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: 5JZ4Z

Calculation Name: 2OER-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OER

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I3U1

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1896959.579247
FMO2-HF: Nuclear repulsion 1824633.732969
FMO2-HF: Total energy -72325.846278
FMO2-MP2: Total energy -72539.529798


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:21:SER)


Summations of interaction energy for fragment #1(A:21:SER)
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.
-10.135-5.5891.377-2.236-3.6870.014
Interaction energy analysis for fragmet #1(A:21:SER)
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 : -0.004
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].
3A23LEU00.0220.0273.068-1.8390.1860.065-0.897-1.1920.003
4A24VAL00.0090.0032.651-6.290-4.3751.310-1.107-2.1180.010
5A25ALA00.0230.0114.008-1.705-1.2730.002-0.213-0.2220.001
6A26SER0-0.001-0.0045.876-0.091-0.0910.0000.0000.0000.000
7A27ILE00.008-0.0036.670-0.330-0.3300.0000.0000.0000.000
8A28LEU0-0.017-0.0177.044-0.284-0.2840.0000.0000.0000.000
9A29GLU-1-0.873-0.9209.8040.1060.1060.0000.0000.0000.000
10A30ALA00.0360.01911.853-0.082-0.0820.0000.0000.0000.000
11A31ALA0-0.037-0.02812.686-0.077-0.0770.0000.0000.0000.000
12A32VAL00.0350.01313.655-0.064-0.0640.0000.0000.0000.000
13A33GLN00.0060.00115.162-0.051-0.0510.0000.0000.0000.000
14A34VAL0-0.0360.00217.287-0.037-0.0370.0000.0000.0000.000
15A35LEU0-0.015-0.01618.329-0.035-0.0350.0000.0000.0000.000
16A36ALA00.0380.02019.856-0.027-0.0270.0000.0000.0000.000
17A37SER0-0.074-0.05421.266-0.015-0.0150.0000.0000.0000.000
18A38GLU-1-0.867-0.92522.7520.2790.2790.0000.0000.0000.000
19A39GLY00.0180.02323.357-0.010-0.0100.0000.0000.0000.000
20A40ALA00.0480.01322.3150.0240.0240.0000.0000.0000.000
21A41GLN0-0.003-0.00223.3360.0130.0130.0000.0000.0000.000
22A42ARG10.8030.88325.024-0.227-0.2270.0000.0000.0000.000
23A43PHE00.0250.04315.6270.0220.0220.0000.0000.0000.000
24A44THR0-0.005-0.02720.405-0.001-0.0010.0000.0000.0000.000
25A45THR00.0620.02315.119-0.019-0.0190.0000.0000.0000.000
26A46ALA0-0.001-0.00716.4070.0680.0680.0000.0000.0000.000
27A47ARG10.8880.95818.286-0.288-0.2880.0000.0000.0000.000
28A48VAL00.0080.01413.016-0.002-0.0020.0000.0000.0000.000
29A49ALA0-0.024-0.01513.5790.0780.0780.0000.0000.0000.000
30A50GLU-1-0.912-0.95214.6590.5000.5000.0000.0000.0000.000
31A51ARG10.8090.90316.461-0.333-0.3330.0000.0000.0000.000
32A52ALA0-0.007-0.00711.160-0.033-0.0330.0000.0000.0000.000
33A53GLY0-0.0120.02112.4750.0850.0850.0000.0000.0000.000
34A54VAL0-0.055-0.0299.9020.0570.0570.0000.0000.0000.000
35A55SER00.0320.00813.331-0.063-0.0630.0000.0000.0000.000
36A56ILE00.0520.00413.6690.1400.1400.0000.0000.0000.000
37A57GLY0-0.027-0.00814.4670.0500.0500.0000.0000.0000.000
38A58SER00.0010.0019.6820.1150.1150.0000.0000.0000.000
39A59LEU00.0320.0179.9070.2910.2910.0000.0000.0000.000
40A60TYR0-0.028-0.02710.7480.0790.0790.0000.0000.0000.000
41A61GLN0-0.0370.0008.786-0.048-0.0480.0000.0000.0000.000
42A62TYR0-0.035-0.0114.0410.6060.7800.000-0.019-0.1550.000
43A63PHE00.014-0.0057.728-0.260-0.2600.0000.0000.0000.000
44A64PRO00.0210.01311.812-0.046-0.0460.0000.0000.0000.000
45A65ASN0-0.022-0.02214.968-0.082-0.0820.0000.0000.0000.000
46A66LYS10.8580.91416.103-0.233-0.2330.0000.0000.0000.000
47A67ALA00.0770.03517.1760.0140.0140.0000.0000.0000.000
48A68ALA0-0.0180.00113.814-0.017-0.0170.0000.0000.0000.000
49A69ILE0-0.0060.00111.9630.0100.0100.0000.0000.0000.000
50A70LEU0-0.0010.00513.471-0.051-0.0510.0000.0000.0000.000
51A71PHE00.0550.02215.691-0.044-0.0440.0000.0000.0000.000
52A72ARG10.8080.8946.187-0.018-0.0180.0000.0000.0000.000
53A73LEU0-0.010-0.01712.119-0.080-0.0800.0000.0000.0000.000
54A74GLN00.0270.00814.221-0.047-0.0470.0000.0000.0000.000
55A75SER0-0.0040.00813.706-0.055-0.0550.0000.0000.0000.000
56A76ASP-1-0.774-0.87510.132-0.243-0.2430.0000.0000.0000.000
57A77GLU-1-0.721-0.80613.725-0.078-0.0780.0000.0000.0000.000
58A78TRP0-0.038-0.02517.183-0.029-0.0290.0000.0000.0000.000
59A79ARG10.8100.90610.5070.3400.3400.0000.0000.0000.000
60A80ARG10.7010.81016.1860.0080.0080.0000.0000.0000.000
61A81THR00.016-0.01117.519-0.019-0.0190.0000.0000.0000.000
62A82THR0-0.021-0.02420.2950.0020.0020.0000.0000.0000.000
63A83ARG10.8230.91018.6740.2650.2650.0000.0000.0000.000
64A84LEU0-0.004-0.00121.0730.0050.0050.0000.0000.0000.000
65A85LEU00.012-0.01122.8070.0090.0090.0000.0000.0000.000
66A86GLY00.0360.02524.9900.0080.0080.0000.0000.0000.000
67A87GLU-1-0.837-0.90922.411-0.216-0.2160.0000.0000.0000.000
68A88ILE0-0.077-0.04425.8990.0060.0060.0000.0000.0000.000
69A89LEU0-0.021-0.00928.5920.0090.0090.0000.0000.0000.000
70A90GLU-1-0.921-0.95727.523-0.162-0.1620.0000.0000.0000.000
71A91ASP-1-0.808-0.85229.619-0.104-0.1040.0000.0000.0000.000
72A92THR00.0190.00430.9450.0070.0070.0000.0000.0000.000
73A93THR0-0.147-0.09132.7510.0060.0060.0000.0000.0000.000
74A94ARG10.8780.93032.1590.0930.0930.0000.0000.0000.000
75A95PRO00.0640.02637.015-0.003-0.0030.0000.0000.0000.000
76A96PRO00.0490.02037.4160.0000.0000.0000.0000.0000.000
77A97LEU00.0420.02137.4790.0000.0000.0000.0000.0000.000
78A98GLU-1-0.888-0.95336.672-0.057-0.0570.0000.0000.0000.000
79A99ARG10.6950.83033.1770.0930.0930.0000.0000.0000.000
80A100LEU00.0570.03133.073-0.002-0.0020.0000.0000.0000.000
81A101ARG10.8280.86734.2730.0320.0320.0000.0000.0000.000
82A102ARG10.8400.90928.8330.0980.0980.0000.0000.0000.000
83A103LEU00.0230.02228.8530.0010.0010.0000.0000.0000.000
84A104VAL0-0.002-0.00529.9520.0030.0030.0000.0000.0000.000
85A105LEU0-0.009-0.00330.2180.0060.0060.0000.0000.0000.000
86A106ALA0-0.019-0.01126.0330.0050.0050.0000.0000.0000.000
87A107PHE0-0.011-0.00426.4020.0040.0040.0000.0000.0000.000
88A108VAL00.005-0.00227.7790.0090.0090.0000.0000.0000.000
89A109ARG10.7500.85325.7070.0220.0220.0000.0000.0000.000
90A110SER00.0170.00322.5300.0090.0090.0000.0000.0000.000
91A111GLU-1-0.804-0.92324.2030.0220.0220.0000.0000.0000.000
92A112CYS0-0.052-0.02626.6500.0140.0140.0000.0000.0000.000
93A113GLU-1-0.875-0.90520.8730.0280.0280.0000.0000.0000.000
94A114GLU-1-0.832-0.92821.6370.0330.0330.0000.0000.0000.000
95A115ALA0-0.0040.01423.0410.0190.0190.0000.0000.0000.000
96A116ALA0-0.015-0.01022.8360.0150.0150.0000.0000.0000.000
97A117ILE00.002-0.01117.8450.0300.0300.0000.0000.0000.000
98A118ARG10.8900.93121.449-0.045-0.0450.0000.0000.0000.000
99A119VAL0-0.021-0.01324.4050.0080.0080.0000.0000.0000.000
100A120ALA0-0.015-0.00921.2220.0100.0100.0000.0000.0000.000
101A121LEU0-0.013-0.01119.2250.0180.0180.0000.0000.0000.000
102A122SER0-0.0030.02522.990-0.008-0.0080.0000.0000.0000.000
103A123ASP-1-0.848-0.92124.4060.2390.2390.0000.0000.0000.000
104A124ALA0-0.031-0.01521.0360.0070.0070.0000.0000.0000.000
105A125ALA0-0.012-0.00922.0680.0150.0150.0000.0000.0000.000
106A126PRO0-0.026-0.00524.134-0.022-0.0220.0000.0000.0000.000
107A127LEU0-0.008-0.02227.284-0.014-0.0140.0000.0000.0000.000
108A128TYR00.000-0.01222.1140.0010.0010.0000.0000.0000.000
109A129ARG10.7850.88826.086-0.124-0.1240.0000.0000.0000.000
110A130ASP-1-0.908-0.95427.7110.0670.0670.0000.0000.0000.000
111A131ALA0-0.0110.01125.728-0.010-0.0100.0000.0000.0000.000
112A132ASP-1-0.922-0.96825.7400.0090.0090.0000.0000.0000.000
113A133GLU-1-0.794-0.86920.1230.0480.0480.0000.0000.0000.000
114A134ALA00.0900.02124.401-0.013-0.0130.0000.0000.0000.000
115A135ARG10.8240.89825.297-0.017-0.0170.0000.0000.0000.000
116A136GLU-1-0.941-0.95724.069-0.071-0.0710.0000.0000.0000.000
117A137VAL00.0200.01221.865-0.012-0.0120.0000.0000.0000.000
118A138LYS10.9450.96524.5660.0140.0140.0000.0000.0000.000
119A139ALA0-0.0210.00827.970-0.003-0.0030.0000.0000.0000.000
120A140GLU-1-0.874-0.94625.258-0.120-0.1200.0000.0000.0000.000
121A141GLY00.0250.01227.097-0.006-0.0060.0000.0000.0000.000
122A142ALA00.005-0.00128.0190.0000.0000.0000.0000.0000.000
123A143ARG10.9020.95830.0270.0790.0790.0000.0000.0000.000
124A144VAL00.0400.02027.1150.0000.0000.0000.0000.0000.000
125A145PHE00.0120.00730.5510.0010.0010.0000.0000.0000.000
126A146GLN0-0.031-0.03933.1180.0010.0010.0000.0000.0000.000
127A147ALA0-0.074-0.02232.9480.0020.0020.0000.0000.0000.000
128A148PHE00.0120.01033.5320.0020.0020.0000.0000.0000.000
129A149LEU00.0260.01435.3690.0030.0030.0000.0000.0000.000
130A150ARG10.7550.86737.5460.0760.0760.0000.0000.0000.000
131A151GLU-1-0.855-0.88236.429-0.089-0.0890.0000.0000.0000.000
132A152ALA0-0.032-0.02839.0860.0030.0030.0000.0000.0000.000
133A153LEU00.0030.01840.9770.0040.0040.0000.0000.0000.000
134A154PRO00.0030.00943.9960.0010.0010.0000.0000.0000.000
135A155GLU-1-0.959-0.99045.389-0.043-0.0430.0000.0000.0000.000
136A156VAL00.0090.02546.0200.0020.0020.0000.0000.0000.000
137A157ALA00.0190.01546.976-0.003-0.0030.0000.0000.0000.000
138A158GLU-1-0.757-0.86542.058-0.062-0.0620.0000.0000.0000.000
139A159ALA0-0.037-0.00644.335-0.001-0.0010.0000.0000.0000.000
140A160GLU-1-0.879-0.94445.506-0.034-0.0340.0000.0000.0000.000
141A161ARG10.8110.89341.7050.0570.0570.0000.0000.0000.000
142A162SER0-0.021-0.02240.723-0.002-0.0020.0000.0000.0000.000
143A163LEU0-0.0040.00040.7710.0010.0010.0000.0000.0000.000
144A164ALA00.0380.01942.1500.0020.0020.0000.0000.0000.000
145A165GLY00.0560.01238.3140.0010.0010.0000.0000.0000.000
146A166ASP-1-0.878-0.92237.265-0.043-0.0430.0000.0000.0000.000
147A167LEU0-0.0200.00738.0630.0040.0040.0000.0000.0000.000
148A168LEU0-0.0010.00537.6590.0040.0040.0000.0000.0000.000
149A169THR0-0.021-0.02833.3130.0030.0030.0000.0000.0000.000
150A170THR0-0.057-0.03234.1610.0040.0040.0000.0000.0000.000
151A171THR0-0.044-0.03236.1710.0060.0060.0000.0000.0000.000
152A172LEU0-0.017-0.00131.6700.0040.0040.0000.0000.0000.000
153A173GLY00.0130.00231.6670.0040.0040.0000.0000.0000.000
154A174ALA0-0.035-0.01432.6350.0070.0070.0000.0000.0000.000
155A175VAL00.000-0.00535.3730.0060.0060.0000.0000.0000.000
156A176GLY00.0260.01332.1950.0040.0040.0000.0000.0000.000
157A177LYN00.0650.06128.0670.0100.0100.0000.0000.0000.000
158A178GLN0-0.061-0.03031.6290.0040.0040.0000.0000.0000.000
159A179PHE0-0.030-0.01532.1620.0060.0060.0000.0000.0000.000
160A180SER0-0.017-0.02129.0140.0060.0060.0000.0000.0000.000
161A181GLU-1-0.904-0.93730.6630.0480.0480.0000.0000.0000.000
162A182GLN0-0.067-0.03732.8570.0020.0020.0000.0000.0000.000
163A183PRO0-0.020-0.01830.613-0.003-0.0030.0000.0000.0000.000
164A184ARG10.8040.91430.862-0.045-0.0450.0000.0000.0000.000
165A185SER0-0.052-0.05131.0910.0030.0030.0000.0000.0000.000
166A186GLU-1-0.767-0.89028.7490.0130.0130.0000.0000.0000.000
167A187ALA00.002-0.00232.147-0.006-0.0060.0000.0000.0000.000
168A188GLU-1-0.844-0.88334.9140.0370.0370.0000.0000.0000.000
169A189ILE00.0180.00928.934-0.005-0.0050.0000.0000.0000.000
170A190GLU-1-0.857-0.91832.422-0.017-0.0170.0000.0000.0000.000
171A191ARG10.9660.98734.456-0.013-0.0130.0000.0000.0000.000
172A192TYR0-0.043-0.01435.301-0.001-0.0010.0000.0000.0000.000
173A193ALA00.0190.00933.161-0.003-0.0030.0000.0000.0000.000
174A194GLU-1-0.963-0.97835.238-0.016-0.0160.0000.0000.0000.000
175A195ALA00.0230.00938.231-0.002-0.0020.0000.0000.0000.000
176A196LEU0-0.005-0.00234.958-0.001-0.0010.0000.0000.0000.000
177A197ALA00.0140.00436.543-0.003-0.0030.0000.0000.0000.000
178A198ASP-1-0.804-0.87138.339-0.024-0.0240.0000.0000.0000.000
179A199MET0-0.048-0.00940.938-0.001-0.0010.0000.0000.0000.000
180A200LEU0-0.003-0.01036.739-0.001-0.0010.0000.0000.0000.000
181A201CYS0-0.051-0.03139.502-0.004-0.0040.0000.0000.0000.000
182A202ALA0-0.0090.00541.852-0.001-0.0010.0000.0000.0000.000
183A203TYR0-0.013-0.00242.569-0.001-0.0010.0000.0000.0000.000
184A204LEU00.001-0.00739.296-0.001-0.0010.0000.0000.0000.000
185A205ALA0-0.005-0.01443.304-0.002-0.0020.0000.0000.0000.000
186A206ALA00.0000.00546.0580.0000.0000.0000.0000.0000.000
187A207LEU0-0.065-0.03643.9760.0000.0000.0000.0000.0000.000
188A208GLY00.0140.00847.404-0.002-0.0020.0000.0000.0000.000
189A209GLU-1-1.043-1.00148.174-0.028-0.0280.0000.0000.0000.000