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: GNM31

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2608715.386424
FMO2-HF: Nuclear repulsion 2518524.378662
FMO2-HF: Total energy -90191.007762
FMO2-MP2: Total energy -90455.025028


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.
-1.0710.485-0.017-0.729-0.810
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 : -0.021 / q_NPA : -0.028
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-12VAL00.0130.0033.893-1.2660.290-0.017-0.729-0.8100.000
4A-11ASP-1-0.934-0.9616.7250.3550.3550.0000.0000.0000.000
5A-10LEU0-0.054-0.0227.353-0.156-0.1560.0000.0000.0000.000
6A-9GLY00.0570.03311.1890.0940.0940.0000.0000.0000.000
7A-8THR0-0.024-0.02515.006-0.036-0.0360.0000.0000.0000.000
8A-7GLU-1-0.870-0.91917.689-0.056-0.0560.0000.0000.0000.000
9A-6ASN0-0.078-0.05118.692-0.014-0.0140.0000.0000.0000.000
10A-5LEU0-0.036-0.01516.483-0.013-0.0130.0000.0000.0000.000
11A-4TYR0-0.0060.01819.398-0.023-0.0230.0000.0000.0000.000
12A-3PHE0-0.046-0.03123.1770.0180.0180.0000.0000.0000.000
13A-2GLN0-0.002-0.00323.1870.0010.0010.0000.0000.0000.000
14A-1SER00.034-0.00825.5480.0060.0060.0000.0000.0000.000
15A0MET0-0.021-0.00628.4760.0030.0030.0000.0000.0000.000
16A101ASP-1-0.802-0.86730.693-0.096-0.0960.0000.0000.0000.000
17A102ALA00.016-0.00230.4170.0000.0000.0000.0000.0000.000
18A103GLU-1-0.845-0.92032.564-0.102-0.1020.0000.0000.0000.000
19A104SER0-0.047-0.06735.6660.0010.0010.0000.0000.0000.000
20A105LEU00.0500.03032.8690.0020.0020.0000.0000.0000.000
21A106PHE0-0.0170.00235.653-0.002-0.0020.0000.0000.0000.000
22A107ARG10.9930.98737.3250.0700.0700.0000.0000.0000.000
23A108GLU-1-0.930-0.96439.832-0.076-0.0760.0000.0000.0000.000
24A109ALA0-0.026-0.00337.5810.0020.0020.0000.0000.0000.000
25A110LEU0-0.012-0.02539.7160.0020.0020.0000.0000.0000.000
26A111SER0-0.013-0.00642.1090.0040.0040.0000.0000.0000.000
27A112ASN00.0280.00941.2720.0060.0060.0000.0000.0000.000
28A113LYS10.7810.87940.1890.1040.1040.0000.0000.0000.000
29A114VAL0-0.038-0.01444.1320.0010.0010.0000.0000.0000.000
30A115ASP-1-0.859-0.92347.438-0.064-0.0640.0000.0000.0000.000
31A116GLU-1-0.814-0.89343.220-0.094-0.0940.0000.0000.0000.000
32A117LEU0-0.024-0.02247.0500.0010.0010.0000.0000.0000.000
33A118ALA00.0360.01948.5840.0020.0020.0000.0000.0000.000
34A119HIS00.0180.00450.4870.0040.0040.0000.0000.0000.000
35A120PHE0-0.103-0.05549.1200.0010.0010.0000.0000.0000.000
36A121LEU00.0130.00351.2620.0010.0010.0000.0000.0000.000
37A122LEU00.0430.02253.9740.0020.0020.0000.0000.0000.000
38A123ARG10.8560.93448.7620.0730.0730.0000.0000.0000.000
39A124LYS10.8210.88952.5390.0710.0710.0000.0000.0000.000
40A125TYR0-0.095-0.06656.2540.0010.0010.0000.0000.0000.000
41A126ARG10.8770.93555.7970.0560.0560.0000.0000.0000.000
42A127ALA0-0.041-0.01057.8820.0020.0020.0000.0000.0000.000
43A128LYS10.8880.95359.8540.0470.0470.0000.0000.0000.000
44A129GLU-1-0.885-0.91755.268-0.065-0.0650.0000.0000.0000.000
45A130LEU0-0.017-0.01257.4050.0000.0000.0000.0000.0000.000
46A131VAL00.0210.01051.707-0.002-0.0020.0000.0000.0000.000
47A132THR00.0270.02049.875-0.001-0.0010.0000.0000.0000.000
48A133LYS11.0261.00746.0730.0850.0850.0000.0000.0000.000
49A134ALA0-0.0040.00445.704-0.003-0.0030.0000.0000.0000.000
50A135GLU-1-0.749-0.87645.302-0.080-0.0800.0000.0000.0000.000
51A136MET0-0.0160.01946.181-0.002-0.0020.0000.0000.0000.000
52A137LEU0-0.059-0.03742.065-0.004-0.0040.0000.0000.0000.000
53A138GLU-1-0.818-0.89640.166-0.130-0.1300.0000.0000.0000.000
54A139ARG10.8400.92141.6240.0800.0800.0000.0000.0000.000
55A140VAL00.0290.02243.6560.0010.0010.0000.0000.0000.000
56A141ILE0-0.0160.00040.885-0.002-0.0020.0000.0000.0000.000
57A142LYS10.8350.91135.9730.1310.1310.0000.0000.0000.000
58A143ASN00.021-0.00634.488-0.007-0.0070.0000.0000.0000.000
59A144TYR00.0540.02735.205-0.003-0.0030.0000.0000.0000.000
60A145LYS10.9170.95537.0790.1420.1420.0000.0000.0000.000
61A146ARG10.8000.89234.3180.1440.1440.0000.0000.0000.000
62A147CYS0-0.023-0.00939.7760.0030.0030.0000.0000.0000.000
63A148PHE00.0610.02242.1300.0050.0050.0000.0000.0000.000
64A149PRO00.012-0.00244.6510.0040.0040.0000.0000.0000.000
65A150VAL00.0200.01745.0700.0040.0040.0000.0000.0000.000
66A151ILE0-0.015-0.01442.0070.0030.0030.0000.0000.0000.000
67A152PHE00.0340.00846.6760.0030.0030.0000.0000.0000.000
68A153GLY00.0340.03249.5260.0030.0030.0000.0000.0000.000
69A154LYS10.9100.95648.0860.0670.0670.0000.0000.0000.000
70A155ALA00.0120.02250.0750.0030.0030.0000.0000.0000.000
71A156SER0-0.012-0.02551.9880.0030.0030.0000.0000.0000.000
72A157GLU-1-0.862-0.90354.718-0.050-0.0500.0000.0000.0000.000
73A158SER00.008-0.01353.6640.0020.0020.0000.0000.0000.000
74A159LEU0-0.023-0.01054.8460.0020.0020.0000.0000.0000.000
75A160LYS10.8110.89957.8290.0490.0490.0000.0000.0000.000
76A161MET0-0.053-0.03459.4680.0010.0010.0000.0000.0000.000
77A162ILE00.0350.03356.5840.0010.0010.0000.0000.0000.000
78A163PHE00.003-0.01256.2660.0010.0010.0000.0000.0000.000
79A164GLY00.0720.04761.4750.0010.0010.0000.0000.0000.000
80A165ILE0-0.082-0.04259.9930.0000.0000.0000.0000.0000.000
81A166ASP-1-0.801-0.90760.543-0.049-0.0490.0000.0000.0000.000
82A167VAL0-0.036-0.01855.1270.0000.0000.0000.0000.0000.000
83A168LYS10.9310.97758.6020.0470.0470.0000.0000.0000.000
84A169GLU-1-0.826-0.90855.298-0.066-0.0660.0000.0000.0000.000
85A170VAL0-0.076-0.04958.5240.0020.0020.0000.0000.0000.000
86A171ASP-1-0.864-0.92058.811-0.056-0.0560.0000.0000.0000.000
87A172PRO00.034-0.01359.8200.0000.0000.0000.0000.0000.000
88A173THR0-0.0400.02355.141-0.001-0.0010.0000.0000.0000.000
89A174SER0-0.028-0.00754.704-0.001-0.0010.0000.0000.0000.000
90A175ASN0-0.055-0.06650.585-0.005-0.0050.0000.0000.0000.000
91A176THR0-0.0060.00352.599-0.003-0.0030.0000.0000.0000.000
92A177TYR0-0.023-0.03252.2790.0000.0000.0000.0000.0000.000
93A178THR0-0.025-0.02057.0240.0000.0000.0000.0000.0000.000
94A179LEU00.0020.00556.1520.0000.0000.0000.0000.0000.000
95A180VAL0-0.010-0.00760.4690.0010.0010.0000.0000.0000.000
96A181THR00.0390.01163.690-0.001-0.0010.0000.0000.0000.000
97A182CYS0-0.042-0.01764.0370.0000.0000.0000.0000.0000.000
98A183LEU0-0.041-0.03466.6600.0010.0010.0000.0000.0000.000
99A184GLY0-0.0190.00869.2590.0010.0010.0000.0000.0000.000
100A185LEU0-0.0030.01270.2280.0010.0010.0000.0000.0000.000
101A186SER0-0.053-0.03570.313-0.001-0.0010.0000.0000.0000.000
102A187TYR00.0280.03869.715-0.001-0.0010.0000.0000.0000.000
103A188ASP-1-0.747-0.86465.544-0.043-0.0430.0000.0000.0000.000
104A189GLY00.0210.02166.414-0.001-0.0010.0000.0000.0000.000
105A190LEU0-0.110-0.04162.5220.0000.0000.0000.0000.0000.000
106A191LEU00.0270.00266.2950.0000.0000.0000.0000.0000.000
107A192GLY0-0.0140.00968.3300.0000.0000.0000.0000.0000.000
108A193ASN0-0.015-0.02262.540-0.001-0.0010.0000.0000.0000.000
109A194ASN0-0.013-0.01363.260-0.003-0.0030.0000.0000.0000.000
110A195GLN00.0140.01662.8250.0000.0000.0000.0000.0000.000
111A196ILE0-0.024-0.01456.125-0.002-0.0020.0000.0000.0000.000
112A197PHE00.0580.01655.660-0.002-0.0020.0000.0000.0000.000
113A198PRO0-0.0060.00660.4470.0020.0020.0000.0000.0000.000
114A199LYS10.8910.93363.2070.0370.0370.0000.0000.0000.000
115A200THR00.0230.00065.7250.0010.0010.0000.0000.0000.000
116A201GLY0-0.023-0.00364.2640.0010.0010.0000.0000.0000.000
117A202LEU00.0320.02365.3070.0010.0010.0000.0000.0000.000
118A203LEU00.0020.01567.2480.0010.0010.0000.0000.0000.000
119A204ILE0-0.034-0.02867.2030.0010.0010.0000.0000.0000.000
120A205ILE0-0.0030.00364.7880.0010.0010.0000.0000.0000.000
121A206VAL00.0350.03669.4170.0010.0010.0000.0000.0000.000
122A207LEU0-0.028-0.01472.6080.0010.0010.0000.0000.0000.000
123A208GLY0-0.001-0.02072.3040.0010.0010.0000.0000.0000.000
124A209THR00.018-0.00772.0460.0010.0010.0000.0000.0000.000
125A210ILE0-0.031-0.00774.2840.0010.0010.0000.0000.0000.000
126A211ALA0-0.055-0.03276.0140.0010.0010.0000.0000.0000.000
127A212MET0-0.093-0.05571.8490.0000.0000.0000.0000.0000.000
128A213GLU-1-0.903-0.92877.273-0.024-0.0240.0000.0000.0000.000
129A214GLY0-0.0420.00579.9390.0010.0010.0000.0000.0000.000
130A215ASP-1-0.926-0.96182.020-0.023-0.0230.0000.0000.0000.000
131A216SER0-0.113-0.07982.7880.0000.0000.0000.0000.0000.000
132A217ALA00.0780.05678.7100.0000.0000.0000.0000.0000.000
133A218SER0-0.080-0.09480.7410.0000.0000.0000.0000.0000.000
134A219GLU-1-0.725-0.83678.480-0.024-0.0240.0000.0000.0000.000
135A220GLU-1-0.898-0.96177.416-0.022-0.0220.0000.0000.0000.000
136A221GLU-1-0.723-0.81776.178-0.023-0.0230.0000.0000.0000.000
137A222ILE0-0.062-0.02673.984-0.001-0.0010.0000.0000.0000.000
138A223TRP0-0.051-0.05071.339-0.002-0.0020.0000.0000.0000.000
139A224GLU-1-0.949-0.96371.403-0.025-0.0250.0000.0000.0000.000
140A225GLU-1-0.917-0.95368.379-0.033-0.0330.0000.0000.0000.000
141A226LEU0-0.036-0.02868.304-0.002-0.0020.0000.0000.0000.000
142A227GLY00.0310.01066.926-0.001-0.0010.0000.0000.0000.000
143A228VAL0-0.043-0.00665.126-0.001-0.0010.0000.0000.0000.000
144A229MET0-0.064-0.01762.886-0.001-0.0010.0000.0000.0000.000
145A230GLY0-0.064-0.03662.496-0.001-0.0010.0000.0000.0000.000
146A231VAL0-0.056-0.03363.568-0.001-0.0010.0000.0000.0000.000
147A232TYR0-0.032-0.02964.0640.0010.0010.0000.0000.0000.000
148A233ASP-1-0.787-0.88668.882-0.026-0.0260.0000.0000.0000.000
149A234GLY00.0160.01871.7930.0010.0010.0000.0000.0000.000
150A235ARG10.8360.91764.0250.0300.0300.0000.0000.0000.000
151A236GLU-1-0.940-0.97364.764-0.035-0.0350.0000.0000.0000.000
152A237HIS00.0420.03260.636-0.001-0.0010.0000.0000.0000.000
153A238THR0-0.025-0.02357.9050.0000.0000.0000.0000.0000.000
154A239VAL0-0.030-0.00858.2550.0000.0000.0000.0000.0000.000
155A240TYR00.022-0.00860.9320.0000.0000.0000.0000.0000.000
156A241GLY00.0210.02764.3650.0010.0010.0000.0000.0000.000
157A242GLU-1-0.798-0.90866.199-0.029-0.0290.0000.0000.0000.000
158A243PRO00.0010.01368.2960.0000.0000.0000.0000.0000.000
159A244ARG10.8260.88970.6900.0250.0250.0000.0000.0000.000
160A245LYS10.8230.87272.3310.0320.0320.0000.0000.0000.000
161A246LEU0-0.051-0.01568.8780.0000.0000.0000.0000.0000.000
162A247LEU00.001-0.01072.9600.0000.0000.0000.0000.0000.000
163A248THR0-0.011-0.01075.2570.0000.0000.0000.0000.0000.000
164A249GLN0-0.021-0.00277.0410.0010.0010.0000.0000.0000.000
165A250ASP-1-0.842-0.88372.741-0.031-0.0310.0000.0000.0000.000
166A251TRP00.070-0.00169.6990.0000.0000.0000.0000.0000.000
167A252VAL0-0.0060.01976.4390.0000.0000.0000.0000.0000.000
168A253GLN0-0.025-0.01978.9480.0000.0000.0000.0000.0000.000
169A254GLU-1-0.907-0.93974.374-0.032-0.0320.0000.0000.0000.000
170A255ASN0-0.071-0.04578.5480.0000.0000.0000.0000.0000.000
171A256TYR0-0.062-0.07174.3290.0000.0000.0000.0000.0000.000
172A257LEU0-0.010-0.00675.5430.0000.0000.0000.0000.0000.000
173A258GLU-1-0.865-0.91579.764-0.022-0.0220.0000.0000.0000.000
174A259TYR0-0.015-0.04281.0880.0000.0000.0000.0000.0000.000
175A260ARG10.8130.89483.1810.0220.0220.0000.0000.0000.000
176A261GLN00.0440.02786.4540.0000.0000.0000.0000.0000.000
177A262VAL00.0370.03587.2510.0010.0010.0000.0000.0000.000
178A263PRO0-0.088-0.03189.6610.0000.0000.0000.0000.0000.000
179A264GLY00.0320.01091.7910.0010.0010.0000.0000.0000.000
180A265SER0-0.027-0.02692.3580.0000.0000.0000.0000.0000.000
181A266ASN0-0.074-0.05193.6570.0010.0010.0000.0000.0000.000
182A267PRO0-0.048-0.00891.6050.0000.0000.0000.0000.0000.000
183A268ALA00.019-0.00786.9300.0000.0000.0000.0000.0000.000
184A269ARG10.8760.93884.2880.0200.0200.0000.0000.0000.000
185A270TYR0-0.0170.00283.3250.0000.0000.0000.0000.0000.000
186A271GLU-1-0.779-0.87082.360-0.021-0.0210.0000.0000.0000.000
187A272PHE00.002-0.00478.0060.0000.0000.0000.0000.0000.000
188A273LEU00.0200.00881.3630.0000.0000.0000.0000.0000.000
189A274TRP0-0.034-0.03276.111-0.001-0.0010.0000.0000.0000.000
190A275GLY00.0510.04480.3770.0010.0010.0000.0000.0000.000
191A276PRO00.022-0.01481.6750.0000.0000.0000.0000.0000.000
192A277ARG10.8040.89375.0720.0320.0320.0000.0000.0000.000
193A278ALA00.0170.01777.493-0.001-0.0010.0000.0000.0000.000
194A279LEU0-0.030-0.01778.4850.0000.0000.0000.0000.0000.000
195A280ALA0-0.050-0.01080.7980.0000.0000.0000.0000.0000.000
196A281GLU-1-0.749-0.81774.805-0.034-0.0340.0000.0000.0000.000
197A282THR0-0.041-0.02773.714-0.001-0.0010.0000.0000.0000.000
198A283SER00.0340.00676.4060.0010.0010.0000.0000.0000.000
199A284TYR00.0640.02076.472-0.001-0.0010.0000.0000.0000.000
200A285VAL00.000-0.00576.429-0.001-0.0010.0000.0000.0000.000
201A286LYS10.9240.96973.5970.0320.0320.0000.0000.0000.000
202A287VAL00.0440.03171.912-0.001-0.0010.0000.0000.0000.000
203A288LEU00.0270.01571.481-0.001-0.0010.0000.0000.0000.000
204A289GLU-1-0.841-0.90570.897-0.036-0.0360.0000.0000.0000.000
205A290HIS0-0.023-0.00565.105-0.001-0.0010.0000.0000.0000.000
206A291VAL00.0500.02267.163-0.001-0.0010.0000.0000.0000.000
207A292VAL0-0.033-0.00767.088-0.001-0.0010.0000.0000.0000.000
208A293ARG10.8210.88064.5580.0380.0380.0000.0000.0000.000
209A294VAL0-0.007-0.00662.013-0.002-0.0020.0000.0000.0000.000
210A295ASN00.008-0.00162.248-0.002-0.0020.0000.0000.0000.000
211A296ALA0-0.0060.01063.2510.0000.0000.0000.0000.0000.000
212A297ARG10.7790.88957.3560.0460.0460.0000.0000.0000.000
213A298VAL00.016-0.00754.9120.0010.0010.0000.0000.0000.000
214A299ARG10.8620.93854.6030.0420.0420.0000.0000.0000.000
215A300ILE00.0260.02048.918-0.001-0.0010.0000.0000.0000.000
216A301ALA00.0050.00647.9020.0010.0010.0000.0000.0000.000
217A302TYR0-0.033-0.04243.823-0.001-0.0010.0000.0000.0000.000
218A303PRO0-0.0090.01241.1420.0020.0020.0000.0000.0000.000
219A304SER00.017-0.03039.062-0.004-0.0040.0000.0000.0000.000
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