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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: QY6KY

Calculation Name: 4W6R-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4W6R

Chain ID: M

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-19

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1945291.398145
FMO2-HF: Nuclear repulsion 1873263.901428
FMO2-HF: Total energy -72027.496717
FMO2-MP2: Total energy -72239.813493


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(M:6:GLU)


Summations of interaction energy for fragment #1(M:6: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.
-26.67-23.1340.496-1.642-2.390.003
Interaction energy analysis for fragmet #1(M:6:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.940 / q_NPA : -0.991
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].
3M8PHE0-0.017-0.0123.221-8.255-5.725-0.011-1.154-1.3660.001
4M9THR0-0.058-0.0072.558-7.512-6.5480.508-0.486-0.9850.002
5M10GLY0-0.0030.0015.250-1.945-1.903-0.001-0.002-0.0390.000
6M11VAL0-0.012-0.0159.009-0.604-0.6040.0000.0000.0000.000
7M12VAL00.0330.0198.1750.1510.1510.0000.0000.0000.000
8M13PRO0-0.035-0.01411.389-1.214-1.2140.0000.0000.0000.000
9M14ILE00.0140.00513.6960.6290.6290.0000.0000.0000.000
10M15LEU00.0150.01715.896-0.918-0.9180.0000.0000.0000.000
11M16ILE0-0.045-0.01318.1400.3610.3610.0000.0000.0000.000
12M17GLU-1-0.962-0.99720.51011.46211.4620.0000.0000.0000.000
13M18LEU0-0.017-0.00123.2540.2190.2190.0000.0000.0000.000
14M19ASP-1-0.859-0.93625.8269.8579.8570.0000.0000.0000.000
15M20GLY00.011-0.02629.0100.1350.1350.0000.0000.0000.000
16M21ASP-1-0.879-0.93831.6238.2698.2690.0000.0000.0000.000
17M22VAL0-0.009-0.02134.4970.0500.0500.0000.0000.0000.000
18M23ASN0-0.015-0.00136.905-0.016-0.0160.0000.0000.0000.000
19M24GLY0-0.0010.01139.493-0.188-0.1880.0000.0000.0000.000
20M25HIS0-0.026-0.02139.502-0.009-0.0090.0000.0000.0000.000
21M26LYS10.9490.98536.346-7.311-7.3110.0000.0000.0000.000
22M27PHE0-0.050-0.03134.091-0.154-0.1540.0000.0000.0000.000
23M28PHE0-0.0140.02330.0370.1180.1180.0000.0000.0000.000
24M29VAL0-0.038-0.02326.426-0.180-0.1800.0000.0000.0000.000
25M30ARG10.9910.99924.198-11.401-11.4010.0000.0000.0000.000
26M31GLY0-0.049-0.03823.654-0.363-0.3630.0000.0000.0000.000
27M32GLU-1-1.003-0.99921.68112.26112.2610.0000.0000.0000.000
28M33GLY00.0590.04116.833-0.006-0.0060.0000.0000.0000.000
29M43SER0-0.012-0.01718.465-0.010-0.0100.0000.0000.0000.000
30M44LEU0-0.025-0.01717.7720.5000.5000.0000.0000.0000.000
31M45LYS10.8550.94021.511-10.814-10.8140.0000.0000.0000.000
32M46PHE00.0240.00121.7120.2050.2050.0000.0000.0000.000
33M47ILE00.016-0.00726.692-0.380-0.3800.0000.0000.0000.000
34M48ALA00.0250.02529.7920.1830.1830.0000.0000.0000.000
35M49THR0-0.078-0.04830.562-0.221-0.2210.0000.0000.0000.000
36M50THR00.0150.02033.216-0.221-0.2210.0000.0000.0000.000
37M51GLY00.023-0.00335.512-0.253-0.2530.0000.0000.0000.000
38M52LYS10.7820.88936.326-7.778-7.7780.0000.0000.0000.000
39M53LEU0-0.0040.00231.4180.0060.0060.0000.0000.0000.000
40M54PRO0-0.0310.01034.017-0.239-0.2390.0000.0000.0000.000
41M55VAL00.042-0.00133.5610.1710.1710.0000.0000.0000.000
42M56PRO00.0150.02334.3920.1250.1250.0000.0000.0000.000
43M57TRP00.1020.03628.2550.2980.2980.0000.0000.0000.000
44M58PRO00.008-0.00529.3770.3280.3280.0000.0000.0000.000
45M59THR0-0.045-0.04028.8110.2670.2670.0000.0000.0000.000
46M60LEU00.0480.02727.6190.1190.1190.0000.0000.0000.000
47M61VAL00.0340.04723.7950.4070.4070.0000.0000.0000.000
48M62THR0-0.030-0.03822.9000.4720.4720.0000.0000.0000.000
49M63THR0-0.100-0.05522.2670.3750.3750.0000.0000.0000.000
50M64LEU00.0320.02822.1480.3600.3600.0000.0000.0000.000
51M65ALA0-0.029-0.02118.2730.6180.6180.0000.0000.0000.000
52M68VAL00.0820.02313.6690.3190.3190.0000.0000.0000.000
53M69GLN0-0.037-0.02713.679-0.316-0.3160.0000.0000.0000.000
54M70CYS0-0.0030.0118.629-0.273-0.2730.0000.0000.0000.000
55M71PHE00.0760.0448.5871.7091.7090.0000.0000.0000.000
56M72SER0-0.042-0.00210.669-1.041-1.0410.0000.0000.0000.000
57M73ARG10.9640.9949.654-16.795-16.7950.0000.0000.0000.000
58M74TYR00.016-0.0107.455-2.525-2.5250.0000.0000.0000.000
59M75PRO0-0.045-0.02910.4530.7820.7820.0000.0000.0000.000
60M76ASP-1-0.865-0.93912.31121.95321.9530.0000.0000.0000.000
61M77HIS0-0.013-0.02113.4600.9800.9800.0000.0000.0000.000
62M78MET0-0.056-0.02313.189-0.924-0.9240.0000.0000.0000.000
63M79LYS10.9180.9878.746-28.543-28.5430.0000.0000.0000.000
64M80ARG11.0041.0158.575-19.448-19.4480.0000.0000.0000.000
65M96ARG10.8410.89520.311-12.252-12.2520.0000.0000.0000.000
66M97THR0-0.067-0.03525.780-0.267-0.2670.0000.0000.0000.000
67M98ILE0-0.002-0.00926.7070.1170.1170.0000.0000.0000.000
68M99TYR00.0370.01730.465-0.258-0.2580.0000.0000.0000.000
69M100PHE0-0.011-0.00432.0580.1090.1090.0000.0000.0000.000
70M101LYS10.9431.00835.457-7.406-7.4060.0000.0000.0000.000
71M102CYS0-0.133-0.09437.722-0.123-0.1230.0000.0000.0000.000
72M103ASP-1-0.865-0.94638.2827.2937.2930.0000.0000.0000.000
73M104GLY00.0990.04337.878-0.113-0.1130.0000.0000.0000.000
74M105THR0-0.072-0.03834.3470.2150.2150.0000.0000.0000.000
75M106TYR00.0170.00029.603-0.130-0.1300.0000.0000.0000.000
76M107LYS10.9310.96729.735-8.368-8.3680.0000.0000.0000.000
77M108THR00.0080.00324.8800.0160.0160.0000.0000.0000.000
78M109ARG10.8980.94223.395-11.311-11.3110.0000.0000.0000.000
79M110ALA00.0130.00120.033-0.184-0.1840.0000.0000.0000.000
80M111GLU-1-0.870-0.93117.81414.24914.2490.0000.0000.0000.000
81M112VAL00.0420.02912.5930.2180.2180.0000.0000.0000.000
82M113LYS10.8050.89413.536-14.336-14.3360.0000.0000.0000.000
83M114PHE0-0.046-0.01613.621-0.341-0.3410.0000.0000.0000.000
84M115GLU-1-0.867-0.9567.45629.87129.8710.0000.0000.0000.000
85M116GLY0-0.050-0.0109.3161.5421.5420.0000.0000.0000.000
86M117ASP-1-0.922-0.96711.92918.35018.3500.0000.0000.0000.000
87M118THR0-0.042-0.00712.0861.0331.0330.0000.0000.0000.000
88M119LEU0-0.0040.0159.820-0.080-0.0800.0000.0000.0000.000
89M120VAL0-0.017-0.02813.045-1.021-1.0210.0000.0000.0000.000
90M121ASN00.0200.00216.1310.7910.7910.0000.0000.0000.000
91M122ARG10.9581.01218.413-13.621-13.6210.0000.0000.0000.000
92M123ILE0-0.015-0.02121.6140.1520.1520.0000.0000.0000.000
93M124GLU-1-0.878-0.92723.76210.15410.1540.0000.0000.0000.000
94M125LEU0-0.012-0.02327.1090.0660.0660.0000.0000.0000.000
95M126LYS10.9580.98129.679-9.360-9.3600.0000.0000.0000.000
96M127GLY00.009-0.00233.0220.1130.1130.0000.0000.0000.000
97M128ILE0-0.044-0.02435.267-0.187-0.1870.0000.0000.0000.000
98M129ASP-1-0.873-0.94538.0647.4417.4410.0000.0000.0000.000
99M130PHE0-0.0160.02934.7490.0050.0050.0000.0000.0000.000
100M131LYS10.8630.91340.768-6.349-6.3490.0000.0000.0000.000
101M132GLU-1-0.856-0.93343.7406.3016.3010.0000.0000.0000.000
102M133ASP-1-0.845-0.88944.6726.5396.5390.0000.0000.0000.000
103M134GLY00.0420.01443.2510.1540.1540.0000.0000.0000.000
104M135ASN0-0.032-0.04241.334-0.224-0.2240.0000.0000.0000.000
105M136ILE00.0150.01235.2960.1030.1030.0000.0000.0000.000
106M137LEU0-0.020-0.01338.4840.0890.0890.0000.0000.0000.000
107M138GLY00.0260.01940.840-0.078-0.0780.0000.0000.0000.000
108M139HIS0-0.127-0.06939.3430.0690.0690.0000.0000.0000.000
109M140LYS10.8860.95940.268-6.706-6.7060.0000.0000.0000.000
110M141LEU0-0.064-0.02234.2100.0430.0430.0000.0000.0000.000
111M142GLU-1-0.812-0.89835.9197.8427.8420.0000.0000.0000.000
112M143TYR0-0.063-0.03833.1110.2220.2220.0000.0000.0000.000
113M144ASN00.016-0.01930.8570.0420.0420.0000.0000.0000.000
114M145PHE0-0.023-0.00125.825-0.151-0.1510.0000.0000.0000.000
115M146ASN0-0.027-0.02228.4950.1160.1160.0000.0000.0000.000
116M147SER0-0.120-0.13324.2450.3910.3910.0000.0000.0000.000
117M148HIS00.0760.04824.598-0.678-0.6780.0000.0000.0000.000
118M149LYS10.9550.99122.531-9.899-9.8990.0000.0000.0000.000
119M150VAL0-0.007-0.00319.385-0.427-0.4270.0000.0000.0000.000
120M151TYR00.0270.01820.0500.4400.4400.0000.0000.0000.000
121M152ILE00.0410.01915.361-0.186-0.1860.0000.0000.0000.000
122M153THR0-0.035-0.01219.436-0.261-0.2610.0000.0000.0000.000
123M154ALA00.0450.01719.1620.2480.2480.0000.0000.0000.000
124M155ASP-1-0.846-0.94419.97111.25711.2570.0000.0000.0000.000
125M156LYS10.9720.96421.604-11.896-11.8960.0000.0000.0000.000
126M157GLN0-0.0320.02922.7520.0210.0210.0000.0000.0000.000
127M158ASN00.013-0.01321.909-0.365-0.3650.0000.0000.0000.000
128M159ASN0-0.073-0.02719.2580.2420.2420.0000.0000.0000.000
129M160GLY00.0410.01417.2240.7920.7920.0000.0000.0000.000
130M161ILE0-0.035-0.01414.524-0.017-0.0170.0000.0000.0000.000
131M162LYS10.8860.95518.773-11.279-11.2790.0000.0000.0000.000
132M163ALA00.0400.00520.1120.4000.4000.0000.0000.0000.000
133M164ASN0-0.022-0.00622.085-0.192-0.1920.0000.0000.0000.000
134M165PHE0-0.016-0.01023.0200.2300.2300.0000.0000.0000.000
135M166THR00.0040.00426.539-0.208-0.2080.0000.0000.0000.000
136M167ILE0-0.0260.01125.6860.1070.1070.0000.0000.0000.000
137M168ARG10.9430.94729.586-8.583-8.5830.0000.0000.0000.000
138M169HIS0-0.027-0.00729.6610.1640.1640.0000.0000.0000.000
139M170ASN00.0780.04833.802-0.110-0.1100.0000.0000.0000.000
140M171VAL0-0.037-0.01136.3650.0600.0600.0000.0000.0000.000
141M172GLU-1-0.885-0.95239.6037.2147.2140.0000.0000.0000.000
142M173ASP-1-0.948-0.96341.8356.4246.4240.0000.0000.0000.000
143M174GLY0-0.025-0.00942.269-0.124-0.1240.0000.0000.0000.000
144M175SER0-0.064-0.01942.2140.0920.0920.0000.0000.0000.000
145M176VAL00.004-0.02036.2090.1770.1770.0000.0000.0000.000
146M177GLN00.0300.01536.588-0.314-0.3140.0000.0000.0000.000
147M178LEU0-0.025-0.03333.1250.1800.1800.0000.0000.0000.000
148M179ALA00.0580.02530.984-0.129-0.1290.0000.0000.0000.000
149M180ASP-1-0.907-0.92530.3848.9708.9700.0000.0000.0000.000
150M181HIS0-0.008-0.00425.5710.1940.1940.0000.0000.0000.000
151M182TYR0-0.037-0.02027.1480.1120.1120.0000.0000.0000.000
152M183GLN00.0620.03918.697-0.227-0.2270.0000.0000.0000.000
153M201LEU00.002-0.00914.2570.2440.2440.0000.0000.0000.000
154M202SER0-0.065-0.02818.112-0.747-0.7470.0000.0000.0000.000
155M203THR00.017-0.01818.9150.4530.4530.0000.0000.0000.000
156M204GLN00.0320.06820.781-0.312-0.3120.0000.0000.0000.000
157M205THR00.0250.01521.7030.4680.4680.0000.0000.0000.000
158M206ILE00.0040.01324.063-0.423-0.4230.0000.0000.0000.000
159M207LEU0-0.025-0.00125.8790.2930.2930.0000.0000.0000.000
160M208SER0-0.028-0.01028.079-0.277-0.2770.0000.0000.0000.000
161M209LYS10.9600.96930.153-8.023-8.0230.0000.0000.0000.000
162M210ASP-1-0.838-0.91531.0559.2239.2230.0000.0000.0000.000
163M211LEU0-0.019-0.05032.863-0.193-0.1930.0000.0000.0000.000
164M212ASN0-0.068-0.01035.544-0.149-0.1490.0000.0000.0000.000
165M213GLU-1-0.829-0.89631.7569.5109.5100.0000.0000.0000.000
166M214LYS10.9400.95236.103-7.118-7.1180.0000.0000.0000.000
167M215ARG10.9340.98132.053-9.165-9.1650.0000.0000.0000.000
168M216ASP-1-0.712-0.83434.9278.3748.3740.0000.0000.0000.000
169M217HIS0-0.017-0.00330.6320.2970.2970.0000.0000.0000.000
170M218MET00.0060.02026.700-0.085-0.0850.0000.0000.0000.000
171M219VAL00.0180.03026.0130.3530.3530.0000.0000.0000.000
172M220LEU0-0.063-0.03721.839-0.331-0.3310.0000.0000.0000.000
173M221LEU00.0420.01521.4960.5170.5170.0000.0000.0000.000
174M222GLU-1-0.890-0.95718.97312.82712.8270.0000.0000.0000.000
175M223TYR0-0.0100.00817.4560.8830.8830.0000.0000.0000.000
176M224VAL0-0.002-0.00415.495-0.684-0.6840.0000.0000.0000.000
177M225THR00.0040.00314.6660.9950.9950.0000.0000.0000.000
178M226ALA00.0250.02213.925-0.714-0.7140.0000.0000.0000.000
179M227ALA00.011-0.02015.7300.0960.0960.0000.0000.0000.000
180M228GLY0-0.0050.00218.511-0.036-0.0360.0000.0000.0000.000
181M229ILE0-0.0030.00116.789-0.393-0.3930.0000.0000.0000.000
182M230THR0-0.0030.00919.4210.4060.4060.0000.0000.0000.000