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: 539JZ

Calculation Name: 4HKJ-D-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 183
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2050840.442456
FMO2-HF: Nuclear repulsion 1973668.773681
FMO2-HF: Total energy -77171.668774
FMO2-MP2: Total energy -77388.78769


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:ACE )


Summations of interaction energy for fragment #1(D:4:ACE )
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.
-0.0980.784-0.005-0.399-0.478-0.001
Interaction energy analysis for fragmet #1(D:4:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.004
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].
3D153CYS 0-0.081-0.0163.8400.4861.368-0.005-0.399-0.478-0.001
4D7GLU -1-0.887-0.9246.2220.2970.2970.0000.0000.0000.000
5D8LYS 11.0110.9988.573-0.160-0.1600.0000.0000.0000.000
6D9MET 00.0290.01310.635-0.023-0.0230.0000.0000.0000.000
7D10GLU -1-0.830-0.91210.209-0.439-0.4390.0000.0000.0000.000
8D11GLU -1-0.923-0.9747.644-0.673-0.6730.0000.0000.0000.000
9D12GLU -1-0.940-0.96612.207-0.053-0.0530.0000.0000.0000.000
10D13THR 0-0.075-0.04415.4670.0330.0330.0000.0000.0000.000
11D14TRP 0-0.0130.00016.811-0.030-0.0300.0000.0000.0000.000
12D15LYS 10.8890.95319.6360.1730.1730.0000.0000.0000.000
13D16LEU 0-0.0200.00222.145-0.009-0.0090.0000.0000.0000.000
14D17LYS 10.9110.95425.3310.1280.1280.0000.0000.0000.000
15D18ILE 00.0020.00027.516-0.004-0.0040.0000.0000.0000.000
16D19GLY 00.0150.02130.7120.0060.0060.0000.0000.0000.000
17D20MET 00.0140.00732.6260.0010.0010.0000.0000.0000.000
18D168CYS 0-0.105-0.03635.6910.0060.0060.0000.0000.0000.000
19D22ILE 00.0530.02338.6850.0000.0000.0000.0000.0000.000
20D23GLN 0-0.012-0.00742.3650.0000.0000.0000.0000.0000.000
21D24ALA 00.0040.00245.1020.0010.0010.0000.0000.0000.000
22D25LYS 10.9200.95548.6720.0340.0340.0000.0000.0000.000
23D26ASP -1-0.899-0.94651.576-0.030-0.0300.0000.0000.0000.000
24D27PHE 0-0.0130.00050.2370.0010.0010.0000.0000.0000.000
25D28TYR 0-0.034-0.01651.970-0.001-0.0010.0000.0000.0000.000
26D29SER 00.0610.04447.1420.0010.0010.0000.0000.0000.000
27D30LYS 10.9220.95649.5040.0270.0270.0000.0000.0000.000
28D31ARG 10.9520.97244.4900.0350.0350.0000.0000.0000.000
29D32THR 0-0.081-0.05245.9370.0030.0030.0000.0000.0000.000
30D33ASP -1-0.896-0.92144.369-0.034-0.0340.0000.0000.0000.000
31D183CYS 0-0.0330.02037.1620.0020.0020.0000.0000.0000.000
32D35SER 0-0.033-0.02243.1590.0000.0000.0000.0000.0000.000
33D36VAL 0-0.022-0.01438.628-0.002-0.0020.0000.0000.0000.000
34D37HIS 10.8310.92141.9660.0330.0330.0000.0000.0000.000
35D38ARG 10.9560.98039.6800.0300.0300.0000.0000.0000.000
36D39PRO 0-0.070-0.01542.2750.0020.0020.0000.0000.0000.000
37D40ASP -1-0.823-0.92044.690-0.026-0.0260.0000.0000.0000.000
38D41VAL 0-0.077-0.03146.7470.0010.0010.0000.0000.0000.000
39D42GLY 00.0480.01645.3060.0000.0000.0000.0000.0000.000
40D43GLY 00.0260.02341.0860.0000.0000.0000.0000.0000.000
41D44GLY 00.0660.03638.690-0.002-0.0020.0000.0000.0000.000
42D45LEU 0-0.062-0.02936.1680.0020.0020.0000.0000.0000.000
43D46ILE 0-0.005-0.00740.562-0.001-0.0010.0000.0000.0000.000
44D47THR 0-0.054-0.03540.3490.0000.0000.0000.0000.0000.000
45D48GLU -1-0.833-0.92443.023-0.034-0.0340.0000.0000.0000.000
46D49GLY 00.0420.01344.7660.0000.0000.0000.0000.0000.000
47D50ASN 0-0.002-0.00442.4510.0000.0000.0000.0000.0000.000
48D51GLY 0-0.017-0.01346.2460.0000.0000.0000.0000.0000.000
49D52TYR 00.0140.01244.6990.0010.0010.0000.0000.0000.000
50D53ARG 10.9210.97846.0230.0310.0310.0000.0000.0000.000
51D54VAL 0-0.022-0.01840.6930.0000.0000.0000.0000.0000.000
52D55VAL 0-0.0090.00042.9490.0000.0000.0000.0000.0000.000
53D56VAL 0-0.018-0.00336.448-0.002-0.0020.0000.0000.0000.000
54D57HIS 0-0.035-0.03639.6890.0030.0030.0000.0000.0000.000
55D58ASP -1-0.829-0.93335.876-0.053-0.0530.0000.0000.0000.000
56D59GLN 0-0.048-0.02037.0800.0030.0030.0000.0000.0000.000
57D99CYS 0-0.0590.00031.698-0.003-0.0030.0000.0000.0000.000
58D61GLU -1-0.914-0.94938.712-0.030-0.0300.0000.0000.0000.000
59D62GLU -1-0.934-0.97038.934-0.025-0.0250.0000.0000.0000.000
60D63PRO 0-0.058-0.03638.945-0.003-0.0030.0000.0000.0000.000
61D64ASN 00.0260.01434.2020.0020.0020.0000.0000.0000.000
62D65PRO 0-0.053-0.02831.4970.0000.0000.0000.0000.0000.000
63D66PHE 00.0240.01532.688-0.004-0.0040.0000.0000.0000.000
64D67ILE 00.0460.02627.540-0.002-0.0020.0000.0000.0000.000
65D68ILE 0-0.055-0.00629.571-0.007-0.0070.0000.0000.0000.000
66D69ALA 00.0230.00930.1050.0050.0050.0000.0000.0000.000
67D70THR 0-0.065-0.04431.3140.0040.0040.0000.0000.0000.000
68D71THR 00.0410.02232.998-0.004-0.0040.0000.0000.0000.000
69D72LYS 10.9200.97130.4370.0740.0740.0000.0000.0000.000
70D73GLN 00.0840.03536.111-0.001-0.0010.0000.0000.0000.000
71D74THR 00.0200.00737.2060.0020.0020.0000.0000.0000.000
72D75HIS 0-0.049-0.03539.8780.0000.0000.0000.0000.0000.000
73D76PHE 0-0.0260.01437.6670.0000.0000.0000.0000.0000.000
74D77GLY 0-0.0070.00043.3100.0000.0000.0000.0000.0000.000
75D78VAL 00.0190.00146.6820.0010.0010.0000.0000.0000.000
76D79THR 00.0520.02446.1510.0010.0010.0000.0000.0000.000
77D80HIS 0-0.0150.00741.889-0.002-0.0020.0000.0000.0000.000
78D81SER 00.0150.00242.4400.0020.0020.0000.0000.0000.000
79D82TYR 00.0100.00731.867-0.002-0.0020.0000.0000.0000.000
80D83ILE 00.000-0.00336.7670.0030.0030.0000.0000.0000.000
81D84GLU -1-0.897-0.96729.987-0.091-0.0910.0000.0000.0000.000
82D85PHE 00.0140.00632.6180.0040.0040.0000.0000.0000.000
83D86SER 0-0.015-0.02128.414-0.009-0.0090.0000.0000.0000.000
84D87ASN 00.007-0.01526.8500.0070.0070.0000.0000.0000.000
85D88SER 0-0.035-0.01524.125-0.010-0.0100.0000.0000.0000.000
86D89ASN 00.0390.00221.208-0.020-0.0200.0000.0000.0000.000
87D90THR 0-0.0110.00923.1190.0070.0070.0000.0000.0000.000
88D91GLY 00.0250.02721.1820.0100.0100.0000.0000.0000.000
89D92ALA 00.0500.00918.962-0.008-0.0080.0000.0000.0000.000
90D93PRO 00.0320.01020.0770.0170.0170.0000.0000.0000.000
91D94GLU -1-0.960-0.97918.969-0.122-0.1220.0000.0000.0000.000
92D95ASN 0-0.026-0.01221.2250.0160.0160.0000.0000.0000.000
93D96ILE 0-0.051-0.01225.0230.0080.0080.0000.0000.0000.000
94D97PRO 00.0300.00827.458-0.002-0.0020.0000.0000.0000.000
95D98ASP -1-0.869-0.95530.737-0.073-0.0730.0000.0000.0000.000
96D100SER 00.0560.01531.5130.0010.0010.0000.0000.0000.000
97D101LYS 10.8400.93226.5380.0870.0870.0000.0000.0000.000
98D102HIS 0-0.066-0.02931.179-0.004-0.0040.0000.0000.0000.000
99D103ILE 0-0.007-0.00432.8520.0040.0040.0000.0000.0000.000
100D104LEU 0-0.023-0.00935.7040.0000.0000.0000.0000.0000.000
101D105ILE 0-0.002-0.00635.8520.0020.0020.0000.0000.0000.000
102D106SER 0-0.032-0.01640.2260.0010.0010.0000.0000.0000.000
103D107VAL 0-0.013-0.01742.2800.0010.0010.0000.0000.0000.000
104D108TYR 00.0150.00444.9800.0010.0010.0000.0000.0000.000
105D139CYS 0-0.0160.00148.034-0.001-0.0010.0000.0000.0000.000
106D110ASP -1-0.862-0.94750.414-0.030-0.0300.0000.0000.0000.000
107D111GLN 0-0.118-0.08151.5200.0000.0000.0000.0000.0000.000
108D112GLU -1-0.906-0.93853.585-0.026-0.0260.0000.0000.0000.000
109D113ALA 0-0.023-0.01255.2200.0000.0000.0000.0000.0000.000
110D114SER 0-0.015-0.00554.0580.0000.0000.0000.0000.0000.000
111D115GLY 00.0170.00055.5810.0010.0010.0000.0000.0000.000
112D116LEU 0-0.104-0.04954.3240.0000.0000.0000.0000.0000.000
113D117ASP -1-0.882-0.92454.081-0.032-0.0320.0000.0000.0000.000
114D118PHE 0-0.061-0.04348.772-0.002-0.0020.0000.0000.0000.000
115D119HIS 00.0500.03245.1270.0020.0020.0000.0000.0000.000
116D120THR 0-0.034-0.02443.434-0.001-0.0010.0000.0000.0000.000
117D121LEU 0-0.0020.00440.2870.0010.0010.0000.0000.0000.000
118D122LYS 10.9590.97136.7580.0590.0590.0000.0000.0000.000
119D123TYR 0-0.0050.00235.360-0.001-0.0010.0000.0000.0000.000
120D124VAL 0-0.024-0.01029.995-0.005-0.0050.0000.0000.0000.000
121D125GLU -1-0.848-0.93232.076-0.069-0.0690.0000.0000.0000.000
122D126SER 0-0.033-0.01526.890-0.008-0.0080.0000.0000.0000.000
123D127ASN 00.022-0.00825.1220.0150.0150.0000.0000.0000.000
124D128TYR 0-0.039-0.00219.2980.0100.0100.0000.0000.0000.000
125D129LEU 00.0170.00825.9240.0060.0060.0000.0000.0000.000
126D130HIS 10.8810.95829.1400.0780.0780.0000.0000.0000.000
127D131ILE 00.0210.01931.1450.0030.0030.0000.0000.0000.000
128D132THR 0-0.015-0.01034.7420.0010.0010.0000.0000.0000.000
129D133VAL 0-0.009-0.00138.1250.0010.0010.0000.0000.0000.000
130D134LYS 10.9470.98840.7260.0390.0390.0000.0000.0000.000
131D135TYR 00.009-0.00543.6350.0010.0010.0000.0000.0000.000
132D136ASP -1-0.724-0.84746.317-0.032-0.0320.0000.0000.0000.000
133D137THR 0-0.028-0.02048.401-0.001-0.0010.0000.0000.0000.000
134D138SER 0-0.047-0.04650.4330.0010.0010.0000.0000.0000.000
135D140ILE 0-0.008-0.01245.358-0.001-0.0010.0000.0000.0000.000
136D141ASN 0-0.084-0.03247.6630.0010.0010.0000.0000.0000.000
137D142HIS 00.013-0.00739.7600.0000.0000.0000.0000.0000.000
138D143LEU 00.0450.02839.4050.0000.0000.0000.0000.0000.000
139D144GLY 0-0.0160.00037.555-0.001-0.0010.0000.0000.0000.000
140D145VAL 0-0.007-0.01433.0320.0010.0010.0000.0000.0000.000
141D146ASN 0-0.047-0.02328.554-0.011-0.0110.0000.0000.0000.000
142D147TYR 00.0470.01025.5030.0040.0040.0000.0000.0000.000
143D148SER 0-0.0020.00722.954-0.011-0.0110.0000.0000.0000.000
144D149PHE 00.037-0.00523.0040.0100.0100.0000.0000.0000.000
145D150MET 00.0360.03917.588-0.016-0.0160.0000.0000.0000.000
146D151ASN 00.0580.03413.861-0.007-0.0070.0000.0000.0000.000
147D152GLU -1-0.819-0.90514.530-0.246-0.2460.0000.0000.0000.000
148D154GLU -1-0.880-0.95011.576-0.473-0.4730.0000.0000.0000.000
149D155ARG 10.8530.91213.4230.2640.2640.0000.0000.0000.000
150D156LYS 10.7890.8888.1950.7440.7440.0000.0000.0000.000
151D157LEU 0-0.036-0.0247.964-0.039-0.0390.0000.0000.0000.000
152D158THR 0-0.051-0.03412.3010.0460.0460.0000.0000.0000.000
153D159SER 00.0030.00515.8650.0430.0430.0000.0000.0000.000
154D160ILE 0-0.014-0.00716.8120.0320.0320.0000.0000.0000.000
155D161TYR 0-0.047-0.01417.2140.0150.0150.0000.0000.0000.000
156D162GLU -1-0.938-0.95721.342-0.143-0.1430.0000.0000.0000.000
157D163THR 00.018-0.00623.8270.0060.0060.0000.0000.0000.000
158D164ASP -1-0.931-0.96626.359-0.097-0.0970.0000.0000.0000.000
159D165THR 00.0280.00328.5890.0040.0040.0000.0000.0000.000
160D166LEU 0-0.0270.00232.0270.0070.0070.0000.0000.0000.000
161D167THR 0-0.029-0.02134.2450.0010.0010.0000.0000.0000.000
162D169GLY 00.0670.02138.6690.0030.0030.0000.0000.0000.000
163D170ALA 0-0.0370.00036.9160.0030.0030.0000.0000.0000.000
164D171LYS 10.9050.94135.1310.0630.0630.0000.0000.0000.000
165D172ASP -1-0.780-0.86832.191-0.074-0.0740.0000.0000.0000.000
166D173ILE 00.0350.01127.4770.0050.0050.0000.0000.0000.000
167D174GLN 00.0710.03327.1630.0070.0070.0000.0000.0000.000
168D175THR 0-0.103-0.09131.0720.0060.0060.0000.0000.0000.000
169D176ARG 10.8840.94730.0110.0930.0930.0000.0000.0000.000
170D177ASP -1-0.879-0.95830.354-0.087-0.0870.0000.0000.0000.000
171D178LYS 10.8990.96832.6240.0590.0590.0000.0000.0000.000
172D179TYR 0-0.074-0.04534.3290.0040.0040.0000.0000.0000.000
173D180LEU 0-0.0320.01232.3400.0040.0040.0000.0000.0000.000
174D181LYS 10.9110.95536.2770.0440.0440.0000.0000.0000.000
175D182THR 0-0.005-0.01634.946-0.003-0.0030.0000.0000.0000.000
176D184THR 00.0290.00939.2740.0010.0010.0000.0000.0000.000
177D185ASN 00.0170.00741.8690.0000.0000.0000.0000.0000.000
178D186THR 00.0440.01443.7160.0030.0030.0000.0000.0000.000
179D187LYS 10.9400.96347.2670.0200.0200.0000.0000.0000.000
180D188PHE 00.0270.01247.2020.0000.0000.0000.0000.0000.000
181D189ASP -1-0.867-0.93251.007-0.024-0.0240.0000.0000.0000.000
182D190ARG 10.8720.95950.0860.0300.0300.0000.0000.0000.000
183D191NME 0-0.008-0.01054.1140.0000.0000.0000.0000.0000.000