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

tag_button

FMODB ID: JL519

Calculation Name: 3ONM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ONM

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0U1

Base Structure: X-ray

Registration Date: 2023-09-20

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1970617.501982
FMO2-HF: Nuclear repulsion 1896846.461235
FMO2-HF: Total energy -73771.040747
FMO2-MP2: Total energy -73984.610102


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:99:GLY)


Summations of interaction energy for fragment #1(A:99:GLY)
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.
1.2421.8712.426-1.575-1.4790.004
Interaction energy analysis for fragmet #1(A:99:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.007
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].
3A101LEU00.015-0.0013.8160.7031.699-0.013-0.426-0.5580.001
4A102ILE0-0.0050.0156.8320.1420.1420.0000.0000.0000.000
5A103ILE00.0090.00710.4900.1120.1120.0000.0000.0000.000
6A104GLY00.0130.00113.1840.0460.0460.0000.0000.0000.000
7A105ALA00.0210.00416.646-0.002-0.0020.0000.0000.0000.000
8A106SER00.012-0.02219.7380.0170.0170.0000.0000.0000.000
9A107ASP-1-0.849-0.95323.484-0.170-0.1700.0000.0000.0000.000
10A108ASP-1-0.889-0.92125.925-0.178-0.1780.0000.0000.0000.000
11A109THR0-0.015-0.00722.280-0.009-0.0090.0000.0000.0000.000
12A110ALA0-0.033-0.01921.845-0.019-0.0190.0000.0000.0000.000
13A111ASP-1-0.866-0.94422.628-0.212-0.2120.0000.0000.0000.000
14A112THR00.0040.00124.7450.0010.0010.0000.0000.0000.000
15A113LEU0-0.004-0.01021.841-0.010-0.0100.0000.0000.0000.000
16A114LEU0-0.0330.00916.648-0.026-0.0260.0000.0000.0000.000
17A115PRO00.0470.01118.211-0.052-0.0520.0000.0000.0000.000
18A116PHE0-0.045-0.01019.257-0.018-0.0180.0000.0000.0000.000
19A117LEU00.0410.01414.727-0.014-0.0140.0000.0000.0000.000
20A118LEU00.0090.00613.854-0.057-0.0570.0000.0000.0000.000
21A119ASN00.0200.01314.781-0.076-0.0760.0000.0000.0000.000
22A120ARG10.8940.97016.1860.2980.2980.0000.0000.0000.000
23A121VAL00.026-0.0029.857-0.008-0.0080.0000.0000.0000.000
24A122ALA00.0090.00011.660-0.076-0.0760.0000.0000.0000.000
25A123THR0-0.073-0.03212.8980.0280.0280.0000.0000.0000.000
26A124LEU0-0.041-0.02211.5720.0420.0420.0000.0000.0000.000
27A125TYR0-0.012-0.0127.427-0.051-0.0510.0000.0000.0000.000
28A126PRO00.0450.0359.279-0.166-0.1660.0000.0000.0000.000
29A127ARG10.8540.9157.1140.6460.6460.0000.0000.0000.000
30A128LEU00.0130.0264.248-0.469-0.388-0.001-0.034-0.0450.000
31A129ALA0-0.0080.0016.1550.5830.5830.0000.0000.0000.000
32A130ILE0-0.039-0.0267.542-0.473-0.4730.0000.0000.0000.000
33A131ASP-1-0.863-0.90610.039-0.635-0.6350.0000.0000.0000.000
34A132VAL0-0.012-0.02312.031-0.010-0.0100.0000.0000.0000.000
35A133ARG10.8990.95613.0320.5130.5130.0000.0000.0000.000
36A134VAL00.005-0.00217.7130.0040.0040.0000.0000.0000.000
37A135LYS10.9440.95820.0170.2240.2240.0000.0000.0000.000
38A136ARG10.8390.92323.6620.1000.1000.0000.0000.0000.000
39A137SER00.0570.02124.5550.0030.0030.0000.0000.0000.000
40A138PRO00.0200.01124.740-0.004-0.0040.0000.0000.0000.000
41A139PHE00.006-0.00923.6440.0030.0030.0000.0000.0000.000
42A140ILE0-0.0010.00019.925-0.003-0.0030.0000.0000.0000.000
43A141ALA0-0.014-0.00219.866-0.013-0.0130.0000.0000.0000.000
44A142ASP-1-0.922-0.96521.104-0.110-0.1100.0000.0000.0000.000
45A143MET0-0.0080.00817.491-0.005-0.0050.0000.0000.0000.000
46A144LEU0-0.085-0.02214.888-0.014-0.0140.0000.0000.0000.000
47A145SER0-0.038-0.02116.6150.0110.0110.0000.0000.0000.000
48A146SER00.0110.01217.9270.0130.0130.0000.0000.0000.000
49A147GLY00.0320.02813.7060.0300.0300.0000.0000.0000.000
50A148GLU-1-0.985-0.98812.665-0.208-0.2080.0000.0000.0000.000
51A149VAL0-0.116-0.06912.766-0.067-0.0670.0000.0000.0000.000
52A150ASP-1-0.773-0.8878.518-0.776-0.7760.0000.0000.0000.000
53A151LEU0-0.062-0.03810.4490.0770.0770.0000.0000.0000.000
54A152ALA00.0110.01413.275-0.021-0.0210.0000.0000.0000.000
55A153ILE0-0.023-0.00616.7900.0190.0190.0000.0000.0000.000
56A154THR0-0.027-0.02719.2620.0180.0180.0000.0000.0000.000
57A155THR00.030-0.01722.8300.0000.0000.0000.0000.0000.000
58A156ALA0-0.044-0.00325.7940.0140.0140.0000.0000.0000.000
59A157LYS10.9580.97026.7030.0780.0780.0000.0000.0000.000
60A158VAL00.0670.05422.5040.0060.0060.0000.0000.0000.000
61A159ASP-1-0.926-1.05324.168-0.084-0.0840.0000.0000.0000.000
62A160SER0-0.0040.01525.8110.0080.0080.0000.0000.0000.000
63A161HIS0-0.0220.04019.9100.0220.0220.0000.0000.0000.000
64A162PRO00.0200.03418.4180.0030.0030.0000.0000.0000.000
65A163HIS0-0.039-0.04219.618-0.022-0.0220.0000.0000.0000.000
66A164VAL00.0210.02618.1440.0150.0150.0000.0000.0000.000
67A165ILE00.0110.00220.806-0.012-0.0120.0000.0000.0000.000
68A166LEU0-0.022-0.01318.429-0.004-0.0040.0000.0000.0000.000
69A167ARG10.8680.92122.6080.1930.1930.0000.0000.0000.000
70A168THR0-0.0110.01426.259-0.005-0.0050.0000.0000.0000.000
71A169SER0-0.061-0.04929.7120.0000.0000.0000.0000.0000.000
72A170PRO00.0590.02832.0330.0030.0030.0000.0000.0000.000
73A171THR0-0.025-0.02134.651-0.011-0.0110.0000.0000.0000.000
74A172LEU0-0.016-0.00736.2540.0060.0060.0000.0000.0000.000
75A173TRP00.0340.01639.146-0.004-0.0040.0000.0000.0000.000
76A174TYR0-0.015-0.03535.8630.0010.0010.0000.0000.0000.000
77A175CYS0-0.016-0.01242.1210.0030.0030.0000.0000.0000.000
78A176SER00.0580.03844.243-0.003-0.0030.0000.0000.0000.000
79A177VAL00.011-0.00245.7480.0020.0020.0000.0000.0000.000
80A178ASP-1-0.923-0.95647.538-0.058-0.0580.0000.0000.0000.000
81A179TYR0-0.013-0.00748.2210.0030.0030.0000.0000.0000.000
82A180GLN0-0.054-0.03450.3900.0020.0020.0000.0000.0000.000
83A181PHE0-0.015-0.01149.9260.0000.0000.0000.0000.0000.000
84A182GLN0-0.006-0.01552.5340.0010.0010.0000.0000.0000.000
85A183PRO00.0280.00954.4710.0000.0000.0000.0000.0000.000
86A184GLY0-0.056-0.01855.4660.0000.0000.0000.0000.0000.000
87A185GLU-1-0.907-0.95354.833-0.040-0.0400.0000.0000.0000.000
88A186PRO0-0.0510.00251.927-0.001-0.0010.0000.0000.0000.000
89A187VAL00.0280.00446.444-0.001-0.0010.0000.0000.0000.000
90A188PRO0-0.014-0.01248.3230.0000.0000.0000.0000.0000.000
91A189LEU0-0.0160.00042.723-0.003-0.0030.0000.0000.0000.000
92A190VAL00.0080.02440.4750.0010.0010.0000.0000.0000.000
93A191VAL0-0.0170.00938.441-0.005-0.0050.0000.0000.0000.000
94A192MET0-0.007-0.01030.917-0.001-0.0010.0000.0000.0000.000
95A193ASP-1-0.790-0.87435.304-0.084-0.0840.0000.0000.0000.000
96A194GLU-1-0.983-0.95635.574-0.066-0.0660.0000.0000.0000.000
97A195PRO00.0240.00831.9050.0000.0000.0000.0000.0000.000
98A196SER00.013-0.04032.704-0.009-0.0090.0000.0000.0000.000
99A197LEU00.0850.04930.2020.0050.0050.0000.0000.0000.000
100A198TYR00.006-0.01630.2520.0020.0020.0000.0000.0000.000
101A199ARG10.8710.94735.1270.0730.0730.0000.0000.0000.000
102A200GLU-1-0.887-0.94936.403-0.062-0.0620.0000.0000.0000.000
103A201MET00.0140.03134.4770.0030.0030.0000.0000.0000.000
104A202ALA0-0.025-0.00938.1360.0040.0040.0000.0000.0000.000
105A203ILE00.0270.00540.7870.0030.0030.0000.0000.0000.000
106A204GLU-1-0.908-0.94038.667-0.066-0.0660.0000.0000.0000.000
107A205HIS0-0.025-0.03939.1870.0040.0040.0000.0000.0000.000
108A206LEU0-0.020-0.00343.8210.0020.0020.0000.0000.0000.000
109A207THR0-0.024-0.02745.8560.0030.0030.0000.0000.0000.000
110A208GLN0-0.071-0.03842.8770.0030.0030.0000.0000.0000.000
111A209ALA0-0.047-0.01847.5590.0020.0020.0000.0000.0000.000
112A210GLY0-0.0090.00949.4990.0010.0010.0000.0000.0000.000
113A211VAL0-0.035-0.00749.5190.0010.0010.0000.0000.0000.000
114A212PRO00.0110.01050.016-0.001-0.0010.0000.0000.0000.000
115A213TRP00.019-0.00846.138-0.002-0.0020.0000.0000.0000.000
116A214ARG10.9880.99648.5640.0520.0520.0000.0000.0000.000
117A215ILE0-0.005-0.00543.326-0.003-0.0030.0000.0000.0000.000
118A216ALA0-0.040-0.01445.8780.0020.0020.0000.0000.0000.000
119A217TYR0-0.013-0.01640.7160.0000.0000.0000.0000.0000.000
120A218VAL00.0200.01639.357-0.003-0.0030.0000.0000.0000.000
121A219ALA00.0010.00437.6150.0010.0010.0000.0000.0000.000
122A220SER00.015-0.00633.913-0.001-0.0010.0000.0000.0000.000
123A221SER00.008-0.00231.327-0.006-0.0060.0000.0000.0000.000
124A222LEU00.0750.03329.8980.0090.0090.0000.0000.0000.000
125A223SER0-0.044-0.02431.2860.0040.0040.0000.0000.0000.000
126A224ALA00.0200.01433.5910.0050.0050.0000.0000.0000.000
127A225ILE0-0.0070.00635.3400.0060.0060.0000.0000.0000.000
128A226ARG10.9700.96831.1890.1430.1430.0000.0000.0000.000
129A227ALA0-0.033-0.00237.1840.0040.0040.0000.0000.0000.000
130A228ALA00.0470.02039.5190.0040.0040.0000.0000.0000.000
131A229VAL0-0.0040.00039.8750.0040.0040.0000.0000.0000.000
132A230ARG10.9120.95836.6810.1060.1060.0000.0000.0000.000
133A231ALA0-0.033-0.00542.6670.0030.0030.0000.0000.0000.000
134A232GLY00.0030.00645.3110.0030.0030.0000.0000.0000.000
135A233LEU0-0.062-0.03944.4800.0030.0030.0000.0000.0000.000
136A234GLY0-0.031-0.01446.0170.0020.0020.0000.0000.0000.000
137A235VAL0-0.0150.00543.828-0.003-0.0030.0000.0000.0000.000
138A236THR0-0.053-0.04838.216-0.002-0.0020.0000.0000.0000.000
139A237ALA00.0460.04038.5780.0010.0010.0000.0000.0000.000
140A238ARG10.8950.93731.2080.1150.1150.0000.0000.0000.000
141A239PRO00.0250.02630.4730.0050.0050.0000.0000.0000.000
142A240ILE00.0570.03332.5650.0000.0000.0000.0000.0000.000
143A241GLU-1-0.782-0.86528.386-0.154-0.1540.0000.0000.0000.000
144A242MET0-0.076-0.01631.692-0.002-0.0020.0000.0000.0000.000
145A243MET0-0.0240.03233.7870.0040.0040.0000.0000.0000.000
146A244SER0-0.037-0.05235.855-0.006-0.0060.0000.0000.0000.000
147A245PRO00.017-0.00938.5270.0040.0040.0000.0000.0000.000
148A246ASP-1-0.907-0.97040.696-0.084-0.0840.0000.0000.0000.000
149A247LEU0-0.047-0.00638.8270.0020.0020.0000.0000.0000.000
150A248ARG10.9030.95342.8250.0590.0590.0000.0000.0000.000
151A249VAL00.003-0.01141.489-0.002-0.0020.0000.0000.0000.000
152A250LEU0-0.056-0.01744.1820.0030.0030.0000.0000.0000.000
153A251GLY00.027-0.01645.236-0.003-0.0030.0000.0000.0000.000
154A252GLU-1-0.913-0.95647.155-0.049-0.0490.0000.0000.0000.000
155A253THR0-0.024-0.00849.8040.0020.0020.0000.0000.0000.000
156A254GLU-1-0.871-0.92649.553-0.056-0.0560.0000.0000.0000.000
157A255GLY00.0130.00851.7190.0010.0010.0000.0000.0000.000
158A256LEU0-0.043-0.01346.0430.0000.0000.0000.0000.0000.000
159A257PRO00.0040.02144.6230.0000.0000.0000.0000.0000.000
160A258GLY00.014-0.00843.333-0.003-0.0030.0000.0000.0000.000
161A259LEU0-0.043-0.01438.6530.0010.0010.0000.0000.0000.000
162A260PRO00.0200.00735.811-0.001-0.0010.0000.0000.0000.000
163A261GLU-1-0.919-0.94933.330-0.103-0.1030.0000.0000.0000.000
164A262THR0-0.008-0.00329.0670.0000.0000.0000.0000.0000.000
165A263ARG10.9640.97327.3110.1200.1200.0000.0000.0000.000
166A264TYR0-0.032-0.03423.654-0.004-0.0040.0000.0000.0000.000
167A265VAL0-0.017-0.00922.321-0.002-0.0020.0000.0000.0000.000
168A266LEU00.001-0.00214.665-0.015-0.0150.0000.0000.0000.000
169A267CYS0-0.031-0.01417.6460.0390.0390.0000.0000.0000.000
170A268LYS11.0011.00513.8780.0910.0910.0000.0000.0000.000
171A269ASP-1-0.816-0.91915.016-0.065-0.0650.0000.0000.0000.000
172A270LYS10.8160.87816.2320.0770.0770.0000.0000.0000.000
173A271GLN0-0.053-0.02517.0580.0000.0000.0000.0000.0000.000
174A272CYS0-0.0400.01611.1170.0160.0160.0000.0000.0000.000
175A273ASP-1-0.874-0.94011.0940.1910.1910.0000.0000.0000.000
176A274ASN0-0.006-0.0075.2860.3100.3100.0000.0000.0000.000
177A275GLU-1-0.919-0.9875.1180.6870.6870.0000.0000.0000.000
178A276LEU00.0300.0162.093-0.183-0.6312.440-1.115-0.8760.003
179A277ALA00.0010.0035.613-0.064-0.0640.0000.0000.0000.000
180A278LEU0-0.023-0.0198.5350.0480.0480.0000.0000.0000.000
181A279ALA00.0060.0148.7260.0400.0400.0000.0000.0000.000
182A280ILE00.0260.0057.8950.0380.0380.0000.0000.0000.000
183A281PHE0-0.0020.00611.1770.0670.0670.0000.0000.0000.000
184A282SER00.022-0.00313.4330.0450.0450.0000.0000.0000.000
185A283ALA0-0.052-0.01013.6660.0340.0340.0000.0000.0000.000
186A284LEU0-0.016-0.02214.7810.0270.0270.0000.0000.0000.000
187A285GLN00.007-0.01517.1930.0250.0250.0000.0000.0000.000
188A286ASN0-0.081-0.03717.7650.0360.0360.0000.0000.0000.000
189A287SER0-0.058-0.02119.4430.0020.0020.0000.0000.0000.000
190A288TYR0-0.041-0.02320.6270.0000.0000.0000.0000.0000.000
191A289GLN00.0200.03522.2110.0110.0110.0000.0000.0000.000