FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: ZYLMN

Calculation Name: 2WGL-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WGL

Chain ID: C

ChEMBL ID:

UniProt ID: Q09065

Base Structure: X-ray

Registration Date: 2023-03-14

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2493655.556297
FMO2-HF: Nuclear repulsion 2410665.107431
FMO2-HF: Total energy -82990.448866
FMO2-MP2: Total energy -83231.543706


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:25:ASN)


Summations of interaction energy for fragment #1(C:25:ASN)
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.
-0.7682.8910.125-1.708-2.0750.003
Interaction energy analysis for fragmet #1(C:25:ASN)
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 : 0.000
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].
3C27ALA0-0.025-0.0192.9020.2823.5260.124-1.669-1.6990.003
4C28HIS0-0.016-0.0054.3770.3920.6620.002-0.035-0.2360.000
5C29VAL0-0.022-0.0116.7080.5640.5640.0000.0000.0000.000
6C30ASP-1-0.815-0.9027.8170.4690.4690.0000.0000.0000.000
7C31ASN00.027-0.0129.555-0.327-0.3270.0000.0000.0000.000
8C32GLU-1-0.856-0.90911.5630.3740.3740.0000.0000.0000.000
9C33PHE0-0.033-0.01214.051-0.036-0.0360.0000.0000.0000.000
10C34LEU00.0320.02311.0950.0120.0120.0000.0000.0000.000
11C35ILE00.003-0.00714.3810.0160.0160.0000.0000.0000.000
12C36LEU0-0.031-0.00816.6680.0160.0160.0000.0000.0000.000
13C37GLN00.0160.00815.711-0.017-0.0170.0000.0000.0000.000
14C38VAL0-0.049-0.02816.470-0.012-0.0120.0000.0000.0000.000
15C39ASN0-0.082-0.07319.3130.0340.0340.0000.0000.0000.000
16C40ASP-1-0.833-0.90622.311-0.145-0.1450.0000.0000.0000.000
17C41ALA0-0.045-0.02524.286-0.003-0.0030.0000.0000.0000.000
18C42VAL0-0.055-0.02725.254-0.004-0.0040.0000.0000.0000.000
19C43PHE00.0250.02618.250-0.034-0.0340.0000.0000.0000.000
20C44PRO00.0150.02822.0200.0320.0320.0000.0000.0000.000
21C45ILE0-0.044-0.02422.562-0.007-0.0070.0000.0000.0000.000
22C46GLY00.011-0.00625.2170.0090.0090.0000.0000.0000.000
23C47SER0-0.029-0.02929.0390.0060.0060.0000.0000.0000.000
24C48TYR00.0130.00826.1770.0140.0140.0000.0000.0000.000
25C49THR00.003-0.01431.4840.0010.0010.0000.0000.0000.000
26C50HIS10.8130.89830.625-0.027-0.0270.0000.0000.0000.000
27C51SER00.0330.02135.8100.0050.0050.0000.0000.0000.000
28C52PHE00.009-0.00337.122-0.001-0.0010.0000.0000.0000.000
29C53GLY00.0340.03540.0050.0010.0010.0000.0000.0000.000
30C54LEU0-0.0460.00141.2240.0050.0050.0000.0000.0000.000
31C55GLU-1-0.848-0.92643.150-0.013-0.0130.0000.0000.0000.000
32C56THR00.0500.01645.6420.0010.0010.0000.0000.0000.000
33C57TYR0-0.012-0.00945.3210.0020.0020.0000.0000.0000.000
34C58ILE00.0100.02445.1020.0010.0010.0000.0000.0000.000
35C59GLN0-0.036-0.02048.3630.0020.0020.0000.0000.0000.000
36C60GLN0-0.010-0.00651.731-0.003-0.0030.0000.0000.0000.000
37C61LYS10.8480.91152.7470.0040.0040.0000.0000.0000.000
38C62LYS10.9050.95650.478-0.019-0.0190.0000.0000.0000.000
39C63VAL0-0.0040.00245.3370.0030.0030.0000.0000.0000.000
40C64THR0-0.007-0.01048.769-0.003-0.0030.0000.0000.0000.000
41C65ASN00.0510.04949.048-0.001-0.0010.0000.0000.0000.000
42C66LYS10.9060.94344.586-0.026-0.0260.0000.0000.0000.000
43C67GLU-1-0.840-0.90745.2830.0290.0290.0000.0000.0000.000
44C68SER00.035-0.00846.5710.0030.0030.0000.0000.0000.000
45C69ALA00.0210.00843.2040.0020.0020.0000.0000.0000.000
46C70LEU0-0.0070.00440.6700.0030.0030.0000.0000.0000.000
47C71GLU-1-0.790-0.89142.0590.0670.0670.0000.0000.0000.000
48C72TYR0-0.022-0.02140.6230.0050.0050.0000.0000.0000.000
49C73LEU0-0.008-0.00937.3460.0030.0030.0000.0000.0000.000
50C74LYS10.8150.89438.684-0.061-0.0610.0000.0000.0000.000
51C75ALA00.0170.03439.6250.0080.0080.0000.0000.0000.000
52C76ASN00.0020.01536.6130.0050.0050.0000.0000.0000.000
53C77LEU0-0.025-0.02533.3850.0060.0060.0000.0000.0000.000
54C78SER0-0.038-0.04735.2860.0110.0110.0000.0000.0000.000
55C79SER00.014-0.01137.6520.0040.0040.0000.0000.0000.000
56C80GLN0-0.002-0.00736.2290.0030.0030.0000.0000.0000.000
57C81PHE0-0.021-0.00829.4630.0050.0050.0000.0000.0000.000
58C82LEU00.0240.01232.1030.0100.0100.0000.0000.0000.000
59C83TYR00.0470.02032.0890.0150.0150.0000.0000.0000.000
60C84THR00.0460.03831.8410.0060.0060.0000.0000.0000.000
61C85GLU-1-0.818-0.88929.0240.0720.0720.0000.0000.0000.000
62C86MET0-0.029-0.00827.6240.0100.0100.0000.0000.0000.000
63C87LEU00.0280.02627.2320.0300.0300.0000.0000.0000.000
64C88SER0-0.018-0.02427.4690.0230.0230.0000.0000.0000.000
65C89LEU0-0.040-0.00521.8770.0240.0240.0000.0000.0000.000
66C90LYS10.7950.89522.909-0.291-0.2910.0000.0000.0000.000
67C91LEU00.0350.02723.4680.0440.0440.0000.0000.0000.000
68C92THR0-0.081-0.05421.6160.0340.0340.0000.0000.0000.000
69C93TYR0-0.012-0.01616.6150.0480.0480.0000.0000.0000.000
70C94GLU-1-0.817-0.91818.9480.4900.4900.0000.0000.0000.000
71C95SER0-0.037-0.02320.4460.0440.0440.0000.0000.0000.000
72C96ALA0-0.007-0.00616.6310.0140.0140.0000.0000.0000.000
73C97LEU0-0.0060.00314.5550.1000.1000.0000.0000.0000.000
74C98GLN0-0.031-0.00716.5930.0330.0330.0000.0000.0000.000
75C99GLN0-0.021-0.01013.995-0.042-0.0420.0000.0000.0000.000
76C100ASP-1-0.781-0.86817.9010.2740.2740.0000.0000.0000.000
77C101LEU00.009-0.01219.494-0.033-0.0330.0000.0000.0000.000
78C102LYS10.9330.97221.700-0.226-0.2260.0000.0000.0000.000
79C103LYS10.8260.88524.476-0.411-0.4110.0000.0000.0000.000
80C104ILE0-0.0220.00819.598-0.025-0.0250.0000.0000.0000.000
81C105LEU0-0.012-0.00623.468-0.031-0.0310.0000.0000.0000.000
82C106GLY0-0.0010.00625.958-0.023-0.0230.0000.0000.0000.000
83C107VAL00.0210.01126.578-0.017-0.0170.0000.0000.0000.000
84C108GLU-1-0.729-0.80323.9370.0870.0870.0000.0000.0000.000
85C109GLU-1-0.907-0.93928.3040.0700.0700.0000.0000.0000.000
86C110VAL00.0300.00731.325-0.012-0.0120.0000.0000.0000.000
87C111ILE00.0370.02428.821-0.009-0.0090.0000.0000.0000.000
88C112MET0-0.098-0.02132.015-0.014-0.0140.0000.0000.0000.000
89C113LEU0-0.017-0.02433.644-0.009-0.0090.0000.0000.0000.000
90C114SER0-0.031-0.01435.8050.0000.0000.0000.0000.0000.000
91C115THR0-0.096-0.04434.572-0.002-0.0020.0000.0000.0000.000
92C116SER0-0.039-0.01737.074-0.008-0.0080.0000.0000.0000.000
93C117PRO00.0570.00940.2150.0030.0030.0000.0000.0000.000
94C118MET00.0340.03539.0790.0030.0030.0000.0000.0000.000
95C119GLU-1-0.867-0.94737.837-0.017-0.0170.0000.0000.0000.000
96C120LEU0-0.0020.00735.401-0.008-0.0080.0000.0000.0000.000
97C121ARG10.8890.93133.538-0.008-0.0080.0000.0000.0000.000
98C122LEU0-0.008-0.00933.116-0.003-0.0030.0000.0000.0000.000
99C123ALA0-0.055-0.02232.598-0.012-0.0120.0000.0000.0000.000
100C124ASN00.0540.02330.562-0.016-0.0160.0000.0000.0000.000
101C125GLN00.0170.01428.724-0.005-0.0050.0000.0000.0000.000
102C126LYS10.9060.95427.6940.0760.0760.0000.0000.0000.000
103C127LEU0-0.012-0.00426.786-0.019-0.0190.0000.0000.0000.000
104C128GLY00.0570.03024.190-0.011-0.0110.0000.0000.0000.000
105C129ASN0-0.010-0.00622.822-0.029-0.0290.0000.0000.0000.000
106C130ARG10.8540.92522.5910.2010.2010.0000.0000.0000.000
107C131PHE00.0250.02918.120-0.052-0.0520.0000.0000.0000.000
108C132ILE00.0120.00917.985-0.046-0.0460.0000.0000.0000.000
109C133LYS10.8650.92517.7570.1780.1780.0000.0000.0000.000
110C134THR0-0.037-0.02919.022-0.067-0.0670.0000.0000.0000.000
111C135LEU0-0.008-0.00514.093-0.074-0.0740.0000.0000.0000.000
112C136GLN00.0140.00014.382-0.078-0.0780.0000.0000.0000.000
113C137ALA0-0.0170.00615.330-0.091-0.0910.0000.0000.0000.000
114C138MET0-0.065-0.01513.745-0.051-0.0510.0000.0000.0000.000
115C139ASN0-0.016-0.02912.148-0.274-0.2740.0000.0000.0000.000
116C140GLU-1-0.921-0.9419.306-2.067-2.0670.0000.0000.0000.000
117C141LEU0-0.058-0.0227.796-0.809-0.8090.0000.0000.0000.000
118C142ASP-1-0.846-0.9184.752-0.853-0.708-0.001-0.004-0.1400.000
119C143MET0-0.053-0.0156.7380.5030.5030.0000.0000.0000.000
120C144GLY00.0610.0337.6660.4850.4850.0000.0000.0000.000
121C145GLU-1-0.929-0.9708.533-0.123-0.1230.0000.0000.0000.000
122C146PHE0-0.0090.00611.234-0.129-0.1290.0000.0000.0000.000
123C147PHE00.0640.02812.211-0.121-0.1210.0000.0000.0000.000
124C148ASN0-0.002-0.01211.028-0.135-0.1350.0000.0000.0000.000
125C149ALA0-0.011-0.01014.464-0.036-0.0360.0000.0000.0000.000
126C150TYR0-0.022-0.04816.745-0.024-0.0240.0000.0000.0000.000
127C151ALA0-0.017-0.01016.855-0.028-0.0280.0000.0000.0000.000
128C152GLN0-0.047-0.01418.063-0.034-0.0340.0000.0000.0000.000
129C153LYS10.8540.92520.460-0.072-0.0720.0000.0000.0000.000
130C154THR0-0.023-0.03422.0320.0060.0060.0000.0000.0000.000
131C155LYS10.8440.92024.101-0.081-0.0810.0000.0000.0000.000
132C156ASP-1-0.818-0.91027.680-0.006-0.0060.0000.0000.0000.000
133C157PRO00.0090.03523.5340.0160.0160.0000.0000.0000.000
134C158THR00.006-0.02025.115-0.016-0.0160.0000.0000.0000.000
135C159HIS00.007-0.00522.7900.0010.0010.0000.0000.0000.000
136C160ALA00.0350.02423.1790.0090.0090.0000.0000.0000.000
137C161THR0-0.001-0.00923.1790.0230.0230.0000.0000.0000.000
138C162SER00.0420.00320.0990.0330.0330.0000.0000.0000.000
139C163TYR0-0.061-0.02718.6670.0170.0170.0000.0000.0000.000
140C164GLY00.0470.02418.4990.0490.0490.0000.0000.0000.000
141C165VAL00.008-0.00315.9760.0930.0930.0000.0000.0000.000
142C166PHE00.0060.00013.8530.1230.1230.0000.0000.0000.000
143C167ALA00.0140.00513.6340.0990.0990.0000.0000.0000.000
144C168ALA0-0.0110.00014.0300.1520.1520.0000.0000.0000.000
145C169SER0-0.056-0.04611.2590.2380.2380.0000.0000.0000.000
146C170LEU0-0.0070.0088.6450.3000.3000.0000.0000.0000.000
147C171GLY0-0.0010.0079.8630.2280.2280.0000.0000.0000.000
148C172ILE0-0.033-0.00511.562-0.072-0.0720.0000.0000.0000.000
149C173GLU-1-0.757-0.88014.1680.4720.4720.0000.0000.0000.000
150C174LEU00.0660.04117.437-0.095-0.0950.0000.0000.0000.000
151C175LYS10.8620.89220.173-0.420-0.4200.0000.0000.0000.000
152C176LYS10.7430.87216.847-0.394-0.3940.0000.0000.0000.000
153C177ALA00.0350.02018.363-0.065-0.0650.0000.0000.0000.000
154C178LEU00.0270.01920.051-0.066-0.0660.0000.0000.0000.000
155C179ARG10.8480.92221.568-0.387-0.3870.0000.0000.0000.000
156C180HIS0-0.023-0.01020.2610.0010.0010.0000.0000.0000.000
157C181TYR00.021-0.00323.071-0.033-0.0330.0000.0000.0000.000
158C182LEU0-0.0040.00224.504-0.028-0.0280.0000.0000.0000.000
159C183TYR00.0080.01826.800-0.018-0.0180.0000.0000.0000.000
160C184ALA00.0560.03325.350-0.018-0.0180.0000.0000.0000.000
161C185GLN00.0370.02326.091-0.027-0.0270.0000.0000.0000.000
162C186THR0-0.008-0.02229.769-0.008-0.0080.0000.0000.0000.000
163C187SER0-0.0230.00030.390-0.009-0.0090.0000.0000.0000.000
164C188ASN0-0.002-0.00431.2200.0000.0000.0000.0000.0000.000
165C189MET00.0260.01832.835-0.005-0.0050.0000.0000.0000.000
166C190VAL00.0070.01635.589-0.003-0.0030.0000.0000.0000.000
167C191ILE0-0.001-0.00534.620-0.005-0.0050.0000.0000.0000.000
168C192ASN0-0.011-0.00737.2070.0000.0000.0000.0000.0000.000
169C193CYS00.0130.01239.0150.0000.0000.0000.0000.0000.000
170C194VAL0-0.037-0.02439.975-0.002-0.0020.0000.0000.0000.000
171C195LYS10.9230.95836.9720.0550.0550.0000.0000.0000.000
172C196SER0-0.028-0.02042.483-0.005-0.0050.0000.0000.0000.000
173C197VAL0-0.0600.00245.0300.0010.0010.0000.0000.0000.000
174C198PRO0-0.0100.01046.0600.0000.0000.0000.0000.0000.000
175C199LEU0-0.026-0.02742.9880.0050.0050.0000.0000.0000.000
176C200SER0-0.010-0.03745.072-0.006-0.0060.0000.0000.0000.000
177C201GLN00.0900.01739.8810.0040.0040.0000.0000.0000.000
178C202ASN00.0370.01640.5090.0020.0020.0000.0000.0000.000
179C203ASP-1-0.818-0.88042.1150.0150.0150.0000.0000.0000.000
180C204GLY00.0870.04539.6620.0060.0060.0000.0000.0000.000
181C205GLN0-0.019-0.00636.1570.0090.0090.0000.0000.0000.000
182C206LYS10.8240.90138.551-0.004-0.0040.0000.0000.0000.000
183C207ILE0-0.0080.01438.5990.0080.0080.0000.0000.0000.000
184C208LEU00.0260.00633.2900.0080.0080.0000.0000.0000.000
185C209LEU00.0030.00935.8050.0100.0100.0000.0000.0000.000
186C210SER0-0.062-0.05037.4970.0090.0090.0000.0000.0000.000
187C211LEU0-0.012-0.00435.5860.0050.0050.0000.0000.0000.000
188C212GLN00.0110.01132.9900.0020.0020.0000.0000.0000.000
189C213SER0-0.022-0.00933.7020.0160.0160.0000.0000.0000.000
190C214PRO00.004-0.01035.1630.0110.0110.0000.0000.0000.000
191C215PHE00.0290.00330.7210.0060.0060.0000.0000.0000.000
192C216ASN00.002-0.00530.0540.0300.0300.0000.0000.0000.000
193C217GLN00.0170.01731.7590.0090.0090.0000.0000.0000.000
194C218LEU00.0150.01132.3890.0050.0050.0000.0000.0000.000
195C219ILE0-0.0160.01126.5340.0090.0090.0000.0000.0000.000
196C220GLU-1-0.807-0.89229.1280.3200.3200.0000.0000.0000.000
197C221LYS10.9280.97031.049-0.153-0.1530.0000.0000.0000.000
198C222THR0-0.030-0.04127.602-0.005-0.0050.0000.0000.0000.000
199C223LEU0-0.038-0.03025.2930.0190.0190.0000.0000.0000.000
200C224GLU-1-0.980-0.97628.9070.2170.2170.0000.0000.0000.000
201C225LEU0-0.040-0.01031.129-0.017-0.0170.0000.0000.0000.000
202C226ASP-1-0.791-0.88130.2440.2460.2460.0000.0000.0000.000
203C227GLU-1-0.852-0.95628.7810.2690.2690.0000.0000.0000.000
204C228SER0-0.139-0.08432.001-0.023-0.0230.0000.0000.0000.000
205C229HIS00.0290.01234.524-0.011-0.0110.0000.0000.0000.000
206C230LEU00.0000.01530.603-0.009-0.0090.0000.0000.0000.000
207C231CYS0-0.049-0.03434.003-0.009-0.0090.0000.0000.0000.000
208C232THR0-0.077-0.03636.056-0.011-0.0110.0000.0000.0000.000
209C233ALA0-0.0230.00038.538-0.005-0.0050.0000.0000.0000.000