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: 4L94N

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 OptAll
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 -2338851.417274
FMO2-HF: Nuclear repulsion 2254946.45689
FMO2-HF: Total energy -83904.960384
FMO2-MP2: Total energy -84141.949532


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.
-0.4183.0720.03-1.824-1.6970.003
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 : 0.039 / q_NPA : 0.017
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-1-0.749-0.8583.367-3.593-0.2090.031-1.820-1.5950.003
4A36PRO00.0550.0114.646-0.0830.023-0.001-0.004-0.1020.000
5A37ILE00.0390.0367.1990.1240.1240.0000.0000.0000.000
6A38ASP-1-0.794-0.8778.003-1.492-1.4920.0000.0000.0000.000
7A39VAL0-0.059-0.0126.393-0.010-0.0100.0000.0000.0000.000
8A40ALA00.0490.0249.3990.1760.1760.0000.0000.0000.000
9A41MET00.0020.00212.3860.1400.1400.0000.0000.0000.000
10A42ARG10.8970.9367.5641.9511.9510.0000.0000.0000.000
11A43GLN00.001-0.00512.0470.0860.0860.0000.0000.0000.000
12A44CYS0-0.072-0.01815.1170.0870.0870.0000.0000.0000.000
13A45LEU0-0.006-0.00515.9960.0520.0520.0000.0000.0000.000
14A46ALA00.0240.02717.1710.0380.0380.0000.0000.0000.000
15A47ARG10.8020.89019.0300.3390.3390.0000.0000.0000.000
16A48ARG11.0191.00121.6020.1810.1810.0000.0000.0000.000
17A49ASP-1-0.821-0.88424.447-0.244-0.2440.0000.0000.0000.000
18A50ARG10.7650.84721.8030.3090.3090.0000.0000.0000.000
19A51SER00.0180.02224.361-0.013-0.0130.0000.0000.0000.000
20A52SER00.0210.02425.718-0.003-0.0030.0000.0000.0000.000
21A53THR00.0500.00226.475-0.010-0.0100.0000.0000.0000.000
22A54ALA00.0150.01126.510-0.017-0.0170.0000.0000.0000.000
23A55GLY00.0500.02925.562-0.008-0.0080.0000.0000.0000.000
24A56GLN0-0.020-0.05021.380-0.050-0.0500.0000.0000.0000.000
25A57ILE00.015-0.01221.696-0.034-0.0340.0000.0000.0000.000
26A58GLN0-0.046-0.01222.793-0.009-0.0090.0000.0000.0000.000
27A60MET00.0000.00818.301-0.039-0.0390.0000.0000.0000.000
28A61ASP-1-0.764-0.83819.445-0.315-0.3150.0000.0000.0000.000
29A62GLU-1-0.728-0.83719.069-0.325-0.3250.0000.0000.0000.000
30A63ALA0-0.0010.01115.056-0.004-0.0040.0000.0000.0000.000
31A64ARG10.8350.89816.0930.3130.3130.0000.0000.0000.000
32A65GLN0-0.025-0.01418.5000.0140.0140.0000.0000.0000.000
33A66GLN0-0.016-0.01514.075-0.007-0.0070.0000.0000.0000.000
34A67TRP00.027-0.0059.4930.0830.0830.0000.0000.0000.000
35A68GLN0-0.035-0.03615.5160.0080.0080.0000.0000.0000.000
36A69GLY00.0180.01217.4800.0350.0350.0000.0000.0000.000
37A70GLU-1-0.815-0.90511.791-0.232-0.2320.0000.0000.0000.000
38A71VAL0-0.078-0.02115.1580.0400.0400.0000.0000.0000.000
39A72ASP-1-0.843-0.92018.035-0.136-0.1360.0000.0000.0000.000
40A73ALA00.0070.00615.7850.0370.0370.0000.0000.0000.000
41A74ALA00.0010.00014.9580.0500.0500.0000.0000.0000.000
42A75TYR00.0190.00516.7540.0420.0420.0000.0000.0000.000
43A76GLN0-0.009-0.02020.4370.0410.0410.0000.0000.0000.000
44A77ARG10.8280.87313.136-0.105-0.1050.0000.0000.0000.000
45A78LEU00.0130.03519.2470.0250.0250.0000.0000.0000.000
46A79VAL0-0.063-0.04020.9320.0140.0140.0000.0000.0000.000
47A80LYS10.8610.93322.1180.0030.0030.0000.0000.0000.000
48A81THR0-0.025-0.01919.6490.0130.0130.0000.0000.0000.000
49A82ALA00.0000.02122.8550.0090.0090.0000.0000.0000.000
50A83PRO00.0040.00824.412-0.002-0.0020.0000.0000.0000.000
51A84ALA00.0250.00027.816-0.012-0.0120.0000.0000.0000.000
52A85ASP-1-0.858-0.92629.0640.0120.0120.0000.0000.0000.000
53A86ALA00.0790.02425.007-0.010-0.0100.0000.0000.0000.000
54A87ARG10.9080.98126.170-0.033-0.0330.0000.0000.0000.000
55A88ARG10.8980.93427.187-0.008-0.0080.0000.0000.0000.000
56A89GLY00.0180.01928.381-0.009-0.0090.0000.0000.0000.000
57A90TRP00.0950.01319.498-0.021-0.0210.0000.0000.0000.000
58A91GLN0-0.014-0.00225.383-0.013-0.0130.0000.0000.0000.000
59A92GLU-1-0.790-0.85527.642-0.084-0.0840.0000.0000.0000.000
60A93SER0-0.008-0.01224.464-0.016-0.0160.0000.0000.0000.000
61A94GLN00.0770.04122.258-0.025-0.0250.0000.0000.0000.000
62A95ARG10.8650.92025.8160.0560.0560.0000.0000.0000.000
63A96ARG10.8690.92028.7710.0840.0840.0000.0000.0000.000
64A97TRP00.0270.01621.4710.0020.0020.0000.0000.0000.000
65A98LEU0-0.005-0.00725.586-0.011-0.0110.0000.0000.0000.000
66A99ALA0-0.0150.00027.913-0.002-0.0020.0000.0000.0000.000
67A100TRP0-0.012-0.01823.533-0.007-0.0070.0000.0000.0000.000
68A101ARG10.9010.95224.1850.2620.2620.0000.0000.0000.000
69A102LYS10.7650.87028.0110.1240.1240.0000.0000.0000.000
70A103ASP-1-0.831-0.90931.446-0.126-0.1260.0000.0000.0000.000
71A104GLU-1-0.771-0.86827.364-0.219-0.2190.0000.0000.0000.000
72A105ALA0-0.0120.00029.647-0.009-0.0090.0000.0000.0000.000
73A106HIS00.0340.02330.667-0.003-0.0030.0000.0000.0000.000
74A107LEU0-0.0130.01331.5240.0030.0030.0000.0000.0000.000
75A108VAL00.007-0.00727.873-0.002-0.0020.0000.0000.0000.000
76A109ARG10.8650.93431.0740.1460.1460.0000.0000.0000.000
77A110ALA00.0320.01933.6260.0020.0020.0000.0000.0000.000
78A111VAL0-0.051-0.01531.9470.0050.0050.0000.0000.0000.000
79A112TYR00.014-0.01226.8620.0030.0030.0000.0000.0000.000
80A113GLU-1-0.892-0.93633.545-0.142-0.1420.0000.0000.0000.000
81A114THR0-0.041-0.01036.8610.0070.0070.0000.0000.0000.000
82A115THR0-0.074-0.04734.045-0.001-0.0010.0000.0000.0000.000
83A116GLN00.0550.01236.2740.0030.0030.0000.0000.0000.000
84A117GLY00.0440.02233.9290.0000.0000.0000.0000.0000.000
85A118THR0-0.002-0.01129.527-0.008-0.0080.0000.0000.0000.000
86A119MET00.0260.02227.976-0.020-0.0200.0000.0000.0000.000
87A120TYR00.0570.02227.731-0.021-0.0210.0000.0000.0000.000
88A121ALA00.0160.01428.800-0.010-0.0100.0000.0000.0000.000
89A122MET00.009-0.00122.050-0.006-0.0060.0000.0000.0000.000
90A123ALA00.0140.00923.961-0.030-0.0300.0000.0000.0000.000
91A124SER0-0.0220.00125.198-0.009-0.0090.0000.0000.0000.000
92A125ALA0-0.008-0.01623.138-0.003-0.0030.0000.0000.0000.000
93A126ASP-1-0.859-0.93518.955-0.577-0.5770.0000.0000.0000.000
94A127MET0-0.041-0.01421.011-0.010-0.0100.0000.0000.0000.000
95A128ARG10.7890.88423.3100.3060.3060.0000.0000.0000.000
96A129LEU0-0.049-0.02015.8940.0060.0060.0000.0000.0000.000
97A130GLN00.0260.00215.638-0.074-0.0740.0000.0000.0000.000
98A131PRO00.0330.01817.663-0.012-0.0120.0000.0000.0000.000
99A132VAL0-0.059-0.01817.9970.0280.0280.0000.0000.0000.000
100A133ARG10.8410.90510.0261.3181.3180.0000.0000.0000.000
101A134GLU-1-0.897-0.95814.166-0.512-0.5120.0000.0000.0000.000
102A135ARG10.8220.91315.8310.2260.2260.0000.0000.0000.000
103A136ALA00.0210.00614.2470.0480.0480.0000.0000.0000.000
104A137LEU0-0.021-0.0099.2150.0520.0520.0000.0000.0000.000
105A138ALA00.0140.00812.6030.0790.0790.0000.0000.0000.000
106A139LEU0-0.048-0.02315.6220.0670.0670.0000.0000.0000.000
107A140ARG10.7580.8508.1390.6270.6270.0000.0000.0000.000
108A141GLY00.0460.03313.1070.0850.0850.0000.0000.0000.000
109A142ALA0-0.0160.01213.8510.0420.0420.0000.0000.0000.000
110A143ALA0-0.001-0.01315.9940.0380.0380.0000.0000.0000.000
111A144ASP-1-0.772-0.86112.4180.2890.2890.0000.0000.0000.000
112A145ARG10.7530.87014.9440.1000.1000.0000.0000.0000.000
113A146TYR0-0.025-0.02617.0950.0010.0010.0000.0000.0000.000
114A147ALA0-0.0190.00316.9730.0020.0020.0000.0000.0000.000
115A148GLN0-0.025-0.00815.0430.0400.0400.0000.0000.0000.000
116A149PRO00.031-0.00518.953-0.043-0.0430.0000.0000.0000.000
117A150GLY0-0.0100.00422.0900.0020.0020.0000.0000.0000.000
118A151GLY00.0400.02420.842-0.023-0.0230.0000.0000.0000.000
119A152GLY00.0200.01021.861-0.023-0.0230.0000.0000.0000.000
120A153LYS10.9070.94124.358-0.133-0.1330.0000.0000.0000.000
121A154GLY00.0120.00925.4480.0020.0020.0000.0000.0000.000
122A155ALA0-0.0180.00224.167-0.011-0.0110.0000.0000.0000.000
123A156VAL0-0.0080.00525.162-0.016-0.0160.0000.0000.0000.000
124A157HIS10.8250.91125.7400.0640.0640.0000.0000.0000.000
125A158ARG10.9090.94729.7420.0240.0240.0000.0000.0000.000
126A159VAL00.0910.05031.406-0.002-0.0020.0000.0000.0000.000
127A160ARG10.9720.98830.5520.0490.0490.0000.0000.0000.000
128A161PRO00.0470.00932.766-0.007-0.0070.0000.0000.0000.000
129A162CYS0-0.0230.00027.730-0.012-0.0120.0000.0000.0000.000
130A163MET00.1040.05632.3970.0000.0000.0000.0000.0000.000
131A164ARG10.8340.90933.7250.0510.0510.0000.0000.0000.000
132A165ASP-1-0.818-0.90627.687-0.113-0.1130.0000.0000.0000.000
133A166ALA00.0320.02430.769-0.005-0.0050.0000.0000.0000.000
134A167ALA00.0070.00825.579-0.008-0.0080.0000.0000.0000.000
135A169GLU-1-0.860-0.94628.602-0.104-0.1040.0000.0000.0000.000
136A170HIS0-0.021-0.00928.6650.0070.0070.0000.0000.0000.000
137A171ALA00.0130.00626.578-0.006-0.0060.0000.0000.0000.000
138A172LEU00.009-0.00528.452-0.007-0.0070.0000.0000.0000.000
139A173PHE00.0060.00631.3130.0020.0020.0000.0000.0000.000
140A174ASP-1-0.768-0.87929.823-0.170-0.1700.0000.0000.0000.000
141A175MET0-0.057-0.00429.345-0.006-0.0060.0000.0000.0000.000
142A176ASN00.000-0.01930.9070.0010.0010.0000.0000.0000.000
143A177ARG10.8350.91231.5410.1650.1650.0000.0000.0000.000
144A178TYR0-0.028-0.03130.4910.0010.0010.0000.0000.0000.000
145A179TYR00.0110.01433.4120.0010.0010.0000.0000.0000.000
146A180GLU-1-0.758-0.85934.819-0.109-0.1090.0000.0000.0000.000
147A181LYS10.8190.93233.5390.1790.1790.0000.0000.0000.000
148A182LEU00.000-0.01232.9530.0010.0010.0000.0000.0000.000
149A183ARG10.8370.88836.4010.1120.1120.0000.0000.0000.000
150A184ALA0-0.015-0.00839.3000.0050.0050.0000.0000.0000.000
151A185ARG10.8860.93336.3130.1520.1520.0000.0000.0000.000
152A186MET0-0.031-0.00237.238-0.002-0.0020.0000.0000.0000.000
153A187PRO00.0700.03540.1780.0060.0060.0000.0000.0000.000
154A188ALA0-0.025-0.02042.989-0.002-0.0020.0000.0000.0000.000
155A189ASP-1-0.882-0.93644.488-0.097-0.0970.0000.0000.0000.000
156A190SER00.0300.01239.6260.0010.0010.0000.0000.0000.000
157A191ARG10.8970.96739.7560.1010.1010.0000.0000.0000.000
158A192GLN00.0500.01339.943-0.005-0.0050.0000.0000.0000.000
159A193THR0-0.028-0.02436.340-0.004-0.0040.0000.0000.0000.000
160A194LEU00.0200.02234.271-0.005-0.0050.0000.0000.0000.000
161A195VAL0-0.034-0.02135.761-0.003-0.0030.0000.0000.0000.000
162A196ALA0-0.029-0.01337.1160.0010.0010.0000.0000.0000.000
163A197ALA00.0690.03131.7580.0000.0000.0000.0000.0000.000
164A198GLN00.0080.00831.242-0.018-0.0180.0000.0000.0000.000
165A199ARG10.9660.99633.1930.1040.1040.0000.0000.0000.000
166A200GLU-1-0.869-0.93232.196-0.120-0.1200.0000.0000.0000.000
167A201TRP00.0370.00525.5550.0090.0090.0000.0000.0000.000
168A202ALA00.0010.00729.290-0.003-0.0030.0000.0000.0000.000
169A203ALA00.0210.00931.1560.0040.0040.0000.0000.0000.000
170A204PHE0-0.023-0.02022.4030.0060.0060.0000.0000.0000.000
171A205SER00.0290.01426.750-0.002-0.0020.0000.0000.0000.000
172A206ASP-1-0.928-0.96127.830-0.097-0.0970.0000.0000.0000.000
173A207ALA0-0.057-0.04028.6490.0100.0100.0000.0000.0000.000
174A208MET00.0080.00820.8030.0120.0120.0000.0000.0000.000
175A209THR0-0.016-0.00225.2810.0070.0070.0000.0000.0000.000
176A210PRO0-0.069-0.04326.9110.0060.0060.0000.0000.0000.000
177A211LEU0-0.036-0.00924.0580.0170.0170.0000.0000.0000.000
178A212VAL0-0.0060.02420.4610.0070.0070.0000.0000.0000.000
179A213SER0-0.035-0.04519.7540.0080.0080.0000.0000.0000.000
180A214GLU-1-0.846-0.93022.431-0.107-0.1070.0000.0000.0000.000
181A215GLY00.0330.02220.600-0.010-0.0100.0000.0000.0000.000
182A216GLU-1-0.680-0.79617.571-0.157-0.1570.0000.0000.0000.000
183A217ARG10.7920.88520.0660.0890.0890.0000.0000.0000.000
184A218VAL00.0170.00422.905-0.007-0.0070.0000.0000.0000.000
185A219ASP-1-0.884-0.93817.918-0.354-0.3540.0000.0000.0000.000
186A220LEU0-0.057-0.03020.658-0.019-0.0190.0000.0000.0000.000
187A221ILE0-0.017-0.00722.4360.0000.0000.0000.0000.0000.000
188A222GLY00.0340.01722.6400.0020.0020.0000.0000.0000.000
189A223ALA00.0480.02120.416-0.006-0.0060.0000.0000.0000.000
190A224ARG10.7720.86922.1880.2120.2120.0000.0000.0000.000
191A225VAL0-0.012-0.00925.7290.0090.0090.0000.0000.0000.000
192A226ALA0-0.0010.00022.8880.0080.0080.0000.0000.0000.000
193A227THR0-0.052-0.03224.204-0.001-0.0010.0000.0000.0000.000
194A228LEU00.0110.00326.1010.0100.0100.0000.0000.0000.000
195A229LYS10.8570.92027.2030.2500.2500.0000.0000.0000.000
196A230ARG10.9991.01322.3730.3700.3700.0000.0000.0000.000
197A231PHE00.0380.01628.1840.0100.0100.0000.0000.0000.000
198A232SER0-0.015-0.00631.3010.0140.0140.0000.0000.0000.000
199A233GLU-1-0.887-0.94429.984-0.204-0.2040.0000.0000.0000.000
200A234THR0-0.067-0.02830.548-0.008-0.0080.0000.0000.0000.000
201A235VAL0-0.031-0.01133.0170.0050.0050.0000.0000.0000.000
202A236ASN0-0.037-0.01736.1390.0070.0070.0000.0000.0000.000
203A237ASN0-0.026-0.01039.4080.0110.0110.0000.0000.0000.000