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: JLK99

Calculation Name: 3H3B-C-Xray372

Preferred Name: Receptor protein-tyrosine kinase erbB-2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3H3B

Chain ID: C

ChEMBL ID: CHEMBL1824

UniProt ID: P04626

Base Structure: X-ray

Registration Date: 2023-06-26

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2879090.102985
FMO2-HF: Nuclear repulsion 2788348.395951
FMO2-HF: Total energy -90741.707034
FMO2-MP2: Total energy -91006.214409


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:-2:GLN)


Summations of interaction energy for fragment #1(C:-2:GLN)
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.
-0.7291.058-0.011-0.852-0.9240
Interaction energy analysis for fragmet #1(C:-2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.025
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].
3C0ALA00.0040.0063.849-0.4221.365-0.011-0.852-0.9240.000
4C1ASP-1-0.849-0.9265.5670.2950.2950.0000.0000.0000.000
5C2ILE0-0.049-0.0108.8210.0900.0900.0000.0000.0000.000
6C3VAL0-0.0020.00810.973-0.052-0.0520.0000.0000.0000.000
7C4LEU00.002-0.00513.8510.0540.0540.0000.0000.0000.000
8C5THR00.0190.00116.905-0.047-0.0470.0000.0000.0000.000
9C6GLN00.010-0.00819.1750.0130.0130.0000.0000.0000.000
10C7THR0-0.061-0.00722.638-0.010-0.0100.0000.0000.0000.000
11C8PRO00.0520.02225.5350.0080.0080.0000.0000.0000.000
12C9SER00.0390.01627.3570.0050.0050.0000.0000.0000.000
13C10SER00.000-0.02928.464-0.001-0.0010.0000.0000.0000.000
14C11LEU0-0.039-0.01931.3010.0020.0020.0000.0000.0000.000
15C12PRO0-0.0080.00734.2040.0000.0000.0000.0000.0000.000
16C13VAL0-0.006-0.00737.0150.0030.0030.0000.0000.0000.000
17C14SER00.004-0.02039.828-0.004-0.0040.0000.0000.0000.000
18C15VAL0-0.068-0.04942.4960.0030.0030.0000.0000.0000.000
19C16GLY00.0170.01543.106-0.003-0.0030.0000.0000.0000.000
20C17GLU-1-0.784-0.85440.1630.0730.0730.0000.0000.0000.000
21C18LYS10.9370.98534.673-0.110-0.1100.0000.0000.0000.000
22C19VAL00.0090.00933.359-0.001-0.0010.0000.0000.0000.000
23C20THR0-0.023-0.03729.3580.0010.0010.0000.0000.0000.000
24C21MET0-0.0330.00927.277-0.004-0.0040.0000.0000.0000.000
25C22THR00.0180.00322.4410.0090.0090.0000.0000.0000.000
26C23CYS0-0.046-0.01419.867-0.008-0.0080.0000.0000.0000.000
27C24LYS10.8430.91516.955-0.380-0.3800.0000.0000.0000.000
28C25SER0-0.001-0.01912.758-0.049-0.0490.0000.0000.0000.000
29C26SER0-0.0020.0059.8350.0240.0240.0000.0000.0000.000
30C27GLN0-0.015-0.0146.6050.3120.3120.0000.0000.0000.000
31C28THR00.0030.0089.439-0.267-0.2670.0000.0000.0000.000
32C29LEU0-0.006-0.01011.010-0.023-0.0230.0000.0000.0000.000
33C30LEU0-0.0640.00513.797-0.063-0.0630.0000.0000.0000.000
34C31TYR00.0280.01112.0290.0860.0860.0000.0000.0000.000
35C32SER00.0560.00913.961-0.033-0.0330.0000.0000.0000.000
36C33ASN0-0.042-0.01814.153-0.033-0.0330.0000.0000.0000.000
37C34ASN00.004-0.01217.728-0.015-0.0150.0000.0000.0000.000
38C35GLN0-0.0010.00718.0280.0130.0130.0000.0000.0000.000
39C36LYS10.8630.93619.372-0.217-0.2170.0000.0000.0000.000
40C37ASN00.049-0.00117.3510.0810.0810.0000.0000.0000.000
41C38TYR0-0.0140.00215.162-0.039-0.0390.0000.0000.0000.000
42C39LEU0-0.014-0.00316.7540.0050.0050.0000.0000.0000.000
43C40ALA0-0.009-0.00419.167-0.016-0.0160.0000.0000.0000.000
44C41TRP00.009-0.00322.4640.0020.0020.0000.0000.0000.000
45C42TYR0-0.033-0.03923.256-0.006-0.0060.0000.0000.0000.000
46C43GLN00.004-0.00927.684-0.002-0.0020.0000.0000.0000.000
47C44GLN0-0.009-0.02330.7900.0010.0010.0000.0000.0000.000
48C45LYS10.8990.95932.464-0.084-0.0840.0000.0000.0000.000
49C46PRO00.019-0.00536.1420.0000.0000.0000.0000.0000.000
50C47GLY00.0070.01037.714-0.001-0.0010.0000.0000.0000.000
51C48GLN0-0.028-0.00636.7510.0000.0000.0000.0000.0000.000
52C49SER00.0160.02232.8770.0020.0020.0000.0000.0000.000
53C50PRO0-0.025-0.00728.902-0.001-0.0010.0000.0000.0000.000
54C51LYS10.8890.94531.041-0.091-0.0910.0000.0000.0000.000
55C52LEU0-0.0020.01226.1390.0020.0020.0000.0000.0000.000
56C53LEU0-0.051-0.01328.859-0.007-0.0070.0000.0000.0000.000
57C54ILE0-0.009-0.01325.775-0.004-0.0040.0000.0000.0000.000
58C55SER00.0310.01923.8610.0060.0060.0000.0000.0000.000
59C56TRP0-0.010-0.00719.1610.0030.0030.0000.0000.0000.000
60C57ALA00.0000.00121.1940.0040.0040.0000.0000.0000.000
61C58PHE0-0.016-0.01323.083-0.011-0.0110.0000.0000.0000.000
62C59THR0-0.027-0.00426.356-0.015-0.0150.0000.0000.0000.000
63C60ARG10.8840.94728.256-0.117-0.1170.0000.0000.0000.000
64C61LYS10.9330.98430.843-0.108-0.1080.0000.0000.0000.000
65C62SER00.010-0.01132.006-0.005-0.0050.0000.0000.0000.000
66C63GLY00.0280.01335.565-0.001-0.0010.0000.0000.0000.000
67C64VAL0-0.055-0.01632.904-0.003-0.0030.0000.0000.0000.000
68C65PRO00.002-0.00636.0750.0020.0020.0000.0000.0000.000
69C66ASP-1-0.881-0.95136.2630.0960.0960.0000.0000.0000.000
70C67ARG10.7890.86836.284-0.082-0.0820.0000.0000.0000.000
71C68PHE00.0000.00832.4990.0030.0030.0000.0000.0000.000
72C69THR00.0200.00430.8430.0020.0020.0000.0000.0000.000
73C70GLY00.0150.01527.2850.0000.0000.0000.0000.0000.000
74C71SER00.021-0.00325.886-0.009-0.0090.0000.0000.0000.000
75C72GLY00.0220.00822.3440.0030.0030.0000.0000.0000.000
76C73SER0-0.004-0.01519.499-0.002-0.0020.0000.0000.0000.000
77C74GLY00.0420.03615.1890.0110.0110.0000.0000.0000.000
78C75THR00.023-0.00412.8800.0430.0430.0000.0000.0000.000
79C76ASP-1-0.826-0.87115.5120.3660.3660.0000.0000.0000.000
80C77PHE00.0280.01216.674-0.021-0.0210.0000.0000.0000.000
81C78THR00.002-0.00421.769-0.008-0.0080.0000.0000.0000.000
82C79LEU0-0.031-0.00725.3030.0010.0010.0000.0000.0000.000
83C80THR00.0000.00228.115-0.007-0.0070.0000.0000.0000.000
84C81ILE0-0.0070.01331.7620.0000.0000.0000.0000.0000.000
85C82GLY0-0.012-0.01435.115-0.003-0.0030.0000.0000.0000.000
86C83SER0-0.041-0.04637.741-0.004-0.0040.0000.0000.0000.000
87C84VAL00.0170.02437.3220.0000.0000.0000.0000.0000.000
88C85LYS10.8820.92139.975-0.081-0.0810.0000.0000.0000.000
89C86ALA00.0530.01741.2330.0020.0020.0000.0000.0000.000
90C87GLU-1-0.851-0.90940.1070.0810.0810.0000.0000.0000.000
91C88ASP-1-0.730-0.84536.9860.0920.0920.0000.0000.0000.000
92C89LEU0-0.0080.02736.3300.0050.0050.0000.0000.0000.000
93C90ALA00.003-0.00533.919-0.002-0.0020.0000.0000.0000.000
94C91VAL0-0.027-0.00328.9480.0010.0010.0000.0000.0000.000
95C92TYR0-0.009-0.01528.4870.0020.0020.0000.0000.0000.000
96C93TYR00.0000.00424.300-0.002-0.0020.0000.0000.0000.000
97C95GLN0-0.020-0.03818.261-0.007-0.0070.0000.0000.0000.000
98C96GLN00.0300.01112.8340.0410.0410.0000.0000.0000.000
99C97TYR00.022-0.00316.028-0.019-0.0190.0000.0000.0000.000
100C98SER0-0.021-0.00111.407-0.012-0.0120.0000.0000.0000.000
101C99ASN00.0150.0057.162-0.021-0.0210.0000.0000.0000.000
102C100TYR0-0.061-0.03210.352-0.004-0.0040.0000.0000.0000.000
103C101PRO00.0170.0049.623-0.025-0.0250.0000.0000.0000.000
104C102TRP00.0330.01613.170-0.006-0.0060.0000.0000.0000.000
105C103THR0-0.048-0.03714.118-0.015-0.0150.0000.0000.0000.000
106C104PHE00.011-0.01416.8390.0100.0100.0000.0000.0000.000
107C105GLY00.0510.03318.9660.0040.0040.0000.0000.0000.000
108C106GLY0-0.042-0.03320.651-0.015-0.0150.0000.0000.0000.000
109C107GLY00.001-0.01623.063-0.013-0.0130.0000.0000.0000.000
110C108THR0-0.037-0.02825.8930.0060.0060.0000.0000.0000.000
111C109ARG10.8110.88828.651-0.072-0.0720.0000.0000.0000.000
112C110LEU0-0.0120.00932.137-0.001-0.0010.0000.0000.0000.000
113C111GLU-1-0.820-0.88434.7830.0690.0690.0000.0000.0000.000
114C112ILE00.0390.02738.2210.0000.0000.0000.0000.0000.000
115C135GLU-1-0.835-0.89937.7380.0850.0850.0000.0000.0000.000
116C136VAL0-0.062-0.02633.180-0.002-0.0020.0000.0000.0000.000
117C137GLN0-0.019-0.00636.640-0.002-0.0020.0000.0000.0000.000
118C138LEU00.001-0.01730.5220.0010.0010.0000.0000.0000.000
119C139GLN0-0.015-0.00634.903-0.002-0.0020.0000.0000.0000.000
120C140GLN00.008-0.01932.3950.0040.0040.0000.0000.0000.000
121C141SER00.0250.03336.283-0.002-0.0020.0000.0000.0000.000
122C142GLY00.0130.01037.7780.0020.0020.0000.0000.0000.000
123C143PRO0-0.044-0.02438.2860.0020.0020.0000.0000.0000.000
124C144GLU-1-0.858-0.94036.8580.0440.0440.0000.0000.0000.000
125C145VAL0-0.039-0.02038.2140.0010.0010.0000.0000.0000.000
126C146VAL00.0380.03136.327-0.002-0.0020.0000.0000.0000.000
127C147LYS10.9580.98739.164-0.025-0.0250.0000.0000.0000.000
128C148THR00.026-0.01034.8360.0030.0030.0000.0000.0000.000
129C149GLY0-0.023-0.00734.893-0.002-0.0020.0000.0000.0000.000
130C150ALA0-0.0280.00235.7510.0010.0010.0000.0000.0000.000
131C151SER0-0.032-0.03033.5840.0030.0030.0000.0000.0000.000
132C152VAL00.0130.02032.837-0.002-0.0020.0000.0000.0000.000
133C153LYS10.9240.96132.704-0.064-0.0640.0000.0000.0000.000
134C154ILE00.0200.03530.794-0.002-0.0020.0000.0000.0000.000
135C155SER00.020-0.00432.9030.0020.0020.0000.0000.0000.000
136C156CYS0-0.0010.00727.9250.0040.0040.0000.0000.0000.000
137C157LYS10.9200.98833.940-0.064-0.0640.0000.0000.0000.000
138C158ALA00.0110.00433.5550.0010.0010.0000.0000.0000.000
139C159SER0-0.011-0.01935.639-0.005-0.0050.0000.0000.0000.000
140C160GLY00.0410.01936.9150.0030.0030.0000.0000.0000.000
141C161TYR0-0.015-0.00330.8020.0010.0010.0000.0000.0000.000
142C162SER00.0120.00533.621-0.003-0.0030.0000.0000.0000.000
143C163PHE00.0550.01331.4360.0060.0060.0000.0000.0000.000
144C164THR00.0410.00730.1720.0060.0060.0000.0000.0000.000
145C165GLY0-0.0110.01628.6030.0050.0050.0000.0000.0000.000
146C166TYR0-0.102-0.07826.3150.0050.0050.0000.0000.0000.000
147C167PHE0-0.0070.01120.320-0.004-0.0040.0000.0000.0000.000
148C168ILE0-0.018-0.00324.645-0.005-0.0050.0000.0000.0000.000
149C169ASN00.011-0.02421.4840.0160.0160.0000.0000.0000.000
150C170TRP00.0280.01523.280-0.013-0.0130.0000.0000.0000.000
151C171VAL0-0.013-0.01223.1310.0080.0080.0000.0000.0000.000
152C172LYS10.8720.94724.425-0.077-0.0770.0000.0000.0000.000
153C173LYS10.8720.93325.779-0.091-0.0910.0000.0000.0000.000
154C174ASN00.0280.00728.115-0.003-0.0030.0000.0000.0000.000
155C175SER00.0260.01030.0700.0030.0030.0000.0000.0000.000
156C176GLY0-0.001-0.00831.314-0.002-0.0020.0000.0000.0000.000
157C177LYS10.9560.98826.057-0.063-0.0630.0000.0000.0000.000
158C178SER00.0470.03422.442-0.003-0.0030.0000.0000.0000.000
159C179PRO0-0.057-0.02823.726-0.008-0.0080.0000.0000.0000.000
160C180GLU-1-0.848-0.89620.8680.1010.1010.0000.0000.0000.000
161C181TRP00.0150.00915.580-0.006-0.0060.0000.0000.0000.000
162C182ILE0-0.019-0.00819.1260.0020.0020.0000.0000.0000.000
163C183GLY00.0520.00118.8100.0040.0040.0000.0000.0000.000
164C184HIS0-0.0510.00618.1390.0040.0040.0000.0000.0000.000
165C185ILE00.0010.00721.1330.0070.0070.0000.0000.0000.000
166C186SER00.0260.02021.942-0.008-0.0080.0000.0000.0000.000
167C187SER0-0.025-0.03723.752-0.006-0.0060.0000.0000.0000.000
168C188SER0-0.025-0.02426.923-0.005-0.0050.0000.0000.0000.000
169C189TYR0-0.014-0.00124.277-0.007-0.0070.0000.0000.0000.000
170C190ALA0-0.0160.00025.1130.0030.0030.0000.0000.0000.000
171C191THR0-0.0030.00119.4610.0020.0020.0000.0000.0000.000
172C192SER0-0.020-0.00921.2900.0050.0050.0000.0000.0000.000
173C193THR00.0040.01615.0540.0110.0110.0000.0000.0000.000
174C194TYR00.0260.01317.481-0.015-0.0150.0000.0000.0000.000
175C195ASN00.0100.00015.4140.0190.0190.0000.0000.0000.000
176C196GLN00.0640.02412.8540.0200.0200.0000.0000.0000.000
177C197LYS10.8430.90315.262-0.097-0.0970.0000.0000.0000.000
178C198PHE00.003-0.01718.062-0.012-0.0120.0000.0000.0000.000
179C199LYS10.9180.97814.920-0.191-0.1910.0000.0000.0000.000
180C200ASN00.0300.01919.7650.0090.0090.0000.0000.0000.000
181C201LYS10.7600.88922.756-0.061-0.0610.0000.0000.0000.000
182C202ALA00.019-0.01323.478-0.006-0.0060.0000.0000.0000.000
183C203ALA00.0150.01623.9000.0070.0070.0000.0000.0000.000
184C204PHE0-0.046-0.01621.289-0.008-0.0080.0000.0000.0000.000
185C205THR0-0.004-0.00926.627-0.003-0.0030.0000.0000.0000.000
186C206VAL0-0.009-0.01228.6900.0010.0010.0000.0000.0000.000
187C207ASP-1-0.740-0.82031.1940.0620.0620.0000.0000.0000.000
188C208THR00.0270.00233.1570.0020.0020.0000.0000.0000.000
189C209SER0-0.052-0.03334.906-0.001-0.0010.0000.0000.0000.000
190C210SER0-0.060-0.04438.092-0.001-0.0010.0000.0000.0000.000
191C211SER0-0.054-0.02735.2650.0010.0010.0000.0000.0000.000
192C212THR00.0130.00134.8810.0010.0010.0000.0000.0000.000
193C213ALA00.0130.01129.5660.0020.0020.0000.0000.0000.000
194C214PHE0-0.019-0.03930.439-0.006-0.0060.0000.0000.0000.000
195C215MET0-0.0090.01226.6260.0090.0090.0000.0000.0000.000
196C216GLN0-0.025-0.00229.220-0.003-0.0030.0000.0000.0000.000
197C217LEU0-0.019-0.00727.2670.0060.0060.0000.0000.0000.000
198C218ASN00.004-0.00526.807-0.010-0.0100.0000.0000.0000.000
199C219SER00.0500.01129.452-0.001-0.0010.0000.0000.0000.000
200C220LEU0-0.065-0.02430.6310.0000.0000.0000.0000.0000.000
201C221THR00.0330.00129.945-0.005-0.0050.0000.0000.0000.000
202C222SER00.0630.01532.4610.0020.0020.0000.0000.0000.000
203C223GLU-1-0.905-0.94126.7880.0410.0410.0000.0000.0000.000
204C224ASP-1-0.817-0.87328.0590.0590.0590.0000.0000.0000.000
205C225SER00.0060.02329.9800.0030.0030.0000.0000.0000.000
206C226ALA0-0.055-0.02329.8590.0010.0010.0000.0000.0000.000
207C227VAL00.0100.01631.733-0.002-0.0020.0000.0000.0000.000
208C228TYR0-0.017-0.03526.9580.0070.0070.0000.0000.0000.000
209C229TYR00.001-0.00128.471-0.003-0.0030.0000.0000.0000.000
210C231VAL00.006-0.02425.731-0.003-0.0030.0000.0000.0000.000
211C232ARG10.7830.88826.312-0.113-0.1130.0000.0000.0000.000
212C233SER00.0460.02822.1350.0020.0020.0000.0000.0000.000
213C234GLY00.0250.00924.605-0.006-0.0060.0000.0000.0000.000
214C235ASN0-0.002-0.00222.5500.0210.0210.0000.0000.0000.000
215C236TYR00.0260.00023.000-0.005-0.0050.0000.0000.0000.000
216C237GLU-1-0.782-0.88523.2720.1930.1930.0000.0000.0000.000
217C238GLU-1-0.816-0.86925.5100.1260.1260.0000.0000.0000.000
218C239TYR0-0.029-0.00215.409-0.002-0.0020.0000.0000.0000.000
219C240ALA00.0330.02221.4610.0050.0050.0000.0000.0000.000
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221C242ASP-1-0.753-0.84724.6470.1270.1270.0000.0000.0000.000
222C243TYR0-0.069-0.05428.371-0.003-0.0030.0000.0000.0000.000
223C244TRP0-0.003-0.00825.6310.0020.0020.0000.0000.0000.000
224C245GLY00.0580.03531.073-0.004-0.0040.0000.0000.0000.000
225C246GLN0-0.035-0.03033.6020.0050.0050.0000.0000.0000.000
226C247GLY00.002-0.01033.4020.0000.0000.0000.0000.0000.000
227C248THR0-0.034-0.01733.614-0.002-0.0020.0000.0000.0000.000
228C249SER0-0.035-0.01533.6660.0030.0030.0000.0000.0000.000
229C250VAL00.0630.03432.823-0.002-0.0020.0000.0000.0000.000
230C251THR0-0.041-0.02934.7270.0000.0000.0000.0000.0000.000
231C252VAL00.0140.02133.530-0.001-0.0010.0000.0000.0000.000
232C253SER0-0.042-0.03036.735-0.005-0.0050.0000.0000.0000.000