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: G6471

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1966852.331645
FMO2-HF: Nuclear repulsion 1890481.501904
FMO2-HF: Total energy -76370.82974
FMO2-MP2: Total energy -76591.732733


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.
-49.119-53.37616.776-6.953-5.5660.073
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 : -0.909 / q_NPA : -0.959
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].
3H3GLN0-0.046-0.0341.673-30.032-34.52216.780-6.871-5.4200.073
4H4LEU00.028-0.0015.532-6.287-6.280-0.001-0.003-0.0020.000
5H5VAL00.0050.0187.4610.6840.6840.0000.0000.0000.000
6H6GLN00.011-0.0279.887-1.414-1.4140.0000.0000.0000.000
7H7SER00.0220.03013.5480.2800.2800.0000.0000.0000.000
8H8GLY00.002-0.00216.4110.1470.1470.0000.0000.0000.000
9H9ALA0-0.034-0.01618.224-0.307-0.3070.0000.0000.0000.000
10H11GLU-1-0.869-0.93620.94712.78812.7880.0000.0000.0000.000
11H12VAL0-0.058-0.03824.189-0.173-0.1730.0000.0000.0000.000
12H13LYS10.8500.93427.568-10.865-10.8650.0000.0000.0000.000
13H14LYS10.8690.92730.432-9.006-9.0060.0000.0000.0000.000
14H15PRO0-0.024-0.03233.5910.1210.1210.0000.0000.0000.000
15H16GLY0-0.0130.00834.960-0.250-0.2500.0000.0000.0000.000
16H17GLU-1-0.828-0.91132.1069.9799.9790.0000.0000.0000.000
17H18SER0-0.044-0.03030.7850.0920.0920.0000.0000.0000.000
18H19LEU0-0.018-0.00224.1610.0520.0520.0000.0000.0000.000
19H20LYS10.8810.95022.802-13.071-13.0710.0000.0000.0000.000
20H21ILE0-0.0010.02319.3870.1730.1730.0000.0000.0000.000
21H22SER00.003-0.02517.0680.1000.1000.0000.0000.0000.000
22H23CYS0-0.0420.00313.7290.5130.5130.0000.0000.0000.000
23H24LYS10.8870.95710.342-22.928-22.9280.0000.0000.0000.000
24H25GLY00.0190.0089.3642.4452.4450.0000.0000.0000.000
25H26SER0-0.023-0.0244.663-2.675-2.549-0.001-0.008-0.1170.000
26H27GLY00.0360.0203.9203.4523.449-0.001-0.0590.0620.000
27H28TYR0-0.008-0.0114.7830.4580.561-0.001-0.012-0.0890.000
28H29SER00.0190.0137.747-0.995-0.9950.0000.0000.0000.000
29H30PHE00.0850.03411.412-0.920-0.9200.0000.0000.0000.000
30H35THR0-0.033-0.03413.099-0.813-0.8130.0000.0000.0000.000
31H36SER0-0.0060.01014.146-0.996-0.9960.0000.0000.0000.000
32H37TYR00.0060.01811.6630.2580.2580.0000.0000.0000.000
33H38TRP0-0.023-0.00115.764-0.161-0.1610.0000.0000.0000.000
34H39ILE0-0.018-0.01113.9381.4111.4110.0000.0000.0000.000
35H40GLY00.0270.02017.264-1.324-1.3240.0000.0000.0000.000
36H41TRP0-0.014-0.01417.5231.1691.1690.0000.0000.0000.000
37H42VAL0-0.001-0.01319.118-0.798-0.7980.0000.0000.0000.000
38H43ARG10.8240.86720.604-11.074-11.0740.0000.0000.0000.000
39H44GLN0-0.0010.00421.1160.5450.5450.0000.0000.0000.000
40H45MET0-0.0050.00723.718-0.117-0.1170.0000.0000.0000.000
41H46PRO00.0490.01226.2940.1960.1960.0000.0000.0000.000
42H47GLY0-0.009-0.00326.607-0.442-0.4420.0000.0000.0000.000
43H48LYS10.8910.95327.020-10.698-10.6980.0000.0000.0000.000
44H49GLY00.0390.02325.3100.4580.4580.0000.0000.0000.000
45H50LEU0-0.002-0.00220.072-0.069-0.0690.0000.0000.0000.000
46H51GLU-1-0.767-0.85423.83711.01911.0190.0000.0000.0000.000
47H52TRP00.0320.02322.2990.2130.2130.0000.0000.0000.000
48H53MET0-0.051-0.00323.536-0.386-0.3860.0000.0000.0000.000
49H54GLY00.039-0.00823.577-0.682-0.6820.0000.0000.0000.000
50H55ILE0-0.083-0.02419.6250.8110.8110.0000.0000.0000.000
51H56ILE0-0.0130.00220.159-0.665-0.6650.0000.0000.0000.000
52H57TYR00.001-0.02219.0810.9020.9020.0000.0000.0000.000
53H58PRO0-0.014-0.00616.766-0.703-0.7030.0000.0000.0000.000
54H59GLY00.0190.01819.923-0.331-0.3310.0000.0000.0000.000
55H62ASP-1-0.866-0.94021.11811.70011.7000.0000.0000.0000.000
56H63SER0-0.065-0.03323.308-0.326-0.3260.0000.0000.0000.000
57H64ASP-1-0.726-0.79524.59811.08211.0820.0000.0000.0000.000
58H65THR0-0.032-0.03724.6300.7420.7420.0000.0000.0000.000
59H66ARG10.7630.84525.913-11.704-11.7040.0000.0000.0000.000
60H67TYR00.0360.02026.5800.5570.5570.0000.0000.0000.000
61H68SER00.0130.02027.912-0.460-0.4600.0000.0000.0000.000
62H69PRO00.032-0.00829.567-0.077-0.0770.0000.0000.0000.000
63H70SER00.0020.00731.796-0.282-0.2820.0000.0000.0000.000
64H71PHE0-0.003-0.00727.909-0.103-0.1030.0000.0000.0000.000
65H72GLN00.0400.02930.8310.2290.2290.0000.0000.0000.000
66H74GLY0-0.024-0.01032.550-0.259-0.2590.0000.0000.0000.000
67H75GLN0-0.072-0.04031.831-0.260-0.2600.0000.0000.0000.000
68H76VAL0-0.049-0.02426.2950.1530.1530.0000.0000.0000.000
69H77THR0-0.042-0.01827.576-0.202-0.2020.0000.0000.0000.000
70H78ILE00.0080.00522.1890.4030.4030.0000.0000.0000.000
71H79SER00.003-0.00723.024-0.395-0.3950.0000.0000.0000.000
72H80ALA00.017-0.01019.4760.7830.7830.0000.0000.0000.000
73H81ASP-1-0.815-0.87019.34913.58013.5800.0000.0000.0000.000
74H82LYS10.8760.92117.776-12.364-12.3640.0000.0000.0000.000
75H83SER0-0.075-0.04917.1380.7530.7530.0000.0000.0000.000
76H84ILE00.0190.01215.7970.6610.6610.0000.0000.0000.000
77H85SER0-0.021-0.00112.2731.3841.3840.0000.0000.0000.000
78H86THR0-0.010-0.00413.2821.7781.7780.0000.0000.0000.000
79H87ALA00.0050.00315.753-1.149-1.1490.0000.0000.0000.000
80H88TYR0-0.005-0.03117.9220.5820.5820.0000.0000.0000.000
81H89LEU00.0240.03720.663-0.388-0.3880.0000.0000.0000.000
82H90GLN00.0170.00022.6490.3590.3590.0000.0000.0000.000
83H91TRP00.0590.02523.369-0.224-0.2240.0000.0000.0000.000
84H92SER00.012-0.00329.1770.0670.0670.0000.0000.0000.000
85H93SER0-0.008-0.01032.333-0.273-0.2730.0000.0000.0000.000
86H94LEU0-0.0170.01927.993-0.036-0.0360.0000.0000.0000.000
87H95LYS10.9090.93732.133-10.254-10.2540.0000.0000.0000.000
88H96ALA00.0700.01832.1430.2910.2910.0000.0000.0000.000
89H97SER0-0.009-0.00132.1070.1650.1650.0000.0000.0000.000
90H98ASP-1-0.839-0.89128.63610.53010.5300.0000.0000.0000.000
91H99THR0-0.0080.00427.4610.5610.5610.0000.0000.0000.000
92H100ALA0-0.041-0.02024.781-0.202-0.2020.0000.0000.0000.000
93H101MET00.0230.03718.8360.3370.3370.0000.0000.0000.000
94H102TYR0-0.035-0.05020.079-0.479-0.4790.0000.0000.0000.000
95H103TYR00.0320.02015.1220.8280.8280.0000.0000.0000.000
96H105ALA00.025-0.00713.5561.4301.4300.0000.0000.0000.000
97H106ARG10.8570.9109.547-28.160-28.1600.0000.0000.0000.000
98H107PRO0-0.0120.00513.3600.8240.8240.0000.0000.0000.000
99H108HIS0-0.059-0.03211.8530.0350.0350.0000.0000.0000.000
100H109TYR0-0.025-0.00913.2270.5180.5180.0000.0000.0000.000
101H110TYR0-0.038-0.02714.6690.0730.0730.0000.0000.0000.000
102H111ASP-1-0.852-0.92116.23614.26914.2690.0000.0000.0000.000
103H112SER0-0.045-0.03718.869-1.072-1.0720.0000.0000.0000.000
104H112LEU0-0.054-0.03519.2710.6310.6310.0000.0000.0000.000
105H113ASP-1-0.850-0.89818.04415.01715.0170.0000.0000.0000.000
106H114ALA00.008-0.01018.1830.2870.2870.0000.0000.0000.000
107H115PHE0-0.048-0.03415.2730.4900.4900.0000.0000.0000.000
108H116ASP-1-0.721-0.83010.72326.93226.9320.0000.0000.0000.000
109H117ILE0-0.0180.0087.1252.5762.5760.0000.0000.0000.000
110H118TRP0-0.017-0.0239.928-4.130-4.1300.0000.0000.0000.000
111H119GLY00.0490.0309.5463.2503.2500.0000.0000.0000.000
112H120GLN0-0.031-0.01810.3330.5990.5990.0000.0000.0000.000
113H121GLY0-0.008-0.00211.902-1.527-1.5270.0000.0000.0000.000
114H122THR0-0.052-0.03315.4570.4190.4190.0000.0000.0000.000
115H123MET0-0.016-0.00718.163-0.514-0.5140.0000.0000.0000.000
116H124VAL00.0070.00721.387-0.109-0.1090.0000.0000.0000.000
117H125THR0-0.019-0.01624.497-0.319-0.3190.0000.0000.0000.000
118H126VAL00.0000.01027.802-0.111-0.1110.0000.0000.0000.000
119H127SER00.015-0.01130.899-0.317-0.3170.0000.0000.0000.000
120H128SER00.0270.00734.0790.0810.0810.0000.0000.0000.000
121H129ALA00.0140.02135.866-0.224-0.2240.0000.0000.0000.000
122H130SER00.014-0.00235.9190.2510.2510.0000.0000.0000.000
123H131THR0-0.027-0.00933.1290.0010.0010.0000.0000.0000.000
124H132LYS10.8270.90935.253-8.293-8.2930.0000.0000.0000.000
125H133GLY00.0690.05036.0080.2470.2470.0000.0000.0000.000
126H134PRO0-0.051-0.01235.375-0.211-0.2110.0000.0000.0000.000
127H135SER0-0.005-0.00138.152-0.114-0.1140.0000.0000.0000.000
128H136VAL00.003-0.00338.4910.1180.1180.0000.0000.0000.000
129H137PHE00.002-0.00241.180-0.215-0.2150.0000.0000.0000.000
130H138PRO0-0.0090.00642.8680.1840.1840.0000.0000.0000.000
131H139LEU0-0.032-0.00941.423-0.109-0.1090.0000.0000.0000.000
132H140ALA00.011-0.00445.0490.0690.0690.0000.0000.0000.000
133H141PRO00.0400.03047.334-0.087-0.0870.0000.0000.0000.000
134H150THR0-0.009-0.01743.720-0.014-0.0140.0000.0000.0000.000
135H151ALA0-0.0080.00046.428-0.050-0.0500.0000.0000.0000.000
136H152ALA0-0.011-0.00242.4990.1580.1580.0000.0000.0000.000
137H153LEU0-0.0030.00842.158-0.206-0.2060.0000.0000.0000.000
138H154GLY00.0430.00640.4810.2510.2510.0000.0000.0000.000
139H155CYS0-0.0560.01037.398-0.114-0.1140.0000.0000.0000.000
140H156LEU00.0140.00239.0050.2080.2080.0000.0000.0000.000
141H157VAL0-0.025-0.01935.260-0.151-0.1510.0000.0000.0000.000
142H158LYS10.9010.91637.271-7.426-7.4260.0000.0000.0000.000
143H159ASP-1-0.814-0.87938.8627.6947.6940.0000.0000.0000.000
144H160TYR0-0.020-0.03431.321-0.244-0.2440.0000.0000.0000.000
145H161PHE00.0330.02431.8120.1690.1690.0000.0000.0000.000
146H162PRO00.0200.01729.118-0.230-0.2300.0000.0000.0000.000
147H163GLU-1-0.760-0.86227.35610.96210.9620.0000.0000.0000.000
148H164PRO0-0.009-0.00824.5690.1630.1630.0000.0000.0000.000
149H165VAL00.006-0.01127.739-0.183-0.1830.0000.0000.0000.000
150H166THR0-0.068-0.03826.2790.4080.4080.0000.0000.0000.000
151H167VAL00.0300.00229.361-0.336-0.3360.0000.0000.0000.000
152H168SER0-0.0370.00030.9100.1990.1990.0000.0000.0000.000
153H169TRP00.0630.01632.604-0.371-0.3710.0000.0000.0000.000
154H170ASN0-0.0040.00935.4450.0800.0800.0000.0000.0000.000
155H171SER00.009-0.01534.347-0.019-0.0190.0000.0000.0000.000
156H172GLY0-0.012-0.00232.0410.1330.1330.0000.0000.0000.000
157H173ALA0-0.0080.01432.4980.1520.1520.0000.0000.0000.000
158H174LEU0-0.031-0.00934.960-0.002-0.0020.0000.0000.0000.000
159H175THR00.0370.00530.4570.0300.0300.0000.0000.0000.000
160H176SER00.0040.00133.0210.1610.1610.0000.0000.0000.000
161H177GLY00.0350.01034.968-0.243-0.2430.0000.0000.0000.000
162H178VAL0-0.056-0.02232.928-0.113-0.1130.0000.0000.0000.000
163H179HIS00.0110.02232.7870.4900.4900.0000.0000.0000.000
164H180THR0-0.0010.00030.730-0.451-0.4510.0000.0000.0000.000
165H181PHE0-0.020-0.00331.0600.3330.3330.0000.0000.0000.000
166H182PRO00.011-0.00529.3480.0660.0660.0000.0000.0000.000
167H183ALA0-0.0060.01330.640-0.398-0.3980.0000.0000.0000.000
168H184VAL0-0.0030.00132.3600.1140.1140.0000.0000.0000.000
169H185LEU0-0.038-0.02433.289-0.038-0.0380.0000.0000.0000.000
170H186GLN0-0.041-0.02035.650-0.354-0.3540.0000.0000.0000.000
171H187SER00.0340.00738.9000.1410.1410.0000.0000.0000.000
172H188SER0-0.001-0.00341.1260.0100.0100.0000.0000.0000.000
173H189GLY00.0170.01837.588-0.017-0.0170.0000.0000.0000.000
174H190LEU0-0.076-0.02936.2700.2680.2680.0000.0000.0000.000
175H191TYR00.0340.01430.308-0.079-0.0790.0000.0000.0000.000
176H192SER00.007-0.01835.464-0.301-0.3010.0000.0000.0000.000
177H193LEU00.0120.03631.7580.1050.1050.0000.0000.0000.000
178H194SER00.0240.00935.664-0.348-0.3480.0000.0000.0000.000
179H195SER0-0.034-0.02634.0070.2160.2160.0000.0000.0000.000
180H196VAL00.0310.00436.105-0.271-0.2710.0000.0000.0000.000
181H197VAL00.0350.02036.9710.1350.1350.0000.0000.0000.000
182H208THR0-0.002-0.01445.948-0.095-0.0950.0000.0000.0000.000
183H209TYR0-0.009-0.02841.7720.0180.0180.0000.0000.0000.000
184H210ILE00.005-0.00239.5060.0720.0720.0000.0000.0000.000
185H212ASN00.0050.00734.546-0.140-0.1400.0000.0000.0000.000
186H213VAL00.0250.01633.9350.3750.3750.0000.0000.0000.000
187H214ASN0-0.042-0.03229.8630.0960.0960.0000.0000.0000.000
188H215HIS00.0330.00130.8240.1150.1150.0000.0000.0000.000
189H216LYS10.9340.96025.477-12.142-12.1420.0000.0000.0000.000
190H217PRO00.0260.02728.326-0.148-0.1480.0000.0000.0000.000
191H218SER00.0330.01330.480-0.214-0.2140.0000.0000.0000.000
192H219ASN0-0.025-0.00232.311-0.223-0.2230.0000.0000.0000.000
193H220THR00.0280.02533.846-0.323-0.3230.0000.0000.0000.000
194H221LYS10.8650.91232.432-9.338-9.3380.0000.0000.0000.000
195H222VAL0-0.029-0.00836.097-0.249-0.2490.0000.0000.0000.000
196H223ASP-1-0.822-0.89937.3028.8648.8640.0000.0000.0000.000
197H224LYS10.9080.96039.646-7.435-7.4350.0000.0000.0000.000