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: 3J9QL

Calculation Name: 2O8V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O8V

Chain ID: A

ChEMBL ID:

UniProt ID: P17854

Base Structure: X-ray

Registration Date: 2023-09-21

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2843956.782429
FMO2-HF: Nuclear repulsion 2753829.178444
FMO2-HF: Total energy -90127.603985
FMO2-MP2: Total energy -90396.991591


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
0.1841.36-0.004-0.466-0.7060.002
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.021
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].
3A4LEU00.0160.0093.811-2.563-1.387-0.004-0.466-0.7060.002
4A5ASP-1-0.843-0.9156.0560.5600.5600.0000.0000.0000.000
5A6LEU0-0.028-0.0297.826-0.109-0.1090.0000.0000.0000.000
6A7ASN0-0.034-0.03011.3080.0100.0100.0000.0000.0000.000
7A8ALA00.0930.05610.2850.0040.0040.0000.0000.0000.000
8A9LEU0-0.011-0.0079.783-0.002-0.0020.0000.0000.0000.000
9A10ASN0-0.106-0.05913.2050.0140.0140.0000.0000.0000.000
10A11GLU-1-0.954-0.94915.262-0.085-0.0850.0000.0000.0000.000
11A12LEU0-0.011-0.00312.859-0.032-0.0320.0000.0000.0000.000
12A13PRO00.0040.00317.2580.0350.0350.0000.0000.0000.000
13A14LYS10.9580.96818.9330.1180.1180.0000.0000.0000.000
14A15VAL00.015-0.01320.374-0.005-0.0050.0000.0000.0000.000
15A16ASP-1-0.777-0.89216.738-0.324-0.3240.0000.0000.0000.000
16A17ARG10.8980.97715.3670.1220.1220.0000.0000.0000.000
17A18ILE0-0.049-0.03315.556-0.033-0.0330.0000.0000.0000.000
18A19LEU00.0100.00317.388-0.003-0.0030.0000.0000.0000.000
19A20ALA00.0450.02811.960-0.030-0.0300.0000.0000.0000.000
20A21LEU0-0.016-0.02812.434-0.065-0.0650.0000.0000.0000.000
21A22ALA0-0.036-0.00113.5140.0140.0140.0000.0000.0000.000
22A23GLU-1-0.921-0.95512.064-0.692-0.6920.0000.0000.0000.000
23A24THR0-0.0130.0009.503-0.084-0.0840.0000.0000.0000.000
24A25ASN0-0.006-0.03211.5220.1060.1060.0000.0000.0000.000
25A26ALA00.0180.02214.9570.0490.0490.0000.0000.0000.000
26A27GLU-1-0.943-0.96411.613-0.421-0.4210.0000.0000.0000.000
27A28LEU0-0.008-0.00812.1280.0610.0610.0000.0000.0000.000
28A29GLU-1-0.928-0.95815.301-0.120-0.1200.0000.0000.0000.000
29A30LYS10.8520.92116.4490.3620.3620.0000.0000.0000.000
30A31LEU0-0.0270.00813.8930.0220.0220.0000.0000.0000.000
31A32ASP-1-0.832-0.92018.416-0.023-0.0230.0000.0000.0000.000
32A33ALA0-0.047-0.03619.4370.0050.0050.0000.0000.0000.000
33A34GLU-1-0.852-0.94519.9140.0450.0450.0000.0000.0000.000
34A35GLY00.0500.03416.7830.0350.0350.0000.0000.0000.000
35A36ARG10.7620.85615.0760.1110.1110.0000.0000.0000.000
36A37VAL0-0.019-0.00915.0690.0310.0310.0000.0000.0000.000
37A38ALA00.0180.00514.8160.0680.0680.0000.0000.0000.000
38A39TRP00.0100.0028.0710.2020.2020.0000.0000.0000.000
39A40ALA0-0.008-0.02510.4160.1140.1140.0000.0000.0000.000
40A41LEU0-0.061-0.03311.8280.1200.1200.0000.0000.0000.000
41A42ASP-1-0.890-0.9318.8252.2192.2190.0000.0000.0000.000
42A43ASN0-0.036-0.0125.7810.3590.3590.0000.0000.0000.000
43A44LEU0-0.066-0.0197.005-0.174-0.1740.0000.0000.0000.000
44A45PRO00.0230.0039.3460.2380.2380.0000.0000.0000.000
45A46GLY00.012-0.00611.042-0.129-0.1290.0000.0000.0000.000
46A47GLU-1-0.859-0.91714.3450.3730.3730.0000.0000.0000.000
47A48TYR00.0130.01411.480-0.109-0.1090.0000.0000.0000.000
48A49VAL0-0.0030.00318.155-0.021-0.0210.0000.0000.0000.000
49A50LEU00.0160.00721.427-0.015-0.0150.0000.0000.0000.000
50A51SER0-0.0080.02023.934-0.007-0.0070.0000.0000.0000.000
51A52SER0-0.006-0.00226.779-0.014-0.0140.0000.0000.0000.000
52A53SER0-0.026-0.01729.7420.0020.0020.0000.0000.0000.000
53A54PHE00.0350.00231.969-0.002-0.0020.0000.0000.0000.000
54A55GLY00.0460.02534.616-0.003-0.0030.0000.0000.0000.000
55A56ILE0-0.003-0.01936.5840.0030.0030.0000.0000.0000.000
56A57GLN00.0760.03531.698-0.003-0.0030.0000.0000.0000.000
57A58ALA0-0.0100.02131.4690.0010.0010.0000.0000.0000.000
58A59ALA00.0550.01630.7880.0070.0070.0000.0000.0000.000
59A60VAL00.0080.01728.3630.0050.0050.0000.0000.0000.000
60A61SER00.0370.01126.0480.0020.0020.0000.0000.0000.000
61A62LEU0-0.042-0.01225.9690.0130.0130.0000.0000.0000.000
62A63HIS00.0240.01527.1260.0200.0200.0000.0000.0000.000
63A64LEU0-0.0110.01022.2530.0110.0110.0000.0000.0000.000
64A65VAL00.010-0.01921.0140.0120.0120.0000.0000.0000.000
65A66ASN0-0.008-0.00322.6090.0380.0380.0000.0000.0000.000
66A67GLN0-0.055-0.01524.4510.0040.0040.0000.0000.0000.000
67A68ILE0-0.068-0.02818.6370.0110.0110.0000.0000.0000.000
68A69ARG10.9190.95416.589-0.421-0.4210.0000.0000.0000.000
69A70PRO00.0320.01221.455-0.012-0.0120.0000.0000.0000.000
70A71ASP-1-0.895-0.94423.9860.2060.2060.0000.0000.0000.000
71A72ILE0-0.0330.00120.7010.0200.0200.0000.0000.0000.000
72A73PRO0-0.001-0.02222.435-0.027-0.0270.0000.0000.0000.000
73A74VAL00.0350.02925.009-0.006-0.0060.0000.0000.0000.000
74A75ILE0-0.041-0.02025.138-0.008-0.0080.0000.0000.0000.000
75A76LEU00.0130.00328.758-0.010-0.0100.0000.0000.0000.000
76A77THR0-0.037-0.02231.1940.0020.0020.0000.0000.0000.000
77A78ASP-1-0.848-0.92133.8360.0470.0470.0000.0000.0000.000
78A79THR0-0.021-0.06037.5410.0010.0010.0000.0000.0000.000
79A80GLY00.0080.02239.451-0.001-0.0010.0000.0000.0000.000
80A81TYR0-0.079-0.03242.656-0.001-0.0010.0000.0000.0000.000
81A82LEU00.0210.01038.069-0.004-0.0040.0000.0000.0000.000
82A83PHE0-0.029-0.01242.682-0.001-0.0010.0000.0000.0000.000
83A84PRO00.0380.01543.7340.0030.0030.0000.0000.0000.000
84A85GLU-1-0.826-0.94844.9630.0310.0310.0000.0000.0000.000
85A86THR0-0.037-0.01939.1760.0000.0000.0000.0000.0000.000
86A87TYR00.006-0.00240.0260.0020.0020.0000.0000.0000.000
87A88ARG10.9790.99640.676-0.034-0.0340.0000.0000.0000.000
88A89PHE00.0450.03136.1750.0020.0020.0000.0000.0000.000
89A90ILE0-0.024-0.02035.4000.0030.0030.0000.0000.0000.000
90A91ASP-1-0.908-0.95736.9640.0730.0730.0000.0000.0000.000
91A92GLU-1-0.979-0.96639.3960.0500.0500.0000.0000.0000.000
92A93LEU0-0.034-0.03133.8960.0030.0030.0000.0000.0000.000
93A94THR0-0.061-0.04333.4030.0060.0060.0000.0000.0000.000
94A95ASP-1-0.888-0.92234.6490.0910.0910.0000.0000.0000.000
95A96LYS10.9170.96436.167-0.053-0.0530.0000.0000.0000.000
96A97LEU0-0.115-0.09130.9920.0010.0010.0000.0000.0000.000
97A98LYS10.9300.97931.071-0.099-0.0990.0000.0000.0000.000
98A99LEU0-0.0010.00428.7100.0090.0090.0000.0000.0000.000
99A100ASN00.0360.03526.481-0.020-0.0200.0000.0000.0000.000
100A101LEU0-0.026-0.02228.7520.0060.0060.0000.0000.0000.000
101A102LYS10.8910.95727.569-0.168-0.1680.0000.0000.0000.000
102A103VAL00.0330.01430.972-0.006-0.0060.0000.0000.0000.000
103A104TYR0-0.055-0.03129.0380.0040.0040.0000.0000.0000.000
104A105ARG10.9961.00534.041-0.080-0.0800.0000.0000.0000.000
105A106ALA0-0.007-0.01136.5700.0030.0030.0000.0000.0000.000
106A107THR0-0.0120.00537.7220.0040.0040.0000.0000.0000.000
107A108GLU-1-0.858-0.93439.4580.0420.0420.0000.0000.0000.000
108A109SER00.013-0.01242.4610.0000.0000.0000.0000.0000.000
109A110ALA00.0770.03344.805-0.002-0.0020.0000.0000.0000.000
110A111ALA00.0520.02046.693-0.002-0.0020.0000.0000.0000.000
111A112TRP0-0.014-0.00146.004-0.001-0.0010.0000.0000.0000.000
112A113GLN0-0.010-0.02141.828-0.005-0.0050.0000.0000.0000.000
113A114GLU-1-0.912-0.95146.9330.0220.0220.0000.0000.0000.000
114A115ALA0-0.0070.01350.233-0.002-0.0020.0000.0000.0000.000
115A116ARG10.8500.94243.045-0.035-0.0350.0000.0000.0000.000
116A117TYR0-0.039-0.03243.407-0.002-0.0020.0000.0000.0000.000
117A118GLY00.0560.03349.235-0.002-0.0020.0000.0000.0000.000
118A119LYS10.9360.95549.057-0.014-0.0140.0000.0000.0000.000
119A120LEU0-0.004-0.00343.918-0.002-0.0020.0000.0000.0000.000
120A121TRP00.001-0.00946.055-0.002-0.0020.0000.0000.0000.000
121A122GLU-1-0.940-0.97047.2200.0080.0080.0000.0000.0000.000
122A123GLN0-0.075-0.02948.528-0.002-0.0020.0000.0000.0000.000
123A124GLY00.0270.01848.042-0.001-0.0010.0000.0000.0000.000
124A125VAL00.022-0.00542.9950.0020.0020.0000.0000.0000.000
125A126GLU-1-0.775-0.88542.753-0.007-0.0070.0000.0000.0000.000
126A127GLY00.0010.01543.0880.0030.0030.0000.0000.0000.000
127A128ILE0-0.022-0.02840.9570.0040.0040.0000.0000.0000.000
128A129GLU-1-0.951-0.97038.834-0.005-0.0050.0000.0000.0000.000
129A130LYS10.9580.98838.725-0.018-0.0180.0000.0000.0000.000
130A131TYR00.0020.00540.1720.0050.0050.0000.0000.0000.000
131A132ASN00.006-0.02536.3930.0080.0080.0000.0000.0000.000
132A133ASP-1-0.932-0.95534.6850.0270.0270.0000.0000.0000.000
133A134ILE00.0110.00835.2800.0050.0050.0000.0000.0000.000
134A135ASN0-0.073-0.04437.4600.0080.0080.0000.0000.0000.000
135A136LYS10.9020.95633.498-0.021-0.0210.0000.0000.0000.000
136A137VAL0-0.041-0.01630.5530.0070.0070.0000.0000.0000.000
137A138GLU-1-0.868-0.91930.6090.0720.0720.0000.0000.0000.000
138A139PRO00.0310.01331.0930.0090.0090.0000.0000.0000.000
139A140MET00.0150.01526.8470.0150.0150.0000.0000.0000.000
140A141ASN0-0.148-0.09826.5170.0090.0090.0000.0000.0000.000
141A142ARG10.9070.97426.509-0.077-0.0770.0000.0000.0000.000
142A143ALA00.0230.01427.4710.0140.0140.0000.0000.0000.000
143A144LEU0-0.043-0.03221.8270.0150.0150.0000.0000.0000.000
144A145LYS10.9440.96922.478-0.079-0.0790.0000.0000.0000.000
145A146GLU-1-0.880-0.93623.8500.1460.1460.0000.0000.0000.000
146A147LEU0-0.048-0.02923.5700.0120.0120.0000.0000.0000.000
147A148ASN0-0.031-0.01119.7000.0180.0180.0000.0000.0000.000
148A149ALA0-0.006-0.00218.4970.0470.0470.0000.0000.0000.000
149A150GLN0-0.052-0.02013.425-0.055-0.0550.0000.0000.0000.000
150A151THR0-0.0190.01213.957-0.084-0.0840.0000.0000.0000.000
151A152TRP0-0.061-0.05516.281-0.006-0.0060.0000.0000.0000.000
152A153PHE00.0090.01515.987-0.043-0.0430.0000.0000.0000.000
153A154ALA00.008-0.01020.9840.0010.0010.0000.0000.0000.000
154A155GLY00.0320.00023.818-0.010-0.0100.0000.0000.0000.000
155A156LEU0-0.071-0.03225.120-0.005-0.0050.0000.0000.0000.000
156A157ARG10.9220.95925.9140.0100.0100.0000.0000.0000.000
157A158ARG10.7910.87021.7100.1160.1160.0000.0000.0000.000
158A159GLU-1-0.853-0.94428.595-0.034-0.0340.0000.0000.0000.000
159A160GLN0-0.071-0.02331.0030.0040.0040.0000.0000.0000.000
160A161SER0-0.0020.00632.9120.0010.0010.0000.0000.0000.000
161A162GLY00.0400.00032.386-0.003-0.0030.0000.0000.0000.000
162A163SER0-0.0190.00226.8750.0000.0000.0000.0000.0000.000
163A164ARG11.0481.02527.2510.1060.1060.0000.0000.0000.000
164A165ALA00.0390.01824.8740.0000.0000.0000.0000.0000.000
165A166ASN0-0.023-0.01324.436-0.023-0.0230.0000.0000.0000.000
166A167LEU0-0.070-0.03023.2660.0000.0000.0000.0000.0000.000
167A168PRO0-0.0130.00618.4300.0080.0080.0000.0000.0000.000
168A169VAL00.0710.04317.2200.0220.0220.0000.0000.0000.000
169A170LEU00.0170.03311.9260.0460.0460.0000.0000.0000.000
170A171ALA0-0.018-0.03016.359-0.035-0.0350.0000.0000.0000.000
171A172ILE00.0450.04313.9380.0290.0290.0000.0000.0000.000
172A173GLN0-0.080-0.03117.814-0.014-0.0140.0000.0000.0000.000
173A174ARG10.9420.96021.443-0.049-0.0490.0000.0000.0000.000
174A175GLY00.0330.02517.8330.0220.0220.0000.0000.0000.000
175A176VAL00.003-0.00216.8140.0320.0320.0000.0000.0000.000
176A177PHE00.036-0.00510.324-0.057-0.0570.0000.0000.0000.000
177A178LYS10.8150.93315.6860.0430.0430.0000.0000.0000.000
178A179VAL00.0670.01415.625-0.040-0.0400.0000.0000.0000.000
179A180LEU0-0.067-0.04318.3090.0220.0220.0000.0000.0000.000
180A181PRO00.0830.04819.963-0.023-0.0230.0000.0000.0000.000
181A182ILE0-0.0090.01420.943-0.016-0.0160.0000.0000.0000.000
182A183ILE0-0.006-0.01521.5860.0010.0010.0000.0000.0000.000
183A184ASP-1-0.854-0.92323.286-0.080-0.0800.0000.0000.0000.000
184A185TRP00.0100.01824.6130.0090.0090.0000.0000.0000.000
185A186ASP-1-0.780-0.87828.239-0.036-0.0360.0000.0000.0000.000
186A187ASN0-0.045-0.05431.9710.0090.0090.0000.0000.0000.000
187A188ARG10.9450.99235.0280.0290.0290.0000.0000.0000.000
188A189THR00.0480.01629.0740.0040.0040.0000.0000.0000.000
189A190ILE0-0.031-0.01130.1680.0070.0070.0000.0000.0000.000
190A191TYR0-0.0040.00832.7360.0070.0070.0000.0000.0000.000
191A192GLN0-0.005-0.02033.9810.0020.0020.0000.0000.0000.000
192A193TYR0-0.0110.01127.5850.0040.0040.0000.0000.0000.000
193A194LEU0-0.021-0.02532.6150.0070.0070.0000.0000.0000.000
194A195GLN0-0.0100.00035.2100.0010.0010.0000.0000.0000.000
195A196LYS10.9260.96530.508-0.014-0.0140.0000.0000.0000.000
196A197HIS00.0320.01829.0570.0050.0050.0000.0000.0000.000
197A198GLY0-0.0150.01234.2390.0050.0050.0000.0000.0000.000
198A199LEU0-0.101-0.04531.9260.0030.0030.0000.0000.0000.000
199A200LYS10.9550.96436.609-0.036-0.0360.0000.0000.0000.000
200A201TYR00.0260.01136.9820.0020.0020.0000.0000.0000.000
201A202HIS0-0.0020.00838.8190.0000.0000.0000.0000.0000.000
202A203PRO00.035-0.00340.539-0.003-0.0030.0000.0000.0000.000
203A204LEU00.0070.01643.651-0.002-0.0020.0000.0000.0000.000
204A205TRP0-0.049-0.03740.870-0.003-0.0030.0000.0000.0000.000
205A206ASP-1-0.976-0.96843.5780.0120.0120.0000.0000.0000.000
206A207GLU-1-0.945-0.97246.4420.0180.0180.0000.0000.0000.000
207A208GLY0-0.019-0.01547.320-0.002-0.0020.0000.0000.0000.000
208A209TYR0-0.085-0.04044.504-0.003-0.0030.0000.0000.0000.000
209A210LEU00.0360.03641.6710.0010.0010.0000.0000.0000.000
210A211SER0-0.006-0.03138.889-0.001-0.0010.0000.0000.0000.000
211A212VAL00.0480.03039.860-0.001-0.0010.0000.0000.0000.000
212A213GLY0-0.045-0.04139.1310.0000.0000.0000.0000.0000.000
213A214ASP-1-0.795-0.87440.1080.0330.0330.0000.0000.0000.000
214A215THR00.0350.01542.644-0.004-0.0040.0000.0000.0000.000
215A216HIS10.8570.92443.667-0.023-0.0230.0000.0000.0000.000
216A217THR00.0370.03047.3760.0000.0000.0000.0000.0000.000
217A218THR0-0.064-0.01642.142-0.001-0.0010.0000.0000.0000.000
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