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

tag_button

FMODB ID: JQK69

Calculation Name: 3P01-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P01

Chain ID: A

ChEMBL ID:

UniProt ID: Q8YLP5

Base Structure: X-ray

Registration Date: 2023-09-23

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1761074.620194
FMO2-HF: Nuclear repulsion 1692462.209483
FMO2-HF: Total energy -68612.410711
FMO2-MP2: Total energy -68812.874455


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:137:GLN)


Summations of interaction energy for fragment #1(A:137:GLN)
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.
-2.4253.3112.317-2.805-5.246-0.001
Interaction energy analysis for fragmet #1(A:137:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.004
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].
3A139ALA00.0130.0182.482-3.0620.6192.029-2.077-3.6320.003
4A140ALA0-0.011-0.0082.707-2.084-0.3400.288-0.689-1.342-0.004
5A141GLU-1-0.805-0.8644.1640.7831.0940.000-0.039-0.2720.000
6A142THR00.004-0.0106.3450.9920.9920.0000.0000.0000.000
7A143TYR00.0000.0007.3780.2690.2690.0000.0000.0000.000
8A144ASP-1-0.808-0.8998.824-0.700-0.7000.0000.0000.0000.000
9A145LEU00.0220.00510.6040.2450.2450.0000.0000.0000.000
10A146LEU00.0010.01011.9910.1330.1330.0000.0000.0000.000
11A147LYS10.8380.92812.5870.9460.9460.0000.0000.0000.000
12A148GLN0-0.004-0.00113.4740.0460.0460.0000.0000.0000.000
13A149ARG10.9670.99816.4350.2730.2730.0000.0000.0000.000
14A150THR0-0.006-0.02117.1840.0320.0320.0000.0000.0000.000
15A151GLU-1-0.783-0.86019.357-0.310-0.3100.0000.0000.0000.000
16A152GLU-1-0.902-0.96720.149-0.210-0.2100.0000.0000.0000.000
17A153LEU0-0.045-0.01822.2000.0280.0280.0000.0000.0000.000
18A154ARG10.8860.94623.5550.3070.3070.0000.0000.0000.000
19A155ARG10.8620.90223.0490.2920.2920.0000.0000.0000.000
20A156ALA00.0420.02226.7920.0170.0170.0000.0000.0000.000
21A157ASN0-0.015-0.02127.1540.0310.0310.0000.0000.0000.000
22A158ALA0-0.0110.00029.7280.0100.0100.0000.0000.0000.000
23A159GLN00.0210.00431.0250.0070.0070.0000.0000.0000.000
24A160MET00.0140.00932.7570.0120.0120.0000.0000.0000.000
25A161SER0-0.0460.00434.0240.0120.0120.0000.0000.0000.000
26A162LEU00.0840.05135.7760.0060.0060.0000.0000.0000.000
27A163LEU0-0.011-0.02037.3460.0090.0090.0000.0000.0000.000
28A164THR0-0.051-0.04137.5720.0080.0080.0000.0000.0000.000
29A165VAL00.0090.00539.8790.0060.0060.0000.0000.0000.000
30A166LEU00.0170.00841.9500.0060.0060.0000.0000.0000.000
31A167VAL0-0.0060.02543.3250.0060.0060.0000.0000.0000.000
32A168GLN0-0.043-0.03141.8320.0010.0010.0000.0000.0000.000
33A169VAL00.0250.01645.7830.0030.0030.0000.0000.0000.000
34A170THR0-0.021-0.02347.7100.0030.0030.0000.0000.0000.000
35A171GLN0-0.073-0.04048.6360.0040.0040.0000.0000.0000.000
36A172ALA0-0.024-0.00450.1130.0020.0020.0000.0000.0000.000
37A173SER0-0.045-0.02351.7970.0000.0000.0000.0000.0000.000
38A174ASN0-0.027-0.02354.1650.0040.0040.0000.0000.0000.000
39A175SER0-0.0010.00356.9400.0020.0020.0000.0000.0000.000
40A176LEU00.0630.02055.734-0.002-0.0020.0000.0000.0000.000
41A177GLU-1-0.891-0.96055.386-0.052-0.0520.0000.0000.0000.000
42A178ALA0-0.058-0.02455.229-0.003-0.0030.0000.0000.0000.000
43A179ILE00.0240.02750.400-0.004-0.0040.0000.0000.0000.000
44A180LEU0-0.0100.00150.347-0.004-0.0040.0000.0000.0000.000
45A181THR00.0440.01949.806-0.002-0.0020.0000.0000.0000.000
46A182PRO00.0060.02547.649-0.006-0.0060.0000.0000.0000.000
47A183ILE00.0450.02945.760-0.006-0.0060.0000.0000.0000.000
48A184ALA00.0230.00944.875-0.005-0.0050.0000.0000.0000.000
49A185THR0-0.028-0.04843.862-0.005-0.0050.0000.0000.0000.000
50A186ALA0-0.0180.00141.751-0.008-0.0080.0000.0000.0000.000
51A187PHE0-0.014-0.02740.277-0.007-0.0070.0000.0000.0000.000
52A188ALA00.010-0.01639.579-0.007-0.0070.0000.0000.0000.000
53A189GLU-1-0.926-0.96038.187-0.159-0.1590.0000.0000.0000.000
54A190SER0-0.059-0.03735.759-0.012-0.0120.0000.0000.0000.000
55A191PHE0-0.058-0.02534.684-0.007-0.0070.0000.0000.0000.000
56A192ALA0-0.0010.01234.639-0.003-0.0030.0000.0000.0000.000
57A193VAL0-0.0500.02136.606-0.001-0.0010.0000.0000.0000.000
58A194ASN00.008-0.00239.656-0.007-0.0070.0000.0000.0000.000
59A195ALA0-0.017-0.01742.1750.0020.0020.0000.0000.0000.000
60A196CYS0-0.050-0.00243.6820.0000.0000.0000.0000.0000.000
61A197ILE00.0100.00545.5180.0020.0020.0000.0000.0000.000
62A198LEU00.0050.00848.2600.0010.0010.0000.0000.0000.000
63A199GLN00.021-0.00450.116-0.001-0.0010.0000.0000.0000.000
64A200MET0-0.028-0.00952.8050.0020.0020.0000.0000.0000.000
65A201LEU00.0160.01254.518-0.001-0.0010.0000.0000.0000.000
66A202GLU-1-0.880-0.91357.780-0.039-0.0390.0000.0000.0000.000
67A203GLY0-0.015-0.01461.4150.0000.0000.0000.0000.0000.000
68A204GLN0-0.024-0.02158.4450.0000.0000.0000.0000.0000.000
69A205THR0-0.0060.00959.090-0.001-0.0010.0000.0000.0000.000
70A206LEU0-0.023-0.00654.3890.0000.0000.0000.0000.0000.000
71A207SER0-0.031-0.03258.2420.0010.0010.0000.0000.0000.000
72A208THR00.018-0.00258.770-0.003-0.0030.0000.0000.0000.000
73A209ILE0-0.015-0.00557.375-0.003-0.0030.0000.0000.0000.000
74A210GLN00.012-0.00554.154-0.003-0.0030.0000.0000.0000.000
75A211GLY00.0150.01652.2540.0010.0010.0000.0000.0000.000
76A212PHE0-0.044-0.03049.3470.0000.0000.0000.0000.0000.000
77A213TYR00.0370.01543.0840.0000.0000.0000.0000.0000.000
78A214SER00.014-0.00545.914-0.001-0.0010.0000.0000.0000.000
79A215GLN0-0.0060.00639.693-0.005-0.0050.0000.0000.0000.000
80A216GLN0-0.082-0.03344.8690.0020.0020.0000.0000.0000.000
81A217GLY00.0070.00547.9450.0010.0010.0000.0000.0000.000
82A218THR0-0.049-0.03851.2190.0050.0050.0000.0000.0000.000
83A219VAL00.0130.01650.287-0.004-0.0040.0000.0000.0000.000
84A220ASN0-0.029-0.02151.4970.0060.0060.0000.0000.0000.000
85A221ASN0-0.027-0.01852.103-0.001-0.0010.0000.0000.0000.000
86A222TRP00.0220.01048.3930.0040.0040.0000.0000.0000.000
87A223LEU00.0380.01149.7140.0010.0010.0000.0000.0000.000
88A224ASN00.0130.00553.5050.0000.0000.0000.0000.0000.000
89A225GLN0-0.063-0.03455.8840.0010.0010.0000.0000.0000.000
90A226ASP-1-0.696-0.78649.911-0.068-0.0680.0000.0000.0000.000
91A227PRO0-0.017-0.01251.1470.0020.0020.0000.0000.0000.000
92A228LEU0-0.0210.00544.6050.0030.0030.0000.0000.0000.000
93A229THR00.013-0.04049.1600.0010.0010.0000.0000.0000.000
94A230ASN0-0.034-0.01550.8740.0030.0030.0000.0000.0000.000
95A231GLU-1-0.924-0.95648.879-0.043-0.0430.0000.0000.0000.000
96A232ALA0-0.010-0.00448.4770.0020.0020.0000.0000.0000.000
97A233ILE0-0.007-0.01949.9670.0020.0020.0000.0000.0000.000
98A234ALA0-0.0260.00253.4400.0020.0020.0000.0000.0000.000
99A235THR0-0.054-0.03849.6040.0020.0020.0000.0000.0000.000
100A236GLY0-0.003-0.00150.4450.0020.0020.0000.0000.0000.000
101A237GLN0-0.026-0.00645.035-0.001-0.0010.0000.0000.0000.000
102A238ILE0-0.021-0.02539.991-0.002-0.0020.0000.0000.0000.000
103A239GLN0-0.0190.00944.0370.0010.0010.0000.0000.0000.000
104A240VAL0-0.009-0.01237.695-0.006-0.0060.0000.0000.0000.000
105A241ALA00.0400.03741.1470.0030.0030.0000.0000.0000.000
106A242ALA00.008-0.01136.126-0.004-0.0040.0000.0000.0000.000
107A243ASN00.003-0.02936.801-0.006-0.0060.0000.0000.0000.000
108A244ILE00.0640.04739.5880.0050.0050.0000.0000.0000.000
109A245ALA0-0.018-0.00441.9010.0040.0040.0000.0000.0000.000
110A246LYS10.8750.92736.5340.1040.1040.0000.0000.0000.000
111A247ASP-1-0.795-0.89043.000-0.058-0.0580.0000.0000.0000.000
112A248PRO00.0070.00745.409-0.001-0.0010.0000.0000.0000.000
113A249LYS10.8660.94647.9800.0550.0550.0000.0000.0000.000
114A250LEU0-0.033-0.03045.5810.0000.0000.0000.0000.0000.000
115A251ALA0-0.030-0.01446.768-0.002-0.0020.0000.0000.0000.000
116A252SER0-0.044-0.02448.311-0.001-0.0010.0000.0000.0000.000
117A253ILE0-0.0300.01051.1780.0020.0020.0000.0000.0000.000
118A254SER00.022-0.00251.712-0.003-0.0030.0000.0000.0000.000
119A255GLN00.0490.03152.621-0.003-0.0030.0000.0000.0000.000
120A256TYR0-0.020-0.03546.106-0.005-0.0050.0000.0000.0000.000
121A257GLN0-0.031-0.01747.963-0.003-0.0030.0000.0000.0000.000
122A258ASP-1-0.867-0.93348.981-0.080-0.0800.0000.0000.0000.000
123A259ASN0-0.073-0.04448.397-0.003-0.0030.0000.0000.0000.000
124A260GLY0-0.0130.00545.644-0.006-0.0060.0000.0000.0000.000
125A261ILE0-0.053-0.02643.697-0.006-0.0060.0000.0000.0000.000
126A262GLN00.024-0.01039.7920.0000.0000.0000.0000.0000.000
127A263SER0-0.055-0.02438.3440.0010.0010.0000.0000.0000.000
128A264HIS0-0.0060.00340.565-0.002-0.0020.0000.0000.0000.000
129A265VAL00.0060.01038.8640.0030.0030.0000.0000.0000.000
130A266VAL00.0060.00542.214-0.002-0.0020.0000.0000.0000.000
131A267ILE0-0.010-0.00842.4560.0030.0030.0000.0000.0000.000
132A268PRO00.0130.01445.516-0.001-0.0010.0000.0000.0000.000
133A269ILE0-0.013-0.01447.084-0.001-0.0010.0000.0000.0000.000
134A270THR00.0240.00249.0740.0010.0010.0000.0000.0000.000
135A271TYR00.0090.00949.9270.0010.0010.0000.0000.0000.000
136A272ARG10.9070.94651.5980.0270.0270.0000.0000.0000.000
137A273ASN00.013-0.01352.256-0.001-0.0010.0000.0000.0000.000
138A274GLU-1-0.951-0.95554.533-0.031-0.0310.0000.0000.0000.000
139A275MET0-0.0310.01052.164-0.003-0.0030.0000.0000.0000.000
140A276LEU0-0.008-0.00153.1360.0000.0000.0000.0000.0000.000
141A277GLY00.0370.00452.9910.0000.0000.0000.0000.0000.000
142A278VAL0-0.0110.01449.7430.0010.0010.0000.0000.0000.000
143A279LEU00.0100.00443.583-0.001-0.0010.0000.0000.0000.000
144A280SER0-0.045-0.02845.850-0.001-0.0010.0000.0000.0000.000
145A281LEU00.009-0.00739.557-0.003-0.0030.0000.0000.0000.000
146A282GLN00.0590.01942.603-0.001-0.0010.0000.0000.0000.000
147A283TRP00.0390.01736.6960.0000.0000.0000.0000.0000.000
148A284GLN00.015-0.00239.952-0.001-0.0010.0000.0000.0000.000
149A285GLN0-0.028-0.00535.755-0.002-0.0020.0000.0000.0000.000
150A286PRO0-0.021-0.00635.0250.0040.0040.0000.0000.0000.000
151A287ILE00.0010.02333.689-0.012-0.0120.0000.0000.0000.000
152A288SER0-0.034-0.04229.8460.0120.0120.0000.0000.0000.000
153A289LEU0-0.036-0.00130.555-0.011-0.0110.0000.0000.0000.000
154A290ARG10.8000.87725.8250.2000.2000.0000.0000.0000.000
155A291GLU-1-0.906-0.96128.943-0.068-0.0680.0000.0000.0000.000
156A292ASP-1-0.817-0.89428.026-0.163-0.1630.0000.0000.0000.000
157A293GLU-1-0.819-0.91530.355-0.169-0.1690.0000.0000.0000.000
158A294LEU00.0250.01332.6980.0070.0070.0000.0000.0000.000
159A295THR0-0.026-0.00733.1980.0110.0110.0000.0000.0000.000
160A296LEU0-0.0140.00334.2770.0060.0060.0000.0000.0000.000
161A297ILE00.0250.02636.0690.0040.0040.0000.0000.0000.000
162A298HIS00.0340.00938.2950.0060.0060.0000.0000.0000.000
163A299LEU00.0080.00537.8380.0050.0050.0000.0000.0000.000
164A300SER0-0.048-0.03638.9720.0020.0020.0000.0000.0000.000
165A301ALA00.0360.02441.4500.0020.0020.0000.0000.0000.000
166A302GLN0-0.015-0.00843.2720.0020.0020.0000.0000.0000.000
167A303LEU0-0.034-0.01142.3310.0040.0040.0000.0000.0000.000
168A304VAL00.0380.01245.0630.0020.0020.0000.0000.0000.000
169A305ALA00.0570.03547.3670.0020.0020.0000.0000.0000.000
170A306ILE0-0.072-0.02347.5980.0040.0040.0000.0000.0000.000
171A307ALA00.0070.00748.5430.0020.0020.0000.0000.0000.000
172A308LEU00.0150.00250.5360.0020.0020.0000.0000.0000.000
173A309THR0-0.038-0.04453.2900.0020.0020.0000.0000.0000.000
174A310SER0-0.071-0.02853.0920.0020.0020.0000.0000.0000.000
175A311SER00.029-0.00353.7880.0000.0000.0000.0000.0000.000
176A312ARG10.8860.96456.2870.0400.0400.0000.0000.0000.000
177A313CYS0-0.045-0.02358.9390.0030.0030.0000.0000.0000.000
178A314SER00.0040.01560.794-0.001-0.0010.0000.0000.0000.000