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: 4JR5N

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1894441.861657
FMO2-HF: Nuclear repulsion 1822116.817524
FMO2-HF: Total energy -72325.044133
FMO2-MP2: Total energy -72538.830927


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.
-11.289-6.1831.785-2.677-4.2130.015
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 : 0.007 / q_NPA : -0.009
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].
3A23LEU00.0030.0112.919-2.0000.1690.154-0.950-1.3730.004
4A24VAL00.0060.0012.415-6.922-4.9291.623-1.353-2.2620.010
5A25ALA00.0180.0153.518-1.834-1.1640.008-0.343-0.3350.001
6A26SER00.0180.0165.389-0.111-0.030-0.001-0.004-0.0760.000
7A27ILE00.003-0.0036.764-0.383-0.3830.0000.0000.0000.000
8A28LEU0-0.007-0.0156.458-0.286-0.2860.0000.0000.0000.000
9A29GLU-1-0.901-0.9359.297-0.023-0.0230.0000.0000.0000.000
10A30ALA00.009-0.00311.342-0.070-0.0700.0000.0000.0000.000
11A31ALA0-0.040-0.03812.312-0.066-0.0660.0000.0000.0000.000
12A32VAL00.003-0.01912.876-0.050-0.0500.0000.0000.0000.000
13A33GLN00.0180.02414.107-0.046-0.0460.0000.0000.0000.000
14A34VAL00.0120.03516.622-0.029-0.0290.0000.0000.0000.000
15A35LEU0-0.029-0.02817.809-0.040-0.0400.0000.0000.0000.000
16A36ALA00.0620.04719.168-0.023-0.0230.0000.0000.0000.000
17A37SER0-0.091-0.06720.650-0.013-0.0130.0000.0000.0000.000
18A38GLU-1-0.876-0.94122.0980.2550.2550.0000.0000.0000.000
19A39GLY00.0430.02522.932-0.002-0.0020.0000.0000.0000.000
20A40ALA0-0.036-0.03121.5450.0250.0250.0000.0000.0000.000
21A41GLN00.0540.02322.5690.0140.0140.0000.0000.0000.000
22A42ARG10.8270.88824.677-0.204-0.2040.0000.0000.0000.000
23A43PHE00.0110.03915.2590.0260.0260.0000.0000.0000.000
24A44THR0-0.011-0.02220.0840.0060.0060.0000.0000.0000.000
25A45THR00.0710.03215.340-0.009-0.0090.0000.0000.0000.000
26A46ALA0-0.014-0.00916.6550.0520.0520.0000.0000.0000.000
27A47ARG10.8960.94718.309-0.270-0.2700.0000.0000.0000.000
28A48VAL00.0020.01212.944-0.001-0.0010.0000.0000.0000.000
29A49ALA0-0.010-0.01413.4620.0800.0800.0000.0000.0000.000
30A50GLU-1-0.939-0.95314.5270.4900.4900.0000.0000.0000.000
31A51ARG10.8580.93016.154-0.302-0.3020.0000.0000.0000.000
32A52ALA0-0.041-0.02511.002-0.028-0.0280.0000.0000.0000.000
33A53GLY00.0170.03512.3880.0910.0910.0000.0000.0000.000
34A54VAL0-0.060-0.0299.6750.1060.1060.0000.0000.0000.000
35A55SER00.0560.01913.099-0.090-0.0900.0000.0000.0000.000
36A56ILE00.0490.00613.3740.1540.1540.0000.0000.0000.000
37A57GLY0-0.016-0.00514.4450.0340.0340.0000.0000.0000.000
38A58SER00.0030.0169.6090.1350.1350.0000.0000.0000.000
39A59LEU00.0480.0109.8260.2950.2950.0000.0000.0000.000
40A60TYR0-0.050-0.03210.5580.0800.0800.0000.0000.0000.000
41A61GLN0-0.055-0.0138.986-0.121-0.1210.0000.0000.0000.000
42A62TYR0-0.044-0.0183.9300.5890.7820.001-0.027-0.1670.000
43A63PHE0-0.001-0.0117.429-0.288-0.2880.0000.0000.0000.000
44A64PRO00.0410.02711.534-0.022-0.0220.0000.0000.0000.000
45A65ASN0-0.017-0.02514.793-0.065-0.0650.0000.0000.0000.000
46A66LYS10.9150.94115.484-0.227-0.2270.0000.0000.0000.000
47A67ALA00.0810.04016.692-0.004-0.0040.0000.0000.0000.000
48A68ALA00.0000.01113.554-0.026-0.0260.0000.0000.0000.000
49A69ILE0-0.010-0.00711.584-0.016-0.0160.0000.0000.0000.000
50A70LEU0-0.0060.01013.122-0.059-0.0590.0000.0000.0000.000
51A71PHE00.0390.02415.221-0.049-0.0490.0000.0000.0000.000
52A72ARG10.8130.8965.8170.2450.2450.0000.0000.0000.000
53A73LEU0-0.023-0.01911.733-0.087-0.0870.0000.0000.0000.000
54A74GLN00.006-0.00513.743-0.051-0.0510.0000.0000.0000.000
55A75SER00.0200.00813.528-0.062-0.0620.0000.0000.0000.000
56A76ASP-1-0.822-0.8879.657-0.447-0.4470.0000.0000.0000.000
57A77GLU-1-0.733-0.82313.269-0.163-0.1630.0000.0000.0000.000
58A78TRP0-0.021-0.01116.644-0.024-0.0240.0000.0000.0000.000
59A79ARG10.8370.91110.6090.5040.5040.0000.0000.0000.000
60A80ARG10.7550.84615.6670.1040.1040.0000.0000.0000.000
61A81THR00.021-0.00517.208-0.013-0.0130.0000.0000.0000.000
62A82THR0-0.005-0.01420.2150.0120.0120.0000.0000.0000.000
63A83ARG10.8150.90417.9730.3580.3580.0000.0000.0000.000
64A84LEU0-0.007-0.00420.7240.0100.0100.0000.0000.0000.000
65A85LEU00.003-0.01822.5770.0120.0120.0000.0000.0000.000
66A86GLY00.0170.00824.5410.0110.0110.0000.0000.0000.000
67A87GLU-1-0.838-0.90621.930-0.291-0.2910.0000.0000.0000.000
68A88ILE0-0.096-0.04825.5320.0110.0110.0000.0000.0000.000
69A89LEU0-0.009-0.01128.3580.0110.0110.0000.0000.0000.000
70A90GLU-1-0.919-0.93927.461-0.198-0.1980.0000.0000.0000.000
71A91ASP-1-0.804-0.86029.266-0.137-0.1370.0000.0000.0000.000
72A92THR0-0.002-0.01630.7310.0080.0080.0000.0000.0000.000
73A93THR0-0.129-0.07432.6070.0070.0070.0000.0000.0000.000
74A94ARG10.8700.93231.2720.1270.1270.0000.0000.0000.000
75A95PRO00.0800.03436.295-0.004-0.0040.0000.0000.0000.000
76A96PRO00.0710.02936.971-0.001-0.0010.0000.0000.0000.000
77A97LEU00.0300.01437.219-0.001-0.0010.0000.0000.0000.000
78A98GLU-1-0.920-0.96736.413-0.080-0.0800.0000.0000.0000.000
79A99ARG10.7120.83032.7380.1200.1200.0000.0000.0000.000
80A100LEU00.0390.02332.937-0.003-0.0030.0000.0000.0000.000
81A101ARG10.8690.89433.9900.0540.0540.0000.0000.0000.000
82A102ARG10.8640.93028.6450.1320.1320.0000.0000.0000.000
83A103LEU00.0220.01828.569-0.002-0.0020.0000.0000.0000.000
84A104VAL00.0020.00529.6330.0020.0020.0000.0000.0000.000
85A105LEU00.0000.00529.7430.0050.0050.0000.0000.0000.000
86A106ALA0-0.037-0.02225.7320.0060.0060.0000.0000.0000.000
87A107PHE00.0200.00525.924-0.001-0.0010.0000.0000.0000.000
88A108VAL00.0140.00727.3440.0080.0080.0000.0000.0000.000
89A109ARG10.7570.85125.4450.0610.0610.0000.0000.0000.000
90A110SER00.0300.01422.0000.0070.0070.0000.0000.0000.000
91A111GLU-1-0.830-0.92123.569-0.019-0.0190.0000.0000.0000.000
92A112CYS0-0.058-0.03626.0110.0160.0160.0000.0000.0000.000
93A113GLU-1-0.947-0.95420.260-0.029-0.0290.0000.0000.0000.000
94A114GLU-1-0.834-0.92821.228-0.028-0.0280.0000.0000.0000.000
95A115ALA0-0.0090.01422.6100.0200.0200.0000.0000.0000.000
96A116ALA00.001-0.00522.5320.0160.0160.0000.0000.0000.000
97A117ILE00.026-0.00317.4060.0310.0310.0000.0000.0000.000
98A118ARG10.9110.95121.007-0.010-0.0100.0000.0000.0000.000
99A119VAL0-0.013-0.01323.8280.0130.0130.0000.0000.0000.000
100A120ALA0-0.0320.00320.9790.0100.0100.0000.0000.0000.000
101A121LEU0-0.018-0.01818.7810.0210.0210.0000.0000.0000.000
102A122SER0-0.0130.01122.3550.0000.0000.0000.0000.0000.000
103A123ASP-1-0.897-0.93824.5070.2090.2090.0000.0000.0000.000
104A124ALA0-0.033-0.02121.0990.0070.0070.0000.0000.0000.000
105A125ALA0-0.021-0.01721.8620.0140.0140.0000.0000.0000.000
106A126PRO0-0.0030.01023.932-0.021-0.0210.0000.0000.0000.000
107A127LEU0-0.010-0.02527.269-0.013-0.0130.0000.0000.0000.000
108A128TYR0-0.036-0.03121.7950.0020.0020.0000.0000.0000.000
109A129ARG10.8130.89625.694-0.102-0.1020.0000.0000.0000.000
110A130ASP-1-0.936-0.95927.3680.0410.0410.0000.0000.0000.000
111A131ALA00.0020.02025.306-0.010-0.0100.0000.0000.0000.000
112A132ASP-1-0.919-0.97925.814-0.026-0.0260.0000.0000.0000.000
113A133GLU-1-0.799-0.86120.213-0.007-0.0070.0000.0000.0000.000
114A134ALA00.0860.01623.967-0.016-0.0160.0000.0000.0000.000
115A135ARG10.8340.90724.8900.0130.0130.0000.0000.0000.000
116A136GLU-1-0.935-0.95023.965-0.110-0.1100.0000.0000.0000.000
117A137VAL00.0300.02121.476-0.014-0.0140.0000.0000.0000.000
118A138LYS10.9340.96224.4000.0470.0470.0000.0000.0000.000
119A139ALA0-0.050-0.01727.834-0.003-0.0030.0000.0000.0000.000
120A140GLU-1-0.893-0.95525.002-0.159-0.1590.0000.0000.0000.000
121A141GLY00.0210.01127.094-0.006-0.0060.0000.0000.0000.000
122A142ALA00.008-0.00527.9920.0000.0000.0000.0000.0000.000
123A143ARG10.9170.96230.0850.1070.1070.0000.0000.0000.000
124A144VAL00.0320.01727.0440.0020.0020.0000.0000.0000.000
125A145PHE00.0320.01030.4920.0020.0020.0000.0000.0000.000
126A146GLN0-0.021-0.01432.9690.0030.0030.0000.0000.0000.000
127A147ALA0-0.068-0.03533.0680.0040.0040.0000.0000.0000.000
128A148PHE00.0210.02733.4340.0020.0020.0000.0000.0000.000
129A149LEU00.0180.01935.2920.0040.0040.0000.0000.0000.000
130A150ARG10.7930.89437.1210.0990.0990.0000.0000.0000.000
131A151GLU-1-0.865-0.89335.805-0.114-0.1140.0000.0000.0000.000
132A152ALA0-0.017-0.01538.9580.0030.0030.0000.0000.0000.000
133A153LEU0-0.017-0.00140.7310.0050.0050.0000.0000.0000.000
134A154PRO0-0.003-0.00143.6530.0010.0010.0000.0000.0000.000
135A155GLU-1-0.947-0.97445.211-0.055-0.0550.0000.0000.0000.000
136A156VAL0-0.0040.01645.8150.0020.0020.0000.0000.0000.000
137A157ALA00.0150.00646.719-0.003-0.0030.0000.0000.0000.000
138A158GLU-1-0.739-0.86042.059-0.081-0.0810.0000.0000.0000.000
139A159ALA0-0.052-0.01444.417-0.001-0.0010.0000.0000.0000.000
140A160GLU-1-0.884-0.95145.545-0.047-0.0470.0000.0000.0000.000
141A161ARG10.8490.91841.4330.0760.0760.0000.0000.0000.000
142A162SER0-0.028-0.03240.710-0.003-0.0030.0000.0000.0000.000
143A163LEU00.0170.01940.7760.0000.0000.0000.0000.0000.000
144A164ALA00.0080.01242.0340.0010.0010.0000.0000.0000.000
145A165GLY00.044-0.00538.2520.0000.0000.0000.0000.0000.000
146A166ASP-1-0.914-0.95737.157-0.066-0.0660.0000.0000.0000.000
147A167LEU0-0.0080.01137.9380.0020.0020.0000.0000.0000.000
148A168LEU0-0.0040.00037.1490.0030.0030.0000.0000.0000.000
149A169THR0-0.024-0.02133.0830.0010.0010.0000.0000.0000.000
150A170THR0-0.042-0.02333.7020.0020.0020.0000.0000.0000.000
151A171THR0-0.046-0.02835.8550.0070.0070.0000.0000.0000.000
152A172LEU0-0.015-0.00131.1550.0040.0040.0000.0000.0000.000
153A173GLY00.0090.00131.0770.0030.0030.0000.0000.0000.000
154A174ALA0-0.046-0.02532.0540.0060.0060.0000.0000.0000.000
155A175VAL00.0080.00334.7150.0060.0060.0000.0000.0000.000
156A176GLY0-0.004-0.00231.5600.0050.0050.0000.0000.0000.000
157A177LYN00.0830.07327.9790.0100.0100.0000.0000.0000.000
158A178GLN0-0.0120.00431.1860.0040.0040.0000.0000.0000.000
159A179PHE0-0.044-0.02231.9690.0060.0060.0000.0000.0000.000
160A180SER0-0.011-0.02028.5940.0070.0070.0000.0000.0000.000
161A181GLU-1-0.942-0.96629.9890.0250.0250.0000.0000.0000.000
162A182GLN0-0.089-0.04732.2400.0060.0060.0000.0000.0000.000
163A183PRO0-0.013-0.01330.018-0.004-0.0040.0000.0000.0000.000
164A184ARG10.8190.92730.250-0.017-0.0170.0000.0000.0000.000
165A185SER0-0.023-0.03830.6280.0000.0000.0000.0000.0000.000
166A186GLU-1-0.799-0.89028.213-0.028-0.0280.0000.0000.0000.000
167A187ALA00.0450.00931.320-0.006-0.0060.0000.0000.0000.000
168A188GLU-1-0.853-0.89334.3870.0150.0150.0000.0000.0000.000
169A189ILE00.010-0.00728.563-0.004-0.0040.0000.0000.0000.000
170A190GLU-1-0.906-0.93832.286-0.043-0.0430.0000.0000.0000.000
171A191ARG10.9730.98534.1860.0060.0060.0000.0000.0000.000
172A192TYR0-0.025-0.00735.035-0.001-0.0010.0000.0000.0000.000
173A193ALA00.0310.00932.855-0.003-0.0030.0000.0000.0000.000
174A194GLU-1-0.967-0.96934.939-0.038-0.0380.0000.0000.0000.000
175A195ALA00.0300.00537.902-0.002-0.0020.0000.0000.0000.000
176A196LEU00.0040.00134.584-0.001-0.0010.0000.0000.0000.000
177A197ALA00.0160.00536.271-0.003-0.0030.0000.0000.0000.000
178A198ASP-1-0.826-0.87638.069-0.042-0.0420.0000.0000.0000.000
179A199MET0-0.059-0.01840.5770.0010.0010.0000.0000.0000.000
180A200LEU0-0.008-0.01736.195-0.001-0.0010.0000.0000.0000.000
181A201CYS0-0.061-0.04239.111-0.004-0.0040.0000.0000.0000.000
182A202ALA0-0.0040.01241.385-0.001-0.0010.0000.0000.0000.000
183A203TYR0-0.0010.00342.1050.0000.0000.0000.0000.0000.000
184A204LEU0-0.004-0.00639.252-0.001-0.0010.0000.0000.0000.000
185A205ALA0-0.005-0.02643.122-0.001-0.0010.0000.0000.0000.000
186A206ALA00.0020.01545.9270.0000.0000.0000.0000.0000.000
187A207LEU0-0.063-0.02743.8340.0010.0010.0000.0000.0000.000
188A208GLY00.0090.01346.750-0.001-0.0010.0000.0000.0000.000
189A209GLU-1-1.069-1.02847.622-0.039-0.0390.0000.0000.0000.000