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: J3JJ9

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 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 452
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6755094.702408
FMO2-HF: Nuclear repulsion 6580495.928556
FMO2-HF: Total energy -174598.773852
FMO2-MP2: Total energy -175111.080338


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.
-16.095-5.0561.573-5.101-7.508-0.018
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 : 0.015 / q_NPA : 0.002
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].
3D6ILE00.1080.0573.123-3.0000.3290.133-1.403-2.0580.001
4D7TYR0-0.0210.0104.7750.1450.259-0.001-0.004-0.1090.000
5D8GLN0-0.121-0.0623.8130.4180.6740.001-0.029-0.2280.000
6D9LEU00.0530.0433.518-0.485-0.0950.010-0.070-0.3300.000
7D10ALA00.0940.0335.0710.0300.063-0.001-0.004-0.0280.000
8D11LYS10.9050.9627.930-0.261-0.2610.0000.0000.0000.000
9D12GLU-1-1.040-1.0326.635-0.824-0.8240.0000.0000.0000.000
10D13LEU0-0.008-0.0018.4730.0340.0340.0000.0000.0000.000
11D14GLY0-0.047-0.01110.8780.0320.0320.0000.0000.0000.000
12D15MET0-0.271-0.23411.4980.0440.0440.0000.0000.0000.000
13D16GLU-1-0.802-0.86313.184-0.073-0.0730.0000.0000.0000.000
14D17CYS0-0.009-0.09311.886-0.056-0.0560.0000.0000.0000.000
15D18GLN0-0.104-0.01413.354-0.030-0.0300.0000.0000.0000.000
16D19GLU-1-0.855-0.76115.409-0.385-0.3850.0000.0000.0000.000
17D20LEU00.1630.0147.390-0.059-0.0590.0000.0000.0000.000
18D21LEU0-0.062-0.04410.661-0.084-0.0840.0000.0000.0000.000
19D22GLU-1-0.789-0.88212.513-0.413-0.4130.0000.0000.0000.000
20D23LEU00.0090.01511.323-0.035-0.0350.0000.0000.0000.000
21D24LEU00.1110.0148.298-0.099-0.0990.0000.0000.0000.000
22D25ASP-1-0.262-0.57712.420-0.457-0.4570.0000.0000.0000.000
23D26GLN0-0.084-0.05615.6220.0400.0400.0000.0000.0000.000
24D27MET0-0.066-0.02516.4490.0600.0600.0000.0000.0000.000
25D28GLY0-0.064-0.03615.6590.0580.0580.0000.0000.0000.000
26D29VAL0-0.779-0.40011.444-0.059-0.0590.0000.0000.0000.000
27D30ALA0-0.016-0.00112.9080.1130.1130.0000.0000.0000.000
28D31TYR0-0.0100.03610.334-0.043-0.0430.0000.0000.0000.000
29D32LYS10.9190.97311.822-0.110-0.1100.0000.0000.0000.000
30D33SER00.019-0.05211.7600.0750.0750.0000.0000.0000.000
31D34HIS00.1510.0729.629-0.099-0.0990.0000.0000.0000.000
32D35ALA0-0.049-0.0347.9680.0690.0690.0000.0000.0000.000
33D36SER0-0.066-0.0437.3470.5740.5740.0000.0000.0000.000
34D37THR0-0.032-0.0622.221-1.3610.0931.066-1.046-1.4740.002
35D38LEU00.0040.0152.688-1.8840.4670.147-0.929-1.569-0.005
36D39GLU-1-0.918-0.9503.022-7.344-4.6030.220-1.587-1.373-0.016
37D40GLU-1-0.923-0.9684.629-1.848-1.701-0.001-0.006-0.1390.000
38D41LYS10.9800.9915.6151.1181.1180.0000.0000.0000.000
39D42ASP-1-0.828-0.9047.272-1.418-1.4180.0000.0000.0000.000
40D43ALA0-0.012-0.0234.054-0.0020.1450.000-0.020-0.1270.000
41D44GLU-1-0.973-1.0086.191-0.740-0.7400.0000.0000.0000.000
42D45ALA0-0.024-0.0288.6350.2380.2380.0000.0000.0000.000
43D46VAL00.0100.0228.3100.1780.1780.0000.0000.0000.000
44D47ARG10.9070.9364.3821.7911.868-0.001-0.003-0.0730.000
45D48GLU-1-0.954-0.98210.294-0.403-0.4030.0000.0000.0000.000
46D49LEU0-0.0440.00013.2660.0990.0990.0000.0000.0000.000
47D50VAL0-0.0140.00611.3120.0600.0600.0000.0000.0000.000
48D51LYS10.9750.97614.3470.4780.4780.0000.0000.0000.000
49D52GLU-1-0.932-0.93116.485-0.337-0.3370.0000.0000.0000.000
50D53GLN00.022-0.01718.3240.0290.0290.0000.0000.0000.000
51D54ARG10.9991.01014.9530.3660.3660.0000.0000.0000.000
52D55GLY0-0.026-0.01219.4240.0350.0350.0000.0000.0000.000
53D56LEU0-0.045-0.04721.9450.0310.0310.0000.0000.0000.000
54D57GLN00.007-0.00619.7990.0190.0190.0000.0000.0000.000
55D58GLU-1-0.900-0.93923.247-0.172-0.1720.0000.0000.0000.000
56D59LYS10.9110.97325.7690.2130.2130.0000.0000.0000.000
57D60LEU00.0400.02726.6800.0130.0130.0000.0000.0000.000
58D61ALA00.0430.02827.2420.0110.0110.0000.0000.0000.000
59D62GLU-1-0.886-0.97529.178-0.107-0.1070.0000.0000.0000.000
60D63GLU-1-1.095-1.04031.367-0.141-0.1410.0000.0000.0000.000
61D64GLU-1-0.992-1.03932.074-0.091-0.0910.0000.0000.0000.000
62D65ARG11.0731.08431.8000.1140.1140.0000.0000.0000.000
63D66ARG10.8761.02534.8700.1130.1130.0000.0000.0000.000
64D67LYS10.9310.95336.1860.1080.1080.0000.0000.0000.000
65D68SER0-0.117-0.13237.0440.0040.0040.0000.0000.0000.000
66D69LEU0-0.0020.05739.0600.0050.0050.0000.0000.0000.000
67D70PRO00.012-0.01341.6970.0020.0020.0000.0000.0000.000
68D71ARG10.9850.98845.0430.0470.0470.0000.0000.0000.000
69D72ARG10.8430.93348.1680.0550.0550.0000.0000.0000.000
70D73PRO0-0.034-0.01550.0050.0000.0000.0000.0000.0000.000
71D74PRO0-0.022-0.01453.797-0.001-0.0010.0000.0000.0000.000
72D75VAL00.0120.02254.8110.0020.0020.0000.0000.0000.000
73D76VAL00.0240.00057.440-0.001-0.0010.0000.0000.0000.000
74D77VAL00.0200.00660.8790.0010.0010.0000.0000.0000.000
75D78ILE00.0010.00863.7900.0000.0000.0000.0000.0000.000
76D79MET0-0.043-0.02465.8300.0000.0000.0000.0000.0000.000
77D80GLY00.0790.02669.0890.0000.0000.0000.0000.0000.000
78D81HIS00.068-0.01472.313-0.001-0.0010.0000.0000.0000.000
79D82VAL0-0.104-0.07275.9130.0000.0000.0000.0000.0000.000
80D83ASP-1-0.889-0.94676.899-0.023-0.0230.0000.0000.0000.000
81D84HIS0-0.117-0.05076.4850.0000.0000.0000.0000.0000.000
82D85GLY00.0250.00476.7580.0000.0000.0000.0000.0000.000
83D86LYS10.9891.02571.4740.0290.0290.0000.0000.0000.000
84D87THR00.0400.01872.8020.0000.0000.0000.0000.0000.000
85D88THR0-0.033-0.02874.0360.0010.0010.0000.0000.0000.000
86D89LEU0-0.010-0.01769.9900.0010.0010.0000.0000.0000.000
87D90LEU00.0440.00867.2880.0000.0000.0000.0000.0000.000
88D91ASP-1-0.863-0.93370.651-0.025-0.0250.0000.0000.0000.000
89D92TYR0-0.087-0.03171.8700.0010.0010.0000.0000.0000.000
90D93LEU00.0610.00766.9100.0000.0000.0000.0000.0000.000
91D94ARG00.0240.19068.168-0.001-0.0010.0000.0000.0000.000
92D95LYS10.8620.94569.6830.0210.0210.0000.0000.0000.000
93D96SER0-0.067-0.05968.9660.0000.0000.0000.0000.0000.000
94D97ARG0-0.109-0.14361.3250.0000.0000.0000.0000.0000.000
95D98ILE0-0.1520.10265.5880.0000.0000.0000.0000.0000.000
96D99ALA0-0.036-0.01267.8500.0010.0010.0000.0000.0000.000
97D107THR0-0.030-0.02768.7190.0000.0000.0000.0000.0000.000
98D108GLN00.0500.01366.7480.0000.0000.0000.0000.0000.000
99D109HIS0-0.0030.00066.9060.0000.0000.0000.0000.0000.000
100D110VAL00.0090.03160.3510.0000.0000.0000.0000.0000.000
101D111GLY0-0.007-0.02461.966-0.001-0.0010.0000.0000.0000.000
102D112ALA0-0.061-0.03160.3500.0000.0000.0000.0000.0000.000
103D113PHE0-0.0300.00361.7650.0000.0000.0000.0000.0000.000
104D114GLU-1-0.820-0.90257.620-0.033-0.0330.0000.0000.0000.000
105D115VAL00.0990.14161.6890.0020.0020.0000.0000.0000.000
106D116LYS10.8510.94356.5830.0320.0320.0000.0000.0000.000
107D117THR0-0.021-0.01860.7710.0010.0010.0000.0000.0000.000
108D118PRO00.010-0.03359.862-0.001-0.0010.0000.0000.0000.000
109D119GLN0-0.046-0.03058.449-0.001-0.0010.0000.0000.0000.000
110D120GLY00.0160.01056.878-0.002-0.0020.0000.0000.0000.000
111D121THR00.003-0.00656.3780.0020.0020.0000.0000.0000.000
112D122VAL00.0250.04757.019-0.002-0.0020.0000.0000.0000.000
113D123VAL00.0480.01857.5600.0020.0020.0000.0000.0000.000
114D124PHE0-0.019-0.02259.758-0.001-0.0010.0000.0000.0000.000
115D125ILE0-0.020-0.01059.7800.0010.0010.0000.0000.0000.000
116D126ASH0-0.111-0.20063.4910.0010.0010.0000.0000.0000.000
117D127THR0-0.090-0.10265.4700.0000.0000.0000.0000.0000.000
118D128PRO0-0.037-0.01066.910-0.001-0.0010.0000.0000.0000.000
119D129GLY00.0550.03268.9650.0000.0000.0000.0000.0000.000
120D130HIS0-0.071-0.03767.6200.0020.0020.0000.0000.0000.000
121D131GLU-1-0.797-0.87865.657-0.036-0.0360.0000.0000.0000.000
122D132ALA0-0.0200.00267.2440.0000.0000.0000.0000.0000.000
123D133PHE0-0.010-0.01559.705-0.001-0.0010.0000.0000.0000.000
124D134THR0-0.0010.00865.0370.0000.0000.0000.0000.0000.000
125D135THR0-0.047-0.02663.6190.0000.0000.0000.0000.0000.000
126D136ILE00.035-0.00160.325-0.001-0.0010.0000.0000.0000.000
127D137ARG00.010-0.01759.409-0.001-0.0010.0000.0000.0000.000
128D138GLN00.0750.02058.479-0.002-0.0020.0000.0000.0000.000
129D139ARG00.1730.26658.5020.0010.0010.0000.0000.0000.000
130D140GLY0-0.0200.00256.418-0.001-0.0010.0000.0000.0000.000
131D141ALA0-0.0210.00253.961-0.002-0.0020.0000.0000.0000.000
132D142LYS10.8940.93951.8590.0550.0550.0000.0000.0000.000
133D143VAL0-0.023-0.01953.934-0.001-0.0010.0000.0000.0000.000
134D144ALA00.0260.00855.7260.0000.0000.0000.0000.0000.000
135D145ASP-1-0.827-0.88054.097-0.051-0.0510.0000.0000.0000.000
136D146ILE0-0.007-0.02356.214-0.001-0.0010.0000.0000.0000.000
137D147ALA00.0150.01459.6830.0010.0010.0000.0000.0000.000
138D148VAL00.0100.00663.2070.0000.0000.0000.0000.0000.000
139D149ILE0-0.019-0.01266.4110.0010.0010.0000.0000.0000.000
140D150VAL0-0.013-0.02069.1950.0010.0010.0000.0000.0000.000
141D151ILE0-0.0200.00072.1340.0000.0000.0000.0000.0000.000
142D152ALA00.0060.00074.9980.0000.0000.0000.0000.0000.000
143D153ALA0-0.010-0.02478.7080.0000.0000.0000.0000.0000.000
144D154ASP-1-0.994-0.99680.320-0.022-0.0220.0000.0000.0000.000
145D155ASP-1-0.824-0.92581.552-0.024-0.0240.0000.0000.0000.000
146D156GLY0-0.014-0.00479.0200.0000.0000.0000.0000.0000.000
147D157ILE0-0.080-0.05973.8990.0000.0000.0000.0000.0000.000
148D158MET0-0.0270.01577.1510.0010.0010.0000.0000.0000.000
149D159PRO00.061-0.03676.187-0.001-0.0010.0000.0000.0000.000
150D160GLN00.1000.09274.773-0.001-0.0010.0000.0000.0000.000
151D161THR00.003-0.00672.4160.0000.0000.0000.0000.0000.000
152D162GLU-1-0.949-0.92971.367-0.032-0.0320.0000.0000.0000.000
153D163GLU-1-0.955-0.96570.086-0.034-0.0340.0000.0000.0000.000
154D164ALA0-0.012-0.01768.377-0.001-0.0010.0000.0000.0000.000
155D165ILE00.0160.00566.482-0.001-0.0010.0000.0000.0000.000
156D166ALA0-0.0040.00065.262-0.001-0.0010.0000.0000.0000.000
157D167HIS0-0.183-0.25064.274-0.003-0.0030.0000.0000.0000.000
158D168ALA00.006-0.00162.417-0.001-0.0010.0000.0000.0000.000
159D169LYS10.9020.95460.8820.0430.0430.0000.0000.0000.000
160D170ALA0-0.057-0.01359.781-0.002-0.0020.0000.0000.0000.000
161D171ALA0-0.0020.00157.702-0.002-0.0020.0000.0000.0000.000
162D172GLY0-0.036-0.00655.923-0.001-0.0010.0000.0000.0000.000
163D173ALA0-0.0250.00556.055-0.001-0.0010.0000.0000.0000.000
164D174LYS10.9280.96656.1840.0490.0490.0000.0000.0000.000
165D175LEU0-0.009-0.02459.2040.0010.0010.0000.0000.0000.000
166D176ILE00.0640.05061.8680.0000.0000.0000.0000.0000.000
167D177PHE0-0.0170.00265.4530.0010.0010.0000.0000.0000.000
168D178ALA0-0.128-0.31669.1120.0010.0010.0000.0000.0000.000
169D179ILE00.044-0.00971.1760.0000.0000.0000.0000.0000.000
170D180ASN00.1620.04674.7720.0010.0010.0000.0000.0000.000
171D181LYS10.8030.89077.0180.0230.0230.0000.0000.0000.000
172D182ILE00.0770.05776.4870.0000.0000.0000.0000.0000.000
173D183ASP-1-0.852-0.92680.661-0.021-0.0210.0000.0000.0000.000
174D184LEU0-0.090-0.03683.2170.0010.0010.0000.0000.0000.000
175D185PRO0-0.024-0.00685.6950.0000.0000.0000.0000.0000.000
176D186GLN00.029-0.01187.9020.0000.0000.0000.0000.0000.000
177D187ALA0-0.0190.02682.1870.0000.0000.0000.0000.0000.000
178D188ASP-1-0.753-0.90182.916-0.024-0.0240.0000.0000.0000.000
179D189PRO00.023-0.00278.092-0.001-0.0010.0000.0000.0000.000
180D190GLU-1-0.937-0.97178.022-0.025-0.0250.0000.0000.0000.000
181D191LYS10.8470.94079.2190.0230.0230.0000.0000.0000.000
182D192VAL00.0520.04175.297-0.001-0.0010.0000.0000.0000.000
183D193LYS10.9430.97273.6930.0270.0270.0000.0000.0000.000
184D194ARG10.9040.94674.6470.0250.0250.0000.0000.0000.000
185D195GLN0-0.034-0.00576.243-0.001-0.0010.0000.0000.0000.000
186D196LEU00.0550.03370.237-0.001-0.0010.0000.0000.0000.000
187D197MET0-0.031-0.01071.456-0.001-0.0010.0000.0000.0000.000
188D198GLU-1-0.997-0.98972.238-0.031-0.0310.0000.0000.0000.000
189D199ARG10.8370.92971.4030.0310.0310.0000.0000.0000.000
190D200GLY0-0.0050.00368.084-0.001-0.0010.0000.0000.0000.000
191D201PHE0-0.052-0.02365.157-0.002-0.0020.0000.0000.0000.000
192D202VAL00.0670.02767.3800.0010.0010.0000.0000.0000.000
193D203PRO00.0460.00567.279-0.001-0.0010.0000.0000.0000.000
194D204GLU-1-0.839-0.89963.788-0.037-0.0370.0000.0000.0000.000
195D205GLU-1-0.976-0.98167.133-0.029-0.0290.0000.0000.0000.000
196D206TYR0-0.085-0.05970.0510.0010.0010.0000.0000.0000.000
197D207GLY0-0.057-0.01367.4910.0000.0000.0000.0000.0000.000
198D208GLY0-0.035-0.03666.229-0.001-0.0010.0000.0000.0000.000
199D209ASP-1-0.948-0.97361.565-0.044-0.0440.0000.0000.0000.000
200D210ALA0-0.029-0.02763.2110.0000.0000.0000.0000.0000.000
201D211ILE00.0540.02761.4390.0020.0020.0000.0000.0000.000
202D212VAL0-0.066-0.04365.8710.0010.0010.0000.0000.0000.000
203D213ILE00.0780.01566.2470.0000.0000.0000.0000.0000.000
204D214PRO00.0250.33870.4980.0000.0000.0000.0000.0000.000
205D215ILE0-0.036-0.01371.4210.0000.0000.0000.0000.0000.000
206D216SER00.0180.01674.7090.0000.0000.0000.0000.0000.000
207D217ALA0-0.0110.00874.7350.0000.0000.0000.0000.0000.000
208D218LYS10.8720.93376.3700.0210.0210.0000.0000.0000.000
209D219THR00.0150.00279.5920.0000.0000.0000.0000.0000.000
210D220GLY00.0510.00275.2540.0000.0000.0000.0000.0000.000
211D221GLN00.0180.01674.2550.0000.0000.0000.0000.0000.000
212D222GLY00.0740.00972.2880.0000.0000.0000.0000.0000.000
213D223VAL0-0.019-0.01669.476-0.001-0.0010.0000.0000.0000.000
214D224GLN0-0.041-0.03968.507-0.001-0.0010.0000.0000.0000.000
215D225ASP-1-0.802-0.88767.066-0.028-0.0280.0000.0000.0000.000
216D226LEU0-0.060-0.01665.805-0.001-0.0010.0000.0000.0000.000
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