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: 94GQ2

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2935896.438708
FMO2-HF: Nuclear repulsion 2841119.147868
FMO2-HF: Total energy -94777.290839
FMO2-MP2: Total energy -95043.822064


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.
-2.1270.5420.347-1.116-1.9010.004
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 : -0.004
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].
3D25GLN00.0130.0103.7620.3301.4290.000-0.463-0.6370.000
4D26ARG10.9530.9752.525-3.526-2.1780.348-0.598-1.0980.004
5D27VAL00.0120.0224.3280.1090.331-0.001-0.055-0.1660.000
6D28LEU00.0680.0416.6080.5450.5450.0000.0000.0000.000
7D29GLN00.0050.0048.4520.2890.2890.0000.0000.0000.000
8D30SER0-0.111-0.0668.9020.0870.0870.0000.0000.0000.000
9D31LEU00.0240.00710.6060.0870.0870.0000.0000.0000.000
10D32LEU00.0360.01512.7220.0680.0680.0000.0000.0000.000
11D33ARG10.8960.94912.4780.0840.0840.0000.0000.0000.000
12D34LEU0-0.015-0.00113.8690.0340.0340.0000.0000.0000.000
13D35GLU-1-0.757-0.84216.914-0.205-0.2050.0000.0000.0000.000
14D36GLU-1-0.911-0.96119.376-0.075-0.0750.0000.0000.0000.000
15D37ARG10.7340.86520.2650.1760.1760.0000.0000.0000.000
16D38TYR0-0.066-0.06018.616-0.002-0.0020.0000.0000.0000.000
17D39VAL00.0560.05023.261-0.001-0.0010.0000.0000.0000.000
18D40PRO0-0.034-0.01925.4460.0090.0090.0000.0000.0000.000
19D41ARG10.9750.98028.9100.0830.0830.0000.0000.0000.000
20D42ALA0-0.005-0.00130.9430.0060.0060.0000.0000.0000.000
21D43SER00.0730.04134.171-0.005-0.0050.0000.0000.0000.000
22D44TYR0-0.022-0.05134.0040.0080.0080.0000.0000.0000.000
23D45PHE00.005-0.00837.5090.0030.0030.0000.0000.0000.000
24D46GLN00.0000.00840.4430.0010.0010.0000.0000.0000.000
25D47CYS0-0.027-0.00238.9270.0030.0030.0000.0000.0000.000
26D48VAL0-0.003-0.00140.6120.0020.0020.0000.0000.0000.000
27D49GLN00.0320.02143.5450.0000.0000.0000.0000.0000.000
28D50ARG10.8960.94846.1310.0420.0420.0000.0000.0000.000
29D51GLU-1-0.880-0.94246.715-0.047-0.0470.0000.0000.0000.000
30D52ILE00.0160.01740.4210.0000.0000.0000.0000.0000.000
31D53LYS10.9500.97143.2820.0460.0460.0000.0000.0000.000
32D54PRO00.0580.01539.888-0.002-0.0020.0000.0000.0000.000
33D55HIS00.0490.03139.885-0.005-0.0050.0000.0000.0000.000
34D56MET0-0.015-0.00541.329-0.001-0.0010.0000.0000.0000.000
35D57ARG10.7700.87930.9660.1030.1030.0000.0000.0000.000
36D58LYS10.9060.95136.7810.0670.0670.0000.0000.0000.000
37D59MET00.0040.00037.532-0.003-0.0030.0000.0000.0000.000
38D60LEU0-0.028-0.01436.417-0.001-0.0010.0000.0000.0000.000
39D61ALA00.0200.00333.326-0.004-0.0040.0000.0000.0000.000
40D62TYR00.023-0.00134.090-0.003-0.0030.0000.0000.0000.000
41D63TRP00.0220.02336.112-0.005-0.0050.0000.0000.0000.000
42D64MET0-0.054-0.03932.367-0.004-0.0040.0000.0000.0000.000
43D65LEU00.0300.02030.192-0.007-0.0070.0000.0000.0000.000
44D66GLU-1-0.905-0.95632.688-0.082-0.0820.0000.0000.0000.000
45D67VAL0-0.020-0.01233.614-0.002-0.0020.0000.0000.0000.000
46D68CYS0-0.067-0.03829.129-0.005-0.0050.0000.0000.0000.000
47D69GLU-1-0.815-0.87329.965-0.132-0.1320.0000.0000.0000.000
48D70GLU-1-0.943-0.96631.988-0.087-0.0870.0000.0000.0000.000
49D71GLN0-0.074-0.03131.9080.0070.0070.0000.0000.0000.000
50D72ARG10.7400.83429.2380.1210.1210.0000.0000.0000.000
51D73CYS0-0.034-0.01427.310-0.002-0.0020.0000.0000.0000.000
52D74GLU-1-0.910-0.95521.688-0.252-0.2520.0000.0000.0000.000
53D75GLU-1-0.874-0.94122.775-0.189-0.1890.0000.0000.0000.000
54D76GLU-1-0.859-0.90717.284-0.394-0.3940.0000.0000.0000.000
55D77VAL0-0.010-0.00621.9560.0050.0050.0000.0000.0000.000
56D78PHE00.0410.01525.0620.0090.0090.0000.0000.0000.000
57D79PRO00.030-0.00423.4390.0100.0100.0000.0000.0000.000
58D80LEU0-0.0140.00821.5630.0070.0070.0000.0000.0000.000
59D81ALA0-0.0010.00924.9440.0110.0110.0000.0000.0000.000
60D82MET0-0.0140.00028.3180.0140.0140.0000.0000.0000.000
61D83ASN0-0.006-0.00724.7760.0070.0070.0000.0000.0000.000
62D84TYR0-0.020-0.04123.6220.0130.0130.0000.0000.0000.000
63D85LEU00.0280.01429.1430.0110.0110.0000.0000.0000.000
64D86ASP-1-0.730-0.83230.377-0.098-0.0980.0000.0000.0000.000
65D87ARG10.8410.93924.8350.1670.1670.0000.0000.0000.000
66D88TYR00.0190.00430.8170.0080.0080.0000.0000.0000.000
67D89LEU00.002-0.01233.7310.0080.0080.0000.0000.0000.000
68D90SER0-0.064-0.04532.9070.0060.0060.0000.0000.0000.000
69D91CYS0-0.106-0.03634.0800.0050.0050.0000.0000.0000.000
70D92VAL0-0.026-0.02236.6360.0040.0040.0000.0000.0000.000
71D93PRO00.0050.00839.141-0.002-0.0020.0000.0000.0000.000
72D94THR0-0.0140.00439.9130.0030.0030.0000.0000.0000.000
73D95ARG10.9570.97242.5570.0480.0480.0000.0000.0000.000
74D96LYS10.9850.97944.2440.0430.0430.0000.0000.0000.000
75D97ALA0-0.016-0.01344.983-0.002-0.0020.0000.0000.0000.000
76D98GLN0-0.004-0.00342.793-0.001-0.0010.0000.0000.0000.000
77D99LEU00.0030.02039.109-0.003-0.0030.0000.0000.0000.000
78D100GLN00.0820.04139.327-0.005-0.0050.0000.0000.0000.000
79D101LEU0-0.0010.00839.213-0.004-0.0040.0000.0000.0000.000
80D102LEU0-0.018-0.01035.389-0.004-0.0040.0000.0000.0000.000
81D103GLY00.0480.02635.043-0.006-0.0060.0000.0000.0000.000
82D104ALA00.0480.02134.274-0.007-0.0070.0000.0000.0000.000
83D105VAL0-0.029-0.01333.755-0.005-0.0050.0000.0000.0000.000
84D106CYS0-0.082-0.03331.086-0.007-0.0070.0000.0000.0000.000
85D107MET00.0500.02429.789-0.012-0.0120.0000.0000.0000.000
86D108LEU0-0.046-0.01429.872-0.007-0.0070.0000.0000.0000.000
87D109LEU0-0.028-0.02628.567-0.007-0.0070.0000.0000.0000.000
88D110ALA0-0.024-0.00625.701-0.012-0.0120.0000.0000.0000.000
89D111SER0-0.012-0.02824.904-0.013-0.0130.0000.0000.0000.000
90D112LYS10.7900.85625.5540.1110.1110.0000.0000.0000.000
91D113LEU0-0.053-0.00621.300-0.001-0.0010.0000.0000.0000.000
92D114ARG10.7490.82717.2970.3370.3370.0000.0000.0000.000
93D115GLU-1-0.709-0.80221.518-0.179-0.1790.0000.0000.0000.000
94D116THR0-0.005-0.00722.0850.0060.0060.0000.0000.0000.000
95D117THR0-0.086-0.05524.3770.0150.0150.0000.0000.0000.000
96D118PRO0-0.0010.01926.5880.0060.0060.0000.0000.0000.000
97D119LEU00.0100.01328.9190.0120.0120.0000.0000.0000.000
98D120THR00.0210.00532.1790.0010.0010.0000.0000.0000.000
99D121ILE00.013-0.02235.2850.0010.0010.0000.0000.0000.000
100D122GLU-1-0.958-0.97537.631-0.072-0.0720.0000.0000.0000.000
101D123LYS10.9110.93934.6690.1030.1030.0000.0000.0000.000
102D124LEU00.0210.02533.7130.0010.0010.0000.0000.0000.000
103D125CYS0-0.084-0.02637.9720.0040.0040.0000.0000.0000.000
104D126ILE00.0390.01340.4030.0030.0030.0000.0000.0000.000
105D127TYR00.0600.03236.2930.0040.0040.0000.0000.0000.000
106D128THR0-0.121-0.06440.4510.0010.0010.0000.0000.0000.000
107D129ASP-1-0.880-0.94542.785-0.053-0.0530.0000.0000.0000.000
108D130HIS0-0.035-0.02645.0870.0020.0020.0000.0000.0000.000
109D131ALA0-0.050-0.00746.1220.0010.0010.0000.0000.0000.000
110D132VAL0-0.055-0.02041.1970.0010.0010.0000.0000.0000.000
111D133SER00.0470.00943.579-0.002-0.0020.0000.0000.0000.000
112D134PRO00.0580.00841.994-0.002-0.0020.0000.0000.0000.000
113D135ARG10.9060.96242.3480.0500.0500.0000.0000.0000.000
114D136GLN00.1180.07042.274-0.003-0.0030.0000.0000.0000.000
115D137LEU00.0330.02736.935-0.001-0.0010.0000.0000.0000.000
116D138ARG10.9090.95137.5920.0660.0660.0000.0000.0000.000
117D139ASP-1-0.891-0.95038.182-0.068-0.0680.0000.0000.0000.000
118D140TRP00.003-0.02738.266-0.001-0.0010.0000.0000.0000.000
119D141GLU-1-0.771-0.86332.641-0.118-0.1180.0000.0000.0000.000
120D142VAL00.0200.00734.150-0.005-0.0050.0000.0000.0000.000
121D143LEU0-0.038-0.00435.480-0.001-0.0010.0000.0000.0000.000
122D144VAL0-0.001-0.01131.7940.0010.0010.0000.0000.0000.000
123D145LEU00.0330.02729.331-0.004-0.0040.0000.0000.0000.000
124D146GLY0-0.0020.00331.279-0.002-0.0020.0000.0000.0000.000
125D147LYS10.8300.90533.2000.0700.0700.0000.0000.0000.000
126D148LEU0-0.022-0.00128.5990.0020.0020.0000.0000.0000.000
127D149LYS10.9090.94928.2420.0730.0730.0000.0000.0000.000
128D150TRP00.0170.00027.347-0.004-0.0040.0000.0000.0000.000
129D151ASP-1-0.792-0.82922.565-0.195-0.1950.0000.0000.0000.000
130D152LEU00.0490.00824.3310.0010.0010.0000.0000.0000.000
131D153ALA0-0.0110.01918.658-0.007-0.0070.0000.0000.0000.000
132D154ALA0-0.022-0.01718.761-0.025-0.0250.0000.0000.0000.000
133D155VAL00.0160.01515.344-0.018-0.0180.0000.0000.0000.000
134D156ILE0-0.042-0.02518.0560.0490.0490.0000.0000.0000.000
135D157ALA00.013-0.00118.026-0.038-0.0380.0000.0000.0000.000
136D158HIS00.000-0.02117.7350.0130.0130.0000.0000.0000.000
137D159ASP-1-0.754-0.83714.281-0.440-0.4400.0000.0000.0000.000
138D160PHE00.009-0.01013.121-0.128-0.1280.0000.0000.0000.000
139D161LEU00.0110.01213.588-0.033-0.0330.0000.0000.0000.000
140D162ALA00.0180.01011.4690.0210.0210.0000.0000.0000.000
141D163PHE00.008-0.0036.677-0.042-0.0420.0000.0000.0000.000
142D164ILE0-0.002-0.00110.3010.0530.0530.0000.0000.0000.000
143D165LEU00.0210.01513.1850.0710.0710.0000.0000.0000.000
144D166HIS0-0.040-0.0239.7340.1190.1190.0000.0000.0000.000
145D167ARG10.8600.9398.9140.1490.1490.0000.0000.0000.000
146D168LEU00.0450.04112.2690.0570.0570.0000.0000.0000.000
147D169SER0-0.032-0.01315.6810.0020.0020.0000.0000.0000.000
148D170LEU0-0.014-0.01117.0890.0070.0070.0000.0000.0000.000
149D171PRO00.0040.02316.654-0.025-0.0250.0000.0000.0000.000
150D172ARG10.9250.91610.9560.3450.3450.0000.0000.0000.000
151D173ASP-1-0.901-0.94817.913-0.102-0.1020.0000.0000.0000.000
152D174ARG10.9290.95320.9220.0760.0760.0000.0000.0000.000
153D175GLN0-0.011-0.00114.524-0.029-0.0290.0000.0000.0000.000
154D176ALA0-0.0140.00620.029-0.010-0.0100.0000.0000.0000.000
155D177LEU00.009-0.00322.222-0.004-0.0040.0000.0000.0000.000
156D178VAL00.0360.02121.0610.0010.0010.0000.0000.0000.000
157D179LYS10.8790.94217.9210.2720.2720.0000.0000.0000.000
158D180LYS11.0111.00521.1580.1310.1310.0000.0000.0000.000
159D181HIS00.0190.01324.4640.0000.0000.0000.0000.0000.000
160D182ALA00.0640.03021.8980.0060.0060.0000.0000.0000.000
161D183GLN0-0.011-0.00521.912-0.005-0.0050.0000.0000.0000.000
162D184THR0-0.052-0.02224.2470.0090.0090.0000.0000.0000.000
163D185PHE00.0600.02626.1220.0070.0070.0000.0000.0000.000
164D186LEU0-0.0020.00520.7410.0010.0010.0000.0000.0000.000
165D187ALA00.0010.00625.4140.0030.0030.0000.0000.0000.000
166D188LEU00.0170.01428.2370.0050.0050.0000.0000.0000.000
167D189CYS0-0.013-0.01226.7180.0060.0060.0000.0000.0000.000
168D190ALA0-0.0100.00827.0620.0040.0040.0000.0000.0000.000
169D191THR0-0.044-0.03228.8640.0090.0090.0000.0000.0000.000
170D192ASP-1-0.794-0.89132.029-0.070-0.0700.0000.0000.0000.000
171D193TYR0-0.029-0.02932.048-0.002-0.0020.0000.0000.0000.000
172D194THR0-0.080-0.05633.134-0.001-0.0010.0000.0000.0000.000
173D195PHE00.0720.04028.0420.0010.0010.0000.0000.0000.000
174D196ALA0-0.034-0.00728.094-0.009-0.0090.0000.0000.0000.000
175D197MET0-0.050-0.02828.552-0.006-0.0060.0000.0000.0000.000
176D198TYR0-0.033-0.03625.7580.0040.0040.0000.0000.0000.000
177D199PRO00.0380.01421.631-0.011-0.0110.0000.0000.0000.000
178D200PRO0-0.002-0.00419.077-0.002-0.0020.0000.0000.0000.000
179D201SER0-0.014-0.04516.861-0.001-0.0010.0000.0000.0000.000
180D202MET00.0260.01218.4150.0040.0040.0000.0000.0000.000
181D203ILE00.0230.01021.7200.0050.0050.0000.0000.0000.000
182D204ALA0-0.0260.00918.1920.0060.0060.0000.0000.0000.000
183D205THR0-0.001-0.00718.5180.0000.0000.0000.0000.0000.000
184D206GLY00.0510.03320.1040.0170.0170.0000.0000.0000.000
185D207SER0-0.050-0.05322.8240.0030.0030.0000.0000.0000.000
186D208ILE0-0.013-0.02117.9020.0040.0040.0000.0000.0000.000
187D209GLY00.0440.02921.8650.0090.0090.0000.0000.0000.000
188D210ALA00.0150.01623.5730.0100.0100.0000.0000.0000.000
189D211ALA0-0.055-0.01523.8830.0080.0080.0000.0000.0000.000
190D212VAL0-0.018-0.02720.8800.0060.0060.0000.0000.0000.000
191D213GLN0-0.005-0.00224.2470.0140.0140.0000.0000.0000.000
192D214GLY0-0.032-0.01527.4250.0080.0080.0000.0000.0000.000
193D215LEU0-0.065-0.03325.5970.0000.0000.0000.0000.0000.000
194D216GLY00.0000.00827.8410.0020.0020.0000.0000.0000.000
195D217ALA0-0.064-0.01723.1270.0060.0060.0000.0000.0000.000
196D218CYS00.004-0.01821.945-0.013-0.0130.0000.0000.0000.000
197D219SER0-0.018-0.00723.1080.0090.0090.0000.0000.0000.000
198D220MET0-0.0260.00126.060-0.003-0.0030.0000.0000.0000.000
199D221SER0-0.015-0.02927.5890.0020.0020.0000.0000.0000.000
200D222GLY00.0860.03526.983-0.005-0.0050.0000.0000.0000.000
201D223ASP-1-0.871-0.91626.641-0.021-0.0210.0000.0000.0000.000
202D224GLU-1-0.816-0.89624.261-0.001-0.0010.0000.0000.0000.000
203D225LEU0-0.036-0.01322.370-0.003-0.0030.0000.0000.0000.000
204D226THR00.014-0.01921.661-0.009-0.0090.0000.0000.0000.000
205D227GLU-1-0.885-0.94222.1540.0020.0020.0000.0000.0000.000
206D228LEU0-0.038-0.01617.7970.0080.0080.0000.0000.0000.000
207D229LEU0-0.028-0.01317.427-0.013-0.0130.0000.0000.0000.000
208D230ALA00.0300.03517.829-0.023-0.0230.0000.0000.0000.000
209D231GLY0-0.008-0.00317.4200.0000.0000.0000.0000.0000.000
210D232ILE0-0.126-0.05612.5570.0020.0020.0000.0000.0000.000
211D233THR0-0.030-0.03213.265-0.039-0.0390.0000.0000.0000.000
212D234GLY0-0.034-0.00215.647-0.002-0.0020.0000.0000.0000.000
213D235THR0-0.040-0.02917.6820.0140.0140.0000.0000.0000.000
214D236GLU-1-0.875-0.94120.760-0.009-0.0090.0000.0000.0000.000
215D237VAL00.0330.00523.686-0.012-0.0120.0000.0000.0000.000
216D238ASP-1-0.900-0.94025.244-0.020-0.0200.0000.0000.0000.000
217D239CYS0-0.048-0.03425.804-0.005-0.0050.0000.0000.0000.000
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