FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: K95K3

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1946986.854913
FMO2-HF: Nuclear repulsion 1874958.131377
FMO2-HF: Total energy -72028.723536
FMO2-MP2: Total energy -72240.984866


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.
-26.148-22.3090.358-1.664-2.5330.004
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 : -0.918 / q_NPA : -0.981
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].
3M8PHE0-0.019-0.0133.018-8.322-5.715-0.001-1.184-1.4210.001
4M9THR0-0.051-0.0052.638-7.468-6.2600.360-0.478-1.0910.003
5M10GLY0-0.011-0.0025.268-2.412-2.388-0.001-0.002-0.0210.000
6M11VAL0-0.020-0.0199.029-0.490-0.4900.0000.0000.0000.000
7M12VAL00.0320.0167.932-0.015-0.0150.0000.0000.0000.000
8M13PRO0-0.0100.00311.303-1.057-1.0570.0000.0000.0000.000
9M14ILE0-0.018-0.01513.3610.5510.5510.0000.0000.0000.000
10M15LEU00.0020.01415.683-0.978-0.9780.0000.0000.0000.000
11M16ILE0-0.038-0.01617.9260.3590.3590.0000.0000.0000.000
12M17GLU-1-0.891-0.95920.30011.59111.5910.0000.0000.0000.000
13M18LEU0-0.0120.00223.0540.2330.2330.0000.0000.0000.000
14M19ASP-1-0.869-0.93325.6289.9669.9660.0000.0000.0000.000
15M20GLY00.022-0.01628.8160.1440.1440.0000.0000.0000.000
16M21ASP-1-0.904-0.95731.4378.2268.2260.0000.0000.0000.000
17M22VAL0-0.002-0.01834.3210.0550.0550.0000.0000.0000.000
18M23ASN0-0.023-0.00136.731-0.029-0.0290.0000.0000.0000.000
19M24GLY00.0040.01139.321-0.190-0.1900.0000.0000.0000.000
20M25HIS0-0.027-0.01539.247-0.018-0.0180.0000.0000.0000.000
21M26LYS10.9480.98736.167-7.378-7.3780.0000.0000.0000.000
22M27PHE0-0.032-0.02533.990-0.162-0.1620.0000.0000.0000.000
23M28PHE0-0.0150.01229.9150.1090.1090.0000.0000.0000.000
24M29VAL0-0.035-0.01826.540-0.170-0.1700.0000.0000.0000.000
25M30ARG10.9710.98923.778-11.512-11.5120.0000.0000.0000.000
26M31GLY0-0.041-0.02823.441-0.358-0.3580.0000.0000.0000.000
27M32GLU-1-1.001-0.99721.49312.10612.1060.0000.0000.0000.000
28M33GLY00.0600.04316.6120.1250.1250.0000.0000.0000.000
29M43SER0-0.009-0.01118.2770.0090.0090.0000.0000.0000.000
30M44LEU0-0.035-0.02517.4440.5070.5070.0000.0000.0000.000
31M45LYS10.8180.91621.326-10.654-10.6540.0000.0000.0000.000
32M46PHE00.025-0.00121.3110.1990.1990.0000.0000.0000.000
33M47ILE00.014-0.00526.493-0.355-0.3550.0000.0000.0000.000
34M48ALA00.0170.02229.5850.1810.1810.0000.0000.0000.000
35M49THR0-0.056-0.03730.464-0.223-0.2230.0000.0000.0000.000
36M50THR00.0310.01933.003-0.212-0.2120.0000.0000.0000.000
37M51GLY0-0.001-0.01135.283-0.255-0.2550.0000.0000.0000.000
38M52LYS10.7980.89336.032-7.818-7.8180.0000.0000.0000.000
39M53LEU0-0.0040.00131.078-0.001-0.0010.0000.0000.0000.000
40M54PRO0-0.0410.01233.968-0.215-0.2150.0000.0000.0000.000
41M55VAL00.034-0.00333.2960.1910.1910.0000.0000.0000.000
42M56PRO00.0340.02634.1960.1170.1170.0000.0000.0000.000
43M57TRP00.0850.01127.8680.3380.3380.0000.0000.0000.000
44M58PRO00.0190.00129.2070.3370.3370.0000.0000.0000.000
45M59THR0-0.045-0.02428.6620.2690.2690.0000.0000.0000.000
46M60LEU00.0440.02327.5070.1350.1350.0000.0000.0000.000
47M61VAL00.0280.03023.7010.3920.3920.0000.0000.0000.000
48M62THR0-0.030-0.03922.7610.4740.4740.0000.0000.0000.000
49M63THR0-0.091-0.05222.1220.4340.4340.0000.0000.0000.000
50M64LEU00.0330.03321.9800.3730.3730.0000.0000.0000.000
51M65ALA0-0.018-0.02718.1120.6150.6150.0000.0000.0000.000
52M68VAL00.0700.03013.2880.2810.2810.0000.0000.0000.000
53M69GLN0-0.019-0.01813.525-0.148-0.1480.0000.0000.0000.000
54M70CYS0-0.0020.0248.483-0.300-0.3000.0000.0000.0000.000
55M71PHE00.0900.0458.4481.8171.8170.0000.0000.0000.000
56M72SER0-0.060-0.02110.527-1.096-1.0960.0000.0000.0000.000
57M73ARG10.9600.9919.620-17.130-17.1300.0000.0000.0000.000
58M74TYR00.018-0.0077.686-2.609-2.6090.0000.0000.0000.000
59M75PRO0-0.035-0.02110.4940.8360.8360.0000.0000.0000.000
60M76ASP-1-0.825-0.92812.41924.17724.1770.0000.0000.0000.000
61M77HIS0-0.004-0.01113.6111.1951.1950.0000.0000.0000.000
62M78MET0-0.062-0.02813.480-1.030-1.0300.0000.0000.0000.000
63M79LYS10.8590.9678.762-28.314-28.3140.0000.0000.0000.000
64M80ARG11.0061.0148.694-19.937-19.9370.0000.0000.0000.000
65M96ARG10.8490.91220.216-12.443-12.4430.0000.0000.0000.000
66M97THR0-0.065-0.03425.663-0.302-0.3020.0000.0000.0000.000
67M98ILE0-0.017-0.02126.4080.1210.1210.0000.0000.0000.000
68M99TYR00.0300.01730.346-0.286-0.2860.0000.0000.0000.000
69M100PHE0-0.021-0.00931.4210.1070.1070.0000.0000.0000.000
70M101LYS10.9471.00335.336-7.491-7.4910.0000.0000.0000.000
71M102CYS0-0.141-0.09737.614-0.129-0.1290.0000.0000.0000.000
72M103ASP-1-0.826-0.93438.3947.2727.2720.0000.0000.0000.000
73M104GLY00.1180.08437.830-0.116-0.1160.0000.0000.0000.000
74M105THR0-0.082-0.04334.2400.2420.2420.0000.0000.0000.000
75M106TYR00.010-0.00229.552-0.108-0.1080.0000.0000.0000.000
76M107LYS10.9280.96829.589-8.351-8.3510.0000.0000.0000.000
77M108THR00.0060.00024.700-0.005-0.0050.0000.0000.0000.000
78M109ARG10.8570.91423.327-11.475-11.4750.0000.0000.0000.000
79M110ALA00.007-0.00720.068-0.184-0.1840.0000.0000.0000.000
80M111GLU-1-0.862-0.93217.74014.17414.1740.0000.0000.0000.000
81M112VAL00.0230.02412.6720.1840.1840.0000.0000.0000.000
82M113LYS10.8010.89213.327-14.441-14.4410.0000.0000.0000.000
83M114PHE0-0.043-0.01013.820-0.123-0.1230.0000.0000.0000.000
84M115GLU-1-0.869-0.9617.45230.38430.3840.0000.0000.0000.000
85M116GLY0-0.035-0.0099.3191.5261.5260.0000.0000.0000.000
86M117ASP-1-0.916-0.96011.84017.46017.4600.0000.0000.0000.000
87M118THR0-0.0390.00112.0861.0991.0990.0000.0000.0000.000
88M119LEU0-0.0150.0059.858-0.046-0.0460.0000.0000.0000.000
89M120VAL0-0.024-0.02912.941-1.046-1.0460.0000.0000.0000.000
90M121ASN00.0300.00716.0240.9820.9820.0000.0000.0000.000
91M122ARG10.9140.97918.212-13.585-13.5850.0000.0000.0000.000
92M123ILE0-0.005-0.01420.9800.1720.1720.0000.0000.0000.000
93M124GLU-1-0.789-0.86223.57910.13310.1330.0000.0000.0000.000
94M125LEU0-0.007-0.01626.9830.0840.0840.0000.0000.0000.000
95M126LYS10.8860.94329.509-9.746-9.7460.0000.0000.0000.000
96M127GLY00.009-0.00332.8590.1190.1190.0000.0000.0000.000
97M128ILE0-0.063-0.03934.889-0.183-0.1830.0000.0000.0000.000
98M129ASP-1-0.845-0.93937.9167.5807.5800.0000.0000.0000.000
99M130PHE0-0.0100.01034.5290.0020.0020.0000.0000.0000.000
100M131LYS10.8510.91240.619-6.424-6.4240.0000.0000.0000.000
101M132GLU-1-0.849-0.93843.5886.3656.3650.0000.0000.0000.000
102M133ASP-1-0.845-0.88444.8116.5696.5690.0000.0000.0000.000
103M134GLY00.0430.01842.7410.1580.1580.0000.0000.0000.000
104M135ASN0-0.010-0.02940.533-0.215-0.2150.0000.0000.0000.000
105M136ILE0-0.0280.00535.6200.1160.1160.0000.0000.0000.000
106M137LEU0-0.012-0.00338.3310.0880.0880.0000.0000.0000.000
107M138GLY00.0300.02340.677-0.085-0.0850.0000.0000.0000.000
108M139HIS0-0.159-0.07838.9360.0810.0810.0000.0000.0000.000
109M140LYS10.9070.94540.107-6.717-6.7170.0000.0000.0000.000
110M141LEU0-0.056-0.01634.2360.0520.0520.0000.0000.0000.000
111M142GLU-1-0.798-0.88335.8177.9467.9460.0000.0000.0000.000
112M143TYR0-0.082-0.04832.9950.2610.2610.0000.0000.0000.000
113M144ASN00.004-0.02330.722-0.012-0.0120.0000.0000.0000.000
114M145PHE0-0.0200.00125.152-0.167-0.1670.0000.0000.0000.000
115M146ASN0-0.009-0.01228.3790.1140.1140.0000.0000.0000.000
116M147SER0-0.065-0.05524.4530.2900.2900.0000.0000.0000.000
117M148HIS00.0730.04324.525-0.679-0.6790.0000.0000.0000.000
118M149LYS10.9230.96822.481-10.104-10.1040.0000.0000.0000.000
119M150VAL0-0.016-0.00919.492-0.397-0.3970.0000.0000.0000.000
120M151TYR00.0340.02520.0170.4750.4750.0000.0000.0000.000
121M152ILE00.0300.01415.462-0.177-0.1770.0000.0000.0000.000
122M153THR0-0.020-0.00819.420-0.262-0.2620.0000.0000.0000.000
123M154ALA00.0390.01919.1630.2550.2550.0000.0000.0000.000
124M155ASP-1-0.800-0.90620.00011.29011.2900.0000.0000.0000.000
125M156LYS11.0020.97821.618-12.084-12.0840.0000.0000.0000.000
126M157GLN0-0.0300.02722.8070.0390.0390.0000.0000.0000.000
127M158ASN00.004-0.02621.975-0.311-0.3110.0000.0000.0000.000
128M159ASN0-0.072-0.01919.4070.4580.4580.0000.0000.0000.000
129M160GLY00.0540.01917.2930.8020.8020.0000.0000.0000.000
130M161ILE0-0.040-0.01214.6690.0010.0010.0000.0000.0000.000
131M162LYS10.8250.91118.745-11.705-11.7050.0000.0000.0000.000
132M163ALA00.010-0.00719.9350.4160.4160.0000.0000.0000.000
133M164ASN0-0.0060.00522.031-0.263-0.2630.0000.0000.0000.000
134M165PHE0-0.007-0.01222.2690.2420.2420.0000.0000.0000.000
135M166THR0-0.0080.00426.472-0.210-0.2100.0000.0000.0000.000
136M167ILE0-0.0280.00425.4550.1100.1100.0000.0000.0000.000
137M168ARG10.9460.95929.488-8.758-8.7580.0000.0000.0000.000
138M169HIS0-0.0110.00229.8440.1750.1750.0000.0000.0000.000
139M170ASN00.0590.02833.683-0.110-0.1100.0000.0000.0000.000
140M171VAL0-0.038-0.01436.2480.0650.0650.0000.0000.0000.000
141M172GLU-1-0.897-0.95739.4777.2227.2220.0000.0000.0000.000
142M173ASP-1-0.953-0.96941.7046.5526.5520.0000.0000.0000.000
143M174GLY0-0.017-0.00542.161-0.127-0.1270.0000.0000.0000.000
144M175SER0-0.061-0.01842.1130.0980.0980.0000.0000.0000.000
145M176VAL00.001-0.02336.1360.1710.1710.0000.0000.0000.000
146M177GLN00.0270.02336.610-0.254-0.2540.0000.0000.0000.000
147M178LEU0-0.032-0.04133.1380.1860.1860.0000.0000.0000.000
148M179ALA00.0630.02830.881-0.138-0.1380.0000.0000.0000.000
149M180ASP-1-0.885-0.91830.2839.0859.0850.0000.0000.0000.000
150M181HIS00.0060.01225.2080.2170.2170.0000.0000.0000.000
151M182TYR0-0.049-0.03127.0420.1670.1670.0000.0000.0000.000
152M183GLN00.0550.02918.602-0.189-0.1890.0000.0000.0000.000
153M201LEU00.002-0.01914.4210.1540.1540.0000.0000.0000.000
154M202SER0-0.065-0.01018.081-0.792-0.7920.0000.0000.0000.000
155M203THR00.002-0.03018.8570.4850.4850.0000.0000.0000.000
156M204GLN0-0.0060.00920.693-0.398-0.3980.0000.0000.0000.000
157M205THR0-0.013-0.02521.5960.4280.4280.0000.0000.0000.000
158M206ILE00.0090.01223.944-0.431-0.4310.0000.0000.0000.000
159M207LEU0-0.0210.00425.7340.2870.2870.0000.0000.0000.000
160M208SER0-0.026-0.01227.853-0.261-0.2610.0000.0000.0000.000
161M209LYS10.9820.97829.983-8.000-8.0000.0000.0000.0000.000
162M210ASP-1-0.790-0.87930.8019.3659.3650.0000.0000.0000.000
163M211LEU0-0.017-0.05332.684-0.159-0.1590.0000.0000.0000.000
164M212ASN0-0.087-0.02434.558-0.210-0.2100.0000.0000.0000.000
165M213GLU-1-0.748-0.83131.5829.2249.2240.0000.0000.0000.000
166M214LYS10.9360.94635.908-7.112-7.1120.0000.0000.0000.000
167M215ARG10.8610.92731.826-9.200-9.2000.0000.0000.0000.000
168M216ASP-1-0.722-0.82834.8258.4418.4410.0000.0000.0000.000
169M217HIS0-0.023-0.01730.5490.3120.3120.0000.0000.0000.000
170M218MET00.0010.01526.451-0.067-0.0670.0000.0000.0000.000
171M219VAL00.0090.02725.8420.3380.3380.0000.0000.0000.000
172M220LEU0-0.055-0.03721.560-0.288-0.2880.0000.0000.0000.000
173M221LEU00.0420.01921.3780.5210.5210.0000.0000.0000.000
174M222GLU-1-0.855-0.91718.75812.80012.8000.0000.0000.0000.000
175M223TYR0-0.0020.01217.3650.8750.8750.0000.0000.0000.000
176M224VAL00.000-0.00515.440-0.675-0.6750.0000.0000.0000.000
177M225THR0-0.003-0.00314.6321.0771.0770.0000.0000.0000.000
178M226ALA00.0310.02513.889-0.754-0.7540.0000.0000.0000.000
179M227ALA00.016-0.01815.7310.1230.1230.0000.0000.0000.000
180M228GLY00.0050.00418.545-0.038-0.0380.0000.0000.0000.000
181M229ILE0-0.010-0.00716.910-0.405-0.4050.0000.0000.0000.000
182M230THR00.0040.01319.5150.4670.4670.0000.0000.0000.000