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: 2J55R

Calculation Name: 4ZTP-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZTP

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166479.157903
FMO2-HF: Nuclear repulsion 2083465.83295
FMO2-HF: Total energy -83013.324954
FMO2-MP2: Total energy -83251.311529


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(H:1:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
-10.195-3.1638.441-5.87-9.603-0.041
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.018
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].
3H3LEU00.017-0.0133.865-0.4661.481-0.019-0.980-0.9470.004
4H4GLU-1-0.925-0.9597.062-0.587-0.5870.0000.0000.0000.000
5H5GLU-1-0.775-0.87010.386-1.103-1.1030.0000.0000.0000.000
6H6SER0-0.016-0.01413.8410.0810.0810.0000.0000.0000.000
7H7GLY00.0360.00817.0260.0010.0010.0000.0000.0000.000
8H8GLY00.0170.01620.1190.0200.0200.0000.0000.0000.000
9H9GLY00.0130.00121.9000.0190.0190.0000.0000.0000.000
10H10PRO0-0.039-0.01625.343-0.004-0.0040.0000.0000.0000.000
11H11VAL00.0270.00727.9600.0100.0100.0000.0000.0000.000
12H12LYS10.8490.92630.7280.1520.1520.0000.0000.0000.000
13H13PRO00.012-0.01533.161-0.005-0.0050.0000.0000.0000.000
14H14GLY0-0.0130.00534.2630.0090.0090.0000.0000.0000.000
15H15GLY0-0.0100.00632.0390.0050.0050.0000.0000.0000.000
16H16THR0-0.029-0.03527.648-0.002-0.0020.0000.0000.0000.000
17H17LEU00.0050.01123.8230.0040.0040.0000.0000.0000.000
18H18THR0-0.036-0.03820.7830.0170.0170.0000.0000.0000.000
19H19LEU0-0.0020.03217.8510.0050.0050.0000.0000.0000.000
20H20THR0-0.007-0.01415.5600.0140.0140.0000.0000.0000.000
21H21CYS0-0.020-0.00910.2640.0000.0000.0000.0000.0000.000
22H22LYS10.8960.9658.4770.2020.2020.0000.0000.0000.000
23H23ALA00.0550.0195.608-0.297-0.2970.0000.0000.0000.000
24H24SER0-0.002-0.0224.4140.3740.518-0.001-0.032-0.1110.000
25H25GLY00.0340.0152.458-2.431-1.0672.324-1.779-1.910-0.016
26H26ILE0-0.035-0.0152.261-5.866-3.9454.984-2.617-4.288-0.025
27H27ASP-1-0.720-0.8143.5431.8331.8270.0120.175-0.1810.000
28H28PHE0-0.059-0.0445.759-0.442-0.4420.0000.0000.0000.000
29H29SER0-0.081-0.0559.270-0.170-0.1700.0000.0000.0000.000
30H30SER00.0170.0118.650-0.125-0.1250.0000.0000.0000.000
31H31PHE0-0.034-0.02510.287-0.094-0.0940.0000.0000.0000.000
32H32TYR0-0.025-0.0265.9500.0710.0710.0000.0000.0000.000
33H33TYR00.0150.0129.9270.0380.0380.0000.0000.0000.000
34H34MET0-0.006-0.0028.057-0.277-0.2770.0000.0000.0000.000
35H34CYS0-0.069-0.01710.9020.0820.0820.0000.0000.0000.000
36H35TRP00.0220.01112.917-0.153-0.1530.0000.0000.0000.000
37H36VAL0-0.002-0.00615.2140.0830.0830.0000.0000.0000.000
38H37ARG10.7520.85017.3050.2990.2990.0000.0000.0000.000
39H38GLN00.005-0.00319.847-0.040-0.0400.0000.0000.0000.000
40H39ALA00.0500.03321.8060.0060.0060.0000.0000.0000.000
41H40PRO0-0.001-0.01825.426-0.010-0.0100.0000.0000.0000.000
42H41GLY00.0290.03326.2190.0260.0260.0000.0000.0000.000
43H42LYS10.8380.91325.6350.3130.3130.0000.0000.0000.000
44H43GLY00.0610.03423.291-0.028-0.0280.0000.0000.0000.000
45H44LEU00.0100.00516.5800.0060.0060.0000.0000.0000.000
46H45GLU-1-0.824-0.87820.604-0.295-0.2950.0000.0000.0000.000
47H46TRP00.002-0.02117.210-0.010-0.0100.0000.0000.0000.000
48H47ILE0-0.031-0.00919.1880.0480.0480.0000.0000.0000.000
49H48ALA00.021-0.00118.5920.0530.0530.0000.0000.0000.000
50H50ILE0-0.001-0.00513.9610.0550.0550.0000.0000.0000.000
51H51VAL00.0320.03713.559-0.073-0.0730.0000.0000.0000.000
52H51THR0-0.014-0.0149.154-0.002-0.0020.0000.0000.0000.000
53H51ASP-1-0.785-0.85612.4660.1080.1080.0000.0000.0000.000
54H52ILE0-0.034-0.03115.240-0.034-0.0340.0000.0000.0000.000
55H53THR0-0.035-0.04318.555-0.028-0.0280.0000.0000.0000.000
56H54GLY0-0.0090.01017.525-0.012-0.0120.0000.0000.0000.000
57H55GLU-1-0.846-0.88818.596-0.089-0.0890.0000.0000.0000.000
58H56SER0-0.008-0.01818.205-0.031-0.0310.0000.0000.0000.000
59H57TYR0-0.071-0.05917.3150.0060.0060.0000.0000.0000.000
60H58TYR00.0190.00920.190-0.046-0.0460.0000.0000.0000.000
61H59ALA00.0340.02522.6260.0260.0260.0000.0000.0000.000
62H60THR0-0.014-0.04324.3460.0080.0080.0000.0000.0000.000
63H61TRP00.0120.01623.1950.0230.0230.0000.0000.0000.000
64H62ALA00.0300.02524.3060.0040.0040.0000.0000.0000.000
65H63LYS10.8720.93326.2430.1770.1770.0000.0000.0000.000
66H64GLY00.0250.02627.5260.0100.0100.0000.0000.0000.000
67H65ARG10.8070.87628.5110.2170.2170.0000.0000.0000.000
68H66PHE0-0.010-0.00722.694-0.009-0.0090.0000.0000.0000.000
69H67ALA00.0150.01323.0240.0150.0150.0000.0000.0000.000
70H68ILE0-0.036-0.00615.036-0.022-0.0220.0000.0000.0000.000
71H69SER0-0.003-0.00517.8960.0460.0460.0000.0000.0000.000
72H70LYS10.8900.93913.361-0.049-0.0490.0000.0000.0000.000
73H71THR0-0.002-0.00715.2780.0310.0310.0000.0000.0000.000
74H72SER00.005-0.00913.3480.0500.0500.0000.0000.0000.000
75H73SER00.0050.00211.922-0.051-0.0510.0000.0000.0000.000
76H74THR0-0.019-0.0018.3470.0200.0200.0000.0000.0000.000
77H75THR0-0.0180.0059.881-0.079-0.0790.0000.0000.0000.000
78H76VAL00.0310.02811.3100.0730.0730.0000.0000.0000.000
79H77THR0-0.025-0.01413.532-0.044-0.0440.0000.0000.0000.000
80H78LEU00.0210.00516.7230.0060.0060.0000.0000.0000.000
81H79GLN0-0.0100.00719.2290.0090.0090.0000.0000.0000.000
82H80MET0-0.031-0.01122.568-0.019-0.0190.0000.0000.0000.000
83H81THR00.0240.00325.1280.0150.0150.0000.0000.0000.000
84H81SER00.0230.00228.964-0.002-0.0020.0000.0000.0000.000
85H81LEU0-0.0330.00726.751-0.003-0.0030.0000.0000.0000.000
86H82THR00.0290.00130.7620.0190.0190.0000.0000.0000.000
87H83ALA00.0170.00331.016-0.015-0.0150.0000.0000.0000.000
88H84ALA00.002-0.00730.930-0.014-0.0140.0000.0000.0000.000
89H85ASP-1-0.735-0.81626.868-0.260-0.2600.0000.0000.0000.000
90H86THR0-0.053-0.01926.136-0.022-0.0220.0000.0000.0000.000
91H87ALA00.005-0.00522.9160.0060.0060.0000.0000.0000.000
92H88THR00.0130.01718.1060.0340.0340.0000.0000.0000.000
93H89TYR0-0.035-0.04018.3860.0120.0120.0000.0000.0000.000
94H90PHE00.0220.00413.4180.0080.0080.0000.0000.0000.000
95H92ALA00.005-0.0079.234-0.254-0.2540.0000.0000.0000.000
96H93ARG10.9000.9383.324-0.1220.7280.062-0.263-0.649-0.002
97H94GLY00.0230.0177.851-0.275-0.2750.0000.0000.0000.000
98H95ASP-1-0.798-0.8846.8590.3270.3270.0000.0000.0000.000
99H96THR0-0.022-0.0259.407-0.058-0.0580.0000.0000.0000.000
100H97TYR0-0.027-0.00912.7430.0500.0500.0000.0000.0000.000
101H98GLY00.0240.02615.0470.0330.0330.0000.0000.0000.000
102H99TYR0-0.051-0.04215.674-0.065-0.0650.0000.0000.0000.000
103H99GLY0-0.038-0.01016.991-0.035-0.0350.0000.0000.0000.000
104H99ASP-1-0.886-0.94015.3800.4050.4050.0000.0000.0000.000
105H99THR0-0.025-0.01710.5840.0960.0960.0000.0000.0000.000
106H99VAL0-0.002-0.0048.212-0.152-0.1520.0000.0000.0000.000
107H99TYR0-0.025-0.0039.893-0.218-0.2180.0000.0000.0000.000
108H99ALA0-0.012-0.02211.169-0.008-0.0080.0000.0000.0000.000
109H99LEU0-0.027-0.01510.029-0.034-0.0340.0000.0000.0000.000
110H100ASN0-0.039-0.0155.346-0.804-0.8040.0000.0000.0000.000
111H101LEU0-0.0090.0082.345-1.701-0.8891.079-0.374-1.517-0.002
112H102TRP00.002-0.0255.7250.9880.9880.0000.0000.0000.000
113H103GLY00.0310.0357.781-0.637-0.6370.0000.0000.0000.000
114H104PRO0-0.046-0.02610.0260.1030.1030.0000.0000.0000.000
115H105GLY00.0010.00013.1680.1330.1330.0000.0000.0000.000
116H106THR0-0.046-0.02815.4390.0910.0910.0000.0000.0000.000
117H107LEU0-0.034-0.00918.4210.0110.0110.0000.0000.0000.000
118H108VAL00.0230.01522.1080.0280.0280.0000.0000.0000.000
119H109THR0-0.077-0.05324.7240.0030.0030.0000.0000.0000.000
120H110VAL00.0070.02828.4800.0150.0150.0000.0000.0000.000
121H111SER0-0.017-0.02330.9680.0080.0080.0000.0000.0000.000
122H112SER00.0520.01434.3130.0010.0010.0000.0000.0000.000
123H113GLY00.0050.01137.3640.0080.0080.0000.0000.0000.000
124H114GLN00.0490.02436.012-0.010-0.0100.0000.0000.0000.000
125H115PRO0-0.006-0.00532.2810.0000.0000.0000.0000.0000.000
126H116LYS10.8310.91134.3910.1540.1540.0000.0000.0000.000
127H117ALA00.0800.04434.575-0.010-0.0100.0000.0000.0000.000
128H118PRO0-0.040-0.00133.5980.0060.0060.0000.0000.0000.000
129H119SER0-0.008-0.00836.4890.0070.0070.0000.0000.0000.000
130H120VAL00.0240.01336.369-0.005-0.0050.0000.0000.0000.000
131H121PHE0-0.030-0.02039.1340.0100.0100.0000.0000.0000.000
132H122PRO00.0600.03140.173-0.008-0.0080.0000.0000.0000.000
133H123LEU0-0.064-0.03138.8120.0010.0010.0000.0000.0000.000
134H124ALA00.0280.01041.780-0.003-0.0030.0000.0000.0000.000
135H125PRO00.0330.02744.362-0.002-0.0020.0000.0000.0000.000
136H126CYM-1-0.814-0.86146.849-0.080-0.0800.0000.0000.0000.000
137H127CYS0-0.038-0.02950.5290.0010.0010.0000.0000.0000.000
138H128GLY0-0.038-0.04952.8500.0030.0030.0000.0000.0000.000
139H129ASP-1-0.937-0.95648.501-0.088-0.0880.0000.0000.0000.000
140H130THR0-0.045-0.02751.6510.0040.0040.0000.0000.0000.000
141H131PRO0-0.037-0.02249.937-0.003-0.0030.0000.0000.0000.000
142H132SER00.0320.01545.4840.0030.0030.0000.0000.0000.000
143H133SER00.0060.00745.703-0.001-0.0010.0000.0000.0000.000
144H134THR0-0.039-0.01040.974-0.001-0.0010.0000.0000.0000.000
145H135VAL00.0840.05441.6190.0020.0020.0000.0000.0000.000
146H136THR0-0.018-0.02238.179-0.011-0.0110.0000.0000.0000.000
147H137LEU00.0230.02238.7030.0060.0060.0000.0000.0000.000
148H138GLY00.029-0.00637.078-0.011-0.0110.0000.0000.0000.000
149H139CYS0-0.0610.00334.2810.0060.0060.0000.0000.0000.000
150H140LEU0-0.0060.00936.451-0.011-0.0110.0000.0000.0000.000
151H141VAL00.014-0.00132.8810.0090.0090.0000.0000.0000.000
152H142LYS10.9940.98635.6060.1200.1200.0000.0000.0000.000
153H143GLY00.0430.01637.9840.0060.0060.0000.0000.0000.000
154H144TYR0-0.021-0.02630.2090.0160.0160.0000.0000.0000.000
155H145LEU0-0.0020.00733.178-0.006-0.0060.0000.0000.0000.000
156H146PRO00.0070.00528.6690.0160.0160.0000.0000.0000.000
157H147GLU-1-0.724-0.81426.844-0.287-0.2870.0000.0000.0000.000
158H148PRO0-0.0030.00023.404-0.001-0.0010.0000.0000.0000.000
159H149VAL0-0.020-0.01826.5550.0210.0210.0000.0000.0000.000
160H150THR0-0.013-0.00924.372-0.025-0.0250.0000.0000.0000.000
161H151VAL0-0.030-0.02927.3100.0220.0220.0000.0000.0000.000
162H152THR0-0.020-0.00726.778-0.020-0.0200.0000.0000.0000.000
163H153TRP00.0270.01229.4320.0170.0170.0000.0000.0000.000
164H154ASN00.018-0.00831.586-0.004-0.0040.0000.0000.0000.000
165H155SER0-0.018-0.01130.9200.0050.0050.0000.0000.0000.000
166H156GLY00.0200.02028.026-0.003-0.0030.0000.0000.0000.000
167H157THR0-0.065-0.03828.636-0.002-0.0020.0000.0000.0000.000
168H158LEU0-0.036-0.00931.1420.0040.0040.0000.0000.0000.000
169H159THR00.0380.00325.909-0.010-0.0100.0000.0000.0000.000
170H160ASN00.0250.01228.290-0.022-0.0220.0000.0000.0000.000
171H161GLY00.0600.03029.6230.0120.0120.0000.0000.0000.000
172H162VAL0-0.047-0.01728.8160.0090.0090.0000.0000.0000.000
173H163ARG10.8270.91829.3710.1650.1650.0000.0000.0000.000
174H164THR00.0150.01227.7780.0240.0240.0000.0000.0000.000
175H165PHE0-0.0150.00628.521-0.020-0.0200.0000.0000.0000.000
176H166PRO00.022-0.00127.553-0.005-0.0050.0000.0000.0000.000
177H167SER0-0.050-0.04329.0920.0210.0210.0000.0000.0000.000
178H168VAL00.0110.00731.129-0.004-0.0040.0000.0000.0000.000
179H169ARG10.8530.93132.4320.2250.2250.0000.0000.0000.000
180H170GLN0-0.008-0.00235.0350.0080.0080.0000.0000.0000.000
181H171SER00.0490.01638.308-0.005-0.0050.0000.0000.0000.000
182H172SER00.0010.00240.830-0.001-0.0010.0000.0000.0000.000
183H173GLY00.0170.01436.7540.0010.0010.0000.0000.0000.000
184H174LEU0-0.042-0.00435.449-0.012-0.0120.0000.0000.0000.000
185H175TYR00.0270.00829.5600.0000.0000.0000.0000.0000.000
186H176SER0-0.008-0.01634.7470.0150.0150.0000.0000.0000.000
187H177LEU00.0170.02429.604-0.007-0.0070.0000.0000.0000.000
188H178SER00.0190.00633.4310.0110.0110.0000.0000.0000.000
189H179SER00.011-0.00530.861-0.012-0.0120.0000.0000.0000.000
190H180VAL00.0270.01633.2950.0150.0150.0000.0000.0000.000
191H181VAL00.0200.01833.182-0.014-0.0140.0000.0000.0000.000
192H182SER0-0.010-0.01834.8030.0080.0080.0000.0000.0000.000
193H183VAL0-0.026-0.00335.907-0.005-0.0050.0000.0000.0000.000
194H184THR00.0390.01038.4650.0000.0000.0000.0000.0000.000
195H185SER0-0.045-0.03341.198-0.002-0.0020.0000.0000.0000.000
196H186SER0-0.014-0.02142.2680.0040.0040.0000.0000.0000.000
197H187SER00.0190.00345.029-0.001-0.0010.0000.0000.0000.000
198H188GLN0-0.0130.01539.0100.0020.0020.0000.0000.0000.000
199H189PRO00.0220.02340.883-0.003-0.0030.0000.0000.0000.000
200H190VAL00.0290.01837.364-0.004-0.0040.0000.0000.0000.000
201H191THR00.0270.01336.5890.0040.0040.0000.0000.0000.000
202H193ASN00.0700.02231.5270.0010.0010.0000.0000.0000.000
203H194VAL0-0.026-0.00931.523-0.016-0.0160.0000.0000.0000.000
204H195ALA00.0140.00528.5200.0140.0140.0000.0000.0000.000
205H196HIS00.0140.01129.336-0.005-0.0050.0000.0000.0000.000
206H197PRO00.0500.02124.8770.0160.0160.0000.0000.0000.000
207H198ALA0-0.0010.00627.3650.0120.0120.0000.0000.0000.000
208H199THR0-0.024-0.02928.9830.0140.0140.0000.0000.0000.000
209H200ASN00.0080.00329.8310.0070.0070.0000.0000.0000.000
210H201THR00.0150.00830.8230.0090.0090.0000.0000.0000.000
211H202LYS10.8700.91729.8120.1350.1350.0000.0000.0000.000
212H203VAL0-0.037-0.01633.4340.0110.0110.0000.0000.0000.000
213H204ASP-1-0.824-0.89135.578-0.137-0.1370.0000.0000.0000.000
214H205LYS10.8520.89837.2700.1200.1200.0000.0000.0000.000
215H206THR0-0.020-0.01239.124-0.004-0.0040.0000.0000.0000.000
216H207VAL0-0.036-0.02439.5730.0030.0030.0000.0000.0000.000
217H208ALA00.0000.00542.3270.0030.0030.0000.0000.0000.000
218H209PRO0-0.010-0.02845.139-0.002-0.0020.0000.0000.0000.000
219H210SER0-0.051-0.01446.3240.0010.0010.0000.0000.0000.000
220H211THR00.0300.02449.1870.0020.0020.0000.0000.0000.000