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: 852NY

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2397144.068495
FMO2-HF: Nuclear repulsion 2305028.376725
FMO2-HF: Total energy -92115.691769
FMO2-MP2: Total energy -92381.669781


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.
-234.446-232.18234.968-17.45-19.781-0.194
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 : 0.799 / q_NPA : 0.861
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].
3B252ILE0-0.0100.0033.5166.0658.1600.010-0.749-1.3570.001
4B253ILE0-0.013-0.0155.479-4.531-4.5310.0000.0000.0000.000
5B254VAL00.0040.0235.089-1.304-1.3040.0000.0000.0000.000
6B255VAL0-0.050-0.0317.2031.6061.6060.0000.0000.0000.000
7B256LEU00.0220.0039.036-0.047-0.0470.0000.0000.0000.000
8B257ASP-1-0.744-0.88312.529-15.315-15.3150.0000.0000.0000.000
9B258PRO0-0.016-0.01916.282-0.106-0.1060.0000.0000.0000.000
10B259VAL00.0150.00418.4910.0690.0690.0000.0000.0000.000
11B260LEU00.0210.01113.4860.2590.2590.0000.0000.0000.000
12B261LEU0-0.041-0.02312.791-0.146-0.1460.0000.0000.0000.000
13B262GLN0-0.070-0.02716.6630.2210.2210.0000.0000.0000.000
14B263MET0-0.0190.01417.6561.0601.0600.0000.0000.0000.000
15B264GLU-1-0.892-0.94419.429-13.837-13.8370.0000.0000.0000.000
16B265GLY00.0310.02317.3790.0120.0120.0000.0000.0000.000
17B266GLY0-0.017-0.00415.139-1.527-1.5270.0000.0000.0000.000
18B267GLY00.0230.00013.949-1.480-1.4800.0000.0000.0000.000
19B268GLN0-0.025-0.01813.899-1.257-1.2570.0000.0000.0000.000
20B269LEU00.0290.0159.261-1.898-1.8980.0000.0000.0000.000
21B270LEU00.0170.0169.324-3.509-3.5090.0000.0000.0000.000
22B271GLY00.0150.0059.347-2.429-2.4290.0000.0000.0000.000
23B272ALA0-0.024-0.0158.726-1.634-1.6340.0000.0000.0000.000
24B273LEU00.036-0.0054.629-6.064-5.988-0.001-0.003-0.0720.000
25B274GLN00.016-0.0104.816-6.870-6.838-0.001-0.003-0.0270.000
26B275THR0-0.080-0.0337.2130.7900.7900.0000.0000.0000.000
27B276MET0-0.0610.0042.409-14.219-16.76110.073-3.625-3.906-0.051
28B277GLU-1-0.816-0.8933.015-60.648-58.8740.102-0.728-1.148-0.005
29B278CYS0-0.037-0.0032.260-12.931-17.82512.792-4.095-3.803-0.047
30B279ARG10.8640.9084.01343.31343.5030.003-0.054-0.1390.000
31B280CYS0-0.049-0.0097.0041.8771.8770.0000.0000.0000.000
32B281VAL00.0360.0448.7582.7252.7250.0000.0000.0000.000
33B282ILE00.006-0.00312.011-0.576-0.5760.0000.0000.0000.000
34B283GLU-1-0.847-0.90314.766-18.721-18.7210.0000.0000.0000.000
35B284ALA0-0.021-0.01216.837-0.551-0.5510.0000.0000.0000.000
36B285GLN0-0.0030.01215.297-0.377-0.3770.0000.0000.0000.000
37B286ALA0-0.029-0.01618.6460.8090.8090.0000.0000.0000.000
38B287VAL0-0.020-0.01919.5960.8970.8970.0000.0000.0000.000
39B288PRO00.0220.01619.546-0.827-0.8270.0000.0000.0000.000
40B289CYS0-0.038-0.00817.984-0.022-0.0220.0000.0000.0000.000
41B290SER0-0.004-0.01115.655-0.430-0.4300.0000.0000.0000.000
42B291VAL0-0.022-0.0109.202-0.163-0.1630.0000.0000.0000.000
43B292THR00.0200.00211.2740.1370.1370.0000.0000.0000.000
44B293TRP00.034-0.0125.699-1.032-1.0320.0000.0000.0000.000
45B294ARG10.7870.8359.25521.19621.1960.0000.0000.0000.000
46B307VAL0-0.003-0.0227.5460.8330.8330.0000.0000.0000.000
47B308GLU-1-0.934-0.9248.502-19.180-19.1800.0000.0000.0000.000
48B309GLU-1-0.884-0.93710.304-21.988-21.9880.0000.0000.0000.000
49B310PRO0-0.061-0.0158.9781.5031.5030.0000.0000.0000.000
50B311THR0-0.021-0.01311.9540.2620.2620.0000.0000.0000.000
51B312VAL0-0.021-0.00311.573-1.848-1.8480.0000.0000.0000.000
52B313LEU0-0.012-0.01013.134-0.445-0.4450.0000.0000.0000.000
53B314VAL0-0.0090.01111.5060.8670.8670.0000.0000.0000.000
54B315LEU0-0.020-0.02414.0420.0200.0200.0000.0000.0000.000
55B316LEU00.0140.00714.161-0.187-0.1870.0000.0000.0000.000
56B317ARG10.8950.96618.16812.87812.8780.0000.0000.0000.000
57B318ALA00.0610.03021.303-0.393-0.3930.0000.0000.0000.000
58B319GLU-1-0.872-0.92123.829-11.131-11.1310.0000.0000.0000.000
59B349ASP-1-0.807-0.88725.379-11.085-11.0850.0000.0000.0000.000
60B350ILE0-0.013-0.04425.861-0.482-0.4820.0000.0000.0000.000
61B351THR00.0030.00127.632-0.188-0.1880.0000.0000.0000.000
62B352ALA00.0560.04122.012-0.164-0.1640.0000.0000.0000.000
63B353LYS10.8630.93922.76412.93812.9380.0000.0000.0000.000
64B354THR0-0.067-0.06024.1700.2690.2690.0000.0000.0000.000
65B355ALA00.0270.01423.8590.1020.1020.0000.0000.0000.000
66B356GLY00.0350.03220.529-0.236-0.2360.0000.0000.0000.000
67B357LYS10.8320.90920.68411.56511.5650.0000.0000.0000.000
68B358ALA0-0.007-0.01320.2280.1150.1150.0000.0000.0000.000
69B359LEU0-0.0050.00117.964-0.652-0.6520.0000.0000.0000.000
70B360SER0-0.027-0.01218.273-0.825-0.8250.0000.0000.0000.000
71B361LEU00.0310.00615.349-0.914-0.9140.0000.0000.0000.000
72B362VAL0-0.0140.00416.128-1.072-1.0720.0000.0000.0000.000
73B363ILE00.000-0.00313.8450.5240.5240.0000.0000.0000.000
74B364VAL0-0.046-0.02516.814-0.172-0.1720.0000.0000.0000.000
75B365ASP-1-0.773-0.88815.192-20.073-20.0730.0000.0000.0000.000
76B366GLN0-0.040-0.03717.5820.6520.6520.0000.0000.0000.000
77B367GLU-1-0.679-0.84917.943-17.127-17.1270.0000.0000.0000.000
78B368LYS10.7710.86020.56913.17813.1780.0000.0000.0000.000
79B404SER00.004-0.01136.303-0.046-0.0460.0000.0000.0000.000
80B405ARG10.8400.89328.48710.51610.5160.0000.0000.0000.000
81B406VAL00.0440.02331.852-0.281-0.2810.0000.0000.0000.000
82B407ASP-1-0.867-0.92533.578-9.006-9.0060.0000.0000.0000.000
83B408ALA0-0.029-0.01628.518-0.159-0.1590.0000.0000.0000.000
84B409GLU-1-0.835-0.90529.190-10.696-10.6960.0000.0000.0000.000
85B410GLU-1-0.930-0.96830.275-8.927-8.9270.0000.0000.0000.000
86B411ALA0-0.0040.00530.106-0.050-0.0500.0000.0000.0000.000
87B412LEU0-0.037-0.01724.182-0.247-0.2470.0000.0000.0000.000
88B413VAL0-0.007-0.00827.297-0.231-0.2310.0000.0000.0000.000
89B414ASP-1-0.870-0.93429.681-9.769-9.7690.0000.0000.0000.000
90B415LEU00.004-0.00123.860-0.119-0.1190.0000.0000.0000.000
91B416GLN0-0.043-0.03025.254-0.165-0.1650.0000.0000.0000.000
92B417LEU0-0.070-0.02526.5770.0310.0310.0000.0000.0000.000
93B418HIS0-0.094-0.03829.3450.4500.4500.0000.0000.0000.000
94B419THR0-0.107-0.06724.000-0.112-0.1120.0000.0000.0000.000
95B420GLU-1-0.839-0.90521.927-13.352-13.3520.0000.0000.0000.000
96B421ALA0-0.0210.00420.538-0.752-0.7520.0000.0000.0000.000
97B422GLN0-0.029-0.00817.4290.3800.3800.0000.0000.0000.000
98B423ALA00.0250.00419.106-0.473-0.4730.0000.0000.0000.000
99B424GLN0-0.076-0.03015.3090.7440.7440.0000.0000.0000.000
100B425ILE0-0.032-0.02719.9650.1730.1730.0000.0000.0000.000
101B426VAL0-0.0040.01416.288-0.262-0.2620.0000.0000.0000.000
102B427GLN0-0.030-0.02319.6720.9260.9260.0000.0000.0000.000
103B428SER0-0.077-0.06618.6500.2000.2000.0000.0000.0000.000
104B429TRP0-0.0090.00116.843-0.503-0.5030.0000.0000.0000.000
105B430LYS10.7790.86412.52421.43521.4350.0000.0000.0000.000
106B431GLU-1-0.835-0.88313.639-18.058-18.0580.0000.0000.0000.000
107B432LEU00.0490.04312.672-1.922-1.9220.0000.0000.0000.000
108B433ALA0-0.0060.00210.869-2.617-2.6170.0000.0000.0000.000
109B434ASP-1-0.787-0.8749.100-29.343-29.3430.0000.0000.0000.000
110B435PHE00.0000.0068.770-3.847-3.8470.0000.0000.0000.000
111B436THR00.034-0.0017.621-2.241-2.2410.0000.0000.0000.000
112B437CYS0-0.073-0.0324.912-7.132-7.1320.0000.0000.0000.000
113B438ALA0-0.003-0.0064.288-11.708-11.594-0.001-0.023-0.0910.000
114B439PHE00.0030.0076.278-1.774-1.7740.0000.0000.0000.000
115B440THR00.007-0.0042.0910.6890.8662.228-1.023-1.382-0.009
116B441LYS10.7920.8891.8535.9357.7878.312-5.303-4.860-0.071
117B442ALA00.0320.0123.7754.4944.7990.003-0.039-0.2690.000
118B443VAL0-0.003-0.0086.6083.0063.0060.0000.0000.0000.000
119B444ALA0-0.045-0.0122.5881.3611.7841.324-0.616-1.131-0.003
120B445GLU-1-0.860-0.9153.204-52.634-50.1280.124-1.166-1.464-0.009
121B446ALA00.0230.0105.7554.0354.0350.0000.0000.0000.000
122B447PRO0-0.0090.0308.553-0.296-0.2960.0000.0000.0000.000
123B448PHE0-0.048-0.0383.7792.0392.1950.000-0.023-0.1320.000
124B449LYS10.9500.9628.76118.36618.3660.0000.0000.0000.000
125B450LYS10.8840.93112.24715.52015.5200.0000.0000.0000.000
126B451LEU00.0970.07414.4910.7830.7830.0000.0000.0000.000
127B452ARG10.8030.88817.48311.43111.4310.0000.0000.0000.000
128B453ASP-1-0.823-0.91120.598-11.795-11.7950.0000.0000.0000.000
129B454GLU-1-0.824-0.87919.750-13.478-13.4780.0000.0000.0000.000
130B455THR0-0.020-0.01323.2830.4980.4980.0000.0000.0000.000
131B456THR00.035-0.00524.400-0.229-0.2290.0000.0000.0000.000
132B457PHE0-0.0080.00325.603-0.105-0.1050.0000.0000.0000.000
133B458SER00.012-0.02021.2610.0830.0830.0000.0000.0000.000
134B459PHE00.0560.03418.892-0.268-0.2680.0000.0000.0000.000
135B460CYS0-0.140-0.07221.040-0.120-0.1200.0000.0000.0000.000
136B461LEU0-0.068-0.03820.6520.1820.1820.0000.0000.0000.000
137B462GLU-1-0.908-0.92615.452-17.584-17.5840.0000.0000.0000.000
138B463SER0-0.096-0.06614.9000.4230.4230.0000.0000.0000.000
139B464ASP-1-0.809-0.90315.717-16.240-16.2400.0000.0000.0000.000
140B465TRP00.0030.00011.304-0.306-0.3060.0000.0000.0000.000
141B466ALA0-0.034-0.00516.6720.2500.2500.0000.0000.0000.000
142B467GLY00.0230.02518.1600.4620.4620.0000.0000.0000.000
143B468GLY00.0150.00918.8010.7640.7640.0000.0000.0000.000
144B469VAL0-0.058-0.04021.268-0.111-0.1110.0000.0000.0000.000
145B470LYS10.9510.97419.03414.21414.2140.0000.0000.0000.000
146B471VAL0-0.008-0.00124.4490.2810.2810.0000.0000.0000.000
147B472ASP-1-0.774-0.86027.464-9.241-9.2410.0000.0000.0000.000
148B473LEU00.028-0.00529.6310.1100.1100.0000.0000.0000.000
149B474ALA0-0.039-0.00632.0520.2480.2480.0000.0000.0000.000
150B475GLY00.0230.01632.4360.1820.1820.0000.0000.0000.000
151B476ARG10.8590.90132.0768.5238.5230.0000.0000.0000.000
152B477GLY00.0910.02829.549-0.339-0.3390.0000.0000.0000.000
153B478LEU00.0040.00030.324-0.164-0.1640.0000.0000.0000.000
154B479ALA00.0270.01831.9480.0090.0090.0000.0000.0000.000
155B480LEU0-0.018-0.00526.7850.0250.0250.0000.0000.0000.000
156B481VAL0-0.0010.00127.277-0.229-0.2290.0000.0000.0000.000
157B482TRP00.0150.00029.355-0.153-0.1530.0000.0000.0000.000
158B483ARG10.9220.95928.74910.14210.1420.0000.0000.0000.000
159B484ARG10.8450.89622.18512.65212.6520.0000.0000.0000.000
160B485GLN00.0150.00928.8920.0430.0430.0000.0000.0000.000
161B486ILE00.0260.02130.4640.0110.0110.0000.0000.0000.000
162B487GLN0-0.002-0.01828.8310.0580.0580.0000.0000.0000.000
163B488GLN0-0.037-0.00325.621-0.439-0.4390.0000.0000.0000.000
164B489LEU0-0.0270.00729.0500.0250.0250.0000.0000.0000.000
165B490ASN00.0550.01630.091-0.185-0.1850.0000.0000.0000.000
166B491ARG10.8570.88832.1098.7258.7250.0000.0000.0000.000
167B492VAL00.0000.02432.6880.2210.2210.0000.0000.0000.000
168B493SER00.0410.01331.954-0.292-0.2920.0000.0000.0000.000
169B494LEU00.0250.00229.8140.1150.1150.0000.0000.0000.000
170B495GLU-1-0.888-0.96032.322-8.474-8.4740.0000.0000.0000.000
171B496MET0-0.037-0.00935.9770.2070.2070.0000.0000.0000.000
172B497ALA00.0560.03133.4370.1880.1880.0000.0000.0000.000
173B498SER0-0.022-0.01235.1530.0580.0580.0000.0000.0000.000
174B499ALA0-0.032-0.01136.4990.1740.1740.0000.0000.0000.000
175B500VAL00.0110.00638.2040.1940.1940.0000.0000.0000.000
176B501VAL00.0060.00335.3420.1380.1380.0000.0000.0000.000
177B502ASN0-0.112-0.05338.6800.1480.1480.0000.0000.0000.000
178B503ALA0-0.0090.00241.2380.1520.1520.0000.0000.0000.000
179B504TYR00.0170.00641.7280.1960.1960.0000.0000.0000.000
180B505PRO00.0330.02139.404-0.193-0.1930.0000.0000.0000.000
181B506SER0-0.017-0.02438.057-0.141-0.1410.0000.0000.0000.000
182B507PRO00.0560.02435.8280.1520.1520.0000.0000.0000.000
183B508GLN00.0180.01638.7340.2270.2270.0000.0000.0000.000
184B509LEU00.0170.01441.9320.1520.1520.0000.0000.0000.000
185B510LEU0-0.0080.00539.9980.1320.1320.0000.0000.0000.000
186B511VAL00.0200.00740.9840.1180.1180.0000.0000.0000.000
187B512GLN00.0220.00243.7390.0920.0920.0000.0000.0000.000
188B513ALA00.0000.01646.2980.1730.1730.0000.0000.0000.000
189B514TYR00.0440.00742.1060.0670.0670.0000.0000.0000.000
190B515GLN0-0.047-0.03447.0490.0210.0210.0000.0000.0000.000
191B516GLN0-0.042-0.02349.8380.2140.2140.0000.0000.0000.000
192B517CYS0-0.0720.00150.7840.0530.0530.0000.0000.0000.000
193B518PHE00.0110.00852.8950.0280.0280.0000.0000.0000.000
194B519SER0-0.040-0.05454.3820.0070.0070.0000.0000.0000.000
195B520ASP-1-0.747-0.86049.136-6.270-6.2700.0000.0000.0000.000
196B521LYS10.8910.96450.0065.8185.8180.0000.0000.0000.000
197B522GLU-1-0.804-0.87851.270-5.762-5.7620.0000.0000.0000.000
198B523ARG10.8560.92547.6815.8785.8780.0000.0000.0000.000
199B524GLN00.005-0.00745.750-0.214-0.2140.0000.0000.0000.000
200B525ASN0-0.049-0.03346.067-0.050-0.0500.0000.0000.0000.000
201B526LEU00.0320.03946.350-0.002-0.0020.0000.0000.0000.000
202B527LEU00.002-0.01440.992-0.042-0.0420.0000.0000.0000.000
203B528ALA0-0.073-0.03144.262-0.120-0.1200.0000.0000.0000.000
204B529ASP-1-0.872-0.92946.030-6.343-6.3430.0000.0000.0000.000
205B530ILE0-0.0260.00342.7830.0660.0660.0000.0000.0000.000
206B531GLN00.0350.01544.140-0.269-0.2690.0000.0000.0000.000
207B532VAL00.0290.00239.1950.0010.0010.0000.0000.0000.000
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