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: 856KY

Calculation Name: 4ZD3-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZD3

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1965609.208241
FMO2-HF: Nuclear repulsion 1889237.9476
FMO2-HF: Total energy -76371.260641
FMO2-MP2: Total energy -76592.144863


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:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-48.264-52.08915.947-6.614-5.510.064
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.889 / q_NPA : -0.944
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].
3H3GLN0-0.047-0.0361.692-28.246-32.41615.950-6.500-5.2810.064
4H4LEU00.022-0.0065.511-5.567-5.5670.0000.0000.0000.000
5H5VAL00.0050.0077.3451.1271.1270.0000.0000.0000.000
6H6GLN0-0.001-0.02710.094-1.188-1.1880.0000.0000.0000.000
7H7SER00.0100.02213.9040.2790.2790.0000.0000.0000.000
8H8GLY00.0100.00416.7630.2290.2290.0000.0000.0000.000
9H9ALA0-0.042-0.02018.392-0.363-0.3630.0000.0000.0000.000
10H11GLU-1-0.853-0.93621.20912.25712.2570.0000.0000.0000.000
11H12VAL0-0.072-0.04424.575-0.197-0.1970.0000.0000.0000.000
12H13LYS10.8140.90527.486-10.671-10.6710.0000.0000.0000.000
13H14LYS10.8680.92231.007-8.783-8.7830.0000.0000.0000.000
14H15PRO0-0.039-0.03234.1380.1140.1140.0000.0000.0000.000
15H16GLY00.0220.02035.662-0.231-0.2310.0000.0000.0000.000
16H17GLU-1-0.794-0.86332.2269.7689.7680.0000.0000.0000.000
17H18SER0-0.014-0.01830.7850.0740.0740.0000.0000.0000.000
18H19LEU0-0.031-0.01024.4280.0680.0680.0000.0000.0000.000
19H20LYS10.8690.93322.266-12.848-12.8480.0000.0000.0000.000
20H21ILE00.0180.03919.8390.2480.2480.0000.0000.0000.000
21H22SER00.003-0.02316.9470.0400.0400.0000.0000.0000.000
22H23CYS0-0.0200.00313.7070.2840.2840.0000.0000.0000.000
23H24LYS10.8930.9669.830-22.562-22.5620.0000.0000.0000.000
24H25GLY00.0450.0218.9041.6691.6690.0000.0000.0000.000
25H26SER0-0.027-0.0254.184-2.513-2.348-0.001-0.014-0.1510.000
26H27GLY00.0450.0234.2242.5892.625-0.001-0.0850.0500.000
27H28TYR0-0.038-0.0174.970-0.300-0.156-0.001-0.015-0.1280.000
28H29SER00.010-0.0048.257-0.966-0.9660.0000.0000.0000.000
29H30PHE00.0620.01511.562-0.839-0.8390.0000.0000.0000.000
30H35THR0-0.032-0.03413.307-0.963-0.9630.0000.0000.0000.000
31H36SER00.0250.04215.042-0.687-0.6870.0000.0000.0000.000
32H37TYR00.0010.00312.1670.7190.7190.0000.0000.0000.000
33H38TRP0-0.045-0.01115.579-0.091-0.0910.0000.0000.0000.000
34H39ILE0-0.024-0.01513.7581.3041.3040.0000.0000.0000.000
35H40GLY00.0150.01116.857-1.236-1.2360.0000.0000.0000.000
36H41TRP0-0.014-0.01517.6811.0941.0940.0000.0000.0000.000
37H42VAL00.001-0.00619.447-0.791-0.7910.0000.0000.0000.000
38H43ARG10.8140.87520.919-10.869-10.8690.0000.0000.0000.000
39H44GLN00.0140.01421.3420.6740.6740.0000.0000.0000.000
40H45MET0-0.0060.00724.031-0.100-0.1000.0000.0000.0000.000
41H46PRO00.0290.00126.8880.1780.1780.0000.0000.0000.000
42H47GLY00.0090.01426.990-0.471-0.4710.0000.0000.0000.000
43H48LYS10.8580.93127.139-10.749-10.7490.0000.0000.0000.000
44H49GLY00.0590.03125.5790.4560.4560.0000.0000.0000.000
45H50LEU00.0080.00619.860-0.047-0.0470.0000.0000.0000.000
46H51GLU-1-0.771-0.85823.92910.86410.8640.0000.0000.0000.000
47H52TRP00.0280.01322.1590.1430.1430.0000.0000.0000.000
48H53MET0-0.026-0.00123.772-0.420-0.4200.0000.0000.0000.000
49H54GLY00.0410.00423.734-0.632-0.6320.0000.0000.0000.000
50H55ILE0-0.087-0.02119.3180.7510.7510.0000.0000.0000.000
51H56ILE00.0040.01619.752-0.677-0.6770.0000.0000.0000.000
52H57TYR00.011-0.00519.1420.9090.9090.0000.0000.0000.000
53H58PRO0-0.014-0.02016.407-0.678-0.6780.0000.0000.0000.000
54H59GLY00.0100.02119.559-0.196-0.1960.0000.0000.0000.000
55H62ASP-1-0.887-0.94021.26011.62011.6200.0000.0000.0000.000
56H63SER0-0.041-0.01723.319-0.263-0.2630.0000.0000.0000.000
57H64ASP-1-0.750-0.81624.47310.84310.8430.0000.0000.0000.000
58H65THR0-0.028-0.03824.4260.7750.7750.0000.0000.0000.000
59H66ARG10.7620.84625.598-11.525-11.5250.0000.0000.0000.000
60H67TYR00.0470.02526.1000.5780.5780.0000.0000.0000.000
61H68SER0-0.0210.00327.347-0.408-0.4080.0000.0000.0000.000
62H69PRO00.028-0.00829.070-0.122-0.1220.0000.0000.0000.000
63H70SER00.0030.00431.665-0.267-0.2670.0000.0000.0000.000
64H71PHE00.007-0.00728.459-0.099-0.0990.0000.0000.0000.000
65H72GLN00.0150.01731.0630.2510.2510.0000.0000.0000.000
66H74GLY00.0000.00432.123-0.307-0.3070.0000.0000.0000.000
67H75GLN0-0.077-0.04332.206-0.243-0.2430.0000.0000.0000.000
68H76VAL0-0.045-0.01726.4910.1530.1530.0000.0000.0000.000
69H77THR0-0.056-0.02526.944-0.347-0.3470.0000.0000.0000.000
70H78ILE00.0350.01721.8140.3830.3830.0000.0000.0000.000
71H79SER00.000-0.00222.429-0.434-0.4340.0000.0000.0000.000
72H80ALA00.003-0.01418.8200.7220.7220.0000.0000.0000.000
73H81ASP-1-0.814-0.87618.81413.29513.2950.0000.0000.0000.000
74H82LYS10.8910.93217.131-12.261-12.2610.0000.0000.0000.000
75H83SER0-0.079-0.04816.8950.7130.7130.0000.0000.0000.000
76H84ILE00.0290.01815.8660.5060.5060.0000.0000.0000.000
77H85SER0-0.051-0.01812.2291.4181.4180.0000.0000.0000.000
78H86THR0-0.010-0.00412.7971.8221.8220.0000.0000.0000.000
79H87ALA00.0160.01215.220-1.125-1.1250.0000.0000.0000.000
80H88TYR0-0.016-0.03417.3460.5500.5500.0000.0000.0000.000
81H89LEU00.0030.01720.017-0.309-0.3090.0000.0000.0000.000
82H90GLN00.007-0.00222.5530.3730.3730.0000.0000.0000.000
83H91TRP00.0570.01924.000-0.159-0.1590.0000.0000.0000.000
84H92SER00.0270.00929.3650.0820.0820.0000.0000.0000.000
85H93SER0-0.031-0.01732.438-0.213-0.2130.0000.0000.0000.000
86H94LEU0-0.0110.01328.3990.0330.0330.0000.0000.0000.000
87H95LYS10.8800.92232.504-10.084-10.0840.0000.0000.0000.000
88H96ALA00.0580.02032.7240.2690.2690.0000.0000.0000.000
89H97SER0-0.020-0.01932.6570.1230.1230.0000.0000.0000.000
90H98ASP-1-0.803-0.87829.07610.28710.2870.0000.0000.0000.000
91H99THR0-0.0120.01127.7900.5370.5370.0000.0000.0000.000
92H100ALA0-0.039-0.02125.308-0.222-0.2220.0000.0000.0000.000
93H101MET00.0110.03619.0820.3080.3080.0000.0000.0000.000
94H102TYR0-0.028-0.05020.430-0.557-0.5570.0000.0000.0000.000
95H103TYR00.022-0.00415.5710.7630.7630.0000.0000.0000.000
96H105ALA00.0230.00213.3751.4841.4840.0000.0000.0000.000
97H106ARG10.8870.94010.015-27.275-27.2750.0000.0000.0000.000
98H107PRO0-0.034-0.00313.3320.7990.7990.0000.0000.0000.000
99H108HIS0-0.053-0.03112.273-0.070-0.0700.0000.0000.0000.000
100H109TYR0-0.028-0.01013.3600.6070.6070.0000.0000.0000.000
101H110TYR0-0.009-0.01014.999-0.049-0.0490.0000.0000.0000.000
102H111ASP-1-0.818-0.91716.29414.21114.2110.0000.0000.0000.000
103H112SER0-0.046-0.02518.654-1.090-1.0900.0000.0000.0000.000
104H112LEU0-0.031-0.03719.1640.5280.5280.0000.0000.0000.000
105H113ASP-1-0.859-0.89817.85214.98014.9800.0000.0000.0000.000
106H114ALA00.012-0.00818.4480.3190.3190.0000.0000.0000.000
107H115PHE0-0.032-0.03014.8550.4570.4570.0000.0000.0000.000
108H116ASP-1-0.744-0.83310.97226.18126.1810.0000.0000.0000.000
109H117ILE0-0.0210.0026.6831.9951.9950.0000.0000.0000.000
110H118TRP0-0.033-0.0469.681-3.971-3.9710.0000.0000.0000.000
111H119GLY00.0310.0209.7333.0283.0280.0000.0000.0000.000
112H120GLN0-0.030-0.01510.4170.5800.5800.0000.0000.0000.000
113H121GLY0-0.0040.00111.995-1.367-1.3670.0000.0000.0000.000
114H122THR0-0.067-0.04015.6770.4470.4470.0000.0000.0000.000
115H123MET0-0.011-0.00318.585-0.485-0.4850.0000.0000.0000.000
116H124VAL00.0250.01621.773-0.003-0.0030.0000.0000.0000.000
117H125THR0-0.029-0.01924.857-0.261-0.2610.0000.0000.0000.000
118H126VAL00.0130.01128.252-0.112-0.1120.0000.0000.0000.000
119H127SER00.011-0.00231.544-0.322-0.3220.0000.0000.0000.000
120H128SER00.0250.00334.8100.0870.0870.0000.0000.0000.000
121H129ALA00.0050.01936.210-0.168-0.1680.0000.0000.0000.000
122H130SER00.014-0.00536.4200.2300.2300.0000.0000.0000.000
123H131THR0-0.022-0.00433.590-0.048-0.0480.0000.0000.0000.000
124H132LYS10.8430.92435.729-8.179-8.1790.0000.0000.0000.000
125H133GLY00.0610.04136.0670.2460.2460.0000.0000.0000.000
126H134PRO0-0.070-0.02035.381-0.234-0.2340.0000.0000.0000.000
127H135SER00.0080.00438.170-0.087-0.0870.0000.0000.0000.000
128H136VAL0-0.003-0.00638.7990.1050.1050.0000.0000.0000.000
129H137PHE00.012-0.00441.475-0.203-0.2030.0000.0000.0000.000
130H138PRO0-0.015-0.00343.1130.1680.1680.0000.0000.0000.000
131H139LEU0-0.026-0.01041.632-0.150-0.1500.0000.0000.0000.000
132H140ALA00.0500.02645.2810.0870.0870.0000.0000.0000.000
133H141PRO0-0.017-0.00447.552-0.175-0.1750.0000.0000.0000.000
134H150THR0-0.018-0.02144.034-0.015-0.0150.0000.0000.0000.000
135H151ALA00.0090.01346.962-0.002-0.0020.0000.0000.0000.000
136H152ALA0-0.008-0.00742.7720.1730.1730.0000.0000.0000.000
137H153LEU0-0.0120.00042.088-0.210-0.2100.0000.0000.0000.000
138H154GLY00.0390.00540.4970.2470.2470.0000.0000.0000.000
139H155CYS0-0.063-0.00137.366-0.086-0.0860.0000.0000.0000.000
140H156LEU00.0330.03938.7360.2490.2490.0000.0000.0000.000
141H157VAL0-0.034-0.02235.315-0.131-0.1310.0000.0000.0000.000
142H158LYS10.9000.90837.233-7.323-7.3230.0000.0000.0000.000
143H159ASP-1-0.817-0.87339.3547.5867.5860.0000.0000.0000.000
144H160TYR0-0.027-0.03131.486-0.235-0.2350.0000.0000.0000.000
145H161PHE00.0470.02032.3150.1240.1240.0000.0000.0000.000
146H162PRO00.0230.02229.243-0.220-0.2200.0000.0000.0000.000
147H163GLU-1-0.748-0.86227.52910.79810.7980.0000.0000.0000.000
148H164PRO0-0.026-0.00824.6050.1390.1390.0000.0000.0000.000
149H165VAL0-0.023-0.02127.638-0.182-0.1820.0000.0000.0000.000
150H166THR0-0.072-0.04126.2790.4960.4960.0000.0000.0000.000
151H167VAL00.001-0.01729.410-0.341-0.3410.0000.0000.0000.000
152H168SER0-0.0170.00730.9650.2690.2690.0000.0000.0000.000
153H169TRP00.0740.02532.804-0.380-0.3800.0000.0000.0000.000
154H170ASN00.0240.03335.4160.0650.0650.0000.0000.0000.000
155H171SER0-0.003-0.01434.750-0.032-0.0320.0000.0000.0000.000
156H172GLY00.0010.00632.0040.2610.2610.0000.0000.0000.000
157H173ALA0-0.030-0.01132.6170.1630.1630.0000.0000.0000.000
158H174LEU0-0.049-0.01635.070-0.173-0.1730.0000.0000.0000.000
159H175THR00.0310.00330.4400.0480.0480.0000.0000.0000.000
160H176SER00.0190.00533.2230.1180.1180.0000.0000.0000.000
161H177GLY00.0380.01135.155-0.215-0.2150.0000.0000.0000.000
162H178VAL0-0.046-0.01133.060-0.146-0.1460.0000.0000.0000.000
163H179HIS0-0.0020.00732.9280.4700.4700.0000.0000.0000.000
164H180THR0-0.017-0.01330.646-0.442-0.4420.0000.0000.0000.000
165H181PHE00.0030.00930.9020.3500.3500.0000.0000.0000.000
166H182PRO00.014-0.00629.0740.0750.0750.0000.0000.0000.000
167H183ALA0-0.0120.00830.455-0.388-0.3880.0000.0000.0000.000
168H184VAL0-0.016-0.01032.3470.1090.1090.0000.0000.0000.000
169H185LEU0-0.029-0.01433.373-0.110-0.1100.0000.0000.0000.000
170H186GLN0-0.023-0.01735.687-0.319-0.3190.0000.0000.0000.000
171H187SER00.0310.00439.2580.1220.1220.0000.0000.0000.000
172H188SER0-0.006-0.00141.485-0.014-0.0140.0000.0000.0000.000
173H189GLY00.0220.01538.015-0.015-0.0150.0000.0000.0000.000
174H190LEU0-0.053-0.02036.7150.2550.2550.0000.0000.0000.000
175H191TYR00.0320.01130.170-0.102-0.1020.0000.0000.0000.000
176H192SER0-0.004-0.01335.545-0.315-0.3150.0000.0000.0000.000
177H193LEU00.0320.03531.6510.1210.1210.0000.0000.0000.000
178H194SER0-0.002-0.01635.364-0.417-0.4170.0000.0000.0000.000
179H195SER0-0.011-0.00234.0180.2240.2240.0000.0000.0000.000
180H196VAL00.0170.00436.143-0.299-0.2990.0000.0000.0000.000
181H197VAL00.0460.03437.1170.1310.1310.0000.0000.0000.000
182H208THR00.003-0.01245.886-0.073-0.0730.0000.0000.0000.000
183H209TYR0-0.008-0.01741.513-0.081-0.0810.0000.0000.0000.000
184H210ILE00.0320.03539.4900.0610.0610.0000.0000.0000.000
185H212ASN00.004-0.01434.672-0.158-0.1580.0000.0000.0000.000
186H213VAL00.0180.01034.0360.3690.3690.0000.0000.0000.000
187H214ASN0-0.013-0.00129.9190.1130.1130.0000.0000.0000.000
188H215HIS00.015-0.01030.8510.1430.1430.0000.0000.0000.000
189H216LYS10.9500.96525.344-12.040-12.0400.0000.0000.0000.000
190H217PRO00.0270.02428.397-0.158-0.1580.0000.0000.0000.000
191H218SER00.0350.01730.526-0.199-0.1990.0000.0000.0000.000
192H219ASN0-0.014-0.00532.560-0.224-0.2240.0000.0000.0000.000
193H220THR00.0440.02733.654-0.289-0.2890.0000.0000.0000.000
194H221LYS10.8370.90932.989-9.070-9.0700.0000.0000.0000.000
195H222VAL0-0.023-0.01136.132-0.249-0.2490.0000.0000.0000.000
196H223ASP-1-0.810-0.88737.3378.8138.8130.0000.0000.0000.000
197H224LYS10.8580.91039.637-7.409-7.4090.0000.0000.0000.000