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: 821YY

Calculation Name: 2WA0-A-Xray372

Preferred Name: Melanoma-associated antigen 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2WA0

Chain ID: A

ChEMBL ID: CHEMBL4296022

UniProt ID: P43358

Base Structure: X-ray

Registration Date: 2023-06-21

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2612407.725113
FMO2-HF: Nuclear repulsion 2522215.587894
FMO2-HF: Total energy -90192.137219
FMO2-MP2: Total energy -90456.111369


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(A:-14:SER)


Summations of interaction energy for fragment #1(A:-14:SER)
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.
-0.9080.191-0.011-0.462-0.6270.002
Interaction energy analysis for fragmet #1(A:-14:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.023
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].
3A-12VAL0-0.012-0.0113.871-0.9190.180-0.011-0.462-0.6270.002
4A-11ASP-1-0.869-0.9386.7080.3160.3160.0000.0000.0000.000
5A-10LEU0-0.045-0.0267.847-0.238-0.2380.0000.0000.0000.000
6A-9GLY00.0050.02011.6800.0380.0380.0000.0000.0000.000
7A-8THR0-0.021-0.02715.476-0.051-0.0510.0000.0000.0000.000
8A-7GLU-1-0.876-0.92017.896-0.041-0.0410.0000.0000.0000.000
9A-6ASN0-0.066-0.04119.201-0.013-0.0130.0000.0000.0000.000
10A-5LEU0-0.037-0.01916.639-0.014-0.0140.0000.0000.0000.000
11A-4TYR0-0.0090.00620.044-0.023-0.0230.0000.0000.0000.000
12A-3PHE0-0.045-0.01423.2470.0170.0170.0000.0000.0000.000
13A-2GLN0-0.009-0.03323.2510.0030.0030.0000.0000.0000.000
14A-1SER00.0170.00525.8730.0080.0080.0000.0000.0000.000
15A0MET0-0.019-0.00829.1040.0000.0000.0000.0000.0000.000
16A101ASP-1-0.778-0.84231.055-0.093-0.0930.0000.0000.0000.000
17A102ALA00.0200.00731.187-0.003-0.0030.0000.0000.0000.000
18A103GLU-1-0.848-0.92133.326-0.097-0.0970.0000.0000.0000.000
19A104SER0-0.047-0.06636.5100.0010.0010.0000.0000.0000.000
20A105LEU00.0680.04133.4020.0000.0000.0000.0000.0000.000
21A106PHE0-0.012-0.00235.939-0.002-0.0020.0000.0000.0000.000
22A107ARG10.9360.95337.6650.0690.0690.0000.0000.0000.000
23A108GLU-1-0.919-0.95840.249-0.072-0.0720.0000.0000.0000.000
24A109ALA0-0.038-0.01138.1700.0020.0020.0000.0000.0000.000
25A110LEU0-0.017-0.02140.2930.0020.0020.0000.0000.0000.000
26A111SER00.005-0.00442.6350.0030.0030.0000.0000.0000.000
27A112ASN00.0040.00442.2760.0050.0050.0000.0000.0000.000
28A113LYS10.7900.87440.5900.1030.1030.0000.0000.0000.000
29A114VAL0-0.028-0.01144.5640.0010.0010.0000.0000.0000.000
30A115ASP-1-0.832-0.89447.935-0.063-0.0630.0000.0000.0000.000
31A116GLU-1-0.802-0.89043.663-0.094-0.0940.0000.0000.0000.000
32A117LEU0-0.036-0.02447.4830.0000.0000.0000.0000.0000.000
33A118ALA00.0460.02449.0970.0020.0020.0000.0000.0000.000
34A119HIS00.033-0.00250.7460.0040.0040.0000.0000.0000.000
35A120PHE0-0.121-0.03649.4180.0000.0000.0000.0000.0000.000
36A121LEU00.0220.00351.5640.0010.0010.0000.0000.0000.000
37A122LEU00.0210.01254.4870.0020.0020.0000.0000.0000.000
38A123ARG10.8330.89948.6670.0740.0740.0000.0000.0000.000
39A124LYS10.7780.87152.7480.0720.0720.0000.0000.0000.000
40A125TYR0-0.039-0.04556.5790.0010.0010.0000.0000.0000.000
41A126ARG10.8650.93855.6410.0560.0560.0000.0000.0000.000
42A127ALA00.0040.00558.2890.0020.0020.0000.0000.0000.000
43A128LYS10.8520.93260.2450.0480.0480.0000.0000.0000.000
44A129GLU-1-0.895-0.92255.138-0.067-0.0670.0000.0000.0000.000
45A130LEU0-0.005-0.00257.9580.0000.0000.0000.0000.0000.000
46A131VAL00.0070.00252.217-0.002-0.0020.0000.0000.0000.000
47A132THR00.0200.01350.3450.0000.0000.0000.0000.0000.000
48A133LYS10.9490.96746.9630.0820.0820.0000.0000.0000.000
49A134ALA00.0010.00046.104-0.004-0.0040.0000.0000.0000.000
50A135GLU-1-0.743-0.85945.582-0.081-0.0810.0000.0000.0000.000
51A136MET0-0.0110.02146.109-0.003-0.0030.0000.0000.0000.000
52A137LEU0-0.0030.00242.606-0.003-0.0030.0000.0000.0000.000
53A138GLU-1-0.789-0.88440.022-0.137-0.1370.0000.0000.0000.000
54A139ARG10.8470.91141.8180.0790.0790.0000.0000.0000.000
55A140VAL00.0230.03044.0530.0030.0030.0000.0000.0000.000
56A141ILE0-0.016-0.00941.451-0.003-0.0030.0000.0000.0000.000
57A142LYS10.8200.91036.3910.1320.1320.0000.0000.0000.000
58A143ASN00.022-0.00434.129-0.003-0.0030.0000.0000.0000.000
59A144TYR00.0320.01135.507-0.003-0.0030.0000.0000.0000.000
60A145LYS10.8450.93037.9980.1360.1360.0000.0000.0000.000
61A146ARG10.8240.89434.8030.1420.1420.0000.0000.0000.000
62A147CYS0-0.019-0.00540.0950.0040.0040.0000.0000.0000.000
63A148PHE00.0520.01342.5120.0050.0050.0000.0000.0000.000
64A149PRO00.0150.00045.3100.0040.0040.0000.0000.0000.000
65A150VAL00.0110.01445.3670.0040.0040.0000.0000.0000.000
66A151ILE0-0.007-0.00642.5180.0030.0030.0000.0000.0000.000
67A152PHE00.0550.01347.2000.0030.0030.0000.0000.0000.000
68A153GLY00.0320.03650.0700.0030.0030.0000.0000.0000.000
69A154LYS10.8820.94448.1920.0660.0660.0000.0000.0000.000
70A155ALA00.0010.01850.5340.0030.0030.0000.0000.0000.000
71A156SER0-0.002-0.02352.4320.0020.0020.0000.0000.0000.000
72A157GLU-1-0.860-0.90355.082-0.049-0.0490.0000.0000.0000.000
73A158SER0-0.007-0.01953.8400.0020.0020.0000.0000.0000.000
74A159LEU0-0.044-0.02055.3530.0020.0020.0000.0000.0000.000
75A160LYS10.8380.91258.3530.0490.0490.0000.0000.0000.000
76A161MET0-0.060-0.02859.8490.0020.0020.0000.0000.0000.000
77A162ILE00.0320.03056.8190.0010.0010.0000.0000.0000.000
78A163PHE00.0210.01156.7110.0010.0010.0000.0000.0000.000
79A164GLY00.0610.04061.9720.0010.0010.0000.0000.0000.000
80A165ILE0-0.065-0.03060.6770.0010.0010.0000.0000.0000.000
81A166ASP-1-0.801-0.90860.965-0.048-0.0480.0000.0000.0000.000
82A167VAL0-0.030-0.01955.573-0.001-0.0010.0000.0000.0000.000
83A168LYS10.9380.97959.0450.0470.0470.0000.0000.0000.000
84A169GLU-1-0.766-0.88555.622-0.067-0.0670.0000.0000.0000.000
85A170VAL0-0.056-0.04458.7970.0020.0020.0000.0000.0000.000
86A171ASP-1-0.893-0.96159.247-0.055-0.0550.0000.0000.0000.000
87A172PRO00.0400.01659.928-0.001-0.0010.0000.0000.0000.000
88A173THR0-0.049-0.00155.472-0.001-0.0010.0000.0000.0000.000
89A174SER0-0.0280.00055.415-0.002-0.0020.0000.0000.0000.000
90A175ASN0-0.033-0.02950.772-0.005-0.0050.0000.0000.0000.000
91A176THR00.005-0.00352.607-0.004-0.0040.0000.0000.0000.000
92A177TYR0-0.058-0.04052.5260.0010.0010.0000.0000.0000.000
93A178THR0-0.001-0.00457.3560.0000.0000.0000.0000.0000.000
94A179LEU0-0.0130.00156.6060.0000.0000.0000.0000.0000.000
95A180VAL0-0.007-0.00660.9720.0010.0010.0000.0000.0000.000
96A181THR00.0320.01364.299-0.001-0.0010.0000.0000.0000.000
97A182CYS0-0.035-0.01564.6050.0000.0000.0000.0000.0000.000
98A183LEU0-0.023-0.02067.2730.0010.0010.0000.0000.0000.000
99A184GLY0-0.0130.00370.0850.0010.0010.0000.0000.0000.000
100A185LEU00.0080.02170.7240.0010.0010.0000.0000.0000.000
101A186SER0-0.079-0.05470.818-0.001-0.0010.0000.0000.0000.000
102A187TYR00.0410.03270.1060.0000.0000.0000.0000.0000.000
103A188ASP-1-0.758-0.84765.687-0.043-0.0430.0000.0000.0000.000
104A189GLY00.0740.04267.0480.0000.0000.0000.0000.0000.000
105A190LEU0-0.105-0.04462.5220.0000.0000.0000.0000.0000.000
106A191LEU00.0240.00866.6690.0000.0000.0000.0000.0000.000
107A192GLY00.0020.00367.5620.0010.0010.0000.0000.0000.000
108A193ASN0-0.043-0.02763.063-0.001-0.0010.0000.0000.0000.000
109A194ASN00.0150.00163.554-0.003-0.0030.0000.0000.0000.000
110A195GLN00.0160.01062.6750.0000.0000.0000.0000.0000.000
111A196ILE0-0.045-0.01756.516-0.002-0.0020.0000.0000.0000.000
112A197PHE00.0450.01256.335-0.002-0.0020.0000.0000.0000.000
113A198PRO0-0.027-0.00460.9220.0020.0020.0000.0000.0000.000
114A199LYS10.9140.94763.6250.0360.0360.0000.0000.0000.000
115A200THR00.005-0.01666.1480.0010.0010.0000.0000.0000.000
116A201GLY0-0.0100.00164.7160.0010.0010.0000.0000.0000.000
117A202LEU00.0150.01565.7640.0010.0010.0000.0000.0000.000
118A203LEU00.0120.01767.5740.0010.0010.0000.0000.0000.000
119A204ILE0-0.031-0.02467.8650.0010.0010.0000.0000.0000.000
120A205ILE00.0010.00865.1370.0010.0010.0000.0000.0000.000
121A206VAL00.0290.03169.7780.0010.0010.0000.0000.0000.000
122A207LEU0-0.018-0.01272.9480.0010.0010.0000.0000.0000.000
123A208GLY00.008-0.01372.7210.0010.0010.0000.0000.0000.000
124A209THR0-0.007-0.01772.4950.0010.0010.0000.0000.0000.000
125A210ILE00.0020.00274.6780.0010.0010.0000.0000.0000.000
126A211ALA0-0.061-0.03176.4220.0010.0010.0000.0000.0000.000
127A212MET0-0.087-0.04572.0510.0000.0000.0000.0000.0000.000
128A213GLU-1-0.910-0.93477.770-0.023-0.0230.0000.0000.0000.000
129A214GLY0-0.023-0.00980.4680.0010.0010.0000.0000.0000.000
130A215ASP-1-0.944-0.96282.458-0.022-0.0220.0000.0000.0000.000
131A216SER0-0.116-0.07083.1060.0000.0000.0000.0000.0000.000
132A217ALA00.0810.05579.1840.0000.0000.0000.0000.0000.000
133A218SER0-0.075-0.08081.1850.0000.0000.0000.0000.0000.000
134A219GLU-1-0.768-0.85478.884-0.023-0.0230.0000.0000.0000.000
135A220GLU-1-0.859-0.95077.801-0.021-0.0210.0000.0000.0000.000
136A221GLU-1-0.732-0.82976.677-0.022-0.0220.0000.0000.0000.000
137A222ILE0-0.046-0.02074.324-0.001-0.0010.0000.0000.0000.000
138A223TRP0-0.042-0.04671.814-0.002-0.0020.0000.0000.0000.000
139A224GLU-1-0.967-0.96772.038-0.023-0.0230.0000.0000.0000.000
140A225GLU-1-0.904-0.94668.862-0.031-0.0310.0000.0000.0000.000
141A226LEU0-0.042-0.03268.702-0.002-0.0020.0000.0000.0000.000
142A227GLY00.0340.01567.444-0.001-0.0010.0000.0000.0000.000
143A228VAL0-0.034-0.00665.784-0.001-0.0010.0000.0000.0000.000
144A229MET0-0.067-0.01563.654-0.001-0.0010.0000.0000.0000.000
145A230GLY0-0.038-0.01762.968-0.001-0.0010.0000.0000.0000.000
146A231VAL0-0.082-0.05164.034-0.001-0.0010.0000.0000.0000.000
147A232TYR0-0.023-0.03164.7200.0010.0010.0000.0000.0000.000
148A233ASP-1-0.774-0.88469.547-0.025-0.0250.0000.0000.0000.000
149A234GLY0-0.0020.01371.7250.0000.0000.0000.0000.0000.000
150A235ARG10.8410.92564.6430.0290.0290.0000.0000.0000.000
151A236GLU-1-0.878-0.94565.248-0.034-0.0340.0000.0000.0000.000
152A237HIS00.0510.03961.105-0.001-0.0010.0000.0000.0000.000
153A238THR0-0.028-0.02758.3070.0000.0000.0000.0000.0000.000
154A239VAL0-0.030-0.01058.592-0.001-0.0010.0000.0000.0000.000
155A240TYR0-0.016-0.03761.2260.0000.0000.0000.0000.0000.000
156A241GLY00.0010.01564.7850.0010.0010.0000.0000.0000.000
157A242GLU-1-0.816-0.91566.669-0.028-0.0280.0000.0000.0000.000
158A243PRO0-0.0020.01468.6360.0000.0000.0000.0000.0000.000
159A244ARG10.8230.87371.0630.0240.0240.0000.0000.0000.000
160A245LYS10.7700.86272.9720.0310.0310.0000.0000.0000.000
161A246LEU0-0.034-0.01969.3680.0000.0000.0000.0000.0000.000
162A247LEU0-0.003-0.00273.2630.0000.0000.0000.0000.0000.000
163A248THR0-0.021-0.01475.7260.0000.0000.0000.0000.0000.000
164A249GLN0-0.033-0.00177.4830.0010.0010.0000.0000.0000.000
165A250ASP-1-0.786-0.86473.237-0.031-0.0310.0000.0000.0000.000
166A251TRP00.045-0.01369.9780.0000.0000.0000.0000.0000.000
167A252VAL00.0100.02676.6610.0000.0000.0000.0000.0000.000
168A253GLN0-0.025-0.02079.0650.0000.0000.0000.0000.0000.000
169A254GLU-1-0.896-0.93774.432-0.032-0.0320.0000.0000.0000.000
170A255ASN0-0.047-0.03178.4890.0000.0000.0000.0000.0000.000
171A256TYR0-0.063-0.06674.6470.0000.0000.0000.0000.0000.000
172A257LEU0-0.019-0.00576.0920.0000.0000.0000.0000.0000.000
173A258GLU-1-0.821-0.89280.148-0.022-0.0220.0000.0000.0000.000
174A259TYR0-0.032-0.04981.3880.0000.0000.0000.0000.0000.000
175A260ARG10.7820.86883.6530.0210.0210.0000.0000.0000.000
176A261GLN00.0560.04186.5260.0000.0000.0000.0000.0000.000
177A262VAL00.0080.01887.6300.0010.0010.0000.0000.0000.000
178A263PRO0-0.063-0.01689.9090.0000.0000.0000.0000.0000.000
179A264GLY00.027-0.00191.9670.0010.0010.0000.0000.0000.000
180A265SER0-0.033-0.03092.4550.0000.0000.0000.0000.0000.000
181A266ASN0-0.073-0.05093.9280.0010.0010.0000.0000.0000.000
182A267PRO0-0.045-0.00191.9550.0000.0000.0000.0000.0000.000
183A268ALA00.015-0.00687.4040.0000.0000.0000.0000.0000.000
184A269ARG10.8660.93584.8590.0200.0200.0000.0000.0000.000
185A270TYR0-0.0130.00083.5940.0000.0000.0000.0000.0000.000
186A271GLU-1-0.761-0.87282.574-0.020-0.0200.0000.0000.0000.000
187A272PHE0-0.024-0.00678.2030.0000.0000.0000.0000.0000.000
188A273LEU00.0440.01381.4930.0000.0000.0000.0000.0000.000
189A274TRP0-0.030-0.03176.520-0.001-0.0010.0000.0000.0000.000
190A275GLY00.0270.02780.6960.0010.0010.0000.0000.0000.000
191A276PRO00.004-0.01981.9190.0000.0000.0000.0000.0000.000
192A277ARG10.7840.86575.4570.0320.0320.0000.0000.0000.000
193A278ALA00.0110.00677.664-0.001-0.0010.0000.0000.0000.000
194A279LEU0-0.020-0.01378.647-0.001-0.0010.0000.0000.0000.000
195A280ALA0-0.0230.01481.0020.0000.0000.0000.0000.0000.000
196A281GLU-1-0.718-0.78875.313-0.034-0.0340.0000.0000.0000.000
197A282THR0-0.050-0.03774.067-0.001-0.0010.0000.0000.0000.000
198A283SER00.0560.01876.6440.0010.0010.0000.0000.0000.000
199A284TYR00.0640.01776.801-0.001-0.0010.0000.0000.0000.000
200A285VAL0-0.0080.00076.700-0.001-0.0010.0000.0000.0000.000
201A286LYS10.8550.93673.8880.0330.0330.0000.0000.0000.000
202A287VAL00.0090.01072.150-0.001-0.0010.0000.0000.0000.000
203A288LEU00.0520.03071.784-0.001-0.0010.0000.0000.0000.000
204A289GLU-1-0.853-0.90171.020-0.035-0.0350.0000.0000.0000.000
205A290HIS0-0.028-0.01965.374-0.001-0.0010.0000.0000.0000.000
206A291VAL00.0600.03167.366-0.001-0.0010.0000.0000.0000.000
207A292VAL00.0040.00967.510-0.001-0.0010.0000.0000.0000.000
208A293ARG10.8110.88164.9990.0370.0370.0000.0000.0000.000
209A294VAL0-0.006-0.00862.428-0.002-0.0020.0000.0000.0000.000
210A295ASN0-0.023-0.00162.521-0.002-0.0020.0000.0000.0000.000
211A296ALA00.0060.00563.3390.0000.0000.0000.0000.0000.000
212A297ARG10.7530.86457.4420.0450.0450.0000.0000.0000.000
213A298VAL00.0250.00155.2800.0000.0000.0000.0000.0000.000
214A299ARG10.8540.92655.2330.0410.0410.0000.0000.0000.000
215A300ILE0-0.0020.01349.446-0.001-0.0010.0000.0000.0000.000
216A301ALA00.0470.02748.3310.0010.0010.0000.0000.0000.000
217A302TYR0-0.005-0.03144.4930.0000.0000.0000.0000.0000.000
218A303PRO0-0.0330.00341.7010.0020.0020.0000.0000.0000.000
219A304SER00.049-0.01939.156-0.004-0.0040.0000.0000.0000.000
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