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: 3916L

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1974067.153777
FMO2-HF: Nuclear repulsion 1900295.202887
FMO2-HF: Total energy -73771.95089
FMO2-MP2: Total energy -73985.528003


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.
2.1574.1721.396-1.748-1.6610.006
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 : 0.045 / q_NPA : 0.023
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].
3A101LEU0-0.026-0.0173.8160.1051.976-0.014-0.999-0.8580.005
4A102ILE0-0.0040.0126.8300.0270.0270.0000.0000.0000.000
5A103ILE00.0100.00810.4900.1780.1780.0000.0000.0000.000
6A104GLY00.0130.00213.1820.0140.0140.0000.0000.0000.000
7A105ALA00.0170.00216.6460.0220.0220.0000.0000.0000.000
8A106SER00.0170.00619.7360.0030.0030.0000.0000.0000.000
9A107ASP-1-0.826-0.93823.482-0.201-0.2010.0000.0000.0000.000
10A108ASP-1-0.898-0.94025.922-0.176-0.1760.0000.0000.0000.000
11A109THR0-0.011-0.00822.3190.0000.0000.0000.0000.0000.000
12A110ALA0-0.030-0.01521.832-0.015-0.0150.0000.0000.0000.000
13A111ASP-1-0.777-0.88822.620-0.226-0.2260.0000.0000.0000.000
14A112THR00.0000.00624.7100.0060.0060.0000.0000.0000.000
15A113LEU0-0.011-0.01821.972-0.005-0.0050.0000.0000.0000.000
16A114LEU0-0.0140.02116.655-0.013-0.0130.0000.0000.0000.000
17A115PRO00.0370.00818.201-0.043-0.0430.0000.0000.0000.000
18A116PHE0-0.050-0.01419.245-0.010-0.0100.0000.0000.0000.000
19A117LEU00.0460.01714.6050.0050.0050.0000.0000.0000.000
20A118LEU00.0230.01313.623-0.029-0.0290.0000.0000.0000.000
21A119ASN00.0070.00714.767-0.062-0.0620.0000.0000.0000.000
22A120ARG10.8710.96016.1930.1620.1620.0000.0000.0000.000
23A121VAL00.016-0.0069.8840.0310.0310.0000.0000.0000.000
24A122ALA00.0120.00211.629-0.016-0.0160.0000.0000.0000.000
25A123THR0-0.071-0.03912.6770.0410.0410.0000.0000.0000.000
26A124LEU0-0.042-0.01911.5090.0600.0600.0000.0000.0000.000
27A125TYR0-0.011-0.0147.0270.0380.0380.0000.0000.0000.000
28A126PRO00.0470.0359.098-0.271-0.2710.0000.0000.0000.000
29A127ARG10.8550.9187.1570.7490.7490.0000.0000.0000.000
30A128LEU00.0070.0224.117-0.689-0.5960.000-0.037-0.0550.000
31A129ALA0-0.0100.0016.3690.6310.6310.0000.0000.0000.000
32A130ILE0-0.032-0.0267.631-0.536-0.5360.0000.0000.0000.000
33A131ASP-1-0.816-0.88310.060-0.741-0.7410.0000.0000.0000.000
34A132VAL0-0.005-0.01312.0310.0380.0380.0000.0000.0000.000
35A133ARG10.7910.89612.8790.7740.7740.0000.0000.0000.000
36A134VAL0-0.006-0.01217.7130.0270.0270.0000.0000.0000.000
37A135LYS10.8390.89619.4230.3540.3540.0000.0000.0000.000
38A136ARG10.8600.90923.6620.1410.1410.0000.0000.0000.000
39A137SER00.0550.02424.515-0.001-0.0010.0000.0000.0000.000
40A138PRO00.0040.00024.742-0.002-0.0020.0000.0000.0000.000
41A139PHE00.0080.00023.6890.0050.0050.0000.0000.0000.000
42A140ILE00.004-0.00719.816-0.007-0.0070.0000.0000.0000.000
43A141ALA0-0.024-0.00619.870-0.009-0.0090.0000.0000.0000.000
44A142ASP-1-0.909-0.95721.110-0.151-0.1510.0000.0000.0000.000
45A143MET0-0.0440.02717.409-0.013-0.0130.0000.0000.0000.000
46A144LEU0-0.075-0.02414.917-0.020-0.0200.0000.0000.0000.000
47A145SER0-0.023-0.01316.6230.0250.0250.0000.0000.0000.000
48A146SER0-0.023-0.01417.9230.0130.0130.0000.0000.0000.000
49A147GLY00.0230.02613.7010.0160.0160.0000.0000.0000.000
50A148GLU-1-0.827-0.91012.661-0.471-0.4710.0000.0000.0000.000
51A149VAL0-0.040-0.04812.759-0.105-0.1050.0000.0000.0000.000
52A150ASP-1-0.764-0.8658.511-0.904-0.9040.0000.0000.0000.000
53A151LEU0-0.057-0.03610.7450.1400.1400.0000.0000.0000.000
54A152ALA00.0060.01313.276-0.064-0.0640.0000.0000.0000.000
55A153ILE0-0.030-0.00916.7900.0430.0430.0000.0000.0000.000
56A154THR0-0.016-0.02619.2590.0010.0010.0000.0000.0000.000
57A155THR00.018-0.01222.8280.0090.0090.0000.0000.0000.000
58A156ALA0-0.031-0.00225.7930.0140.0140.0000.0000.0000.000
59A157LYS10.9570.97126.7030.0620.0620.0000.0000.0000.000
60A158VAL00.0480.04422.6010.0030.0030.0000.0000.0000.000
61A159ASP-1-0.885-1.02924.126-0.001-0.0010.0000.0000.0000.000
62A160SER0-0.0100.01625.8050.0080.0080.0000.0000.0000.000
63A161HIS0-0.0380.03119.4580.0280.0280.0000.0000.0000.000
64A162PRO00.0260.04018.3370.0060.0060.0000.0000.0000.000
65A163HIS0-0.008-0.02419.620-0.030-0.0300.0000.0000.0000.000
66A164VAL00.0140.02518.0490.0180.0180.0000.0000.0000.000
67A165ILE00.0220.00720.802-0.025-0.0250.0000.0000.0000.000
68A166LEU0-0.016-0.00718.4700.0030.0030.0000.0000.0000.000
69A167ARG10.8720.92622.6010.1490.1490.0000.0000.0000.000
70A168THR0-0.021-0.00326.251-0.005-0.0050.0000.0000.0000.000
71A169SER0-0.075-0.06129.7060.0020.0020.0000.0000.0000.000
72A170PRO00.0490.02332.0260.0020.0020.0000.0000.0000.000
73A171THR0-0.025-0.02034.644-0.012-0.0120.0000.0000.0000.000
74A172LEU0-0.013-0.00136.2490.0070.0070.0000.0000.0000.000
75A173TRP00.0270.00439.141-0.007-0.0070.0000.0000.0000.000
76A174TYR0-0.028-0.03335.8460.0020.0020.0000.0000.0000.000
77A175CYS0-0.016-0.01642.1150.0020.0020.0000.0000.0000.000
78A176SER00.0360.01944.236-0.002-0.0020.0000.0000.0000.000
79A177VAL00.009-0.01045.7410.0030.0030.0000.0000.0000.000
80A178ASP-1-0.904-0.93447.530-0.065-0.0650.0000.0000.0000.000
81A179TYR00.0050.01248.2610.0030.0030.0000.0000.0000.000
82A180GLN0-0.059-0.04150.3840.0040.0040.0000.0000.0000.000
83A181PHE0-0.002-0.00749.3420.0000.0000.0000.0000.0000.000
84A182GLN0-0.010-0.01252.5280.0020.0020.0000.0000.0000.000
85A183PRO00.0350.00854.4480.0000.0000.0000.0000.0000.000
86A184GLY0-0.063-0.01855.4620.0010.0010.0000.0000.0000.000
87A185GLU-1-0.913-0.96054.758-0.045-0.0450.0000.0000.0000.000
88A186PRO0-0.0490.00651.8950.0000.0000.0000.0000.0000.000
89A187VAL00.0330.00246.532-0.002-0.0020.0000.0000.0000.000
90A188PRO0-0.019-0.01448.321-0.001-0.0010.0000.0000.0000.000
91A189LEU0-0.0130.00742.922-0.003-0.0030.0000.0000.0000.000
92A190VAL00.0040.01940.047-0.001-0.0010.0000.0000.0000.000
93A191VAL0-0.0030.00538.430-0.003-0.0030.0000.0000.0000.000
94A192MET0-0.024-0.01630.834-0.001-0.0010.0000.0000.0000.000
95A193ASP-1-0.792-0.84835.249-0.113-0.1130.0000.0000.0000.000
96A194GLU-1-0.866-0.89835.575-0.077-0.0770.0000.0000.0000.000
97A195PRO00.0160.00531.982-0.002-0.0020.0000.0000.0000.000
98A196SER00.026-0.03432.703-0.009-0.0090.0000.0000.0000.000
99A197LEU00.0670.04629.9810.0070.0070.0000.0000.0000.000
100A198TYR00.024-0.02130.1160.0030.0030.0000.0000.0000.000
101A199ARG10.8020.90135.1250.0850.0850.0000.0000.0000.000
102A200GLU-1-0.888-0.95036.389-0.060-0.0600.0000.0000.0000.000
103A201MET0-0.0270.00934.1520.0050.0050.0000.0000.0000.000
104A202ALA00.004-0.00138.1350.0050.0050.0000.0000.0000.000
105A203ILE00.0430.01540.7860.0040.0040.0000.0000.0000.000
106A204GLU-1-0.927-0.95138.642-0.052-0.0520.0000.0000.0000.000
107A205HIS0-0.027-0.04039.3470.0060.0060.0000.0000.0000.000
108A206LEU0-0.0070.00143.8190.0030.0030.0000.0000.0000.000
109A207THR0-0.016-0.02145.9430.0030.0030.0000.0000.0000.000
110A208GLN0-0.065-0.02443.0190.0040.0040.0000.0000.0000.000
111A209ALA0-0.041-0.01847.5590.0020.0020.0000.0000.0000.000
112A210GLY0-0.0080.00749.4980.0010.0010.0000.0000.0000.000
113A211VAL0-0.043-0.01349.4140.0010.0010.0000.0000.0000.000
114A212PRO00.0090.00550.015-0.002-0.0020.0000.0000.0000.000
115A213TRP00.021-0.00946.101-0.003-0.0030.0000.0000.0000.000
116A214ARG10.9760.98948.5740.0570.0570.0000.0000.0000.000
117A215ILE0-0.001-0.00443.202-0.003-0.0030.0000.0000.0000.000
118A216ALA0-0.036-0.00445.8900.0010.0010.0000.0000.0000.000
119A217TYR0-0.002-0.01240.965-0.002-0.0020.0000.0000.0000.000
120A218VAL00.0170.01339.439-0.002-0.0020.0000.0000.0000.000
121A219ALA00.0030.00537.727-0.001-0.0010.0000.0000.0000.000
122A220SER00.026-0.01633.9350.0010.0010.0000.0000.0000.000
123A221SER0-0.017-0.01531.314-0.009-0.0090.0000.0000.0000.000
124A222LEU00.0610.02829.3290.0130.0130.0000.0000.0000.000
125A223SER0-0.037-0.02131.3330.0080.0080.0000.0000.0000.000
126A224ALA00.0220.01633.5860.0070.0070.0000.0000.0000.000
127A225ILE0-0.0050.00635.4040.0070.0070.0000.0000.0000.000
128A226ARG10.8650.90530.1070.1750.1750.0000.0000.0000.000
129A227ALA0-0.025-0.00237.1780.0060.0060.0000.0000.0000.000
130A228ALA00.0460.01939.5130.0060.0060.0000.0000.0000.000
131A229VAL0-0.0020.00039.9860.0050.0050.0000.0000.0000.000
132A230ARG10.8680.91837.0590.1190.1190.0000.0000.0000.000
133A231ALA0-0.029-0.00342.6600.0030.0030.0000.0000.0000.000
134A232GLY00.0060.00845.3050.0030.0030.0000.0000.0000.000
135A233LEU0-0.057-0.03744.2660.0030.0030.0000.0000.0000.000
136A234GLY0-0.037-0.02246.0010.0020.0020.0000.0000.0000.000
137A235VAL0-0.0190.00143.816-0.003-0.0030.0000.0000.0000.000
138A236THR0-0.054-0.04138.213-0.003-0.0030.0000.0000.0000.000
139A237ALA00.0460.04238.5770.0020.0020.0000.0000.0000.000
140A238ARG10.8930.93230.6510.1230.1230.0000.0000.0000.000
141A239PRO00.0240.02330.4620.0070.0070.0000.0000.0000.000
142A240ILE00.0570.03732.591-0.003-0.0030.0000.0000.0000.000
143A241GLU-1-0.760-0.84828.369-0.128-0.1280.0000.0000.0000.000
144A242MET0-0.081-0.02131.684-0.006-0.0060.0000.0000.0000.000
145A243MET0-0.0140.02833.7800.0010.0010.0000.0000.0000.000
146A244SER0-0.029-0.03635.846-0.010-0.0100.0000.0000.0000.000
147A245PRO00.0210.00238.5180.0040.0040.0000.0000.0000.000
148A246ASP-1-0.884-0.94640.772-0.094-0.0940.0000.0000.0000.000
149A247LEU0-0.046-0.00638.7340.0000.0000.0000.0000.0000.000
150A248ARG10.8940.93642.8170.0580.0580.0000.0000.0000.000
151A249VAL00.002-0.01041.442-0.003-0.0030.0000.0000.0000.000
152A250LEU0-0.069-0.01844.1750.0030.0030.0000.0000.0000.000
153A251GLY00.027-0.01645.230-0.002-0.0020.0000.0000.0000.000
154A252GLU-1-0.912-0.95347.150-0.035-0.0350.0000.0000.0000.000
155A253THR0-0.039-0.01749.7990.0020.0020.0000.0000.0000.000
156A254GLU-1-0.838-0.90649.806-0.050-0.0500.0000.0000.0000.000
157A255GLY0-0.0030.00451.6980.0000.0000.0000.0000.0000.000
158A256LEU0-0.047-0.01346.0560.0000.0000.0000.0000.0000.000
159A257PRO00.0040.01644.8920.0010.0010.0000.0000.0000.000
160A258GLY00.0160.00343.328-0.003-0.0030.0000.0000.0000.000
161A259LEU0-0.029-0.00738.5730.0000.0000.0000.0000.0000.000
162A260PRO00.0070.00235.8550.0010.0010.0000.0000.0000.000
163A261GLU-1-0.876-0.91432.362-0.063-0.0630.0000.0000.0000.000
164A262THR0-0.005-0.00328.977-0.002-0.0020.0000.0000.0000.000
165A263ARG10.9200.95327.0150.0600.0600.0000.0000.0000.000
166A264TYR0-0.055-0.04923.704-0.010-0.0100.0000.0000.0000.000
167A265VAL0-0.017-0.01522.3020.0090.0090.0000.0000.0000.000
168A266LEU00.0000.00314.586-0.027-0.0270.0000.0000.0000.000
169A267CYS0-0.040-0.01617.6360.0470.0470.0000.0000.0000.000
170A268LYS11.0001.00513.867-0.174-0.1740.0000.0000.0000.000
171A269ASP-1-0.767-0.90115.019-0.001-0.0010.0000.0000.0000.000
172A270LYS10.7980.87316.2400.0380.0380.0000.0000.0000.000
173A271GLN0-0.077-0.03617.0690.0170.0170.0000.0000.0000.000
174A272CYS0-0.0520.00111.4180.0290.0290.0000.0000.0000.000
175A273ASP-1-0.869-0.93711.1070.3690.3690.0000.0000.0000.000
176A274ASN0-0.014-0.0165.2670.7190.7190.0000.0000.0000.000
177A275GLU-1-0.921-0.9865.1213.1253.1250.0000.0000.0000.000
178A276LEU00.0190.0112.232-0.592-0.5411.410-0.712-0.7480.001
179A277ALA00.0120.0065.611-0.264-0.2640.0000.0000.0000.000
180A278LEU0-0.015-0.0138.536-0.032-0.0320.0000.0000.0000.000
181A279ALA00.0100.0308.653-0.049-0.0490.0000.0000.0000.000
182A280ILE00.0300.0087.900-0.069-0.0690.0000.0000.0000.000
183A281PHE00.0080.00711.1710.0070.0070.0000.0000.0000.000
184A282SER00.004-0.02313.427-0.010-0.0100.0000.0000.0000.000
185A283ALA0-0.045-0.00713.5990.0010.0010.0000.0000.0000.000
186A284LEU0-0.013-0.02114.715-0.015-0.0150.0000.0000.0000.000
187A285GLN00.010-0.01017.1880.0100.0100.0000.0000.0000.000
188A286ASN0-0.094-0.04917.800-0.005-0.0050.0000.0000.0000.000
189A287SER0-0.054-0.01419.361-0.010-0.0100.0000.0000.0000.000
190A288TYR0-0.054-0.04020.602-0.011-0.0110.0000.0000.0000.000
191A289GLN00.0280.03722.242-0.006-0.0060.0000.0000.0000.000