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: ZN2NN

Calculation Name: 1G3N-C-Xray372

Preferred Name: Cyclin-dependent kinase 6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1G3N

Chain ID: C

ChEMBL ID: CHEMBL2508

UniProt ID: Q00534

Base Structure: X-ray

Registration Date: 2023-09-26

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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2911682.503421
FMO2-HF: Nuclear repulsion 2820229.148664
FMO2-HF: Total energy -91453.354757
FMO2-MP2: Total energy -91720.423799


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(C:16:LEU)


Summations of interaction energy for fragment #1(C:16:LEU)
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.
-0.4622.10.03-0.699-1.8950.001
Interaction energy analysis for fragmet #1(C:16:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.017
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].
3C18GLU-1-0.785-0.8963.871-1.2110.153-0.002-0.517-0.8460.001
4C19ASP-1-0.809-0.8983.407-1.848-1.1600.017-0.099-0.6060.000
5C20ARG10.8280.9363.3631.4851.9950.015-0.083-0.4430.000
6C21ILE00.0150.0105.6280.4210.4210.0000.0000.0000.000
7C22PHE00.0330.0098.2920.1470.1470.0000.0000.0000.000
8C23TYR0-0.007-0.0308.2620.0630.0630.0000.0000.0000.000
9C24ASN00.013-0.0069.7800.0370.0370.0000.0000.0000.000
10C25ILE0-0.003-0.00311.8040.0870.0870.0000.0000.0000.000
11C26LEU00.0360.02312.6100.0590.0590.0000.0000.0000.000
12C27GLU-1-0.860-0.90414.014-0.326-0.3260.0000.0000.0000.000
13C28ILE0-0.066-0.02616.3500.0430.0430.0000.0000.0000.000
14C29GLU-1-0.768-0.86117.750-0.146-0.1460.0000.0000.0000.000
15C30PRO00.0230.00119.4750.0220.0220.0000.0000.0000.000
16C31ARG10.7540.86420.0850.1560.1560.0000.0000.0000.000
17C32PHE0-0.019-0.00120.4840.0120.0120.0000.0000.0000.000
18C33LEU0-0.0050.02124.9340.0070.0070.0000.0000.0000.000
19C34THR0-0.054-0.02826.9430.0080.0080.0000.0000.0000.000
20C35SER00.0450.00930.677-0.003-0.0030.0000.0000.0000.000
21C36ASP-1-0.811-0.87833.583-0.028-0.0280.0000.0000.0000.000
22C37SER0-0.021-0.02436.3710.0030.0030.0000.0000.0000.000
23C38VAL00.0340.03236.5230.0020.0020.0000.0000.0000.000
24C39PHE00.0170.00137.6310.0030.0030.0000.0000.0000.000
25C40GLY0-0.010-0.01442.0400.0020.0020.0000.0000.0000.000
26C41THR0-0.066-0.03441.9720.0000.0000.0000.0000.0000.000
27C42PHE00.0080.02140.2490.0010.0010.0000.0000.0000.000
28C43GLN0-0.001-0.01340.3790.0040.0040.0000.0000.0000.000
29C44GLN00.0050.02844.1040.0020.0020.0000.0000.0000.000
30C45SER0-0.053-0.03647.4480.0020.0020.0000.0000.0000.000
31C46LEU0-0.021-0.01042.6580.0020.0020.0000.0000.0000.000
32C47THR0-0.003-0.01544.213-0.001-0.0010.0000.0000.0000.000
33C48SER00.0590.00438.7500.0020.0020.0000.0000.0000.000
34C49HIS00.0520.02740.4610.0000.0000.0000.0000.0000.000
35C50MET0-0.017-0.01242.5980.0020.0020.0000.0000.0000.000
36C51ARG10.7550.83933.2040.0210.0210.0000.0000.0000.000
37C52LYS10.8260.92236.9070.0220.0220.0000.0000.0000.000
38C53LEU0-0.021-0.00739.2250.0020.0020.0000.0000.0000.000
39C54LEU0-0.024-0.00439.1000.0020.0020.0000.0000.0000.000
40C55GLY00.0490.01436.3650.0020.0020.0000.0000.0000.000
41C56THR0-0.009-0.00936.0920.0030.0030.0000.0000.0000.000
42C57TRP0-0.012-0.00338.1710.0020.0020.0000.0000.0000.000
43C58MET0-0.035-0.01634.2860.0020.0020.0000.0000.0000.000
44C59PHE00.0520.01531.0440.0040.0040.0000.0000.0000.000
45C60SER0-0.015-0.01134.7420.0040.0040.0000.0000.0000.000
46C61VAL00.0220.01237.3100.0030.0030.0000.0000.0000.000
47C62CYS0-0.066-0.02632.1950.0030.0030.0000.0000.0000.000
48C63GLN00.019-0.00329.4490.0030.0030.0000.0000.0000.000
49C64GLU-1-0.966-0.96633.8640.0270.0270.0000.0000.0000.000
50C65TYR0-0.043-0.03436.5590.0030.0030.0000.0000.0000.000
51C66ASN0-0.094-0.04533.3960.0050.0050.0000.0000.0000.000
52C67LEU0-0.0210.00131.0130.0050.0050.0000.0000.0000.000
53C68GLU-1-0.752-0.88825.4770.0660.0660.0000.0000.0000.000
54C69PRO00.0200.00524.399-0.007-0.0070.0000.0000.0000.000
55C70ASN00.0300.00920.552-0.017-0.0170.0000.0000.0000.000
56C71VAL00.0030.01424.882-0.008-0.0080.0000.0000.0000.000
57C72VAL00.0290.01628.443-0.007-0.0070.0000.0000.0000.000
58C73ALA00.0120.00025.121-0.006-0.0060.0000.0000.0000.000
59C74LEU0-0.021-0.00325.554-0.008-0.0080.0000.0000.0000.000
60C75ALA00.006-0.00127.405-0.005-0.0050.0000.0000.0000.000
61C76LEU0-0.012-0.00730.262-0.003-0.0030.0000.0000.0000.000
62C77ASN00.0200.01626.883-0.002-0.0020.0000.0000.0000.000
63C78LEU0-0.026-0.01529.368-0.004-0.0040.0000.0000.0000.000
64C79LEU00.0260.00331.411-0.001-0.0010.0000.0000.0000.000
65C80ASP-1-0.788-0.87232.125-0.025-0.0250.0000.0000.0000.000
66C81ARG10.8200.89627.5470.0330.0330.0000.0000.0000.000
67C82LEU0-0.0230.00132.643-0.001-0.0010.0000.0000.0000.000
68C83LEU0-0.033-0.02435.9260.0000.0000.0000.0000.0000.000
69C84LEU0-0.011-0.00232.3320.0000.0000.0000.0000.0000.000
70C85ILE0-0.046-0.01834.977-0.001-0.0010.0000.0000.0000.000
71C86LYS10.8190.90638.1200.0120.0120.0000.0000.0000.000
72C87GLN0-0.046-0.01041.0110.0010.0010.0000.0000.0000.000
73C88VAL0-0.005-0.00541.3200.0020.0020.0000.0000.0000.000
74C89SER00.0250.00444.5870.0000.0000.0000.0000.0000.000
75C90LYS10.9360.94546.7640.0110.0110.0000.0000.0000.000
76C91GLU-1-0.929-0.94648.030-0.003-0.0030.0000.0000.0000.000
77C92HIS00.0380.01946.1860.0020.0020.0000.0000.0000.000
78C93PHE00.0300.02639.7890.0010.0010.0000.0000.0000.000
79C94GLN00.0810.03341.961-0.001-0.0010.0000.0000.0000.000
80C95LYS10.8370.94341.8760.0010.0010.0000.0000.0000.000
81C96THR0-0.024-0.02439.0840.0010.0010.0000.0000.0000.000
82C97GLY00.0600.02637.6030.0000.0000.0000.0000.0000.000
83C98SER0-0.004-0.02137.1470.0020.0020.0000.0000.0000.000
84C99ALA0-0.016-0.00937.9270.0030.0030.0000.0000.0000.000
85C100CYS0-0.063-0.01533.8000.0000.0000.0000.0000.0000.000
86C101LEU00.017-0.00133.1820.0010.0010.0000.0000.0000.000
87C102LEU0-0.044-0.00833.6550.0040.0040.0000.0000.0000.000
88C103VAL00.0120.00431.3750.0040.0040.0000.0000.0000.000
89C104ALA00.0220.01529.4890.0020.0020.0000.0000.0000.000
90C105SER0-0.020-0.01328.9760.0060.0060.0000.0000.0000.000
91C106LYS10.7700.85630.013-0.015-0.0150.0000.0000.0000.000
92C107LEU0-0.058-0.01826.5590.0010.0010.0000.0000.0000.000
93C108ARG10.7150.80520.726-0.009-0.0090.0000.0000.0000.000
94C109SER00.0070.00825.8660.0040.0040.0000.0000.0000.000
95C110LEU0-0.044-0.01925.1670.0010.0010.0000.0000.0000.000
96C111THR0-0.041-0.01629.0360.0000.0000.0000.0000.0000.000
97C112PRO00.0020.01831.900-0.004-0.0040.0000.0000.0000.000
98C113ILE00.0470.02933.6050.0000.0000.0000.0000.0000.000
99C114SER00.000-0.00936.640-0.003-0.0030.0000.0000.0000.000
100C115THR00.0570.00039.979-0.001-0.0010.0000.0000.0000.000
101C116SER00.0070.00042.011-0.002-0.0020.0000.0000.0000.000
102C117SER0-0.0280.00941.100-0.001-0.0010.0000.0000.0000.000
103C118LEU00.0600.02637.768-0.001-0.0010.0000.0000.0000.000
104C119CYS0-0.063-0.02441.994-0.001-0.0010.0000.0000.0000.000
105C120TYR00.0180.01145.348-0.001-0.0010.0000.0000.0000.000
106C121ALA00.0190.01042.416-0.001-0.0010.0000.0000.0000.000
107C122ALA0-0.030-0.00544.204-0.001-0.0010.0000.0000.0000.000
108C123ALA0-0.024-0.00845.793-0.001-0.0010.0000.0000.0000.000
109C124ASP-1-0.945-0.97848.5320.0110.0110.0000.0000.0000.000
110C125SER0-0.100-0.05248.183-0.001-0.0010.0000.0000.0000.000
111C126PHE00.009-0.00943.599-0.001-0.0010.0000.0000.0000.000
112C127SER00.0570.03048.3990.0020.0020.0000.0000.0000.000
113C128ARG10.9720.95445.294-0.019-0.0190.0000.0000.0000.000
114C129GLN0-0.049-0.03045.4910.0020.0020.0000.0000.0000.000
115C130GLU-1-0.787-0.88046.0880.0030.0030.0000.0000.0000.000
116C131LEU0-0.0070.01940.363-0.001-0.0010.0000.0000.0000.000
117C132ILE00.0150.00641.6400.0000.0000.0000.0000.0000.000
118C133ASP-1-0.857-0.92241.8840.0030.0030.0000.0000.0000.000
119C134GLN00.005-0.00541.808-0.004-0.0040.0000.0000.0000.000
120C135GLU-1-0.794-0.87736.7310.0130.0130.0000.0000.0000.000
121C136LYS10.8780.93037.923-0.004-0.0040.0000.0000.0000.000
122C137GLU-1-0.829-0.90139.354-0.013-0.0130.0000.0000.0000.000
123C138LEU00.0310.01134.200-0.003-0.0030.0000.0000.0000.000
124C139LEU0-0.002-0.00233.342-0.003-0.0030.0000.0000.0000.000
125C140GLU-1-0.931-0.96435.327-0.010-0.0100.0000.0000.0000.000
126C141LYS10.8000.90437.0460.0090.0090.0000.0000.0000.000
127C142LEU0-0.0140.00131.515-0.004-0.0040.0000.0000.0000.000
128C143ALA0-0.009-0.00831.943-0.002-0.0020.0000.0000.0000.000
129C144TRP0-0.024-0.02931.8900.0010.0010.0000.0000.0000.000
130C145ARG10.8950.98522.4830.0610.0610.0000.0000.0000.000
131C146THR00.014-0.01028.373-0.007-0.0070.0000.0000.0000.000
132C147GLU-1-0.752-0.85523.1650.0000.0000.0000.0000.0000.000
133C148ALA0-0.043-0.02822.951-0.010-0.0100.0000.0000.0000.000
134C149VAL0-0.0160.00217.5100.0100.0100.0000.0000.0000.000
135C150LEU0-0.0070.01820.011-0.006-0.0060.0000.0000.0000.000
136C151ALA00.015-0.00219.602-0.007-0.0070.0000.0000.0000.000
137C152THR00.029-0.00319.986-0.009-0.0090.0000.0000.0000.000
138C153ASP-1-0.810-0.86016.9900.0250.0250.0000.0000.0000.000
139C154VAL0-0.033-0.01714.2540.0090.0090.0000.0000.0000.000
140C155THR00.008-0.00714.7500.0020.0020.0000.0000.0000.000
141C156SER0-0.0030.00514.2880.0140.0140.0000.0000.0000.000
142C157PHE00.0130.0006.7030.0290.0290.0000.0000.0000.000
143C158LEU0-0.006-0.00311.208-0.023-0.0230.0000.0000.0000.000
144C159LEU00.0260.01613.5860.0010.0010.0000.0000.0000.000
145C160LEU0-0.022-0.00710.1690.0130.0130.0000.0000.0000.000
146C161LYS10.7940.8896.0650.5420.5420.0000.0000.0000.000
147C162LEU0-0.0190.01611.924-0.022-0.0220.0000.0000.0000.000
148C163VAL00.014-0.00615.6540.0040.0040.0000.0000.0000.000
149C164GLY00.0110.02213.0260.0350.0350.0000.0000.0000.000
150C165GLY0-0.059-0.04913.5730.0180.0180.0000.0000.0000.000
151C166SER0-0.037-0.02914.2210.0640.0640.0000.0000.0000.000
152C167GLN00.0120.01916.655-0.008-0.0080.0000.0000.0000.000
153C168HIS00.019-0.01219.6160.0030.0030.0000.0000.0000.000
154C169LEU00.0120.02414.608-0.019-0.0190.0000.0000.0000.000
155C170ASP-1-0.850-0.94118.7490.1770.1770.0000.0000.0000.000
156C171PHE0-0.042-0.01120.859-0.014-0.0140.0000.0000.0000.000
157C172TRP00.0580.01020.732-0.014-0.0140.0000.0000.0000.000
158C173HIS00.0340.02018.097-0.020-0.0200.0000.0000.0000.000
159C174HIS0-0.046-0.02120.674-0.011-0.0110.0000.0000.0000.000
160C175GLU-1-0.874-0.92424.2200.0300.0300.0000.0000.0000.000
161C176VAL00.0040.00020.816-0.009-0.0090.0000.0000.0000.000
162C177ASN0-0.027-0.03320.075-0.021-0.0210.0000.0000.0000.000
163C178THR00.0060.00923.993-0.006-0.0060.0000.0000.0000.000
164C179LEU0-0.049-0.00125.843-0.004-0.0040.0000.0000.0000.000
165C180ILE0-0.004-0.00822.448-0.005-0.0050.0000.0000.0000.000
166C181THR0-0.030-0.03625.898-0.004-0.0040.0000.0000.0000.000
167C182LYS10.9090.97528.332-0.010-0.0100.0000.0000.0000.000
168C183ALA00.0420.02327.944-0.002-0.0020.0000.0000.0000.000
169C184LEU0-0.0080.00825.608-0.004-0.0040.0000.0000.0000.000
170C185VAL0-0.0060.01029.9960.0000.0000.0000.0000.0000.000
171C186ASP-1-0.789-0.87733.009-0.027-0.0270.0000.0000.0000.000
172C187PRO00.004-0.00732.564-0.003-0.0030.0000.0000.0000.000
173C188LEU0-0.041-0.00332.810-0.005-0.0050.0000.0000.0000.000
174C189THR00.0610.01827.712-0.007-0.0070.0000.0000.0000.000
175C190GLY00.0140.01528.259-0.006-0.0060.0000.0000.0000.000
176C191SER0-0.044-0.03128.745-0.003-0.0030.0000.0000.0000.000
177C192LEU0-0.043-0.01225.172-0.008-0.0080.0000.0000.0000.000
178C193PRO0-0.006-0.01021.0380.0040.0040.0000.0000.0000.000
179C194ALA00.0280.01819.7360.0040.0040.0000.0000.0000.000
180C195SER00.013-0.03416.5220.0120.0120.0000.0000.0000.000
181C196ILE00.0020.00618.2360.0080.0080.0000.0000.0000.000
182C197ILE00.0080.00221.0870.0110.0110.0000.0000.0000.000
183C198SER0-0.014-0.02418.1040.0120.0120.0000.0000.0000.000
184C199ALA00.0290.01718.0160.0140.0140.0000.0000.0000.000
185C200ALA00.0070.00019.5770.0100.0100.0000.0000.0000.000
186C201GLY00.016-0.00322.9490.0080.0080.0000.0000.0000.000
187C202CYS0-0.065-0.03618.8570.0140.0140.0000.0000.0000.000
188C203ALA0-0.010-0.01721.3130.0090.0090.0000.0000.0000.000
189C204LEU0-0.051-0.01023.0750.0040.0040.0000.0000.0000.000
190C205LEU0-0.044-0.01424.6950.0060.0060.0000.0000.0000.000
191C206VAL0-0.020-0.00120.1270.0080.0080.0000.0000.0000.000
192C207PRO0-0.0100.01323.345-0.010-0.0100.0000.0000.0000.000
193C208ALA00.052-0.00723.0680.0040.0040.0000.0000.0000.000
194C209ASN0-0.043-0.02123.097-0.001-0.0010.0000.0000.0000.000
195C210VAL0-0.053-0.02420.6640.0100.0100.0000.0000.0000.000
196C211ILE00.0160.01817.9210.0070.0070.0000.0000.0000.000
197C212PRO0-0.0200.01014.7890.0010.0010.0000.0000.0000.000
198C213GLN0-0.055-0.04817.921-0.029-0.0290.0000.0000.0000.000
199C214ASP-1-0.883-0.94420.253-0.030-0.0300.0000.0000.0000.000
200C215THR0-0.0120.01422.6070.0010.0010.0000.0000.0000.000
201C216HIS00.033-0.00122.789-0.009-0.0090.0000.0000.0000.000
202C217SER0-0.071-0.04323.831-0.008-0.0080.0000.0000.0000.000
203C218GLY00.0490.04119.570-0.010-0.0100.0000.0000.0000.000
204C219GLY00.0240.00919.035-0.002-0.0020.0000.0000.0000.000
205C220VAL00.0290.00619.507-0.015-0.0150.0000.0000.0000.000
206C221VAL00.0570.03719.104-0.014-0.0140.0000.0000.0000.000
207C222PRO00.004-0.01119.625-0.015-0.0150.0000.0000.0000.000
208C223GLN0-0.023-0.00414.870-0.018-0.0180.0000.0000.0000.000
209C224LEU00.0210.00514.815-0.034-0.0340.0000.0000.0000.000
210C225ALA00.001-0.00415.590-0.030-0.0300.0000.0000.0000.000
211C226SER0-0.028-0.01413.265-0.017-0.0170.0000.0000.0000.000
212C227ILE0-0.074-0.02610.406-0.055-0.0550.0000.0000.0000.000
213C228LEU0-0.028-0.03011.925-0.062-0.0620.0000.0000.0000.000
214C229GLY0-0.0320.01014.637-0.017-0.0170.0000.0000.0000.000
215C230CYS0-0.052-0.02615.2130.0190.0190.0000.0000.0000.000
216C231ASP-1-0.884-0.94118.953-0.143-0.1430.0000.0000.0000.000
217C232VAL00.027-0.00620.7580.0050.0050.0000.0000.0000.000
218C233SER00.0010.00322.6390.0060.0060.0000.0000.0000.000
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