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: LJ889

Calculation Name: 4KJZ-D-Xray372

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate

ligand 3-letter code: GDP

PDB ID: 4KJZ

Chain ID: D

ChEMBL ID:

UniProt ID: P48515

Base Structure: X-ray

Registration Date: 2023-06-20

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 452
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6750833.184782
FMO2-HF: Nuclear repulsion 6576211.473566
FMO2-HF: Total energy -174621.711216
FMO2-MP2: Total energy -175131.948118


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:VAL)


Summations of interaction energy for fragment #1(D:4:VAL)
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.
-11.142-3.8070.4-3.022-4.7130
Interaction energy analysis for fragmet #1(D:4:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.006
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].
3D6ILE00.0840.0513.562-2.207-0.1820.004-0.962-1.0680.002
4D7TYR00.0460.0105.3510.2740.386-0.001-0.003-0.1080.000
5D8GLN0-0.113-0.0603.4630.2580.9840.040-0.272-0.494-0.001
6D9LEU00.0570.0383.243-0.4160.0550.022-0.088-0.4060.000
7D10ALA00.0470.0254.9060.0980.133-0.001-0.005-0.0290.000
8D11LYS10.9280.9588.251-0.065-0.0650.0000.0000.0000.000
9D12GLU-1-0.923-0.9325.805-1.321-1.3210.0000.0000.0000.000
10D13LEU00.004-0.0018.2610.0430.0430.0000.0000.0000.000
11D14GLY0-0.042-0.00910.6040.0560.0560.0000.0000.0000.000
12D15MET0-0.0240.01311.242-0.013-0.0130.0000.0000.0000.000
13D16GLU-1-0.834-0.90712.684-0.104-0.1040.0000.0000.0000.000
14D17CYS0-0.092-0.07011.934-0.051-0.0510.0000.0000.0000.000
15D18GLN0-0.036-0.03413.016-0.047-0.0470.0000.0000.0000.000
16D19GLU-1-0.890-0.94714.596-0.346-0.3460.0000.0000.0000.000
17D20LEU0-0.006-0.0037.049-0.049-0.0490.0000.0000.0000.000
18D21LEU0-0.075-0.04110.980-0.065-0.0650.0000.0000.0000.000
19D22GLU-1-0.853-0.90612.569-0.326-0.3260.0000.0000.0000.000
20D23LEU00.0460.01211.431-0.019-0.0190.0000.0000.0000.000
21D24LEU0-0.059-0.0318.654-0.086-0.0860.0000.0000.0000.000
22D25ASP-1-0.857-0.92212.766-0.309-0.3090.0000.0000.0000.000
23D26GLN0-0.101-0.04816.0990.0430.0430.0000.0000.0000.000
24D27MET0-0.069-0.03116.9890.0310.0310.0000.0000.0000.000
25D28GLY0-0.021-0.01015.9210.0450.0450.0000.0000.0000.000
26D29VAL0-0.0210.00310.546-0.067-0.0670.0000.0000.0000.000
27D30ALA00.0530.03013.2270.0750.0750.0000.0000.0000.000
28D31TYR0-0.076-0.05310.9750.0160.0160.0000.0000.0000.000
29D32LYS10.9360.97011.960-0.253-0.2530.0000.0000.0000.000
30D33SER00.009-0.00612.1670.0450.0450.0000.0000.0000.000
31D34HIS00.1670.0919.752-0.037-0.0370.0000.0000.0000.000
32D35ALA0-0.061-0.0338.272-0.065-0.0650.0000.0000.0000.000
33D36SER0-0.033-0.0387.6620.6450.6450.0000.0000.0000.000
34D37THR0-0.039-0.0273.033-1.553-0.2370.275-0.655-0.9360.005
35D38LEU00.0080.0133.201-0.3000.5580.010-0.237-0.6300.000
36D39GLU-1-0.861-0.9143.341-4.576-3.1700.052-0.766-0.692-0.006
37D40GLU-1-0.931-0.9744.745-1.913-1.761-0.001-0.005-0.1460.000
38D41LYS10.8230.8855.6401.1051.1050.0000.0000.0000.000
39D42ASP-1-0.809-0.8947.686-1.045-1.0450.0000.0000.0000.000
40D43ALA00.003-0.0034.031-0.0630.0910.001-0.025-0.1300.000
41D44GLU-1-0.870-0.9205.924-1.058-1.0580.0000.0000.0000.000
42D45ALA0-0.024-0.0148.6130.2230.2230.0000.0000.0000.000
43D46VAL00.0100.0098.2190.1560.1560.0000.0000.0000.000
44D47ARG10.7810.8454.6021.8821.962-0.001-0.004-0.0740.000
45D48GLU-1-0.820-0.88810.112-0.424-0.4240.0000.0000.0000.000
46D49LEU0-0.005-0.00213.3220.0970.0970.0000.0000.0000.000
47D50VAL00.0220.01011.5490.0760.0760.0000.0000.0000.000
48D51LYS10.7830.87114.2050.5940.5940.0000.0000.0000.000
49D52GLU-1-0.907-0.95715.989-0.298-0.2980.0000.0000.0000.000
50D53GLN0-0.022-0.01918.0170.0460.0460.0000.0000.0000.000
51D54ARG10.9020.94915.9890.3650.3650.0000.0000.0000.000
52D55GLY00.0000.00819.4010.0340.0340.0000.0000.0000.000
53D56LEU0-0.053-0.04221.8050.0340.0340.0000.0000.0000.000
54D57GLN00.0240.01719.3720.0210.0210.0000.0000.0000.000
55D58GLU-1-0.864-0.92721.351-0.218-0.2180.0000.0000.0000.000
56D59LYS10.8820.95525.0170.2240.2240.0000.0000.0000.000
57D60LEU00.0430.03026.6780.0150.0150.0000.0000.0000.000
58D61ALA00.0280.01327.1070.0140.0140.0000.0000.0000.000
59D62GLU-1-0.793-0.85129.002-0.108-0.1080.0000.0000.0000.000
60D63GLU-1-0.936-0.98930.665-0.140-0.1400.0000.0000.0000.000
61D64GLU-1-1.006-0.98531.906-0.091-0.0910.0000.0000.0000.000
62D65ARG10.9650.96532.0780.1190.1190.0000.0000.0000.000
63D66ARG10.8130.89434.8180.1160.1160.0000.0000.0000.000
64D67LYS10.8720.92334.3580.1140.1140.0000.0000.0000.000
65D68SER0-0.055-0.03636.5950.0060.0060.0000.0000.0000.000
66D69LEU0-0.048-0.00938.5610.0050.0050.0000.0000.0000.000
67D70PRO00.0230.00641.1270.0020.0020.0000.0000.0000.000
68D71ARG10.8680.92744.5440.0500.0500.0000.0000.0000.000
69D72ARG10.7970.87847.7030.0570.0570.0000.0000.0000.000
70D73PRO0-0.0030.00249.9480.0000.0000.0000.0000.0000.000
71D74PRO00.0060.00853.461-0.002-0.0020.0000.0000.0000.000
72D75VAL00.0070.01554.6450.0020.0020.0000.0000.0000.000
73D76VAL0-0.010-0.00257.125-0.001-0.0010.0000.0000.0000.000
74D77VAL00.0130.01160.5830.0010.0010.0000.0000.0000.000
75D78ILE0-0.007-0.00163.4710.0000.0000.0000.0000.0000.000
76D79MET0-0.037-0.01265.3590.0000.0000.0000.0000.0000.000
77D80GLY00.0590.02468.9680.0000.0000.0000.0000.0000.000
78D81HIS00.005-0.01972.147-0.001-0.0010.0000.0000.0000.000
79D82VAL0-0.039-0.02675.6350.0000.0000.0000.0000.0000.000
80D83ASP-1-0.833-0.91276.774-0.024-0.0240.0000.0000.0000.000
81D84HIS0-0.086-0.05575.9340.0000.0000.0000.0000.0000.000
82D85GLY00.0220.01376.7930.0000.0000.0000.0000.0000.000
83D86LYS10.9110.97271.4210.0290.0290.0000.0000.0000.000
84D87THR00.0410.02272.0560.0000.0000.0000.0000.0000.000
85D88THR0-0.035-0.02073.6990.0010.0010.0000.0000.0000.000
86D89LEU00.0330.01769.8870.0000.0000.0000.0000.0000.000
87D90LEU00.0340.02367.1330.0000.0000.0000.0000.0000.000
88D91ASP-1-0.848-0.94270.329-0.026-0.0260.0000.0000.0000.000
89D92TYR0-0.136-0.06671.8710.0010.0010.0000.0000.0000.000
90D93LEU00.0390.02366.7110.0000.0000.0000.0000.0000.000
91D94ARG00.0240.07068.3090.0000.0000.0000.0000.0000.000
92D95LYS10.8480.93169.4020.0230.0230.0000.0000.0000.000
93D96SER0-0.044-0.03768.8460.0010.0010.0000.0000.0000.000
94D97ARG00.0580.09861.1750.0000.0000.0000.0000.0000.000
95D98ILE0-0.012-0.01365.3130.0000.0000.0000.0000.0000.000
96D99ALA0-0.0240.00167.7780.0010.0010.0000.0000.0000.000
97D107THR0-0.0020.01068.0860.0000.0000.0000.0000.0000.000
98D108GLN00.017-0.02166.2900.0000.0000.0000.0000.0000.000
99D109HIS0-0.0110.00166.9450.0000.0000.0000.0000.0000.000
100D110VAL00.0080.02560.4870.0000.0000.0000.0000.0000.000
101D111GLY00.0330.02261.503-0.001-0.0010.0000.0000.0000.000
102D112ALA0-0.024-0.01660.2200.0000.0000.0000.0000.0000.000
103D113PHE0-0.040-0.01962.3770.0010.0010.0000.0000.0000.000
104D114GLU-1-0.811-0.90157.903-0.037-0.0370.0000.0000.0000.000
105D115VAL00.015-0.00761.2720.0020.0020.0000.0000.0000.000
106D116LYS10.8830.94456.0260.0340.0340.0000.0000.0000.000
107D117THR0-0.0030.00160.7910.0010.0010.0000.0000.0000.000
108D118PRO0-0.047-0.03859.780-0.001-0.0010.0000.0000.0000.000
109D119GLN00.001-0.00558.345-0.001-0.0010.0000.0000.0000.000
110D120GLY00.0210.01556.785-0.002-0.0020.0000.0000.0000.000
111D121THR0-0.064-0.03655.8570.0020.0020.0000.0000.0000.000
112D122VAL00.0240.01557.066-0.002-0.0020.0000.0000.0000.000
113D123VAL00.0030.00556.6570.0010.0010.0000.0000.0000.000
114D124PHE00.0480.01859.440-0.001-0.0010.0000.0000.0000.000
115D125ILE0-0.004-0.01859.2130.0010.0010.0000.0000.0000.000
116D126ASH0-0.111-0.09963.0640.0010.0010.0000.0000.0000.000
117D127THR0-0.030-0.00365.1790.0010.0010.0000.0000.0000.000
118D128PRO0-0.037-0.00466.237-0.001-0.0010.0000.0000.0000.000
119D129GLY00.0300.01268.7550.0000.0000.0000.0000.0000.000
120D130HIS0-0.052-0.02267.4420.0010.0010.0000.0000.0000.000
121D131GLU-1-0.797-0.86965.157-0.038-0.0380.0000.0000.0000.000
122D132ALA0-0.010-0.00866.6800.0000.0000.0000.0000.0000.000
123D133PHE00.0180.01858.893-0.001-0.0010.0000.0000.0000.000
124D134THR0-0.035-0.02364.2740.0010.0010.0000.0000.0000.000
125D135THR0-0.009-0.01963.2410.0000.0000.0000.0000.0000.000
126D136ILE00.015-0.00260.276-0.001-0.0010.0000.0000.0000.000
127D137ARG00.0390.00959.017-0.003-0.0030.0000.0000.0000.000
128D138GLN0-0.009-0.02258.165-0.002-0.0020.0000.0000.0000.000
129D139ARG00.0040.01558.215-0.001-0.0010.0000.0000.0000.000
130D140GLY0-0.035-0.00555.897-0.001-0.0010.0000.0000.0000.000
131D141ALA0-0.016-0.00453.573-0.003-0.0030.0000.0000.0000.000
132D142LYS10.8900.94351.7520.0560.0560.0000.0000.0000.000
133D143VAL0-0.022-0.01053.560-0.001-0.0010.0000.0000.0000.000
134D144ALA00.0080.00255.6330.0000.0000.0000.0000.0000.000
135D145ASP-1-0.804-0.87653.177-0.054-0.0540.0000.0000.0000.000
136D146ILE00.0150.02156.0790.0000.0000.0000.0000.0000.000
137D147ALA00.006-0.00259.5470.0010.0010.0000.0000.0000.000
138D148VAL00.0050.00062.9640.0000.0000.0000.0000.0000.000
139D149ILE00.0140.00166.0270.0010.0010.0000.0000.0000.000
140D150VAL0-0.027-0.01968.7690.0010.0010.0000.0000.0000.000
141D151ILE0-0.025-0.01071.7160.0000.0000.0000.0000.0000.000
142D152ALA0-0.031-0.01774.8370.0000.0000.0000.0000.0000.000
143D153ALA00.0460.00778.4350.0000.0000.0000.0000.0000.000
144D154ASP-1-0.806-0.89780.154-0.023-0.0230.0000.0000.0000.000
145D155ASP-1-0.876-0.91281.129-0.024-0.0240.0000.0000.0000.000
146D156GLY00.0000.00879.1870.0000.0000.0000.0000.0000.000
147D157ILE0-0.062-0.04873.3040.0000.0000.0000.0000.0000.000
148D158MET00.0190.01776.6880.0000.0000.0000.0000.0000.000
149D159PRO00.0660.01575.880-0.001-0.0010.0000.0000.0000.000
150D160GLN00.0590.03974.196-0.001-0.0010.0000.0000.0000.000
151D161THR0-0.014-0.00372.579-0.001-0.0010.0000.0000.0000.000
152D162GLU-1-0.829-0.90571.148-0.031-0.0310.0000.0000.0000.000
153D163GLU-1-0.891-0.93569.849-0.035-0.0350.0000.0000.0000.000
154D164ALA0-0.020-0.01268.303-0.001-0.0010.0000.0000.0000.000
155D165ILE00.0170.00766.539-0.001-0.0010.0000.0000.0000.000
156D166ALA0-0.016-0.00265.185-0.002-0.0020.0000.0000.0000.000
157D167HIS0-0.057-0.03564.122-0.002-0.0020.0000.0000.0000.000
158D168ALA00.0220.00462.211-0.002-0.0020.0000.0000.0000.000
159D169LYS10.9150.96160.5860.0420.0420.0000.0000.0000.000
160D170ALA0-0.045-0.01659.449-0.002-0.0020.0000.0000.0000.000
161D171ALA00.0030.00857.747-0.002-0.0020.0000.0000.0000.000
162D172GLY0-0.028-0.00555.499-0.001-0.0010.0000.0000.0000.000
163D173ALA0-0.048-0.01955.714-0.001-0.0010.0000.0000.0000.000
164D174LYS10.8870.93155.7990.0490.0490.0000.0000.0000.000
165D175LEU0-0.021-0.02758.8190.0010.0010.0000.0000.0000.000
166D176ILE00.0260.01862.1220.0000.0000.0000.0000.0000.000
167D177PHE0-0.006-0.00565.1720.0010.0010.0000.0000.0000.000
168D178ALA00.0360.01468.8680.0010.0010.0000.0000.0000.000
169D179ILE0-0.020-0.01670.9060.0010.0010.0000.0000.0000.000
170D180ASN00.0370.01274.4730.0010.0010.0000.0000.0000.000
171D181LYS10.7670.86176.4500.0240.0240.0000.0000.0000.000
172D182ILE00.0600.03376.6850.0010.0010.0000.0000.0000.000
173D183ASP-1-0.849-0.89280.426-0.021-0.0210.0000.0000.0000.000
174D184LEU0-0.065-0.02783.0690.0010.0010.0000.0000.0000.000
175D185PRO0-0.017-0.01485.4930.0000.0000.0000.0000.0000.000
176D186GLN0-0.015-0.01687.6810.0000.0000.0000.0000.0000.000
177D187ALA0-0.0200.01482.2590.0000.0000.0000.0000.0000.000
178D188ASP-1-0.768-0.88582.612-0.023-0.0230.0000.0000.0000.000
179D189PRO00.042-0.00577.782-0.001-0.0010.0000.0000.0000.000
180D190GLU-1-0.849-0.91077.687-0.025-0.0250.0000.0000.0000.000
181D191LYS10.8090.90678.7430.0230.0230.0000.0000.0000.000
182D192VAL00.0460.03174.496-0.001-0.0010.0000.0000.0000.000
183D193LYS10.8420.90874.0760.0260.0260.0000.0000.0000.000
184D194ARG10.8410.90774.3610.0240.0240.0000.0000.0000.000
185D195GLN00.0270.01875.8830.0000.0000.0000.0000.0000.000
186D196LEU00.0180.00970.036-0.001-0.0010.0000.0000.0000.000
187D197MET0-0.023-0.00971.245-0.001-0.0010.0000.0000.0000.000
188D198GLU-1-0.946-0.97172.016-0.029-0.0290.0000.0000.0000.000
189D199ARG10.7010.84070.8160.0300.0300.0000.0000.0000.000
190D200GLY0-0.0150.00667.685-0.001-0.0010.0000.0000.0000.000
191D201PHE0-0.022-0.01664.391-0.002-0.0020.0000.0000.0000.000
192D202VAL00.0340.00967.6300.0010.0010.0000.0000.0000.000
193D203PRO00.0210.00167.313-0.001-0.0010.0000.0000.0000.000
194D204GLU-1-0.812-0.90763.984-0.035-0.0350.0000.0000.0000.000
195D205GLU-1-0.859-0.91766.852-0.028-0.0280.0000.0000.0000.000
196D206TYR0-0.068-0.04169.7800.0010.0010.0000.0000.0000.000
197D207GLY0-0.032-0.00666.8340.0000.0000.0000.0000.0000.000
198D208GLY0-0.047-0.02465.233-0.001-0.0010.0000.0000.0000.000
199D209ASP-1-0.930-0.97061.367-0.041-0.0410.0000.0000.0000.000
200D210ALA0-0.034-0.01063.0760.0000.0000.0000.0000.0000.000
201D211ILE00.0210.01460.8520.0010.0010.0000.0000.0000.000
202D212VAL0-0.051-0.02065.4510.0000.0000.0000.0000.0000.000
203D213ILE00.0310.02065.8000.0000.0000.0000.0000.0000.000
204D214PRO0-0.031-0.00270.3340.0000.0000.0000.0000.0000.000
205D215ILE0-0.012-0.01171.0760.0000.0000.0000.0000.0000.000
206D216SER0-0.016-0.04974.5010.0000.0000.0000.0000.0000.000
207D217ALA0-0.0020.00374.9080.0000.0000.0000.0000.0000.000
208D218LYS10.8530.92376.0260.0230.0230.0000.0000.0000.000
209D219THR0-0.006-0.00478.3450.0000.0000.0000.0000.0000.000
210D220GLY00.0590.01874.6370.0000.0000.0000.0000.0000.000
211D221GLN0-0.029-0.00373.858-0.001-0.0010.0000.0000.0000.000
212D222GLY00.0890.04272.0920.0000.0000.0000.0000.0000.000
213D223VAL0-0.043-0.03069.458-0.001-0.0010.0000.0000.0000.000
214D224GLN0-0.016-0.00768.0220.0000.0000.0000.0000.0000.000
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