FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: KK3R3

Calculation Name: 3REB-C-Xray540

Preferred Name: Tyrosine-protein kinase HCK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3REB

Chain ID: C

ChEMBL ID: CHEMBL3234

UniProt ID: P08631

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 209
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -979914.566856
FMO2-HF: Nuclear repulsion 932782.160656
FMO2-HF: Total energy -47132.406199
FMO2-MP2: Total energy -47271.636049


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:69:GLU)


Summations of interaction energy for fragment #1(C:69:GLU)
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.
0.6413.066-0.004-1.419-1.0040.005
Interaction energy analysis for fragmet #1(C:69:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.188 / q_NPA : 0.044
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].
4C70VAL0-0.0840.0974.158-0.0110.5270.002-0.294-0.2460.001
5C71GLY00.023-0.1163.950-0.1611.726-0.006-1.125-0.7580.004
6C72PHE00.0070.0206.0320.3380.3380.0000.0000.0000.000
7C72PHE0-0.1060.0627.7030.0850.0850.0000.0000.0000.000
8C73PRO00.068-0.0778.4850.0540.0540.0000.0000.0000.000
9C74VAL00.075-0.00210.9470.0680.0680.0000.0000.0000.000
10C74VAL0-0.0670.10514.4430.0060.0060.0000.0000.0000.000
11C75ARG00.010-0.12713.201-0.089-0.0890.0000.0000.0000.000
12C75ARG10.9181.06615.3450.2800.2800.0000.0000.0000.000
13C76PRO00.036-0.08611.2830.0710.0710.0000.0000.0000.000
14C77GLN00.1530.03813.783-0.010-0.0100.0000.0000.0000.000
15C77GLN0-0.1120.08016.6990.0310.0310.0000.0000.0000.000
16C78VAL0-0.022-0.11916.758-0.034-0.0340.0000.0000.0000.000
17C78VAL0-0.0530.12218.361-0.006-0.0060.0000.0000.0000.000
18C79PRO00.018-0.11218.0910.0360.0360.0000.0000.0000.000
19C80LEU00.1680.04020.524-0.003-0.0030.0000.0000.0000.000
20C80LEU0-0.0940.10323.4510.0030.0030.0000.0000.0000.000
21C81ARG0-0.026-0.12223.834-0.008-0.0080.0000.0000.0000.000
22C81ARG10.7771.01325.4820.1820.1820.0000.0000.0000.000
23C82PRO00.012-0.09726.9480.0080.0080.0000.0000.0000.000
24C83MET00.1510.00930.740-0.012-0.0120.0000.0000.0000.000
25C83MET0-0.0870.13531.833-0.002-0.0020.0000.0000.0000.000
26C84THR0-0.067-0.13432.7600.0040.0040.0000.0000.0000.000
27C84THR0-0.0120.07633.519-0.001-0.0010.0000.0000.0000.000
28C85TYR00.195-0.02335.630-0.001-0.0010.0000.0000.0000.000
29C85TYR0-0.1520.05039.767-0.002-0.0020.0000.0000.0000.000
30C86LYS00.104-0.09436.6270.0040.0040.0000.0000.0000.000
31C86LYS10.7210.98435.4670.1190.1190.0000.0000.0000.000
32C87ALA00.132-0.08332.687-0.001-0.0010.0000.0000.0000.000
33C87ALA0-0.0810.09231.875-0.001-0.0010.0000.0000.0000.000
34C88ALA00.160-0.08933.686-0.004-0.0040.0000.0000.0000.000
35C88ALA0-0.0400.12436.2620.0020.0020.0000.0000.0000.000
36C89LEU00.113-0.06935.8520.0040.0040.0000.0000.0000.000
37C89LEU0-0.1130.10338.2670.0000.0000.0000.0000.0000.000
38C90ASP00.085-0.10533.9980.0050.0050.0000.0000.0000.000
39C90ASP-1-0.917-0.79733.243-0.127-0.1270.0000.0000.0000.000
40C91ILE00.082-0.08832.936-0.003-0.0030.0000.0000.0000.000
41C91ILE0-0.0870.10030.4530.0000.0000.0000.0000.0000.000
42C92SER00.022-0.12233.7050.0020.0020.0000.0000.0000.000
43C92SER0-0.0590.05837.9450.0040.0040.0000.0000.0000.000
44C93HIS00.113-0.08337.2830.0060.0060.0000.0000.0000.000
45C93HIS0-0.1380.09836.824-0.002-0.0020.0000.0000.0000.000
46C94PHE00.092-0.06933.0020.0040.0040.0000.0000.0000.000
47C94PHE0-0.1130.06928.757-0.003-0.0030.0000.0000.0000.000
48C95LEU00.043-0.10434.351-0.002-0.0020.0000.0000.0000.000
49C95LEU0-0.0800.08731.7270.0010.0010.0000.0000.0000.000
50C96LYS00.072-0.10035.3370.0050.0050.0000.0000.0000.000
51C96LYS10.7451.01139.4410.0580.0580.0000.0000.0000.000
52C97GLU00.063-0.12637.2220.0070.0070.0000.0000.0000.000
53C97GLU-1-1.014-0.85536.157-0.088-0.0880.0000.0000.0000.000
54C98LYS00.068-0.09334.0260.0010.0010.0000.0000.0000.000
55C98LYS10.8031.04829.4690.0910.0910.0000.0000.0000.000
56C99GLY0-0.007-0.08635.2650.0040.0040.0000.0000.0000.000
57C100GLY0-0.026-0.03136.238-0.002-0.0020.0000.0000.0000.000
58C101LEU00.075-0.02536.9220.0030.0030.0000.0000.0000.000
59C101LEU0-0.0560.12636.311-0.001-0.0010.0000.0000.0000.000
60C102GLU00.096-0.11338.9080.0040.0040.0000.0000.0000.000
61C102GLU-1-0.864-0.77642.304-0.048-0.0480.0000.0000.0000.000
62C103GLY0-0.034-0.10742.4890.0010.0010.0000.0000.0000.000
63C104LEU00.109-0.00340.4820.0040.0040.0000.0000.0000.000
64C104LEU0-0.1300.10237.5310.0000.0000.0000.0000.0000.000
65C105ILE00.109-0.09541.986-0.002-0.0020.0000.0000.0000.000
66C105ILE0-0.0980.10743.2430.0000.0000.0000.0000.0000.000
67C106TRP00.126-0.08940.8650.0000.0000.0000.0000.0000.000
68C106TRP0-0.0560.10339.5170.0030.0030.0000.0000.0000.000
69C107SER0-0.035-0.10939.8770.0030.0030.0000.0000.0000.000
70C107SER0-0.0150.07138.9470.0020.0020.0000.0000.0000.000
71C108GLN00.163-0.04838.334-0.004-0.0040.0000.0000.0000.000
72C108GLN0-0.1400.06536.102-0.002-0.0020.0000.0000.0000.000
73C109ARG00.092-0.08734.789-0.004-0.0040.0000.0000.0000.000
74C109ARG10.8211.03628.663-0.013-0.0130.0000.0000.0000.000
75C110ARG00.054-0.11233.7460.0000.0000.0000.0000.0000.000
76C110ARG10.8191.01636.1320.0120.0120.0000.0000.0000.000
77C111GLN00.146-0.07734.031-0.006-0.0060.0000.0000.0000.000
78C111GLN0-0.0740.12635.2620.0030.0030.0000.0000.0000.000
79C112GLU00.072-0.12632.283-0.009-0.0090.0000.0000.0000.000
80C112GLU-1-0.882-0.77631.5370.0110.0110.0000.0000.0000.000
81C113ILE00.078-0.07029.442-0.003-0.0030.0000.0000.0000.000
82C113ILE0-0.1200.07429.1120.0010.0010.0000.0000.0000.000
83C114LEU00.109-0.08729.006-0.008-0.0080.0000.0000.0000.000
84C114LEU0-0.1150.09531.6260.0000.0000.0000.0000.0000.000
85C115ASP00.092-0.10129.740-0.013-0.0130.0000.0000.0000.000
86C115ASP-1-0.866-0.79431.185-0.047-0.0470.0000.0000.0000.000
87C116LEU00.069-0.11926.955-0.012-0.0120.0000.0000.0000.000
88C116LEU0-0.0680.10625.9220.0030.0030.0000.0000.0000.000
89C117TRP00.082-0.06425.172-0.008-0.0080.0000.0000.0000.000
90C117TRP0-0.0700.08024.6440.0030.0030.0000.0000.0000.000
91C118ILE00.102-0.07525.070-0.020-0.0200.0000.0000.0000.000
92C118ILE0-0.0890.09628.408-0.001-0.0010.0000.0000.0000.000
93C119TYR00.059-0.10425.431-0.022-0.0220.0000.0000.0000.000
94C119TYR0-0.0470.11422.900-0.001-0.0010.0000.0000.0000.000
95C120HIS00.072-0.09121.468-0.018-0.0180.0000.0000.0000.000
96C120HIS0-0.1190.07117.7700.0010.0010.0000.0000.0000.000
97C121THR00.010-0.09820.583-0.027-0.0270.0000.0000.0000.000
98C121THR0-0.1130.02222.424-0.003-0.0030.0000.0000.0000.000
99C122GLN0-0.020-0.11422.490-0.032-0.0320.0000.0000.0000.000
100C122GLN0-0.0630.09424.4740.0010.0010.0000.0000.0000.000
101C123GLY00.099-0.05323.504-0.006-0.0060.0000.0000.0000.000
102C124TYR00.0770.00624.1640.0060.0060.0000.0000.0000.000
103C124TYR0-0.0910.08728.448-0.004-0.0040.0000.0000.0000.000
104C125PHE00.162-0.07627.4080.0020.0020.0000.0000.0000.000
105C125PHE0-0.0910.10626.4870.0000.0000.0000.0000.0000.000
106C126PRO0-0.053-0.12927.470-0.002-0.0020.0000.0000.0000.000
107C127ASP00.030-0.03030.4230.0090.0090.0000.0000.0000.000
108C127ASP-1-0.895-0.82732.543-0.053-0.0530.0000.0000.0000.000
109C128TRP00.109-0.05733.6020.0050.0050.0000.0000.0000.000
110C128TRP0-0.0530.09931.087-0.002-0.0020.0000.0000.0000.000
111C129GLN00.035-0.06235.1550.0000.0000.0000.0000.0000.000
112C129GLN0-0.0420.10934.5100.0030.0030.0000.0000.0000.000
113C130ASN00.139-0.09036.9150.0040.0040.0000.0000.0000.000
114C130ASN0-0.1220.05637.6540.0040.0040.0000.0000.0000.000
115C131TYR00.017-0.11339.952-0.004-0.0040.0000.0000.0000.000
116C131TYR0-0.0930.06639.059-0.001-0.0010.0000.0000.0000.000
117C132THR00.036-0.07343.4460.0020.0020.0000.0000.0000.000
118C132THR0-0.0150.09047.399-0.001-0.0010.0000.0000.0000.000
119C133PRO00.025-0.08047.0140.0010.0010.0000.0000.0000.000
120C134GLY0-0.0090.00548.958-0.002-0.0020.0000.0000.0000.000
121C135PRO0-0.033-0.02151.7260.0010.0010.0000.0000.0000.000
122C136GLY00.013-0.00752.971-0.001-0.0010.0000.0000.0000.000
123C137ILE00.112-0.00850.1610.0010.0010.0000.0000.0000.000
124C137ILE0-0.1240.07849.1640.0000.0000.0000.0000.0000.000
125C138ARG00.042-0.10146.7020.0000.0000.0000.0000.0000.000
126C138ARG10.7431.01945.8510.0150.0150.0000.0000.0000.000
127C139TYR00.106-0.08646.106-0.002-0.0020.0000.0000.0000.000
128C139TYR0-0.0370.11547.619-0.001-0.0010.0000.0000.0000.000
129C140PRO00.009-0.09841.8290.0030.0030.0000.0000.0000.000
130C141LEU00.089-0.02042.396-0.001-0.0010.0000.0000.0000.000
131C141LEU0-0.0740.13141.7100.0000.0000.0000.0000.0000.000
132C142THR0-0.005-0.08838.9240.0000.0000.0000.0000.0000.000
133C142THR0-0.1070.03137.021-0.001-0.0010.0000.0000.0000.000
134C143PHE00.144-0.08640.416-0.002-0.0020.0000.0000.0000.000
135C143PHE0-0.0800.10442.881-0.001-0.0010.0000.0000.0000.000
136C144GLY00.024-0.09640.042-0.004-0.0040.0000.0000.0000.000
137C145TRP00.1310.02938.869-0.005-0.0050.0000.0000.0000.000
138C145TRP0-0.1280.07036.064-0.003-0.0030.0000.0000.0000.000
139C146CYS00.026-0.12139.6290.0050.0050.0000.0000.0000.000
140C146CYS0-0.1520.07641.183-0.001-0.0010.0000.0000.0000.000
141C147PHE00.074-0.10741.1280.0010.0010.0000.0000.0000.000
142C147PHE0-0.0650.09138.4850.0000.0000.0000.0000.0000.000
143C148LYS00.134-0.06142.3410.0000.0000.0000.0000.0000.000
144C148LYS10.7440.99245.9200.0360.0360.0000.0000.0000.000
145C149LEU00.071-0.09144.719-0.002-0.0020.0000.0000.0000.000
146C149LEU0-0.0870.09941.4210.0010.0010.0000.0000.0000.000
147C150VAL00.078-0.10845.4450.0020.0020.0000.0000.0000.000
148C150VAL0-0.1190.07347.679-0.001-0.0010.0000.0000.0000.000
149C151PRO00.036-0.08548.7610.0000.0000.0000.0000.0000.000
150C152VAL0-0.026-0.01650.984-0.002-0.0020.0000.0000.0000.000
151C152VAL0-0.0380.08650.082-0.001-0.0010.0000.0000.0000.000
152C153GLU00.089-0.11152.7620.0010.0010.0000.0000.0000.000
153C153GLU-1-0.944-0.81854.956-0.017-0.0170.0000.0000.0000.000
154C154PRO0-0.066-0.13952.613-0.001-0.0010.0000.0000.0000.000
155C155GLU0-0.162-0.10753.2010.0020.0020.0000.0000.0000.000
156C155GLU-1-0.819-0.86653.901-0.006-0.0060.0000.0000.0000.000
157C181GLU00.1420.00155.0360.0010.0010.0000.0000.0000.000
158C181GLU-1-1.032-0.86455.458-0.002-0.0020.0000.0000.0000.000
159C182LYS00.057-0.12351.8010.0010.0010.0000.0000.0000.000
160C182LYS10.8451.04648.0530.0000.0000.0000.0000.0000.000
161C183GLU00.054-0.09151.2650.0000.0000.0000.0000.0000.000
162C183GLU-1-0.856-0.78350.594-0.013-0.0130.0000.0000.0000.000
163C184VAL00.110-0.07848.2190.0010.0010.0000.0000.0000.000
164C184VAL0-0.0490.13247.2180.0000.0000.0000.0000.0000.000
165C185LEU00.027-0.12046.410-0.001-0.0010.0000.0000.0000.000
166C185LEU0-0.0540.09745.5360.0000.0000.0000.0000.0000.000
167C186VAL00.056-0.09244.4680.0020.0020.0000.0000.0000.000
168C186VAL0-0.0420.11245.2260.0000.0000.0000.0000.0000.000
169C187TRP00.101-0.09641.4420.0000.0000.0000.0000.0000.000
170C187TRP0-0.1100.09437.2060.0010.0010.0000.0000.0000.000
171C188ARG00.126-0.08042.9250.0000.0000.0000.0000.0000.000
172C188ARG10.7941.05146.5160.0300.0300.0000.0000.0000.000
173C189PHE00.125-0.07843.7400.0000.0000.0000.0000.0000.000
174C189PHE0-0.0760.08341.074-0.001-0.0010.0000.0000.0000.000
175C190ASP00.045-0.10744.4640.0020.0020.0000.0000.0000.000
176C190ASP-1-0.886-0.77847.261-0.042-0.0420.0000.0000.0000.000
177C191SER00.120-0.04245.801-0.001-0.0010.0000.0000.0000.000
178C191SER0-0.0270.06246.8240.0010.0010.0000.0000.0000.000
179C192LYS00.052-0.09946.863-0.003-0.0030.0000.0000.0000.000
180C192LYS10.7991.01550.4200.0420.0420.0000.0000.0000.000
181C193LEU00.047-0.09445.6940.0000.0000.0000.0000.0000.000
182C193LEU0-0.0650.10944.9870.0010.0010.0000.0000.0000.000
183C194ALA00.154-0.09543.906-0.001-0.0010.0000.0000.0000.000
184C194ALA0-0.0520.12044.095-0.001-0.0010.0000.0000.0000.000
185C195PHE0-0.050-0.12444.884-0.004-0.0040.0000.0000.0000.000
186C195PHE0-0.0810.08346.9470.0000.0000.0000.0000.0000.000
187C196HIS00.118-0.07048.1290.0000.0000.0000.0000.0000.000
188C196HIS0-0.1090.06550.357-0.001-0.0010.0000.0000.0000.000
189C197HIS00.087-0.06847.295-0.001-0.0010.0000.0000.0000.000
190C197HIS0-0.1180.06544.645-0.001-0.0010.0000.0000.0000.000
191C198MET00.115-0.10348.1760.0010.0010.0000.0000.0000.000
192C198MET0-0.1200.07548.9160.0000.0000.0000.0000.0000.000
193C199ALA00.136-0.07747.0580.0030.0030.0000.0000.0000.000
194C199ALA0-0.0660.11546.5260.0000.0000.0000.0000.0000.000
195C200ARG00.071-0.06648.4150.0030.0030.0000.0000.0000.000
196C200ARG10.8511.03446.7550.0440.0440.0000.0000.0000.000
197C201GLU00.034-0.12149.5600.0010.0010.0000.0000.0000.000
198C201GLU-1-0.982-0.84652.830-0.034-0.0340.0000.0000.0000.000
199C202LEU00.018-0.10952.1470.0010.0010.0000.0000.0000.000
200C202LEU0-0.0980.08252.0340.0000.0000.0000.0000.0000.000
201C203HIS00.121-0.11051.6310.0020.0020.0000.0000.0000.000
202C203HIS0-0.0460.10750.8040.0000.0000.0000.0000.0000.000
203C204PRO0-0.001-0.08750.369-0.002-0.0020.0000.0000.0000.000
204C205GLU00.014-0.03747.2530.0020.0020.0000.0000.0000.000
205C205GLU-1-0.894-0.79946.509-0.028-0.0280.0000.0000.0000.000
206C206TYR00.059-0.08045.9640.0000.0000.0000.0000.0000.000
207C206TYR0-0.1560.04943.826-0.002-0.0020.0000.0000.0000.000
208C207TYR0-0.057-0.12145.8660.0030.0030.0000.0000.0000.000
209C207TYR00.0190.00943.708-0.001-0.0010.0000.0000.0000.000