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: K2963

Calculation Name: 6AR7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6AR7

Chain ID: A

ChEMBL ID:

UniProt ID: Q2T081

Base Structure: X-ray

Registration Date: 2023-09-26

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2328857.373637
FMO2-HF: Nuclear repulsion 2244952.620126
FMO2-HF: Total energy -83904.75351
FMO2-MP2: Total energy -84141.847411


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:33:MET)


Summations of interaction energy for fragment #1(A:33:MET)
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.
-0.5983.0310.046-1.862-1.8120.002
Interaction energy analysis for fragmet #1(A:33:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.015
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].
3A35ASP-1-0.739-0.8483.305-3.801-0.2890.047-1.858-1.7010.002
4A36PRO00.0530.0094.625-0.1140.003-0.001-0.004-0.1110.000
5A37ILE00.0370.0306.9770.1350.1350.0000.0000.0000.000
6A38ASP-1-0.814-0.8978.127-1.555-1.5550.0000.0000.0000.000
7A39VAL0-0.057-0.0306.1470.1050.1050.0000.0000.0000.000
8A40ALA00.0400.0239.1080.1970.1970.0000.0000.0000.000
9A41MET00.0010.01012.0830.1500.1500.0000.0000.0000.000
10A42ARG10.9440.9708.1671.7931.7930.0000.0000.0000.000
11A43GLN00.0110.00211.7640.0910.0910.0000.0000.0000.000
12A44CYS0-0.091-0.02415.1430.0910.0910.0000.0000.0000.000
13A45LEU0-0.019-0.00916.1620.0560.0560.0000.0000.0000.000
14A46ALA00.0220.02317.6030.0370.0370.0000.0000.0000.000
15A47ARG10.7940.87819.3850.3430.3430.0000.0000.0000.000
16A48ARG11.0060.99521.7860.1850.1850.0000.0000.0000.000
17A49ASP-1-0.831-0.88824.213-0.241-0.2410.0000.0000.0000.000
18A50ARG10.7760.84021.3500.3140.3140.0000.0000.0000.000
19A51SER00.0330.03824.220-0.015-0.0150.0000.0000.0000.000
20A52SER00.0120.01425.680-0.007-0.0070.0000.0000.0000.000
21A53THR00.0740.01626.506-0.011-0.0110.0000.0000.0000.000
22A54ALA00.0090.00526.675-0.016-0.0160.0000.0000.0000.000
23A55GLY00.0340.02625.556-0.009-0.0090.0000.0000.0000.000
24A56GLN0-0.011-0.03821.472-0.050-0.0500.0000.0000.0000.000
25A57ILE00.016-0.00821.711-0.035-0.0350.0000.0000.0000.000
26A58GLN0-0.030-0.00422.897-0.005-0.0050.0000.0000.0000.000
27A60MET0-0.0040.00118.337-0.034-0.0340.0000.0000.0000.000
28A61ASP-1-0.795-0.86619.251-0.333-0.3330.0000.0000.0000.000
29A62GLU-1-0.750-0.84618.691-0.331-0.3310.0000.0000.0000.000
30A63ALA00.0140.01314.811-0.005-0.0050.0000.0000.0000.000
31A64ARG10.8490.91216.0230.3240.3240.0000.0000.0000.000
32A65GLN0-0.027-0.01818.3740.0160.0160.0000.0000.0000.000
33A66GLN0-0.009-0.00713.979-0.006-0.0060.0000.0000.0000.000
34A67TRP00.024-0.0059.1670.0770.0770.0000.0000.0000.000
35A68GLN0-0.048-0.03815.4610.0150.0150.0000.0000.0000.000
36A69GLY00.0230.01317.4540.0380.0380.0000.0000.0000.000
37A70GLU-1-0.821-0.90611.846-0.227-0.2270.0000.0000.0000.000
38A71VAL0-0.078-0.02315.0970.0480.0480.0000.0000.0000.000
39A72ASP-1-0.858-0.92217.851-0.139-0.1390.0000.0000.0000.000
40A73ALA00.0090.00215.8600.0390.0390.0000.0000.0000.000
41A74ALA00.000-0.00214.9350.0530.0530.0000.0000.0000.000
42A75TYR00.012-0.00316.8460.0410.0410.0000.0000.0000.000
43A76GLN0-0.003-0.00920.3150.0420.0420.0000.0000.0000.000
44A77ARG10.8740.91212.957-0.138-0.1380.0000.0000.0000.000
45A78LEU0-0.0080.02418.9350.0240.0240.0000.0000.0000.000
46A79VAL0-0.053-0.03420.6880.0120.0120.0000.0000.0000.000
47A80LYS10.8680.93022.6230.0010.0010.0000.0000.0000.000
48A81THR0-0.023-0.01619.9280.0130.0130.0000.0000.0000.000
49A82ALA0-0.0300.01722.8580.0100.0100.0000.0000.0000.000
50A83PRO00.0200.01224.048-0.002-0.0020.0000.0000.0000.000
51A84ALA00.028-0.00227.364-0.013-0.0130.0000.0000.0000.000
52A85ASP-1-0.919-0.96829.0490.0100.0100.0000.0000.0000.000
53A86ALA00.1100.04924.724-0.011-0.0110.0000.0000.0000.000
54A87ARG10.9260.99425.826-0.032-0.0320.0000.0000.0000.000
55A88ARG10.9230.95026.856-0.010-0.0100.0000.0000.0000.000
56A89GLY00.0270.02428.092-0.010-0.0100.0000.0000.0000.000
57A90TRP00.0980.01619.260-0.022-0.0220.0000.0000.0000.000
58A91GLN0-0.033-0.01625.242-0.012-0.0120.0000.0000.0000.000
59A92GLU-1-0.790-0.86227.503-0.087-0.0870.0000.0000.0000.000
60A93SER00.003-0.00324.415-0.016-0.0160.0000.0000.0000.000
61A94GLN00.0840.04022.098-0.025-0.0250.0000.0000.0000.000
62A95ARG10.8670.92625.6490.0590.0590.0000.0000.0000.000
63A96ARG10.8590.92428.5730.0880.0880.0000.0000.0000.000
64A97TRP00.0250.00821.1190.0000.0000.0000.0000.0000.000
65A98LEU0-0.005-0.00825.259-0.012-0.0120.0000.0000.0000.000
66A99ALA0-0.0020.00327.635-0.003-0.0030.0000.0000.0000.000
67A100TRP00.0150.00023.503-0.009-0.0090.0000.0000.0000.000
68A101ARG10.9000.95723.8180.2740.2740.0000.0000.0000.000
69A102LYS10.7470.87527.6030.1290.1290.0000.0000.0000.000
70A103ASP-1-0.836-0.91830.844-0.131-0.1310.0000.0000.0000.000
71A104GLU-1-0.789-0.87227.212-0.223-0.2230.0000.0000.0000.000
72A105ALA0-0.0070.00029.350-0.008-0.0080.0000.0000.0000.000
73A106HIS00.0380.02030.487-0.003-0.0030.0000.0000.0000.000
74A107LEU0-0.0170.01531.4890.0050.0050.0000.0000.0000.000
75A108VAL0-0.007-0.01327.861-0.002-0.0020.0000.0000.0000.000
76A109ARG10.8890.93831.1790.1520.1520.0000.0000.0000.000
77A110ALA00.0250.02133.7500.0040.0040.0000.0000.0000.000
78A111VAL0-0.032-0.01132.3150.0040.0040.0000.0000.0000.000
79A112TYR00.024-0.01027.474-0.003-0.0030.0000.0000.0000.000
80A113GLU-1-0.918-0.93733.665-0.143-0.1430.0000.0000.0000.000
81A114THR0-0.044-0.01236.8790.0070.0070.0000.0000.0000.000
82A115THR0-0.080-0.05133.609-0.002-0.0020.0000.0000.0000.000
83A116GLN00.0560.01436.1730.0040.0040.0000.0000.0000.000
84A117GLY00.0550.03134.290-0.002-0.0020.0000.0000.0000.000
85A118THR0-0.001-0.01629.650-0.008-0.0080.0000.0000.0000.000
86A119MET00.0190.01828.422-0.020-0.0200.0000.0000.0000.000
87A120TYR00.0560.01727.966-0.021-0.0210.0000.0000.0000.000
88A121ALA00.0040.00828.896-0.010-0.0100.0000.0000.0000.000
89A122MET00.001-0.00422.351-0.007-0.0070.0000.0000.0000.000
90A123ALA0-0.0060.00824.093-0.029-0.0290.0000.0000.0000.000
91A124SER0-0.0040.00124.798-0.016-0.0160.0000.0000.0000.000
92A125ALA0-0.010-0.01223.377-0.004-0.0040.0000.0000.0000.000
93A126ASP-1-0.831-0.92018.795-0.603-0.6030.0000.0000.0000.000
94A127MET0-0.055-0.02520.873-0.014-0.0140.0000.0000.0000.000
95A128ARG10.8260.91023.2540.3130.3130.0000.0000.0000.000
96A129LEU0-0.048-0.02315.8450.0080.0080.0000.0000.0000.000
97A130GLN00.022-0.00815.445-0.086-0.0860.0000.0000.0000.000
98A131PRO00.0200.01217.357-0.021-0.0210.0000.0000.0000.000
99A132VAL0-0.051-0.01117.8280.0230.0230.0000.0000.0000.000
100A133ARG10.8540.9209.5411.4681.4680.0000.0000.0000.000
101A134GLU-1-0.902-0.95414.088-0.527-0.5270.0000.0000.0000.000
102A135ARG10.8110.89415.7590.2450.2450.0000.0000.0000.000
103A136ALA00.0150.00113.8120.0510.0510.0000.0000.0000.000
104A137LEU0-0.006-0.0079.1940.0580.0580.0000.0000.0000.000
105A138ALA00.0170.02012.5400.0770.0770.0000.0000.0000.000
106A139LEU0-0.051-0.02315.5840.0720.0720.0000.0000.0000.000
107A140ARG10.7640.8458.0990.6550.6550.0000.0000.0000.000
108A141GLY00.0420.03312.7290.0920.0920.0000.0000.0000.000
109A142ALA0-0.035-0.01613.5440.0760.0760.0000.0000.0000.000
110A143ALA0-0.017-0.01715.7330.0430.0430.0000.0000.0000.000
111A144ASP-1-0.805-0.88711.1620.3450.3450.0000.0000.0000.000
112A145ARG10.8990.96214.6150.0830.0830.0000.0000.0000.000
113A146TYR0-0.032-0.04416.9480.0010.0010.0000.0000.0000.000
114A147ALA00.0050.02716.657-0.001-0.0010.0000.0000.0000.000
115A148GLN0-0.059-0.01115.0150.0230.0230.0000.0000.0000.000
116A149PRO00.0510.00718.856-0.044-0.0440.0000.0000.0000.000
117A150GLY0-0.0100.00021.8350.0070.0070.0000.0000.0000.000
118A151GLY00.0330.01320.692-0.026-0.0260.0000.0000.0000.000
119A152GLY00.0110.01121.747-0.025-0.0250.0000.0000.0000.000
120A153LYS10.9220.94423.936-0.132-0.1320.0000.0000.0000.000
121A154GLY0-0.0010.00325.1570.0000.0000.0000.0000.0000.000
122A155ALA0-0.0130.01024.319-0.012-0.0120.0000.0000.0000.000
123A156VAL0-0.0110.00925.286-0.018-0.0180.0000.0000.0000.000
124A157HIS10.8200.91125.2500.0700.0700.0000.0000.0000.000
125A158ARG10.9220.94629.6080.0290.0290.0000.0000.0000.000
126A159VAL00.0840.04730.690-0.003-0.0030.0000.0000.0000.000
127A160ARG10.9510.98030.6860.0480.0480.0000.0000.0000.000
128A161PRO00.0600.01332.303-0.008-0.0080.0000.0000.0000.000
129A162CYS00.0060.01627.673-0.013-0.0130.0000.0000.0000.000
130A163MET00.0880.04732.112-0.001-0.0010.0000.0000.0000.000
131A164ARG10.8380.91633.4110.0520.0520.0000.0000.0000.000
132A165ASP-1-0.823-0.91027.448-0.118-0.1180.0000.0000.0000.000
133A166ALA00.0340.02030.767-0.007-0.0070.0000.0000.0000.000
134A167ALA00.0100.00925.580-0.008-0.0080.0000.0000.0000.000
135A169GLU-1-0.885-0.95828.586-0.108-0.1080.0000.0000.0000.000
136A170HIS0-0.017-0.00928.2860.0080.0080.0000.0000.0000.000
137A171ALA00.0120.00826.467-0.007-0.0070.0000.0000.0000.000
138A172LEU00.005-0.01028.362-0.006-0.0060.0000.0000.0000.000
139A173PHE0-0.007-0.00131.1800.0030.0030.0000.0000.0000.000
140A174ASP-1-0.783-0.88529.582-0.177-0.1770.0000.0000.0000.000
141A175MET0-0.059-0.00729.259-0.005-0.0050.0000.0000.0000.000
142A176ASN00.026-0.00530.964-0.001-0.0010.0000.0000.0000.000
143A177ARG10.8750.94131.7560.1680.1680.0000.0000.0000.000
144A178TYR0-0.023-0.03330.4970.0020.0020.0000.0000.0000.000
145A179TYR00.0020.00833.5170.0020.0020.0000.0000.0000.000
146A180GLU-1-0.786-0.88434.766-0.111-0.1110.0000.0000.0000.000
147A181LYS10.8490.94033.4250.1800.1800.0000.0000.0000.000
148A182LEU0-0.015-0.02032.8340.0010.0010.0000.0000.0000.000
149A183ARG10.8700.91236.4070.1150.1150.0000.0000.0000.000
150A184ALA0-0.032-0.01539.1740.0050.0050.0000.0000.0000.000
151A185ARG10.8940.93636.4860.1540.1540.0000.0000.0000.000
152A186MET0-0.0270.00037.195-0.003-0.0030.0000.0000.0000.000
153A187PRO00.0620.03340.2580.0060.0060.0000.0000.0000.000
154A188ALA0-0.014-0.01942.719-0.002-0.0020.0000.0000.0000.000
155A189ASP-1-0.886-0.93144.103-0.100-0.1000.0000.0000.0000.000
156A190SER00.0430.01739.1250.0000.0000.0000.0000.0000.000
157A191ARG10.9170.98339.5870.1030.1030.0000.0000.0000.000
158A192GLN00.0410.00939.988-0.005-0.0050.0000.0000.0000.000
159A193THR0-0.036-0.03036.623-0.004-0.0040.0000.0000.0000.000
160A194LEU00.0240.02434.164-0.007-0.0070.0000.0000.0000.000
161A195VAL0-0.046-0.02735.601-0.003-0.0030.0000.0000.0000.000
162A196ALA0-0.032-0.01637.0270.0000.0000.0000.0000.0000.000
163A197ALA00.0600.03031.863-0.001-0.0010.0000.0000.0000.000
164A198GLN00.0200.01230.909-0.017-0.0170.0000.0000.0000.000
165A199ARG10.9660.99332.8810.1060.1060.0000.0000.0000.000
166A200GLU-1-0.844-0.92531.957-0.127-0.1270.0000.0000.0000.000
167A201TRP00.0410.01125.2110.0080.0080.0000.0000.0000.000
168A202ALA00.0040.00429.147-0.003-0.0030.0000.0000.0000.000
169A203ALA00.0300.01931.1860.0050.0050.0000.0000.0000.000
170A204PHE0-0.033-0.03122.3620.0050.0050.0000.0000.0000.000
171A205SER0-0.003-0.00726.593-0.002-0.0020.0000.0000.0000.000
172A206ASP-1-0.927-0.97327.675-0.103-0.1030.0000.0000.0000.000
173A207ALA0-0.082-0.04228.1640.0100.0100.0000.0000.0000.000
174A208MET00.0220.01920.7890.0140.0140.0000.0000.0000.000
175A209THR0-0.0130.01025.2060.0050.0050.0000.0000.0000.000
176A210PRO0-0.056-0.03926.6740.0060.0060.0000.0000.0000.000
177A211LEU0-0.028-0.01023.6490.0170.0170.0000.0000.0000.000
178A212VAL0-0.0260.00820.4800.0070.0070.0000.0000.0000.000
179A213SER0-0.049-0.04419.4210.0130.0130.0000.0000.0000.000
180A214GLU-1-0.808-0.90522.080-0.118-0.1180.0000.0000.0000.000
181A215GLY00.0270.01420.462-0.010-0.0100.0000.0000.0000.000
182A216GLU-1-0.745-0.85417.339-0.202-0.2020.0000.0000.0000.000
183A217ARG10.7820.87819.9480.0960.0960.0000.0000.0000.000
184A218VAL00.003-0.00422.817-0.007-0.0070.0000.0000.0000.000
185A219ASP-1-0.883-0.93717.857-0.370-0.3700.0000.0000.0000.000
186A220LEU0-0.063-0.03020.710-0.021-0.0210.0000.0000.0000.000
187A221ILE0-0.015-0.01022.311-0.003-0.0030.0000.0000.0000.000
188A222GLY00.0330.01622.9120.0020.0020.0000.0000.0000.000
189A223ALA00.0330.01820.195-0.008-0.0080.0000.0000.0000.000
190A224ARG10.7690.85422.0450.2190.2190.0000.0000.0000.000
191A225VAL0-0.018-0.01625.5850.0100.0100.0000.0000.0000.000
192A226ALA00.0030.00522.9210.0100.0100.0000.0000.0000.000
193A227THR0-0.045-0.01924.167-0.001-0.0010.0000.0000.0000.000
194A228LEU00.0180.00926.1020.0120.0120.0000.0000.0000.000
195A229LYS10.8690.92527.1680.2570.2570.0000.0000.0000.000
196A230ARG10.9911.00722.7580.3640.3640.0000.0000.0000.000
197A231PHE00.0260.00828.5110.0100.0100.0000.0000.0000.000
198A232SER0-0.044-0.01731.2840.0150.0150.0000.0000.0000.000
199A233GLU-1-0.909-0.95029.763-0.213-0.2130.0000.0000.0000.000
200A234THR0-0.071-0.03030.653-0.004-0.0040.0000.0000.0000.000
201A235VAL0-0.034-0.01033.1840.0060.0060.0000.0000.0000.000
202A236ASN0-0.025-0.00736.1520.0070.0070.0000.0000.0000.000
203A237ASN0-0.015-0.00639.4220.0100.0100.0000.0000.0000.000