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: 49ZQN

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1947495.578891
FMO2-HF: Nuclear repulsion 1875465.783725
FMO2-HF: Total energy -72029.795166
FMO2-MP2: Total energy -72241.976718


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.
-27.033-23.3670.363-1.604-2.4240.003
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 : -0.897 / q_NPA : -0.965
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].
3M8PHE0-0.0020.0013.200-8.271-5.9000.000-1.077-1.2930.001
4M9THR0-0.059-0.0272.620-5.695-4.4300.364-0.524-1.1050.002
5M10GLY0-0.028-0.0085.168-2.829-2.799-0.001-0.003-0.0260.000
6M11VAL0-0.021-0.0228.937-1.214-1.2140.0000.0000.0000.000
7M12VAL00.0180.0177.9080.0250.0250.0000.0000.0000.000
8M13PRO0-0.0030.00111.213-0.863-0.8630.0000.0000.0000.000
9M14ILE0-0.013-0.00713.4570.7380.7380.0000.0000.0000.000
10M15LEU0-0.027-0.00415.708-1.006-1.0060.0000.0000.0000.000
11M16ILE0-0.038-0.00218.1540.3780.3780.0000.0000.0000.000
12M17GLU-1-0.775-0.87820.57211.56611.5660.0000.0000.0000.000
13M18LEU0-0.0040.00323.3860.2880.2880.0000.0000.0000.000
14M19ASP-1-0.876-0.93925.87110.05410.0540.0000.0000.0000.000
15M20GLY00.023-0.01729.0280.1700.1700.0000.0000.0000.000
16M21ASP-1-0.923-0.96031.6578.1538.1530.0000.0000.0000.000
17M22VAL00.002-0.01034.2670.1230.1230.0000.0000.0000.000
18M23ASN0-0.036-0.02636.752-0.031-0.0310.0000.0000.0000.000
19M24GLY0-0.0020.00939.266-0.197-0.1970.0000.0000.0000.000
20M25HIS0-0.025-0.00339.2190.0100.0100.0000.0000.0000.000
21M26LYS10.9440.98136.036-7.457-7.4570.0000.0000.0000.000
22M27PHE0-0.018-0.01234.303-0.183-0.1830.0000.0000.0000.000
23M28PHE0-0.0150.00230.1980.1400.1400.0000.0000.0000.000
24M29VAL0-0.031-0.01227.008-0.194-0.1940.0000.0000.0000.000
25M30ARG10.8740.92823.318-11.537-11.5370.0000.0000.0000.000
26M31GLY00.002-0.01423.421-0.378-0.3780.0000.0000.0000.000
27M32GLU-1-0.969-0.97421.53611.87611.8760.0000.0000.0000.000
28M33GLY00.0680.04216.8170.3390.3390.0000.0000.0000.000
29M43SER0-0.004-0.00418.2920.0100.0100.0000.0000.0000.000
30M44LEU0-0.054-0.03117.4380.5160.5160.0000.0000.0000.000
31M45LYS10.8110.90021.252-10.635-10.6350.0000.0000.0000.000
32M46PHE00.0350.00421.4140.3160.3160.0000.0000.0000.000
33M47ILE00.003-0.01326.463-0.361-0.3610.0000.0000.0000.000
34M48ALA00.0520.03629.6740.2000.2000.0000.0000.0000.000
35M49THR0-0.041-0.02730.217-0.196-0.1960.0000.0000.0000.000
36M50THR0-0.034-0.02432.807-0.138-0.1380.0000.0000.0000.000
37M51GLY0-0.0100.00035.565-0.247-0.2470.0000.0000.0000.000
38M52LYS10.7880.88636.375-7.825-7.8250.0000.0000.0000.000
39M53LEU00.0080.00231.584-0.013-0.0130.0000.0000.0000.000
40M54PRO0-0.0240.01334.533-0.201-0.2010.0000.0000.0000.000
41M55VAL00.0310.00434.1820.1800.1800.0000.0000.0000.000
42M56PRO00.0290.02534.5780.1630.1630.0000.0000.0000.000
43M57TRP00.0710.01927.8970.3460.3460.0000.0000.0000.000
44M58PRO0-0.010-0.00729.4120.3490.3490.0000.0000.0000.000
45M59THR0-0.045-0.02329.0570.2710.2710.0000.0000.0000.000
46M60LEU00.0420.02627.5050.2000.2000.0000.0000.0000.000
47M61VAL00.0380.03923.5660.4020.4020.0000.0000.0000.000
48M62THR0-0.007-0.02722.5840.4850.4850.0000.0000.0000.000
49M63THR0-0.082-0.04922.2410.3840.3840.0000.0000.0000.000
50M64LEU00.0110.01621.9910.2810.2810.0000.0000.0000.000
51M65ALA00.000-0.01118.3010.5960.5960.0000.0000.0000.000
52M68VAL00.0840.02713.6970.1370.1370.0000.0000.0000.000
53M69GLN00.0040.00713.5790.1690.1690.0000.0000.0000.000
54M70CYS0-0.0090.0358.837-0.374-0.3740.0000.0000.0000.000
55M71PHE00.0940.0418.6531.8571.8570.0000.0000.0000.000
56M72SER0-0.078-0.04310.719-0.983-0.9830.0000.0000.0000.000
57M73ARG10.9690.99910.024-17.513-17.5130.0000.0000.0000.000
58M74TYR00.008-0.0108.720-2.497-2.4970.0000.0000.0000.000
59M75PRO0-0.005-0.00911.1781.0441.0440.0000.0000.0000.000
60M76ASP-1-0.829-0.92912.83924.56024.5600.0000.0000.0000.000
61M77HIS0-0.009-0.00513.7511.2951.2950.0000.0000.0000.000
62M78MET0-0.063-0.03013.531-1.006-1.0060.0000.0000.0000.000
63M79LYS10.8870.9648.586-29.159-29.1590.0000.0000.0000.000
64M80ARG10.9911.0128.369-20.108-20.1080.0000.0000.0000.000
65M96ARG10.8290.90920.700-12.496-12.4960.0000.0000.0000.000
66M97THR0-0.0110.01125.771-0.387-0.3870.0000.0000.0000.000
67M98ILE00.003-0.00726.5420.2560.2560.0000.0000.0000.000
68M99TYR00.0010.00130.454-0.312-0.3120.0000.0000.0000.000
69M100PHE0-0.0200.00131.5150.1020.1020.0000.0000.0000.000
70M101LYS10.9510.96335.581-7.583-7.5830.0000.0000.0000.000
71M102CYS0-0.083-0.04938.228-0.125-0.1250.0000.0000.0000.000
72M103ASP-1-0.749-0.87638.7497.2417.2410.0000.0000.0000.000
73M104GLY00.0690.02838.192-0.130-0.1300.0000.0000.0000.000
74M105THR0-0.071-0.05434.3120.2580.2580.0000.0000.0000.000
75M106TYR00.0390.01329.714-0.111-0.1110.0000.0000.0000.000
76M107LYS10.8790.93129.850-8.360-8.3600.0000.0000.0000.000
77M108THR0-0.016-0.02925.097-0.084-0.0840.0000.0000.0000.000
78M109ARG10.7970.87922.682-11.805-11.8050.0000.0000.0000.000
79M110ALA00.0200.01220.186-0.175-0.1750.0000.0000.0000.000
80M111GLU-1-0.840-0.91918.14613.84813.8480.0000.0000.0000.000
81M112VAL0-0.0100.00512.6670.0860.0860.0000.0000.0000.000
82M113LYS10.8310.91113.286-13.957-13.9570.0000.0000.0000.000
83M114PHE0-0.025-0.00813.613-0.436-0.4360.0000.0000.0000.000
84M115GLU-1-0.870-0.9557.60129.92729.9270.0000.0000.0000.000
85M116GLY0-0.033-0.0109.0001.6741.6740.0000.0000.0000.000
86M117ASP-1-0.905-0.93911.33717.56717.5670.0000.0000.0000.000
87M118THR0-0.038-0.02612.5500.5060.5060.0000.0000.0000.000
88M119LEU0-0.0110.0049.911-0.087-0.0870.0000.0000.0000.000
89M120VAL0-0.024-0.01313.107-1.100-1.1000.0000.0000.0000.000
90M121ASN00.012-0.00215.9771.0281.0280.0000.0000.0000.000
91M122ARG10.8720.93217.997-13.550-13.5500.0000.0000.0000.000
92M123ILE0-0.014-0.01520.7640.2670.2670.0000.0000.0000.000
93M124GLU-1-0.792-0.86023.58310.19710.1970.0000.0000.0000.000
94M125LEU0-0.002-0.02726.9230.1570.1570.0000.0000.0000.000
95M126LYS10.8810.94829.144-9.884-9.8840.0000.0000.0000.000
96M127GLY00.0160.00132.5470.1280.1280.0000.0000.0000.000
97M128ILE0-0.033-0.02034.848-0.176-0.1760.0000.0000.0000.000
98M129ASP-1-0.843-0.91537.9627.7637.7630.0000.0000.0000.000
99M130PHE0-0.046-0.00234.445-0.085-0.0850.0000.0000.0000.000
100M131LYS10.8790.92240.531-6.458-6.4580.0000.0000.0000.000
101M132GLU-1-0.845-0.92943.3406.4236.4230.0000.0000.0000.000
102M133ASP-1-0.830-0.89144.8606.5666.5660.0000.0000.0000.000
103M134GLY00.0110.00642.9600.1570.1570.0000.0000.0000.000
104M135ASN0-0.038-0.02840.762-0.227-0.2270.0000.0000.0000.000
105M136ILE0-0.0220.00835.8250.1020.1020.0000.0000.0000.000
106M137LEU0-0.020-0.01138.8720.1100.1100.0000.0000.0000.000
107M138GLY00.0230.01241.100-0.076-0.0760.0000.0000.0000.000
108M139HIS0-0.113-0.07138.9460.0970.0970.0000.0000.0000.000
109M140LYS10.8660.95239.739-6.568-6.5680.0000.0000.0000.000
110M141LEU0-0.038-0.02835.0500.0510.0510.0000.0000.0000.000
111M142GLU-1-0.822-0.90036.0028.0098.0090.0000.0000.0000.000
112M143TYR0-0.075-0.03933.3870.2720.2720.0000.0000.0000.000
113M144ASN0-0.011-0.02631.1500.0430.0430.0000.0000.0000.000
114M145PHE0-0.0060.00024.970-0.173-0.1730.0000.0000.0000.000
115M146ASN0-0.023-0.02428.3730.1440.1440.0000.0000.0000.000
116M147SER0-0.041-0.03124.7740.3190.3190.0000.0000.0000.000
117M148HIS00.0520.03324.604-0.713-0.7130.0000.0000.0000.000
118M149LYS10.8990.95022.677-10.220-10.2200.0000.0000.0000.000
119M150VAL0-0.0020.00219.817-0.470-0.4700.0000.0000.0000.000
120M151TYR00.0460.03520.2840.4540.4540.0000.0000.0000.000
121M152ILE00.0160.00115.950-0.108-0.1080.0000.0000.0000.000
122M153THR0-0.041-0.01819.688-0.280-0.2800.0000.0000.0000.000
123M154ALA00.0550.02218.9850.3020.3020.0000.0000.0000.000
124M155ASP-1-0.800-0.89919.95511.37811.3780.0000.0000.0000.000
125M156LYS10.9820.96821.834-12.144-12.1440.0000.0000.0000.000
126M157GLN0-0.0260.00023.373-0.051-0.0510.0000.0000.0000.000
127M158ASN0-0.018-0.01822.003-0.378-0.3780.0000.0000.0000.000
128M159ASN0-0.072-0.02819.5370.5070.5070.0000.0000.0000.000
129M160GLY00.0870.04917.2140.8580.8580.0000.0000.0000.000
130M161ILE0-0.058-0.02514.5940.0240.0240.0000.0000.0000.000
131M162LYS10.8590.93718.681-11.816-11.8160.0000.0000.0000.000
132M163ALA00.012-0.00220.1600.4440.4440.0000.0000.0000.000
133M164ASN0-0.023-0.00122.255-0.231-0.2310.0000.0000.0000.000
134M165PHE0-0.010-0.00622.4170.2420.2420.0000.0000.0000.000
135M166THR0-0.008-0.00326.654-0.181-0.1810.0000.0000.0000.000
136M167ILE0-0.0220.01425.3710.0120.0120.0000.0000.0000.000
137M168ARG10.9410.96429.445-8.876-8.8760.0000.0000.0000.000
138M169HIS00.0130.00529.7550.2130.2130.0000.0000.0000.000
139M170ASN00.0300.01133.763-0.084-0.0840.0000.0000.0000.000
140M171VAL0-0.023-0.01036.5990.0900.0900.0000.0000.0000.000
141M172GLU-1-0.901-0.95639.8747.2117.2110.0000.0000.0000.000
142M173ASP-1-0.950-0.97142.0376.5746.5740.0000.0000.0000.000
143M174GLY0-0.0090.00442.616-0.121-0.1210.0000.0000.0000.000
144M175SER0-0.056-0.02042.1860.0450.0450.0000.0000.0000.000
145M176VAL00.010-0.02136.1490.1750.1750.0000.0000.0000.000
146M177GLN00.0010.01936.648-0.254-0.2540.0000.0000.0000.000
147M178LEU0-0.029-0.02533.2380.1770.1770.0000.0000.0000.000
148M179ALA00.0480.02730.918-0.174-0.1740.0000.0000.0000.000
149M180ASP-1-0.895-0.92730.2519.1929.1920.0000.0000.0000.000
150M181HIS00.000-0.00725.0820.1890.1890.0000.0000.0000.000
151M182TYR0-0.021-0.02127.1640.1880.1880.0000.0000.0000.000
152M183GLN00.0380.01718.732-0.093-0.0930.0000.0000.0000.000
153M201LEU0-0.022-0.02214.3670.0030.0030.0000.0000.0000.000
154M202SER0-0.0010.01218.142-0.779-0.7790.0000.0000.0000.000
155M203THR0-0.014-0.02819.1610.5390.5390.0000.0000.0000.000
156M204GLN0-0.0070.00521.007-0.501-0.5010.0000.0000.0000.000
157M205THR00.000-0.01821.8860.4630.4630.0000.0000.0000.000
158M206ILE0-0.011-0.00224.271-0.429-0.4290.0000.0000.0000.000
159M207LEU0-0.0140.00425.9720.2870.2870.0000.0000.0000.000
160M208SER0-0.034-0.01727.792-0.217-0.2170.0000.0000.0000.000
161M209LYS10.9760.97730.161-8.039-8.0390.0000.0000.0000.000
162M210ASP-1-0.783-0.87931.0099.4089.4080.0000.0000.0000.000
163M211LEU0-0.028-0.03432.985-0.171-0.1710.0000.0000.0000.000
164M212ASN0-0.047-0.01734.375-0.230-0.2300.0000.0000.0000.000
165M213GLU-1-0.766-0.83931.8759.0799.0790.0000.0000.0000.000
166M214LYS10.9120.94635.747-7.076-7.0760.0000.0000.0000.000
167M215ARG10.8630.91531.880-9.203-9.2030.0000.0000.0000.000
168M216ASP-1-0.721-0.83734.8338.4928.4920.0000.0000.0000.000
169M217HIS0-0.004-0.00430.6020.3030.3030.0000.0000.0000.000
170M218MET00.0010.02026.500-0.022-0.0220.0000.0000.0000.000
171M219VAL0-0.0030.00325.9680.2840.2840.0000.0000.0000.000
172M220LEU0-0.023-0.00921.534-0.330-0.3300.0000.0000.0000.000
173M221LEU00.0210.01021.6400.5290.5290.0000.0000.0000.000
174M222GLU-1-0.857-0.91919.05512.78412.7840.0000.0000.0000.000
175M223TYR0-0.0050.00317.7450.8480.8480.0000.0000.0000.000
176M224VAL00.006-0.00415.488-0.653-0.6530.0000.0000.0000.000
177M225THR0-0.024-0.01114.8550.9850.9850.0000.0000.0000.000
178M226ALA00.0050.00813.691-0.906-0.9060.0000.0000.0000.000
179M227ALA00.006-0.01915.540-0.012-0.0120.0000.0000.0000.000
180M228GLY00.005-0.00118.679-0.008-0.0080.0000.0000.0000.000
181M229ILE0-0.0060.00217.093-0.393-0.3930.0000.0000.0000.000
182M230THR00.0030.01219.6280.3880.3880.0000.0000.0000.000