Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LZJR9

Calculation Name: 3G33-D-Xray372

Preferred Name: G1/S-specific cyclin D3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3G33

Chain ID: D

ChEMBL ID: CHEMBL2422

UniProt ID: P30281

Base Structure: X-ray

Registration Date: 2023-06-21

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2928292.678769
FMO2-HF: Nuclear repulsion 2833516.141462
FMO2-HF: Total energy -94776.537307
FMO2-MP2: Total energy -95043.104388


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:23:GLY)


Summations of interaction energy for fragment #1(D:23:GLY)
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.
-4.024-0.9910.728-1.382-2.3790.008
Interaction energy analysis for fragmet #1(D:23:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.022
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].
3D25GLN0-0.020-0.0193.586-0.2940.9900.000-0.536-0.7480.001
4D26ARG10.9480.9692.430-3.953-2.3720.729-0.811-1.4990.007
5D27VAL00.0290.0244.655-0.272-0.104-0.001-0.035-0.1320.000
6D28LEU00.0680.0396.6560.3430.3430.0000.0000.0000.000
7D29GLN00.0060.0098.3400.1810.1810.0000.0000.0000.000
8D30SER0-0.094-0.0469.129-0.033-0.0330.0000.0000.0000.000
9D31LEU00.0340.01310.6920.0390.0390.0000.0000.0000.000
10D32LEU00.0230.00712.7140.0390.0390.0000.0000.0000.000
11D33ARG10.9030.95313.006-0.086-0.0860.0000.0000.0000.000
12D34LEU0-0.0180.00014.2470.0120.0120.0000.0000.0000.000
13D35GLU-1-0.748-0.84217.189-0.086-0.0860.0000.0000.0000.000
14D36GLU-1-0.911-0.95719.374-0.005-0.0050.0000.0000.0000.000
15D37ARG10.7440.86520.7410.1230.1230.0000.0000.0000.000
16D38TYR0-0.123-0.08318.974-0.005-0.0050.0000.0000.0000.000
17D39VAL00.0750.05223.286-0.008-0.0080.0000.0000.0000.000
18D40PRO0-0.029-0.01625.6350.0070.0070.0000.0000.0000.000
19D41ARG10.9720.97929.1360.0480.0480.0000.0000.0000.000
20D42ALA0-0.007-0.00430.9690.0060.0060.0000.0000.0000.000
21D43SER00.0640.04334.043-0.004-0.0040.0000.0000.0000.000
22D44TYR00.024-0.01934.2590.0050.0050.0000.0000.0000.000
23D45PHE0-0.017-0.01138.1680.0010.0010.0000.0000.0000.000
24D46GLN00.0190.00041.1100.0010.0010.0000.0000.0000.000
25D47CYS0-0.058-0.01939.5000.0020.0020.0000.0000.0000.000
26D48VAL0-0.019-0.01140.7070.0000.0000.0000.0000.0000.000
27D49GLN00.0420.02143.677-0.001-0.0010.0000.0000.0000.000
28D50ARG10.9100.96146.3930.0300.0300.0000.0000.0000.000
29D51GLU-1-0.849-0.93647.192-0.036-0.0360.0000.0000.0000.000
30D52ILE0-0.0100.01340.850-0.001-0.0010.0000.0000.0000.000
31D53LYS10.9590.96943.6790.0320.0320.0000.0000.0000.000
32D54PRO00.0540.02740.298-0.003-0.0030.0000.0000.0000.000
33D55HIS00.0460.01440.363-0.004-0.0040.0000.0000.0000.000
34D56MET0-0.009-0.00442.140-0.001-0.0010.0000.0000.0000.000
35D57ARG10.7640.87531.6180.0710.0710.0000.0000.0000.000
36D58LYS10.8790.94237.2370.0410.0410.0000.0000.0000.000
37D59MET0-0.004-0.00538.378-0.002-0.0020.0000.0000.0000.000
38D60LEU0-0.041-0.01437.240-0.001-0.0010.0000.0000.0000.000
39D61ALA00.0250.00734.199-0.004-0.0040.0000.0000.0000.000
40D62TYR00.0360.00534.984-0.004-0.0040.0000.0000.0000.000
41D63TRP00.0220.02737.162-0.004-0.0040.0000.0000.0000.000
42D64MET0-0.045-0.03033.200-0.005-0.0050.0000.0000.0000.000
43D65LEU00.0190.01431.138-0.007-0.0070.0000.0000.0000.000
44D66GLU-1-0.901-0.95233.640-0.070-0.0700.0000.0000.0000.000
45D67VAL00.0000.00234.310-0.003-0.0030.0000.0000.0000.000
46D68CYS0-0.059-0.02929.922-0.005-0.0050.0000.0000.0000.000
47D69GLU-1-0.810-0.86730.390-0.121-0.1210.0000.0000.0000.000
48D70GLU-1-0.966-0.97032.636-0.079-0.0790.0000.0000.0000.000
49D71GLN0-0.092-0.05332.2600.0030.0030.0000.0000.0000.000
50D72ARG10.7270.83629.4920.1110.1110.0000.0000.0000.000
51D73CYS0-0.053-0.02727.795-0.003-0.0030.0000.0000.0000.000
52D74GLU-1-0.920-0.96422.212-0.246-0.2460.0000.0000.0000.000
53D75GLU-1-0.934-0.98122.750-0.152-0.1520.0000.0000.0000.000
54D76GLU-1-0.898-0.93318.345-0.345-0.3450.0000.0000.0000.000
55D77VAL0-0.010-0.00322.7610.0090.0090.0000.0000.0000.000
56D78PHE00.0550.02025.7530.0080.0080.0000.0000.0000.000
57D79PRO00.0530.01024.3960.0090.0090.0000.0000.0000.000
58D80LEU00.0040.01122.4580.0080.0080.0000.0000.0000.000
59D81ALA0-0.013-0.00325.4800.0100.0100.0000.0000.0000.000
60D82MET0-0.015-0.01029.0800.0120.0120.0000.0000.0000.000
61D83ASN0-0.029-0.01224.8610.0060.0060.0000.0000.0000.000
62D84TYR0-0.030-0.04424.2660.0120.0120.0000.0000.0000.000
63D85LEU00.0190.01129.6280.0100.0100.0000.0000.0000.000
64D86ASP-1-0.724-0.82930.665-0.067-0.0670.0000.0000.0000.000
65D87ARG10.8680.94925.3720.1300.1300.0000.0000.0000.000
66D88TYR00.008-0.00331.2150.0070.0070.0000.0000.0000.000
67D89LEU0-0.021-0.02334.1610.0060.0060.0000.0000.0000.000
68D90SER0-0.054-0.04333.3700.0060.0060.0000.0000.0000.000
69D91CYS0-0.089-0.03734.3610.0040.0040.0000.0000.0000.000
70D92VAL0-0.043-0.01836.9340.0040.0040.0000.0000.0000.000
71D93PRO0-0.026-0.01239.290-0.001-0.0010.0000.0000.0000.000
72D94THR0-0.0060.01140.5530.0020.0020.0000.0000.0000.000
73D95ARG10.9660.97442.9810.0390.0390.0000.0000.0000.000
74D96LYS10.9850.98244.8720.0330.0330.0000.0000.0000.000
75D97ALA0-0.023-0.01945.771-0.002-0.0020.0000.0000.0000.000
76D98GLN0-0.015-0.00743.591-0.001-0.0010.0000.0000.0000.000
77D99LEU00.0020.01740.011-0.003-0.0030.0000.0000.0000.000
78D100GLN00.0840.03540.240-0.004-0.0040.0000.0000.0000.000
79D101LEU0-0.0080.00240.094-0.003-0.0030.0000.0000.0000.000
80D102LEU0-0.026-0.01436.106-0.004-0.0040.0000.0000.0000.000
81D103GLY00.0410.01036.009-0.006-0.0060.0000.0000.0000.000
82D104ALA00.0540.03135.017-0.007-0.0070.0000.0000.0000.000
83D105VAL0-0.0290.00134.272-0.007-0.0070.0000.0000.0000.000
84D106CYS0-0.056-0.01731.605-0.007-0.0070.0000.0000.0000.000
85D107MET00.0470.03230.464-0.011-0.0110.0000.0000.0000.000
86D108LEU0-0.039-0.01930.303-0.009-0.0090.0000.0000.0000.000
87D109LEU0-0.031-0.01929.107-0.009-0.0090.0000.0000.0000.000
88D110ALA00.003-0.00126.279-0.012-0.0120.0000.0000.0000.000
89D111SER0-0.011-0.03725.467-0.015-0.0150.0000.0000.0000.000
90D112LYS10.7980.84326.1150.1080.1080.0000.0000.0000.000
91D113LEU0-0.085-0.02522.138-0.006-0.0060.0000.0000.0000.000
92D114ARG10.7550.83717.9710.2890.2890.0000.0000.0000.000
93D115GLU-1-0.707-0.79822.072-0.178-0.1780.0000.0000.0000.000
94D116THR0-0.015-0.01322.5720.0090.0090.0000.0000.0000.000
95D117THR0-0.060-0.02924.7560.0120.0120.0000.0000.0000.000
96D118PRO0-0.0010.02027.0690.0080.0080.0000.0000.0000.000
97D119LEU00.0020.01229.2770.0110.0110.0000.0000.0000.000
98D120THR00.020-0.00232.6370.0010.0010.0000.0000.0000.000
99D121ILE00.014-0.01935.6710.0020.0020.0000.0000.0000.000
100D122GLU-1-0.953-0.97938.102-0.069-0.0690.0000.0000.0000.000
101D123LYS10.9400.97135.5850.1030.1030.0000.0000.0000.000
102D124LEU00.0460.02634.2290.0030.0030.0000.0000.0000.000
103D125CYS0-0.086-0.02638.5810.0040.0040.0000.0000.0000.000
104D126ILE00.0310.00241.5570.0030.0030.0000.0000.0000.000
105D127TYR00.0480.01637.0530.0040.0040.0000.0000.0000.000
106D128THR0-0.125-0.05541.1040.0020.0020.0000.0000.0000.000
107D129ASP-1-0.877-0.94243.486-0.048-0.0480.0000.0000.0000.000
108D130HIS0-0.045-0.01745.7440.0020.0020.0000.0000.0000.000
109D131ALA0-0.034-0.00546.6370.0020.0020.0000.0000.0000.000
110D132VAL0-0.062-0.02742.0560.0010.0010.0000.0000.0000.000
111D133SER00.020-0.00444.575-0.002-0.0020.0000.0000.0000.000
112D134PRO00.0800.00742.688-0.002-0.0020.0000.0000.0000.000
113D135ARG10.9030.94242.5580.0470.0470.0000.0000.0000.000
114D136GLN00.0930.06543.535-0.002-0.0020.0000.0000.0000.000
115D137LEU00.0300.02137.643-0.001-0.0010.0000.0000.0000.000
116D138ARG10.9510.98138.5970.0660.0660.0000.0000.0000.000
117D139ASP-1-0.893-0.94038.863-0.064-0.0640.0000.0000.0000.000
118D140TRP0-0.006-0.03138.972-0.001-0.0010.0000.0000.0000.000
119D141GLU-1-0.793-0.86633.047-0.113-0.1130.0000.0000.0000.000
120D142VAL00.0100.00034.526-0.004-0.0040.0000.0000.0000.000
121D143LEU0-0.062-0.01735.9810.0010.0010.0000.0000.0000.000
122D144VAL00.006-0.01632.3120.0020.0020.0000.0000.0000.000
123D145LEU00.0520.03629.614-0.002-0.0020.0000.0000.0000.000
124D146GLY00.0000.01231.529-0.002-0.0020.0000.0000.0000.000
125D147LYS10.8760.93933.5960.0570.0570.0000.0000.0000.000
126D148LEU0-0.0180.00929.0110.0040.0040.0000.0000.0000.000
127D149LYS10.9160.95128.6120.0570.0570.0000.0000.0000.000
128D150TRP0-0.014-0.01827.931-0.005-0.0050.0000.0000.0000.000
129D151ASP-1-0.793-0.83722.836-0.164-0.1640.0000.0000.0000.000
130D152LEU00.0520.01524.4400.0070.0070.0000.0000.0000.000
131D153ALA00.0020.03718.929-0.006-0.0060.0000.0000.0000.000
132D154ALA0-0.024-0.03119.193-0.013-0.0130.0000.0000.0000.000
133D155VAL00.0010.00415.947-0.023-0.0230.0000.0000.0000.000
134D156ILE00.001-0.00918.6550.0430.0430.0000.0000.0000.000
135D157ALA00.0350.01718.762-0.030-0.0300.0000.0000.0000.000
136D158HIS00.0680.03218.5070.0080.0080.0000.0000.0000.000
137D159ASP-1-0.798-0.86115.211-0.361-0.3610.0000.0000.0000.000
138D160PHE00.002-0.02313.916-0.094-0.0940.0000.0000.0000.000
139D161LEU0-0.0070.00814.291-0.008-0.0080.0000.0000.0000.000
140D162ALA00.0410.01212.3190.0130.0130.0000.0000.0000.000
141D163PHE00.0060.0057.3600.0050.0050.0000.0000.0000.000
142D164ILE00.002-0.00510.8610.0730.0730.0000.0000.0000.000
143D165LEU0-0.0020.00813.5390.0590.0590.0000.0000.0000.000
144D166HIS0-0.013-0.0179.7300.0600.0600.0000.0000.0000.000
145D167ARG10.8530.9408.399-0.349-0.3490.0000.0000.0000.000
146D168LEU00.0500.04112.0900.0460.0460.0000.0000.0000.000
147D169SER0-0.022-0.00715.3030.0070.0070.0000.0000.0000.000
148D170LEU00.0040.00417.254-0.001-0.0010.0000.0000.0000.000
149D171PRO0-0.0140.00616.776-0.014-0.0140.0000.0000.0000.000
150D172ARG10.9270.91611.4300.3930.3930.0000.0000.0000.000
151D173ASP-1-0.901-0.94217.972-0.094-0.0940.0000.0000.0000.000
152D174ARG10.9380.95421.0640.0510.0510.0000.0000.0000.000
153D175GLN00.0020.00514.740-0.028-0.0280.0000.0000.0000.000
154D176ALA0-0.0240.00420.352-0.008-0.0080.0000.0000.0000.000
155D177LEU00.0300.00222.829-0.004-0.0040.0000.0000.0000.000
156D178VAL00.0310.01521.3920.0010.0010.0000.0000.0000.000
157D179LYS10.9550.98418.6660.2710.2710.0000.0000.0000.000
158D180LYS10.9991.00321.6630.1090.1090.0000.0000.0000.000
159D181HIS00.0130.01025.047-0.002-0.0020.0000.0000.0000.000
160D182ALA00.0560.01522.3880.0060.0060.0000.0000.0000.000
161D183GLN0-0.013-0.02022.1330.0040.0040.0000.0000.0000.000
162D184THR0-0.0240.00324.9800.0050.0050.0000.0000.0000.000
163D185PHE00.0610.02726.4420.0060.0060.0000.0000.0000.000
164D186LEU0-0.0100.00521.1470.0010.0010.0000.0000.0000.000
165D187ALA00.002-0.00125.7380.0020.0020.0000.0000.0000.000
166D188LEU00.0090.01128.6140.0050.0050.0000.0000.0000.000
167D189CYS00.0030.00127.2720.0070.0070.0000.0000.0000.000
168D190ALA0-0.0060.01427.8080.0040.0040.0000.0000.0000.000
169D191THR0-0.046-0.03129.5960.0060.0060.0000.0000.0000.000
170D192ASP-1-0.771-0.88732.596-0.040-0.0400.0000.0000.0000.000
171D193TYR0-0.025-0.03232.6360.0010.0010.0000.0000.0000.000
172D194THR0-0.075-0.04633.6080.0000.0000.0000.0000.0000.000
173D195PHE00.0620.03228.5590.0030.0030.0000.0000.0000.000
174D196ALA0-0.047-0.01328.534-0.006-0.0060.0000.0000.0000.000
175D197MET0-0.056-0.03028.510-0.007-0.0070.0000.0000.0000.000
176D198TYR0-0.046-0.03426.0450.0060.0060.0000.0000.0000.000
177D199PRO00.0410.02321.918-0.012-0.0120.0000.0000.0000.000
178D200PRO00.005-0.00219.424-0.001-0.0010.0000.0000.0000.000
179D201SER0-0.005-0.03917.369-0.002-0.0020.0000.0000.0000.000
180D202MET00.0060.00318.9010.0030.0030.0000.0000.0000.000
181D203ILE00.0390.01722.0770.0010.0010.0000.0000.0000.000
182D204ALA0-0.0250.01318.576-0.001-0.0010.0000.0000.0000.000
183D205THR0-0.009-0.01618.5750.0020.0020.0000.0000.0000.000
184D206GLY00.0540.03420.0980.0140.0140.0000.0000.0000.000
185D207SER0-0.046-0.05523.3120.0010.0010.0000.0000.0000.000
186D208ILE0-0.030-0.02217.995-0.004-0.0040.0000.0000.0000.000
187D209GLY00.0370.01622.0530.0040.0040.0000.0000.0000.000
188D210ALA00.0130.01223.7200.0060.0060.0000.0000.0000.000
189D211ALA0-0.062-0.01823.9800.0020.0020.0000.0000.0000.000
190D212VAL0-0.007-0.01421.1460.0030.0030.0000.0000.0000.000
191D213GLN00.0360.03024.5570.0100.0100.0000.0000.0000.000
192D214GLY0-0.0220.00227.5870.0050.0050.0000.0000.0000.000
193D215LEU0-0.067-0.03725.817-0.004-0.0040.0000.0000.0000.000
194D216GLY0-0.0120.01828.1210.0010.0010.0000.0000.0000.000
195D217ALA0-0.085-0.05723.2160.0040.0040.0000.0000.0000.000
196D218CYS00.019-0.01321.670-0.004-0.0040.0000.0000.0000.000
197D219SER0-0.042-0.01723.3860.0100.0100.0000.0000.0000.000
198D220MET0-0.023-0.01126.286-0.007-0.0070.0000.0000.0000.000
199D221SER00.0120.01327.1750.0030.0030.0000.0000.0000.000
200D222GLY00.0700.04626.963-0.003-0.0030.0000.0000.0000.000
201D223ASP-1-0.833-0.90726.6200.0370.0370.0000.0000.0000.000
202D224GLU-1-0.856-0.94524.5290.0620.0620.0000.0000.0000.000
203D225LEU0-0.033-0.01122.2400.0060.0060.0000.0000.0000.000
204D226THR00.009-0.02621.7520.0030.0030.0000.0000.0000.000
205D227GLU-1-0.898-0.95222.2810.0910.0910.0000.0000.0000.000
206D228LEU0-0.048-0.01617.6630.0230.0230.0000.0000.0000.000
207D229LEU0-0.041-0.02417.3420.0080.0080.0000.0000.0000.000
208D230ALA00.0160.01817.643-0.004-0.0040.0000.0000.0000.000
209D231GLY00.0100.00817.4630.0140.0140.0000.0000.0000.000
210D232ILE0-0.134-0.05112.2420.0560.0560.0000.0000.0000.000
211D233THR0-0.044-0.03113.6990.0300.0300.0000.0000.0000.000
212D234GLY0-0.0200.00415.7970.0000.0000.0000.0000.0000.000
213D235THR0-0.037-0.01717.684-0.004-0.0040.0000.0000.0000.000
214D236GLU-1-0.902-0.95620.9210.0780.0780.0000.0000.0000.000
215D237VAL00.014-0.01223.830-0.013-0.0130.0000.0000.0000.000
216D238ASP-1-0.905-0.94725.4520.0410.0410.0000.0000.0000.000
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218D240LEU0-0.0190.00521.753-0.012-0.0120.0000.0000.0000.000
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