Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: ZV31N

Calculation Name: 4HKJ-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HKJ

Chain ID: D

ChEMBL ID:

UniProt ID: P61769

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:


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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2048802.170123
FMO2-HF: Nuclear repulsion 1971799.932802
FMO2-HF: Total energy -77002.23732
FMO2-MP2: Total energy -77219.024492


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:5:ARG)


Summations of interaction energy for fragment #1(D:5:ARG)
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.
-194.989-200.63830.103-14.165-10.289-0.149
Interaction energy analysis for fragmet #1(D:5:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.889
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].
3D7GLU-1-0.845-0.9283.756-39.876-37.492-0.015-1.320-1.0480.003
4D8LYS10.8100.8955.45127.18827.1880.0000.0000.0000.000
5D9MET00.0380.0116.5150.7570.7570.0000.0000.0000.000
6D10GLU-1-0.803-0.8776.589-33.156-33.1560.0000.0000.0000.000
7D11GLU-1-0.791-0.8681.701-142.524-151.05230.075-12.751-8.796-0.152
8D12GLU-1-0.806-0.8846.093-26.087-26.0870.0000.0000.0000.000
9D13THR0-0.065-0.0359.0923.8103.8100.0000.0000.0000.000
10D14TRP00.0090.0109.258-0.352-0.3520.0000.0000.0000.000
11D15LYS10.8160.90713.29321.41321.4130.0000.0000.0000.000
12D16LEU00.0160.01216.420-0.249-0.2490.0000.0000.0000.000
13D17LYS10.8130.90019.41113.57313.5730.0000.0000.0000.000
14D18ILE00.0310.01122.003-0.221-0.2210.0000.0000.0000.000
15D19GLY00.0060.01724.9080.3720.3720.0000.0000.0000.000
16D20MET0-0.014-0.00627.0430.0670.0670.0000.0000.0000.000
17D21CYS0-0.084-0.03030.5670.3940.3940.0000.0000.0000.000
18D22ILE00.0490.02033.0850.0080.0080.0000.0000.0000.000
19D23GLN0-0.0040.01136.810-0.021-0.0210.0000.0000.0000.000
20D24ALA00.0310.00939.7900.0470.0470.0000.0000.0000.000
21D25LYS10.8360.91743.3346.6716.6710.0000.0000.0000.000
22D26ASP-1-0.875-0.94846.159-6.380-6.3800.0000.0000.0000.000
23D27PHE0-0.0180.00544.9290.1110.1110.0000.0000.0000.000
24D28TYR0-0.017-0.01546.661-0.089-0.0890.0000.0000.0000.000
25D29SER00.0250.02941.7250.1190.1190.0000.0000.0000.000
26D30LYS10.8950.94844.7026.5906.5900.0000.0000.0000.000
27D31ARG10.9270.96439.6877.4267.4260.0000.0000.0000.000
28D32THR0-0.085-0.04741.1270.2700.2700.0000.0000.0000.000
29D33ASP-1-0.895-0.93039.499-7.932-7.9320.0000.0000.0000.000
30D34CYS0-0.067-0.00132.3370.2610.2610.0000.0000.0000.000
31D35SER0-0.015-0.00438.321-0.085-0.0850.0000.0000.0000.000
32D36VAL0-0.026-0.01233.194-0.112-0.1120.0000.0000.0000.000
33D37HIS10.7920.87336.5768.2078.2070.0000.0000.0000.000
34D38ARG10.9200.93433.4018.6058.6050.0000.0000.0000.000
35D39PRO0-0.065-0.01335.8220.1620.1620.0000.0000.0000.000
36D40ASP-1-0.793-0.89238.214-8.222-8.2220.0000.0000.0000.000
37D41VAL0-0.054-0.01840.1350.0590.0590.0000.0000.0000.000
38D42GLY00.0380.01638.3070.0910.0910.0000.0000.0000.000
39D43GLY00.0380.02833.979-0.074-0.0740.0000.0000.0000.000
40D44GLY00.0430.03532.014-0.115-0.1150.0000.0000.0000.000
41D45LEU0-0.067-0.03430.3820.0930.0930.0000.0000.0000.000
42D46ILE00.004-0.00134.2840.1070.1070.0000.0000.0000.000
43D47THR0-0.049-0.03434.497-0.079-0.0790.0000.0000.0000.000
44D48GLU-1-0.739-0.85237.270-7.784-7.7840.0000.0000.0000.000
45D49GLY00.016-0.01039.451-0.109-0.1090.0000.0000.0000.000
46D50ASN0-0.021-0.03037.7780.1250.1250.0000.0000.0000.000
47D51GLY00.0630.04140.9560.0000.0000.0000.0000.0000.000
48D52TYR0-0.032-0.01339.9670.1730.1730.0000.0000.0000.000
49D53ARG10.8730.93139.9957.4177.4170.0000.0000.0000.000
50D54VAL0-0.017-0.01134.6990.0350.0350.0000.0000.0000.000
51D55VAL00.0030.01136.769-0.086-0.0860.0000.0000.0000.000
52D56VAL0-0.013-0.01830.205-0.103-0.1030.0000.0000.0000.000
53D57HIS0-0.033-0.03132.7920.2230.2230.0000.0000.0000.000
54D58ASP-1-0.802-0.89128.370-11.209-11.2090.0000.0000.0000.000
55D59GLN0-0.021-0.01629.8580.2990.2990.0000.0000.0000.000
56D60CYS0-0.070-0.01924.302-0.091-0.0910.0000.0000.0000.000
57D61GLU-1-0.923-0.95731.380-8.416-8.4160.0000.0000.0000.000
58D62GLU-1-0.916-0.95031.627-9.170-9.1700.0000.0000.0000.000
59D63PRO0-0.024-0.01631.713-0.306-0.3060.0000.0000.0000.000
60D64ASN0-0.012-0.01327.105-0.562-0.5620.0000.0000.0000.000
61D65PRO0-0.051-0.02524.2360.2420.2420.0000.0000.0000.000
62D66PHE00.0180.00825.235-0.412-0.4120.0000.0000.0000.000
63D67ILE00.0540.03220.167-0.243-0.2430.0000.0000.0000.000
64D68ILE0-0.063-0.01423.026-0.550-0.5500.0000.0000.0000.000
65D69ALA00.0500.02224.2510.3540.3540.0000.0000.0000.000
66D70THR0-0.073-0.04526.1560.2020.2020.0000.0000.0000.000
67D71THR00.004-0.00827.834-0.056-0.0560.0000.0000.0000.000
68D72LYS10.8820.94825.08112.22812.2280.0000.0000.0000.000
69D73GLN00.0580.02931.2610.1140.1140.0000.0000.0000.000
70D74THR0-0.033-0.02832.7270.0630.0630.0000.0000.0000.000
71D75HIS0-0.015-0.00735.100-0.106-0.1060.0000.0000.0000.000
72D76PHE00.0020.01133.2570.0050.0050.0000.0000.0000.000
73D77GLY00.0080.00438.7450.0610.0610.0000.0000.0000.000
74D78VAL0-0.009-0.01242.1160.0470.0470.0000.0000.0000.000
75D79THR00.0510.02641.1630.1320.1320.0000.0000.0000.000
76D80HIS00.0080.03237.022-0.125-0.1250.0000.0000.0000.000
77D81SER0-0.017-0.02537.0210.1490.1490.0000.0000.0000.000
78D82TYR0-0.027-0.02526.565-0.076-0.0760.0000.0000.0000.000
79D83ILE00.0160.00531.8110.1450.1450.0000.0000.0000.000
80D84GLU-1-0.773-0.86825.838-12.367-12.3670.0000.0000.0000.000
81D85PHE00.0500.02726.9480.1790.1790.0000.0000.0000.000
82D86SER0-0.034-0.03723.285-0.458-0.4580.0000.0000.0000.000
83D87ASN00.007-0.00820.9510.2590.2590.0000.0000.0000.000
84D88SER0-0.0040.00519.592-0.687-0.6870.0000.0000.0000.000
85D89ASN00.022-0.01415.185-2.139-2.1390.0000.0000.0000.000
86D90THR0-0.040-0.00916.2340.7190.7190.0000.0000.0000.000
87D91GLY00.0080.02314.4320.5350.5350.0000.0000.0000.000
88D92ALA00.0370.01311.2890.3920.3920.0000.0000.0000.000
89D93PRO00.0410.00812.6591.3941.3940.0000.0000.0000.000
90D94GLU-1-0.915-0.96211.835-22.928-22.9280.0000.0000.0000.000
91D95ASN0-0.082-0.03713.8281.4921.4920.0000.0000.0000.000
92D96ILE0-0.0240.00717.6700.8770.8770.0000.0000.0000.000
93D97PRO00.0350.00820.189-0.010-0.0100.0000.0000.0000.000
94D98ASP-1-0.835-0.93122.777-13.381-13.3810.0000.0000.0000.000
95D100SER00.026-0.00724.5490.2340.2340.0000.0000.0000.000
96D101LYS10.8050.91419.52414.93614.9360.0000.0000.0000.000
97D102HIS0-0.082-0.04524.1190.1160.1160.0000.0000.0000.000
98D103ILE0-0.0050.00025.7130.4050.4050.0000.0000.0000.000
99D104LEU0-0.005-0.00528.8490.1170.1170.0000.0000.0000.000
100D105ILE0-0.002-0.00229.5300.1100.1100.0000.0000.0000.000
101D106SER0-0.028-0.02233.7320.2340.2340.0000.0000.0000.000
102D107VAL0-0.019-0.00836.3580.0290.0290.0000.0000.0000.000
103D108TYR00.0200.00038.8980.2020.2020.0000.0000.0000.000
104D109CYS00.0100.00542.272-0.061-0.0610.0000.0000.0000.000
105D110ASP-1-0.811-0.89144.754-7.135-7.1350.0000.0000.0000.000
106D111GLN0-0.093-0.06346.613-0.014-0.0140.0000.0000.0000.000
107D112GLU-1-0.853-0.90548.531-6.015-6.0150.0000.0000.0000.000
108D113ALA0-0.028-0.02450.075-0.081-0.0810.0000.0000.0000.000
109D114SER0-0.055-0.02548.4140.0090.0090.0000.0000.0000.000
110D115GLY00.0320.00949.8450.1130.1130.0000.0000.0000.000
111D116LEU0-0.090-0.04747.7470.0420.0420.0000.0000.0000.000
112D117ASP-1-0.897-0.92947.886-6.645-6.6450.0000.0000.0000.000
113D118PHE0-0.045-0.03442.619-0.186-0.1860.0000.0000.0000.000
114D119HIS00.0670.05138.0890.1630.1630.0000.0000.0000.000
115D120THR0-0.017-0.03337.069-0.110-0.1100.0000.0000.0000.000
116D121LEU0-0.0060.01133.3590.0790.0790.0000.0000.0000.000
117D122LYS10.8610.91329.25610.52610.5260.0000.0000.0000.000
118D123TYR0-0.008-0.02129.059-0.052-0.0520.0000.0000.0000.000
119D124VAL0-0.018-0.00223.521-0.270-0.2700.0000.0000.0000.000
120D125GLU-1-0.791-0.87225.149-11.535-11.5350.0000.0000.0000.000
121D126SER0-0.023-0.02120.017-0.564-0.5640.0000.0000.0000.000
122D127ASN00.021-0.00717.8350.9410.9410.0000.0000.0000.000
123D128TYR0-0.0020.01311.933-0.062-0.0620.0000.0000.0000.000
124D129LEU00.0070.01218.7110.3060.3060.0000.0000.0000.000
125D130HIS10.8700.94122.11712.79212.7920.0000.0000.0000.000
126D131ILE00.0060.00724.7420.0960.0960.0000.0000.0000.000
127D132THR0-0.035-0.01428.1690.1920.1920.0000.0000.0000.000
128D133VAL0-0.007-0.00731.736-0.052-0.0520.0000.0000.0000.000
129D134LYS10.9160.98634.2707.7487.7480.0000.0000.0000.000
130D135TYR0-0.001-0.01237.572-0.135-0.1350.0000.0000.0000.000
131D136ASP-1-0.738-0.84040.208-6.775-6.7750.0000.0000.0000.000
132D137THR0-0.004-0.02042.364-0.009-0.0090.0000.0000.0000.000
133D138SER0-0.032-0.03244.4910.1120.1120.0000.0000.0000.000
134D140ILE0-0.018-0.01039.606-0.096-0.0960.0000.0000.0000.000
135D141ASN0-0.071-0.03542.0190.1610.1610.0000.0000.0000.000
136D142HIS0-0.008-0.01934.156-0.064-0.0640.0000.0000.0000.000
137D143LEU00.0420.02533.5270.0000.0000.0000.0000.0000.000
138D144GLY00.0020.01632.083-0.030-0.0300.0000.0000.0000.000
139D145VAL0-0.012-0.01526.8490.0260.0260.0000.0000.0000.000
140D146ASN0-0.047-0.02922.860-0.461-0.4610.0000.0000.0000.000
141D147TYR00.019-0.01219.6620.0420.0420.0000.0000.0000.000
142D148SER0-0.0020.01017.193-0.597-0.5970.0000.0000.0000.000
143D149PHE00.0400.00215.1430.4570.4570.0000.0000.0000.000
144D150MET0-0.0010.01911.629-0.447-0.4470.0000.0000.0000.000
145D151ASN00.0430.0357.061-0.865-0.8650.0000.0000.0000.000
146D152GLU-1-0.747-0.8449.852-21.312-21.3120.0000.0000.0000.000
147D154GLU-1-0.834-0.9276.211-29.863-29.8630.0000.0000.0000.000
148D155ARG10.8720.9167.94623.74723.7470.0000.0000.0000.000
149D156LYS10.7730.8685.93036.69736.6970.0000.0000.0000.000
150D157LEU0-0.022-0.0123.0471.2361.7310.043-0.094-0.4450.000
151D158THR0-0.047-0.0377.6902.1662.1660.0000.0000.0000.000
152D159SER0-0.030-0.02311.1762.1902.1900.0000.0000.0000.000
153D160ILE0-0.036-0.01213.0891.2391.2390.0000.0000.0000.000
154D161TYR0-0.037-0.01212.5740.6410.6410.0000.0000.0000.000
155D162GLU-1-0.941-0.96816.852-13.275-13.2750.0000.0000.0000.000
156D163THR00.001-0.00918.3950.4100.4100.0000.0000.0000.000
157D164ASP-1-0.848-0.89321.077-11.790-11.7900.0000.0000.0000.000
158D165THR00.0400.00923.3910.1680.1680.0000.0000.0000.000
159D166LEU00.0030.02326.8770.4820.4820.0000.0000.0000.000
160D167THR0-0.028-0.02029.229-0.002-0.0020.0000.0000.0000.000
161D169GLY00.0560.01833.6990.1960.1960.0000.0000.0000.000
162D170ALA0-0.0300.00832.0910.1970.1970.0000.0000.0000.000
163D171LYS10.8740.91631.9119.2709.2700.0000.0000.0000.000
164D172ASP-1-0.748-0.84628.205-10.027-10.0270.0000.0000.0000.000
165D173ILE00.0680.02822.9800.2770.2770.0000.0000.0000.000
166D174GLN00.0600.03523.0600.3570.3570.0000.0000.0000.000
167D175THR0-0.103-0.08526.7050.2350.2350.0000.0000.0000.000
168D176ARG10.7820.86125.56211.61011.6100.0000.0000.0000.000
169D177ASP-1-0.811-0.91024.678-11.876-11.8760.0000.0000.0000.000
170D178LYS10.8590.93728.0749.7009.7000.0000.0000.0000.000
171D179TYR0-0.007-0.01430.1440.2350.2350.0000.0000.0000.000
172D180LEU0-0.0310.01827.6820.3410.3410.0000.0000.0000.000
173D181LYS10.8420.92031.6889.1829.1820.0000.0000.0000.000
174D182THR00.022-0.00130.160-0.095-0.0950.0000.0000.0000.000
175D184THR00.0350.00834.594-0.108-0.1080.0000.0000.0000.000
176D185ASN00.0360.02737.0900.1660.1660.0000.0000.0000.000
177D186THR00.0140.01138.7810.2150.2150.0000.0000.0000.000
178D187LYS10.9650.97442.4466.5686.5680.0000.0000.0000.000
179D188PHE00.0490.01141.738-0.033-0.0330.0000.0000.0000.000
180D189ASP-1-0.841-0.89546.132-6.609-6.6090.0000.0000.0000.000
181D190ARG10.7490.85344.3307.2357.2350.0000.0000.0000.000