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: 493VN

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 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 454
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7344126.907736
FMO2-HF: Nuclear repulsion 7170519.151858
FMO2-HF: Total energy -173607.755879
FMO2-MP2: Total energy -174120.076232


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.
4.9485.07524.045-12.672-11.4970.113
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 : -0.841 / q_NPA : -0.924
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].
3D6LYS10.7560.8641.846-139.815-142.85223.227-11.004-9.1850.116
4D7LEU00.0010.0124.6944.9815.076-0.001-0.012-0.0820.000
5D8VAL00.0120.0146.659-2.689-2.6890.0000.0000.0000.000
6D9ILE00.0070.0039.154-0.995-0.9950.0000.0000.0000.000
7D10TRP0-0.058-0.04512.588-1.227-1.2270.0000.0000.0000.000
8D11ILE00.0340.00515.618-0.572-0.5720.0000.0000.0000.000
9D12ASN0-0.001-0.01119.2590.2750.2750.0000.0000.0000.000
10D13GLY00.0630.02622.597-0.072-0.0720.0000.0000.0000.000
11D14ASP-1-0.826-0.90024.46011.12811.1280.0000.0000.0000.000
12D15LYS10.8930.94823.632-11.344-11.3440.0000.0000.0000.000
13D16GLY00.0370.03424.7970.1050.1050.0000.0000.0000.000
14D17TYR0-0.005-0.01920.1440.3860.3860.0000.0000.0000.000
15D18ASN0-0.040-0.04320.2771.2001.2000.0000.0000.0000.000
16D19GLY00.0430.02021.9010.2790.2790.0000.0000.0000.000
17D20LEU0-0.002-0.00117.1780.2500.2500.0000.0000.0000.000
18D21ALA00.0230.01117.3880.9480.9480.0000.0000.0000.000
19D22GLU-1-0.858-0.90618.20215.02715.0270.0000.0000.0000.000
20D23VAL00.0040.01117.8550.1780.1780.0000.0000.0000.000
21D24GLY00.007-0.00415.1330.5280.5280.0000.0000.0000.000
22D25LYS10.8180.88615.250-14.288-14.2880.0000.0000.0000.000
23D26LYS10.7470.85417.500-14.422-14.4220.0000.0000.0000.000
24D27PHE00.0760.03510.240-0.164-0.1640.0000.0000.0000.000
25D28GLU-1-0.788-0.86112.88724.00024.0000.0000.0000.0000.000
26D29LYS10.8840.93614.190-13.865-13.8650.0000.0000.0000.000
27D30ASP-1-0.784-0.84617.06614.62014.6200.0000.0000.0000.000
28D31THR0-0.017-0.01412.2380.4830.4830.0000.0000.0000.000
29D32GLY0-0.041-0.00912.5360.7060.7060.0000.0000.0000.000
30D33ILE0-0.048-0.0206.7982.6732.6730.0000.0000.0000.000
31D34LYS10.8220.8888.857-26.508-26.5080.0000.0000.0000.000
32D35VAL00.0040.0178.8552.8092.8090.0000.0000.0000.000
33D36THR0-0.063-0.02610.623-1.484-1.4840.0000.0000.0000.000
34D37VAL0-0.005-0.00312.1780.5670.5670.0000.0000.0000.000
35D38GLU-1-0.896-0.93912.49622.99922.9990.0000.0000.0000.000
36D39HIS00.0160.00016.534-0.486-0.4860.0000.0000.0000.000
37D40PRO0-0.0160.00516.784-0.828-0.8280.0000.0000.0000.000
38D41ASP-1-0.797-0.91620.03811.87511.8750.0000.0000.0000.000
39D42LYS10.7570.86522.241-11.360-11.3600.0000.0000.0000.000
40D43LEU00.0590.03718.2180.2470.2470.0000.0000.0000.000
41D44GLU-1-0.788-0.87619.05613.03713.0370.0000.0000.0000.000
42D45GLU-1-0.843-0.90321.39811.35511.3550.0000.0000.0000.000
43D46LYS10.8550.91517.835-14.393-14.3930.0000.0000.0000.000
44D47PHE00.0280.02113.1040.4310.4310.0000.0000.0000.000
45D48PRO0-0.001-0.01115.7880.7000.7000.0000.0000.0000.000
46D49GLN0-0.055-0.02917.4130.0150.0150.0000.0000.0000.000
47D50VAL0-0.0040.00512.9090.1330.1330.0000.0000.0000.000
48D51ALA00.0290.02212.1891.1611.1610.0000.0000.0000.000
49D52ALA0-0.055-0.02413.0620.4650.4650.0000.0000.0000.000
50D53THR0-0.098-0.08413.072-0.943-0.9430.0000.0000.0000.000
51D54GLY0-0.028-0.0029.7390.8470.8470.0000.0000.0000.000
52D55ASP-1-0.898-0.9028.07630.15230.1520.0000.0000.0000.000
53D56GLY0-0.017-0.0259.771-1.790-1.7900.0000.0000.0000.000
54D57PRO0-0.050-0.0108.6062.7292.7290.0000.0000.0000.000
55D58ASP-1-0.733-0.8426.08338.99338.9930.0000.0000.0000.000
56D59ILE0-0.030-0.0148.948-1.831-1.8310.0000.0000.0000.000
57D60ILE0-0.017-0.00112.6870.2580.2580.0000.0000.0000.000
58D61PHE00.0280.00015.819-0.676-0.6760.0000.0000.0000.000
59D62TRP0-0.018-0.02219.360-0.005-0.0050.0000.0000.0000.000
60D63ALA00.0330.03222.429-0.072-0.0720.0000.0000.0000.000
61D64HIS00.016-0.00124.5200.4780.4780.0000.0000.0000.000
62D65ASP-1-0.878-0.94425.59210.90210.9020.0000.0000.0000.000
63D66ARG10.8430.89922.946-11.906-11.9060.0000.0000.0000.000
64D67PHE0-0.001-0.00419.6240.2960.2960.0000.0000.0000.000
65D68GLY00.0420.03622.4820.2240.2240.0000.0000.0000.000
66D69GLY0-0.006-0.00124.794-0.030-0.0300.0000.0000.0000.000
67D70TYR0-0.023-0.03618.9910.1570.1570.0000.0000.0000.000
68D71ALA00.0220.02020.2680.3790.3790.0000.0000.0000.000
69D72GLN0-0.0350.00121.648-0.176-0.1760.0000.0000.0000.000
70D73SER0-0.079-0.04920.808-0.323-0.3230.0000.0000.0000.000
71D74GLY0-0.018-0.00319.4970.3740.3740.0000.0000.0000.000
72D75LEU0-0.009-0.00516.0110.6670.6670.0000.0000.0000.000
73D76LEU0-0.049-0.01415.0081.0341.0340.0000.0000.0000.000
74D77ALA0-0.007-0.01113.724-0.494-0.4940.0000.0000.0000.000
75D78GLU-1-0.830-0.90015.85712.02512.0250.0000.0000.0000.000
76D79ILE0-0.050-0.00716.5710.4910.4910.0000.0000.0000.000
77D80THR00.003-0.01217.243-0.544-0.5440.0000.0000.0000.000
78D81PRO00.0150.04419.4810.1380.1380.0000.0000.0000.000
79D82ASP-1-0.818-0.90621.28211.29211.2920.0000.0000.0000.000
80D83LYS10.8280.87224.065-9.196-9.1960.0000.0000.0000.000
81D84ALA0-0.0020.00427.097-0.254-0.2540.0000.0000.0000.000
82D85PHE00.0040.00421.901-0.080-0.0800.0000.0000.0000.000
83D86GLN0-0.069-0.04724.761-0.421-0.4210.0000.0000.0000.000
84D87ASP-1-0.797-0.87226.8138.9868.9860.0000.0000.0000.000
85D88LYS10.9010.98122.824-12.469-12.4690.0000.0000.0000.000
86D89LEU00.0250.01824.923-0.079-0.0790.0000.0000.0000.000
87D90TYR0-0.058-0.04829.000-0.367-0.3670.0000.0000.0000.000
88D91PRO0-0.015-0.00230.9890.2030.2030.0000.0000.0000.000
89D92PHE00.0310.00331.2570.2240.2240.0000.0000.0000.000
90D93THR0-0.003-0.01128.5480.2260.2260.0000.0000.0000.000
91D94TRP00.019-0.01722.8190.5150.5150.0000.0000.0000.000
92D95ASP-1-0.795-0.86227.8179.3499.3490.0000.0000.0000.000
93D96ALA00.0070.01428.4600.0000.0000.0000.0000.0000.000
94D97VAL0-0.039-0.00723.6710.1970.1970.0000.0000.0000.000
95D98ARG10.8210.90324.491-9.353-9.3530.0000.0000.0000.000
96D99TYR00.020-0.01724.945-0.376-0.3760.0000.0000.0000.000
97D100ASN0-0.032-0.01726.281-0.004-0.0040.0000.0000.0000.000
98D101GLY00.0050.00228.533-0.001-0.0010.0000.0000.0000.000
99D102LYS10.8180.89822.926-11.946-11.9460.0000.0000.0000.000
100D103LEU00.0390.02822.737-0.061-0.0610.0000.0000.0000.000
101D104ILE0-0.019-0.01519.9650.4950.4950.0000.0000.0000.000
102D105ALA0-0.003-0.01119.1300.7030.7030.0000.0000.0000.000
103D106TYR0-0.019-0.03516.483-0.446-0.4460.0000.0000.0000.000
104D107PRO00.0080.00921.0940.2320.2320.0000.0000.0000.000
105D108ILE0-0.020-0.01220.4400.2010.2010.0000.0000.0000.000
106D109ALA0-0.016-0.00424.576-0.293-0.2930.0000.0000.0000.000
107D110VAL0-0.054-0.02727.9450.1040.1040.0000.0000.0000.000
108D111GLU-1-0.880-0.94531.0469.4279.4270.0000.0000.0000.000
109D112ALA00.020-0.00333.226-0.005-0.0050.0000.0000.0000.000
110D113LEU0-0.0290.00836.699-0.063-0.0630.0000.0000.0000.000
111D114SER00.0130.00539.974-0.044-0.0440.0000.0000.0000.000
112D115LEU00.0030.00042.667-0.040-0.0400.0000.0000.0000.000
113D116ILE0-0.023-0.00442.6380.0340.0340.0000.0000.0000.000
114D117TYR00.003-0.00447.013-0.137-0.1370.0000.0000.0000.000
115D118ASN00.0530.01750.3830.0660.0660.0000.0000.0000.000
116D119LYS10.8530.90649.730-6.404-6.4040.0000.0000.0000.000
117D120ASP-1-0.838-0.91454.6355.6595.6590.0000.0000.0000.000
118D121LEU0-0.105-0.04756.258-0.120-0.1200.0000.0000.0000.000
119D122LEU0-0.030-0.02054.547-0.091-0.0910.0000.0000.0000.000
120D123PRO00.0040.01855.3900.1140.1140.0000.0000.0000.000
121D124ASN0-0.061-0.03655.5220.0150.0150.0000.0000.0000.000
122D125PRO00.0160.02151.422-0.073-0.0730.0000.0000.0000.000
123D126PRO00.0020.01053.476-0.040-0.0400.0000.0000.0000.000
124D127LYS10.9420.95452.943-5.533-5.5330.0000.0000.0000.000
125D128THR0-0.095-0.03353.3960.0350.0350.0000.0000.0000.000
126D129TRP00.0660.00048.362-0.044-0.0440.0000.0000.0000.000
127D130GLU-1-0.796-0.91454.6295.5535.5530.0000.0000.0000.000
128D131GLU-1-0.815-0.88057.1565.4195.4190.0000.0000.0000.000
129D132ILE00.0170.01653.396-0.067-0.0670.0000.0000.0000.000
130D133PRO00.0020.00257.876-0.042-0.0420.0000.0000.0000.000
131D134ALA0-0.030-0.02060.583-0.090-0.0900.0000.0000.0000.000
132D135LEU00.0530.02257.443-0.058-0.0580.0000.0000.0000.000
133D136ASP-1-0.732-0.84159.1525.3075.3070.0000.0000.0000.000
134D137LYS10.8910.95660.870-4.960-4.9600.0000.0000.0000.000
135D138GLU-1-0.879-0.92263.7334.9204.9200.0000.0000.0000.000
136D139LEU00.007-0.00258.497-0.033-0.0330.0000.0000.0000.000
137D140LYS10.7900.89059.260-5.317-5.3170.0000.0000.0000.000
138D141ALA0-0.051-0.01963.892-0.044-0.0440.0000.0000.0000.000
139D142LYS10.8170.90462.911-5.074-5.0740.0000.0000.0000.000
140D143GLY0-0.0080.00863.9580.0430.0430.0000.0000.0000.000
141D144LYS10.8340.91758.456-5.343-5.3430.0000.0000.0000.000
142D145SER00.0470.01556.122-0.046-0.0460.0000.0000.0000.000
143D146ALA00.002-0.00956.8220.0480.0480.0000.0000.0000.000
144D147LEU0-0.039-0.01849.9710.0760.0760.0000.0000.0000.000
145D148MET0-0.0150.01151.511-0.102-0.1020.0000.0000.0000.000
146D149PHE00.0440.01646.0470.0860.0860.0000.0000.0000.000
147D150ASN00.0240.00742.117-0.214-0.2140.0000.0000.0000.000
148D151LEU00.009-0.00645.7120.0630.0630.0000.0000.0000.000
149D152GLN0-0.028-0.01745.535-0.029-0.0290.0000.0000.0000.000
150D153GLU-1-0.815-0.89239.8877.8057.8050.0000.0000.0000.000
151D154PRO0-0.028-0.01341.245-0.012-0.0120.0000.0000.0000.000
152D155TYR0-0.031-0.01535.576-0.073-0.0730.0000.0000.0000.000
153D156PHE00.0470.00839.3730.0270.0270.0000.0000.0000.000
154D157THR0-0.0060.01142.756-0.102-0.1020.0000.0000.0000.000
155D158TRP0-0.014-0.02241.241-0.251-0.2510.0000.0000.0000.000
156D159PRO00.0250.01442.492-0.078-0.0780.0000.0000.0000.000
157D160LEU00.0030.02044.777-0.079-0.0790.0000.0000.0000.000
158D161ILE0-0.060-0.02546.341-0.099-0.0990.0000.0000.0000.000
159D162ALA00.0500.01544.386-0.105-0.1050.0000.0000.0000.000
160D163ALA00.0150.02346.4080.0150.0150.0000.0000.0000.000
161D164ASP-1-0.846-0.91548.0585.8385.8380.0000.0000.0000.000
162D165GLY00.0210.01847.298-0.079-0.0790.0000.0000.0000.000
163D166GLY0-0.0410.00046.459-0.011-0.0110.0000.0000.0000.000
164D167TYR0-0.036-0.04341.3630.0090.0090.0000.0000.0000.000
165D168ALA0-0.033-0.01838.537-0.112-0.1120.0000.0000.0000.000
166D169PHE0-0.004-0.02637.239-0.078-0.0780.0000.0000.0000.000
167D170LYS10.8070.88838.882-6.873-6.8730.0000.0000.0000.000
168D171TYR0-0.041-0.04532.0320.1480.1480.0000.0000.0000.000
169D172GLU-1-0.968-0.98035.1848.1708.1700.0000.0000.0000.000
170D173ASN0-0.063-0.03733.8790.0640.0640.0000.0000.0000.000
171D174GLY00.0850.03230.7130.1590.1590.0000.0000.0000.000
172D175LYS10.7920.92630.029-9.314-9.3140.0000.0000.0000.000
173D176TYR00.0580.02531.602-0.098-0.0980.0000.0000.0000.000
174D177ASP-1-0.774-0.87635.2687.6757.6750.0000.0000.0000.000
175D178ILE0-0.070-0.05035.2370.0390.0390.0000.0000.0000.000
176D179LYS10.8610.91938.338-7.071-7.0710.0000.0000.0000.000
177D180ASP-1-0.792-0.84242.0206.7626.7620.0000.0000.0000.000
178D181VAL00.026-0.00241.3390.1790.1790.0000.0000.0000.000
179D182GLY0-0.0260.00443.635-0.180-0.1800.0000.0000.0000.000
180D183VAL0-0.007-0.01843.564-0.073-0.0730.0000.0000.0000.000
181D184ASP-1-0.833-0.92046.2756.0096.0090.0000.0000.0000.000
182D185ASN0-0.023-0.00747.807-0.194-0.1940.0000.0000.0000.000
183D186ALA00.008-0.01650.780-0.028-0.0280.0000.0000.0000.000
184D187GLY00.0320.03050.749-0.080-0.0800.0000.0000.0000.000
185D188ALA00.0390.01647.973-0.027-0.0270.0000.0000.0000.000
186D189LYS10.8090.91549.774-5.807-5.8070.0000.0000.0000.000
187D190ALA0-0.0240.00453.272-0.086-0.0860.0000.0000.0000.000
188D191GLY00.0520.02651.111-0.070-0.0700.0000.0000.0000.000
189D192LEU0-0.001-0.01150.031-0.014-0.0140.0000.0000.0000.000
190D193THR0-0.029-0.02752.158-0.075-0.0750.0000.0000.0000.000
191D194PHE00.0140.01454.511-0.077-0.0770.0000.0000.0000.000
192D195LEU00.0080.00349.546-0.034-0.0340.0000.0000.0000.000
193D196VAL0-0.002-0.00953.654-0.046-0.0460.0000.0000.0000.000
194D197ASP-1-0.849-0.94155.8965.1655.1650.0000.0000.0000.000
195D198LEU0-0.024-0.00754.303-0.106-0.1060.0000.0000.0000.000
196D199ILE0-0.0060.00953.347-0.048-0.0480.0000.0000.0000.000
197D200LYS10.8920.96057.788-5.344-5.3440.0000.0000.0000.000
198D201ASN0-0.116-0.06861.088-0.170-0.1700.0000.0000.0000.000
199D202LYS10.9290.97160.541-4.913-4.9130.0000.0000.0000.000
200D203HIS0-0.060-0.05158.262-0.061-0.0610.0000.0000.0000.000
201D204MET0-0.0150.00650.7810.0550.0550.0000.0000.0000.000
202D205ASN0-0.030-0.02754.777-0.182-0.1820.0000.0000.0000.000
203D206ALA00.0100.00453.5750.1180.1180.0000.0000.0000.000
204D207ASP-1-0.833-0.90051.4845.8955.8950.0000.0000.0000.000
205D208THR0-0.029-0.01749.6890.0210.0210.0000.0000.0000.000
206D209ASP-1-0.774-0.89445.4747.0037.0030.0000.0000.0000.000
207D210TYR0-0.062-0.03640.414-0.031-0.0310.0000.0000.0000.000
208D211SER00.007-0.00144.6620.0200.0200.0000.0000.0000.000
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451D454ARG10.8950.965108.836-2.994-2.9940.0000.0000.0000.000
452D455LEU0-0.0220.001115.411-0.033-0.0330.0000.0000.0000.000
453D456ARG10.8950.939118.256-2.709-2.7090.0000.0000.0000.000
454D457ARG10.8780.945112.008-2.911-2.9110.0000.0000.0000.000