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: G6NY1

Calculation Name: 2ZIW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZIW

Chain ID: B

ChEMBL ID:

UniProt ID: Q96AY2

Base Structure: X-ray

Registration Date: 2023-06-21

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2395396.818767
FMO2-HF: Nuclear repulsion 2303283.431712
FMO2-HF: Total energy -92113.387056
FMO2-MP2: Total energy -92379.656173


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(B:250:LYS)


Summations of interaction energy for fragment #1(B:250:LYS)
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.
-199.095-199.05630.595-12.929-17.707-0.135
Interaction energy analysis for fragmet #1(B:250:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.877
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].
3B252ILE00.0040.0213.5453.8176.728-0.016-1.262-1.632-0.001
4B253ILE0-0.013-0.0235.624-5.365-5.3650.0000.0000.0000.000
5B254VAL00.0140.0054.751-0.800-0.721-0.001-0.001-0.0760.000
6B255VAL0-0.024-0.0017.6500.3610.3610.0000.0000.0000.000
7B256LEU00.0290.0068.8340.0040.0040.0000.0000.0000.000
8B257ASP-1-0.744-0.89612.404-15.468-15.4680.0000.0000.0000.000
9B258PRO0-0.004-0.00216.102-0.080-0.0800.0000.0000.0000.000
10B259VAL00.0230.00018.416-0.007-0.0070.0000.0000.0000.000
11B260LEU00.0150.00813.1600.2050.2050.0000.0000.0000.000
12B261LEU0-0.040-0.02812.395-0.196-0.1960.0000.0000.0000.000
13B262GLN0-0.084-0.02716.2730.2610.2610.0000.0000.0000.000
14B263MET0-0.0080.01317.1961.1361.1360.0000.0000.0000.000
15B264GLU-1-0.932-0.97319.244-13.691-13.6910.0000.0000.0000.000
16B265GLY00.0340.02417.1110.0720.0720.0000.0000.0000.000
17B266GLY0-0.045-0.01614.772-1.595-1.5950.0000.0000.0000.000
18B267GLY00.0180.00213.803-1.324-1.3240.0000.0000.0000.000
19B268GLN0-0.008-0.01513.594-1.152-1.1520.0000.0000.0000.000
20B269LEU00.0020.0039.312-1.997-1.9970.0000.0000.0000.000
21B270LEU00.0390.0189.070-3.761-3.7610.0000.0000.0000.000
22B271GLY00.0080.0059.224-2.095-2.0950.0000.0000.0000.000
23B272ALA0-0.020-0.0107.880-1.367-1.3670.0000.0000.0000.000
24B273LEU00.015-0.0184.411-6.559-6.460-0.001-0.009-0.0890.000
25B274GLN00.0180.0064.767-6.116-6.071-0.001-0.005-0.0390.000
26B275THR0-0.0430.0066.7491.4251.4250.0000.0000.0000.000
27B276MET0-0.094-0.0232.343-17.899-22.50313.599-4.676-4.320-0.061
28B277GLU-1-0.785-0.8952.493-48.008-45.9670.650-0.808-1.884-0.008
29B278CYS0-0.100-0.0272.285-17.689-22.28212.738-4.105-4.041-0.047
30B279ARG10.8910.9474.09839.70039.8630.002-0.047-0.1190.000
31B280CYS0-0.044-0.0196.9361.1401.1400.0000.0000.0000.000
32B281VAL00.0320.0368.8342.3842.3840.0000.0000.0000.000
33B282ILE00.0020.00412.289-0.593-0.5930.0000.0000.0000.000
34B283GLU-1-0.870-0.92114.725-18.182-18.1820.0000.0000.0000.000
35B284ALA00.0090.00317.326-0.293-0.2930.0000.0000.0000.000
36B285GLN0-0.0020.00515.158-0.909-0.9090.0000.0000.0000.000
37B286ALA0-0.023-0.00918.8230.7030.7030.0000.0000.0000.000
38B287VAL0-0.028-0.01119.3270.8600.8600.0000.0000.0000.000
39B288PRO00.0320.01719.381-0.775-0.7750.0000.0000.0000.000
40B289CYS0-0.041-0.00717.450-0.128-0.1280.0000.0000.0000.000
41B290SER00.013-0.01915.398-0.362-0.3620.0000.0000.0000.000
42B291VAL0-0.030-0.0048.905-0.181-0.1810.0000.0000.0000.000
43B292THR00.0120.00311.688-0.127-0.1270.0000.0000.0000.000
44B293TRP00.002-0.0275.648-1.013-1.0130.0000.0000.0000.000
45B294ARG10.7530.8628.74520.99320.9930.0000.0000.0000.000
46B307VAL0-0.030-0.0407.5840.7970.7970.0000.0000.0000.000
47B308GLU-1-0.882-0.9208.538-19.709-19.7090.0000.0000.0000.000
48B309GLU-1-0.900-0.96010.242-21.148-21.1480.0000.0000.0000.000
49B310PRO0-0.0260.0008.9751.2121.2120.0000.0000.0000.000
50B311THR0-0.016-0.01112.1270.4670.4670.0000.0000.0000.000
51B312VAL0-0.066-0.03811.417-1.145-1.1450.0000.0000.0000.000
52B313LEU00.0210.00813.7020.0270.0270.0000.0000.0000.000
53B314VAL0-0.0090.02411.1711.1941.1940.0000.0000.0000.000
54B315LEU0-0.022-0.01814.0210.3770.3770.0000.0000.0000.000
55B316LEU00.0420.00813.937-0.185-0.1850.0000.0000.0000.000
56B317ARG10.9010.97017.94912.66112.6610.0000.0000.0000.000
57B318ALA00.0740.03621.334-0.279-0.2790.0000.0000.0000.000
58B319GLU-1-0.868-0.91823.384-11.237-11.2370.0000.0000.0000.000
59B349ASP-1-0.833-0.91426.310-10.958-10.9580.0000.0000.0000.000
60B350ILE00.022-0.00626.205-0.430-0.4300.0000.0000.0000.000
61B351THR0-0.001-0.00427.385-0.218-0.2180.0000.0000.0000.000
62B352ALA00.0470.03121.920-0.162-0.1620.0000.0000.0000.000
63B353LYS10.8980.95322.63312.64512.6450.0000.0000.0000.000
64B354THR0-0.117-0.08424.2830.1230.1230.0000.0000.0000.000
65B355ALA0-0.016-0.02324.3120.0090.0090.0000.0000.0000.000
66B356GLY00.0410.04321.133-0.151-0.1510.0000.0000.0000.000
67B357LYS10.8870.97021.50411.61911.6190.0000.0000.0000.000
68B358ALA0-0.033-0.04320.709-0.162-0.1620.0000.0000.0000.000
69B359LEU00.0320.00718.437-0.594-0.5940.0000.0000.0000.000
70B360SER0-0.0050.01418.209-0.927-0.9270.0000.0000.0000.000
71B361LEU00.0130.01015.443-0.876-0.8760.0000.0000.0000.000
72B362VAL00.007-0.00316.200-1.101-1.1010.0000.0000.0000.000
73B363ILE00.0110.00613.7590.5750.5750.0000.0000.0000.000
74B364VAL0-0.057-0.04516.546-0.380-0.3800.0000.0000.0000.000
75B365ASP-1-0.795-0.89514.979-20.261-20.2610.0000.0000.0000.000
76B366GLN0-0.048-0.02717.1640.4720.4720.0000.0000.0000.000
77B367GLU-1-0.676-0.84817.442-17.777-17.7770.0000.0000.0000.000
78B368LYS10.7800.86820.29813.31913.3190.0000.0000.0000.000
79B404SER00.010-0.00735.419-0.069-0.0690.0000.0000.0000.000
80B405ARG10.8470.91727.88810.72410.7240.0000.0000.0000.000
81B406VAL00.0410.00731.551-0.274-0.2740.0000.0000.0000.000
82B407ASP-1-0.859-0.92133.208-9.082-9.0820.0000.0000.0000.000
83B408ALA0-0.062-0.03428.303-0.204-0.2040.0000.0000.0000.000
84B409GLU-1-0.818-0.90629.035-10.658-10.6580.0000.0000.0000.000
85B410GLU-1-0.919-0.96130.024-8.950-8.9500.0000.0000.0000.000
86B411ALA00.0370.03229.895-0.049-0.0490.0000.0000.0000.000
87B412LEU00.0060.00624.218-0.220-0.2200.0000.0000.0000.000
88B413VAL0-0.033-0.02827.393-0.206-0.2060.0000.0000.0000.000
89B414ASP-1-0.908-0.96929.607-9.599-9.5990.0000.0000.0000.000
90B415LEU0-0.039-0.01323.940-0.070-0.0700.0000.0000.0000.000
91B416GLN0-0.054-0.03725.211-0.244-0.2440.0000.0000.0000.000
92B417LEU0-0.070-0.02126.6350.0320.0320.0000.0000.0000.000
93B418HIS0-0.079-0.02829.1880.5100.5100.0000.0000.0000.000
94B419THR0-0.111-0.05924.180-0.055-0.0550.0000.0000.0000.000
95B420GLU-1-0.865-0.92522.239-12.886-12.8860.0000.0000.0000.000
96B421ALA0-0.028-0.00420.820-0.787-0.7870.0000.0000.0000.000
97B422GLN0-0.0160.00217.1920.3290.3290.0000.0000.0000.000
98B423ALA0-0.001-0.01819.575-0.147-0.1470.0000.0000.0000.000
99B424GLN0-0.058-0.00714.8801.1381.1380.0000.0000.0000.000
100B425ILE0-0.010-0.02019.5880.0350.0350.0000.0000.0000.000
101B426VAL0-0.0160.01016.045-0.142-0.1420.0000.0000.0000.000
102B427GLN0-0.022-0.02619.3480.8570.8570.0000.0000.0000.000
103B428SER0-0.079-0.06218.1120.1270.1270.0000.0000.0000.000
104B429TRP00.0340.05216.243-0.332-0.3320.0000.0000.0000.000
105B430LYS10.7940.86712.12722.19922.1990.0000.0000.0000.000
106B431GLU-1-0.811-0.88413.189-18.760-18.7600.0000.0000.0000.000
107B432LEU00.0450.03912.346-2.220-2.2200.0000.0000.0000.000
108B433ALA00.0010.01210.210-2.616-2.6160.0000.0000.0000.000
109B434ASP-1-0.812-0.9028.758-30.591-30.5910.0000.0000.0000.000
110B435PHE0-0.022-0.0048.805-3.381-3.3810.0000.0000.0000.000
111B436THR00.0450.0027.290-1.949-1.9490.0000.0000.0000.000
112B437CYS0-0.093-0.0454.657-7.271-7.182-0.001-0.006-0.0820.000
113B438ALA0-0.021-0.0143.858-12.739-12.5070.000-0.092-0.141-0.001
114B439PHE0-0.007-0.0086.220-0.962-0.9620.0000.0000.0000.000
115B440THR00.003-0.0112.124-1.459-1.4561.898-0.562-1.338-0.008
116B441LYS10.7620.8552.25840.01041.7741.359-0.869-2.254-0.005
117B442ALA00.0030.0093.6425.4965.8420.011-0.023-0.334-0.001
118B443VAL0-0.0020.0056.6872.8392.8390.0000.0000.0000.000
119B444ALA0-0.049-0.0172.8491.9592.6500.357-0.313-0.735-0.002
120B445GLU-1-0.885-0.9234.010-45.517-44.9200.001-0.125-0.473-0.001
121B446ALA0-0.0010.0186.2643.2803.2800.0000.0000.0000.000
122B447PRO0-0.2270.0179.6870.4490.4490.0000.0000.0000.000
123B448PHE00.2270.0833.7861.4041.5800.000-0.026-0.1500.000
124B449LYS10.9600.8848.79416.19416.1940.0000.0000.0000.000
125B450LYS10.8610.90113.06015.64915.6490.0000.0000.0000.000
126B451LEU00.0990.06814.8960.4840.4840.0000.0000.0000.000
127B452ARG10.8040.89217.86011.35211.3520.0000.0000.0000.000
128B453ASP-1-0.820-0.90121.003-11.485-11.4850.0000.0000.0000.000
129B454GLU-1-0.885-0.93219.916-13.598-13.5980.0000.0000.0000.000
130B455THR0-0.012-0.01523.6070.4060.4060.0000.0000.0000.000
131B456THR00.0510.00524.746-0.229-0.2290.0000.0000.0000.000
132B457PHE0-0.006-0.00425.965-0.119-0.1190.0000.0000.0000.000
133B458SER00.0370.01721.9710.0370.0370.0000.0000.0000.000
134B459PHE00.0500.03419.034-0.109-0.1090.0000.0000.0000.000
135B460CYS0-0.120-0.05920.838-0.219-0.2190.0000.0000.0000.000
136B461LEU0-0.063-0.02720.8030.0490.0490.0000.0000.0000.000
137B462GLU-1-0.932-0.94316.139-16.748-16.7480.0000.0000.0000.000
138B463SER0-0.086-0.05114.9170.4260.4260.0000.0000.0000.000
139B464ASP-1-0.844-0.92716.220-16.053-16.0530.0000.0000.0000.000
140B465TRP00.015-0.00311.341-0.408-0.4080.0000.0000.0000.000
141B466ALA0-0.0240.00117.1000.2200.2200.0000.0000.0000.000
142B467GLY00.0330.03218.1730.2990.2990.0000.0000.0000.000
143B468GLY00.008-0.00418.7780.7340.7340.0000.0000.0000.000
144B469VAL0-0.070-0.04021.459-0.297-0.2970.0000.0000.0000.000
145B470LYS10.9710.98019.39414.18214.1820.0000.0000.0000.000
146B471VAL0-0.012-0.00824.4030.3050.3050.0000.0000.0000.000
147B472ASP-1-0.778-0.86327.617-9.238-9.2380.0000.0000.0000.000
148B473LEU00.0540.00629.4700.1290.1290.0000.0000.0000.000
149B474ALA0-0.056-0.01231.8260.2180.2180.0000.0000.0000.000
150B475GLY00.0330.02232.2410.2110.2110.0000.0000.0000.000
151B476ARG10.8700.91332.3698.5918.5910.0000.0000.0000.000
152B477GLY00.0650.02029.705-0.297-0.2970.0000.0000.0000.000
153B478LEU00.0370.01230.070-0.203-0.2030.0000.0000.0000.000
154B479ALA0-0.0100.00731.783-0.011-0.0110.0000.0000.0000.000
155B480LEU0-0.029-0.01527.0730.0250.0250.0000.0000.0000.000
156B481VAL00.0090.00327.193-0.227-0.2270.0000.0000.0000.000
157B482TRP0-0.010-0.02329.346-0.118-0.1180.0000.0000.0000.000
158B483ARG10.9480.95828.84310.11710.1170.0000.0000.0000.000
159B484ARG10.8570.91021.97412.64212.6420.0000.0000.0000.000
160B485GLN00.0040.01228.745-0.017-0.0170.0000.0000.0000.000
161B486ILE00.0210.01830.2890.0220.0220.0000.0000.0000.000
162B487GLN0-0.007-0.01229.1420.0450.0450.0000.0000.0000.000
163B488GLN0-0.0310.00425.586-0.422-0.4220.0000.0000.0000.000
164B489LEU0-0.0150.01429.0470.0310.0310.0000.0000.0000.000
165B490ASN00.0470.01030.635-0.254-0.2540.0000.0000.0000.000
166B491ARG10.8460.88532.5358.6988.6980.0000.0000.0000.000
167B492VAL00.0200.03833.1180.2500.2500.0000.0000.0000.000
168B493SER00.0420.01832.096-0.296-0.2960.0000.0000.0000.000
169B494LEU00.0180.00030.1700.0890.0890.0000.0000.0000.000
170B495GLU-1-0.889-0.96432.402-8.437-8.4370.0000.0000.0000.000
171B496MET0-0.045-0.02035.9840.1720.1720.0000.0000.0000.000
172B497ALA00.0700.03433.8260.1900.1900.0000.0000.0000.000
173B498SER0-0.054-0.01635.3490.1010.1010.0000.0000.0000.000
174B499ALA0-0.009-0.00636.6860.1610.1610.0000.0000.0000.000
175B500VAL00.0110.00938.3180.1840.1840.0000.0000.0000.000
176B501VAL00.0160.00235.3440.1330.1330.0000.0000.0000.000
177B502ASN0-0.093-0.03638.4650.1820.1820.0000.0000.0000.000
178B503ALA0-0.0100.00940.9170.1540.1540.0000.0000.0000.000
179B504TYR00.008-0.00141.6410.2020.2020.0000.0000.0000.000
180B505PRO00.0260.02439.290-0.201-0.2010.0000.0000.0000.000
181B506SER0-0.005-0.02438.099-0.110-0.1100.0000.0000.0000.000
182B507PRO00.0670.03336.0020.1540.1540.0000.0000.0000.000
183B508GLN00.0340.01138.8330.2230.2230.0000.0000.0000.000
184B509LEU00.0030.01142.0420.1760.1760.0000.0000.0000.000
185B510LEU0-0.030-0.01539.8470.1270.1270.0000.0000.0000.000
186B511VAL00.0290.00940.9580.0900.0900.0000.0000.0000.000
187B512GLN00.0170.00843.7240.0710.0710.0000.0000.0000.000
188B513ALA00.0040.02346.2010.1630.1630.0000.0000.0000.000
189B514TYR00.0630.02442.0610.0570.0570.0000.0000.0000.000
190B515GLN0-0.064-0.04247.1360.0000.0000.0000.0000.0000.000
191B516GLN0-0.056-0.02550.0230.2030.2030.0000.0000.0000.000
192B517CYS0-0.084-0.00850.7680.0400.0400.0000.0000.0000.000
193B518PHE00.009-0.01353.0580.0530.0530.0000.0000.0000.000
194B519SER0-0.022-0.03654.3430.0440.0440.0000.0000.0000.000
195B520ASP-1-0.770-0.88249.492-6.212-6.2120.0000.0000.0000.000
196B521LYS10.8880.95650.2705.8185.8180.0000.0000.0000.000
197B522GLU-1-0.832-0.89851.009-5.770-5.7700.0000.0000.0000.000
198B523ARG10.8780.94347.8705.8885.8880.0000.0000.0000.000
199B524GLN0-0.021-0.01845.960-0.209-0.2090.0000.0000.0000.000
200B525ASN0-0.055-0.04246.351-0.036-0.0360.0000.0000.0000.000
201B526LEU00.0170.02446.4030.0340.0340.0000.0000.0000.000
202B527LEU00.006-0.00441.399-0.016-0.0160.0000.0000.0000.000
203B528ALA0-0.049-0.02444.861-0.105-0.1050.0000.0000.0000.000
204B529ASP-1-0.929-0.95446.397-6.351-6.3510.0000.0000.0000.000
205B530ILE0-0.0080.02343.2830.0750.0750.0000.0000.0000.000
206B531GLN00.0430.01344.943-0.221-0.2210.0000.0000.0000.000
207B532VAL00.015-0.00239.331-0.030-0.0300.0000.0000.0000.000
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