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: 173VZ

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1966812.95255
FMO2-HF: Nuclear repulsion 1890442.74458
FMO2-HF: Total energy -76370.20797
FMO2-MP2: Total energy -76591.10315


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.
-42.862-65.81744.45-13.091-8.4040.086
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 : -0.901 / q_NPA : -0.960
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].
3H3GLN0-0.053-0.0331.549-24.020-47.21344.454-13.007-8.2530.086
4H4LEU00.010-0.0125.055-7.406-7.389-0.001-0.007-0.0090.000
5H5VAL00.0090.0206.8690.8170.8170.0000.0000.0000.000
6H6GLN00.011-0.0199.355-1.670-1.6700.0000.0000.0000.000
7H7SER00.0310.03713.0500.3890.3890.0000.0000.0000.000
8H8GLY00.002-0.00315.8930.1290.1290.0000.0000.0000.000
9H9ALA0-0.024-0.01317.799-0.330-0.3300.0000.0000.0000.000
10H11GLU-1-0.879-0.93820.59013.46313.4630.0000.0000.0000.000
11H12VAL0-0.056-0.03423.783-0.192-0.1920.0000.0000.0000.000
12H13LYS10.8990.95626.923-11.524-11.5240.0000.0000.0000.000
13H14LYS10.9110.96230.009-9.254-9.2540.0000.0000.0000.000
14H15PRO0-0.026-0.03033.1400.1290.1290.0000.0000.0000.000
15H16GLY0-0.0140.01034.496-0.259-0.2590.0000.0000.0000.000
16H17GLU-1-0.881-0.93831.5799.9799.9790.0000.0000.0000.000
17H18SER0-0.042-0.02930.1360.1080.1080.0000.0000.0000.000
18H19LEU0-0.033-0.01123.6010.0400.0400.0000.0000.0000.000
19H20LYS10.9180.97022.533-13.228-13.2280.0000.0000.0000.000
20H21ILE00.0030.02419.0820.1860.1860.0000.0000.0000.000
21H22SER00.008-0.02516.1810.0060.0060.0000.0000.0000.000
22H23CYS0-0.064-0.00513.2200.5800.5800.0000.0000.0000.000
23H24LYS10.9400.99310.397-23.998-23.9980.0000.0000.0000.000
24H25GLY00.0080.0049.2482.8342.8340.0000.0000.0000.000
25H26SER0-0.065-0.0355.1800.3620.481-0.001-0.008-0.1100.000
26H27GLY00.0790.0343.8693.5943.598-0.001-0.0580.0540.000
27H28TYR0-0.012-0.0154.733-0.0680.030-0.001-0.011-0.0860.000
28H29SER0-0.0020.0007.683-0.826-0.8260.0000.0000.0000.000
29H30PHE00.0750.03111.351-0.998-0.9980.0000.0000.0000.000
30H35THR0-0.027-0.02813.037-0.855-0.8550.0000.0000.0000.000
31H36SER00.0150.02513.935-0.626-0.6260.0000.0000.0000.000
32H37TYR00.0060.02311.5460.0480.0480.0000.0000.0000.000
33H38TRP0-0.0220.00915.718-0.078-0.0780.0000.0000.0000.000
34H39ILE0-0.017-0.01213.8081.4391.4390.0000.0000.0000.000
35H40GLY00.0220.01816.962-1.379-1.3790.0000.0000.0000.000
36H41TRP00.006-0.00617.1651.2361.2360.0000.0000.0000.000
37H42VAL00.006-0.01318.956-0.845-0.8450.0000.0000.0000.000
38H43ARG10.8540.90720.341-11.267-11.2670.0000.0000.0000.000
39H44GLN0-0.0070.00021.0710.4510.4510.0000.0000.0000.000
40H45MET00.0060.00923.567-0.085-0.0850.0000.0000.0000.000
41H46PRO00.0520.01426.2110.2130.2130.0000.0000.0000.000
42H47GLY00.0000.00226.491-0.443-0.4430.0000.0000.0000.000
43H48LYS10.8800.94826.948-10.757-10.7570.0000.0000.0000.000
44H49GLY00.0340.01625.1650.4480.4480.0000.0000.0000.000
45H50LEU0-0.006-0.00420.247-0.044-0.0440.0000.0000.0000.000
46H51GLU-1-0.815-0.90223.75811.04411.0440.0000.0000.0000.000
47H52TRP00.0250.02622.0140.2460.2460.0000.0000.0000.000
48H53MET0-0.051-0.00723.243-0.392-0.3920.0000.0000.0000.000
49H54GLY00.043-0.00923.236-0.702-0.7020.0000.0000.0000.000
50H55ILE0-0.086-0.02719.7190.8410.8410.0000.0000.0000.000
51H56ILE0-0.020-0.00420.131-0.671-0.6710.0000.0000.0000.000
52H57TYR0-0.017-0.07019.4241.0021.0020.0000.0000.0000.000
53H58PRO0-0.023-0.00616.773-0.725-0.7250.0000.0000.0000.000
54H59GLY00.0070.00319.861-0.327-0.3270.0000.0000.0000.000
55H62ASP-1-0.871-0.95421.05512.01412.0140.0000.0000.0000.000
56H63SER0-0.065-0.03723.250-0.346-0.3460.0000.0000.0000.000
57H64ASP-1-0.756-0.82024.55111.15411.1540.0000.0000.0000.000
58H65THR0-0.021-0.03524.6300.7780.7780.0000.0000.0000.000
59H66ARG10.7820.86825.787-11.895-11.8950.0000.0000.0000.000
60H67TYR00.0420.03126.2250.6130.6130.0000.0000.0000.000
61H68SER00.0240.02127.589-0.476-0.4760.0000.0000.0000.000
62H69PRO00.022-0.01129.248-0.080-0.0800.0000.0000.0000.000
63H70SER0-0.0120.00031.637-0.295-0.2950.0000.0000.0000.000
64H71PHE00.007-0.00427.671-0.083-0.0830.0000.0000.0000.000
65H72GLN00.0460.02830.4590.2030.2030.0000.0000.0000.000
66H74GLY0-0.034-0.01232.081-0.270-0.2700.0000.0000.0000.000
67H75GLN0-0.063-0.03431.261-0.208-0.2080.0000.0000.0000.000
68H76VAL0-0.036-0.02025.8160.1480.1480.0000.0000.0000.000
69H77THR0-0.044-0.01526.904-0.270-0.2700.0000.0000.0000.000
70H78ILE00.000-0.00221.6710.4380.4380.0000.0000.0000.000
71H79SER0-0.016-0.01022.555-0.381-0.3810.0000.0000.0000.000
72H80ALA00.029-0.00719.3460.8500.8500.0000.0000.0000.000
73H81ASP-1-0.816-0.86919.22414.03014.0300.0000.0000.0000.000
74H82LYS10.9160.95717.622-12.600-12.6000.0000.0000.0000.000
75H83SER0-0.083-0.05516.9940.7770.7770.0000.0000.0000.000
76H84ILE00.0060.00815.6320.6810.6810.0000.0000.0000.000
77H85SER0-0.040-0.02712.0921.5131.5130.0000.0000.0000.000
78H86THR0-0.010-0.00613.1631.9651.9650.0000.0000.0000.000
79H87ALA00.0000.00015.621-1.251-1.2510.0000.0000.0000.000
80H88TYR0-0.029-0.04217.3970.6340.6340.0000.0000.0000.000
81H89LEU00.0240.03920.070-0.425-0.4250.0000.0000.0000.000
82H90GLN00.005-0.00922.1210.2730.2730.0000.0000.0000.000
83H91TRP00.0540.02123.151-0.195-0.1950.0000.0000.0000.000
84H92SER00.000-0.01028.6570.0600.0600.0000.0000.0000.000
85H93SER00.008-0.00131.781-0.193-0.1930.0000.0000.0000.000
86H94LEU0-0.0170.01727.563-0.024-0.0240.0000.0000.0000.000
87H95LYS10.9670.97431.680-10.079-10.0790.0000.0000.0000.000
88H96ALA00.0490.01631.7730.2970.2970.0000.0000.0000.000
89H97SER00.000-0.01331.8030.1690.1690.0000.0000.0000.000
90H98ASP-1-0.851-0.90528.23410.87810.8780.0000.0000.0000.000
91H99THR0-0.0300.02827.1300.6180.6180.0000.0000.0000.000
92H100ALA0-0.024-0.01424.487-0.217-0.2170.0000.0000.0000.000
93H101MET00.0270.03118.6790.3920.3920.0000.0000.0000.000
94H102TYR0-0.056-0.07819.773-0.512-0.5120.0000.0000.0000.000
95H103TYR00.0180.01914.6970.8480.8480.0000.0000.0000.000
96H105ALA00.032-0.00213.2891.5081.5080.0000.0000.0000.000
97H106ARG10.8770.9278.948-28.583-28.5830.0000.0000.0000.000
98H107PRO0-0.0120.01113.3620.7580.7580.0000.0000.0000.000
99H108HIS0-0.0230.00611.5960.4180.4180.0000.0000.0000.000
100H109TYR0-0.030-0.01113.2440.5380.5380.0000.0000.0000.000
101H110TYR0-0.024-0.02514.6290.0260.0260.0000.0000.0000.000
102H111ASP-1-0.840-0.88016.16514.30914.3090.0000.0000.0000.000
103H112SER0-0.0180.00218.861-1.073-1.0730.0000.0000.0000.000
104H112LEU0-0.061-0.03819.2800.6540.6540.0000.0000.0000.000
105H113ASP-1-0.865-0.93118.06015.01915.0190.0000.0000.0000.000
106H114ALA0-0.007-0.01718.1300.2970.2970.0000.0000.0000.000
107H115PHE0-0.049-0.03315.2490.4410.4410.0000.0000.0000.000
108H116ASP-1-0.761-0.89210.79226.54126.5410.0000.0000.0000.000
109H117ILE0-0.0250.0117.2682.6422.6420.0000.0000.0000.000
110H118TRP0-0.013-0.0179.843-3.989-3.9890.0000.0000.0000.000
111H119GLY00.0380.0229.3753.5113.5110.0000.0000.0000.000
112H120GLN0-0.014-0.01110.1670.4230.4230.0000.0000.0000.000
113H121GLY0-0.007-0.00211.717-1.690-1.6900.0000.0000.0000.000
114H122THR0-0.047-0.03115.2040.4810.4810.0000.0000.0000.000
115H123MET0-0.016-0.00517.822-0.538-0.5380.0000.0000.0000.000
116H124VAL00.0040.00621.105-0.100-0.1000.0000.0000.0000.000
117H125THR0-0.018-0.01624.152-0.320-0.3200.0000.0000.0000.000
118H126VAL0-0.0040.00527.487-0.115-0.1150.0000.0000.0000.000
119H127SER00.017-0.01030.543-0.332-0.3320.0000.0000.0000.000
120H128SER00.0110.00033.7450.0670.0670.0000.0000.0000.000
121H129ALA00.0200.02335.579-0.227-0.2270.0000.0000.0000.000
122H130SER0-0.007-0.02235.5730.2300.2300.0000.0000.0000.000
123H131THR0-0.024-0.01332.7240.0260.0260.0000.0000.0000.000
124H132LYS10.8810.95234.949-8.332-8.3320.0000.0000.0000.000
125H133GLY00.0560.04035.7970.2580.2580.0000.0000.0000.000
126H134PRO0-0.064-0.02435.234-0.202-0.2020.0000.0000.0000.000
127H135SER0-0.009-0.00438.023-0.198-0.1980.0000.0000.0000.000
128H136VAL00.0090.00038.4000.1210.1210.0000.0000.0000.000
129H137PHE0-0.011-0.00541.048-0.210-0.2100.0000.0000.0000.000
130H138PRO0-0.0070.00942.5870.1780.1780.0000.0000.0000.000
131H139LEU0-0.042-0.00840.845-0.105-0.1050.0000.0000.0000.000
132H140ALA00.015-0.00744.6370.0660.0660.0000.0000.0000.000
133H141PRO00.0340.02946.747-0.091-0.0910.0000.0000.0000.000
134H150THR00.001-0.01643.418-0.074-0.0740.0000.0000.0000.000
135H151ALA0-0.0130.00146.019-0.049-0.0490.0000.0000.0000.000
136H152ALA0-0.008-0.00141.9860.1590.1590.0000.0000.0000.000
137H153LEU00.0010.00641.738-0.205-0.2050.0000.0000.0000.000
138H154GLY00.0390.00139.9850.2520.2520.0000.0000.0000.000
139H155CYS0-0.0570.01636.963-0.119-0.1190.0000.0000.0000.000
140H156LEU00.0100.00038.6700.2050.2050.0000.0000.0000.000
141H157VAL0-0.026-0.01735.031-0.148-0.1480.0000.0000.0000.000
142H158LYS10.9260.96737.171-7.502-7.5020.0000.0000.0000.000
143H159ASP-1-0.820-0.91938.7577.7817.7810.0000.0000.0000.000
144H160TYR0-0.024-0.02331.259-0.206-0.2060.0000.0000.0000.000
145H161PHE00.0230.02231.5140.1750.1750.0000.0000.0000.000
146H162PRO00.0240.01428.825-0.238-0.2380.0000.0000.0000.000
147H163GLU-1-0.770-0.88527.26411.14311.1430.0000.0000.0000.000
148H164PRO0-0.011-0.01224.3900.1990.1990.0000.0000.0000.000
149H165VAL00.007-0.01527.624-0.180-0.1800.0000.0000.0000.000
150H166THR0-0.071-0.03126.1940.3870.3870.0000.0000.0000.000
151H167VAL00.0220.00129.162-0.339-0.3390.0000.0000.0000.000
152H168SER0-0.035-0.00230.6700.1890.1890.0000.0000.0000.000
153H169TRP00.0520.00532.170-0.372-0.3720.0000.0000.0000.000
154H170ASN00.0060.03734.8960.0660.0660.0000.0000.0000.000
155H171SER00.012-0.00433.943-0.012-0.0120.0000.0000.0000.000
156H172GLY0-0.0120.00031.4930.1310.1310.0000.0000.0000.000
157H173ALA00.0000.01732.0150.1470.1470.0000.0000.0000.000
158H174LEU0-0.028-0.00834.533-0.006-0.0060.0000.0000.0000.000
159H175THR00.0300.00330.0320.0340.0340.0000.0000.0000.000
160H176SER00.0100.00132.5900.1710.1710.0000.0000.0000.000
161H177GLY00.0250.00634.591-0.244-0.2440.0000.0000.0000.000
162H178VAL0-0.054-0.01731.933-0.109-0.1090.0000.0000.0000.000
163H179HIS00.0180.02232.3090.4900.4900.0000.0000.0000.000
164H180THR00.003-0.00730.289-0.452-0.4520.0000.0000.0000.000
165H181PHE0-0.031-0.01330.5620.3340.3340.0000.0000.0000.000
166H182PRO00.018-0.00229.1320.0840.0840.0000.0000.0000.000
167H183ALA0-0.0060.01530.433-0.411-0.4110.0000.0000.0000.000
168H184VAL0-0.0090.00232.2090.1160.1160.0000.0000.0000.000
169H185LEU0-0.035-0.02433.313-0.034-0.0340.0000.0000.0000.000
170H186GLN0-0.071-0.05135.531-0.373-0.3730.0000.0000.0000.000
171H187SER00.0290.00438.7280.1380.1380.0000.0000.0000.000
172H188SER0-0.003-0.00540.8510.0240.0240.0000.0000.0000.000
173H189GLY00.0240.02237.362-0.015-0.0150.0000.0000.0000.000
174H190LEU0-0.081-0.02536.0420.2840.2840.0000.0000.0000.000
175H191TYR00.0360.01530.369-0.079-0.0790.0000.0000.0000.000
176H192SER00.002-0.01535.337-0.328-0.3280.0000.0000.0000.000
177H193LEU00.0210.03731.3850.1090.1090.0000.0000.0000.000
178H194SER00.0240.00735.443-0.355-0.3550.0000.0000.0000.000
179H195SER0-0.0320.00033.7340.2010.2010.0000.0000.0000.000
180H196VAL00.0390.00935.663-0.274-0.2740.0000.0000.0000.000
181H197VAL00.0320.01736.4280.1240.1240.0000.0000.0000.000
182H208THR00.007-0.02245.601-0.055-0.0550.0000.0000.0000.000
183H209TYR0-0.005-0.03840.9330.0400.0400.0000.0000.0000.000
184H210ILE00.0100.00239.4820.0690.0690.0000.0000.0000.000
185H212ASN0-0.006-0.00434.261-0.190-0.1900.0000.0000.0000.000
186H213VAL00.0320.01433.6560.3790.3790.0000.0000.0000.000
187H214ASN0-0.045-0.03829.961-0.226-0.2260.0000.0000.0000.000
188H215HIS00.0460.03530.7530.0930.0930.0000.0000.0000.000
189H216LYS10.9800.98024.865-12.846-12.8460.0000.0000.0000.000
190H217PRO0-0.0020.01527.871-0.144-0.1440.0000.0000.0000.000
191H218SER0-0.010-0.01630.221-0.242-0.2420.0000.0000.0000.000
192H219ASN0-0.064-0.03232.070-0.191-0.1910.0000.0000.0000.000
193H220THR00.0230.01833.631-0.349-0.3490.0000.0000.0000.000
194H221LYS10.9290.94631.498-9.747-9.7470.0000.0000.0000.000
195H222VAL0-0.025-0.00436.006-0.258-0.2580.0000.0000.0000.000
196H223ASP-1-0.829-0.90637.1778.9408.9400.0000.0000.0000.000
197H224LYS10.9000.94439.435-7.509-7.5090.0000.0000.0000.000