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: 3JG3L

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1761548.453114
FMO2-HF: Nuclear repulsion 1692935.370863
FMO2-HF: Total energy -68613.082252
FMO2-MP2: Total energy -68813.43513


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.
-6.6230.4342.964-3.935-6.0890.01
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 : 0.069 / q_NPA : 0.032
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].
3A139ALA00.0150.0132.445-4.8400.0822.672-3.148-4.4480.013
4A140ALA0-0.009-0.0082.699-2.399-0.5750.292-0.748-1.368-0.003
5A141GLU-1-0.816-0.8674.179-0.896-0.5850.000-0.039-0.2730.000
6A142THR00.010-0.0026.3460.9850.9850.0000.0000.0000.000
7A143TYR0-0.002-0.0017.3740.2300.2300.0000.0000.0000.000
8A144ASP-1-0.797-0.8938.833-0.985-0.9850.0000.0000.0000.000
9A145LEU00.0160.00310.7190.2120.2120.0000.0000.0000.000
10A146LEU00.0030.01311.9860.1240.1240.0000.0000.0000.000
11A147LYS10.8180.90713.1040.9970.9970.0000.0000.0000.000
12A148GLN00.0080.01013.9640.0360.0360.0000.0000.0000.000
13A149ARG10.8960.93516.4340.2570.2570.0000.0000.0000.000
14A150THR0-0.022-0.02217.2350.0250.0250.0000.0000.0000.000
15A151GLU-1-0.743-0.80919.361-0.289-0.2890.0000.0000.0000.000
16A152GLU-1-0.834-0.90720.073-0.232-0.2320.0000.0000.0000.000
17A153LEU0-0.028-0.01322.1950.0270.0270.0000.0000.0000.000
18A154ARG10.8520.89523.5520.2900.2900.0000.0000.0000.000
19A155ARG10.8580.90622.8160.3090.3090.0000.0000.0000.000
20A156ALA00.0100.00626.7890.0150.0150.0000.0000.0000.000
21A157ASN0-0.007-0.01727.0610.0260.0260.0000.0000.0000.000
22A158ALA00.0010.00829.7280.0100.0100.0000.0000.0000.000
23A159GLN00.0100.00530.7240.0090.0090.0000.0000.0000.000
24A160MET00.0220.00732.7610.0100.0100.0000.0000.0000.000
25A161SER0-0.0040.01334.0320.0080.0080.0000.0000.0000.000
26A162LEU00.0120.02235.7740.0060.0060.0000.0000.0000.000
27A163LEU0-0.004-0.01636.7590.0070.0070.0000.0000.0000.000
28A164THR0-0.036-0.02537.6210.0090.0090.0000.0000.0000.000
29A165VAL00.0000.00039.7050.0050.0050.0000.0000.0000.000
30A166LEU00.0180.00941.6930.0050.0050.0000.0000.0000.000
31A167VAL0-0.0020.02243.3560.0050.0050.0000.0000.0000.000
32A168GLN0-0.028-0.02641.9070.0000.0000.0000.0000.0000.000
33A169VAL00.0200.01245.8260.0030.0030.0000.0000.0000.000
34A170THR0-0.012-0.02747.7470.0020.0020.0000.0000.0000.000
35A171GLN0-0.079-0.03948.5230.0040.0040.0000.0000.0000.000
36A172ALA0-0.031-0.00850.0070.0020.0020.0000.0000.0000.000
37A173SER0-0.040-0.01151.7930.0000.0000.0000.0000.0000.000
38A174ASN0-0.044-0.03654.1640.0040.0040.0000.0000.0000.000
39A175SER0-0.030-0.02856.9380.0010.0010.0000.0000.0000.000
40A176LEU00.0570.01855.612-0.002-0.0020.0000.0000.0000.000
41A177GLU-1-0.859-0.92455.389-0.047-0.0470.0000.0000.0000.000
42A178ALA0-0.040-0.01855.290-0.003-0.0030.0000.0000.0000.000
43A179ILE00.0220.03450.317-0.003-0.0030.0000.0000.0000.000
44A180LEU0-0.021-0.00450.352-0.004-0.0040.0000.0000.0000.000
45A181THR00.0490.01749.895-0.003-0.0030.0000.0000.0000.000
46A182PRO00.0140.02347.641-0.005-0.0050.0000.0000.0000.000
47A183ILE00.0380.02745.793-0.005-0.0050.0000.0000.0000.000
48A184ALA00.0220.00844.883-0.005-0.0050.0000.0000.0000.000
49A185THR0-0.026-0.03343.879-0.006-0.0060.0000.0000.0000.000
50A186ALA0-0.0130.00241.757-0.007-0.0070.0000.0000.0000.000
51A187PHE0-0.005-0.01940.285-0.007-0.0070.0000.0000.0000.000
52A188ALA00.015-0.00739.794-0.008-0.0080.0000.0000.0000.000
53A189GLU-1-0.874-0.92538.254-0.140-0.1400.0000.0000.0000.000
54A190SER0-0.080-0.04635.777-0.010-0.0100.0000.0000.0000.000
55A191PHE0-0.042-0.02834.867-0.009-0.0090.0000.0000.0000.000
56A192ALA0-0.0110.01234.875-0.006-0.0060.0000.0000.0000.000
57A193VAL0-0.0460.01736.811-0.004-0.0040.0000.0000.0000.000
58A194ASN00.0100.01439.887-0.003-0.0030.0000.0000.0000.000
59A195ALA0-0.002-0.01342.3930.0040.0040.0000.0000.0000.000
60A196CYS0-0.061-0.01643.867-0.001-0.0010.0000.0000.0000.000
61A197ILE00.0140.00845.7670.0030.0030.0000.0000.0000.000
62A198LEU00.0100.01348.786-0.001-0.0010.0000.0000.0000.000
63A199GLN00.0180.00450.388-0.001-0.0010.0000.0000.0000.000
64A200MET0-0.018-0.00352.9490.0010.0010.0000.0000.0000.000
65A201LEU00.0190.01054.648-0.001-0.0010.0000.0000.0000.000
66A202GLU-1-0.878-0.90358.108-0.042-0.0420.0000.0000.0000.000
67A203GLY0-0.012-0.01661.7490.0000.0000.0000.0000.0000.000
68A204GLN0-0.021-0.01858.728-0.002-0.0020.0000.0000.0000.000
69A205THR0-0.0050.00959.459-0.002-0.0020.0000.0000.0000.000
70A206LEU0-0.028-0.00654.7170.0000.0000.0000.0000.0000.000
71A207SER0-0.022-0.03058.5570.0010.0010.0000.0000.0000.000
72A208THR00.012-0.00759.061-0.003-0.0030.0000.0000.0000.000
73A209ILE0-0.0050.00457.558-0.002-0.0020.0000.0000.0000.000
74A210GLN0-0.004-0.01454.389-0.004-0.0040.0000.0000.0000.000
75A211GLY00.0180.01452.3680.0020.0020.0000.0000.0000.000
76A212PHE0-0.042-0.03149.575-0.001-0.0010.0000.0000.0000.000
77A213TYR0-0.032-0.02942.1140.0030.0030.0000.0000.0000.000
78A214SER00.006-0.00846.109-0.003-0.0030.0000.0000.0000.000
79A215GLN00.0000.00239.4190.0000.0000.0000.0000.0000.000
80A216GLN0-0.070-0.03145.0010.0030.0030.0000.0000.0000.000
81A217GLY00.0030.00448.1120.0020.0020.0000.0000.0000.000
82A218THR0-0.061-0.04551.3970.0050.0050.0000.0000.0000.000
83A219VAL00.0200.02050.445-0.004-0.0040.0000.0000.0000.000
84A220ASN0-0.029-0.02351.7330.0060.0060.0000.0000.0000.000
85A221ASN0-0.033-0.03852.368-0.003-0.0030.0000.0000.0000.000
86A222TRP00.0180.00748.6070.0040.0040.0000.0000.0000.000
87A223LEU00.0390.01050.0070.0000.0000.0000.0000.0000.000
88A224ASN00.001-0.00153.830-0.001-0.0010.0000.0000.0000.000
89A225GLN0-0.048-0.01956.2300.0000.0000.0000.0000.0000.000
90A226ASP-1-0.706-0.81150.259-0.085-0.0850.0000.0000.0000.000
91A227PRO0-0.008-0.00651.4540.0020.0020.0000.0000.0000.000
92A228LEU0-0.0180.00644.8770.0020.0020.0000.0000.0000.000
93A229THR00.022-0.03549.4840.0010.0010.0000.0000.0000.000
94A230ASN0-0.034-0.01051.2440.0040.0040.0000.0000.0000.000
95A231GLU-1-0.868-0.92049.059-0.071-0.0710.0000.0000.0000.000
96A232ALA0-0.0080.01548.7540.0020.0020.0000.0000.0000.000
97A233ILE0-0.005-0.02050.3030.0030.0030.0000.0000.0000.000
98A234ALA0-0.0280.00253.8000.0030.0030.0000.0000.0000.000
99A235THR0-0.059-0.05550.0020.0020.0020.0000.0000.0000.000
100A236GLY0-0.019-0.00950.7620.0010.0010.0000.0000.0000.000
101A237GLN0-0.034-0.01945.274-0.003-0.0030.0000.0000.0000.000
102A238ILE0-0.015-0.01440.226-0.001-0.0010.0000.0000.0000.000
103A239GLN0-0.0110.01044.301-0.002-0.0020.0000.0000.0000.000
104A240VAL0-0.013-0.01437.971-0.004-0.0040.0000.0000.0000.000
105A241ALA00.0420.03541.4550.0010.0010.0000.0000.0000.000
106A242ALA00.007-0.00936.408-0.002-0.0020.0000.0000.0000.000
107A243ASN00.002-0.03236.861-0.003-0.0030.0000.0000.0000.000
108A244ILE00.0670.04539.8610.0030.0030.0000.0000.0000.000
109A245ALA0-0.0170.00042.0480.0040.0040.0000.0000.0000.000
110A246LYS10.8790.93036.6010.1540.1540.0000.0000.0000.000
111A247ASP-1-0.792-0.88943.138-0.088-0.0880.0000.0000.0000.000
112A248PRO00.0090.01145.5670.0010.0010.0000.0000.0000.000
113A249LYS10.8220.90747.9730.0830.0830.0000.0000.0000.000
114A250LEU0-0.025-0.02445.9300.0020.0020.0000.0000.0000.000
115A251ALA0-0.023-0.00647.0260.0000.0000.0000.0000.0000.000
116A252SER0-0.036-0.02248.552-0.001-0.0010.0000.0000.0000.000
117A253ILE0-0.0370.00551.4740.0040.0040.0000.0000.0000.000
118A254SER00.014-0.01052.043-0.003-0.0030.0000.0000.0000.000
119A255GLN00.0390.01853.009-0.004-0.0040.0000.0000.0000.000
120A256TYR0-0.001-0.01546.346-0.005-0.0050.0000.0000.0000.000
121A257GLN0-0.054-0.02848.258-0.003-0.0030.0000.0000.0000.000
122A258ASP-1-0.860-0.92049.257-0.089-0.0890.0000.0000.0000.000
123A259ASN0-0.064-0.03248.693-0.001-0.0010.0000.0000.0000.000
124A260GLY00.0030.01145.897-0.005-0.0050.0000.0000.0000.000
125A261ILE0-0.058-0.02944.036-0.007-0.0070.0000.0000.0000.000
126A262GLN00.013-0.01040.158-0.003-0.0030.0000.0000.0000.000
127A263SER0-0.062-0.03138.621-0.002-0.0020.0000.0000.0000.000
128A264HIS0-0.0110.00440.9010.0030.0030.0000.0000.0000.000
129A265VAL0-0.020-0.00139.1570.0000.0000.0000.0000.0000.000
130A266VAL00.0060.00942.5680.0010.0010.0000.0000.0000.000
131A267ILE0-0.006-0.00543.1180.0010.0010.0000.0000.0000.000
132A268PRO00.0230.02345.8770.0010.0010.0000.0000.0000.000
133A269ILE0-0.014-0.01047.103-0.001-0.0010.0000.0000.0000.000
134A270THR00.009-0.00649.4200.0020.0020.0000.0000.0000.000
135A271TYR00.0470.03550.2090.0020.0020.0000.0000.0000.000
136A272ARG10.8850.92951.8060.0300.0300.0000.0000.0000.000
137A273ASN0-0.011-0.01952.621-0.001-0.0010.0000.0000.0000.000
138A274GLU-1-0.940-0.95154.911-0.038-0.0380.0000.0000.0000.000
139A275MET0-0.0310.00452.559-0.002-0.0020.0000.0000.0000.000
140A276LEU0-0.018-0.00452.8940.0010.0010.0000.0000.0000.000
141A277GLY00.0450.00553.3290.0010.0010.0000.0000.0000.000
142A278VAL0-0.0240.00750.0900.0000.0000.0000.0000.0000.000
143A279LEU00.0120.00444.0370.0010.0010.0000.0000.0000.000
144A280SER0-0.027-0.01946.166-0.002-0.0020.0000.0000.0000.000
145A281LEU00.004-0.00839.888-0.001-0.0010.0000.0000.0000.000
146A282GLN00.0670.01842.915-0.003-0.0030.0000.0000.0000.000
147A283TRP00.0380.00836.9620.0010.0010.0000.0000.0000.000
148A284GLN00.008-0.00340.2020.0000.0000.0000.0000.0000.000
149A285GLN0-0.027-0.00435.967-0.001-0.0010.0000.0000.0000.000
150A286PRO0-0.018-0.00835.4600.0040.0040.0000.0000.0000.000
151A287ILE0-0.0060.01633.997-0.013-0.0130.0000.0000.0000.000
152A288SER0-0.026-0.03530.0560.0060.0060.0000.0000.0000.000
153A289LEU0-0.0320.00030.919-0.012-0.0120.0000.0000.0000.000
154A290ARG10.7650.84626.1850.2160.2160.0000.0000.0000.000
155A291GLU-1-0.897-0.95829.164-0.135-0.1350.0000.0000.0000.000
156A292ASP-1-0.814-0.89428.050-0.186-0.1860.0000.0000.0000.000
157A293GLU-1-0.777-0.88330.843-0.191-0.1910.0000.0000.0000.000
158A294LEU00.0240.01333.0380.0100.0100.0000.0000.0000.000
159A295THR0-0.025-0.01033.6040.0130.0130.0000.0000.0000.000
160A296LEU0-0.0140.00534.0320.0090.0090.0000.0000.0000.000
161A297ILE00.0040.01836.3170.0070.0070.0000.0000.0000.000
162A298HIS00.0230.01038.5940.0090.0090.0000.0000.0000.000
163A299LEU00.0110.00937.6850.0060.0060.0000.0000.0000.000
164A300SER0-0.029-0.03938.9990.0050.0050.0000.0000.0000.000
165A301ALA00.0480.03441.5380.0040.0040.0000.0000.0000.000
166A302GLN0-0.013-0.00843.4040.0030.0030.0000.0000.0000.000
167A303LEU0-0.030-0.01042.4280.0050.0050.0000.0000.0000.000
168A304VAL00.0280.00945.0110.0030.0030.0000.0000.0000.000
169A305ALA00.0520.03447.3670.0030.0030.0000.0000.0000.000
170A306ILE0-0.071-0.03947.6650.0040.0040.0000.0000.0000.000
171A307ALA00.0020.01148.5250.0030.0030.0000.0000.0000.000
172A308LEU00.0200.00550.5340.0030.0030.0000.0000.0000.000
173A309THR0-0.038-0.03853.2900.0020.0020.0000.0000.0000.000
174A310SER0-0.069-0.03253.0440.0030.0030.0000.0000.0000.000
175A311SER00.0310.00053.7890.0010.0010.0000.0000.0000.000
176A312ARG10.8920.96656.2850.0400.0400.0000.0000.0000.000
177A313CYS0-0.065-0.02358.5320.0020.0020.0000.0000.0000.000
178A314SER00.0120.01360.7900.0000.0000.0000.0000.0000.000