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: R8MN8

Calculation Name: 2ZSK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZSK

Chain ID: A

ChEMBL ID:

UniProt ID: O59384

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:


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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2891575.483605
FMO2-HF: Nuclear repulsion 2801843.510749
FMO2-HF: Total energy -89731.972857
FMO2-MP2: Total energy -89997.674069


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-18.062-9.9979.235-5.544-11.754-0.029
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : 0.006
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].
3A3LYS10.9170.9653.6542.0574.130-0.003-0.982-1.0870.005
4A4ILE00.0350.0205.6780.2870.2870.0000.0000.0000.000
5A5GLY00.0160.0057.8760.1460.1460.0000.0000.0000.000
6A6ILE0-0.014-0.00411.5730.0200.0200.0000.0000.0000.000
7A7ILE00.0090.00214.3980.0160.0160.0000.0000.0000.000
8A8GLY00.0700.01518.0470.0210.0210.0000.0000.0000.000
9A9GLY00.0060.00020.147-0.017-0.0170.0000.0000.0000.000
10A10THR0-0.074-0.02123.023-0.001-0.0010.0000.0000.0000.000
11A11THR0-0.019-0.00824.8870.0050.0050.0000.0000.0000.000
12A12PRO00.017-0.02023.5500.0060.0060.0000.0000.0000.000
13A13GLU-1-0.814-0.90423.2710.0510.0510.0000.0000.0000.000
14A14SER0-0.005-0.00821.9990.0240.0240.0000.0000.0000.000
15A15THR00.020-0.00218.1390.0040.0040.0000.0000.0000.000
16A16LEU0-0.044-0.02218.7940.0340.0340.0000.0000.0000.000
17A17TYR0-0.071-0.06919.9100.0460.0460.0000.0000.0000.000
18A18TYR00.029-0.01515.2410.0380.0380.0000.0000.0000.000
19A19TYR00.0210.01513.4810.0670.0670.0000.0000.0000.000
20A20LYS10.9430.97715.271-0.164-0.1640.0000.0000.0000.000
21A21LYS10.8550.94115.831-0.191-0.1910.0000.0000.0000.000
22A22TYR00.005-0.0338.295-0.080-0.0800.0000.0000.0000.000
23A23ILE0-0.062-0.02811.1870.1900.1900.0000.0000.0000.000
24A24GLU-1-0.923-0.98212.4180.3680.3680.0000.0000.0000.000
25A25ILE00.0520.0239.3270.0250.0250.0000.0000.0000.000
26A26SER00.000-0.0077.8550.2170.2170.0000.0000.0000.000
27A27ARG10.8270.9058.491-0.575-0.5750.0000.0000.0000.000
28A28GLU-1-0.910-0.93611.1540.3020.3020.0000.0000.0000.000
29A29LYS10.9150.9935.308-0.213-0.2130.0000.0000.0000.000
30A30PHE0-0.023-0.0212.770-0.8280.0950.263-0.315-0.871-0.003
31A31GLU-1-0.910-0.9446.5940.9170.9170.0000.0000.0000.000
32A32LYS10.9120.9498.860-0.416-0.4160.0000.0000.0000.000
33A33TYR0-0.040-0.04810.840-0.021-0.0210.0000.0000.0000.000
34A34PHE00.0100.0202.761-2.034-2.8064.348-0.890-2.6860.005
35A35TYR00.0130.0107.448-0.415-0.4150.0000.0000.0000.000
36A36PRO00.0240.0433.345-0.7430.0810.398-0.299-0.9220.002
37A37GLU-1-0.882-0.9334.577-2.628-2.5180.001-0.029-0.0820.000
38A38LEU0-0.012-0.0056.333-0.412-0.4120.0000.0000.0000.000
39A39ILE0-0.037-0.0139.0710.0430.0430.0000.0000.0000.000
40A40ILE00.002-0.00812.086-0.017-0.0170.0000.0000.0000.000
41A41TYR00.0120.01115.3400.0000.0000.0000.0000.0000.000
42A42SER0-0.020-0.01318.5450.0020.0020.0000.0000.0000.000
43A43ILE0-0.0100.00721.409-0.001-0.0010.0000.0000.0000.000
44A44ASN00.0560.01024.3920.0210.0210.0000.0000.0000.000
45A45PHE00.0700.02727.561-0.007-0.0070.0000.0000.0000.000
46A46LYS10.9871.01028.8610.0220.0220.0000.0000.0000.000
47A47GLU-1-0.966-0.98530.717-0.061-0.0610.0000.0000.0000.000
48A48PHE0-0.0060.00226.581-0.008-0.0080.0000.0000.0000.000
49A49PHE0-0.003-0.01330.191-0.003-0.0030.0000.0000.0000.000
50A50GLN0-0.034-0.02032.1730.0000.0000.0000.0000.0000.000
51A51ASN00.0250.02931.9550.0010.0010.0000.0000.0000.000
52A52PRO00.004-0.00635.0420.0010.0010.0000.0000.0000.000
53A53GLU-1-0.914-0.95935.172-0.087-0.0870.0000.0000.0000.000
54A54GLY00.0200.01135.428-0.005-0.0050.0000.0000.0000.000
55A55TRP00.021-0.02927.720-0.004-0.0040.0000.0000.0000.000
56A56GLU-1-0.916-0.94531.118-0.130-0.1300.0000.0000.0000.000
57A57GLY00.0540.03231.953-0.008-0.0080.0000.0000.0000.000
58A58ARG10.7750.89028.5780.0630.0630.0000.0000.0000.000
59A59LYS10.9660.98926.8350.1240.1240.0000.0000.0000.000
60A60LYS10.9981.00326.3040.1120.1120.0000.0000.0000.000
61A61ILE0-0.021-0.00125.338-0.015-0.0150.0000.0000.0000.000
62A62LEU0-0.013-0.00322.504-0.010-0.0100.0000.0000.0000.000
63A63ILE00.0600.03721.663-0.025-0.0250.0000.0000.0000.000
64A64ASN0-0.086-0.03621.919-0.027-0.0270.0000.0000.0000.000
65A65ALA00.0250.01020.113-0.019-0.0190.0000.0000.0000.000
66A66ALA00.0270.01617.627-0.030-0.0300.0000.0000.0000.000
67A67LYS11.0170.99817.2710.2240.2240.0000.0000.0000.000
68A68ALA0-0.096-0.03718.508-0.035-0.0350.0000.0000.0000.000
69A69LEU0-0.004-0.01413.844-0.029-0.0290.0000.0000.0000.000
70A70GLU-1-0.836-0.92413.948-0.656-0.6560.0000.0000.0000.000
71A71ARG10.8760.93814.3820.2390.2390.0000.0000.0000.000
72A72ALA0-0.069-0.02214.2690.0110.0110.0000.0000.0000.000
73A73GLY0-0.012-0.00410.709-0.013-0.0130.0000.0000.0000.000
74A74ALA0-0.051-0.0179.509-0.380-0.3800.0000.0000.0000.000
75A75GLU-1-0.822-0.9225.905-4.333-4.3330.0000.0000.0000.000
76A76LEU0-0.015-0.0107.7090.0890.0890.0000.0000.0000.000
77A77ILE00.0270.0259.9620.1210.1210.0000.0000.0000.000
78A78ALA00.0230.01112.9970.0230.0230.0000.0000.0000.000
79A79PHE00.0190.01315.1670.0170.0170.0000.0000.0000.000
80A80ALA00.0450.02317.2920.0160.0160.0000.0000.0000.000
81A81ALA0-0.003-0.02018.7810.0190.0190.0000.0000.0000.000
82A82ASN00.0440.02422.162-0.020-0.0200.0000.0000.0000.000
83A83THR00.0320.01224.695-0.014-0.0140.0000.0000.0000.000
84A84PRO00.0290.00923.040-0.007-0.0070.0000.0000.0000.000
85A85HIS00.013-0.00120.177-0.032-0.0320.0000.0000.0000.000
86A86LEU0-0.072-0.01924.370-0.004-0.0040.0000.0000.0000.000
87A87VAL0-0.025-0.00925.7090.0010.0010.0000.0000.0000.000
88A88PHE00.017-0.00318.262-0.012-0.0120.0000.0000.0000.000
89A89ASP-1-0.830-0.89922.851-0.187-0.1870.0000.0000.0000.000
90A90ASP-1-0.941-1.01824.780-0.170-0.1700.0000.0000.0000.000
91A91VAL0-0.035-0.02820.732-0.010-0.0100.0000.0000.0000.000
92A92GLN00.060-0.00517.347-0.029-0.0290.0000.0000.0000.000
93A93ARG10.8350.96321.0370.1670.1670.0000.0000.0000.000
94A94GLU-1-0.975-0.98423.294-0.241-0.2410.0000.0000.0000.000
95A95VAL0-0.077-0.02316.980-0.013-0.0130.0000.0000.0000.000
96A96ASN0-0.042-0.00217.9190.0090.0090.0000.0000.0000.000
97A97VAL0-0.026-0.01812.312-0.103-0.1030.0000.0000.0000.000
98A98PRO0-0.049-0.01711.8390.0840.0840.0000.0000.0000.000
99A99MET00.0010.01713.327-0.048-0.0480.0000.0000.0000.000
100A100VAL00.0270.00712.0740.0180.0180.0000.0000.0000.000
101A101SER00.0190.00615.0960.0510.0510.0000.0000.0000.000
102A102ILE00.0080.00018.3240.0060.0060.0000.0000.0000.000
103A103ILE00.0220.00319.4110.0160.0160.0000.0000.0000.000
104A104ASP-1-0.893-0.95619.050-0.180-0.1800.0000.0000.0000.000
105A105ALA0-0.026-0.01016.7620.0050.0050.0000.0000.0000.000
106A106VAL0-0.022-0.00718.3870.0190.0190.0000.0000.0000.000
107A107ALA00.0460.01921.4380.0100.0100.0000.0000.0000.000
108A108GLU-1-0.885-0.91716.529-0.159-0.1590.0000.0000.0000.000
109A109GLU-1-0.841-0.93817.7230.0360.0360.0000.0000.0000.000
110A110ILE0-0.024-0.01820.2540.0090.0090.0000.0000.0000.000
111A111LEU0-0.034-0.01723.5150.0050.0050.0000.0000.0000.000
112A112LYS10.9110.96515.8830.0140.0140.0000.0000.0000.000
113A113ARG10.7300.84320.415-0.047-0.0470.0000.0000.0000.000
114A114GLY0-0.058-0.02023.8420.0050.0050.0000.0000.0000.000
115A115VAL0-0.0010.01826.7230.0000.0000.0000.0000.0000.000
116A116ARG10.8230.88427.0230.0280.0280.0000.0000.0000.000
117A117LYS10.8900.96430.7970.0080.0080.0000.0000.0000.000
118A118VAL0-0.012-0.00728.3780.0060.0060.0000.0000.0000.000
119A119LEU00.0370.01831.795-0.003-0.0030.0000.0000.0000.000
120A120LEU0-0.024-0.00729.1280.0050.0050.0000.0000.0000.000
121A121LEU00.026-0.01430.8480.0000.0000.0000.0000.0000.000
122A122GLY00.012-0.01730.2110.0010.0010.0000.0000.0000.000
123A123THR00.0260.01631.380-0.002-0.0020.0000.0000.0000.000
124A124LYS10.9230.92733.5430.0010.0010.0000.0000.0000.000
125A125THR0-0.0120.00232.345-0.003-0.0030.0000.0000.0000.000
126A126THR0-0.028-0.01728.762-0.003-0.0030.0000.0000.0000.000
127A127MET0-0.0800.00531.452-0.002-0.0020.0000.0000.0000.000
128A128THR0-0.004-0.01834.074-0.002-0.0020.0000.0000.0000.000
129A129ALA0-0.0120.01230.930-0.004-0.0040.0000.0000.0000.000
130A130ASP-1-0.855-0.92832.374-0.048-0.0480.0000.0000.0000.000
131A131PHE0-0.004-0.01126.558-0.001-0.0010.0000.0000.0000.000
132A132TYR0-0.0200.01524.255-0.004-0.0040.0000.0000.0000.000
133A133ILE00.0610.01629.198-0.002-0.0020.0000.0000.0000.000
134A134LYS10.9050.95431.7800.0840.0840.0000.0000.0000.000
135A135THR0-0.057-0.05326.042-0.007-0.0070.0000.0000.0000.000
136A136LEU0-0.029-0.01725.841-0.007-0.0070.0000.0000.0000.000
137A137GLU-1-0.842-0.92128.300-0.045-0.0450.0000.0000.0000.000
138A138GLU-1-0.929-0.94929.821-0.098-0.0980.0000.0000.0000.000
139A139LYS10.8430.92922.7020.1450.1450.0000.0000.0000.000
140A140GLY0-0.062-0.02127.979-0.002-0.0020.0000.0000.0000.000
141A141LEU0-0.075-0.03326.4100.0060.0060.0000.0000.0000.000
142A142GLU-1-0.911-0.94630.969-0.027-0.0270.0000.0000.0000.000
143A143VAL0-0.058-0.04630.8880.0060.0060.0000.0000.0000.000
144A144VAL00.0400.04633.699-0.001-0.0010.0000.0000.0000.000
145A145VAL0-0.023-0.03434.9470.0030.0030.0000.0000.0000.000
146A146PRO00.0160.01536.4720.0000.0000.0000.0000.0000.000
147A147ASN00.0700.05139.684-0.003-0.0030.0000.0000.0000.000
148A148ASP-1-0.876-0.96542.225-0.011-0.0110.0000.0000.0000.000
149A149GLU-1-0.986-0.98943.3750.0080.0080.0000.0000.0000.000
150A150GLU-1-0.717-0.86840.9280.0090.0090.0000.0000.0000.000
151A151LYS10.8010.90138.2030.0140.0140.0000.0000.0000.000
152A152GLU-1-0.859-0.91239.0500.0010.0010.0000.0000.0000.000
153A153GLU-1-0.764-0.85041.0560.0230.0230.0000.0000.0000.000
154A154LEU0-0.013-0.00734.1300.0040.0040.0000.0000.0000.000
155A155ASN00.0410.00536.2650.0020.0020.0000.0000.0000.000
156A156ARG10.7680.86637.175-0.023-0.0230.0000.0000.0000.000
157A157ILE0-0.0130.00536.0330.0040.0040.0000.0000.0000.000
158A158ILE0-0.033-0.01831.9640.0050.0050.0000.0000.0000.000
159A159PHE0-0.049-0.02934.1750.0040.0040.0000.0000.0000.000
160A160GLU-1-0.911-0.97236.1120.0240.0240.0000.0000.0000.000
161A161GLU-1-0.889-0.92437.3150.0400.0400.0000.0000.0000.000
162A162LEU0-0.021-0.01431.6890.0050.0050.0000.0000.0000.000
163A163ALA00.0560.05631.8320.0080.0080.0000.0000.0000.000
164A164PHE0-0.098-0.05232.7740.0030.0030.0000.0000.0000.000
165A165GLY0-0.039-0.01231.9490.0050.0050.0000.0000.0000.000
166A166ASN0-0.048-0.01832.8460.0030.0030.0000.0000.0000.000
167A167LEU00.039-0.00231.546-0.003-0.0030.0000.0000.0000.000
168A168LYS10.9310.96835.586-0.041-0.0410.0000.0000.0000.000
169A169ASN0-0.053-0.03938.479-0.003-0.0030.0000.0000.0000.000
170A170LYS10.9740.98832.140-0.080-0.0800.0000.0000.0000.000
171A171GLU-1-0.895-0.95536.3760.0400.0400.0000.0000.0000.000
172A172TRP00.001-0.01138.383-0.002-0.0020.0000.0000.0000.000
173A173ILE00.0190.00633.475-0.003-0.0030.0000.0000.0000.000
174A174VAL00.0140.01134.375-0.002-0.0020.0000.0000.0000.000
175A175ARG10.9330.96636.308-0.033-0.0330.0000.0000.0000.000
176A176LEU0-0.0380.00836.315-0.003-0.0030.0000.0000.0000.000
177A177ILE00.029-0.00832.067-0.004-0.0040.0000.0000.0000.000
178A178GLU-1-0.783-0.86835.6740.0310.0310.0000.0000.0000.000
179A179LYS10.8710.94738.156-0.010-0.0100.0000.0000.0000.000
180A180TYR0-0.042-0.06037.611-0.003-0.0030.0000.0000.0000.000
181A181ARG10.9340.99135.112-0.026-0.0260.0000.0000.0000.000
182A182GLU-1-1.008-1.00837.9950.0080.0080.0000.0000.0000.000
183A183SER0-0.0320.00441.522-0.002-0.0020.0000.0000.0000.000
184A184GLU-1-0.976-1.00539.455-0.012-0.0120.0000.0000.0000.000
185A185GLY00.0390.03238.778-0.003-0.0030.0000.0000.0000.000
186A186ILE0-0.059-0.00633.920-0.002-0.0020.0000.0000.0000.000
187A187GLU-1-0.798-0.90331.459-0.006-0.0060.0000.0000.0000.000
188A188GLY00.019-0.01729.2090.0050.0050.0000.0000.0000.000
189A189VAL0-0.020-0.00128.774-0.005-0.0050.0000.0000.0000.000
190A190ILE00.0160.00825.8200.0060.0060.0000.0000.0000.000
191A191LEU0-0.025-0.00425.335-0.002-0.0020.0000.0000.0000.000
192A192GLY00.0300.00325.5400.0040.0040.0000.0000.0000.000
193A193CYS0-0.075-0.03226.241-0.006-0.0060.0000.0000.0000.000
194A194THR00.0410.00822.5780.0010.0010.0000.0000.0000.000
195A195GLU-1-0.876-0.94025.1300.0780.0780.0000.0000.0000.000
196A196LEU00.021-0.00628.5450.0050.0050.0000.0000.0000.000
197A197PRO00.0190.02623.8720.0010.0010.0000.0000.0000.000
198A198LEU0-0.037-0.02125.6370.0130.0130.0000.0000.0000.000
199A199ALA0-0.045-0.02327.7830.0020.0020.0000.0000.0000.000
200A200ILE0-0.012-0.00728.531-0.002-0.0020.0000.0000.0000.000
201A201LYS10.8480.92325.029-0.111-0.1110.0000.0000.0000.000
202A202GLN00.0840.01424.015-0.009-0.0090.0000.0000.0000.000
203A203GLY0-0.037-0.00726.122-0.007-0.0070.0000.0000.0000.000
204A204ASP-1-0.879-0.93028.8030.0840.0840.0000.0000.0000.000
205A205VAL0-0.039-0.01930.401-0.005-0.0050.0000.0000.0000.000
206A206SER0-0.121-0.08231.6100.0020.0020.0000.0000.0000.000
207A207VAL0-0.065-0.01130.736-0.003-0.0030.0000.0000.0000.000
208A208GLU-1-0.785-0.88224.7680.0580.0580.0000.0000.0000.000
209A209VAL0-0.023-0.00324.816-0.006-0.0060.0000.0000.0000.000
210A210PHE0-0.012-0.00322.4200.0100.0100.0000.0000.0000.000
211A211ASP-1-0.748-0.86020.7610.1180.1180.0000.0000.0000.000
212A212SER00.0360.01420.3770.0080.0080.0000.0000.0000.000
213A213ALA00.0320.00819.196-0.006-0.0060.0000.0000.0000.000
214A214GLU-1-0.918-0.95316.2390.2290.2290.0000.0000.0000.000
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