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: LZK19

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1979790.372268
FMO2-HF: Nuclear repulsion 1906017.78159
FMO2-HF: Total energy -73772.590678
FMO2-MP2: Total energy -73986.114538


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.
1.3853.9480.35-1.36-1.5520.002
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 : 0.046 / q_NPA : 0.026
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].
3A101LEU0-0.024-0.0083.863-0.0781.741-0.012-1.023-0.7840.004
4A102ILE0-0.0090.0086.9340.0660.0660.0000.0000.0000.000
5A103ILE00.001-0.00510.5310.1560.1560.0000.0000.0000.000
6A104GLY00.0230.01813.6330.0240.0240.0000.0000.0000.000
7A105ALA00.009-0.00716.9810.0140.0140.0000.0000.0000.000
8A106SER00.0470.01620.0770.0150.0150.0000.0000.0000.000
9A107ASP-1-0.829-0.92723.884-0.208-0.2080.0000.0000.0000.000
10A108ASP-1-0.812-0.88726.547-0.182-0.1820.0000.0000.0000.000
11A109THR0-0.017-0.01322.632-0.002-0.0020.0000.0000.0000.000
12A110ALA0-0.019-0.01621.972-0.018-0.0180.0000.0000.0000.000
13A111ASP-1-0.782-0.88122.805-0.247-0.2470.0000.0000.0000.000
14A112THR0-0.0050.00725.319-0.004-0.0040.0000.0000.0000.000
15A113LEU0-0.021-0.03222.3190.0080.0080.0000.0000.0000.000
16A114LEU0-0.0110.02116.774-0.017-0.0170.0000.0000.0000.000
17A115PRO00.0340.01118.279-0.051-0.0510.0000.0000.0000.000
18A116PHE0-0.0140.00818.976-0.021-0.0210.0000.0000.0000.000
19A117LEU00.0390.01815.153-0.002-0.0020.0000.0000.0000.000
20A118LEU00.0250.00913.588-0.050-0.0500.0000.0000.0000.000
21A119ASN0-0.036-0.02414.172-0.054-0.0540.0000.0000.0000.000
22A120ARG10.8570.94215.6480.2200.2200.0000.0000.0000.000
23A121VAL00.0310.0089.5230.0280.0280.0000.0000.0000.000
24A122ALA0-0.002-0.00310.774-0.060-0.0600.0000.0000.0000.000
25A123THR0-0.059-0.04712.2820.0530.0530.0000.0000.0000.000
26A124LEU0-0.050-0.01410.8710.0690.0690.0000.0000.0000.000
27A125TYR00.0170.0056.5590.0260.0260.0000.0000.0000.000
28A126PRO00.0430.0318.502-0.327-0.3270.0000.0000.0000.000
29A127ARG10.8530.9107.5270.9180.9180.0000.0000.0000.000
30A128LEU0-0.0180.0143.497-0.680-0.4830.003-0.074-0.1260.000
31A129ALA0-0.010-0.0026.0810.6380.6380.0000.0000.0000.000
32A130ILE0-0.021-0.0157.446-0.535-0.5350.0000.0000.0000.000
33A131ASP-1-0.816-0.88710.095-0.700-0.7000.0000.0000.0000.000
34A132VAL0-0.022-0.02012.1620.0340.0340.0000.0000.0000.000
35A133ARG10.7880.87513.2040.7470.7470.0000.0000.0000.000
36A134VAL00.0050.00117.9130.0330.0330.0000.0000.0000.000
37A135LYS10.8320.90319.6520.3530.3530.0000.0000.0000.000
38A136ARG10.8440.89723.6130.1460.1460.0000.0000.0000.000
39A137SER00.0590.02524.5710.0010.0010.0000.0000.0000.000
40A138PRO00.0010.00224.637-0.004-0.0040.0000.0000.0000.000
41A139PHE00.0220.00323.6990.0040.0040.0000.0000.0000.000
42A140ILE0-0.049-0.02019.904-0.012-0.0120.0000.0000.0000.000
43A141ALA0-0.012-0.00119.945-0.010-0.0100.0000.0000.0000.000
44A142ASP-1-0.900-0.93421.344-0.158-0.1580.0000.0000.0000.000
45A143MET0-0.035-0.00217.367-0.013-0.0130.0000.0000.0000.000
46A144LEU0-0.041-0.00914.931-0.019-0.0190.0000.0000.0000.000
47A145SER0-0.043-0.01816.7500.0270.0270.0000.0000.0000.000
48A146SER0-0.052-0.02818.5730.0170.0170.0000.0000.0000.000
49A147GLY00.0270.02414.1690.0190.0190.0000.0000.0000.000
50A148GLU-1-0.831-0.90413.392-0.441-0.4410.0000.0000.0000.000
51A149VAL0-0.019-0.03212.542-0.100-0.1000.0000.0000.0000.000
52A150ASP-1-0.774-0.8628.161-1.005-1.0050.0000.0000.0000.000
53A151LEU0-0.039-0.02810.9370.1280.1280.0000.0000.0000.000
54A152ALA00.0050.00813.411-0.043-0.0430.0000.0000.0000.000
55A153ILE0-0.029-0.00916.9040.0290.0290.0000.0000.0000.000
56A154THR0-0.016-0.02119.5970.0080.0080.0000.0000.0000.000
57A155THR00.017-0.01123.2810.0050.0050.0000.0000.0000.000
58A156ALA0-0.023-0.00425.7510.0150.0150.0000.0000.0000.000
59A157LYS10.8940.94527.3040.0760.0760.0000.0000.0000.000
60A158VAL0-0.010-0.01123.0540.0050.0050.0000.0000.0000.000
61A159ASP-1-0.868-0.93025.092-0.037-0.0370.0000.0000.0000.000
62A160SER0-0.0190.00826.1890.0080.0080.0000.0000.0000.000
63A161HIS00.0330.02419.5880.0270.0270.0000.0000.0000.000
64A162PRO0-0.0010.02218.4020.0010.0010.0000.0000.0000.000
65A163HIS0-0.004-0.01619.490-0.031-0.0310.0000.0000.0000.000
66A164VAL00.0140.01418.6700.0210.0210.0000.0000.0000.000
67A165ILE00.0180.00821.425-0.023-0.0230.0000.0000.0000.000
68A166LEU0-0.0130.00218.690-0.001-0.0010.0000.0000.0000.000
69A167ARG10.8550.92022.8230.1810.1810.0000.0000.0000.000
70A168THR0-0.012-0.00526.488-0.005-0.0050.0000.0000.0000.000
71A169SER0-0.055-0.05129.9520.0020.0020.0000.0000.0000.000
72A170PRO00.0110.00432.2260.0020.0020.0000.0000.0000.000
73A171THR0-0.021-0.02334.765-0.013-0.0130.0000.0000.0000.000
74A172LEU0-0.014-0.00236.5550.0070.0070.0000.0000.0000.000
75A173TRP00.0280.00739.370-0.007-0.0070.0000.0000.0000.000
76A174TYR0-0.049-0.05336.3220.0010.0010.0000.0000.0000.000
77A175CYS00.0010.00042.3310.0020.0020.0000.0000.0000.000
78A176SER00.0490.01144.475-0.002-0.0020.0000.0000.0000.000
79A177VAL0-0.005-0.00945.9910.0040.0040.0000.0000.0000.000
80A178ASP-1-0.868-0.90847.534-0.070-0.0700.0000.0000.0000.000
81A179TYR0-0.0090.00248.4000.0040.0040.0000.0000.0000.000
82A180GLN0-0.049-0.03650.5210.0040.0040.0000.0000.0000.000
83A181PHE00.001-0.00649.4210.0010.0010.0000.0000.0000.000
84A182GLN0-0.013-0.01352.6410.0030.0030.0000.0000.0000.000
85A183PRO00.005-0.00854.5650.0000.0000.0000.0000.0000.000
86A184GLY0-0.0340.00255.6030.0010.0010.0000.0000.0000.000
87A185GLU-1-0.843-0.91354.511-0.050-0.0500.0000.0000.0000.000
88A186PRO0-0.065-0.01852.106-0.001-0.0010.0000.0000.0000.000
89A187VAL00.0550.01346.804-0.002-0.0020.0000.0000.0000.000
90A188PRO00.009-0.00548.381-0.002-0.0020.0000.0000.0000.000
91A189LEU00.0110.01943.014-0.004-0.0040.0000.0000.0000.000
92A190VAL00.0090.02040.634-0.001-0.0010.0000.0000.0000.000
93A191VAL0-0.006-0.00538.758-0.005-0.0050.0000.0000.0000.000
94A192MET0-0.0250.00330.8840.0010.0010.0000.0000.0000.000
95A193ASP-1-0.750-0.83235.236-0.118-0.1180.0000.0000.0000.000
96A194GLU-1-0.850-0.89135.766-0.083-0.0830.0000.0000.0000.000
97A195PRO00.0120.00831.821-0.001-0.0010.0000.0000.0000.000
98A196SER00.031-0.02232.580-0.010-0.0100.0000.0000.0000.000
99A197LEU00.0390.02830.0560.0070.0070.0000.0000.0000.000
100A198TYR00.043-0.01330.4780.0020.0020.0000.0000.0000.000
101A199ARG10.7730.88235.4000.0920.0920.0000.0000.0000.000
102A200GLU-1-0.885-0.94136.334-0.070-0.0700.0000.0000.0000.000
103A201MET0-0.0390.00134.2590.0050.0050.0000.0000.0000.000
104A202ALA00.0440.01338.2430.0050.0050.0000.0000.0000.000
105A203ILE00.0310.02141.1470.0040.0040.0000.0000.0000.000
106A204GLU-1-0.864-0.93538.353-0.065-0.0650.0000.0000.0000.000
107A205HIS0-0.038-0.03639.2400.0060.0060.0000.0000.0000.000
108A206LEU0-0.0080.00343.7700.0030.0030.0000.0000.0000.000
109A207THR0-0.001-0.01646.0620.0030.0030.0000.0000.0000.000
110A208GLN0-0.063-0.02143.1450.0050.0050.0000.0000.0000.000
111A209ALA0-0.034-0.01147.5650.0030.0030.0000.0000.0000.000
112A210GLY0-0.019-0.00549.6640.0020.0020.0000.0000.0000.000
113A211VAL0-0.0190.00049.5570.0010.0010.0000.0000.0000.000
114A212PRO00.0090.00650.201-0.002-0.0020.0000.0000.0000.000
115A213TRP0-0.007-0.02246.027-0.003-0.0030.0000.0000.0000.000
116A214ARG10.8610.91948.8010.0600.0600.0000.0000.0000.000
117A215ILE0-0.022-0.00143.301-0.003-0.0030.0000.0000.0000.000
118A216ALA0-0.034-0.00945.7520.0030.0030.0000.0000.0000.000
119A217TYR0-0.007-0.01140.949-0.002-0.0020.0000.0000.0000.000
120A218VAL00.0040.00239.589-0.001-0.0010.0000.0000.0000.000
121A219ALA00.0120.00737.8800.0000.0000.0000.0000.0000.000
122A220SER00.003-0.02633.720-0.002-0.0020.0000.0000.0000.000
123A221SER0-0.011-0.01731.085-0.008-0.0080.0000.0000.0000.000
124A222LEU00.0490.02029.8640.0120.0120.0000.0000.0000.000
125A223SER0-0.024-0.01631.2900.0070.0070.0000.0000.0000.000
126A224ALA00.0230.03133.6820.0070.0070.0000.0000.0000.000
127A225ILE0-0.0010.00935.8260.0080.0080.0000.0000.0000.000
128A226ARG10.8500.89430.0940.1880.1880.0000.0000.0000.000
129A227ALA00.0030.00537.3780.0060.0060.0000.0000.0000.000
130A228ALA00.0140.00539.6690.0060.0060.0000.0000.0000.000
131A229VAL0-0.004-0.00440.1480.0060.0060.0000.0000.0000.000
132A230ARG10.8610.90737.4680.1250.1250.0000.0000.0000.000
133A231ALA0-0.035-0.01242.9340.0040.0040.0000.0000.0000.000
134A232GLY00.0240.01945.4150.0040.0040.0000.0000.0000.000
135A233LEU0-0.070-0.04544.5350.0030.0030.0000.0000.0000.000
136A234GLY0-0.032-0.02146.3600.0030.0030.0000.0000.0000.000
137A235VAL0-0.028-0.00144.111-0.002-0.0020.0000.0000.0000.000
138A236THR0-0.047-0.03338.511-0.003-0.0030.0000.0000.0000.000
139A237ALA00.0320.02439.0390.0030.0030.0000.0000.0000.000
140A238ARG10.8300.89630.3480.1390.1390.0000.0000.0000.000
141A239PRO00.0410.02630.7100.0070.0070.0000.0000.0000.000
142A240ILE00.0360.03732.889-0.001-0.0010.0000.0000.0000.000
143A241GLU-1-0.751-0.84228.958-0.150-0.1500.0000.0000.0000.000
144A242MET0-0.073-0.01832.199-0.006-0.0060.0000.0000.0000.000
145A243MET00.0070.04534.4870.0030.0030.0000.0000.0000.000
146A244SER0-0.034-0.04736.312-0.010-0.0100.0000.0000.0000.000
147A245PRO00.0120.00138.8620.0040.0040.0000.0000.0000.000
148A246ASP-1-0.867-0.92441.138-0.100-0.1000.0000.0000.0000.000
149A247LEU0-0.058-0.02238.9830.0000.0000.0000.0000.0000.000
150A248ARG10.8710.93043.1070.0650.0650.0000.0000.0000.000
151A249VAL0-0.001-0.00841.724-0.002-0.0020.0000.0000.0000.000
152A250LEU0-0.034-0.01244.3480.0030.0030.0000.0000.0000.000
153A251GLY00.003-0.02545.299-0.003-0.0030.0000.0000.0000.000
154A252GLU-1-0.906-0.94147.475-0.044-0.0440.0000.0000.0000.000
155A253THR0-0.038-0.01850.3100.0020.0020.0000.0000.0000.000
156A254GLU-1-0.834-0.90250.013-0.058-0.0580.0000.0000.0000.000
157A255GLY00.0090.00752.2650.0000.0000.0000.0000.0000.000
158A256LEU0-0.055-0.02146.3750.0000.0000.0000.0000.0000.000
159A257PRO00.0100.01645.4180.0010.0010.0000.0000.0000.000
160A258GLY00.0140.00543.719-0.003-0.0030.0000.0000.0000.000
161A259LEU0-0.034-0.01738.7250.0000.0000.0000.0000.0000.000
162A260PRO00.0150.00435.8390.0010.0010.0000.0000.0000.000
163A261GLU-1-0.860-0.90232.345-0.085-0.0850.0000.0000.0000.000
164A262THR0-0.008-0.00629.238-0.002-0.0020.0000.0000.0000.000
165A263ARG10.9060.94527.2470.0830.0830.0000.0000.0000.000
166A264TYR0-0.035-0.04024.387-0.009-0.0090.0000.0000.0000.000
167A265VAL0-0.040-0.02822.7840.0060.0060.0000.0000.0000.000
168A266LEU00.0100.01315.003-0.027-0.0270.0000.0000.0000.000
169A267CYS0-0.047-0.03217.9460.0510.0510.0000.0000.0000.000
170A268LYS10.9570.98514.140-0.077-0.0770.0000.0000.0000.000
171A269ASP-1-0.752-0.89015.342-0.017-0.0170.0000.0000.0000.000
172A270LYS10.8050.87016.5720.0580.0580.0000.0000.0000.000
173A271GLN0-0.087-0.03717.1020.0190.0190.0000.0000.0000.000
174A272CYS0-0.044-0.00111.6630.0230.0230.0000.0000.0000.000
175A273ASP-1-0.862-0.93811.1500.2760.2760.0000.0000.0000.000
176A274ASN0-0.007-0.0185.0190.6480.6480.0000.0000.0000.000
177A275GLU-1-0.906-0.9665.4232.7742.7740.0000.0000.0000.000
178A276LEU0-0.0040.0112.605-1.002-0.4550.359-0.263-0.642-0.002
179A277ALA00.0270.0085.993-0.243-0.2430.0000.0000.0000.000
180A278LEU0-0.013-0.0098.5980.0010.0010.0000.0000.0000.000
181A279ALA00.0030.0208.910-0.035-0.0350.0000.0000.0000.000
182A280ILE00.0120.0007.844-0.033-0.0330.0000.0000.0000.000
183A281PHE00.0160.00311.4160.0300.0300.0000.0000.0000.000
184A282SER0-0.008-0.02013.7310.0190.0190.0000.0000.0000.000
185A283ALA0-0.029-0.00613.7490.0160.0160.0000.0000.0000.000
186A284LEU0-0.007-0.00614.911-0.005-0.0050.0000.0000.0000.000
187A285GLN00.019-0.00417.3600.0150.0150.0000.0000.0000.000
188A286ASN0-0.072-0.04618.3420.0090.0090.0000.0000.0000.000
189A287SER0-0.064-0.01319.105-0.007-0.0070.0000.0000.0000.000
190A288TYR0-0.053-0.03920.667-0.016-0.0160.0000.0000.0000.000
191A289GLN00.0030.01922.3480.0000.0000.0000.0000.0000.000