FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: QVKQY

Calculation Name: 2B6P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B6P

Chain ID: A

ChEMBL ID:

UniProt ID: Q6J8I9

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 262
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3194135.230627
FMO2-HF: Nuclear repulsion 3096916.602374
FMO2-HF: Total energy -97218.628253
FMO2-MP2: Total energy -97506.212604


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:TRP)


Summations of interaction energy for fragment #1(A:2:TRP)
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.
-14.89-2.6268.567-5.981-14.850.028
Interaction energy analysis for fragmet #1(A:2:TRP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.085 / q_NPA : -0.090
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].
3A4LEU00.0530.0172.282-1.9320.9360.804-1.452-2.220-0.007
4A5ARG10.9100.9733.871-1.690-0.9020.009-0.168-0.629-0.001
5A6SER00.0280.0132.178-0.6400.6992.342-1.235-2.4460.002
6A7ALA00.0830.0263.3820.0350.4300.0500.018-0.463-0.002
7A8SER0-0.040-0.0175.9800.1620.1620.0000.0000.0000.000
8A9PHE00.006-0.0083.478-2.593-0.3780.078-0.385-1.9080.000
9A10TRP00.0610.0232.488-6.886-2.7542.734-1.932-4.9340.027
10A11ARG10.9660.9857.313-0.656-0.6560.0000.0000.0000.000
11A12ALA00.0120.0168.595-0.116-0.1160.0000.0000.0000.000
12A13ILE00.0200.0187.090-0.160-0.1600.0000.0000.0000.000
13A14CYS0-0.018-0.01210.784-0.180-0.1800.0000.0000.0000.000
14A15ALA00.0150.01513.183-0.088-0.0880.0000.0000.0000.000
15A16GLU-1-0.691-0.80712.9980.2370.2370.0000.0000.0000.000
16A17PHE0-0.0210.02314.754-0.065-0.0650.0000.0000.0000.000
17A18PHE00.011-0.01616.167-0.048-0.0480.0000.0000.0000.000
18A19ALA00.0190.01418.498-0.033-0.0330.0000.0000.0000.000
19A20SER00.032-0.01018.520-0.034-0.0340.0000.0000.0000.000
20A21LEU0-0.0330.01020.969-0.025-0.0250.0000.0000.0000.000
21A22PHE00.022-0.01322.149-0.019-0.0190.0000.0000.0000.000
22A23TYR00.0100.00423.666-0.018-0.0180.0000.0000.0000.000
23A24VAL0-0.028-0.01324.594-0.013-0.0130.0000.0000.0000.000
24A25PHE0-0.0230.00626.597-0.011-0.0110.0000.0000.0000.000
25A26PHE0-0.003-0.01827.641-0.008-0.0080.0000.0000.0000.000
26A27GLY00.0170.01729.324-0.006-0.0060.0000.0000.0000.000
27A28LEU0-0.023-0.01829.088-0.007-0.0070.0000.0000.0000.000
28A29GLY00.0280.01432.115-0.006-0.0060.0000.0000.0000.000
29A30ALA0-0.0080.00734.037-0.004-0.0040.0000.0000.0000.000
30A31SER0-0.050-0.04134.396-0.004-0.0040.0000.0000.0000.000
31A32LEU0-0.073-0.01035.115-0.004-0.0040.0000.0000.0000.000
32A33ARG10.8560.91238.442-0.037-0.0370.0000.0000.0000.000
33A34TRP00.006-0.01341.944-0.001-0.0010.0000.0000.0000.000
34A35ALA00.1350.07543.7600.0020.0020.0000.0000.0000.000
35A36PRO0-0.088-0.07744.2640.0000.0000.0000.0000.0000.000
36A37GLY00.0720.04543.640-0.001-0.0010.0000.0000.0000.000
37A38PRO00.0390.02643.9600.0020.0020.0000.0000.0000.000
38A39LEU00.0370.01944.6720.0010.0010.0000.0000.0000.000
39A40HIS0-0.0200.00639.9820.0030.0030.0000.0000.0000.000
40A41VAL00.012-0.01039.2850.0030.0030.0000.0000.0000.000
41A42LEU0-0.0060.00438.8840.0030.0030.0000.0000.0000.000
42A43GLN00.0460.02838.7410.0020.0020.0000.0000.0000.000
43A44VAL00.0140.01435.1030.0040.0040.0000.0000.0000.000
44A45ALA0-0.001-0.01334.5580.0050.0050.0000.0000.0000.000
45A46LEU0-0.0180.00833.8050.0050.0050.0000.0000.0000.000
46A47ALA00.0130.02533.3420.0060.0060.0000.0000.0000.000
47A48PHE00.0200.00828.7620.0070.0070.0000.0000.0000.000
48A49GLY00.0030.01328.9730.0080.0080.0000.0000.0000.000
49A50LEU00.014-0.01229.1430.0080.0080.0000.0000.0000.000
50A51ALA00.0020.02627.6280.0080.0080.0000.0000.0000.000
51A52LEU0-0.001-0.01022.5860.0110.0110.0000.0000.0000.000
52A53ALA00.0230.01724.4820.0130.0130.0000.0000.0000.000
53A54THR0-0.035-0.02725.6970.0080.0080.0000.0000.0000.000
54A55LEU0-0.015-0.01621.7010.0130.0130.0000.0000.0000.000
55A56VAL0-0.004-0.00620.6710.0230.0230.0000.0000.0000.000
56A57GLN0-0.017-0.00520.9660.0100.0100.0000.0000.0000.000
57A58ALA0-0.042-0.01721.6360.0120.0120.0000.0000.0000.000
58A59VAL0-0.015-0.02416.3330.0180.0180.0000.0000.0000.000
59A60GLY00.0640.03416.2030.0350.0350.0000.0000.0000.000
60A61HIS0-0.021-0.01016.3850.0150.0150.0000.0000.0000.000
61A62ILE0-0.069-0.02512.3910.0430.0430.0000.0000.0000.000
62A63SER0-0.069-0.06411.5440.0850.0850.0000.0000.0000.000
63A64GLY00.0420.04112.618-0.012-0.0120.0000.0000.0000.000
64A65ALA0-0.056-0.01615.396-0.041-0.0410.0000.0000.0000.000
65A66HIS00.0310.02113.978-0.026-0.0260.0000.0000.0000.000
66A67VAL0-0.034-0.03017.243-0.029-0.0290.0000.0000.0000.000
67A68ASN00.044-0.00518.594-0.033-0.0330.0000.0000.0000.000
68A69PRO00.0440.03417.810-0.003-0.0030.0000.0000.0000.000
69A70ALA00.0140.01418.731-0.015-0.0150.0000.0000.0000.000
70A71VAL00.0180.01418.619-0.013-0.0130.0000.0000.0000.000
71A72THR00.001-0.01614.0260.0060.0060.0000.0000.0000.000
72A73PHE0-0.026-0.02516.160-0.028-0.0280.0000.0000.0000.000
73A74ALA00.0190.00717.980-0.024-0.0240.0000.0000.0000.000
74A75PHE00.0140.00015.215-0.009-0.0090.0000.0000.0000.000
75A76LEU0-0.047-0.00512.504-0.024-0.0240.0000.0000.0000.000
76A77VAL00.0000.01315.425-0.034-0.0340.0000.0000.0000.000
77A78GLY00.0790.05718.053-0.001-0.0010.0000.0000.0000.000
78A79SER0-0.128-0.08214.6590.0060.0060.0000.0000.0000.000
79A80GLN00.0240.00613.4040.0010.0010.0000.0000.0000.000
80A81MET0-0.069-0.00810.0130.0550.0550.0000.0000.0000.000
81A82SER00.0680.0325.7540.2090.2090.0000.0000.0000.000
82A83LEU00.0390.0048.9770.1780.1780.0000.0000.0000.000
83A84LEU00.0100.0112.317-1.082-0.6342.551-0.816-2.1830.009
84A85ARG10.9610.9775.880-0.068-0.0680.0000.0000.0000.000
85A86ALA00.0480.0267.8460.1460.1460.0000.0000.0000.000
86A87ILE00.0610.0299.1030.0720.0720.0000.0000.0000.000
87A88CYS0-0.018-0.0086.5680.2570.2570.0000.0000.0000.000
88A89TYR0-0.036-0.0339.1550.0600.0600.0000.0000.0000.000
89A90MET0-0.0100.00012.416-0.048-0.0480.0000.0000.0000.000
90A91VAL0-0.0040.00911.435-0.032-0.0320.0000.0000.0000.000
91A92ALA00.005-0.00312.455-0.039-0.0390.0000.0000.0000.000
92A93GLN0-0.014-0.03414.161-0.079-0.0790.0000.0000.0000.000
93A94LEU0-0.034-0.01016.762-0.032-0.0320.0000.0000.0000.000
94A95LEU0-0.008-0.00714.422-0.023-0.0230.0000.0000.0000.000
95A96GLY00.0280.01217.758-0.014-0.0140.0000.0000.0000.000
96A97ALA0-0.010-0.00819.329-0.018-0.0180.0000.0000.0000.000
97A98VAL00.005-0.00521.428-0.012-0.0120.0000.0000.0000.000
98A99ALA00.0450.02921.116-0.012-0.0120.0000.0000.0000.000
99A100GLY00.0140.02023.081-0.009-0.0090.0000.0000.0000.000
100A101ALA0-0.006-0.01625.351-0.008-0.0080.0000.0000.0000.000
101A102ALA0-0.008-0.00225.705-0.008-0.0080.0000.0000.0000.000
102A103VAL00.004-0.01525.545-0.006-0.0060.0000.0000.0000.000
103A104LEU0-0.0080.01828.350-0.005-0.0050.0000.0000.0000.000
104A105TYR00.001-0.02130.712-0.006-0.0060.0000.0000.0000.000
105A106SER0-0.100-0.06530.890-0.003-0.0030.0000.0000.0000.000
106A107VAL00.0000.00632.015-0.003-0.0030.0000.0000.0000.000
107A108THR0-0.0360.00834.539-0.002-0.0020.0000.0000.0000.000
108A109PRO00.0770.03336.793-0.003-0.0030.0000.0000.0000.000
109A110PRO00.1320.04239.8140.0010.0010.0000.0000.0000.000
110A111ALA00.0050.03240.7560.0010.0010.0000.0000.0000.000
111A112VAL0-0.089-0.06240.0010.0000.0000.0000.0000.0000.000
112A113ARG10.8640.93736.272-0.024-0.0240.0000.0000.0000.000
113A114GLY00.0320.02937.1610.0020.0020.0000.0000.0000.000
114A115ASN0-0.013-0.01036.2670.0010.0010.0000.0000.0000.000
115A116LEU00.011-0.01331.2520.0010.0010.0000.0000.0000.000
116A117ALA00.0300.02232.7210.0040.0040.0000.0000.0000.000
117A118LEU00.0290.03031.5810.0040.0040.0000.0000.0000.000
118A119ASN0-0.048-0.00130.5830.0020.0020.0000.0000.0000.000
119A120THR0-0.019-0.02133.415-0.004-0.0040.0000.0000.0000.000
120A121LEU0-0.024-0.00735.2360.0010.0010.0000.0000.0000.000
121A122HIS00.0650.03838.5630.0000.0000.0000.0000.0000.000
122A123PRO00.022-0.00142.170-0.001-0.0010.0000.0000.0000.000
123A124GLY0-0.0150.00644.748-0.001-0.0010.0000.0000.0000.000
124A125VAL0-0.074-0.03340.1520.0000.0000.0000.0000.0000.000
125A126SER00.0310.00541.534-0.001-0.0010.0000.0000.0000.000
126A127VAL00.0950.02135.5400.0020.0020.0000.0000.0000.000
127A128GLY00.0200.02236.4360.0000.0000.0000.0000.0000.000
128A129GLN00.0670.04537.4480.0000.0000.0000.0000.0000.000
129A130ALA00.0270.01636.2650.0020.0020.0000.0000.0000.000
130A131THR0-0.017-0.02731.7690.0030.0030.0000.0000.0000.000
131A132ILE00.0160.01333.2290.0010.0010.0000.0000.0000.000
132A133VAL00.0100.00735.1210.0020.0020.0000.0000.0000.000
133A134GLU-1-0.724-0.84130.7350.0330.0330.0000.0000.0000.000
134A135ILE0-0.0270.01130.4290.0040.0040.0000.0000.0000.000
135A136PHE00.0370.00231.0340.0030.0030.0000.0000.0000.000
136A137LEU0-0.057-0.01531.7640.0040.0040.0000.0000.0000.000
137A138THR00.017-0.00725.9150.0080.0080.0000.0000.0000.000
138A139LEU00.0070.04127.4380.0050.0050.0000.0000.0000.000
139A140GLN0-0.035-0.01728.8120.0050.0050.0000.0000.0000.000
140A141PHE0-0.015-0.00424.2830.0060.0060.0000.0000.0000.000
141A142VAL00.012-0.00522.9140.0080.0080.0000.0000.0000.000
142A143LEU0-0.0100.01824.6290.0050.0050.0000.0000.0000.000
143A144CYS0-0.012-0.00326.8610.0040.0040.0000.0000.0000.000
144A145ILE0-0.0130.01220.9210.0080.0080.0000.0000.0000.000
145A146PHE0-0.023-0.01919.5010.0090.0090.0000.0000.0000.000
146A147ALA00.0350.02322.8810.0070.0070.0000.0000.0000.000
147A148THR0-0.115-0.07424.7930.0070.0070.0000.0000.0000.000
148A149TYR0-0.057-0.03717.9690.0050.0050.0000.0000.0000.000
149A150ASP-1-0.798-0.83020.1080.0940.0940.0000.0000.0000.000
150A151GLU-1-0.859-0.93518.8200.1220.1220.0000.0000.0000.000
151A152ARG10.7020.81221.258-0.066-0.0660.0000.0000.0000.000
152A153ARG10.8320.87923.998-0.090-0.0900.0000.0000.0000.000
153A154ASN0-0.022-0.00926.2500.0040.0040.0000.0000.0000.000
154A155GLY00.1230.08627.6470.0070.0070.0000.0000.0000.000
155A156ARG10.8860.92329.929-0.067-0.0670.0000.0000.0000.000
156A157LEU00.0160.01025.736-0.006-0.0060.0000.0000.0000.000
157A158GLY00.0100.03629.785-0.003-0.0030.0000.0000.0000.000
158A159SER0-0.009-0.00927.2280.0060.0060.0000.0000.0000.000
159A160VAL00.0860.02422.567-0.007-0.0070.0000.0000.0000.000
160A161ALA00.0230.01824.376-0.004-0.0040.0000.0000.0000.000
161A162LEU00.0290.00325.439-0.005-0.0050.0000.0000.0000.000
162A163ALA0-0.0190.01927.966-0.006-0.0060.0000.0000.0000.000
163A164VAL00.0500.01923.611-0.008-0.0080.0000.0000.0000.000
164A165GLY00.0120.00426.905-0.005-0.0050.0000.0000.0000.000
165A166PHE00.014-0.01828.563-0.006-0.0060.0000.0000.0000.000
166A167SER00.0190.02428.845-0.006-0.0060.0000.0000.0000.000
167A168LEU0-0.011-0.01026.974-0.007-0.0070.0000.0000.0000.000
168A169THR0-0.020-0.02930.074-0.004-0.0040.0000.0000.0000.000
169A170LEU00.0040.01133.454-0.005-0.0050.0000.0000.0000.000
170A171GLY00.0420.00232.684-0.004-0.0040.0000.0000.0000.000
171A172HIS10.8350.90330.508-0.056-0.0560.0000.0000.0000.000
172A173LEU00.004-0.00835.277-0.003-0.0030.0000.0000.0000.000
173A174PHE0-0.0210.00537.138-0.003-0.0030.0000.0000.0000.000
174A175GLY00.0690.01836.311-0.003-0.0030.0000.0000.0000.000
175A176MET0-0.083-0.01836.551-0.001-0.0010.0000.0000.0000.000
176A177TYR00.0140.00938.260-0.002-0.0020.0000.0000.0000.000
177A178TYR0-0.0230.00338.794-0.003-0.0030.0000.0000.0000.000
178A179THR0-0.015-0.03434.365-0.002-0.0020.0000.0000.0000.000
179A180GLY00.0360.02835.2260.0010.0010.0000.0000.0000.000
180A181ALA0-0.046-0.03833.2050.0050.0050.0000.0000.0000.000
181A182GLY00.0220.01030.0070.0040.0040.0000.0000.0000.000
182A183MET0-0.139-0.04828.2040.0080.0080.0000.0000.0000.000
183A184ASN00.0380.00822.9140.0050.0050.0000.0000.0000.000
184A185PRO00.0670.04421.9320.0010.0010.0000.0000.0000.000
185A186ALA00.0300.02220.419-0.005-0.0050.0000.0000.0000.000
186A187ARG10.8330.92422.486-0.051-0.0510.0000.0000.0000.000
187A188SER0-0.010-0.02325.852-0.005-0.0050.0000.0000.0000.000
188A189PHE0-0.042-0.03721.444-0.006-0.0060.0000.0000.0000.000
189A190ALA00.0000.01224.324-0.006-0.0060.0000.0000.0000.000
190A191PRO00.0210.01125.778-0.005-0.0050.0000.0000.0000.000
191A192ALA00.0140.02927.986-0.005-0.0050.0000.0000.0000.000
192A193ILE0-0.041-0.02723.470-0.006-0.0060.0000.0000.0000.000
193A194LEU0-0.035-0.01526.375-0.004-0.0040.0000.0000.0000.000
194A195THR0-0.066-0.04329.321-0.004-0.0040.0000.0000.0000.000
195A196ARG10.8890.95127.334-0.001-0.0010.0000.0000.0000.000
196A197ASN00.0460.02631.960-0.005-0.0050.0000.0000.0000.000
197A198PHE00.0340.00426.8750.0030.0030.0000.0000.0000.000
198A199THR00.0170.02431.933-0.004-0.0040.0000.0000.0000.000
199A200ASN00.004-0.01234.3190.0010.0010.0000.0000.0000.000
200A201HIS00.0510.02726.7630.0020.0020.0000.0000.0000.000
201A202TRP00.0560.02528.6300.0020.0020.0000.0000.0000.000
202A203VAL00.0330.00929.184-0.001-0.0010.0000.0000.0000.000
203A204TYR0-0.066-0.05228.5450.0000.0000.0000.0000.0000.000
204A205TRP0-0.045-0.01719.9580.0070.0070.0000.0000.0000.000
205A206VAL00.025-0.00425.4040.0000.0000.0000.0000.0000.000
206A207GLY00.0530.03627.630-0.002-0.0020.0000.0000.0000.000
207A208PRO00.005-0.00825.403-0.001-0.0010.0000.0000.0000.000
208A209VAL00.0230.02221.9080.0030.0030.0000.0000.0000.000
209A210ILE00.0280.01724.454-0.004-0.0040.0000.0000.0000.000
210A211GLY00.0080.00027.204-0.001-0.0010.0000.0000.0000.000
211A212ALA0-0.031-0.02222.7340.0030.0030.0000.0000.0000.000
212A213GLY0-0.010-0.00823.5810.0000.0000.0000.0000.0000.000
213A214LEU00.003-0.01224.579-0.003-0.0030.0000.0000.0000.000
214A215GLY00.0150.00926.7060.0010.0010.0000.0000.0000.000
215A216SER0-0.032-0.00321.432-0.002-0.0020.0000.0000.0000.000
216A217LEU0-0.011-0.01523.735-0.001-0.0010.0000.0000.0000.000
217A218LEU0-0.022-0.00525.8730.0020.0020.0000.0000.0000.000
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