.0000.0000.000
58D61PHE00.031-0.00915.913-0.576-0.5760.0000.0000.0000.000
59D62TRP0-0.034-0.03619.327-0.054-0.0540.0000.0000.0000.000
60D63ALA00.0150.02322.442-0.036-0.0360.0000.0000.0000.000
61D64HIS00.0350.00224.6570.2970.2970.0000.0000.0000.000
62D65ASP-1-0.858-0.93425.70310.01210.0120.0000.0000.0000.000
63D66ARG10.9340.96223.410-11.444-11.4440.0000.0000.0000.000
64D67PHE0-0.026-0.01019.4020.3110.3110.0000.0000.0000.000
65D68GLY00.0140.01622.8730.2140.2140.0000.0000.0000.000
66D69GLY0-0.031-0.01624.9660.0180.0180.0000.0000.0000.000
67D70TYR0-0.031-0.04019.2130.0860.0860.0000.0000.0000.000
68D71ALA00.0640.03120.6670.3020.3020.0000.0000.0000.000
69D72GLN0-0.064-0.01021.7240.1680.1680.0000.0000.0000.000
70D73SER0-0.064-0.03620.873-0.276-0.2760.0000.0000.0000.000
71D74GLY0-0.050-0.02819.7530.3440.3440.0000.0000.0000.000
72D75LEU0-0.009-0.00816.2960.6000.6000.0000.0000.0000.000
73D76LEU0-0.047-0.01115.0770.8970.8970.0000.0000.0000.000
74D77ALA0-0.015-0.01413.634-0.415-0.4150.0000.0000.0000.000
75D78GLU-1-0.956-0.97815.77111.72611.7260.0000.0000.0000.000
76D79ILE0-0.043-0.00317.1820.4580.4580.0000.0000.0000.000
77D80THR0-0.003-0.01718.194-0.486-0.4860.0000.0000.0000.000
78D81PRO0-0.0160.00920.1490.2320.2320.0000.0000.0000.000
79D82ASP-1-0.851-0.93621.90210.98310.9830.0000.0000.0000.000
80D83LYS10.9100.92624.754-8.731-8.7310.0000.0000.0000.000
81D84ALA00.0150.01727.001-0.308-0.3080.0000.0000.0000.000
82D85PHE00.0050.01922.590-0.200-0.2000.0000.0000.0000.000
83D86GLN0-0.038-0.02125.980-0.459-0.4590.0000.0000.0000.000
84D87ASP-1-0.880-0.93627.5908.7698.7690.0000.0000.0000.000
85D88LYS10.9050.94825.393-11.079-11.0790.0000.0000.0000.000
86D89LEU00.0190.02025.450-0.026-0.0260.0000.0000.0000.000
87D90TYR00.0120.00529.695-0.344-0.3440.0000.0000.0000.000
88D91PRO0-0.016-0.01231.6910.1590.1590.0000.0000.0000.000
89D92PHE00.0540.01432.0460.1910.1910.0000.0000.0000.000
90D93THR0-0.020-0.00428.7560.2260.2260.0000.0000.0000.000
91D94TRP00.033-0.01023.6630.4930.4930.0000.0000.0000.000
92D95ASP-1-0.863-0.93828.3578.8638.8630.0000.0000.0000.000
93D96ALA0-0.0090.00528.825-0.062-0.0620.0000.0000.0000.000
94D97VAL0-0.057-0.01023.8200.2380.2380.0000.0000.0000.000
95D98ARG10.8970.95624.875-9.193-9.1930.0000.0000.0000.000
96D99TYR00.0250.01124.963-0.272-0.2720.0000.0000.0000.000
97D100ASN0-0.033-0.03426.301-0.088-0.0880.0000.0000.0000.000
98D101GLY0-0.027-0.01528.1160.1170.1170.0000.0000.0000.000
99D102LYS10.9530.98923.570-10.974-10.9740.0000.0000.0000.000
100D103LEU00.0200.02123.342-0.164-0.1640.0000.0000.0000.000
101D104ILE0-0.020-0.02020.4680.4350.4350.0000.0000.0000.000
102D105ALA0-0.011-0.01619.2460.6660.6660.0000.0000.0000.000
103D106TYR00.006-0.01917.206-0.335-0.3350.0000.0000.0000.000
104D107PRO00.0050.01521.6630.1770.1770.0000.0000.0000.000
105D108ILE0-0.016-0.00321.1030.1890.1890.0000.0000.0000.000
106D109ALA0-0.0080.00425.084-0.230-0.2300.0000.0000.0000.000
107D110VAL0-0.030-0.02428.2400.0960.0960.0000.0000.0000.000
108D111GLU-1-0.932-0.95331.3688.9858.9850.0000.0000.0000.000
109D112ALA00.037-0.00233.728-0.025-0.0250.0000.0000.0000.000
110D113LEU0-0.0440.02337.173-0.077-0.0770.0000.0000.0000.000
111D114SER00.0340.00840.341-0.012-0.0120.0000.0000.0000.000
112D115LEU0-0.0020.00142.897-0.018-0.0180.0000.0000.0000.000
113D116ILE0-0.0310.00042.944-0.027-0.0270.0000.0000.0000.000
114D117TYR0-0.030-0.03147.173-0.058-0.0580.0000.0000.0000.000
115D118ASN00.0760.04650.4780.0320.0320.0000.0000.0000.000
116D119LYS10.9500.96149.873-6.150-6.1500.0000.0000.0000.000
117D120ASP-1-0.878-0.93954.6855.4295.4290.0000.0000.0000.000
118D121LEU0-0.125-0.06156.604-0.117-0.1170.0000.0000.0000.000
119D122LEU0-0.026-0.02155.330-0.086-0.0860.0000.0000.0000.000
120D123PRO00.0300.03755.4770.1130.1130.0000.0000.0000.000
121D124ASN0-0.072-0.05055.5170.0370.0370.0000.0000.0000.000
122D125PRO00.0110.02451.754-0.072-0.0720.0000.0000.0000.000
123D126PRO00.0440.03053.878-0.025-0.0250.0000.0000.0000.000
124D127LYS10.9610.96853.065-5.416-5.4160.0000.0000.0000.000
125D128THR0-0.057-0.00853.5380.0380.0380.0000.0000.0000.000
126D129TRP00.069-0.00848.638-0.064-0.0640.0000.0000.0000.000
127D130GLU-1-0.810-0.89754.7205.4175.4170.0000.0000.0000.000
128D131GLU-1-0.930-0.96957.8025.1685.1680.0000.0000.0000.000
129D132ILE00.0160.00653.773-0.050-0.0500.0000.0000.0000.000
130D133PRO00.0100.00658.291-0.052-0.0520.0000.0000.0000.000
131D134ALA0-0.062-0.03661.096-0.058-0.0580.0000.0000.0000.000
132D135LEU00.0820.04358.044-0.054-0.0540.0000.0000.0000.000
133D136ASP-1-0.725-0.85559.6595.1525.1520.0000.0000.0000.000
134D137LYS10.8930.95161.184-4.718-4.7180.0000.0000.0000.000
135D138GLU-1-0.934-0.96463.8164.7424.7420.0000.0000.0000.000
136D139LEU0-0.032-0.01358.794-0.041-0.0410.0000.0000.0000.000
137D140LYS10.8560.92359.863-5.124-5.1240.0000.0000.0000.000
138D141ALA0-0.039-0.00464.189-0.048-0.0480.0000.0000.0000.000
139D142LYS10.8870.94863.686-4.886-4.8860.0000.0000.0000.000
140D143GLY0-0.021-0.00864.2740.0480.0480.0000.0000.0000.000
141D144LYS10.8730.94958.698-5.177-5.1770.0000.0000.0000.000
142D145SER00.020-0.00756.609-0.076-0.0760.0000.0000.0000.000
143D146ALA00.0120.01157.1110.0470.0470.0000.0000.0000.000
144D147LEU0-0.037-0.01550.0340.0710.0710.0000.0000.0000.000
145D148MET0-0.059-0.02451.448-0.090-0.0900.0000.0000.0000.000
146D149PHE00.0500.00346.2700.0850.0850.0000.0000.0000.000
147D150ASN00.0190.00542.653-0.199-0.1990.0000.0000.0000.000
148D151LEU00.0110.00645.9210.0630.0630.0000.0000.0000.000
149D152GLN00.0010.00145.431-0.042-0.0420.0000.0000.0000.000
150D153GLU-1-0.911-0.95239.8767.4737.4730.0000.0000.0000.000
151D154PRO00.018-0.01641.353-0.071-0.0710.0000.0000.0000.000
152D155TYR0-0.0160.00735.902-0.107-0.1070.0000.0000.0000.000
153D156PHE00.0370.00840.2910.0400.0400.0000.0000.0000.000
154D157THR00.0070.01443.171-0.082-0.0820.0000.0000.0000.000
155D158TRP0-0.060-0.03340.910-0.216-0.2160.0000.0000.0000.000
156D159PRO00.0260.00242.294-0.099-0.0990.0000.0000.0000.000
157D160LEU00.0000.01844.724-0.072-0.0720.0000.0000.0000.000
158D161ILE0-0.060-0.02046.893-0.102-0.1020.0000.0000.0000.000
159D162ALA00.0230.00544.424-0.101-0.1010.0000.0000.0000.000
160D163ALA00.0420.03546.4010.0060.0060.0000.0000.0000.000
161D164ASP-1-0.925-0.95647.9485.7155.7150.0000.0000.0000.000
162D165GLY0-0.002-0.00447.868-0.075-0.0750.0000.0000.0000.000
163D166GLY0-0.076-0.01946.811-0.002-0.0020.0000.0000.0000.000
164D167TYR0-0.054-0.03041.6120.0250.0250.0000.0000.0000.000
165D168ALA00.0030.00738.685-0.090-0.0900.0000.0000.0000.000
166D169PHE0-0.016-0.02437.027-0.093-0.0930.0000.0000.0000.000
167D170LYS10.9821.00738.661-6.728-6.7280.0000.0000.0000.000
168D171TYR0-0.007-0.01032.1090.2090.2090.0000.0000.0000.000
169D172GLU-1-0.963-0.98936.4647.7027.7020.0000.0000.0000.000
170D173ASN0-0.051-0.03934.723-0.055-0.0550.0000.0000.0000.000
171D174GLY00.0340.02231.1430.1390.1390.0000.0000.0000.000
172D175LYS10.8310.94229.534-8.944-8.9440.0000.0000.0000.000
173D176TYR00.0900.03831.888-0.041-0.0410.0000.0000.0000.000
174D177ASP-1-0.824-0.91035.6487.3497.3490.0000.0000.0000.000
175D178ILE0-0.058-0.04435.221-0.084-0.0840.0000.0000.0000.000
176D179LYS10.8880.92038.104-6.996-6.9960.0000.0000.0000.000
177D180ASP-1-0.845-0.89441.4486.5586.5580.0000.0000.0000.000
178D181VAL0-0.013-0.02041.7680.1790.1790.0000.0000.0000.000
179D182GLY0-0.049-0.00343.596-0.167-0.1670.0000.0000.0000.000
180D183VAL00.031-0.00543.960-0.030-0.0300.0000.0000.0000.000
181D184ASP-1-0.882-0.96446.6515.7685.7680.0000.0000.0000.000
182D185ASN00.0060.01148.545-0.112-0.1120.0000.0000.0000.000
183D186ALA0-0.039-0.03751.054-0.035-0.0350.0000.0000.0000.000
184D187GLY00.0320.02350.619-0.062-0.0620.0000.0000.0000.000
185D188ALA00.0560.02848.299-0.037-0.0370.0000.0000.0000.000
186D189LYS10.9050.96650.188-5.594-5.5940.0000.0000.0000.000
187D190ALA0-0.0120.00253.613-0.070-0.0700.0000.0000.0000.000
188D191GLY00.0650.03451.591-0.063-0.0630.0000.0000.0000.000
189D192LEU00.009-0.00450.301-0.030-0.0300.0000.0000.0000.000
190D193THR0-0.036-0.02852.555-0.075-0.0750.0000.0000.0000.000
191D194PHE00.0150.01954.411-0.083-0.0830.0000.0000.0000.000
192D195LEU0-0.005-0.00649.940-0.035-0.0350.0000.0000.0000.000
193D196VAL00.010-0.00253.998-0.034-0.0340.0000.0000.0000.000
194D197ASP-1-0.890-0.94656.4005.0325.0320.0000.0000.0000.000
195D198LEU0-0.046-0.02454.603-0.094-0.0940.0000.0000.0000.000
196D199ILE0-0.0030.01053.603-0.046-0.0460.0000.0000.0000.000
197D200LYS10.9360.96857.952-5.107-5.1070.0000.0000.0000.000
198D201ASN0-0.107-0.05361.258-0.168-0.1680.0000.0000.0000.000
199D202LYS10.9250.95861.171-4.730-4.7300.0000.0000.0000.000
200D203HIS0-0.068-0.04658.748-0.045-0.0450.0000.0000.0000.000
201D204MET0-0.032-0.00351.2680.0740.0740.0000.0000.0000.000
202D205ASN0-0.030-0.02155.027-0.178-0.1780.0000.0000.0000.000
203D206ALA00.019-0.00953.9250.0970.0970.0000.0000.0000.000
204D207ASP-1-0.906-0.92551.7095.7475.7470.0000.0000.0000.000
205D208THR00.0010.01049.866-0.011-0.0110.0000.0000.0000.000
206D209ASP-1-0.813-0.92545.9126.5796.5790.0000.0000.0000.000
207D210TYR0-0.041-0.03140.444-0.026-0.0260.0000.0000.0000.000
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