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: 2N68R

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2044031.572079
FMO2-HF: Nuclear repulsion 1967030.785257
FMO2-HF: Total energy -77000.786822
FMO2-MP2: Total energy -77217.380985


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.
-132.518-125.4490.053-3.784-3.336-0.025
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 : 0.930 / q_NPA : 0.949
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-1-0.883-0.9223.802-36.465-34.134-0.030-1.222-1.078-0.001
4D8LYS11.0060.9956.44024.69424.6940.0000.0000.0000.000
5D9MET00.0310.0147.9581.0551.0550.0000.0000.0000.000
6D10GLU-1-0.829-0.9127.001-30.365-30.3650.0000.0000.0000.000
7D11GLU-1-0.925-0.9752.968-78.691-74.4730.065-2.473-1.810-0.024
8D12GLU-1-0.938-0.9657.619-24.310-24.3100.0000.0000.0000.000
9D13THR0-0.075-0.04311.1262.9632.9630.0000.0000.0000.000
10D14TRP0-0.0140.00011.389-0.342-0.3420.0000.0000.0000.000
11D15LYS10.8910.95314.85819.01219.0120.0000.0000.0000.000
12D16LEU0-0.0260.00117.085-0.300-0.3000.0000.0000.0000.000
13D17LYS10.9110.95320.02914.06814.0680.0000.0000.0000.000
14D18ILE00.0060.00222.104-0.156-0.1560.0000.0000.0000.000
15D19GLY00.0100.01925.2080.3410.3410.0000.0000.0000.000
16D20MET00.0160.00727.2040.0840.0840.0000.0000.0000.000
17D21CYS0-0.103-0.03630.8140.3640.3640.0000.0000.0000.000
18D22ILE00.0580.02433.3370.0400.0400.0000.0000.0000.000
19D23GLN0-0.014-0.00836.9750.0260.0260.0000.0000.0000.000
20D24ALA00.0070.00339.7950.0500.0500.0000.0000.0000.000
21D25LYS10.9110.95143.3476.6266.6260.0000.0000.0000.000
22D26ASP-1-0.892-0.94446.221-6.222-6.2220.0000.0000.0000.000
23D27PHE0-0.0120.00044.8750.0920.0920.0000.0000.0000.000
24D28TYR0-0.035-0.01546.822-0.097-0.0970.0000.0000.0000.000
25D29SER00.0580.04341.9460.1050.1050.0000.0000.0000.000
26D30LYS10.9210.95544.4596.3736.3730.0000.0000.0000.000
27D31ARG10.9560.97340.0257.1467.1460.0000.0000.0000.000
28D32THR0-0.084-0.05441.0870.2650.2650.0000.0000.0000.000
29D33ASP-1-0.897-0.91939.714-7.607-7.6070.0000.0000.0000.000
30D34CYS0-0.0320.02032.6240.2450.2450.0000.0000.0000.000
31D35SER0-0.032-0.02138.351-0.060-0.0600.0000.0000.0000.000
32D36VAL0-0.023-0.01533.737-0.129-0.1290.0000.0000.0000.000
33D37HIS10.8300.92237.0897.8157.8150.0000.0000.0000.000
34D38ARG10.9580.98135.0168.4768.4760.0000.0000.0000.000
35D39PRO0-0.071-0.01537.6030.1820.1820.0000.0000.0000.000
36D40ASP-1-0.824-0.92139.743-7.857-7.8570.0000.0000.0000.000
37D41VAL0-0.075-0.03141.8570.0520.0520.0000.0000.0000.000
38D42GLY00.0480.01640.0670.0590.0590.0000.0000.0000.000
39D43GLY00.0250.02335.841-0.052-0.0520.0000.0000.0000.000
40D44GLY00.0650.03533.572-0.096-0.0960.0000.0000.0000.000
41D45LEU0-0.060-0.02931.0900.0730.0730.0000.0000.0000.000
42D46ILE0-0.003-0.00735.5750.0600.0600.0000.0000.0000.000
43D47THR0-0.061-0.03735.064-0.031-0.0310.0000.0000.0000.000
44D48GLU-1-0.827-0.92237.856-7.545-7.5450.0000.0000.0000.000
45D49GLY00.0400.01339.627-0.059-0.0590.0000.0000.0000.000
46D50ASN00.003-0.00337.4370.0430.0430.0000.0000.0000.000
47D51GLY0-0.021-0.01441.0710.0080.0080.0000.0000.0000.000
48D52TYR00.0130.01039.3340.1610.1610.0000.0000.0000.000
49D53ARG10.9240.98040.6727.0887.0880.0000.0000.0000.000
50D54VAL0-0.022-0.01835.2090.0190.0190.0000.0000.0000.000
51D55VAL0-0.012-0.00137.645-0.048-0.0480.0000.0000.0000.000
52D56VAL0-0.014-0.00231.111-0.077-0.0770.0000.0000.0000.000
53D57HIS0-0.040-0.03734.2620.2100.2100.0000.0000.0000.000
54D58ASP-1-0.830-0.93430.410-10.407-10.4070.0000.0000.0000.000
55D59GLN0-0.045-0.02031.4210.2280.2280.0000.0000.0000.000
56D60CYS0-0.0530.00225.926-0.230-0.2300.0000.0000.0000.000
57D61GLU-1-0.916-0.95033.144-8.153-8.1530.0000.0000.0000.000
58D62GLU-1-0.933-0.97033.355-8.671-8.6710.0000.0000.0000.000
59D63PRO0-0.058-0.03633.565-0.236-0.2360.0000.0000.0000.000
60D64ASN00.0260.01428.922-0.182-0.1820.0000.0000.0000.000
61D65PRO0-0.051-0.02826.4720.2050.2050.0000.0000.0000.000
62D66PHE00.0210.01327.565-0.331-0.3310.0000.0000.0000.000
63D67ILE00.0460.02622.105-0.265-0.2650.0000.0000.0000.000
64D68ILE0-0.054-0.00724.603-0.484-0.4840.0000.0000.0000.000
65D69ALA00.0230.00925.5010.2920.2920.0000.0000.0000.000
66D70THR0-0.064-0.04326.5130.2720.2720.0000.0000.0000.000
67D71THR00.0440.02328.057-0.183-0.1830.0000.0000.0000.000
68D72LYS10.9140.96925.89711.40611.4060.0000.0000.0000.000
69D73GLN00.0890.03731.1410.0790.0790.0000.0000.0000.000
70D74THR00.0160.00632.4300.1430.1430.0000.0000.0000.000
71D75HIS0-0.052-0.03535.044-0.004-0.0040.0000.0000.0000.000
72D76PHE0-0.0270.01432.988-0.021-0.0210.0000.0000.0000.000
73D77GLY0-0.0050.00038.5890.0400.0400.0000.0000.0000.000
74D78VAL00.0230.00241.9720.0370.0370.0000.0000.0000.000
75D79THR00.0520.02541.0780.1130.1130.0000.0000.0000.000
76D80HIS0-0.0180.00736.804-0.155-0.1550.0000.0000.0000.000
77D81SER00.0130.00137.2740.0940.0940.0000.0000.0000.000
78D82TYR00.0040.00526.691-0.112-0.1120.0000.0000.0000.000
79D83ILE00.0080.00031.4260.1370.1370.0000.0000.0000.000
80D84GLU-1-0.898-0.96824.921-11.968-11.9680.0000.0000.0000.000
81D85PHE00.0190.00727.2320.1620.1620.0000.0000.0000.000
82D86SER0-0.016-0.02223.418-0.533-0.5330.0000.0000.0000.000
83D87ASN00.006-0.01621.9270.1410.1410.0000.0000.0000.000
84D88SER0-0.035-0.01519.595-0.644-0.6440.0000.0000.0000.000
85D89ASN00.0390.00117.136-1.844-1.8440.0000.0000.0000.000
86D90THR0-0.0130.00917.9830.5180.5180.0000.0000.0000.000
87D91GLY00.0260.02816.4450.4590.4590.0000.0000.0000.000
88D92ALA00.0520.00913.5800.1240.1240.0000.0000.0000.000
89D93PRO00.0320.01014.4281.2431.2430.0000.0000.0000.000
90D94GLU-1-0.962-0.98112.947-22.029-22.0290.0000.0000.0000.000
91D95ASN0-0.026-0.01215.6231.1111.1110.0000.0000.0000.000
92D96ILE0-0.052-0.01219.3180.8330.8330.0000.0000.0000.000
93D97PRO00.0310.00921.912-0.093-0.0930.0000.0000.0000.000
94D98ASP-1-0.871-0.95624.975-12.488-12.4880.0000.0000.0000.000
95D100SER00.0550.01525.9970.2100.2100.0000.0000.0000.000
96D101LYS10.8390.93220.75414.64514.6450.0000.0000.0000.000
97D102HIS0-0.066-0.02925.4910.0820.0820.0000.0000.0000.000
98D103ILE0-0.007-0.00327.1420.2910.2910.0000.0000.0000.000
99D104LEU0-0.024-0.01029.8680.0940.0940.0000.0000.0000.000
100D105ILE0-0.001-0.00530.1800.1070.1070.0000.0000.0000.000
101D106SER0-0.032-0.01634.4460.1810.1810.0000.0000.0000.000
102D107VAL0-0.014-0.01836.672-0.003-0.0030.0000.0000.0000.000
103D108TYR00.0140.00539.3410.1810.1810.0000.0000.0000.000
104D109CYS0-0.0150.00142.552-0.072-0.0720.0000.0000.0000.000
105D110ASP-1-0.860-0.94544.939-6.857-6.8570.0000.0000.0000.000
106D111GLN0-0.121-0.08246.301-0.019-0.0190.0000.0000.0000.000
107D112GLU-1-0.901-0.93748.194-5.949-5.9490.0000.0000.0000.000
108D113ALA0-0.024-0.01249.766-0.069-0.0690.0000.0000.0000.000
109D114SER0-0.016-0.00648.5000.0600.0600.0000.0000.0000.000
110D115GLY00.0160.00049.8860.1230.1230.0000.0000.0000.000
111D116LEU0-0.103-0.04948.4450.0400.0400.0000.0000.0000.000
112D117ASP-1-0.883-0.92448.093-6.563-6.5630.0000.0000.0000.000
113D118PHE0-0.060-0.04342.812-0.172-0.1720.0000.0000.0000.000
114D119HIS00.0500.03138.9240.1460.1460.0000.0000.0000.000
115D120THR0-0.033-0.02437.185-0.172-0.1720.0000.0000.0000.000
116D121LEU0-0.0010.00434.0170.0680.0680.0000.0000.0000.000
117D122LYS10.9560.97130.3129.7369.7360.0000.0000.0000.000
118D123TYR0-0.0030.00229.243-0.003-0.0030.0000.0000.0000.000
119D124VAL0-0.027-0.01023.733-0.245-0.2450.0000.0000.0000.000
120D125GLU-1-0.845-0.93225.633-11.035-11.0350.0000.0000.0000.000
121D126SER0-0.033-0.01420.407-0.535-0.5350.0000.0000.0000.000
122D127ASN00.022-0.00818.7850.8800.8800.0000.0000.0000.000
123D128TYR0-0.036-0.00212.9860.1180.1180.0000.0000.0000.000
124D129LEU00.0160.00919.7920.3060.3060.0000.0000.0000.000
125D130HIS10.8790.95823.01812.15012.1500.0000.0000.0000.000
126D131ILE00.0220.02025.1810.1940.1940.0000.0000.0000.000
127D132THR0-0.018-0.01128.5860.1580.1580.0000.0000.0000.000
128D133VAL0-0.0060.00032.0790.0270.0270.0000.0000.0000.000
129D134LYS10.9470.98934.6467.6267.6260.0000.0000.0000.000
130D135TYR00.007-0.00637.6160.0260.0260.0000.0000.0000.000
131D136ASP-1-0.722-0.84540.421-6.670-6.6700.0000.0000.0000.000
132D137THR0-0.027-0.02042.474-0.017-0.0170.0000.0000.0000.000
133D138SER0-0.048-0.04744.6030.0900.0900.0000.0000.0000.000
134D140ILE0-0.003-0.01039.747-0.106-0.1060.0000.0000.0000.000
135D141ASN0-0.090-0.03342.3440.0930.0930.0000.0000.0000.000
136D142HIS00.018-0.00634.288-0.027-0.0270.0000.0000.0000.000
137D143LEU00.0460.02833.627-0.019-0.0190.0000.0000.0000.000
138D144GLY0-0.0180.00032.077-0.075-0.0750.0000.0000.0000.000
139D145VAL0-0.007-0.01527.1850.0250.0250.0000.0000.0000.000
140D146ASN0-0.045-0.02323.193-0.681-0.6810.0000.0000.0000.000
141D147TYR00.0460.00919.1790.0910.0910.0000.0000.0000.000
142D148SER0-0.0030.00717.490-0.568-0.5680.0000.0000.0000.000
143D149PHE00.040-0.00517.2590.4330.4330.0000.0000.0000.000
144D150MET00.0320.03811.817-0.679-0.6790.0000.0000.0000.000
145D151ASN00.0600.0358.3141.2021.2020.0000.0000.0000.000
146D152GLU-1-0.822-0.90510.041-20.499-20.4990.0000.0000.0000.000
147D154GLU-1-0.882-0.9516.325-30.731-30.7310.0000.0000.0000.000
148D155ARG10.8560.9137.88622.24422.2440.0000.0000.0000.000
149D156LYS10.7900.8885.18135.50335.576-0.001-0.006-0.0650.000
150D157LEU0-0.040-0.0263.300-0.0940.3530.019-0.083-0.3830.000
151D158THR0-0.052-0.0337.8381.5691.5690.0000.0000.0000.000
152D159SER00.0040.00611.3321.3361.3360.0000.0000.0000.000
153D160ILE0-0.014-0.00813.2121.1001.1000.0000.0000.0000.000
154D161TYR0-0.046-0.01412.7810.5490.5490.0000.0000.0000.000
155D162GLU-1-0.939-0.95816.977-13.385-13.3850.0000.0000.0000.000
156D163THR00.018-0.00518.7860.2650.2650.0000.0000.0000.000
157D164ASP-1-0.932-0.96721.393-11.592-11.5920.0000.0000.0000.000
158D165THR00.0280.00323.5500.2900.2900.0000.0000.0000.000
159D166LEU0-0.0270.00227.0930.4720.4720.0000.0000.0000.000
160D167THR0-0.029-0.02129.148-0.003-0.0030.0000.0000.0000.000
161D169GLY00.0650.02033.6480.1450.1450.0000.0000.0000.000
162D170ALA0-0.0360.00032.4020.1970.1970.0000.0000.0000.000
163D171LYS10.9080.94331.5259.1269.1260.0000.0000.0000.000
164D172ASP-1-0.783-0.87028.126-9.859-9.8590.0000.0000.0000.000
165D173ILE00.0390.01323.1510.2400.2400.0000.0000.0000.000
166D174GLN00.0670.03223.3160.3520.3520.0000.0000.0000.000
167D175THR0-0.105-0.09127.0280.2280.2280.0000.0000.0000.000
168D176ARG10.8860.94825.00511.31511.3150.0000.0000.0000.000
169D177ASP-1-0.880-0.95925.654-11.301-11.3010.0000.0000.0000.000
170D178LYS10.9010.96828.2069.2639.2630.0000.0000.0000.000
171D179TYR0-0.075-0.04530.3690.1740.1740.0000.0000.0000.000
172D180LEU0-0.0330.01227.7300.2860.2860.0000.0000.0000.000
173D181LYS10.9110.95531.7828.6178.6170.0000.0000.0000.000
174D182THR0-0.004-0.01530.698-0.131-0.1310.0000.0000.0000.000
175D184THR00.0290.00934.636-0.101-0.1010.0000.0000.0000.000
176D185ASN00.0150.00637.3090.1970.1970.0000.0000.0000.000
177D186THR00.0440.01539.2360.2090.2090.0000.0000.0000.000
178D187LYS10.9390.96342.6046.3846.3840.0000.0000.0000.000
179D188PHE00.0250.00942.227-0.020-0.0200.0000.0000.0000.000
180D189ASP-1-0.888-0.93946.083-6.448-6.4480.0000.0000.0000.000
181D190ARG10.8900.96144.9296.8486.8480.0000.0000.0000.000