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: KG7J3

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1892547.269138
FMO2-HF: Nuclear repulsion 1820223.455748
FMO2-HF: Total energy -72323.813391
FMO2-MP2: Total energy -72537.68425


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.
-11.161-6.0921.567-2.587-4.0480.016
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 : -0.008
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].
3A23LEU0-0.0050.0103.155-1.6820.3980.144-0.936-1.2880.005
4A24VAL00.0130.0022.450-7.176-5.1321.416-1.278-2.1820.010
5A25ALA00.0260.0173.498-1.741-1.0600.008-0.345-0.3420.001
6A26SER00.0280.0235.364-0.0580.018-0.001-0.004-0.0710.000
7A27ILE0-0.019-0.0096.554-0.319-0.3190.0000.0000.0000.000
8A28LEU0-0.007-0.0216.410-0.255-0.2550.0000.0000.0000.000
9A29GLU-1-0.897-0.9339.277-0.131-0.1310.0000.0000.0000.000
10A30ALA0-0.011-0.00911.318-0.048-0.0480.0000.0000.0000.000
11A31ALA0-0.046-0.04212.292-0.057-0.0570.0000.0000.0000.000
12A32VAL00.0490.00312.942-0.036-0.0360.0000.0000.0000.000
13A33GLN00.0050.00915.023-0.079-0.0790.0000.0000.0000.000
14A34VAL00.0060.03516.601-0.023-0.0230.0000.0000.0000.000
15A35LEU0-0.046-0.02217.494-0.032-0.0320.0000.0000.0000.000
16A36ALA00.0760.04619.241-0.017-0.0170.0000.0000.0000.000
17A37SER0-0.093-0.07320.589-0.006-0.0060.0000.0000.0000.000
18A38GLU-1-0.901-0.95822.0870.2330.2330.0000.0000.0000.000
19A39GLY00.0540.03222.9500.0000.0000.0000.0000.0000.000
20A40ALA0-0.044-0.04521.6680.0260.0260.0000.0000.0000.000
21A41GLN00.0740.03222.6640.0130.0130.0000.0000.0000.000
22A42ARG10.8460.89724.643-0.186-0.1860.0000.0000.0000.000
23A43PHE00.0000.03015.3820.0320.0320.0000.0000.0000.000
24A44THR0-0.019-0.01720.0480.0140.0140.0000.0000.0000.000
25A45THR00.0720.02615.169-0.015-0.0150.0000.0000.0000.000
26A46ALA0-0.006-0.00816.6550.0510.0510.0000.0000.0000.000
27A47ARG10.8950.94318.309-0.249-0.2490.0000.0000.0000.000
28A48VAL0-0.0090.01812.936-0.002-0.0020.0000.0000.0000.000
29A49ALA00.004-0.01513.4690.0730.0730.0000.0000.0000.000
30A50GLU-1-0.947-0.95714.5270.4630.4630.0000.0000.0000.000
31A51ARG10.8840.95115.900-0.284-0.2840.0000.0000.0000.000
32A52ALA0-0.043-0.03010.967-0.038-0.0380.0000.0000.0000.000
33A53GLY00.0220.03912.3880.0880.0880.0000.0000.0000.000
34A54VAL0-0.069-0.0319.7490.1250.1250.0000.0000.0000.000
35A55SER00.0490.02113.102-0.095-0.0950.0000.0000.0000.000
36A56ILE00.0680.01313.3740.1490.1490.0000.0000.0000.000
37A57GLY0-0.006-0.00114.4080.0310.0310.0000.0000.0000.000
38A58SER0-0.0130.0009.9540.1630.1630.0000.0000.0000.000
39A59LEU00.0600.0229.7460.2920.2920.0000.0000.0000.000
40A60TYR0-0.046-0.03710.4140.0590.0590.0000.0000.0000.000
41A61GLN0-0.078-0.0208.521-0.255-0.2550.0000.0000.0000.000
42A62TYR0-0.042-0.0183.9780.6360.8240.000-0.024-0.1650.000
43A63PHE00.000-0.0137.413-0.289-0.2890.0000.0000.0000.000
44A64PRO00.0450.03311.370-0.014-0.0140.0000.0000.0000.000
45A65ASN0-0.014-0.02314.644-0.066-0.0660.0000.0000.0000.000
46A66LYS11.0000.98915.364-0.257-0.2570.0000.0000.0000.000
47A67ALA00.0700.04316.688-0.007-0.0070.0000.0000.0000.000
48A68ALA00.0080.01413.362-0.028-0.0280.0000.0000.0000.000
49A69ILE0-0.013-0.00611.924-0.018-0.0180.0000.0000.0000.000
50A70LEU00.0050.00813.117-0.066-0.0660.0000.0000.0000.000
51A71PHE00.0260.02415.153-0.050-0.0500.0000.0000.0000.000
52A72ARG10.8720.9465.5280.2650.2650.0000.0000.0000.000
53A73LEU0-0.013-0.01811.765-0.087-0.0870.0000.0000.0000.000
54A74GLN00.0110.00213.731-0.054-0.0540.0000.0000.0000.000
55A75SER00.0010.00013.853-0.061-0.0610.0000.0000.0000.000
56A76ASP-1-0.847-0.92010.018-0.456-0.4560.0000.0000.0000.000
57A77GLU-1-0.815-0.91713.258-0.188-0.1880.0000.0000.0000.000
58A78TRP00.0140.01916.629-0.021-0.0210.0000.0000.0000.000
59A79ARG10.8290.89710.7620.5320.5320.0000.0000.0000.000
60A80ARG10.8840.95615.6120.1740.1740.0000.0000.0000.000
61A81THR00.0250.00017.193-0.012-0.0120.0000.0000.0000.000
62A82THR00.0270.01320.2100.0150.0150.0000.0000.0000.000
63A83ARG10.8230.91918.1080.4070.4070.0000.0000.0000.000
64A84LEU0-0.020-0.00820.7360.0140.0140.0000.0000.0000.000
65A85LEU0-0.025-0.03022.5610.0140.0140.0000.0000.0000.000
66A86GLY00.0340.01824.5250.0130.0130.0000.0000.0000.000
67A87GLU-1-0.817-0.90821.945-0.321-0.3210.0000.0000.0000.000
68A88ILE0-0.120-0.05925.8200.0120.0120.0000.0000.0000.000
69A89LEU0-0.012-0.01428.5500.0120.0120.0000.0000.0000.000
70A90GLU-1-0.917-0.94027.363-0.212-0.2120.0000.0000.0000.000
71A91ASP-1-0.846-0.90729.489-0.155-0.1550.0000.0000.0000.000
72A92THR0-0.055-0.03530.9840.0110.0110.0000.0000.0000.000
73A93THR0-0.108-0.05332.8110.0090.0090.0000.0000.0000.000
74A94ARG10.9020.95530.9940.1410.1410.0000.0000.0000.000
75A95PRO00.0740.03336.521-0.004-0.0040.0000.0000.0000.000
76A96PRO00.0890.03637.184-0.002-0.0020.0000.0000.0000.000
77A97LEU00.0390.01637.275-0.001-0.0010.0000.0000.0000.000
78A98GLU-1-0.943-0.97236.810-0.091-0.0910.0000.0000.0000.000
79A99ARG10.7360.84532.9360.1310.1310.0000.0000.0000.000
80A100LEU00.0340.01732.920-0.004-0.0040.0000.0000.0000.000
81A101ARG10.8880.92433.9730.0650.0650.0000.0000.0000.000
82A102ARG10.9170.95628.0570.1480.1480.0000.0000.0000.000
83A103LEU00.0210.02128.408-0.004-0.0040.0000.0000.0000.000
84A104VAL00.0030.00729.6150.0010.0010.0000.0000.0000.000
85A105LEU0-0.0010.00629.6380.0040.0040.0000.0000.0000.000
86A106ALA0-0.033-0.02625.7090.0050.0050.0000.0000.0000.000
87A107PHE00.0240.00525.906-0.003-0.0030.0000.0000.0000.000
88A108VAL00.0270.00927.3270.0080.0080.0000.0000.0000.000
89A109ARG10.7910.88625.6410.0860.0860.0000.0000.0000.000
90A110SER00.0480.02922.5560.0010.0010.0000.0000.0000.000
91A111GLU-1-0.870-0.92723.553-0.041-0.0410.0000.0000.0000.000
92A112CYS0-0.061-0.03325.9950.0170.0170.0000.0000.0000.000
93A113GLU-1-0.995-0.98420.230-0.050-0.0500.0000.0000.0000.000
94A114GLU-1-0.882-0.96521.322-0.059-0.0590.0000.0000.0000.000
95A115ALA00.0000.01622.5960.0210.0210.0000.0000.0000.000
96A116ALA00.000-0.00722.4850.0180.0180.0000.0000.0000.000
97A117ILE00.0310.00617.6260.0320.0320.0000.0000.0000.000
98A118ARG10.9130.96320.995-0.004-0.0040.0000.0000.0000.000
99A119VAL0-0.034-0.01823.8180.0140.0140.0000.0000.0000.000
100A120ALA0-0.0240.00821.0120.0110.0110.0000.0000.0000.000
101A121LEU0-0.026-0.01618.9900.0220.0220.0000.0000.0000.000
102A122SER0-0.0170.00722.3490.0020.0020.0000.0000.0000.000
103A123ASP-1-0.967-0.97524.9720.1880.1880.0000.0000.0000.000
104A124ALA0-0.039-0.03121.2020.0100.0100.0000.0000.0000.000
105A125ALA0-0.032-0.01821.9030.0160.0160.0000.0000.0000.000
106A126PRO00.0060.01523.932-0.021-0.0210.0000.0000.0000.000
107A127LEU00.000-0.02427.280-0.013-0.0130.0000.0000.0000.000
108A128TYR0-0.032-0.03221.4100.0000.0000.0000.0000.0000.000
109A129ARG10.7840.88725.695-0.093-0.0930.0000.0000.0000.000
110A130ASP-1-0.937-0.96827.7540.0350.0350.0000.0000.0000.000
111A131ALA00.0060.02325.159-0.008-0.0080.0000.0000.0000.000
112A132ASP-1-0.868-0.95825.945-0.036-0.0360.0000.0000.0000.000
113A133GLU-1-0.838-0.86620.493-0.016-0.0160.0000.0000.0000.000
114A134ALA00.0830.01623.962-0.016-0.0160.0000.0000.0000.000
115A135ARG10.8070.88324.8860.0200.0200.0000.0000.0000.000
116A136GLU-1-0.919-0.94424.245-0.109-0.1090.0000.0000.0000.000
117A137VAL00.0210.01721.352-0.015-0.0150.0000.0000.0000.000
118A138LYS10.9200.95924.3950.0540.0540.0000.0000.0000.000
119A139ALA0-0.041-0.01727.827-0.002-0.0020.0000.0000.0000.000
120A140GLU-1-0.898-0.95624.947-0.166-0.1660.0000.0000.0000.000
121A141GLY00.0260.01727.093-0.006-0.0060.0000.0000.0000.000
122A142ALA00.012-0.00327.9830.0000.0000.0000.0000.0000.000
123A143ARG10.9250.95930.1690.1130.1130.0000.0000.0000.000
124A144VAL00.0280.02126.9640.0030.0030.0000.0000.0000.000
125A145PHE00.0320.01030.4650.0030.0030.0000.0000.0000.000
126A146GLN0-0.003-0.00632.9590.0040.0040.0000.0000.0000.000
127A147ALA0-0.063-0.03833.0420.0050.0050.0000.0000.0000.000
128A148PHE00.0260.02833.5550.0020.0020.0000.0000.0000.000
129A149LEU00.0170.01735.3650.0050.0050.0000.0000.0000.000
130A150ARG10.8390.93236.2360.1090.1090.0000.0000.0000.000
131A151GLU-1-0.878-0.90836.250-0.121-0.1210.0000.0000.0000.000
132A152ALA0-0.017-0.01239.1360.0030.0030.0000.0000.0000.000
133A153LEU0-0.027-0.00540.9100.0050.0050.0000.0000.0000.000
134A154PRO0-0.005-0.00443.8510.0010.0010.0000.0000.0000.000
135A155GLU-1-0.932-0.97345.287-0.059-0.0590.0000.0000.0000.000
136A156VAL0-0.0080.01945.8060.0020.0020.0000.0000.0000.000
137A157ALA00.0200.00246.648-0.003-0.0030.0000.0000.0000.000
138A158GLU-1-0.854-0.95042.165-0.085-0.0850.0000.0000.0000.000
139A159ALA0-0.038-0.01944.410-0.001-0.0010.0000.0000.0000.000
140A160GLU-1-0.889-0.95445.538-0.052-0.0520.0000.0000.0000.000
141A161ARG10.8820.96141.5340.0810.0810.0000.0000.0000.000
142A162SER0-0.010-0.00740.706-0.003-0.0030.0000.0000.0000.000
143A163LEU0-0.0010.00740.7680.0000.0000.0000.0000.0000.000
144A164ALA00.0120.01142.0250.0010.0010.0000.0000.0000.000
145A165GLY00.042-0.00238.2420.0000.0000.0000.0000.0000.000
146A166ASP-1-0.938-0.97037.147-0.069-0.0690.0000.0000.0000.000
147A167LEU0-0.0080.01337.9290.0020.0020.0000.0000.0000.000
148A168LEU0-0.003-0.00337.0580.0020.0020.0000.0000.0000.000
149A169THR0-0.025-0.02132.8790.0010.0010.0000.0000.0000.000
150A170THR0-0.026-0.01133.6910.0010.0010.0000.0000.0000.000
151A171THR0-0.051-0.02835.8440.0070.0070.0000.0000.0000.000
152A172LEU0-0.0220.00031.2520.0040.0040.0000.0000.0000.000
153A173GLY00.0110.00131.0660.0020.0020.0000.0000.0000.000
154A174ALA0-0.042-0.02732.0420.0060.0060.0000.0000.0000.000
155A175VAL00.0060.00534.7040.0060.0060.0000.0000.0000.000
156A176GLY0-0.0010.00031.5440.0040.0040.0000.0000.0000.000
157A177LYN00.0920.05728.3420.0090.0090.0000.0000.0000.000
158A178GLN00.0010.01731.1730.0060.0060.0000.0000.0000.000
159A179PHE0-0.067-0.03232.0170.0060.0060.0000.0000.0000.000
160A180SER0-0.017-0.02528.5640.0060.0060.0000.0000.0000.000
161A181GLU-1-0.936-0.96229.9730.0150.0150.0000.0000.0000.000
162A182GLN0-0.113-0.05632.2260.0090.0090.0000.0000.0000.000
163A183PRO0-0.015-0.01330.040-0.005-0.0050.0000.0000.0000.000
164A184ARG10.8590.93030.231-0.004-0.0040.0000.0000.0000.000
165A185SER0-0.005-0.01430.607-0.001-0.0010.0000.0000.0000.000
166A186GLU-1-0.793-0.89428.811-0.049-0.0490.0000.0000.0000.000
167A187ALA00.0390.00231.297-0.005-0.0050.0000.0000.0000.000
168A188GLU-1-0.904-0.92334.3650.0020.0020.0000.0000.0000.000
169A189ILE00.017-0.00728.436-0.004-0.0040.0000.0000.0000.000
170A190GLU-1-0.935-0.96431.976-0.054-0.0540.0000.0000.0000.000
171A191ARG10.9740.99234.1640.0160.0160.0000.0000.0000.000
172A192TYR0-0.034-0.01835.2290.0000.0000.0000.0000.0000.000
173A193ALA00.0310.00932.864-0.002-0.0020.0000.0000.0000.000
174A194GLU-1-0.975-0.97334.919-0.048-0.0480.0000.0000.0000.000
175A195ALA00.0380.01037.882-0.001-0.0010.0000.0000.0000.000
176A196LEU00.0040.00234.5420.0000.0000.0000.0000.0000.000
177A197ALA00.010-0.00136.232-0.003-0.0030.0000.0000.0000.000
178A198ASP-1-0.846-0.90138.051-0.050-0.0500.0000.0000.0000.000
179A199MET0-0.053-0.01940.4800.0010.0010.0000.0000.0000.000
180A200LEU0-0.012-0.01836.097-0.001-0.0010.0000.0000.0000.000
181A201CYS0-0.057-0.03938.988-0.004-0.0040.0000.0000.0000.000
182A202ALA0-0.0070.01141.3680.0000.0000.0000.0000.0000.000
183A203TYR0-0.0020.00242.1100.0000.0000.0000.0000.0000.000
184A204LEU0-0.008-0.00739.238-0.001-0.0010.0000.0000.0000.000
185A205ALA0-0.013-0.03243.107-0.001-0.0010.0000.0000.0000.000
186A206ALA0-0.020-0.00145.9110.0010.0010.0000.0000.0000.000
187A207LEU0-0.053-0.03943.9160.0010.0010.0000.0000.0000.000
188A208GLY00.0120.02046.764-0.001-0.0010.0000.0000.0000.000
189A209GLU-1-1.043-0.99847.608-0.044-0.0440.0000.0000.0000.000