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: 72J8K

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2160451.94557
FMO2-HF: Nuclear repulsion 2081051.643568
FMO2-HF: Total energy -79400.302001
FMO2-MP2: Total energy -79633.983053


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.
-5.379-0.340.805-2.335-3.509-0.004
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 : 0.034 / q_NPA : 0.006
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].
3A52LEU00.0190.0253.168-3.266-1.0830.022-0.868-1.3370.003
4A53SER00.0310.0192.588-1.843-0.4030.721-0.868-1.293-0.005
5A54GLN0-0.022-0.0173.302-1.1400.2760.062-0.599-0.879-0.002
6A55ALA00.0470.0285.4710.5270.5270.0000.0000.0000.000
7A56GLN0-0.008-0.0207.5600.0140.0140.0000.0000.0000.000
8A57ALA00.0180.0318.3720.1420.1420.0000.0000.0000.000
9A58GLN0-0.021-0.0077.9490.0080.0080.0000.0000.0000.000
10A59ASN00.011-0.01611.1320.0840.0840.0000.0000.0000.000
11A60SER0-0.014-0.01812.2820.0660.0660.0000.0000.0000.000
12A61GLN0-0.024-0.01613.2360.0540.0540.0000.0000.0000.000
13A62TYR0-0.015-0.01313.8030.0200.0200.0000.0000.0000.000
14A63ALA00.0240.01317.3010.0340.0340.0000.0000.0000.000
15A64LEU00.0100.01217.5580.0260.0260.0000.0000.0000.000
16A65ALA00.0040.01119.9230.0230.0230.0000.0000.0000.000
17A66ARG10.8930.94020.5190.1610.1610.0000.0000.0000.000
18A67THR0-0.0210.00222.9410.0170.0170.0000.0000.0000.000
19A68PHE0-0.027-0.01124.6710.0110.0110.0000.0000.0000.000
20A69ALA00.003-0.01025.7750.0110.0110.0000.0000.0000.000
21A70THR00.0510.01927.5090.0100.0100.0000.0000.0000.000
22A71GLN0-0.0190.00329.2150.0030.0030.0000.0000.0000.000
23A72LYS10.8000.90830.5450.0820.0820.0000.0000.0000.000
24A73VAL00.0850.03030.8390.0060.0060.0000.0000.0000.000
25A74SER0-0.007-0.01333.2460.0070.0070.0000.0000.0000.000
26A75LEU0-0.0310.00235.4450.0040.0040.0000.0000.0000.000
27A76GLU-1-0.802-0.90234.512-0.063-0.0630.0000.0000.0000.000
28A77GLU-1-0.762-0.87137.467-0.036-0.0360.0000.0000.0000.000
29A78SER0-0.025-0.01439.2290.0040.0040.0000.0000.0000.000
30A79VAL0-0.013-0.01141.1490.0030.0030.0000.0000.0000.000
31A80LEU00.0390.01740.4700.0030.0030.0000.0000.0000.000
32A81SER0-0.0250.00043.4090.0040.0040.0000.0000.0000.000
33A82GLN0-0.002-0.01145.3030.0010.0010.0000.0000.0000.000
34A83VAL00.0090.00945.5690.0020.0020.0000.0000.0000.000
35A84THR0-0.030-0.02046.5970.0020.0020.0000.0000.0000.000
36A85THR00.0230.01749.1050.0020.0020.0000.0000.0000.000
37A86ALA00.0170.02451.2170.0010.0010.0000.0000.0000.000
38A87ILE00.0280.00249.5430.0010.0010.0000.0000.0000.000
39A88GLN0-0.003-0.01252.3430.0010.0010.0000.0000.0000.000
40A89THR0-0.028-0.01655.1790.0010.0010.0000.0000.0000.000
41A90ALA00.0250.01056.5980.0010.0010.0000.0000.0000.000
42A91GLN0-0.021-0.01855.9310.0010.0010.0000.0000.0000.000
43A92GLU-1-0.859-0.91158.869-0.017-0.0170.0000.0000.0000.000
44A93LYS10.8900.94761.3300.0200.0200.0000.0000.0000.000
45A94ILE0-0.020-0.01760.3270.0010.0010.0000.0000.0000.000
46A95VAL0-0.041-0.02062.1910.0010.0010.0000.0000.0000.000
47A96TYR0-0.088-0.06064.7010.0010.0010.0000.0000.0000.000
48A97ALA0-0.006-0.00266.1460.0010.0010.0000.0000.0000.000
49A98GLY0-0.0110.00467.6370.0000.0000.0000.0000.0000.000
50A99ASN0-0.0060.00968.8160.0010.0010.0000.0000.0000.000
51A100GLY00.0540.01972.1890.0000.0000.0000.0000.0000.000
52A101THR0-0.107-0.06774.9890.0000.0000.0000.0000.0000.000
53A102LEU0-0.0380.00570.7100.0000.0000.0000.0000.0000.000
54A103SER00.0580.03875.2530.0000.0000.0000.0000.0000.000
55A104ASP-1-0.693-0.84174.850-0.014-0.0140.0000.0000.0000.000
56A105ASP-1-0.895-0.93174.048-0.015-0.0150.0000.0000.0000.000
57A106ASP-1-0.894-0.95772.852-0.014-0.0140.0000.0000.0000.000
58A107ARG10.7910.86670.4730.0140.0140.0000.0000.0000.000
59A108ALA00.0500.02969.168-0.001-0.0010.0000.0000.0000.000
60A109SER0-0.033-0.02468.617-0.001-0.0010.0000.0000.0000.000
61A110LEU00.0060.00466.118-0.001-0.0010.0000.0000.0000.000
62A111ALA0-0.0060.00164.734-0.001-0.0010.0000.0000.0000.000
63A112THR0-0.045-0.02663.847-0.001-0.0010.0000.0000.0000.000
64A113ASP-1-0.853-0.92162.957-0.021-0.0210.0000.0000.0000.000
65A114LEU0-0.050-0.03259.842-0.001-0.0010.0000.0000.0000.000
66A115GLN0-0.050-0.03558.9240.0000.0000.0000.0000.0000.000
67A116GLY00.0340.02058.545-0.001-0.0010.0000.0000.0000.000
68A117ILE0-0.017-0.00955.395-0.001-0.0010.0000.0000.0000.000
69A118ARG10.7150.82754.6430.0270.0270.0000.0000.0000.000
70A119ASP-1-0.781-0.88953.808-0.031-0.0310.0000.0000.0000.000
71A120GLN0-0.055-0.02052.640-0.001-0.0010.0000.0000.0000.000
72A121LEU00.0140.00349.766-0.002-0.0020.0000.0000.0000.000
73A122MET0-0.0260.01549.006-0.002-0.0020.0000.0000.0000.000
74A123ASN0-0.084-0.06248.445-0.003-0.0030.0000.0000.0000.000
75A124LEU0-0.0130.01046.258-0.002-0.0020.0000.0000.0000.000
76A125ALA00.0120.01244.587-0.003-0.0030.0000.0000.0000.000
77A126ASN0-0.048-0.03243.807-0.004-0.0040.0000.0000.0000.000
78A127SER00.035-0.00142.052-0.001-0.0010.0000.0000.0000.000
79A128THR0-0.010-0.00239.514-0.001-0.0010.0000.0000.0000.000
80A129ASP-1-0.842-0.92634.361-0.084-0.0840.0000.0000.0000.000
81A130GLY0-0.009-0.00936.4240.0020.0020.0000.0000.0000.000
82A131ASN0-0.102-0.05732.522-0.003-0.0030.0000.0000.0000.000
83A132GLY0-0.016-0.01036.1560.0000.0000.0000.0000.0000.000
84A133ARG10.8570.94632.3760.0960.0960.0000.0000.0000.000
85A134TYR00.003-0.01136.8860.0020.0020.0000.0000.0000.000
86A135ILE0-0.038-0.03136.442-0.003-0.0030.0000.0000.0000.000
87A136PHE00.0150.01937.0340.0000.0000.0000.0000.0000.000
88A137ALA00.0540.01237.8200.0030.0030.0000.0000.0000.000
89A138GLY00.0300.02534.8720.0000.0000.0000.0000.0000.000
90A139TYR00.020-0.00628.334-0.005-0.0050.0000.0000.0000.000
91A140LYS10.7840.90733.5390.0490.0490.0000.0000.0000.000
92A141THR0-0.003-0.03333.8050.0020.0020.0000.0000.0000.000
93A142GLU-1-0.803-0.87135.364-0.083-0.0830.0000.0000.0000.000
94A143ALA0-0.036-0.01438.8020.0020.0020.0000.0000.0000.000
95A144ALA0-0.0090.00941.881-0.001-0.0010.0000.0000.0000.000
96A145PRO00.0010.01141.7120.0010.0010.0000.0000.0000.000
97A146PHE00.0100.01043.6290.0020.0020.0000.0000.0000.000
98A147ASP-1-0.805-0.85147.269-0.034-0.0340.0000.0000.0000.000
99A148GLN00.0500.01350.4650.0000.0000.0000.0000.0000.000
100A149ALA0-0.014-0.01453.1050.0010.0010.0000.0000.0000.000
101A150THR0-0.029-0.04253.5790.0010.0010.0000.0000.0000.000
102A151GLY00.0740.04251.0580.0010.0010.0000.0000.0000.000
103A152GLY0-0.0010.01550.0640.0000.0000.0000.0000.0000.000
104A153TYR0-0.034-0.03539.388-0.002-0.0020.0000.0000.0000.000
105A154HIS10.7990.86244.5820.0390.0390.0000.0000.0000.000
106A155GLY00.0770.04340.691-0.002-0.0020.0000.0000.0000.000
107A156GLY0-0.078-0.03637.0150.0020.0020.0000.0000.0000.000
108A157GLU-1-0.869-0.93637.815-0.040-0.0400.0000.0000.0000.000
109A158LYS10.8800.94332.8360.0460.0460.0000.0000.0000.000
110A159SER00.0800.04431.5180.0000.0000.0000.0000.0000.000
111A160VAL0-0.0130.00228.809-0.003-0.0030.0000.0000.0000.000
112A161THR0-0.0180.01125.9080.0050.0050.0000.0000.0000.000
113A162GLN00.005-0.00922.351-0.014-0.0140.0000.0000.0000.000
114A163GLN00.0210.03618.6670.0200.0200.0000.0000.0000.000
115A164VAL0-0.007-0.00920.160-0.017-0.0170.0000.0000.0000.000
116A165ASP-1-0.841-0.92417.769-0.102-0.1020.0000.0000.0000.000
117A166SER00.0020.00213.673-0.010-0.0100.0000.0000.0000.000
118A167ALA0-0.045-0.00416.4130.0090.0090.0000.0000.0000.000
119A168ARG10.8380.90419.7270.0610.0610.0000.0000.0000.000
120A169THR0-0.014-0.03021.229-0.013-0.0130.0000.0000.0000.000
121A170MET0-0.025-0.00323.7090.0090.0090.0000.0000.0000.000
122A171VAL00.000-0.00626.345-0.008-0.0080.0000.0000.0000.000
123A172ILE0-0.049-0.03126.536-0.001-0.0010.0000.0000.0000.000
124A173GLY00.0710.02130.3430.0000.0000.0000.0000.0000.000
125A174HIS0-0.0170.00733.4890.0000.0000.0000.0000.0000.000
126A175THR0-0.023-0.03136.028-0.001-0.0010.0000.0000.0000.000
127A176GLY00.0860.02438.1770.0020.0020.0000.0000.0000.000
128A177ALA0-0.0010.00541.3270.0030.0030.0000.0000.0000.000
129A178GLN00.0010.00436.0910.0000.0000.0000.0000.0000.000
130A179ILE00.0130.04039.5390.0020.0020.0000.0000.0000.000
131A180PHE0-0.003-0.01843.2920.0020.0020.0000.0000.0000.000
132A181ASN0-0.030-0.01945.5400.0030.0030.0000.0000.0000.000
133A182SER0-0.032-0.01344.0070.0000.0000.0000.0000.0000.000
134A183ILE0-0.014-0.00146.2240.0000.0000.0000.0000.0000.000
135A184THR00.0300.01144.7480.0000.0000.0000.0000.0000.000
136A185SER00.019-0.00446.2890.0000.0000.0000.0000.0000.000
137A186ASN0-0.095-0.05446.9490.0020.0020.0000.0000.0000.000
138A187ALA0-0.056-0.00950.4000.0000.0000.0000.0000.0000.000
139A188VAL00.010-0.00452.2360.0010.0010.0000.0000.0000.000
140A189PRO00.0170.01256.022-0.001-0.0010.0000.0000.0000.000
141A190GLU-1-0.745-0.83157.426-0.015-0.0150.0000.0000.0000.000
142A191PRO0-0.016-0.02060.3120.0010.0010.0000.0000.0000.000
143A192ASP-1-0.859-0.90362.905-0.012-0.0120.0000.0000.0000.000
144A193GLY0-0.040-0.01660.8790.0000.0000.0000.0000.0000.000
145A194SER0-0.097-0.06559.832-0.001-0.0010.0000.0000.0000.000
146A195ASP-1-0.926-0.96554.837-0.015-0.0150.0000.0000.0000.000
147A196SER0-0.019-0.01953.6300.0000.0000.0000.0000.0000.000
148A197GLU-1-0.855-0.91453.693-0.023-0.0230.0000.0000.0000.000
149A198LYS10.9100.92948.2790.0230.0230.0000.0000.0000.000
150A199ASN0-0.050-0.02049.957-0.001-0.0010.0000.0000.0000.000
151A200LEU00.0540.01049.9490.0010.0010.0000.0000.0000.000
152A201PHE00.019-0.00148.5720.0010.0010.0000.0000.0000.000
153A202VAL00.0530.05453.7760.0010.0010.0000.0000.0000.000
154A203MET0-0.0430.02052.4840.0010.0010.0000.0000.0000.000
155A204LEU0-0.0140.00254.6230.0010.0010.0000.0000.0000.000
156A205ASP-1-0.763-0.86257.111-0.025-0.0250.0000.0000.0000.000
157A206THR0-0.061-0.04959.4960.0010.0010.0000.0000.0000.000
158A207ALA00.0200.02361.2880.0010.0010.0000.0000.0000.000
159A208ILE0-0.0040.00159.7990.0010.0010.0000.0000.0000.000
160A209ALA0-0.039-0.02263.7020.0010.0010.0000.0000.0000.000
161A210ALA00.0060.00565.6130.0010.0010.0000.0000.0000.000
162A211LEU0-0.041-0.02665.2690.0010.0010.0000.0000.0000.000
163A212LYS10.9130.95865.5580.0200.0200.0000.0000.0000.000
164A213THR0-0.069-0.00969.6430.0000.0000.0000.0000.0000.000
165A214PRO00.0000.02372.0620.0000.0000.0000.0000.0000.000
166A215VAL0-0.027-0.04773.8080.0000.0000.0000.0000.0000.000
167A216GLU-1-0.962-0.97776.675-0.012-0.0120.0000.0000.0000.000
168A217GLY0-0.031-0.01780.0110.0000.0000.0000.0000.0000.000
169A218ASN0-0.009-0.00278.8060.0000.0000.0000.0000.0000.000
170A219ASN00.0480.00178.2880.0000.0000.0000.0000.0000.000
171A220VAL0-0.0040.01077.2830.0000.0000.0000.0000.0000.000
172A221GLU-1-0.820-0.90773.627-0.013-0.0130.0000.0000.0000.000
173A222LYS10.9110.95773.3960.0110.0110.0000.0000.0000.000
174A223GLU-1-0.939-0.95972.552-0.011-0.0110.0000.0000.0000.000
175A224LYS10.8490.90869.7740.0130.0130.0000.0000.0000.000
176A225ALA00.0030.00169.0160.0000.0000.0000.0000.0000.000
177A226ALA00.007-0.00268.177-0.001-0.0010.0000.0000.0000.000
178A227ALA00.0380.02067.7510.0000.0000.0000.0000.0000.000
179A228ALA0-0.022-0.01264.5990.0000.0000.0000.0000.0000.000
180A229ILE0-0.009-0.00463.424-0.001-0.0010.0000.0000.0000.000
181A230ASP-1-0.867-0.91763.334-0.013-0.0130.0000.0000.0000.000
182A231LYS10.8710.92059.1910.0150.0150.0000.0000.0000.000
183A232THR00.000-0.01158.6360.0000.0000.0000.0000.0000.000
184A233ASN0-0.026-0.00758.4680.0000.0000.0000.0000.0000.000
185A234ARG10.7720.84658.2380.0130.0130.0000.0000.0000.000
186A235GLY00.0400.01555.3200.0000.0000.0000.0000.0000.000
187A236LEU00.0370.00053.936-0.001-0.0010.0000.0000.0000.000
188A237LYS10.8870.95553.5760.0130.0130.0000.0000.0000.000
189A238ASN0-0.0060.00051.8650.0000.0000.0000.0000.0000.000
190A239SER00.0280.01449.574-0.001-0.0010.0000.0000.0000.000
191A240LEU0-0.017-0.01448.642-0.001-0.0010.0000.0000.0000.000
192A241ASN00.0160.02648.226-0.001-0.0010.0000.0000.0000.000
193A242ASN0-0.020-0.00544.1110.0000.0000.0000.0000.0000.000
194A243VAL00.010-0.00644.131-0.002-0.0020.0000.0000.0000.000
195A244LEU0-0.025-0.00243.665-0.002-0.0020.0000.0000.0000.000
196A245THR00.005-0.01941.2200.0000.0000.0000.0000.0000.000
197A246VAL00.0080.00538.548-0.001-0.0010.0000.0000.0000.000
198A247ARG10.8150.89738.7670.0310.0310.0000.0000.0000.000
199A248ALA0-0.0100.01039.278-0.001-0.0010.0000.0000.0000.000
200A249GLU-1-0.918-0.95735.850-0.028-0.0280.0000.0000.0000.000
201A250LEU0-0.022-0.02334.745-0.003-0.0030.0000.0000.0000.000
202A251GLY00.0020.01434.649-0.004-0.0040.0000.0000.0000.000
203A252THR0-0.002-0.00832.476-0.001-0.0010.0000.0000.0000.000
204A253GLN00.006-0.00330.682-0.006-0.0060.0000.0000.0000.000
205A254LEU0-0.024-0.01530.047-0.006-0.0060.0000.0000.0000.000
206A255SER0-0.015-0.00330.921-0.004-0.0040.0000.0000.0000.000
207A256GLU-1-0.861-0.91626.936-0.049-0.0490.0000.0000.0000.000
208A257LEU0-0.002-0.01125.386-0.006-0.0060.0000.0000.0000.000
209A258SER00.0130.00826.130-0.006-0.0060.0000.0000.0000.000
210A259THR0-0.009-0.01226.3240.0020.0020.0000.0000.0000.000
211A260LEU0-0.073-0.04322.0090.0020.0020.0000.0000.0000.000
212A261ASP-1-0.952-0.96922.285-0.128-0.1280.0000.0000.0000.000
213A262SER0-0.044-0.02423.886-0.003-0.0030.0000.0000.0000.000
214A263LEU0-0.111-0.03020.1590.0060.0060.0000.0000.0000.000