Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 72ZKK

Calculation Name: 4X80-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X80

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2279507.503428
FMO2-HF: Nuclear repulsion 2194166.003236
FMO2-HF: Total energy -85341.500192
FMO2-MP2: Total energy -85587.385018


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.
-28.638-25.390.059-1.255-2.0520.006
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 : -0.958 / q_NPA : -0.992
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].
3H3LYS10.8370.9133.066-62.298-59.4740.062-1.142-1.7440.006
4H4LEU00.011-0.0065.068-3.011-2.965-0.001-0.004-0.0410.000
5H5GLU-1-0.821-0.8976.88143.03343.0330.0000.0000.0000.000
6H6GLU-1-0.764-0.87110.19120.79720.7970.0000.0000.0000.000
7H7SER0-0.028-0.01714.020-0.020-0.0200.0000.0000.0000.000
8H8GLY00.012-0.00816.969-0.412-0.4120.0000.0000.0000.000
9H9GLY00.0340.02520.171-0.686-0.6860.0000.0000.0000.000
10H10GLY0-0.011-0.01122.0400.0440.0440.0000.0000.0000.000
11H11LEU0-0.037-0.01825.080-0.079-0.0790.0000.0000.0000.000
12H12VAL0-0.027-0.00528.850-0.070-0.0700.0000.0000.0000.000
13H13GLN00.0210.01731.476-0.111-0.1110.0000.0000.0000.000
14H14PRO00.021-0.01234.3900.1180.1180.0000.0000.0000.000
15H15GLY0-0.046-0.01635.687-0.192-0.1920.0000.0000.0000.000
16H16GLY0-0.0180.00033.802-0.042-0.0420.0000.0000.0000.000
17H17SER0-0.010-0.04130.297-0.073-0.0730.0000.0000.0000.000
18H18MET0-0.033-0.00524.6570.1290.1290.0000.0000.0000.000
19H19LYS10.8510.94420.680-14.280-14.2800.0000.0000.0000.000
20H20LEU00.0310.02919.5420.4120.4120.0000.0000.0000.000
21H21SER0-0.021-0.03317.444-0.663-0.6630.0000.0000.0000.000
22H22CYS0-0.064-0.02012.879-0.129-0.1290.0000.0000.0000.000
23H23ALA00.0190.02910.613-1.124-1.1240.0000.0000.0000.000
24H24ALA00.0540.0178.7451.3021.3020.0000.0000.0000.000
25H25SER0-0.012-0.0084.7160.4400.599-0.001-0.007-0.1520.000
26H26GLY00.0650.0334.1380.6830.7520.000-0.0850.0160.000
27H27PHE0-0.039-0.0244.719-1.817-1.667-0.001-0.017-0.1310.000
28H28THR0-0.003-0.0158.3480.5540.5540.0000.0000.0000.000
29H29SER0-0.006-0.04211.937-0.578-0.5780.0000.0000.0000.000
30H30SER0-0.060-0.02913.610-1.143-1.1430.0000.0000.0000.000
31H31ASP-1-0.801-0.85015.27816.04116.0410.0000.0000.0000.000
32H32ALA0-0.0090.01313.515-0.381-0.3810.0000.0000.0000.000
33H33TRP0-0.057-0.02615.669-0.851-0.8510.0000.0000.0000.000
34H34MET00.0000.01112.6441.0571.0570.0000.0000.0000.000
35H35ASH0-0.010-0.06516.790-1.016-1.0160.0000.0000.0000.000
36H36TRP00.0100.01316.8970.9140.9140.0000.0000.0000.000
37H37VAL0-0.010-0.01119.104-0.834-0.8340.0000.0000.0000.000
38H38ARG10.7840.90220.123-10.358-10.3580.0000.0000.0000.000
39H39GLN00.0350.02520.9570.2450.2450.0000.0000.0000.000
40H40SER0-0.009-0.02323.6710.1520.1520.0000.0000.0000.000
41H41PRO0-0.007-0.00326.9890.0090.0090.0000.0000.0000.000
42H42GLU-1-0.852-0.91129.6559.9139.9130.0000.0000.0000.000
43H43LYS10.8340.90829.106-9.959-9.9590.0000.0000.0000.000
44H44GLY00.0210.02827.4330.0070.0070.0000.0000.0000.000
45H45LEU0-0.024-0.02921.1400.5010.5010.0000.0000.0000.000
46H46GLU-1-0.795-0.87124.6469.9229.9220.0000.0000.0000.000
47H47TRP00.0270.01621.7870.1640.1640.0000.0000.0000.000
48H48VAL0-0.026-0.00923.237-0.583-0.5830.0000.0000.0000.000
49H49ALA00.020-0.00523.062-0.539-0.5390.0000.0000.0000.000
50H50GLU-1-0.788-0.81221.11813.55913.5590.0000.0000.0000.000
51H51ILE0-0.045-0.02219.796-0.674-0.6740.0000.0000.0000.000
52H52ARG10.8630.93020.230-10.940-10.9400.0000.0000.0000.000
53H53ASN00.0680.02321.5320.3330.3330.0000.0000.0000.000
54H54DLY00.0450.04822.324-0.638-0.6380.0000.0000.0000.000
55H55ALA0-0.004-0.01624.2540.0690.0690.0000.0000.0000.000
56H56ASN0-0.0080.01525.885-0.105-0.1050.0000.0000.0000.000
57H57ASN0-0.011-0.02225.125-0.337-0.3370.0000.0000.0000.000
58H58HIS00.0390.03228.603-0.022-0.0220.0000.0000.0000.000
59H59ALA00.0150.00725.7560.2460.2460.0000.0000.0000.000
60H60ARG10.8600.91325.054-10.830-10.8300.0000.0000.0000.000
61H61HIS0-0.026-0.00725.935-0.587-0.5870.0000.0000.0000.000
62H62TYR00.014-0.00326.1900.5710.5710.0000.0000.0000.000
63H63ASN00.0070.01127.779-0.665-0.6650.0000.0000.0000.000
64H64GLU-1-0.754-0.86629.4518.6588.6580.0000.0000.0000.000
65H65SER0-0.027-0.01431.528-0.223-0.2230.0000.0000.0000.000
66H66VAL00.013-0.00927.703-0.116-0.1160.0000.0000.0000.000
67H67LYS10.8230.90031.135-8.642-8.6420.0000.0000.0000.000
68H68GLY0-0.015-0.00332.640-0.224-0.2240.0000.0000.0000.000
69H69ARG10.7190.84331.625-9.543-9.5430.0000.0000.0000.000
70H70PHE00.026-0.00126.3400.1770.1770.0000.0000.0000.000
71H71THR0-0.074-0.04526.643-0.311-0.3110.0000.0000.0000.000
72H72ILE00.0070.03420.1100.2730.2730.0000.0000.0000.000
73H73SER0-0.039-0.04321.859-0.618-0.6180.0000.0000.0000.000
74H74ARG10.8060.87317.399-14.672-14.6720.0000.0000.0000.000
75H75ASP-1-0.785-0.84518.42713.91113.9110.0000.0000.0000.000
76H76ASP-1-0.716-0.82916.33517.34417.3440.0000.0000.0000.000
77H77SER0-0.109-0.07216.3700.5560.5560.0000.0000.0000.000
78H78LYS10.8200.88815.749-14.655-14.6550.0000.0000.0000.000
79H79SER0-0.0180.00510.4000.6150.6150.0000.0000.0000.000
80H80SER00.0000.01112.3380.9580.9580.0000.0000.0000.000
81H81VAL00.014-0.00114.825-1.209-1.2090.0000.0000.0000.000
82H82TYR0-0.039-0.04516.9530.2230.2230.0000.0000.0000.000
83H83LEU00.0140.00419.695-0.405-0.4050.0000.0000.0000.000
84H84GLN00.0300.02122.4390.1900.1900.0000.0000.0000.000
85H85MET0-0.0240.00324.747-0.120-0.1200.0000.0000.0000.000
86H86ASN00.0500.02827.978-0.033-0.0330.0000.0000.0000.000
87H87SER00.0040.00031.753-0.016-0.0160.0000.0000.0000.000
88H88LEU0-0.0130.01528.514-0.092-0.0920.0000.0000.0000.000
89H89ARG10.8770.91832.507-9.187-9.1870.0000.0000.0000.000
90H90ALA00.0640.02932.3820.2740.2740.0000.0000.0000.000
91H91GLU-1-0.809-0.89031.9569.4219.4210.0000.0000.0000.000
92H92ASP-1-0.764-0.83928.65910.21610.2160.0000.0000.0000.000
93H93SER00.0110.00727.3900.4500.4500.0000.0000.0000.000
94H94GLY00.0240.00825.239-0.182-0.1820.0000.0000.0000.000
95H95ILE0-0.041-0.00618.7670.1150.1150.0000.0000.0000.000
96H96TYR0-0.038-0.05320.014-0.312-0.3120.0000.0000.0000.000
97H97TYR00.005-0.01014.9260.7860.7860.0000.0000.0000.000
98H99THR00.002-0.02513.5250.9180.9180.0000.0000.0000.000
99H100ARG10.8010.8799.461-22.987-22.9870.0000.0000.0000.000
100H101THR0-0.022-0.02114.5610.0320.0320.0000.0000.0000.000
101H102TYR00.000-0.02716.612-0.621-0.6210.0000.0000.0000.000
102H103TYR0-0.017-0.01810.4671.6481.6480.0000.0000.0000.000
103H104TYR00.024-0.00212.954-0.286-0.2860.0000.0000.0000.000
104H105GLY00.0320.02517.2620.1860.1860.0000.0000.0000.000
105H106SER0-0.013-0.00920.077-0.099-0.0990.0000.0000.0000.000
106H107SER0-0.028-0.00621.223-0.590-0.5900.0000.0000.0000.000
107H108TYR00.0180.00320.0570.4790.4790.0000.0000.0000.000
108H109GLY0-0.013-0.00620.340-0.479-0.4790.0000.0000.0000.000
109H110TYR0-0.013-0.00616.875-0.531-0.5310.0000.0000.0000.000
110H111CYS0-0.023-0.01215.7730.1330.1330.0000.0000.0000.000
111H112ASP-1-0.776-0.85112.14620.79320.7930.0000.0000.0000.000
112H113VAL0-0.031-0.0028.1821.4431.4430.0000.0000.0000.000
113H114TRP0-0.020-0.03210.285-2.212-2.2120.0000.0000.0000.000
114H115GLY00.0330.0309.8832.3552.3550.0000.0000.0000.000
115H116THR0-0.055-0.03510.294-0.003-0.0030.0000.0000.0000.000
116H117GLY0-0.004-0.00212.514-1.406-1.4060.0000.0000.0000.000
117H118THR0-0.059-0.03415.7780.0190.0190.0000.0000.0000.000
118H119THR00.002-0.00318.314-0.316-0.3160.0000.0000.0000.000
119H120VAL00.0090.01121.965-0.087-0.0870.0000.0000.0000.000
120H121THR0-0.005-0.00124.949-0.216-0.2160.0000.0000.0000.000
121H122VAL00.0030.00328.560-0.066-0.0660.0000.0000.0000.000
122H123SER00.0380.01231.719-0.326-0.3260.0000.0000.0000.000
123H124SER00.0170.00834.9180.1210.1210.0000.0000.0000.000
124H125DAL00.0320.02236.820-0.235-0.2350.0000.0000.0000.000
125H126LYS10.8820.93736.288-7.783-7.7830.0000.0000.0000.000
126H127THR00.0020.00431.799-0.037-0.0370.0000.0000.0000.000
127H128THR0-0.023-0.00734.272-0.283-0.2830.0000.0000.0000.000
128H129PRO00.0240.01433.4730.2510.2510.0000.0000.0000.000
129H130PRO0-0.022-0.00131.991-0.242-0.2420.0000.0000.0000.000
130H131SER00.0030.01235.160-0.124-0.1240.0000.0000.0000.000
131H132VAL0-0.019-0.02234.0360.1140.1140.0000.0000.0000.000
132H133TYR0-0.024-0.01337.231-0.152-0.1520.0000.0000.0000.000
133H134PRO00.0160.00238.6340.1950.1950.0000.0000.0000.000
134H135LEU0-0.041-0.01738.735-0.204-0.2040.0000.0000.0000.000
135H136ALA00.0260.01040.7940.1730.1730.0000.0000.0000.000
136H137PRO00.0100.00143.090-0.112-0.1120.0000.0000.0000.000
137H138GLY00.0370.03046.092-0.061-0.0610.0000.0000.0000.000
138H139SER00.014-0.01849.757-0.003-0.0030.0000.0000.0000.000
139H140ALA00.0110.01852.349-0.053-0.0530.0000.0000.0000.000
140H141ALA0-0.026-0.00548.903-0.052-0.0520.0000.0000.0000.000
141H142GLN0-0.014-0.02251.032-0.015-0.0150.0000.0000.0000.000
142H143THR0-0.062-0.01746.3080.0630.0630.0000.0000.0000.000
143H144ASN00.0420.03445.484-0.183-0.1830.0000.0000.0000.000
144H145SER00.0410.02844.5390.0480.0480.0000.0000.0000.000
145H146MET0-0.051-0.01237.2410.1740.1740.0000.0000.0000.000
146H147VAL00.0330.02640.887-0.181-0.1810.0000.0000.0000.000
147H148THR0-0.007-0.01137.8450.2880.2880.0000.0000.0000.000
148H149LEU0-0.0080.01137.666-0.233-0.2330.0000.0000.0000.000
149H150GLY00.031-0.00136.2550.2170.2170.0000.0000.0000.000
150H151CYS0-0.0580.01031.9570.0920.0920.0000.0000.0000.000
151H152LEU0-0.0100.01335.8890.1220.1220.0000.0000.0000.000
152H153VAL00.0200.00531.781-0.088-0.0880.0000.0000.0000.000
153H154LYS10.8750.91035.157-7.790-7.7900.0000.0000.0000.000
154H155GLY00.0170.01537.507-0.072-0.0720.0000.0000.0000.000
155H156TYR0-0.009-0.02330.162-0.194-0.1940.0000.0000.0000.000
156H157PHE00.0450.02332.8140.0230.0230.0000.0000.0000.000
157H158PRO00.0040.01228.485-0.135-0.1350.0000.0000.0000.000
158H159GLU-1-0.754-0.86426.64311.11411.1140.0000.0000.0000.000
159H160PRO0-0.040-0.01622.7490.1120.1120.0000.0000.0000.000
160H161VAL0-0.027-0.01425.973-0.029-0.0290.0000.0000.0000.000
161H162THR0-0.043-0.02222.0970.4810.4810.0000.0000.0000.000
162H163VAL00.013-0.01425.260-0.395-0.3950.0000.0000.0000.000
163H164THR0-0.025-0.00723.9490.4580.4580.0000.0000.0000.000
164H165TRP00.0270.01227.172-0.618-0.6180.0000.0000.0000.000
165H166ASN00.001-0.02128.4990.2360.2360.0000.0000.0000.000
166H167SER0-0.020-0.01426.7060.0500.0500.0000.0000.0000.000
167H168GLY00.0300.02724.1360.5450.5450.0000.0000.0000.000
168H169SER0-0.033-0.02925.0960.2750.2750.0000.0000.0000.000
169H170LEU0-0.054-0.01627.072-0.270-0.2700.0000.0000.0000.000
170H171SER00.0330.00324.360-0.038-0.0380.0000.0000.0000.000
171H172SER00.0000.00526.4530.2860.2860.0000.0000.0000.000
172H173GLY00.0200.01029.025-0.257-0.2570.0000.0000.0000.000
173H174VAL0-0.037-0.01327.446-0.358-0.3580.0000.0000.0000.000
174H175HIS00.0100.01330.0810.2750.2750.0000.0000.0000.000
175H176THR00.003-0.00527.992-0.372-0.3720.0000.0000.0000.000
176H177PHE0-0.0250.00629.3720.2580.2580.0000.0000.0000.000
177H178PRO00.018-0.00529.1550.0700.0700.0000.0000.0000.000
178H179ALA00.0130.02430.400-0.364-0.3640.0000.0000.0000.000
179H180VAL0-0.017-0.01032.379-0.004-0.0040.0000.0000.0000.000
180H181LEU0-0.013-0.00434.812-0.051-0.0510.0000.0000.0000.000
181H182GLN00.0170.00436.860-0.166-0.1660.0000.0000.0000.000
182H183SER0-0.027-0.02340.5400.0220.0220.0000.0000.0000.000
183H184ASP-1-0.899-0.95338.1978.1768.1760.0000.0000.0000.000
184H185LEU0-0.0330.00136.8990.1810.1810.0000.0000.0000.000
185H186TYR00.0260.00831.345-0.095-0.0950.0000.0000.0000.000
186H187THR0-0.041-0.02135.353-0.284-0.2840.0000.0000.0000.000
187H188LEU00.0470.04329.2290.0320.0320.0000.0000.0000.000
188H189SER00.003-0.00733.557-0.159-0.1590.0000.0000.0000.000
189H190SER00.0210.00230.6090.2930.2930.0000.0000.0000.000
190H191SER00.0350.00433.084-0.376-0.3760.0000.0000.0000.000
191H192VAL0-0.020-0.00832.6110.3180.3180.0000.0000.0000.000
192H193THR0-0.004-0.00834.468-0.266-0.2660.0000.0000.0000.000
193H194VAL0-0.007-0.00735.0220.2790.2790.0000.0000.0000.000
194H195PRO00.0560.02237.104-0.243-0.2430.0000.0000.0000.000
195H196SER00.013-0.01440.2700.1320.1320.0000.0000.0000.000
196H197SER0-0.0110.00742.344-0.082-0.0820.0000.0000.0000.000
197H198THR0-0.058-0.04636.7640.0530.0530.0000.0000.0000.000
198H199TRP0-0.045-0.02539.8860.0860.0860.0000.0000.0000.000
199H200PRO0-0.0150.00041.763-0.091-0.0910.0000.0000.0000.000
200H201SER00.0590.00241.613-0.139-0.1390.0000.0000.0000.000
201H202GLN00.0640.04037.4770.0600.0600.0000.0000.0000.000
202H203THR0-0.049-0.02836.530-0.221-0.2210.0000.0000.0000.000
203H204VAL00.0390.04934.7930.2310.2310.0000.0000.0000.000
204H205THR0-0.019-0.02833.118-0.329-0.3290.0000.0000.0000.000
205H207ASN00.004-0.01128.170-0.026-0.0260.0000.0000.0000.000
206H208VAL00.0160.00128.9750.1790.1790.0000.0000.0000.000
207H209ALA00.0210.00225.576-0.150-0.1500.0000.0000.0000.000
208H210HIS00.0200.02426.9830.1220.1220.0000.0000.0000.000
209H211PRO00.0500.01523.079-0.294-0.2940.0000.0000.0000.000
210H212ALA00.0060.01225.773-0.124-0.1240.0000.0000.0000.000
211H213SER0-0.004-0.02027.939-0.314-0.3140.0000.0000.0000.000
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