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: 3QYYL

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 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 452
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6752448.305063
FMO2-HF: Nuclear repulsion 6577833.434178
FMO2-HF: Total energy -174614.870885
FMO2-MP2: Total energy -175125.440841


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.
-16.11-5.2011.134-4.967-7.078-0.016
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 : 0.002 / q_NPA : 0.001
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].
3D6ILE00.0750.0433.213-3.3020.0880.042-1.542-1.8900.001
4D7TYR00.0280.0245.0440.1790.288-0.001-0.003-0.1050.000
5D8GLN0-0.113-0.0603.9250.4330.7510.002-0.046-0.2750.000
6D9LEU00.0520.0443.556-0.413-0.0650.007-0.061-0.2940.000
7D10ALA00.1070.0375.0350.0100.043-0.001-0.003-0.0290.000
8D11LYS10.8950.9527.866-0.206-0.2060.0000.0000.0000.000
9D12GLU-1-0.942-0.9586.692-1.025-1.0250.0000.0000.0000.000
10D13LEU0-0.011-0.0038.6480.0280.0280.0000.0000.0000.000
11D14GLY0-0.033-0.01010.9690.0310.0310.0000.0000.0000.000
12D15MET0-0.0490.00811.509-0.016-0.0160.0000.0000.0000.000
13D16GLU-1-0.834-0.89813.202-0.025-0.0250.0000.0000.0000.000
14D17CYS0-0.057-0.06312.443-0.030-0.0300.0000.0000.0000.000
15D18GLN0-0.063-0.04313.509-0.033-0.0330.0000.0000.0000.000
16D19GLU-1-0.898-0.95515.140-0.291-0.2910.0000.0000.0000.000
17D20LEU00.010-0.0027.480-0.049-0.0490.0000.0000.0000.000
18D21LEU0-0.069-0.04010.682-0.067-0.0670.0000.0000.0000.000
19D22GLU-1-0.845-0.90612.818-0.321-0.3210.0000.0000.0000.000
20D23LEU00.0630.03011.990-0.029-0.0290.0000.0000.0000.000
21D24LEU0-0.031-0.0218.695-0.084-0.0840.0000.0000.0000.000
22D25ASP-1-0.901-0.96512.756-0.310-0.3100.0000.0000.0000.000
23D26GLN0-0.126-0.05015.9860.0230.0230.0000.0000.0000.000
24D27MET0-0.079-0.03216.4300.0460.0460.0000.0000.0000.000
25D28GLY0-0.012-0.02115.6530.0500.0500.0000.0000.0000.000
26D29VAL00.0090.01610.603-0.076-0.0760.0000.0000.0000.000
27D30ALA00.0060.01612.9760.0960.0960.0000.0000.0000.000
28D31TYR0-0.021-0.01510.411-0.018-0.0180.0000.0000.0000.000
29D32LYS10.9250.97411.918-0.238-0.2380.0000.0000.0000.000
30D33SER00.0380.00011.8790.0500.0500.0000.0000.0000.000
31D34HIS00.1410.0789.934-0.052-0.0520.0000.0000.0000.000
32D35ALA0-0.058-0.0378.2090.0470.0470.0000.0000.0000.000
33D36SER0-0.075-0.0557.3470.6200.6200.0000.0000.0000.000
34D37THR0-0.024-0.0592.416-1.858-0.2680.735-0.928-1.3970.003
35D38LEU0-0.0100.0032.732-1.7680.2540.117-0.762-1.376-0.004
36D39GLU-1-0.864-0.9163.039-6.973-4.2310.235-1.587-1.391-0.016
37D40GLU-1-0.929-0.9704.450-1.978-1.806-0.001-0.009-0.1620.000
38D41LYS10.8560.9265.3991.2961.330-0.0010.000-0.0330.000
39D42ASP-1-0.801-0.8967.524-1.193-1.1930.0000.0000.0000.000
40D43ALA00.015-0.0084.0370.0240.1750.000-0.026-0.1260.000
41D44GLU-1-0.895-0.9466.178-0.993-0.9930.0000.0000.0000.000
42D45ALA0-0.036-0.0358.5240.2380.2380.0000.0000.0000.000
43D46VAL00.0130.0208.4460.1750.1750.0000.0000.0000.000
44D47ARG10.7780.8345.1521.7151.7150.0000.0000.0000.000
45D48GLU-1-0.834-0.90310.277-0.404-0.4040.0000.0000.0000.000
46D49LEU0-0.051-0.00813.2620.1000.1000.0000.0000.0000.000
47D50VAL00.0040.00811.5260.0590.0590.0000.0000.0000.000
48D51LYS10.8230.88914.4060.5620.5620.0000.0000.0000.000
49D52GLU-1-0.909-0.93416.493-0.304-0.3040.0000.0000.0000.000
50D53GLN00.003-0.01418.4090.0470.0470.0000.0000.0000.000
51D54ARG10.9991.01015.1090.3490.3490.0000.0000.0000.000
52D55GLY0-0.016-0.00819.4860.0320.0320.0000.0000.0000.000
53D56LEU0-0.048-0.04521.9640.0310.0310.0000.0000.0000.000
54D57GLN0-0.005-0.01119.8470.0200.0200.0000.0000.0000.000
55D58GLU-1-0.894-0.93722.717-0.175-0.1750.0000.0000.0000.000
56D59LYS10.9010.97325.8200.2060.2060.0000.0000.0000.000
57D60LEU00.0490.02326.7400.0130.0130.0000.0000.0000.000
58D61ALA00.0560.03527.3130.0110.0110.0000.0000.0000.000
59D62GLU-1-0.774-0.87729.262-0.100-0.1000.0000.0000.0000.000
60D63GLU-1-1.038-1.01431.109-0.132-0.1320.0000.0000.0000.000
61D64GLU-1-1.022-1.01832.158-0.086-0.0860.0000.0000.0000.000
62D65ARG10.9981.00931.9670.1080.1080.0000.0000.0000.000
63D66ARG10.7770.90834.8290.1090.1090.0000.0000.0000.000
64D67LYS10.8930.90334.7610.1050.1050.0000.0000.0000.000
65D68SER0-0.050-0.04137.1200.0050.0050.0000.0000.0000.000
66D69LEU0-0.068-0.01038.8490.0050.0050.0000.0000.0000.000
67D70PRO00.0340.00241.7800.0020.0020.0000.0000.0000.000
68D71ARG10.9480.98545.1300.0450.0450.0000.0000.0000.000
69D72ARG10.8300.89848.1700.0530.0530.0000.0000.0000.000
70D73PRO0-0.023-0.01050.0700.0000.0000.0000.0000.0000.000
71D74PRO00.002-0.00853.865-0.001-0.0010.0000.0000.0000.000
72D75VAL00.0020.01154.9660.0020.0020.0000.0000.0000.000
73D76VAL00.0310.01057.4850.0000.0000.0000.0000.0000.000
74D77VAL00.0250.00760.9240.0000.0000.0000.0000.0000.000
75D78ILE0-0.018-0.00463.8250.0000.0000.0000.0000.0000.000
76D79MET0-0.035-0.01665.5400.0000.0000.0000.0000.0000.000
77D80GLY00.0810.02869.1190.0000.0000.0000.0000.0000.000
78D81HIS00.009-0.01872.343-0.001-0.0010.0000.0000.0000.000
79D82VAL0-0.073-0.04875.9380.0000.0000.0000.0000.0000.000
80D83ASP-1-0.892-0.94176.918-0.023-0.0230.0000.0000.0000.000
81D84HIS0-0.083-0.05776.4830.0000.0000.0000.0000.0000.000
82D85GLY00.0370.01576.8040.0000.0000.0000.0000.0000.000
83D86LYS10.9521.01771.5450.0280.0280.0000.0000.0000.000
84D87THR00.0490.01672.8440.0000.0000.0000.0000.0000.000
85D88THR0-0.043-0.03674.0760.0000.0000.0000.0000.0000.000
86D89LEU0-0.017-0.01469.7730.0000.0000.0000.0000.0000.000
87D90LEU00.0370.01167.4460.0000.0000.0000.0000.0000.000
88D91ASP-1-0.849-0.91970.702-0.024-0.0240.0000.0000.0000.000
89D92TYR0-0.084-0.04672.0970.0010.0010.0000.0000.0000.000
90D93LEU00.0430.01267.1360.0000.0000.0000.0000.0000.000
91D94ARG00.0130.07668.230-0.001-0.0010.0000.0000.0000.000
92D95LYS10.8590.93669.7350.0210.0210.0000.0000.0000.000
93D96SER0-0.044-0.03968.8770.0010.0010.0000.0000.0000.000
94D97ARG00.0860.09961.6270.0000.0000.0000.0000.0000.000
95D98ILE0-0.0020.00465.8060.0000.0000.0000.0000.0000.000
96D99ALA0-0.043-0.01167.9170.0010.0010.0000.0000.0000.000
97D107THR0-0.0030.00968.8380.0000.0000.0000.0000.0000.000
98D108GLN00.035-0.01566.7510.0000.0000.0000.0000.0000.000
99D109HIS0-0.027-0.00766.9510.0000.0000.0000.0000.0000.000
100D110VAL00.0210.02660.8170.0000.0000.0000.0000.0000.000
101D111GLY00.0230.00561.969-0.001-0.0010.0000.0000.0000.000
102D112ALA0-0.062-0.03160.3720.0000.0000.0000.0000.0000.000
103D113PHE0-0.033-0.00361.7940.0000.0000.0000.0000.0000.000
104D114GLU-1-0.841-0.93458.008-0.033-0.0330.0000.0000.0000.000
105D115VAL00.007-0.00561.7420.0010.0010.0000.0000.0000.000
106D116LYS10.8890.95156.3750.0300.0300.0000.0000.0000.000
107D117THR00.0020.00960.8980.0010.0010.0000.0000.0000.000
108D118PRO00.007-0.02659.936-0.001-0.0010.0000.0000.0000.000
109D119GLN0-0.054-0.03858.517-0.001-0.0010.0000.0000.0000.000
110D120GLY00.0060.01256.895-0.002-0.0020.0000.0000.0000.000
111D121THR0-0.028-0.01556.2250.0010.0010.0000.0000.0000.000
112D122VAL00.0320.01957.096-0.002-0.0020.0000.0000.0000.000
113D123VAL00.0110.01557.3170.0010.0010.0000.0000.0000.000
114D124PHE00.0260.00959.809-0.001-0.0010.0000.0000.0000.000
115D125ILE0-0.013-0.01959.5850.0010.0010.0000.0000.0000.000
116D126ASH0-0.105-0.09963.5180.0010.0010.0000.0000.0000.000
117D127THR00.0100.00665.3120.0010.0010.0000.0000.0000.000
118D128PRO0-0.056-0.01266.916-0.001-0.0010.0000.0000.0000.000
119D129GLY00.0600.03168.9630.0000.0000.0000.0000.0000.000
120D130HIS0-0.073-0.03267.7250.0010.0010.0000.0000.0000.000
121D131GLU-1-0.778-0.86265.453-0.036-0.0360.0000.0000.0000.000
122D132ALA0-0.009-0.00466.9750.0000.0000.0000.0000.0000.000
123D133PHE00.0060.00459.413-0.001-0.0010.0000.0000.0000.000
124D134THR0-0.020-0.01364.6730.0000.0000.0000.0000.0000.000
125D135THR0-0.037-0.01863.7260.0000.0000.0000.0000.0000.000
126D136ILE00.0450.00460.312-0.001-0.0010.0000.0000.0000.000
127D137ARG00.0300.00059.366-0.002-0.0020.0000.0000.0000.000
128D138GLN00.005-0.01958.445-0.002-0.0020.0000.0000.0000.000
129D139ARG0-0.0260.01258.485-0.001-0.0010.0000.0000.0000.000
130D140GLY0-0.0110.00256.396-0.001-0.0010.0000.0000.0000.000
131D141ALA0-0.030-0.00653.947-0.002-0.0020.0000.0000.0000.000
132D142LYS10.8850.93851.9240.0530.0530.0000.0000.0000.000
133D143VAL0-0.028-0.01553.946-0.001-0.0010.0000.0000.0000.000
134D144ALA00.0300.00855.7480.0000.0000.0000.0000.0000.000
135D145ASP-1-0.824-0.86253.603-0.051-0.0510.0000.0000.0000.000
136D146ILE00.000-0.00256.2580.0000.0000.0000.0000.0000.000
137D147ALA00.0130.00459.7340.0000.0000.0000.0000.0000.000
138D148VAL00.0150.00663.2510.0000.0000.0000.0000.0000.000
139D149ILE0-0.015-0.00966.4630.0000.0000.0000.0000.0000.000
140D150VAL0-0.028-0.02269.2420.0010.0010.0000.0000.0000.000
141D151ILE0-0.022-0.00372.2100.0000.0000.0000.0000.0000.000
142D152ALA00.0020.00675.0500.0000.0000.0000.0000.0000.000
143D153ALA0-0.002-0.01678.7620.0000.0000.0000.0000.0000.000
144D154ASP-1-0.855-0.93780.385-0.021-0.0210.0000.0000.0000.000
145D155ASP-1-0.835-0.89181.582-0.023-0.0230.0000.0000.0000.000
146D156GLY0-0.0110.00279.0680.0000.0000.0000.0000.0000.000
147D157ILE0-0.073-0.04873.8790.0000.0000.0000.0000.0000.000
148D158MET00.0080.02377.1860.0000.0000.0000.0000.0000.000
149D159PRO00.061-0.00276.051-0.001-0.0010.0000.0000.0000.000
150D160GLN00.0320.03174.758-0.001-0.0010.0000.0000.0000.000
151D161THR00.0050.00272.5780.0000.0000.0000.0000.0000.000
152D162GLU-1-0.842-0.90671.392-0.030-0.0300.0000.0000.0000.000
153D163GLU-1-0.934-0.95970.128-0.033-0.0330.0000.0000.0000.000
154D164ALA0-0.013-0.01568.402-0.001-0.0010.0000.0000.0000.000
155D165ILE00.0270.01266.614-0.001-0.0010.0000.0000.0000.000
156D166ALA0-0.003-0.00465.287-0.001-0.0010.0000.0000.0000.000
157D167HIS0-0.0010.00764.282-0.002-0.0020.0000.0000.0000.000
158D168ALA0-0.006-0.01162.436-0.001-0.0010.0000.0000.0000.000
159D169LYS10.9090.95960.9030.0410.0410.0000.0000.0000.000
160D170ALA0-0.065-0.02059.797-0.002-0.0020.0000.0000.0000.000
161D171ALA0-0.0020.00457.699-0.002-0.0020.0000.0000.0000.000
162D172GLY0-0.037-0.01055.945-0.001-0.0010.0000.0000.0000.000
163D173ALA0-0.0270.00756.086-0.001-0.0010.0000.0000.0000.000
164D174LYS10.8890.92155.9610.0460.0460.0000.0000.0000.000
165D175LEU0-0.009-0.01959.2590.0010.0010.0000.0000.0000.000
166D176ILE00.0510.04362.3990.0000.0000.0000.0000.0000.000
167D177PHE0-0.0080.00365.5210.0000.0000.0000.0000.0000.000
168D178ALA00.004-0.24269.1790.0000.0000.0000.0000.0000.000
169D179ILE0-0.007-0.04471.2490.0000.0000.0000.0000.0000.000
170D180ASN00.1170.03474.8450.0010.0010.0000.0000.0000.000
171D181LYS10.7330.85277.0870.0220.0220.0000.0000.0000.000
172D182ILE00.0670.03576.7890.0000.0000.0000.0000.0000.000
173D183ASP-1-0.855-0.90280.743-0.019-0.0190.0000.0000.0000.000
174D184LEU0-0.083-0.03383.3030.0010.0010.0000.0000.0000.000
175D185PRO00.004-0.00885.7710.0000.0000.0000.0000.0000.000
176D186GLN0-0.008-0.01587.9670.0000.0000.0000.0000.0000.000
177D187ALA0-0.0200.02782.3300.0000.0000.0000.0000.0000.000
178D188ASP-1-0.745-0.88583.130-0.022-0.0220.0000.0000.0000.000
179D189PRO00.0420.00478.040-0.001-0.0010.0000.0000.0000.000
180D190GLU-1-0.868-0.92478.100-0.023-0.0230.0000.0000.0000.000
181D191LYS10.7930.90379.2960.0220.0220.0000.0000.0000.000
182D192VAL00.0540.03875.261-0.001-0.0010.0000.0000.0000.000
183D193LYS10.8570.90974.2140.0250.0250.0000.0000.0000.000
184D194ARG10.8370.90274.7180.0230.0230.0000.0000.0000.000
185D195GLN0-0.007-0.00176.307-0.001-0.0010.0000.0000.0000.000
186D196LEU00.0530.02570.510-0.001-0.0010.0000.0000.0000.000
187D197MET0-0.028-0.00671.532-0.001-0.0010.0000.0000.0000.000
188D198GLU-1-1.004-0.99372.297-0.029-0.0290.0000.0000.0000.000
189D199ARG10.7680.87171.5670.0290.0290.0000.0000.0000.000
190D200GLY0-0.0110.00568.131-0.001-0.0010.0000.0000.0000.000
191D201PHE0-0.049-0.02464.586-0.001-0.0010.0000.0000.0000.000
192D202VAL00.0600.02967.4340.0010.0010.0000.0000.0000.000
193D203PRO00.0510.01667.361-0.001-0.0010.0000.0000.0000.000
194D204GLU-1-0.811-0.89264.033-0.033-0.0330.0000.0000.0000.000
195D205GLU-1-0.881-0.91967.237-0.027-0.0270.0000.0000.0000.000
196D206TYR0-0.076-0.05170.1800.0010.0010.0000.0000.0000.000
197D207GLY0-0.069-0.02067.6400.0000.0000.0000.0000.0000.000
198D208GLY0-0.040-0.04066.320-0.001-0.0010.0000.0000.0000.000
199D209ASP-1-0.931-0.97361.669-0.040-0.0400.0000.0000.0000.000
200D210ALA0-0.045-0.03063.2930.0000.0000.0000.0000.0000.000
201D211ILE00.0370.02261.3960.0010.0010.0000.0000.0000.000
202D212VAL0-0.076-0.04565.9570.0000.0000.0000.0000.0000.000
203D213ILE00.0350.00366.1330.0000.0000.0000.0000.0000.000
204D214PRO0-0.0010.32170.5850.0000.0000.0000.0000.0000.000
205D215ILE0-0.011-0.00971.3900.0000.0000.0000.0000.0000.000
206D216SER0-0.023-0.03174.7920.0000.0000.0000.0000.0000.000
207D217ALA00.0070.01775.0120.0000.0000.0000.0000.0000.000
208D218LYS10.8650.92976.4390.0210.0210.0000.0000.0000.000
209D219THR00.001-0.00679.6660.0000.0000.0000.0000.0000.000
210D220GLY00.033-0.00275.3610.0000.0000.0000.0000.0000.000
211D221GLN00.0240.01674.345-0.001-0.0010.0000.0000.0000.000
212D222GLY00.0710.02672.4050.0000.0000.0000.0000.0000.000
213D223VAL0-0.033-0.02669.768-0.001-0.0010.0000.0000.0000.000
214D224GLN0-0.041-0.03068.5980.0000.0000.0000.0000.0000.000
215D225ASP-1-0.787-0.89167.170-0.026-0.0260.0000.0000.0000.000
216D226LEU0-0.035-0.00665.905-0.001-0.0010.0000.0000.0000.000
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