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: 39QGL

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2927842.690546
FMO2-HF: Nuclear repulsion 2833068.080364
FMO2-HF: Total energy -94774.610182
FMO2-MP2: Total energy -95041.356175


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.
-3.738-0.6620.896-1.462-2.5080.008
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 : -0.017 / q_NPA : -0.021
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].
3D25GLN0-0.082-0.0513.579-0.3101.0030.000-0.546-0.7670.001
4D26ARG10.9430.9652.361-3.696-2.1270.897-0.865-1.6000.007
5D27VAL00.0460.0364.633-0.270-0.076-0.001-0.051-0.1410.000
6D28LEU00.0820.0466.6430.3500.3500.0000.0000.0000.000
7D29GLN00.0040.0118.1820.1700.1700.0000.0000.0000.000
8D30SER0-0.100-0.0529.109-0.060-0.0600.0000.0000.0000.000
9D31LEU00.0290.00510.6910.0400.0400.0000.0000.0000.000
10D32LEU00.0140.00412.7000.0390.0390.0000.0000.0000.000
11D33ARG10.9010.95313.211-0.060-0.0600.0000.0000.0000.000
12D34LEU0-0.025-0.00214.4150.0130.0130.0000.0000.0000.000
13D35GLU-1-0.768-0.86617.120-0.087-0.0870.0000.0000.0000.000
14D36GLU-1-0.915-0.95819.361-0.009-0.0090.0000.0000.0000.000
15D37ARG10.7680.87721.0080.1230.1230.0000.0000.0000.000
16D38TYR0-0.128-0.06918.939-0.005-0.0050.0000.0000.0000.000
17D39VAL00.0700.04623.336-0.007-0.0070.0000.0000.0000.000
18D40PRO0-0.041-0.02225.6220.0070.0070.0000.0000.0000.000
19D41ARG10.9650.98029.2970.0500.0500.0000.0000.0000.000
20D42ALA00.0060.00130.9560.0060.0060.0000.0000.0000.000
21D43SER00.0590.03434.030-0.004-0.0040.0000.0000.0000.000
22D44TYR00.025-0.00934.2390.0050.0050.0000.0000.0000.000
23D45PHE0-0.014-0.00837.9840.0010.0010.0000.0000.0000.000
24D46GLN00.013-0.00241.2350.0020.0020.0000.0000.0000.000
25D47CYS0-0.067-0.02139.3450.0020.0020.0000.0000.0000.000
26D48VAL0-0.086-0.08740.573-0.002-0.0020.0000.0000.0000.000
27D49GLN00.013-0.02643.6660.0000.0000.0000.0000.0000.000
28D50ARG10.8970.95146.3810.0300.0300.0000.0000.0000.000
29D51GLU-1-0.841-0.92547.184-0.036-0.0360.0000.0000.0000.000
30D52ILE00.1050.14740.9770.0030.0030.0000.0000.0000.000
31D53LYS10.9380.95243.6780.0320.0320.0000.0000.0000.000
32D54PRO00.0460.02240.366-0.003-0.0030.0000.0000.0000.000
33D55HIS00.0300.00740.363-0.004-0.0040.0000.0000.0000.000
34D56MET0-0.004-0.00242.140-0.001-0.0010.0000.0000.0000.000
35D57ARG10.8350.91931.6600.0710.0710.0000.0000.0000.000
36D58LYS10.9670.98637.1760.0400.0400.0000.0000.0000.000
37D59MET0-0.0020.00138.378-0.002-0.0020.0000.0000.0000.000
38D60LEU0-0.039-0.01337.343-0.001-0.0010.0000.0000.0000.000
39D61ALA00.0200.01134.240-0.004-0.0040.0000.0000.0000.000
40D62TYR00.0700.01734.984-0.006-0.0060.0000.0000.0000.000
41D63TRP00.0120.01937.162-0.004-0.0040.0000.0000.0000.000
42D64MET0-0.058-0.01533.248-0.004-0.0040.0000.0000.0000.000
43D65LEU00.0240.01931.073-0.006-0.0060.0000.0000.0000.000
44D66GLU-1-0.898-0.95033.641-0.071-0.0710.0000.0000.0000.000
45D67VAL00.0020.01334.263-0.003-0.0030.0000.0000.0000.000
46D68CYS0-0.078-0.05029.900-0.005-0.0050.0000.0000.0000.000
47D69GLU-1-0.890-0.94830.214-0.122-0.1220.0000.0000.0000.000
48D70GLU-1-0.978-0.98032.638-0.079-0.0790.0000.0000.0000.000
49D71GLN0-0.068-0.02032.1860.0030.0030.0000.0000.0000.000
50D72ARG10.8220.92629.6920.1120.1120.0000.0000.0000.000
51D73CYS0-0.045-0.00527.857-0.003-0.0030.0000.0000.0000.000
52D74GLU-1-0.926-0.95621.606-0.248-0.2480.0000.0000.0000.000
53D75GLU-1-0.917-0.97422.756-0.151-0.1510.0000.0000.0000.000
54D76GLU-1-0.946-0.96919.148-0.319-0.3190.0000.0000.0000.000
55D77VAL0-0.014-0.00622.7620.0090.0090.0000.0000.0000.000
56D78PHE00.0470.02625.7550.0080.0080.0000.0000.0000.000
57D79PRO00.0430.00424.3830.0100.0100.0000.0000.0000.000
58D80LEU0-0.0090.00622.7230.0080.0080.0000.0000.0000.000
59D81ALA00.000-0.00125.4820.0100.0100.0000.0000.0000.000
60D82MET00.002-0.00629.0840.0110.0110.0000.0000.0000.000
61D83ASN0-0.0100.00725.1440.0040.0040.0000.0000.0000.000
62D84TYR0-0.048-0.04424.3890.0110.0110.0000.0000.0000.000
63D85LEU00.0250.00829.6200.0100.0100.0000.0000.0000.000
64D86ASP-1-0.753-0.85030.585-0.069-0.0690.0000.0000.0000.000
65D87ARG10.8360.92624.9770.1340.1340.0000.0000.0000.000
66D88TYR00.019-0.00131.2050.0080.0080.0000.0000.0000.000
67D89LEU0-0.024-0.02334.1520.0060.0060.0000.0000.0000.000
68D90SER0-0.050-0.04533.4270.0060.0060.0000.0000.0000.000
69D91CYS0-0.088-0.03434.3230.0040.0040.0000.0000.0000.000
70D92VAL0-0.050-0.02136.9890.0040.0040.0000.0000.0000.000
71D93PRO0-0.0110.00139.280-0.001-0.0010.0000.0000.0000.000
72D94THR00.0050.01240.4320.0020.0020.0000.0000.0000.000
73D95ARG10.9580.96842.9720.0400.0400.0000.0000.0000.000
74D96LYS11.0190.99244.8630.0340.0340.0000.0000.0000.000
75D97ALA0-0.044-0.02745.762-0.002-0.0020.0000.0000.0000.000
76D98GLN0-0.013-0.00643.568-0.002-0.0020.0000.0000.0000.000
77D99LEU00.0050.01939.972-0.003-0.0030.0000.0000.0000.000
78D100GLN00.0730.02640.242-0.004-0.0040.0000.0000.0000.000
79D101LEU0-0.0030.00840.095-0.004-0.0040.0000.0000.0000.000
80D102LEU0-0.030-0.01436.093-0.004-0.0040.0000.0000.0000.000
81D103GLY00.034-0.01936.013-0.006-0.0060.0000.0000.0000.000
82D104ALA00.0620.03435.019-0.007-0.0070.0000.0000.0000.000
83D105VAL0-0.0290.00334.188-0.007-0.0070.0000.0000.0000.000
84D106CYS0-0.053-0.01231.555-0.007-0.0070.0000.0000.0000.000
85D107MET00.0670.04030.466-0.012-0.0120.0000.0000.0000.000
86D108LEU0-0.031-0.01730.304-0.009-0.0090.0000.0000.0000.000
87D109LEU0-0.039-0.02429.048-0.009-0.0090.0000.0000.0000.000
88D110ALA00.0010.00326.268-0.012-0.0120.0000.0000.0000.000
89D111SER0-0.002-0.01525.469-0.016-0.0160.0000.0000.0000.000
90D112LYS10.8160.85826.1160.1110.1110.0000.0000.0000.000
91D113LEU0-0.086-0.02622.157-0.007-0.0070.0000.0000.0000.000
92D114ARG10.8280.91418.0130.2860.2860.0000.0000.0000.000
93D115GLU-1-0.725-0.84922.074-0.179-0.1790.0000.0000.0000.000
94D116THR0-0.022-0.01422.5330.0090.0090.0000.0000.0000.000
95D117THR0-0.060-0.02924.7580.0120.0120.0000.0000.0000.000
96D118PRO00.0150.02527.1050.0080.0080.0000.0000.0000.000
97D119LEU00.0060.00929.2780.0110.0110.0000.0000.0000.000
98D120THR00.0160.00032.6380.0010.0010.0000.0000.0000.000
99D121ILE00.004-0.02435.6730.0020.0020.0000.0000.0000.000
100D122GLU-1-0.925-0.97138.104-0.067-0.0670.0000.0000.0000.000
101D123LYS10.9280.97135.7300.1010.1010.0000.0000.0000.000
102D124LEU00.0440.02434.2980.0030.0030.0000.0000.0000.000
103D125CYS0-0.076-0.03338.5830.0040.0040.0000.0000.0000.000
104D126ILE00.0280.00741.2580.0040.0040.0000.0000.0000.000
105D127TYR00.013-0.01737.2250.0030.0030.0000.0000.0000.000
106D128THR0-0.124-0.05841.0950.0020.0020.0000.0000.0000.000
107D129ASP-1-0.873-0.93943.488-0.048-0.0480.0000.0000.0000.000
108D130HIS0-0.053-0.01745.7520.0020.0020.0000.0000.0000.000
109D131ALA0-0.033-0.00946.6440.0020.0020.0000.0000.0000.000
110D132VAL0-0.032-0.00941.9720.0010.0010.0000.0000.0000.000
111D133SER00.0210.01344.577-0.002-0.0020.0000.0000.0000.000
112D134PRO00.0810.01042.675-0.002-0.0020.0000.0000.0000.000
113D135ARG10.8970.93342.5600.0480.0480.0000.0000.0000.000
114D136GLN00.0700.03643.536-0.002-0.0020.0000.0000.0000.000
115D137LEU00.0420.02737.959-0.001-0.0010.0000.0000.0000.000
116D138ARG10.9460.97838.5990.0660.0660.0000.0000.0000.000
117D139ASP-1-0.889-0.93538.859-0.065-0.0650.0000.0000.0000.000
118D140TRP0-0.010-0.02838.944-0.001-0.0010.0000.0000.0000.000
119D141GLU-1-0.819-0.88633.216-0.111-0.1110.0000.0000.0000.000
120D142VAL00.0090.00334.521-0.005-0.0050.0000.0000.0000.000
121D143LEU0-0.071-0.02435.9760.0000.0000.0000.0000.0000.000
122D144VAL00.001-0.01632.2950.0020.0020.0000.0000.0000.000
123D145LEU00.0610.03829.571-0.002-0.0020.0000.0000.0000.000
124D146GLY0-0.0020.01231.523-0.002-0.0020.0000.0000.0000.000
125D147LYS10.8760.93733.5890.0590.0590.0000.0000.0000.000
126D148LEU0-0.0220.00828.9700.0040.0040.0000.0000.0000.000
127D149LYS10.9230.95428.6050.0600.0600.0000.0000.0000.000
128D150TRP0-0.008-0.01427.784-0.005-0.0050.0000.0000.0000.000
129D151ASP-1-0.813-0.86022.860-0.167-0.1670.0000.0000.0000.000
130D152LEU00.0450.01424.4590.0070.0070.0000.0000.0000.000
131D153ALA00.0110.03918.873-0.005-0.0050.0000.0000.0000.000
132D154ALA0-0.026-0.03719.186-0.013-0.0130.0000.0000.0000.000
133D155VAL00.0050.01015.946-0.023-0.0230.0000.0000.0000.000
134D156ILE00.005-0.00218.6450.0410.0410.0000.0000.0000.000
135D157ALA00.0460.02218.762-0.030-0.0300.0000.0000.0000.000
136D158HIS00.0880.04918.5070.0040.0040.0000.0000.0000.000
137D159ASP-1-0.854-0.92015.132-0.384-0.3840.0000.0000.0000.000
138D160PHE0-0.010-0.02413.873-0.091-0.0910.0000.0000.0000.000
139D161LEU0-0.0040.00814.291-0.010-0.0100.0000.0000.0000.000
140D162ALA00.0300.00712.2840.0130.0130.0000.0000.0000.000
141D163PHE00.0020.0017.1320.0270.0270.0000.0000.0000.000
142D164ILE00.013-0.00310.8620.0730.0730.0000.0000.0000.000
143D165LEU0-0.002-0.01613.5390.0590.0590.0000.0000.0000.000
144D166HIS0-0.030-0.0249.6900.0550.0550.0000.0000.0000.000
145D167ARG10.8840.9657.611-0.317-0.3170.0000.0000.0000.000
146D168LEU00.0380.05212.0900.0450.0450.0000.0000.0000.000
147D169SER0-0.016-0.00115.3030.0080.0080.0000.0000.0000.000
148D170LEU0-0.014-0.00917.243-0.002-0.0020.0000.0000.0000.000
149D171PRO00.0280.02616.777-0.014-0.0140.0000.0000.0000.000
150D172ARG10.9350.92311.7800.3790.3790.0000.0000.0000.000
151D173ASP-1-0.910-0.94517.974-0.093-0.0930.0000.0000.0000.000
152D174ARG10.9330.95421.0700.0480.0480.0000.0000.0000.000
153D175GLN00.0020.00714.658-0.023-0.0230.0000.0000.0000.000
154D176ALA0-0.0240.00320.353-0.009-0.0090.0000.0000.0000.000
155D177LEU00.0340.00022.830-0.004-0.0040.0000.0000.0000.000
156D178VAL00.0360.01821.3740.0010.0010.0000.0000.0000.000
157D179LYS10.9720.98917.7970.2870.2870.0000.0000.0000.000
158D180LYS10.9750.99321.6640.1050.1050.0000.0000.0000.000
159D181HIS00.0230.01725.048-0.002-0.0020.0000.0000.0000.000
160D182ALA00.0480.00722.3900.0060.0060.0000.0000.0000.000
161D183GLN0-0.007-0.02621.6820.0070.0070.0000.0000.0000.000
162D184THR0-0.0140.01624.9800.0050.0050.0000.0000.0000.000
163D185PHE00.0540.02626.3810.0070.0070.0000.0000.0000.000
164D186LEU0-0.026-0.01021.2990.0000.0000.0000.0000.0000.000
165D187ALA00.0170.00725.7380.0020.0020.0000.0000.0000.000
166D188LEU00.0320.02228.6140.0050.0050.0000.0000.0000.000
167D189CYS0-0.0020.01527.2930.0070.0070.0000.0000.0000.000
168D190ALA0-0.0230.00327.8540.0040.0040.0000.0000.0000.000
169D191THR0-0.087-0.07029.5960.0050.0050.0000.0000.0000.000
170D192ASP-1-0.838-0.93232.615-0.042-0.0420.0000.0000.0000.000
171D193TYR0-0.047-0.04832.6360.0010.0010.0000.0000.0000.000
172D194THR0-0.025-0.00833.0880.0000.0000.0000.0000.0000.000
173D195PHE00.0320.01928.5590.0030.0030.0000.0000.0000.000
174D196ALA0-0.045-0.01128.534-0.006-0.0060.0000.0000.0000.000
175D197MET0-0.050-0.03428.497-0.007-0.0070.0000.0000.0000.000
176D198TYR0-0.036-0.00926.0400.0050.0050.0000.0000.0000.000
177D199PRO00.0320.01821.933-0.012-0.0120.0000.0000.0000.000
178D200PRO00.0180.00519.3940.0000.0000.0000.0000.0000.000
179D201SER00.010-0.01917.4400.0010.0010.0000.0000.0000.000
180D202MET00.007-0.00818.9010.0040.0040.0000.0000.0000.000
181D203ILE00.0420.01622.0770.0020.0020.0000.0000.0000.000
182D204ALA0-0.0280.00118.5970.0000.0000.0000.0000.0000.000
183D205THR0-0.027-0.01618.6610.0000.0000.0000.0000.0000.000
184D206GLY00.0740.04220.0980.0130.0130.0000.0000.0000.000
185D207SER0-0.045-0.05023.3520.0010.0010.0000.0000.0000.000
186D208ILE0-0.030-0.01517.884-0.005-0.0050.0000.0000.0000.000
187D209GLY00.0240.01122.0540.0050.0050.0000.0000.0000.000
188D210ALA00.0250.01323.7200.0060.0060.0000.0000.0000.000
189D211ALA0-0.065-0.02223.9880.0020.0020.0000.0000.0000.000
190D212VAL00.0040.00121.1610.0030.0030.0000.0000.0000.000
191D213GLN00.0260.02624.5570.0060.0060.0000.0000.0000.000
192D214GLY0-0.025-0.00327.5880.0050.0050.0000.0000.0000.000
193D215LEU0-0.069-0.03425.658-0.004-0.0040.0000.0000.0000.000
194D216GLY00.0020.02328.1220.0010.0010.0000.0000.0000.000
195D217ALA0-0.076-0.06023.3400.0040.0040.0000.0000.0000.000
196D218CYS00.008-0.01721.650-0.003-0.0030.0000.0000.0000.000
197D219SER0-0.045-0.02423.4440.0110.0110.0000.0000.0000.000
198D220MET0-0.028-0.01026.463-0.006-0.0060.0000.0000.0000.000
199D221SER00.0240.02227.1780.0010.0010.0000.0000.0000.000
200D222GLY00.0610.04226.963-0.003-0.0030.0000.0000.0000.000
201D223ASP-1-0.906-0.95526.6200.0350.0350.0000.0000.0000.000
202D224GLU-1-0.864-0.94524.5500.0610.0610.0000.0000.0000.000
203D225LEU0-0.024-0.01221.5700.0060.0060.0000.0000.0000.000
204D226THR0-0.015-0.03521.7510.0030.0030.0000.0000.0000.000
205D227GLU-1-0.894-0.95222.2810.0960.0960.0000.0000.0000.000
206D228LEU0-0.042-0.01417.3450.0220.0220.0000.0000.0000.000
207D229LEU0-0.034-0.01617.3410.0090.0090.0000.0000.0000.000
208D230ALA00.0040.00917.642-0.004-0.0040.0000.0000.0000.000
209D231GLY00.0090.00817.4620.0130.0130.0000.0000.0000.000
210D232ILE0-0.142-0.06212.2500.0570.0570.0000.0000.0000.000
211D233THR0-0.040-0.03713.6980.0320.0320.0000.0000.0000.000
212D234GLY0-0.0060.01215.7970.0000.0000.0000.0000.0000.000
213D235THR0-0.049-0.01617.684-0.008-0.0080.0000.0000.0000.000
214D236GLU-1-0.888-0.95120.9210.0790.0790.0000.0000.0000.000
215D237VAL00.029-0.00323.828-0.014-0.0140.0000.0000.0000.000
216D238ASP-1-0.912-0.95425.4510.0410.0410.0000.0000.0000.000
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218D240LEU0-0.0080.00921.684-0.011-0.0110.0000.0000.0000.000
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