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

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FMODB ID: MVMKZ

Calculation Name: 2D4X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4X

Chain ID: A

ChEMBL ID:

UniProt ID: P16326

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 OptH
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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2160982.871076
FMO2-HF: Nuclear repulsion 2081584.346192
FMO2-HF: Total energy -79398.524884
FMO2-MP2: Total energy -79632.386073


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:50:VAL)


Summations of interaction energy for fragment #1(A:50:VAL)
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.
-7.105-1.9430.909-1.99-4.081-0.006
Interaction energy analysis for fragmet #1(A:50:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.012
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].
3A52LEU00.0180.0263.261-3.102-1.4120.043-0.339-1.3930.005
4A53SER00.0450.0232.798-2.457-1.0730.512-0.735-1.161-0.006
5A54GLN00.0170.0033.002-2.253-0.2750.355-0.909-1.424-0.005
6A55ALA00.0290.0235.0610.4730.583-0.001-0.007-0.1030.000
7A56GLN00.014-0.0067.620-0.051-0.0510.0000.0000.0000.000
8A57ALA00.0530.1018.1130.1470.1470.0000.0000.0000.000
9A58GLN0-0.054-0.0308.041-0.047-0.0470.0000.0000.0000.000
10A59ASN00.029-0.01510.8740.0610.0610.0000.0000.0000.000
11A60SER0-0.094-0.10511.9220.0600.0600.0000.0000.0000.000
12A61GLN0-0.012-0.01213.0900.0630.0630.0000.0000.0000.000
13A62TYR00.0160.01613.5220.0280.0280.0000.0000.0000.000
14A63ALA00.0150.00316.9680.0400.0400.0000.0000.0000.000
15A64LEU0-0.007-0.00317.3360.0300.0300.0000.0000.0000.000
16A65ALA00.0060.01319.5390.0260.0260.0000.0000.0000.000
17A66ARG10.9831.00320.3120.1760.1760.0000.0000.0000.000
18A67THR0-0.0340.00322.9640.0230.0230.0000.0000.0000.000
19A68PHE0-0.015-0.00124.2780.0120.0120.0000.0000.0000.000
20A69ALA00.000-0.01725.4380.0120.0120.0000.0000.0000.000
21A70THR00.0340.01627.0290.0140.0140.0000.0000.0000.000
22A71GLN0-0.024-0.01528.771-0.001-0.0010.0000.0000.0000.000
23A72LYS10.8440.94130.3030.0950.0950.0000.0000.0000.000
24A73VAL00.0760.02730.6300.0060.0060.0000.0000.0000.000
25A74SER00.0170.01233.1250.0080.0080.0000.0000.0000.000
26A75LEU0-0.047-0.00335.1000.0050.0050.0000.0000.0000.000
27A76GLU-1-0.814-0.92334.464-0.074-0.0740.0000.0000.0000.000
28A77GLU-1-0.816-0.91737.206-0.044-0.0440.0000.0000.0000.000
29A78SER0-0.069-0.02638.9990.0060.0060.0000.0000.0000.000
30A79VAL00.0290.00540.8460.0030.0030.0000.0000.0000.000
31A80LEU00.0250.00539.9760.0040.0040.0000.0000.0000.000
32A81SER0-0.061-0.01843.1850.0050.0050.0000.0000.0000.000
33A82GLN00.015-0.00945.0800.0010.0010.0000.0000.0000.000
34A83VAL00.0110.01145.2620.0020.0020.0000.0000.0000.000
35A84THR0-0.023-0.01146.8230.0030.0030.0000.0000.0000.000
36A85THR00.0300.02548.9390.0020.0020.0000.0000.0000.000
37A86ALA00.0120.02050.9870.0020.0020.0000.0000.0000.000
38A87ILE00.018-0.00449.4170.0010.0010.0000.0000.0000.000
39A88GLN0-0.003-0.01051.8620.0010.0010.0000.0000.0000.000
40A89THR0-0.014-0.00755.0310.0020.0020.0000.0000.0000.000
41A90ALA00.0200.00756.4470.0010.0010.0000.0000.0000.000
42A91GLN0-0.005-0.00955.5360.0010.0010.0000.0000.0000.000
43A92GLU-1-0.942-0.96858.751-0.020-0.0200.0000.0000.0000.000
44A93LYS10.9310.97061.1540.0240.0240.0000.0000.0000.000
45A94ILE0-0.008-0.01160.1980.0010.0010.0000.0000.0000.000
46A95VAL0-0.039-0.02062.1020.0010.0010.0000.0000.0000.000
47A96TYR0-0.024-0.01364.6130.0010.0010.0000.0000.0000.000
48A97ALA0-0.005-0.00266.1570.0010.0010.0000.0000.0000.000
49A98GLY0-0.0020.01167.5420.0000.0000.0000.0000.0000.000
50A99ASN0-0.0140.00368.7490.0010.0010.0000.0000.0000.000
51A100GLY00.0600.02172.1050.0000.0000.0000.0000.0000.000
52A101THR0-0.106-0.06274.9190.0000.0000.0000.0000.0000.000
53A102LEU0-0.0280.00970.6350.0000.0000.0000.0000.0000.000
54A103SER00.0730.04575.1060.0000.0000.0000.0000.0000.000
55A104ASP-1-0.675-0.85574.665-0.017-0.0170.0000.0000.0000.000
56A105ASP-1-0.914-0.94773.833-0.018-0.0180.0000.0000.0000.000
57A106ASP-1-0.941-0.97872.707-0.017-0.0170.0000.0000.0000.000
58A107ARG10.8160.89670.2910.0170.0170.0000.0000.0000.000
59A108ALA00.0450.02468.963-0.001-0.0010.0000.0000.0000.000
60A109SER0-0.031-0.01868.364-0.001-0.0010.0000.0000.0000.000
61A110LEU00.0040.00566.081-0.001-0.0010.0000.0000.0000.000
62A111ALA0-0.004-0.00164.511-0.001-0.0010.0000.0000.0000.000
63A112THR0-0.038-0.01263.602-0.001-0.0010.0000.0000.0000.000
64A113ASP-1-0.893-0.94662.621-0.024-0.0240.0000.0000.0000.000
65A114LEU0-0.062-0.04159.794-0.001-0.0010.0000.0000.0000.000
66A115GLN0-0.034-0.02258.6500.0000.0000.0000.0000.0000.000
67A116GLY00.0320.01858.257-0.001-0.0010.0000.0000.0000.000
68A117ILE0-0.012-0.00755.095-0.002-0.0020.0000.0000.0000.000
69A118ARG10.7330.86254.3790.0320.0320.0000.0000.0000.000
70A119ASP-1-0.841-0.92853.543-0.036-0.0360.0000.0000.0000.000
71A120GLN0-0.064-0.03452.260-0.001-0.0010.0000.0000.0000.000
72A121LEU00.0070.00149.558-0.002-0.0020.0000.0000.0000.000
73A122MET0-0.0180.00848.741-0.003-0.0030.0000.0000.0000.000
74A123ASN0-0.029-0.02248.139-0.003-0.0030.0000.0000.0000.000
75A124LEU0-0.029-0.00145.927-0.003-0.0030.0000.0000.0000.000
76A125ALA00.0190.01744.285-0.003-0.0030.0000.0000.0000.000
77A126ASN0-0.037-0.02943.533-0.005-0.0050.0000.0000.0000.000
78A127SER00.017-0.01141.714-0.001-0.0010.0000.0000.0000.000
79A128THR00.0030.00239.168-0.001-0.0010.0000.0000.0000.000
80A129ASP-1-0.848-0.92833.993-0.097-0.0970.0000.0000.0000.000
81A130GLY0-0.024-0.01836.1820.0020.0020.0000.0000.0000.000
82A131ASN0-0.077-0.03731.8370.0010.0010.0000.0000.0000.000
83A132GLY0-0.015-0.00635.9820.0000.0000.0000.0000.0000.000
84A133ARG10.8260.91331.4340.1160.1160.0000.0000.0000.000
85A134TYR0-0.006-0.01436.6120.0030.0030.0000.0000.0000.000
86A135ILE0-0.053-0.03836.019-0.004-0.0040.0000.0000.0000.000
87A136PHE00.0130.02436.780-0.001-0.0010.0000.0000.0000.000
88A137ALA00.0580.01537.5820.0040.0040.0000.0000.0000.000
89A138GLY00.0290.02534.7030.0000.0000.0000.0000.0000.000
90A139TYR00.020-0.00727.2630.0000.0000.0000.0000.0000.000
91A140LYS10.8750.94833.3200.0670.0670.0000.0000.0000.000
92A141THR00.0360.00933.2930.0020.0020.0000.0000.0000.000
93A142GLU-1-0.803-0.88335.340-0.096-0.0960.0000.0000.0000.000
94A143ALA0-0.031-0.01138.5480.0030.0030.0000.0000.0000.000
95A144ALA0-0.0170.00441.557-0.001-0.0010.0000.0000.0000.000
96A145PRO0-0.0060.00841.4820.0010.0010.0000.0000.0000.000
97A146PHE00.0130.01143.3740.0020.0020.0000.0000.0000.000
98A147ASP-1-0.791-0.83747.026-0.041-0.0410.0000.0000.0000.000
99A148GLN00.0750.02450.2030.0000.0000.0000.0000.0000.000
100A149ALA0-0.015-0.00952.8110.0010.0010.0000.0000.0000.000
101A150THR0-0.036-0.06853.3350.0010.0010.0000.0000.0000.000
102A151GLY00.0560.04050.8310.0010.0010.0000.0000.0000.000
103A152GLY00.0060.01549.9140.0000.0000.0000.0000.0000.000
104A153TYR0-0.054-0.04239.188-0.002-0.0020.0000.0000.0000.000
105A154HIS10.7880.86744.4060.0480.0480.0000.0000.0000.000
106A155GLY00.0480.03640.496-0.003-0.0030.0000.0000.0000.000
107A156GLY0-0.105-0.05636.8800.0020.0020.0000.0000.0000.000
108A157GLU-1-0.866-0.94437.815-0.051-0.0510.0000.0000.0000.000
109A158LYS10.8680.94332.8350.0620.0620.0000.0000.0000.000
110A159SER00.0570.03331.931-0.003-0.0030.0000.0000.0000.000
111A160VAL00.0000.01328.577-0.005-0.0050.0000.0000.0000.000
112A161THR0-0.0200.00625.9260.0000.0000.0000.0000.0000.000
113A162GLN00.010-0.00822.308-0.019-0.0190.0000.0000.0000.000
114A163GLN00.0310.03018.6440.0210.0210.0000.0000.0000.000
115A164VAL0-0.017-0.01320.014-0.018-0.0180.0000.0000.0000.000
116A165ASP-1-0.859-0.95117.737-0.146-0.1460.0000.0000.0000.000
117A166SER0-0.048-0.02313.680-0.010-0.0100.0000.0000.0000.000
118A167ALA0-0.047-0.00916.2870.0080.0080.0000.0000.0000.000
119A168ARG10.9340.97119.5190.0810.0810.0000.0000.0000.000
120A169THR0-0.021-0.01221.205-0.016-0.0160.0000.0000.0000.000
121A170MET0-0.0130.00623.7110.0100.0100.0000.0000.0000.000
122A171VAL0-0.008-0.00926.372-0.009-0.0090.0000.0000.0000.000
123A172ILE0-0.055-0.03826.8150.0000.0000.0000.0000.0000.000
124A173GLY00.0830.02530.2110.0000.0000.0000.0000.0000.000
125A174HIS0-0.077-0.03133.3100.0010.0010.0000.0000.0000.000
126A175THR0-0.013-0.02035.8700.0000.0000.0000.0000.0000.000
127A176GLY00.0910.02638.0600.0030.0030.0000.0000.0000.000
128A177ALA0-0.0060.00241.2450.0030.0030.0000.0000.0000.000
129A178GLN00.0150.02836.3710.0000.0000.0000.0000.0000.000
130A179ILE00.0180.04139.7690.0030.0030.0000.0000.0000.000
131A180PHE0-0.007-0.01843.2080.0030.0030.0000.0000.0000.000
132A181ASN0-0.010-0.01445.4780.0040.0040.0000.0000.0000.000
133A182SER0-0.045-0.03844.1020.0000.0000.0000.0000.0000.000
134A183ILE0-0.0010.00246.2510.0010.0010.0000.0000.0000.000
135A184THR00.0340.02445.0350.0000.0000.0000.0000.0000.000
136A185SER0-0.004-0.01646.2140.0000.0000.0000.0000.0000.000
137A186ASN0-0.060-0.02946.9850.0030.0030.0000.0000.0000.000
138A187ALA0-0.054-0.01250.3070.0010.0010.0000.0000.0000.000
139A188VAL0-0.014-0.01752.1890.0010.0010.0000.0000.0000.000
140A189PRO00.0190.01555.975-0.001-0.0010.0000.0000.0000.000
141A190GLU-1-0.736-0.83457.379-0.019-0.0190.0000.0000.0000.000
142A191PRO0-0.038-0.03360.2960.0010.0010.0000.0000.0000.000
143A192ASP-1-0.865-0.90763.039-0.015-0.0150.0000.0000.0000.000
144A193GLY0-0.029-0.01260.8190.0000.0000.0000.0000.0000.000
145A194SER0-0.090-0.05559.792-0.001-0.0010.0000.0000.0000.000
146A195ASP-1-0.942-0.97554.784-0.021-0.0210.0000.0000.0000.000
147A196SER0-0.020-0.01553.6480.0000.0000.0000.0000.0000.000
148A197GLU-1-0.869-0.94654.008-0.029-0.0290.0000.0000.0000.000
149A198LYS10.9000.93847.8520.0310.0310.0000.0000.0000.000
150A199ASN0-0.0240.00849.932-0.001-0.0010.0000.0000.0000.000
151A200LEU00.0440.00349.7590.0010.0010.0000.0000.0000.000
152A201PHE00.009-0.00248.5190.0010.0010.0000.0000.0000.000
153A202VAL00.0480.05853.6240.0010.0010.0000.0000.0000.000
154A203MET0-0.0620.00352.4470.0020.0020.0000.0000.0000.000
155A204LEU0-0.014-0.00754.3730.0010.0010.0000.0000.0000.000
156A205ASP-1-0.771-0.88657.001-0.030-0.0300.0000.0000.0000.000
157A206THR0-0.080-0.05659.3330.0010.0010.0000.0000.0000.000
158A207ALA00.0200.02661.1700.0010.0010.0000.0000.0000.000
159A208ILE00.0000.00659.6200.0010.0010.0000.0000.0000.000
160A209ALA0-0.029-0.01963.5350.0010.0010.0000.0000.0000.000
161A210ALA00.0030.00465.4760.0010.0010.0000.0000.0000.000
162A211LEU0-0.045-0.03065.0260.0010.0010.0000.0000.0000.000
163A212LYS10.9100.95865.6720.0240.0240.0000.0000.0000.000
164A213THR0-0.066-0.00869.4390.0000.0000.0000.0000.0000.000
165A214PRO00.0060.01771.8920.0000.0000.0000.0000.0000.000
166A215VAL0-0.037-0.04173.6710.0000.0000.0000.0000.0000.000
167A216GLU-1-0.980-0.98076.543-0.014-0.0140.0000.0000.0000.000
168A217GLY0-0.023-0.01679.8690.0000.0000.0000.0000.0000.000
169A218ASN00.0080.00978.7150.0000.0000.0000.0000.0000.000
170A219ASN00.0440.00178.213-0.001-0.0010.0000.0000.0000.000
171A220VAL0-0.026-0.00976.6130.0000.0000.0000.0000.0000.000
172A221GLU-1-0.897-0.95873.580-0.017-0.0170.0000.0000.0000.000
173A222LYS10.8920.95473.3260.0130.0130.0000.0000.0000.000
174A223GLU-1-0.955-0.97572.376-0.014-0.0140.0000.0000.0000.000
175A224LYS10.9580.98369.9740.0150.0150.0000.0000.0000.000
176A225ALA00.006-0.00368.943-0.001-0.0010.0000.0000.0000.000
177A226ALA0-0.001-0.00568.114-0.001-0.0010.0000.0000.0000.000
178A227ALA00.0680.04367.7020.0000.0000.0000.0000.0000.000
179A228ALA0-0.040-0.02664.572-0.001-0.0010.0000.0000.0000.000
180A229ILE00.0080.00263.381-0.001-0.0010.0000.0000.0000.000
181A230ASP-1-0.893-0.94063.293-0.016-0.0160.0000.0000.0000.000
182A231LYS10.8910.93558.9690.0210.0210.0000.0000.0000.000
183A232THR0-0.001-0.00558.6500.0000.0000.0000.0000.0000.000
184A233ASN0-0.030-0.01358.4260.0000.0000.0000.0000.0000.000
185A234ARG10.7660.84658.2900.0170.0170.0000.0000.0000.000
186A235GLY00.0460.01855.3360.0000.0000.0000.0000.0000.000
187A236LEU00.0550.00553.922-0.001-0.0010.0000.0000.0000.000
188A237LYS10.9040.96753.5350.0170.0170.0000.0000.0000.000
189A238ASN00.0080.01351.8300.0000.0000.0000.0000.0000.000
190A239SER00.0150.01349.470-0.001-0.0010.0000.0000.0000.000
191A240LEU0-0.020-0.02048.603-0.002-0.0020.0000.0000.0000.000
192A241ASN00.0050.00948.322-0.001-0.0010.0000.0000.0000.000
193A242ASN0-0.013-0.01044.0220.0000.0000.0000.0000.0000.000
194A243VAL00.004-0.01144.125-0.002-0.0020.0000.0000.0000.000
195A244LEU0-0.036-0.00643.600-0.002-0.0020.0000.0000.0000.000
196A245THR00.000-0.01641.1460.0000.0000.0000.0000.0000.000
197A246VAL00.0170.01138.473-0.001-0.0010.0000.0000.0000.000
198A247ARG10.8890.94138.7180.0340.0340.0000.0000.0000.000
199A248ALA00.0080.02839.202-0.001-0.0010.0000.0000.0000.000
200A249GLU-1-0.925-0.96935.906-0.033-0.0330.0000.0000.0000.000
201A250LEU0-0.024-0.02534.653-0.004-0.0040.0000.0000.0000.000
202A251GLY00.0340.03134.541-0.004-0.0040.0000.0000.0000.000
203A252THR0-0.033-0.01632.3360.0000.0000.0000.0000.0000.000
204A253GLN00.0180.00430.661-0.006-0.0060.0000.0000.0000.000
205A254LEU0-0.012-0.01329.955-0.007-0.0070.0000.0000.0000.000
206A255SER0-0.035-0.01030.774-0.003-0.0030.0000.0000.0000.000
207A256GLU-1-0.909-0.97127.251-0.058-0.0580.0000.0000.0000.000
208A257LEU0-0.026-0.02725.496-0.007-0.0070.0000.0000.0000.000
209A258SER00.0380.01025.996-0.008-0.0080.0000.0000.0000.000
210A259THR00.0240.02026.0810.0030.0030.0000.0000.0000.000
211A260LEU0-0.074-0.04721.6340.0080.0080.0000.0000.0000.000
212A261ASP-1-1.058-1.02122.308-0.122-0.1220.0000.0000.0000.000
213A262SER0-0.011-0.00523.932-0.002-0.0020.0000.0000.0000.000
214A263LEU0-0.107-0.03520.2790.0110.0110.0000.0000.0000.000