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: N96GQ

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 OptHSide
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 -2875268.016571
FMO2-HF: Nuclear repulsion 2784526.603441
FMO2-HF: Total energy -90741.41313
FMO2-MP2: Total energy -91005.882885


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.
-2.1430.786-0.025-1.409-1.493-0.003
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 : -0.031 / q_NPA : -0.036
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].
3C0ALA0-0.0110.0033.547-1.5981.284-0.024-1.407-1.450-0.003
4C1ASP-1-0.846-0.9225.3960.3200.367-0.001-0.002-0.0430.000
5C2ILE0-0.040-0.0029.2090.0310.0310.0000.0000.0000.000
6C3VAL0-0.009-0.00510.932-0.046-0.0460.0000.0000.0000.000
7C4LEU00.000-0.00713.8220.0410.0410.0000.0000.0000.000
8C5THR0-0.006-0.01616.787-0.040-0.0400.0000.0000.0000.000
9C6GLN00.015-0.01319.3390.0120.0120.0000.0000.0000.000
10C7THR0-0.0610.00622.854-0.012-0.0120.0000.0000.0000.000
11C8PRO00.0690.03325.7350.0070.0070.0000.0000.0000.000
12C9SER00.0460.01227.2420.0020.0020.0000.0000.0000.000
13C10SER00.009-0.02228.529-0.001-0.0010.0000.0000.0000.000
14C11LEU0-0.064-0.03331.5670.0020.0020.0000.0000.0000.000
15C12PRO00.0080.01234.2880.0000.0000.0000.0000.0000.000
16C13VAL0-0.005-0.01436.8670.0020.0020.0000.0000.0000.000
17C14SER00.0190.01339.695-0.005-0.0050.0000.0000.0000.000
18C15VAL0-0.034-0.04442.1000.0030.0030.0000.0000.0000.000
19C16GLY0-0.036-0.01742.920-0.002-0.0020.0000.0000.0000.000
20C17GLU-1-0.854-0.91139.9540.0770.0770.0000.0000.0000.000
21C18LYS10.9570.98434.875-0.108-0.1080.0000.0000.0000.000
22C19VAL0-0.0030.00133.1690.0000.0000.0000.0000.0000.000
23C20THR0-0.016-0.02528.9110.0020.0020.0000.0000.0000.000
24C21MET0-0.0360.00827.209-0.002-0.0020.0000.0000.0000.000
25C22THR00.008-0.00922.4800.0090.0090.0000.0000.0000.000
26C23CYS0-0.061-0.01319.914-0.005-0.0050.0000.0000.0000.000
27C24LYS10.8590.91617.080-0.329-0.3290.0000.0000.0000.000
28C25SER00.002-0.01512.722-0.042-0.0420.0000.0000.0000.000
29C26SER00.0110.01210.0560.0350.0350.0000.0000.0000.000
30C27GLN00.003-0.0046.3260.2140.2140.0000.0000.0000.000
31C28THR00.0080.0089.697-0.254-0.2540.0000.0000.0000.000
32C29LEU0-0.015-0.01211.119-0.001-0.0010.0000.0000.0000.000
33C30LEU0-0.042-0.00313.816-0.069-0.0690.0000.0000.0000.000
34C31TYR00.0120.00912.2160.0830.0830.0000.0000.0000.000
35C32SER00.028-0.00213.802-0.042-0.0420.0000.0000.0000.000
36C33ASN0-0.026-0.00714.963-0.037-0.0370.0000.0000.0000.000
37C34ASN00.015-0.01317.582-0.008-0.0080.0000.0000.0000.000
38C35GLN00.0000.00518.1720.0140.0140.0000.0000.0000.000
39C36LYS10.8590.93718.816-0.210-0.2100.0000.0000.0000.000
40C37ASN00.030-0.00317.4730.0790.0790.0000.0000.0000.000
41C38TYR0-0.0190.00115.604-0.038-0.0380.0000.0000.0000.000
42C39LEU0-0.013-0.00317.2230.0050.0050.0000.0000.0000.000
43C40ALA0-0.001-0.00719.474-0.016-0.0160.0000.0000.0000.000
44C41TRP00.008-0.00622.6330.0030.0030.0000.0000.0000.000
45C42TYR0-0.034-0.05723.169-0.006-0.0060.0000.0000.0000.000
46C43GLN00.0110.00227.632-0.002-0.0020.0000.0000.0000.000
47C44GLN0-0.017-0.02230.8750.0020.0020.0000.0000.0000.000
48C45LYS10.8930.95432.604-0.087-0.0870.0000.0000.0000.000
49C46PRO00.0410.00536.2560.0000.0000.0000.0000.0000.000
50C47GLY00.0100.00937.524-0.003-0.0030.0000.0000.0000.000
51C48GLN0-0.042-0.01137.1250.0000.0000.0000.0000.0000.000
52C49SER00.0290.02932.9820.0020.0020.0000.0000.0000.000
53C50PRO0-0.009-0.01028.918-0.002-0.0020.0000.0000.0000.000
54C51LYS10.8940.95031.268-0.096-0.0960.0000.0000.0000.000
55C52LEU0-0.0020.00926.4170.0020.0020.0000.0000.0000.000
56C53LEU0-0.035-0.00128.839-0.007-0.0070.0000.0000.0000.000
57C54ILE0-0.011-0.01125.662-0.005-0.0050.0000.0000.0000.000
58C55SER00.0280.02524.1720.0060.0060.0000.0000.0000.000
59C56TRP0-0.032-0.02919.3020.0020.0020.0000.0000.0000.000
60C57ALA00.0230.02721.2290.0050.0050.0000.0000.0000.000
61C58PHE0-0.044-0.04623.092-0.010-0.0100.0000.0000.0000.000
62C59THR0-0.0120.00926.560-0.014-0.0140.0000.0000.0000.000
63C60ARG10.8990.95928.399-0.116-0.1160.0000.0000.0000.000
64C61LYS10.9340.97530.860-0.109-0.1090.0000.0000.0000.000
65C62SER00.013-0.01132.138-0.004-0.0040.0000.0000.0000.000
66C63GLY00.0230.00935.702-0.001-0.0010.0000.0000.0000.000
67C64VAL0-0.054-0.01332.968-0.003-0.0030.0000.0000.0000.000
68C65PRO00.013-0.00236.0860.0010.0010.0000.0000.0000.000
69C66ASP-1-0.898-0.95736.0480.0970.0970.0000.0000.0000.000
70C67ARG10.7770.85436.611-0.086-0.0860.0000.0000.0000.000
71C68PHE0-0.0120.00432.2800.0030.0030.0000.0000.0000.000
72C69THR00.009-0.00830.5520.0000.0000.0000.0000.0000.000
73C70GLY00.0140.02327.0680.0020.0020.0000.0000.0000.000
74C71SER00.0260.00126.062-0.008-0.0080.0000.0000.0000.000
75C72GLY00.0160.00822.5870.0050.0050.0000.0000.0000.000
76C73SER0-0.006-0.01919.8110.0000.0000.0000.0000.0000.000
77C74GLY00.0490.03815.5050.0090.0090.0000.0000.0000.000
78C75THR00.0220.00512.9460.0430.0430.0000.0000.0000.000
79C76ASP-1-0.827-0.88115.6020.3360.3360.0000.0000.0000.000
80C77PHE00.0270.01116.639-0.015-0.0150.0000.0000.0000.000
81C78THR0-0.014-0.00821.759-0.009-0.0090.0000.0000.0000.000
82C79LEU0-0.032-0.00525.3730.0000.0000.0000.0000.0000.000
83C80THR0-0.006-0.00828.105-0.007-0.0070.0000.0000.0000.000
84C81ILE0-0.0030.00731.659-0.001-0.0010.0000.0000.0000.000
85C82GLY0-0.020-0.01134.946-0.003-0.0030.0000.0000.0000.000
86C83SER00.002-0.00637.745-0.004-0.0040.0000.0000.0000.000
87C84VAL00.0140.01837.141-0.001-0.0010.0000.0000.0000.000
88C85LYS10.9130.94639.811-0.082-0.0820.0000.0000.0000.000
89C86ALA00.0560.01540.9020.0020.0020.0000.0000.0000.000
90C87GLU-1-0.860-0.92340.3010.0830.0830.0000.0000.0000.000
91C88ASP-1-0.725-0.82136.7670.0940.0940.0000.0000.0000.000
92C89LEU0-0.0040.03236.2360.0060.0060.0000.0000.0000.000
93C90ALA00.004-0.00234.136-0.003-0.0030.0000.0000.0000.000
94C91VAL0-0.017-0.00128.9160.0010.0010.0000.0000.0000.000
95C92TYR0-0.011-0.02128.4550.0020.0020.0000.0000.0000.000
96C93TYR00.0000.00524.2040.0000.0000.0000.0000.0000.000
97C95GLN0-0.010-0.02818.350-0.004-0.0040.0000.0000.0000.000
98C96GLN00.0650.04012.9770.0180.0180.0000.0000.0000.000
99C97TYR00.005-0.00916.277-0.013-0.0130.0000.0000.0000.000
100C98SER0-0.010-0.00411.823-0.020-0.0200.0000.0000.0000.000
101C99ASN00.0150.0037.700-0.057-0.0570.0000.0000.0000.000
102C100TYR0-0.073-0.02110.532-0.001-0.0010.0000.0000.0000.000
103C101PRO00.022-0.0029.7730.0080.0080.0000.0000.0000.000
104C102TRP00.0350.00313.302-0.008-0.0080.0000.0000.0000.000
105C103THR0-0.029-0.02214.223-0.012-0.0120.0000.0000.0000.000
106C104PHE0-0.004-0.01916.8890.0030.0030.0000.0000.0000.000
107C105GLY00.0480.03519.2000.0070.0070.0000.0000.0000.000
108C106GLY0-0.036-0.03920.758-0.013-0.0130.0000.0000.0000.000
109C107GLY0-0.035-0.02523.375-0.012-0.0120.0000.0000.0000.000
110C108THR0-0.029-0.02326.0230.0020.0020.0000.0000.0000.000
111C109ARG10.8130.88428.775-0.083-0.0830.0000.0000.0000.000
112C110LEU0-0.0180.01432.250-0.002-0.0020.0000.0000.0000.000
113C111GLU-1-0.830-0.89534.9700.0780.0780.0000.0000.0000.000
114C112ILE00.0430.03838.4230.0000.0000.0000.0000.0000.000
115C135GLU-1-0.881-0.95238.5650.0810.0810.0000.0000.0000.000
116C136VAL0-0.049-0.01433.393-0.001-0.0010.0000.0000.0000.000
117C137GLN0-0.021-0.01036.831-0.001-0.0010.0000.0000.0000.000
118C138LEU0-0.003-0.01530.8470.0000.0000.0000.0000.0000.000
119C139GLN0-0.038-0.01935.327-0.002-0.0020.0000.0000.0000.000
120C140GLN00.013-0.02332.3800.0040.0040.0000.0000.0000.000
121C141SER00.0440.04136.422-0.002-0.0020.0000.0000.0000.000
122C142GLY0-0.001-0.00137.9060.0020.0020.0000.0000.0000.000
123C143PRO0-0.043-0.02638.5250.0020.0020.0000.0000.0000.000
124C144GLU-1-0.876-0.94136.7940.0550.0550.0000.0000.0000.000
125C145VAL0-0.027-0.00938.1310.0020.0020.0000.0000.0000.000
126C146VAL00.0300.01536.190-0.002-0.0020.0000.0000.0000.000
127C147LYS10.9910.99638.995-0.035-0.0350.0000.0000.0000.000
128C148THR00.0480.02535.0400.0030.0030.0000.0000.0000.000
129C149GLY0-0.032-0.00634.631-0.003-0.0030.0000.0000.0000.000
130C150ALA0-0.041-0.00235.5870.0000.0000.0000.0000.0000.000
131C151SER0-0.008-0.02633.7990.0050.0050.0000.0000.0000.000
132C152VAL00.0070.01332.618-0.003-0.0030.0000.0000.0000.000
133C153LYS10.9370.97432.794-0.065-0.0650.0000.0000.0000.000
134C154ILE00.0040.02231.012-0.003-0.0030.0000.0000.0000.000
135C155SER00.017-0.00432.8390.0030.0030.0000.0000.0000.000
136C156CYS0-0.0160.00327.8360.0060.0060.0000.0000.0000.000
137C157LYS10.9310.99534.017-0.063-0.0630.0000.0000.0000.000
138C158ALA00.0110.00933.5060.0010.0010.0000.0000.0000.000
139C159SER0-0.024-0.02535.618-0.005-0.0050.0000.0000.0000.000
140C160GLY00.0520.02237.4750.0030.0030.0000.0000.0000.000
141C161TYR0-0.024-0.01730.9960.0020.0020.0000.0000.0000.000
142C162SER00.0110.00933.688-0.002-0.0020.0000.0000.0000.000
143C163PHE00.0710.02731.4210.0050.0050.0000.0000.0000.000
144C164THR00.030-0.00430.1810.0060.0060.0000.0000.0000.000
145C165GLY0-0.0200.00728.7720.0030.0030.0000.0000.0000.000
146C166TYR0-0.112-0.08726.7510.0030.0030.0000.0000.0000.000
147C167PHE0-0.0120.00720.735-0.003-0.0030.0000.0000.0000.000
148C168ILE0-0.011-0.00724.991-0.005-0.0050.0000.0000.0000.000
149C169ASN00.009-0.02421.5050.0190.0190.0000.0000.0000.000
150C170TRP00.0400.01923.330-0.012-0.0120.0000.0000.0000.000
151C171VAL0-0.029-0.02323.1780.0110.0110.0000.0000.0000.000
152C172LYS10.8920.95624.245-0.112-0.1120.0000.0000.0000.000
153C173LYS10.8780.93625.502-0.106-0.1060.0000.0000.0000.000
154C174ASN00.018-0.00628.000-0.003-0.0030.0000.0000.0000.000
155C175SER00.0310.00829.8730.0030.0030.0000.0000.0000.000
156C176GLY0-0.009-0.01331.249-0.002-0.0020.0000.0000.0000.000
157C177LYS10.9740.99725.990-0.089-0.0890.0000.0000.0000.000
158C178SER00.0310.02922.532-0.004-0.0040.0000.0000.0000.000
159C179PRO0-0.055-0.02423.844-0.004-0.0040.0000.0000.0000.000
160C180GLU-1-0.830-0.88820.7320.1510.1510.0000.0000.0000.000
161C181TRP00.0090.01115.595-0.005-0.0050.0000.0000.0000.000
162C182ILE0-0.014-0.00518.8900.0110.0110.0000.0000.0000.000
163C183GLY00.0620.01018.8590.0130.0130.0000.0000.0000.000
164C184HIS0-0.074-0.00118.246-0.003-0.0030.0000.0000.0000.000
165C185ILE00.0190.01220.8270.0090.0090.0000.0000.0000.000
166C186SER00.0040.01122.167-0.008-0.0080.0000.0000.0000.000
167C187SER0-0.013-0.02923.838-0.005-0.0050.0000.0000.0000.000
168C188SER0-0.010-0.00927.117-0.004-0.0040.0000.0000.0000.000
169C189TYR0-0.0010.00024.043-0.007-0.0070.0000.0000.0000.000
170C190ALA0-0.0190.00724.9860.0020.0020.0000.0000.0000.000
171C191THR0-0.020-0.00219.1750.0020.0020.0000.0000.0000.000
172C192SER00.004-0.00120.9110.0000.0000.0000.0000.0000.000
173C193THR0-0.0010.01114.8600.0130.0130.0000.0000.0000.000
174C194TYR00.0200.00416.929-0.022-0.0220.0000.0000.0000.000
175C195ASN00.0100.00115.1970.0450.0450.0000.0000.0000.000
176C196GLN00.0640.02413.139-0.001-0.0010.0000.0000.0000.000
177C197LYS10.8370.90015.254-0.159-0.1590.0000.0000.0000.000
178C198PHE0-0.013-0.02318.020-0.023-0.0230.0000.0000.0000.000
179C199LYS10.9781.01415.975-0.257-0.2570.0000.0000.0000.000
180C200ASN0-0.002-0.00419.869-0.001-0.0010.0000.0000.0000.000
181C201LYS10.7560.88222.908-0.096-0.0960.0000.0000.0000.000
182C202ALA00.019-0.00923.414-0.010-0.0100.0000.0000.0000.000
183C203ALA00.0110.01823.9680.0080.0080.0000.0000.0000.000
184C204PHE0-0.041-0.02121.407-0.009-0.0090.0000.0000.0000.000
185C205THR0-0.001-0.00526.594-0.004-0.0040.0000.0000.0000.000
186C206VAL0-0.009-0.00828.4520.0020.0020.0000.0000.0000.000
187C207ASP-1-0.775-0.84830.8930.0610.0610.0000.0000.0000.000
188C208THR00.001-0.01432.8380.0020.0020.0000.0000.0000.000
189C209SER0-0.029-0.01934.602-0.001-0.0010.0000.0000.0000.000
190C210SER0-0.061-0.05437.802-0.001-0.0010.0000.0000.0000.000
191C211SER0-0.030-0.01335.1360.0010.0010.0000.0000.0000.000
192C212THR00.0120.00534.7290.0020.0020.0000.0000.0000.000
193C213ALA0-0.0050.01129.3990.0010.0010.0000.0000.0000.000
194C214PHE0-0.015-0.04130.546-0.005-0.0050.0000.0000.0000.000
195C215MET00.0030.02326.7370.0100.0100.0000.0000.0000.000
196C216GLN0-0.039-0.02029.129-0.004-0.0040.0000.0000.0000.000
197C217LEU0-0.0110.00027.1200.0070.0070.0000.0000.0000.000
198C218ASN00.0390.02127.236-0.012-0.0120.0000.0000.0000.000
199C219SER00.044-0.00129.2750.0020.0020.0000.0000.0000.000
200C220LEU0-0.076-0.01230.5870.0010.0010.0000.0000.0000.000
201C221THR00.0540.01729.721-0.007-0.0070.0000.0000.0000.000
202C222SER00.0640.00732.2610.0020.0020.0000.0000.0000.000
203C223GLU-1-0.929-0.94826.4480.0750.0750.0000.0000.0000.000
204C224ASP-1-0.811-0.88027.6220.0910.0910.0000.0000.0000.000
205C225SER00.0210.04229.5820.0010.0010.0000.0000.0000.000
206C226ALA0-0.061-0.02329.6060.0030.0030.0000.0000.0000.000
207C227VAL0-0.0210.00131.319-0.004-0.0040.0000.0000.0000.000
208C228TYR00.003-0.02526.7550.0100.0100.0000.0000.0000.000
209C229TYR0-0.0160.00228.305-0.005-0.0050.0000.0000.0000.000
210C231VAL00.015-0.02425.734-0.004-0.0040.0000.0000.0000.000
211C232ARG10.8210.91226.466-0.108-0.1080.0000.0000.0000.000
212C233SER00.0400.02822.3820.0040.0040.0000.0000.0000.000
213C234GLY00.0250.02024.790-0.008-0.0080.0000.0000.0000.000
214C235ASN00.0060.00423.0630.0150.0150.0000.0000.0000.000
215C236TYR00.0440.01123.117-0.002-0.0020.0000.0000.0000.000
216C237GLU-1-0.766-0.88223.6600.1810.1810.0000.0000.0000.000
217C238GLU-1-0.839-0.87126.0230.1200.1200.0000.0000.0000.000
218C239TYR0-0.027-0.00515.694-0.003-0.0030.0000.0000.0000.000
219C240ALA00.0110.01121.8340.0050.0050.0000.0000.0000.000
220C241MET0-0.028-0.01321.078-0.013-0.0130.0000.0000.0000.000
221C242ASP-1-0.743-0.83324.7940.1250.1250.0000.0000.0000.000
222C243TYR0-0.040-0.02328.447-0.002-0.0020.0000.0000.0000.000
223C244TRP0-0.014-0.01025.5560.0020.0020.0000.0000.0000.000
224C245GLY00.0610.04030.954-0.005-0.0050.0000.0000.0000.000
225C246GLN0-0.030-0.02933.3610.0050.0050.0000.0000.0000.000
226C247GLY0-0.006-0.00933.1330.0000.0000.0000.0000.0000.000
227C248THR0-0.011-0.00733.331-0.003-0.0030.0000.0000.0000.000
228C249SER0-0.050-0.01733.6020.0040.0040.0000.0000.0000.000
229C250VAL00.0530.03132.755-0.003-0.0030.0000.0000.0000.000
230C251THR0-0.023-0.01634.4010.0020.0020.0000.0000.0000.000
231C252VAL0-0.012-0.00733.217-0.002-0.0020.0000.0000.0000.000
232C253SER0-0.056-0.05436.403-0.003-0.0030.0000.0000.0000.000