Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: VQQ71

Calculation Name: 2J5U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J5U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y6Y4

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptAll
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2197554.338125
FMO2-HF: Nuclear repulsion 2117706.727982
FMO2-HF: Total energy -79847.610143
FMO2-MP2: Total energy -80081.798123


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:74:THR)


Summations of interaction energy for fragment #1(A:74:THR)
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.
-14.585-9.0949.828-6.311-9.008-0.012
Interaction energy analysis for fragmet #1(A:74:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.015
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].
3A76ASN0-0.032-0.0333.209-0.7461.8670.009-1.152-1.4700.002
4A77GLN00.0100.0122.110-13.314-11.3408.330-4.486-5.818-0.014
5A78HIS00.0500.0382.371-1.072-0.2611.490-0.667-1.6350.000
6A79LEU00.0400.0115.3810.2350.328-0.001-0.006-0.0850.000
7A80LYS10.8400.9167.262-0.032-0.0320.0000.0000.0000.000
8A81GLU-1-0.749-0.8429.047-0.414-0.4140.0000.0000.0000.000
9A82ARG10.8220.8886.2790.8900.8900.0000.0000.0000.000
10A83LEU00.0010.00311.2170.0040.0040.0000.0000.0000.000
11A84GLU-1-0.948-0.96412.9600.0650.0650.0000.0000.0000.000
12A85GLU-1-0.943-0.98314.435-0.233-0.2330.0000.0000.0000.000
13A86LEU0-0.057-0.01514.6700.0040.0040.0000.0000.0000.000
14A87ALA00.0650.03016.4930.0220.0220.0000.0000.0000.000
15A88GLN0-0.035-0.00618.8810.0320.0320.0000.0000.0000.000
16A89LEU0-0.015-0.00817.8530.0070.0070.0000.0000.0000.000
17A90GLU-1-0.964-0.99019.868-0.193-0.1930.0000.0000.0000.000
18A91SER0-0.052-0.04222.3850.0160.0160.0000.0000.0000.000
19A92GLU-1-0.880-0.92723.936-0.107-0.1070.0000.0000.0000.000
20A93VAL0-0.046-0.03524.3270.0060.0060.0000.0000.0000.000
21A94ALA0-0.068-0.03726.5330.0060.0060.0000.0000.0000.000
22A95ASP-1-0.857-0.92328.407-0.057-0.0570.0000.0000.0000.000
23A96LEU00.0000.00228.4510.0040.0040.0000.0000.0000.000
24A97LYS10.8950.95127.4580.1180.1180.0000.0000.0000.000
25A98LYS10.8220.90031.9960.0530.0530.0000.0000.0000.000
26A99GLU-1-0.900-0.94634.458-0.056-0.0560.0000.0000.0000.000
27A100ASN0-0.040-0.03134.7840.0010.0010.0000.0000.0000.000
28A101LYS10.7920.88036.2340.0550.0550.0000.0000.0000.000
29A102ASP-1-0.788-0.89438.022-0.047-0.0470.0000.0000.0000.000
30A103LEU0-0.028-0.01238.5680.0030.0030.0000.0000.0000.000
31A104LYS10.8000.89236.7170.0760.0760.0000.0000.0000.000
32A105GLU-1-0.809-0.87242.090-0.049-0.0490.0000.0000.0000.000
33A106SER0-0.079-0.04043.9680.0030.0030.0000.0000.0000.000
34A107LEU0-0.091-0.04044.4550.0020.0020.0000.0000.0000.000
35A108ASP-1-0.912-0.95146.824-0.041-0.0410.0000.0000.0000.000
36A109ILE0-0.079-0.03842.556-0.001-0.0010.0000.0000.0000.000
37A110THR00.005-0.01042.935-0.002-0.0020.0000.0000.0000.000
38A111ASP-1-0.903-0.94340.997-0.061-0.0610.0000.0000.0000.000
39A112SER00.014-0.00938.355-0.002-0.0020.0000.0000.0000.000
40A113ILE0-0.012-0.02437.248-0.004-0.0040.0000.0000.0000.000
41A114ARG10.8510.91629.4200.1080.1080.0000.0000.0000.000
42A115ASP-1-0.775-0.84533.831-0.086-0.0860.0000.0000.0000.000
43A116TYR0-0.024-0.03428.6620.0000.0000.0000.0000.0000.000
44A117ASP-1-0.793-0.87534.659-0.079-0.0790.0000.0000.0000.000
45A118PRO0-0.052-0.03130.100-0.002-0.0020.0000.0000.0000.000
46A119LEU00.0020.00131.9630.0040.0040.0000.0000.0000.000
47A120ASN0-0.0070.00027.198-0.010-0.0100.0000.0000.0000.000
48A121ALA0-0.035-0.01828.7100.0110.0110.0000.0000.0000.000
49A122SER00.019-0.00627.072-0.011-0.0110.0000.0000.0000.000
50A123VAL0-0.037-0.01826.9110.0130.0130.0000.0000.0000.000
51A124ILE0-0.048-0.02629.1270.0000.0000.0000.0000.0000.000
52A125SER0-0.024-0.00832.0080.0040.0040.0000.0000.0000.000
53A126ARG10.8390.90224.6840.1690.1690.0000.0000.0000.000
54A127ASN00.0540.05631.486-0.001-0.0010.0000.0000.0000.000
55A128PRO00.0380.00330.853-0.003-0.0030.0000.0000.0000.000
56A129THR0-0.069-0.05332.0240.0010.0010.0000.0000.0000.000
57A130ASN0-0.017-0.01434.0890.0020.0020.0000.0000.0000.000
58A131TRP00.0200.03125.0720.0050.0050.0000.0000.0000.000
59A132ASN00.0250.01627.331-0.016-0.0160.0000.0000.0000.000
60A133ASP-1-0.785-0.86629.609-0.109-0.1090.0000.0000.0000.000
61A134GLN00.0010.00332.4360.0030.0030.0000.0000.0000.000
62A135VAL00.0120.01228.289-0.005-0.0050.0000.0000.0000.000
63A136GLU-1-0.890-0.91731.736-0.083-0.0830.0000.0000.0000.000
64A137ILE00.019-0.00430.182-0.008-0.0080.0000.0000.0000.000
65A138ASP-1-0.761-0.88232.201-0.106-0.1060.0000.0000.0000.000
66A139LYS10.8050.90632.9470.1100.1100.0000.0000.0000.000
67A140GLY00.0310.00736.081-0.001-0.0010.0000.0000.0000.000
68A141SER0-0.022-0.01739.5290.0010.0010.0000.0000.0000.000
69A142SER0-0.070-0.05642.6040.0010.0010.0000.0000.0000.000
70A143ASP-1-0.826-0.90037.829-0.077-0.0770.0000.0000.0000.000
71A144GLY00.0120.00838.831-0.003-0.0030.0000.0000.0000.000
72A145VAL0-0.022-0.00736.3030.0000.0000.0000.0000.0000.000
73A146LYS10.9460.94838.9240.0700.0700.0000.0000.0000.000
74A147PRO00.027-0.00538.960-0.004-0.0040.0000.0000.0000.000
75A148ASP-1-0.856-0.94638.298-0.081-0.0810.0000.0000.0000.000
76A149MET0-0.0500.00635.639-0.003-0.0030.0000.0000.0000.000
77A150ALA00.0370.02131.654-0.003-0.0030.0000.0000.0000.000
78A151VAL00.0110.00528.6910.0010.0010.0000.0000.0000.000
79A152THR0-0.002-0.00625.705-0.001-0.0010.0000.0000.0000.000
80A153THR00.0360.01821.199-0.008-0.0080.0000.0000.0000.000
81A154PRO00.035-0.00118.7920.0070.0070.0000.0000.0000.000
82A155SER00.0010.01617.284-0.011-0.0110.0000.0000.0000.000
83A156GLY0-0.011-0.01319.2450.0030.0030.0000.0000.0000.000
84A157LEU0-0.045-0.03222.8730.0030.0030.0000.0000.0000.000
85A158ILE00.0150.00623.922-0.009-0.0090.0000.0000.0000.000
86A159GLY00.0240.00926.6610.0050.0050.0000.0000.0000.000
87A160LYS10.8080.91330.4920.0980.0980.0000.0000.0000.000
88A161VAL00.0350.02433.8310.0000.0000.0000.0000.0000.000
89A162THR0-0.041-0.01736.1190.0030.0030.0000.0000.0000.000
90A163THR00.0190.00539.0400.0050.0050.0000.0000.0000.000
91A164THR0-0.039-0.01139.349-0.004-0.0040.0000.0000.0000.000
92A165GLY00.0530.04041.1630.0040.0040.0000.0000.0000.000
93A166ALA00.000-0.01942.513-0.001-0.0010.0000.0000.0000.000
94A167LYS10.8030.88939.7690.0720.0720.0000.0000.0000.000
95A168SER0-0.0030.02337.160-0.001-0.0010.0000.0000.0000.000
96A169ALA00.031-0.00536.1950.0050.0050.0000.0000.0000.000
97A170THR00.0030.01935.417-0.007-0.0070.0000.0000.0000.000
98A171VAL0-0.011-0.01730.7320.0020.0020.0000.0000.0000.000
99A172GLU-1-0.816-0.87733.460-0.096-0.0960.0000.0000.0000.000
100A173LEU0-0.005-0.00727.785-0.004-0.0040.0000.0000.0000.000
101A174LEU0-0.028-0.04526.8730.0090.0090.0000.0000.0000.000
102A175THR0-0.071-0.05926.0190.0000.0000.0000.0000.0000.000
103A176SER0-0.077-0.04529.3370.0050.0050.0000.0000.0000.000
104A177SER0-0.030-0.03332.9880.0030.0030.0000.0000.0000.000
105A178ASP-1-0.833-0.88035.388-0.071-0.0710.0000.0000.0000.000
106A179VAL00.0400.00937.635-0.002-0.0020.0000.0000.0000.000
107A180LYS10.8160.88539.5160.0740.0740.0000.0000.0000.000
108A181ASN0-0.0150.01133.1870.0030.0030.0000.0000.0000.000
109A182ARG10.8220.86735.7380.0750.0750.0000.0000.0000.000
110A183VAL00.0070.00831.713-0.001-0.0010.0000.0000.0000.000
111A184SER0-0.0110.00834.8860.0000.0000.0000.0000.0000.000
112A185ALA00.0130.01231.690-0.005-0.0050.0000.0000.0000.000
113A186LYS10.8790.92532.0560.1070.1070.0000.0000.0000.000
114A187VAL00.0160.02029.538-0.010-0.0100.0000.0000.0000.000
115A188GLN0-0.009-0.01326.3260.0010.0010.0000.0000.0000.000
116A189GLY00.0440.01029.398-0.004-0.0040.0000.0000.0000.000
117A190LYS10.9290.96231.1050.0730.0730.0000.0000.0000.000
118A191GLU-1-0.892-0.92333.637-0.060-0.0600.0000.0000.0000.000
119A192ASN0-0.041-0.01833.571-0.009-0.0090.0000.0000.0000.000
120A193ALA00.0590.03434.4240.0050.0050.0000.0000.0000.000
121A194PHE0-0.014-0.02734.769-0.007-0.0070.0000.0000.0000.000
122A195GLY00.0670.03736.4740.0030.0030.0000.0000.0000.000
123A196ILE0-0.050-0.02536.615-0.002-0.0020.0000.0000.0000.000
124A197ILE00.0100.00730.1190.0000.0000.0000.0000.0000.000
125A198ASN0-0.059-0.05833.8800.0060.0060.0000.0000.0000.000
126A199GLY00.0640.05033.7890.0060.0060.0000.0000.0000.000
127A200TYR0-0.004-0.00525.007-0.008-0.0080.0000.0000.0000.000
128A201ASP-1-0.791-0.85029.262-0.109-0.1090.0000.0000.0000.000
129A202SER00.004-0.00727.926-0.012-0.0120.0000.0000.0000.000
130A203ASP-1-0.910-0.95026.663-0.118-0.1180.0000.0000.0000.000
131A204THR0-0.124-0.10825.147-0.010-0.0100.0000.0000.0000.000
132A205LYS10.8560.94221.8470.1640.1640.0000.0000.0000.000
133A206LEU0-0.027-0.00723.500-0.015-0.0150.0000.0000.0000.000
134A207LEU00.0340.00926.3710.0100.0100.0000.0000.0000.000
135A208GLU-1-0.839-0.90828.750-0.093-0.0930.0000.0000.0000.000
136A209LEU0-0.038-0.01531.0240.0020.0020.0000.0000.0000.000
137A210LYS10.8580.90533.1050.0910.0910.0000.0000.0000.000
138A211GLN0-0.015-0.02436.835-0.002-0.0020.0000.0000.0000.000
139A212LEU00.0090.03233.1500.0000.0000.0000.0000.0000.000
140A213PRO00.0250.00737.7590.0030.0030.0000.0000.0000.000
141A214TYR00.0310.01239.105-0.003-0.0030.0000.0000.0000.000
142A215ASP-1-0.913-0.94440.857-0.059-0.0590.0000.0000.0000.000
143A216MET00.0080.01636.298-0.002-0.0020.0000.0000.0000.000
144A217LYS10.9460.97534.5240.0620.0620.0000.0000.0000.000
145A218PHE00.0300.00731.241-0.004-0.0040.0000.0000.0000.000
146A219LYS10.9140.95025.9310.1090.1090.0000.0000.0000.000
147A220LYS10.8490.91720.5520.1780.1780.0000.0000.0000.000
148A221GLY0-0.006-0.00622.0090.0010.0010.0000.0000.0000.000
149A222GLN0-0.026-0.02022.969-0.005-0.0050.0000.0000.0000.000
150A223LYS10.9891.00320.1020.2220.2220.0000.0000.0000.000
151A224VAL00.0120.00725.0100.0160.0160.0000.0000.0000.000
152A225VAL0-0.018-0.00326.449-0.013-0.0130.0000.0000.0000.000
153A226THR00.0500.00528.7850.0070.0070.0000.0000.0000.000
154A227SER0-0.024-0.01731.7510.0010.0010.0000.0000.0000.000
155A228GLY00.0340.02335.0270.0040.0040.0000.0000.0000.000
156A229LEU00.009-0.00936.9730.0040.0040.0000.0000.0000.000
157A230GLY00.0280.02539.1550.0030.0030.0000.0000.0000.000
158A231GLY0-0.033-0.01140.5420.0020.0020.0000.0000.0000.000
159A232LYS10.8690.94738.0440.0770.0770.0000.0000.0000.000
160A233PHE00.010-0.00432.918-0.003-0.0030.0000.0000.0000.000
161A234PRO00.0640.05232.5270.0050.0050.0000.0000.0000.000
162A235ALA0-0.0050.01333.438-0.006-0.0060.0000.0000.0000.000
163A236GLY0-0.026-0.02830.1170.0000.0000.0000.0000.0000.000
164A237ILE0-0.0050.01126.833-0.009-0.0090.0000.0000.0000.000
165A238PHE0-0.027-0.01019.8110.0090.0090.0000.0000.0000.000
166A239ILE00.0300.01425.135-0.003-0.0030.0000.0000.0000.000
167A240GLY00.0660.02922.390-0.011-0.0110.0000.0000.0000.000
168A241THR0-0.060-0.02221.0670.0040.0040.0000.0000.0000.000
169A242ILE0-0.0120.00023.218-0.001-0.0010.0000.0000.0000.000
170A243GLU-1-0.822-0.90221.777-0.197-0.1970.0000.0000.0000.000
171A244LYS10.8340.91424.7640.1050.1050.0000.0000.0000.000
172A245VAL0-0.018-0.01728.276-0.002-0.0020.0000.0000.0000.000
173A246GLU-1-0.852-0.90631.849-0.083-0.0830.0000.0000.0000.000
174A247THR00.0300.00935.409-0.001-0.0010.0000.0000.0000.000
175A248ASP-1-0.795-0.87539.090-0.059-0.0590.0000.0000.0000.000
176A249LYS10.9740.96441.0290.0560.0560.0000.0000.0000.000
177A250MET0-0.056-0.02543.8580.0030.0030.0000.0000.0000.000
178A251GLY0-0.0100.00544.2400.0020.0020.0000.0000.0000.000
179A252LEU0-0.047-0.01944.7320.0010.0010.0000.0000.0000.000
180A253SER0-0.088-0.05240.789-0.002-0.0020.0000.0000.0000.000
181A254GLN0-0.073-0.06236.188-0.001-0.0010.0000.0000.0000.000
182A255THR0-0.020-0.00634.2170.0000.0000.0000.0000.0000.000
183A256ALA0-0.026-0.01430.3920.0000.0000.0000.0000.0000.000
184A257PHE00.0410.01728.343-0.002-0.0020.0000.0000.0000.000
185A258ILE0-0.009-0.01825.059-0.005-0.0050.0000.0000.0000.000
186A259LYS11.0191.02015.7610.3430.3430.0000.0000.0000.000
187A260PRO00.0200.00822.007-0.002-0.0020.0000.0000.0000.000
188A261GLY0-0.026-0.02819.696-0.021-0.0210.0000.0000.0000.000
189A262ALA0-0.028-0.00218.388-0.038-0.0380.0000.0000.0000.000
190A263ASP-1-0.807-0.90817.572-0.282-0.2820.0000.0000.0000.000
191A264MET0-0.056-0.02919.4640.0130.0130.0000.0000.0000.000
192A265TYR0-0.0250.00720.4700.0290.0290.0000.0000.0000.000
193A266ASP-1-0.904-0.95219.802-0.236-0.2360.0000.0000.0000.000
194A267LEU0-0.057-0.02921.301-0.011-0.0110.0000.0000.0000.000
195A268ASN0-0.0040.01222.1040.0260.0260.0000.0000.0000.000
196A269HIS00.0470.02921.9970.0240.0240.0000.0000.0000.000
197A270VAL0-0.001-0.00423.518-0.016-0.0160.0000.0000.0000.000
198A271THR0-0.033-0.01726.0770.0040.0040.0000.0000.0000.000
199A272VAL00.0040.00828.315-0.002-0.0020.0000.0000.0000.000
200A273LEU0-0.034-0.02329.0250.0020.0020.0000.0000.0000.000
201A274LYS10.8310.91333.0330.0780.0780.0000.0000.0000.000
202A275ARG10.7780.86136.7110.0760.0760.0000.0000.0000.000
203A276SER00.010-0.00437.6320.0030.0030.0000.0000.0000.000
204A277ALA00.0060.03139.6280.0040.0040.0000.0000.0000.000
205A278GLU-1-0.822-0.90241.590-0.057-0.0570.0000.0000.0000.000
206A279ALA0-0.033-0.00843.756-0.003-0.0030.0000.0000.0000.000
207A280GLY0-0.020-0.01143.6960.0030.0030.0000.0000.0000.000
208A281THR00.005-0.02045.166-0.001-0.0010.0000.0000.0000.000
209A282THR0-0.0140.00146.3760.0010.0010.0000.0000.0000.000
210A283ASP-1-0.838-0.85242.467-0.072-0.0720.0000.0000.0000.000