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: 2N33R

Calculation Name: 2POF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2POF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8X7A5

Base Structure: X-ray

Registration Date: 2023-09-23

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2803713.463657
FMO2-HF: Nuclear repulsion 2715015.709427
FMO2-HF: Total energy -88697.75423
FMO2-MP2: Total energy -88953.810646


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:31:SER)


Summations of interaction energy for fragment #1(A:31: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.
-4.4483.1362.93-4.656-5.857-0.026
Interaction energy analysis for fragmet #1(A:31:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.016
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].
3A33THR00.0470.0363.249-3.2090.990-0.040-2.144-2.015-0.008
4A34LEU00.0540.0195.2670.5280.633-0.001-0.003-0.1010.000
5A35ARG10.8080.9045.5611.5361.5360.0000.0000.0000.000
6A36LYS10.8120.8897.0190.6650.6650.0000.0000.0000.000
7A37ILE00.0460.0499.1480.1460.1460.0000.0000.0000.000
8A38VAL0-0.013-0.02011.3320.1660.1660.0000.0000.0000.000
9A39LEU0-0.061-0.04911.5790.1160.1160.0000.0000.0000.000
10A40GLU-1-0.859-0.91311.801-0.288-0.2880.0000.0000.0000.000
11A41GLU-1-0.896-0.93912.578-0.521-0.5210.0000.0000.0000.000
12A42CYS0-0.144-0.06615.4920.0070.0070.0000.0000.0000.000
13A43LEU00.0180.01417.1140.0490.0490.0000.0000.0000.000
14A44PRO00.003-0.00117.5150.0370.0370.0000.0000.0000.000
15A45ASN00.0440.03719.8520.0580.0580.0000.0000.0000.000
16A46GLN0-0.0050.00121.3880.0130.0130.0000.0000.0000.000
17A47GLN0-0.042-0.04222.9580.0180.0180.0000.0000.0000.000
18A48GLN0-0.0270.01224.1790.0170.0170.0000.0000.0000.000
19A49ASN0-0.066-0.05624.3000.0260.0260.0000.0000.0000.000
20A50GLN0-0.051-0.02026.3490.0080.0080.0000.0000.0000.000
21A51ASN0-0.0010.02623.724-0.014-0.0140.0000.0000.0000.000
22A52PRO00.009-0.00121.392-0.013-0.0130.0000.0000.0000.000
23A53SER0-0.0200.00719.544-0.043-0.0430.0000.0000.0000.000
24A54PRO00.049-0.00314.7720.0110.0110.0000.0000.0000.000
25A56ALA0-0.009-0.01218.3360.0350.0350.0000.0000.0000.000
26A57GLU-1-0.822-0.90020.670-0.176-0.1760.0000.0000.0000.000
27A58VAL00.0050.00519.134-0.036-0.0360.0000.0000.0000.000
28A59LYS10.8880.94021.5990.2090.2090.0000.0000.0000.000
29A60PRO00.0580.02222.008-0.005-0.0050.0000.0000.0000.000
30A61ASN0-0.023-0.01023.045-0.006-0.0060.0000.0000.0000.000
31A62ALA0-0.025-0.00724.4210.0120.0120.0000.0000.0000.000
32A63GLY00.0080.01220.9620.0040.0040.0000.0000.0000.000
33A64TYR0-0.064-0.06218.436-0.023-0.0230.0000.0000.0000.000
34A65VAL00.0220.00715.5340.0210.0210.0000.0000.0000.000
35A66VAL00.0010.00317.662-0.018-0.0180.0000.0000.0000.000
36A67LEU00.0280.01312.4460.0110.0110.0000.0000.0000.000
37A68LYS10.7730.86916.3550.3500.3500.0000.0000.0000.000
38A69ASP-1-0.854-0.93513.451-0.651-0.6510.0000.0000.0000.000
39A70LEU00.0060.00511.3640.0610.0610.0000.0000.0000.000
40A71ASN0-0.045-0.01614.3960.0890.0890.0000.0000.0000.000
41A72GLY00.0990.05416.1640.0030.0030.0000.0000.0000.000
42A73PRO00.0140.00819.698-0.027-0.0270.0000.0000.0000.000
43A74LEU00.016-0.00822.261-0.006-0.0060.0000.0000.0000.000
44A75GLN0-0.0050.02215.683-0.003-0.0030.0000.0000.0000.000
45A76TYR00.0280.02117.447-0.025-0.0250.0000.0000.0000.000
46A77LEU00.0120.01511.1670.0010.0010.0000.0000.0000.000
47A78LEU0-0.0190.00715.3290.0150.0150.0000.0000.0000.000
48A79MET0-0.028-0.01111.288-0.110-0.1100.0000.0000.0000.000
49A80PRO00.0230.02613.1370.0560.0560.0000.0000.0000.000
50A81THR00.0020.00014.909-0.072-0.0720.0000.0000.0000.000
51A82TYR00.0530.01415.5410.0090.0090.0000.0000.0000.000
52A83ARG10.9560.9618.6010.2340.2340.0000.0000.0000.000
53A84ILE00.0470.04711.7750.0930.0930.0000.0000.0000.000
54A85ASN0-0.003-0.0057.780-0.267-0.2670.0000.0000.0000.000
55A86GLY00.0210.0068.323-0.129-0.1290.0000.0000.0000.000
56A87THR00.008-0.00210.8110.0400.0400.0000.0000.0000.000
57A88GLU-1-0.755-0.8579.3200.0180.0180.0000.0000.0000.000
58A89SER0-0.087-0.03212.8740.0340.0340.0000.0000.0000.000
59A90PRO00.1050.03514.344-0.012-0.0120.0000.0000.0000.000
60A91LEU00.0240.01815.939-0.005-0.0050.0000.0000.0000.000
61A92LEU0-0.045-0.00214.968-0.011-0.0110.0000.0000.0000.000
62A93THR0-0.054-0.02919.0050.0080.0080.0000.0000.0000.000
63A94ASP-1-0.841-0.89621.968-0.049-0.0490.0000.0000.0000.000
64A95PRO0-0.025-0.03723.793-0.012-0.0120.0000.0000.0000.000
65A96SER0-0.044-0.03125.147-0.003-0.0030.0000.0000.0000.000
66A97THR0-0.101-0.04919.444-0.017-0.0170.0000.0000.0000.000
67A98PRO00.0290.02220.8620.0060.0060.0000.0000.0000.000
68A99ASN00.0350.02021.581-0.018-0.0180.0000.0000.0000.000
69A100PHE00.017-0.01818.059-0.009-0.0090.0000.0000.0000.000
70A101PHE00.0120.00719.078-0.016-0.0160.0000.0000.0000.000
71A102TRP00.0180.01821.826-0.003-0.0030.0000.0000.0000.000
72A103LEU00.0040.00121.9250.0020.0020.0000.0000.0000.000
73A104ALA0-0.008-0.00919.740-0.008-0.0080.0000.0000.0000.000
74A105TRP00.0150.00621.595-0.002-0.0020.0000.0000.0000.000
75A106GLN00.0260.01124.9420.0060.0060.0000.0000.0000.000
76A107ALA0-0.0260.00022.0160.0040.0040.0000.0000.0000.000
77A108ARG10.8610.90523.7520.1160.1160.0000.0000.0000.000
78A109ASP-1-0.840-0.91225.092-0.142-0.1420.0000.0000.0000.000
79A110PHE0-0.038-0.03422.9490.0030.0030.0000.0000.0000.000
80A111MET0-0.0230.00722.954-0.004-0.0040.0000.0000.0000.000
81A112SER00.0560.02325.0950.0060.0060.0000.0000.0000.000
82A113LYS10.8410.92626.9630.1710.1710.0000.0000.0000.000
83A114LYS10.8490.94122.9690.2420.2420.0000.0000.0000.000
84A115TYR00.009-0.00826.8170.0040.0040.0000.0000.0000.000
85A116GLY00.0010.01429.1300.0080.0080.0000.0000.0000.000
86A117GLN0-0.030-0.00831.8700.0110.0110.0000.0000.0000.000
87A118PRO00.007-0.01531.938-0.008-0.0080.0000.0000.0000.000
88A119VAL00.0250.02727.7840.0050.0050.0000.0000.0000.000
89A120PRO00.0140.00531.0340.0000.0000.0000.0000.0000.000
90A121ASP-1-0.713-0.84930.293-0.110-0.1100.0000.0000.0000.000
91A122ARG10.7910.86329.7110.0600.0600.0000.0000.0000.000
92A123ALA00.0240.01328.8360.0030.0030.0000.0000.0000.000
93A124VAL0-0.0100.00824.287-0.009-0.0090.0000.0000.0000.000
94A125SER0-0.025-0.00222.7740.0120.0120.0000.0000.0000.000
95A126LEU0-0.024-0.00720.248-0.024-0.0240.0000.0000.0000.000
96A127ALA00.0300.01217.7290.0300.0300.0000.0000.0000.000
97A128ILE0-0.0130.00412.873-0.052-0.0520.0000.0000.0000.000
98A129ASN0-0.019-0.01611.5730.0640.0640.0000.0000.0000.000
99A130SER00.0460.02811.710-0.015-0.0150.0000.0000.0000.000
100A131ARG11.0020.9786.962-0.986-0.9860.0000.0000.0000.000
101A132THR0-0.065-0.0268.3000.2070.2070.0000.0000.0000.000
102A133GLY00.0160.02010.9020.0230.0230.0000.0000.0000.000
103A134ARG10.7640.8716.1280.0810.0810.0000.0000.0000.000
104A135THR00.0310.0084.5130.0240.146-0.001-0.017-0.1030.000
105A136GLN00.0180.0172.660-3.276-0.6911.142-1.623-2.104-0.015
106A137ASN0-0.007-0.0112.1340.4100.9421.831-0.861-1.503-0.003
107A138HIS00.0190.0104.6320.2890.330-0.001-0.008-0.0310.000
108A139PHE00.001-0.0077.952-0.020-0.0200.0000.0000.0000.000
109A140HIS0-0.036-0.0357.6900.0440.0440.0000.0000.0000.000
110A141ILE0-0.0340.00812.2200.0520.0520.0000.0000.0000.000
111A142HIS10.8640.93212.1090.3860.3860.0000.0000.0000.000
112A143ILE00.000-0.00316.0820.0480.0480.0000.0000.0000.000
113A144SER00.037-0.02519.128-0.013-0.0130.0000.0000.0000.000
114A145CYS0-0.074-0.03621.1820.0170.0170.0000.0000.0000.000
115A146ILE0-0.0140.01223.059-0.005-0.0050.0000.0000.0000.000
116A147ARG10.8410.89423.2730.0690.0690.0000.0000.0000.000
117A148PRO00.0700.01626.3100.0050.0050.0000.0000.0000.000
118A149ASP-1-0.763-0.84827.920-0.047-0.0470.0000.0000.0000.000
119A150VAL0-0.001-0.00225.3580.0040.0040.0000.0000.0000.000
120A151ARG10.7710.88128.6660.0750.0750.0000.0000.0000.000
121A152GLU-1-0.897-0.94730.635-0.035-0.0350.0000.0000.0000.000
122A153GLN0-0.013-0.01429.6580.0030.0030.0000.0000.0000.000
123A154LEU0-0.012-0.01727.7010.0030.0030.0000.0000.0000.000
124A155ASP-1-0.798-0.85932.277-0.056-0.0560.0000.0000.0000.000
125A156ASN0-0.023-0.01435.4320.0030.0030.0000.0000.0000.000
126A157ASN0-0.0270.00134.5510.0070.0070.0000.0000.0000.000
127A158LEU00.0200.01636.2750.0010.0010.0000.0000.0000.000
128A159ALA0-0.034-0.02637.3090.0000.0000.0000.0000.0000.000
129A160ASN0-0.045-0.02836.8540.0030.0030.0000.0000.0000.000
130A161ILE0-0.0260.00732.4010.0030.0030.0000.0000.0000.000
131A162SER00.0420.01635.166-0.002-0.0020.0000.0000.0000.000
132A163SER0-0.0060.00134.018-0.001-0.0010.0000.0000.0000.000
133A164ARG10.9530.98033.6070.0060.0060.0000.0000.0000.000
134A165TRP00.003-0.00924.753-0.001-0.0010.0000.0000.0000.000
135A166LEU00.006-0.00130.8980.0060.0060.0000.0000.0000.000
136A167PRO0-0.026-0.01429.771-0.004-0.0040.0000.0000.0000.000
137A168LEU00.0180.01529.196-0.002-0.0020.0000.0000.0000.000
138A169PRO00.005-0.00531.3160.0050.0050.0000.0000.0000.000
139A170GLY00.0040.01132.903-0.004-0.0040.0000.0000.0000.000
140A171GLY0-0.051-0.01228.7870.0030.0030.0000.0000.0000.000
141A172LEU00.0150.00025.352-0.008-0.0080.0000.0000.0000.000
142A173ARG10.8710.92021.5960.0460.0460.0000.0000.0000.000
143A174GLY00.0270.02724.8220.0080.0080.0000.0000.0000.000
144A175HIS10.7900.87720.950-0.031-0.0310.0000.0000.0000.000
145A176GLU-1-0.761-0.88625.1810.0520.0520.0000.0000.0000.000
146A177TYR0-0.045-0.05121.060-0.004-0.0040.0000.0000.0000.000
147A178LEU0-0.0170.00525.486-0.002-0.0020.0000.0000.0000.000
148A179ALA00.027-0.00426.500-0.008-0.0080.0000.0000.0000.000
149A180ARG10.8080.88728.9750.0400.0400.0000.0000.0000.000
150A181ARG10.8610.92230.2720.0310.0310.0000.0000.0000.000
151A182VAL0-0.022-0.02228.9970.0030.0030.0000.0000.0000.000
152A183THR00.004-0.02732.427-0.005-0.0050.0000.0000.0000.000
153A184GLU-1-0.794-0.91332.153-0.088-0.0880.0000.0000.0000.000
154A185SER0-0.003-0.00332.602-0.003-0.0030.0000.0000.0000.000
155A186GLU-1-0.795-0.86832.272-0.045-0.0450.0000.0000.0000.000
156A187LEU00.013-0.00226.497-0.002-0.0020.0000.0000.0000.000
157A188VAL0-0.047-0.00828.588-0.008-0.0080.0000.0000.0000.000
158A189GLN0-0.0310.00030.640-0.003-0.0030.0000.0000.0000.000
159A190ARG10.9270.95727.9820.0490.0490.0000.0000.0000.000
160A191SER00.0670.03922.778-0.001-0.0010.0000.0000.0000.000
161A192PRO00.0730.00722.2940.0110.0110.0000.0000.0000.000
162A193PHE00.014-0.00217.1700.0080.0080.0000.0000.0000.000
163A194MET0-0.0120.00721.8880.0150.0150.0000.0000.0000.000
164A195MET00.0080.01125.0870.0080.0080.0000.0000.0000.000
165A196LEU0-0.0220.01621.0310.0060.0060.0000.0000.0000.000
166A197ALA00.005-0.02023.0710.0110.0110.0000.0000.0000.000
167A198GLU-1-0.880-0.93624.8340.0010.0010.0000.0000.0000.000
168A199GLU-1-0.889-0.92728.087-0.022-0.0220.0000.0000.0000.000
169A200VAL0-0.021-0.00725.5360.0030.0030.0000.0000.0000.000
170A201PRO00.0350.00427.1690.0040.0040.0000.0000.0000.000
171A202GLU-1-0.915-0.95325.7080.0820.0820.0000.0000.0000.000
172A203ALA00.0150.01822.8980.0120.0120.0000.0000.0000.000
173A204ARG10.8630.90321.677-0.007-0.0070.0000.0000.0000.000
174A205GLU-1-0.919-0.94821.8350.0950.0950.0000.0000.0000.000
175A206HIS10.8160.90919.060-0.084-0.0840.0000.0000.0000.000
176A207MET00.0640.06617.6120.0070.0070.0000.0000.0000.000
177A208GLY00.013-0.00314.141-0.012-0.0120.0000.0000.0000.000
178A209SER0-0.146-0.07113.9980.0280.0280.0000.0000.0000.000
179A210TYR00.0440.00116.505-0.003-0.0030.0000.0000.0000.000
180A211GLY0-0.0140.01515.736-0.009-0.0090.0000.0000.0000.000
181A212LEU0-0.021-0.01316.9750.0120.0120.0000.0000.0000.000
182A213ALA00.027-0.00318.813-0.029-0.0290.0000.0000.0000.000
183A214MET0-0.041-0.00321.4490.0100.0100.0000.0000.0000.000
184A215VAL00.0410.01924.449-0.014-0.0140.0000.0000.0000.000
185A216ARG10.7910.91527.1610.0910.0910.0000.0000.0000.000
186A217GLN0-0.004-0.03330.5460.0040.0040.0000.0000.0000.000
187A218SER00.0610.01433.626-0.003-0.0030.0000.0000.0000.000
188A219ASP-1-0.764-0.82336.952-0.047-0.0470.0000.0000.0000.000
189A220ASN0-0.064-0.03635.561-0.003-0.0030.0000.0000.0000.000
190A221SER0-0.021-0.01134.795-0.004-0.0040.0000.0000.0000.000
191A222PHE00.005-0.01828.356-0.004-0.0040.0000.0000.0000.000
192A223VAL00.0130.01228.6160.0070.0070.0000.0000.0000.000
193A224LEU0-0.060-0.02224.631-0.012-0.0120.0000.0000.0000.000
194A225LEU00.0120.00023.8750.0110.0110.0000.0000.0000.000
195A226ALA00.0290.00521.756-0.012-0.0120.0000.0000.0000.000
196A227THR0-0.035-0.00619.3350.0150.0150.0000.0000.0000.000
197A228GLN00.0470.01819.523-0.010-0.0100.0000.0000.0000.000
198A229ARG10.9050.95114.692-0.341-0.3410.0000.0000.0000.000
199A230ASN0-0.016-0.01818.6300.0080.0080.0000.0000.0000.000
200A231LEU0-0.008-0.00520.3460.0030.0030.0000.0000.0000.000
201A232LEU00.0250.02121.857-0.002-0.0020.0000.0000.0000.000
202A233THR00.0040.00824.151-0.001-0.0010.0000.0000.0000.000
203A234LEU0-0.0010.00019.772-0.006-0.0060.0000.0000.0000.000
204A235ASN00.0190.02119.470-0.002-0.0020.0000.0000.0000.000
205A236ARG10.8700.90811.445-0.381-0.3810.0000.0000.0000.000
206A237ALA00.0440.01814.4940.0250.0250.0000.0000.0000.000
207A238SER0-0.010-0.01614.504-0.023-0.0230.0000.0000.0000.000
208A239ALA00.0840.03915.686-0.004-0.0040.0000.0000.0000.000
209A240GLU-1-0.826-0.90213.259-0.324-0.3240.0000.0000.0000.000
210A241GLU-1-0.854-0.86717.0750.0010.0010.0000.0000.0000.000
211A242ILE0-0.006-0.00619.3620.0090.0090.0000.0000.0000.000
212A243GLN0-0.065-0.04617.945-0.023-0.0230.0000.0000.0000.000
213A244ASP-1-0.816-0.91321.269-0.115-0.1150.0000.0000.0000.000
214A245HIS0-0.082-0.03615.9230.0080.0080.0000.0000.0000.000
215A246GLN0-0.020-0.02120.675-0.012-0.0120.0000.0000.0000.000
216A248GLU-1-0.819-0.91026.160-0.081-0.0810.0000.0000.0000.000
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