FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 1746Z

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 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 233
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2396866.735685
FMO2-HF: Nuclear repulsion 2304755.773828
FMO2-HF: Total energy -92110.961857
FMO2-MP2: Total energy -92377.612082


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.
-189.34-189.13827.234-10.41-17.025-0.074
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 : 0.892 / q_NPA : 0.918
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].
3B252ILE00.0100.0333.6624.0986.834-0.021-1.190-1.5250.000
4B253ILE0-0.022-0.0315.729-4.634-4.6340.0000.0000.0000.000
5B254VAL00.0110.0125.755-0.486-0.4860.0000.0000.0000.000
6B255VAL0-0.031-0.0078.1310.5040.5040.0000.0000.0000.000
7B256LEU00.0330.0079.422-0.085-0.0850.0000.0000.0000.000
8B257ASP-1-0.722-0.89912.819-15.155-15.1550.0000.0000.0000.000
9B258PRO0-0.0020.00116.472-0.151-0.1510.0000.0000.0000.000
10B259VAL00.0120.00518.8620.0110.0110.0000.0000.0000.000
11B260LEU00.0000.00012.5740.2060.2060.0000.0000.0000.000
12B261LEU0-0.031-0.02413.106-0.237-0.2370.0000.0000.0000.000
13B262GLN0-0.094-0.02816.6250.2560.2560.0000.0000.0000.000
14B263MET0-0.0170.00517.2951.0961.0960.0000.0000.0000.000
15B264GLU-1-0.946-0.97919.445-13.567-13.5670.0000.0000.0000.000
16B265GLY00.0400.03117.1500.0670.0670.0000.0000.0000.000
17B266GLY0-0.040-0.01514.991-1.593-1.5930.0000.0000.0000.000
18B267GLY00.0200.00414.147-1.267-1.2670.0000.0000.0000.000
19B268GLN0-0.017-0.02013.703-1.046-1.0460.0000.0000.0000.000
20B269LEU00.0130.0059.261-1.948-1.9480.0000.0000.0000.000
21B270LEU00.0310.0169.327-3.627-3.6270.0000.0000.0000.000
22B271GLY00.0040.0049.796-1.933-1.9330.0000.0000.0000.000
23B272ALA0-0.030-0.0187.792-1.266-1.2660.0000.0000.0000.000
24B273LEU00.013-0.0214.839-6.010-6.0100.0000.0000.0000.000
25B274GLN00.0440.0145.355-5.371-5.3710.0000.0000.0000.000
26B275THR0-0.0770.0045.9470.5550.5550.0000.0000.0000.000
27B276MET0-0.120-0.0472.399-16.960-24.58815.887-3.773-4.486-0.034
28B277GLU-1-0.822-0.9032.024-52.867-51.4492.239-1.296-2.361-0.006
29B278CYS0-0.128-0.0662.997-9.744-8.5772.039-1.020-2.185-0.013
30B279ARG10.9520.9944.15834.29634.4280.000-0.037-0.0960.000
31B280CYS0-0.038-0.0187.5171.3721.3720.0000.0000.0000.000
32B281VAL00.0040.0239.3062.2622.2620.0000.0000.0000.000
33B282ILE00.0030.00412.670-0.601-0.6010.0000.0000.0000.000
34B283GLU-1-0.876-0.92815.375-17.519-17.5190.0000.0000.0000.000
35B284ALA00.0120.00717.797-0.290-0.2900.0000.0000.0000.000
36B285GLN00.002-0.00214.914-1.326-1.3260.0000.0000.0000.000
37B286ALA0-0.025-0.00919.0930.6670.6670.0000.0000.0000.000
38B287VAL0-0.033-0.01119.0720.8500.8500.0000.0000.0000.000
39B288PRO00.0270.00019.483-0.759-0.7590.0000.0000.0000.000
40B289CYS0-0.029-0.01417.602-0.073-0.0730.0000.0000.0000.000
41B290SER00.0160.00115.433-0.448-0.4480.0000.0000.0000.000
42B291VAL0-0.0030.0148.877-0.075-0.0750.0000.0000.0000.000
43B292THR00.0140.00811.743-0.216-0.2160.0000.0000.0000.000
44B293TRP00.017-0.0175.674-1.080-1.0800.0000.0000.0000.000
45B294ARG10.8310.8688.74720.76320.7630.0000.0000.0000.000
46B307VAL0-0.025-0.0457.649-0.334-0.3340.0000.0000.0000.000
47B308GLU-1-0.869-0.9328.553-19.500-19.5000.0000.0000.0000.000
48B309GLU-1-1.013-0.96310.226-21.271-21.2710.0000.0000.0000.000
49B310PRO0-0.020-0.0039.1091.1531.1530.0000.0000.0000.000
50B311THR00.023-0.05812.0900.5850.5850.0000.0000.0000.000
51B312VAL0-0.053-0.00611.252-1.196-1.1960.0000.0000.0000.000
52B313LEU0-0.0200.01513.6080.0870.0870.0000.0000.0000.000
53B314VAL0-0.0150.02510.6341.1291.1290.0000.0000.0000.000
54B315LEU0-0.027-0.02013.8840.4810.4810.0000.0000.0000.000
55B316LEU00.0440.01213.966-0.193-0.1930.0000.0000.0000.000
56B317ARG10.9050.97317.75912.61012.6100.0000.0000.0000.000
57B318ALA00.0720.03421.074-0.287-0.2870.0000.0000.0000.000
58B319GLU-1-0.879-0.92323.182-11.106-11.1060.0000.0000.0000.000
59B349ASP-1-0.868-0.94926.090-10.938-10.9380.0000.0000.0000.000
60B350ILE00.0540.02726.153-0.425-0.4250.0000.0000.0000.000
61B351THR00.0120.00627.238-0.247-0.2470.0000.0000.0000.000
62B352ALA00.0620.03621.785-0.159-0.1590.0000.0000.0000.000
63B353LYS10.9090.98422.57712.46512.4650.0000.0000.0000.000
64B354THR0-0.141-0.09524.2990.1440.1440.0000.0000.0000.000
65B355ALA0-0.020-0.02624.2500.0120.0120.0000.0000.0000.000
66B356GLY00.0390.04321.100-0.138-0.1380.0000.0000.0000.000
67B357LYS10.9200.97921.56911.39911.3990.0000.0000.0000.000
68B358ALA0-0.041-0.04020.866-0.166-0.1660.0000.0000.0000.000
69B359LEU00.0420.00818.182-0.545-0.5450.0000.0000.0000.000
70B360SER0-0.0030.01918.253-0.955-0.9550.0000.0000.0000.000
71B361LEU00.0150.01115.317-0.771-0.7710.0000.0000.0000.000
72B362VAL00.006-0.00316.410-1.088-1.0880.0000.0000.0000.000
73B363ILE0-0.003-0.00213.9130.5350.5350.0000.0000.0000.000
74B364VAL0-0.058-0.04616.506-0.357-0.3570.0000.0000.0000.000
75B365ASP-1-0.787-0.90114.689-20.592-20.5920.0000.0000.0000.000
76B366GLN0-0.066-0.03416.9760.5150.5150.0000.0000.0000.000
77B367GLU-1-0.678-0.84517.136-18.019-18.0190.0000.0000.0000.000
78B368LYS10.7840.87019.96913.11213.1120.0000.0000.0000.000
79B404SER00.010-0.01135.131-0.122-0.1220.0000.0000.0000.000
80B405ARG10.8590.93027.85310.74210.7420.0000.0000.0000.000
81B406VAL00.012-0.00731.501-0.268-0.2680.0000.0000.0000.000
82B407ASP-1-0.830-0.91233.197-9.137-9.1370.0000.0000.0000.000
83B408ALA0-0.058-0.03228.358-0.202-0.2020.0000.0000.0000.000
84B409GLU-1-0.834-0.91129.065-10.618-10.6180.0000.0000.0000.000
85B410GLU-1-0.913-0.96130.102-8.991-8.9910.0000.0000.0000.000
86B411ALA00.0410.03529.764-0.043-0.0430.0000.0000.0000.000
87B412LEU00.0010.00224.516-0.224-0.2240.0000.0000.0000.000
88B413VAL0-0.033-0.02227.519-0.206-0.2060.0000.0000.0000.000
89B414ASP-1-0.925-0.98229.739-9.629-9.6290.0000.0000.0000.000
90B415LEU0-0.039-0.01424.008-0.058-0.0580.0000.0000.0000.000
91B416GLN0-0.053-0.03725.416-0.208-0.2080.0000.0000.0000.000
92B417LEU0-0.082-0.02826.8450.0350.0350.0000.0000.0000.000
93B418HIS0-0.076-0.02429.3980.5170.5170.0000.0000.0000.000
94B419THR0-0.047-0.03324.6480.0400.0400.0000.0000.0000.000
95B420GLU-1-0.929-0.97322.124-12.513-12.5130.0000.0000.0000.000
96B421ALA0-0.043-0.01120.976-0.781-0.7810.0000.0000.0000.000
97B422GLN0-0.0020.00917.0660.3210.3210.0000.0000.0000.000
98B423ALA0-0.011-0.02719.601-0.126-0.1260.0000.0000.0000.000
99B424GLN0-0.0320.02214.8141.7501.7500.0000.0000.0000.000
100B425ILE0-0.012-0.01919.4890.0590.0590.0000.0000.0000.000
101B426VAL00.0040.02615.868-0.161-0.1610.0000.0000.0000.000
102B427GLN0-0.001-0.02619.1020.8670.8670.0000.0000.0000.000
103B428SER0-0.071-0.02317.8440.1380.1380.0000.0000.0000.000
104B429TRP00.0590.06615.931-0.247-0.2470.0000.0000.0000.000
105B430LYS10.8720.91413.29720.60520.6050.0000.0000.0000.000
106B431GLU-1-0.849-0.94113.142-18.849-18.8490.0000.0000.0000.000
107B432LEU00.0710.04712.127-2.171-2.1710.0000.0000.0000.000
108B433ALA0-0.0270.02210.033-2.620-2.6200.0000.0000.0000.000
109B434ASP-1-0.882-0.9508.451-30.979-30.9790.0000.0000.0000.000
110B435PHE0-0.047-0.0188.375-3.709-3.7090.0000.0000.0000.000
111B436THR00.028-0.0267.050-1.876-1.8760.0000.0000.0000.000
112B437CYS0-0.074-0.0224.241-7.467-7.354-0.001-0.009-0.1030.000
113B438ALA0-0.017-0.0133.610-15.720-15.2640.005-0.248-0.214-0.002
114B439PHE0-0.006-0.0075.926-1.244-1.2440.0000.0000.0000.000
115B440THR0-0.005-0.0192.286-0.6690.0621.057-0.468-1.320-0.007
116B441LYS10.8140.9081.63446.40545.7485.763-1.861-3.244-0.008
117B442ALA00.0350.0253.5925.5426.0640.014-0.139-0.396-0.002
118B443VAL0-0.0040.0076.3942.9402.9400.0000.0000.0000.000
119B444ALA0-0.056-0.0242.8711.8852.5950.253-0.298-0.665-0.002
120B445GLU-1-0.971-0.9834.339-38.351-38.023-0.001-0.040-0.2870.000
121B446ALA0-0.0230.0226.5433.3443.3440.0000.0000.0000.000
122B447PRO0-0.2200.0299.6770.4400.4400.0000.0000.0000.000
123B448PHE00.2590.0973.7250.8821.0560.000-0.031-0.1430.000
124B449LYS10.9380.8398.85516.32116.3210.0000.0000.0000.000
125B450LYS10.8610.92013.09815.70815.7080.0000.0000.0000.000
126B451LEU00.0860.05114.7480.5200.5200.0000.0000.0000.000
127B452ARG10.8760.93817.85611.51311.5130.0000.0000.0000.000
128B453ASP-1-0.906-0.95320.992-11.399-11.3990.0000.0000.0000.000
129B454GLU-1-0.889-0.92520.108-13.853-13.8530.0000.0000.0000.000
130B455THR0-0.013-0.01223.6080.4020.4020.0000.0000.0000.000
131B456THR00.053-0.00124.758-0.326-0.3260.0000.0000.0000.000
132B457PHE0-0.007-0.00125.974-0.116-0.1160.0000.0000.0000.000
133B458SER00.0380.00322.0760.0130.0130.0000.0000.0000.000
134B459PHE00.0540.03619.255-0.073-0.0730.0000.0000.0000.000
135B460CYS0-0.101-0.04020.847-0.231-0.2310.0000.0000.0000.000
136B461LEU0-0.076-0.04020.7280.0520.0520.0000.0000.0000.000
137B462GLU-1-0.923-0.94116.611-16.214-16.2140.0000.0000.0000.000
138B463SER0-0.067-0.04915.1040.2590.2590.0000.0000.0000.000
139B464ASP-1-0.819-0.88416.225-16.489-16.4890.0000.0000.0000.000
140B465TRP0-0.010-0.03611.230-0.385-0.3850.0000.0000.0000.000
141B466ALA0-0.060-0.02316.9340.2580.2580.0000.0000.0000.000
142B467GLY00.0130.01818.1710.2800.2800.0000.0000.0000.000
143B468GLY00.009-0.00118.7750.7600.7600.0000.0000.0000.000
144B469VAL0-0.074-0.04121.453-0.307-0.3070.0000.0000.0000.000
145B470LYS10.9590.97619.76114.14214.1420.0000.0000.0000.000
146B471VAL0-0.007-0.00724.3940.3030.3030.0000.0000.0000.000
147B472ASP-1-0.778-0.85827.609-9.395-9.3950.0000.0000.0000.000
148B473LEU00.0580.00429.4600.1350.1350.0000.0000.0000.000
149B474ALA0-0.059-0.01231.8160.2160.2160.0000.0000.0000.000
150B475GLY00.0370.02332.2300.2180.2180.0000.0000.0000.000
151B476ARG10.8730.91232.3298.6938.6930.0000.0000.0000.000
152B477GLY00.0610.01829.696-0.303-0.3030.0000.0000.0000.000
153B478LEU00.0290.00830.063-0.208-0.2080.0000.0000.0000.000
154B479ALA0-0.0010.01131.777-0.013-0.0130.0000.0000.0000.000
155B480LEU0-0.027-0.01426.8720.0180.0180.0000.0000.0000.000
156B481VAL00.0170.00327.110-0.227-0.2270.0000.0000.0000.000
157B482TRP0-0.020-0.01929.342-0.115-0.1150.0000.0000.0000.000
158B483ARG10.9380.93328.36510.31710.3170.0000.0000.0000.000
159B484ARG10.9020.93522.34312.57412.5740.0000.0000.0000.000
160B485GLN0-0.0010.01528.7440.0610.0610.0000.0000.0000.000
161B486ILE00.0280.02430.2880.0250.0250.0000.0000.0000.000
162B487GLN00.0100.00628.7640.0890.0890.0000.0000.0000.000
163B488GLN0-0.0280.00225.679-0.413-0.4130.0000.0000.0000.000
164B489LEU0-0.0050.01829.0490.0320.0320.0000.0000.0000.000
165B490ASN00.0530.01630.722-0.247-0.2470.0000.0000.0000.000
166B491ARG10.9110.94832.5838.8848.8840.0000.0000.0000.000
167B492VAL00.0200.04333.0900.2540.2540.0000.0000.0000.000
168B493SER00.0420.02332.049-0.304-0.3040.0000.0000.0000.000
169B494LEU00.020-0.00130.2570.0750.0750.0000.0000.0000.000
170B495GLU-1-0.897-0.96932.233-8.460-8.4600.0000.0000.0000.000
171B496MET0-0.043-0.02035.8010.1720.1720.0000.0000.0000.000
172B497ALA00.0620.03133.7290.1890.1890.0000.0000.0000.000
173B498SER0-0.055-0.01335.0310.1230.1230.0000.0000.0000.000
174B499ALA00.010-0.00236.4540.1590.1590.0000.0000.0000.000
175B500VAL0-0.0020.00638.2170.1890.1890.0000.0000.0000.000
176B501VAL00.0140.00135.3290.1320.1320.0000.0000.0000.000
177B502ASN0-0.096-0.04038.4620.2090.2090.0000.0000.0000.000
178B503ALA00.0010.01640.9120.1540.1540.0000.0000.0000.000
179B504TYR0-0.002-0.00741.5900.2100.2100.0000.0000.0000.000
180B505PRO00.0220.01939.305-0.207-0.2070.0000.0000.0000.000
181B506SER0-0.002-0.02138.104-0.111-0.1110.0000.0000.0000.000
182B507PRO00.0670.03235.8280.1690.1690.0000.0000.0000.000
183B508GLN00.0440.01738.8310.2200.2200.0000.0000.0000.000
184B509LEU0-0.0060.00342.0400.1820.1820.0000.0000.0000.000
185B510LEU0-0.024-0.01139.6940.1310.1310.0000.0000.0000.000
186B511VAL00.0360.01041.0030.0940.0940.0000.0000.0000.000
187B512GLN0-0.004-0.00343.7240.0400.0400.0000.0000.0000.000
188B513ALA00.0060.02246.1740.1560.1560.0000.0000.0000.000
189B514TYR00.0320.02342.1180.0640.0640.0000.0000.0000.000
190B515GLN0-0.075-0.05047.281-0.025-0.0250.0000.0000.0000.000
191B516GLN0-0.0160.00350.0240.1970.1970.0000.0000.0000.000
192B517CYS0-0.079-0.01150.6790.0550.0550.0000.0000.0000.000
193B518PHE00.000-0.01653.0590.0620.0620.0000.0000.0000.000
194B519SER0-0.032-0.02854.2660.0540.0540.0000.0000.0000.000
195B520ASP-1-0.821-0.91850.657-6.143-6.1430.0000.0000.0000.000
196B521LYS10.9180.99150.2735.7915.7910.0000.0000.0000.000
197B522GLU-1-0.881-0.97751.012-5.855-5.8550.0000.0000.0000.000
198B523ARG10.8920.96747.8785.9455.9450.0000.0000.0000.000
199B524GLN0-0.027-0.01745.958-0.072-0.0720.0000.0000.0000.000
200B525ASN0-0.021-0.02746.353-0.125-0.1250.0000.0000.0000.000
201B526LEU00.0220.02646.0230.0300.0300.0000.0000.0000.000
202B527LEU0-0.017-0.02241.424-0.029-0.0290.0000.0000.0000.000
203B528ALA0-0.026-0.01744.861-0.107-0.1070.0000.0000.0000.000
204B529ASP-1-0.925-0.94746.398-6.378-6.3780.0000.0000.0000.000
205B530ILE0-0.0130.02343.2160.0700.0700.0000.0000.0000.000
206B531GLN0-0.003-0.01844.815-0.097-0.0970.0000.0000.0000.000
207B532VAL00.0300.00839.231-0.026-0.0260.0000.0000.0000.000
208B533ARG10.9270.95941.5816.9396.9390.0000.0000.0000.000
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