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

tag_button

FMODB ID: 6Y98Z

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2045897.672337
FMO2-HF: Nuclear repulsion 1968895.89384
FMO2-HF: Total energy -77001.778498
FMO2-MP2: Total energy -77218.433772


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.
-196.608-194.55820.139-12.349-9.84-0.129
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 : 0.859 / q_NPA : 0.911
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-1-0.868-0.9343.794-41.285-37.952-0.027-1.878-1.4290.005
4D8LYS10.9660.9815.84924.99924.9990.0000.0000.0000.000
5D9MET00.0430.0196.8881.0401.0400.0000.0000.0000.000
6D10GLU-1-0.804-0.8777.020-33.876-33.8760.0000.0000.0000.000
7D11GLU-1-0.824-0.9071.811-137.914-139.68220.139-10.378-7.992-0.134
8D12GLU-1-0.916-0.9586.384-26.963-26.9630.0000.0000.0000.000
9D13THR0-0.069-0.0359.5723.6313.6310.0000.0000.0000.000
10D14TRP0-0.013-0.00210.127-0.415-0.4150.0000.0000.0000.000
11D15LYS10.8300.91713.85921.13621.1360.0000.0000.0000.000
12D16LEU0-0.0100.00516.705-0.294-0.2940.0000.0000.0000.000
13D17LYS10.8580.91919.61213.94113.9410.0000.0000.0000.000
14D18ILE00.004-0.00122.094-0.122-0.1220.0000.0000.0000.000
15D19GLY00.0020.01725.1160.3550.3550.0000.0000.0000.000
16D20MET00.0170.00727.2040.1080.1080.0000.0000.0000.000
17D21CYS0-0.108-0.04030.7350.3670.3670.0000.0000.0000.000
18D22ILE00.0570.02433.3400.0390.0390.0000.0000.0000.000
19D23GLN00.0000.01036.9280.0440.0440.0000.0000.0000.000
20D24ALA00.0140.00639.7710.0510.0510.0000.0000.0000.000
21D25LYS10.8580.92943.3446.7266.7260.0000.0000.0000.000
22D26ASP-1-0.896-0.95646.090-6.364-6.3640.0000.0000.0000.000
23D27PHE00.0010.00944.8740.1000.1000.0000.0000.0000.000
24D28TYR0-0.033-0.01846.829-0.100-0.1000.0000.0000.0000.000
25D29SER00.0430.03841.8070.1000.1000.0000.0000.0000.000
26D30LYS10.9270.95944.4616.5536.5530.0000.0000.0000.000
27D31ARG10.9510.97739.9107.3617.3610.0000.0000.0000.000
28D32THR0-0.081-0.04841.1030.2710.2710.0000.0000.0000.000
29D33ASP-1-0.901-0.92839.710-7.867-7.8670.0000.0000.0000.000
30D34CYS0-0.0570.00432.6180.2550.2550.0000.0000.0000.000
31D35SER0-0.027-0.01638.344-0.075-0.0750.0000.0000.0000.000
32D36VAL0-0.032-0.01533.370-0.133-0.1330.0000.0000.0000.000
33D37HIS10.7930.89436.7838.1318.1310.0000.0000.0000.000
34D38ARG10.9120.94433.6758.6398.6390.0000.0000.0000.000
35D39PRO0-0.066-0.01936.4320.1900.1900.0000.0000.0000.000
36D40ASP-1-0.804-0.89838.476-8.198-8.1980.0000.0000.0000.000
37D41VAL0-0.069-0.02340.5200.0610.0610.0000.0000.0000.000
38D42GLY00.0510.01938.8220.0680.0680.0000.0000.0000.000
39D43GLY00.0350.02634.535-0.061-0.0610.0000.0000.0000.000
40D44GLY00.0570.03432.431-0.090-0.0900.0000.0000.0000.000
41D45LEU0-0.070-0.03430.4740.0660.0660.0000.0000.0000.000
42D46ILE00.0040.00034.6790.0640.0640.0000.0000.0000.000
43D47THR0-0.055-0.04134.703-0.046-0.0460.0000.0000.0000.000
44D48GLU-1-0.751-0.86237.573-7.746-7.7460.0000.0000.0000.000
45D49GLY00.0320.00439.624-0.076-0.0760.0000.0000.0000.000
46D50ASN00.008-0.01837.5960.0900.0900.0000.0000.0000.000
47D51GLY00.0140.01941.070-0.001-0.0010.0000.0000.0000.000
48D52TYR00.0150.01539.8490.1670.1670.0000.0000.0000.000
49D53ARG10.8740.93240.4347.2957.2950.0000.0000.0000.000
50D54VAL0-0.018-0.01334.8780.0240.0240.0000.0000.0000.000
51D55VAL0-0.014-0.00237.038-0.058-0.0580.0000.0000.0000.000
52D56VAL0-0.014-0.00330.414-0.072-0.0720.0000.0000.0000.000
53D57HIS0-0.041-0.04533.4030.2270.2270.0000.0000.0000.000
54D58ASP-1-0.809-0.92329.032-10.970-10.9700.0000.0000.0000.000
55D59GLN0-0.051-0.02330.2980.2960.2960.0000.0000.0000.000
56D60CYS0-0.062-0.00924.664-0.167-0.1670.0000.0000.0000.000
57D61GLU-1-0.921-0.95031.798-8.342-8.3420.0000.0000.0000.000
58D62GLU-1-0.930-0.96731.994-9.015-9.0150.0000.0000.0000.000
59D63PRO0-0.027-0.01832.104-0.284-0.2840.0000.0000.0000.000
60D64ASN0-0.017-0.00927.514-0.551-0.5510.0000.0000.0000.000
61D65PRO0-0.044-0.01924.8040.2340.2340.0000.0000.0000.000
62D66PHE00.0280.01626.152-0.315-0.3150.0000.0000.0000.000
63D67ILE00.0490.02620.865-0.301-0.3010.0000.0000.0000.000
64D68ILE0-0.058-0.01223.551-0.542-0.5420.0000.0000.0000.000
65D69ALA00.0230.01124.8010.3180.3180.0000.0000.0000.000
66D70THR0-0.063-0.04226.3810.2910.2910.0000.0000.0000.000
67D71THR00.0440.02327.878-0.168-0.1680.0000.0000.0000.000
68D72LYS10.8690.93225.27812.10912.1090.0000.0000.0000.000
69D73GLN00.0750.03531.1360.0810.0810.0000.0000.0000.000
70D74THR0-0.035-0.03532.6130.0980.0980.0000.0000.0000.000
71D75HIS0-0.050-0.02435.044-0.031-0.0310.0000.0000.0000.000
72D76PHE0-0.0030.01633.143-0.008-0.0080.0000.0000.0000.000
73D77GLY0-0.008-0.00238.5940.0470.0470.0000.0000.0000.000
74D78VAL00.015-0.00441.9780.0350.0350.0000.0000.0000.000
75D79THR00.0570.02840.9570.1150.1150.0000.0000.0000.000
76D80HIS0-0.0040.02036.835-0.153-0.1530.0000.0000.0000.000
77D81SER0-0.006-0.01337.2750.1450.1450.0000.0000.0000.000
78D82TYR00.0190.01126.701-0.097-0.0970.0000.0000.0000.000
79D83ILE00.0100.00031.5210.1360.1360.0000.0000.0000.000
80D84GLU-1-0.841-0.91025.125-12.458-12.4580.0000.0000.0000.000
81D85PHE00.0250.00826.9850.1570.1570.0000.0000.0000.000
82D86SER0-0.001-0.01823.548-0.603-0.6030.0000.0000.0000.000
83D87ASN00.009-0.00921.3010.1940.1940.0000.0000.0000.000
84D88SER0-0.017-0.00319.487-0.684-0.6840.0000.0000.0000.000
85D89ASN00.027-0.00715.651-2.145-2.1450.0000.0000.0000.000
86D90THR0-0.0120.01116.7340.6240.6240.0000.0000.0000.000
87D91GLY00.0190.02414.9370.5180.5180.0000.0000.0000.000
88D92ALA00.0540.01312.0070.1920.1920.0000.0000.0000.000
89D93PRO00.0410.01313.2151.3541.3540.0000.0000.0000.000
90D94GLU-1-0.981-0.98212.215-23.279-23.2790.0000.0000.0000.000
91D95ASN0-0.038-0.02314.4431.3531.3530.0000.0000.0000.000
92D96ILE0-0.042-0.00418.0310.8790.8790.0000.0000.0000.000
93D97PRO00.0480.01620.488-0.126-0.1260.0000.0000.0000.000
94D98ASP-1-0.848-0.94323.661-13.067-13.0670.0000.0000.0000.000
95D100SER00.0510.02024.5020.1830.1830.0000.0000.0000.000
96D101LYS10.8220.92119.72515.10815.1080.0000.0000.0000.000
97D102HIS0-0.080-0.04324.4490.0600.0600.0000.0000.0000.000
98D103ILE0-0.013-0.01125.9740.3060.3060.0000.0000.0000.000
99D104LEU0-0.021-0.00729.2830.1300.1300.0000.0000.0000.000
100D105ILE00.0060.00029.6520.0990.0990.0000.0000.0000.000
101D106SER0-0.026-0.01434.0330.2100.2100.0000.0000.0000.000
102D107VAL0-0.020-0.02336.446-0.009-0.0090.0000.0000.0000.000
103D108TYR00.0220.00939.0800.1970.1970.0000.0000.0000.000
104D109CYS00.0010.00042.376-0.054-0.0540.0000.0000.0000.000
105D110ASP-1-0.830-0.90744.842-7.086-7.0860.0000.0000.0000.000
106D111GLN0-0.109-0.08146.480-0.011-0.0110.0000.0000.0000.000
107D112GLU-1-0.876-0.92348.190-6.034-6.0340.0000.0000.0000.000
108D113ALA0-0.026-0.01549.710-0.081-0.0810.0000.0000.0000.000
109D114SER0-0.030-0.00748.501-0.001-0.0010.0000.0000.0000.000
110D115GLY00.010-0.01249.6800.1310.1310.0000.0000.0000.000
111D116LEU0-0.108-0.05148.2250.0470.0470.0000.0000.0000.000
112D117ASP-1-0.891-0.92747.890-6.624-6.6240.0000.0000.0000.000
113D118PHE0-0.048-0.04242.678-0.183-0.1830.0000.0000.0000.000
114D119HIS00.0530.03438.5760.1670.1670.0000.0000.0000.000
115D120THR0-0.027-0.02237.013-0.144-0.1440.0000.0000.0000.000
116D121LEU00.0110.01533.7820.0700.0700.0000.0000.0000.000
117D122LYS10.8740.91529.80710.33810.3380.0000.0000.0000.000
118D123TYR0-0.023-0.02128.995-0.017-0.0170.0000.0000.0000.000
119D124VAL0-0.029-0.01123.557-0.242-0.2420.0000.0000.0000.000
120D125GLU-1-0.791-0.87925.427-11.351-11.3510.0000.0000.0000.000
121D126SER0-0.019-0.00320.259-0.538-0.5380.0000.0000.0000.000
122D127ASN00.030-0.00718.2990.9470.9470.0000.0000.0000.000
123D128TYR0-0.0160.00412.5350.1030.1030.0000.0000.0000.000
124D129LEU00.0130.01119.3380.3100.3100.0000.0000.0000.000
125D130HIS10.8790.94322.61912.62012.6200.0000.0000.0000.000
126D131ILE00.0240.02124.8720.1900.1900.0000.0000.0000.000
127D132THR0-0.015-0.00728.3850.2020.2020.0000.0000.0000.000
128D133VAL0-0.005-0.00431.8700.0150.0150.0000.0000.0000.000
129D134LYS10.9360.98834.4477.7767.7760.0000.0000.0000.000
130D135TYR0-0.001-0.00637.606-0.076-0.0760.0000.0000.0000.000
131D136ASP-1-0.720-0.83640.218-6.773-6.7730.0000.0000.0000.000
132D137THR0-0.001-0.00642.359-0.019-0.0190.0000.0000.0000.000
133D138SER0-0.031-0.03944.3950.1040.1040.0000.0000.0000.000
134D140ILE0-0.021-0.01539.509-0.112-0.1120.0000.0000.0000.000
135D141ASN0-0.088-0.03842.0490.1510.1510.0000.0000.0000.000
136D142HIS00.002-0.01834.209-0.054-0.0540.0000.0000.0000.000
137D143LEU00.0410.02633.284-0.034-0.0340.0000.0000.0000.000
138D144GLY00.0010.02331.867-0.064-0.0640.0000.0000.0000.000
139D145VAL0-0.006-0.01627.0940.0100.0100.0000.0000.0000.000
140D146ASN0-0.053-0.02522.925-0.584-0.5840.0000.0000.0000.000
141D147TYR00.026-0.00719.708-0.048-0.0480.0000.0000.0000.000
142D148SER00.0020.00817.582-0.618-0.6180.0000.0000.0000.000
143D149PHE00.029-0.00716.0880.4280.4280.0000.0000.0000.000
144D150MET00.0280.03711.632-0.605-0.6050.0000.0000.0000.000
145D151ASN00.0500.0406.9410.7880.7880.0000.0000.0000.000
146D152GLU-1-0.749-0.8559.964-21.359-21.3590.0000.0000.0000.000
147D154GLU-1-0.858-0.9466.322-31.143-31.1430.0000.0000.0000.000
148D155ARG10.8610.9127.79524.02424.0240.0000.0000.0000.000
149D156LYS10.7700.8635.51738.34438.3440.0000.0000.0000.000
150D157LEU0-0.036-0.0253.1880.3090.7940.027-0.093-0.4190.000
151D158THR0-0.055-0.0397.8561.9081.9080.0000.0000.0000.000
152D159SER00.0130.01111.3481.6621.6620.0000.0000.0000.000
153D160ILE0-0.031-0.01413.2791.1541.1540.0000.0000.0000.000
154D161TYR0-0.047-0.01212.5230.6750.6750.0000.0000.0000.000
155D162GLU-1-0.936-0.95516.969-13.604-13.6040.0000.0000.0000.000
156D163THR00.016-0.00818.6150.3630.3630.0000.0000.0000.000
157D164ASP-1-0.877-0.92021.213-11.798-11.7980.0000.0000.0000.000
158D165THR00.0400.01223.5600.1880.1880.0000.0000.0000.000
159D166LEU0-0.0040.01427.1010.4940.4940.0000.0000.0000.000
160D167THR0-0.017-0.00929.156-0.034-0.0340.0000.0000.0000.000
161D169GLY00.0650.01733.6550.1450.1450.0000.0000.0000.000
162D170ALA0-0.0380.00032.4260.2070.2070.0000.0000.0000.000
163D171LYS10.8840.91831.7549.2779.2770.0000.0000.0000.000
164D172ASP-1-0.763-0.85328.193-10.054-10.0540.0000.0000.0000.000
165D173ILE00.0690.02523.0730.2540.2540.0000.0000.0000.000
166D174GLN00.0520.02523.2510.3480.3480.0000.0000.0000.000
167D175THR0-0.120-0.09027.0370.2430.2430.0000.0000.0000.000
168D176ARG10.7770.85525.59511.61011.6100.0000.0000.0000.000
169D177ASP-1-0.825-0.92624.837-11.723-11.7230.0000.0000.0000.000
170D178LYS10.8980.97128.2099.4829.4820.0000.0000.0000.000
171D179TYR0-0.036-0.02830.3730.1610.1610.0000.0000.0000.000
172D180LEU0-0.0170.03227.7530.3140.3140.0000.0000.0000.000
173D181LYS10.8720.93431.7819.1819.1810.0000.0000.0000.000
174D182THR00.014-0.00530.638-0.107-0.1070.0000.0000.0000.000
175D184THR00.0340.01534.627-0.115-0.1150.0000.0000.0000.000
176D185ASN00.0340.01837.2150.1510.1510.0000.0000.0000.000
177D186THR00.0260.01138.9110.2070.2070.0000.0000.0000.000
178D187LYS10.9680.98142.4326.5666.5660.0000.0000.0000.000
179D188PHE00.0510.01242.019-0.016-0.0160.0000.0000.0000.000
180D189ASP-1-0.855-0.90646.035-6.584-6.5840.0000.0000.0000.000
181D190ARG10.7520.86945.0037.1217.1210.0000.0000.0000.000