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: M31LZ

Calculation Name: 4EYY-Q-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EYY

Chain ID: Q

ChEMBL ID:

UniProt ID: Q5ZYC9

Base Structure: X-ray

Registration Date: 2023-06-19

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1850651.623995
FMO2-HF: Nuclear repulsion 1776535.096811
FMO2-HF: Total energy -74116.527184
FMO2-MP2: Total energy -74337.183503


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(Q:1:MET)


Summations of interaction energy for fragment #1(Q:1:MET)
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.
0.6542.1970.001-0.616-0.9290.003
Interaction energy analysis for fragmet #1(Q:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.010
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].
3Q3ASP-1-0.910-0.9583.8011.3782.9210.001-0.616-0.9290.003
4Q4GLN00.0110.0155.8740.4810.4810.0000.0000.0000.000
5Q5LEU00.013-0.0057.1440.4770.4770.0000.0000.0000.000
6Q6SER0-0.056-0.0669.645-0.234-0.2340.0000.0000.0000.000
7Q7ASP-1-0.778-0.89212.0110.6430.6430.0000.0000.0000.000
8Q8GLU-1-0.773-0.85812.9790.8140.8140.0000.0000.0000.000
9Q9GLN00.0120.0196.463-0.314-0.3140.0000.0000.0000.000
10Q10LYS10.8160.89811.980-0.781-0.7810.0000.0000.0000.000
11Q11GLU-1-0.883-0.94314.2110.4250.4250.0000.0000.0000.000
12Q12THR0-0.036-0.02813.402-0.073-0.0730.0000.0000.0000.000
13Q13ILE0-0.030-0.01210.480-0.060-0.0600.0000.0000.0000.000
14Q14LEU0-0.013-0.00615.013-0.086-0.0860.0000.0000.0000.000
15Q15LYN00.0410.04318.408-0.069-0.0690.0000.0000.0000.000
16Q16ALA00.0160.01716.803-0.052-0.0520.0000.0000.0000.000
17Q17LEU0-0.032-0.02117.031-0.061-0.0610.0000.0000.0000.000
18Q18ASN0-0.006-0.03320.228-0.051-0.0510.0000.0000.0000.000
19Q19ASP-1-0.783-0.86221.9990.2740.2740.0000.0000.0000.000
20Q20ALA00.005-0.00220.974-0.031-0.0310.0000.0000.0000.000
21Q21ILE0-0.095-0.06023.116-0.031-0.0310.0000.0000.0000.000
22Q22GLU-1-0.996-0.99625.6610.1890.1890.0000.0000.0000.000
23Q23LYS10.8910.94723.340-0.290-0.2900.0000.0000.0000.000
24Q24GLY0-0.026-0.00226.873-0.013-0.0130.0000.0000.0000.000
25Q25PRO00.0210.01227.510-0.009-0.0090.0000.0000.0000.000
26Q26TRP0-0.076-0.05924.169-0.015-0.0150.0000.0000.0000.000
27Q27ASP-1-0.838-0.90230.4750.1360.1360.0000.0000.0000.000
28Q28LYS10.8790.92133.483-0.140-0.1400.0000.0000.0000.000
29Q29SER00.0190.00233.363-0.008-0.0080.0000.0000.0000.000
30Q30ASN0-0.004-0.00534.1870.0120.0120.0000.0000.0000.000
31Q31PHE00.0600.03727.5390.0070.0070.0000.0000.0000.000
32Q32LEU00.0420.01228.1990.0100.0100.0000.0000.0000.000
33Q33ARG11.0051.01129.406-0.111-0.1110.0000.0000.0000.000
34Q34VAL0-0.034-0.01328.9020.0110.0110.0000.0000.0000.000
35Q35ILE0-0.037-0.02024.3820.0160.0160.0000.0000.0000.000
36Q36GLY00.0670.03125.6150.0210.0210.0000.0000.0000.000
37Q37LYS10.9230.95626.977-0.156-0.1560.0000.0000.0000.000
38Q38LYS10.9741.00422.139-0.230-0.2300.0000.0000.0000.000
39Q39LEU00.0530.01821.5430.0260.0260.0000.0000.0000.000
40Q40ILE0-0.0170.00722.9260.0280.0280.0000.0000.0000.000
41Q41ALA00.0190.00824.5920.0110.0110.0000.0000.0000.000
42Q42ILE0-0.041-0.01918.1580.0160.0160.0000.0000.0000.000
43Q43ARG10.9340.95019.729-0.285-0.2850.0000.0000.0000.000
44Q44ASP-1-0.832-0.89020.9570.2950.2950.0000.0000.0000.000
45Q45ARG10.9850.97818.645-0.341-0.3410.0000.0000.0000.000
46Q46PHE0-0.020-0.00813.324-0.005-0.0050.0000.0000.0000.000
47Q47LEU00.0540.02118.0060.0190.0190.0000.0000.0000.000
48Q48LYS10.8030.88820.552-0.298-0.2980.0000.0000.0000.000
49Q49ARG10.9010.95015.171-0.515-0.5150.0000.0000.0000.000
50Q50ILE00.0260.01515.456-0.018-0.0180.0000.0000.0000.000
51Q51GLY00.0000.01418.022-0.024-0.0240.0000.0000.0000.000
52Q52ALA0-0.021-0.00920.560-0.030-0.0300.0000.0000.0000.000
53Q53ALA0-0.037-0.01017.731-0.023-0.0230.0000.0000.0000.000
54Q54SER00.0640.02319.243-0.028-0.0280.0000.0000.0000.000
55Q55GLN00.0310.01422.207-0.015-0.0150.0000.0000.0000.000
56Q56ALA0-0.023-0.01319.726-0.024-0.0240.0000.0000.0000.000
57Q57GLN0-0.066-0.03420.1000.0060.0060.0000.0000.0000.000
58Q58LEU00.022-0.00221.426-0.024-0.0240.0000.0000.0000.000
59Q59GLN0-0.038-0.01824.382-0.020-0.0200.0000.0000.0000.000
60Q60ALA0-0.0170.00121.124-0.018-0.0180.0000.0000.0000.000
61Q61GLU-1-0.838-0.91223.0880.1130.1130.0000.0000.0000.000
62Q62SER0-0.066-0.03225.296-0.014-0.0140.0000.0000.0000.000
63Q63HIS00.0380.01825.127-0.015-0.0150.0000.0000.0000.000
64Q64LEU00.0100.00523.769-0.008-0.0080.0000.0000.0000.000
65Q65ALA00.000-0.01328.292-0.005-0.0050.0000.0000.0000.000
66Q66ASN0-0.031-0.00831.021-0.008-0.0080.0000.0000.0000.000
67Q67GLN00.0150.00328.942-0.004-0.0040.0000.0000.0000.000
68Q68ILE00.003-0.00229.754-0.004-0.0040.0000.0000.0000.000
69Q69ALA0-0.0170.01533.866-0.002-0.0020.0000.0000.0000.000
70Q70LEU00.0390.02035.986-0.002-0.0020.0000.0000.0000.000
71Q71GLN0-0.083-0.03534.050-0.001-0.0010.0000.0000.0000.000
72Q72SER0-0.044-0.03537.4560.0000.0000.0000.0000.0000.000
73Q73GLY0-0.0070.01639.8440.0020.0020.0000.0000.0000.000
74Q74GLN0-0.056-0.03437.3640.0070.0070.0000.0000.0000.000
75Q75GLN00.0150.00039.462-0.005-0.0050.0000.0000.0000.000
76Q76GLU-1-0.756-0.83935.0890.0640.0640.0000.0000.0000.000
77Q77ILE0-0.044-0.01639.237-0.003-0.0030.0000.0000.0000.000
78Q78TYR0-0.005-0.02837.1620.0040.0040.0000.0000.0000.000
79Q79VAL00.0170.00942.795-0.003-0.0030.0000.0000.0000.000
80Q80SER00.0300.02844.5190.0030.0030.0000.0000.0000.000
81Q81LEU0-0.003-0.01043.724-0.002-0.0020.0000.0000.0000.000
82Q82TYR00.006-0.01147.3830.0000.0000.0000.0000.0000.000
83Q83SER00.0040.01647.937-0.001-0.0010.0000.0000.0000.000
84Q84SER00.008-0.01749.923-0.002-0.0020.0000.0000.0000.000
85Q85ASP-1-0.837-0.92149.0480.0700.0700.0000.0000.0000.000
86Q86GLY00.0330.02146.8450.0030.0030.0000.0000.0000.000
87Q87SER00.0270.01345.0670.0030.0030.0000.0000.0000.000
88Q88ASN00.0110.01143.9940.0100.0100.0000.0000.0000.000
89Q89LEU0-0.0010.00438.305-0.001-0.0010.0000.0000.0000.000
90Q90GLN0-0.054-0.03739.6580.0070.0070.0000.0000.0000.000
91Q91SER0-0.127-0.07343.198-0.001-0.0010.0000.0000.0000.000
92Q92TRP00.0530.01842.500-0.004-0.0040.0000.0000.0000.000
93Q93GLU-1-0.810-0.90639.4830.1010.1010.0000.0000.0000.000
94Q94LYS10.8730.92942.842-0.079-0.0790.0000.0000.0000.000
95Q95ILE00.0070.01646.091-0.003-0.0030.0000.0000.0000.000
96Q96VAL00.0180.01441.140-0.003-0.0030.0000.0000.0000.000
97Q97GLY00.0070.01144.555-0.001-0.0010.0000.0000.0000.000
98Q98SER0-0.100-0.06245.764-0.003-0.0030.0000.0000.0000.000
99Q99LEU00.0620.03244.067-0.003-0.0030.0000.0000.0000.000
100Q100PRO0-0.045-0.06046.854-0.003-0.0030.0000.0000.0000.000
101Q101ARG10.9921.04649.481-0.046-0.0460.0000.0000.0000.000
102Q102GLN00.018-0.01550.511-0.001-0.0010.0000.0000.0000.000
103Q103MET0-0.0140.00845.6520.0000.0000.0000.0000.0000.000
104Q104ILE0-0.067-0.02249.699-0.001-0.0010.0000.0000.0000.000
105Q105SER00.0580.03253.048-0.001-0.0010.0000.0000.0000.000
106Q106ARG10.7800.88949.590-0.048-0.0480.0000.0000.0000.000
107Q107PRO00.0130.01450.294-0.001-0.0010.0000.0000.0000.000
108Q108ILE00.0190.00246.4430.0030.0030.0000.0000.0000.000
109Q109TYR0-0.011-0.04045.178-0.002-0.0020.0000.0000.0000.000
110Q110ALA00.0310.00044.3000.0020.0020.0000.0000.0000.000
111Q111ASP-1-0.821-0.90741.7000.0300.0300.0000.0000.0000.000
112Q112GLU-1-0.743-0.82336.8310.0640.0640.0000.0000.0000.000
113Q113GLU-1-0.800-0.88239.1310.0430.0430.0000.0000.0000.000
114Q114ASP-1-0.831-0.92441.7780.0290.0290.0000.0000.0000.000
115Q115ILE0-0.0290.00642.4540.0000.0000.0000.0000.0000.000
116Q116LYS10.7730.86440.209-0.039-0.0390.0000.0000.0000.000
117Q117ALA0-0.032-0.01843.1440.0010.0010.0000.0000.0000.000
118Q118ILE0-0.015-0.00445.7820.0000.0000.0000.0000.0000.000
119Q119LEU0-0.0020.01143.2600.0000.0000.0000.0000.0000.000
120Q120LYS10.9350.96343.543-0.045-0.0450.0000.0000.0000.000
121Q121THR0-0.084-0.05146.8010.0000.0000.0000.0000.0000.000
122Q122LYS10.8230.91849.303-0.046-0.0460.0000.0000.0000.000
123Q123GLU-1-0.891-0.94850.4240.0420.0420.0000.0000.0000.000
124Q124ASN00.0020.00749.7050.0040.0040.0000.0000.0000.000
125Q125LYS10.8660.93545.078-0.050-0.0500.0000.0000.0000.000
126Q126GLN00.0440.01843.7360.0060.0060.0000.0000.0000.000
127Q127ASN0-0.045-0.02846.1100.0050.0050.0000.0000.0000.000
128Q128GLU-1-0.802-0.89046.5590.0480.0480.0000.0000.0000.000
129Q129ALA00.0050.00642.1290.0040.0040.0000.0000.0000.000
130Q130TYR0-0.067-0.06238.465-0.005-0.0050.0000.0000.0000.000
131Q131VAL0-0.0120.00639.5200.0060.0060.0000.0000.0000.000
132Q132ALA00.0140.01736.642-0.005-0.0050.0000.0000.0000.000
133Q133ILE0-0.018-0.02038.5020.0040.0040.0000.0000.0000.000
134Q134TYR0-0.0120.01334.166-0.006-0.0060.0000.0000.0000.000
135Q135ILE0-0.032-0.02339.2470.0000.0000.0000.0000.0000.000
136Q136SER00.0840.02941.984-0.002-0.0020.0000.0000.0000.000
137Q137GLN0-0.032-0.02542.615-0.003-0.0030.0000.0000.0000.000
138Q138SER00.0150.02445.881-0.003-0.0030.0000.0000.0000.000
139Q139ASP-1-0.856-0.95647.3960.0320.0320.0000.0000.0000.000
140Q140ILE0-0.048-0.00945.8720.0010.0010.0000.0000.0000.000
141Q141LEU0-0.016-0.01150.299-0.002-0.0020.0000.0000.0000.000
142Q142HIS00.0040.00048.5890.0000.0000.0000.0000.0000.000
143Q143LEU0-0.0260.00253.805-0.001-0.0010.0000.0000.0000.000
144Q144SER0-0.029-0.03955.1920.0000.0000.0000.0000.0000.000
145Q145ALA00.0700.01255.2440.0010.0010.0000.0000.0000.000
146Q146ASP-1-0.873-0.91256.7600.0110.0110.0000.0000.0000.000
147Q147LYS10.8680.92459.173-0.014-0.0140.0000.0000.0000.000
148Q148ALA0-0.0220.01654.8330.0010.0010.0000.0000.0000.000
149Q149PRO00.0120.00955.7220.0000.0000.0000.0000.0000.000
150Q150VAL00.0140.02854.6870.0000.0000.0000.0000.0000.000
151Q151ASP-1-0.700-0.83150.7110.0330.0330.0000.0000.0000.000
152Q152LYS10.9380.96154.120-0.035-0.0350.0000.0000.0000.000
153Q153LEU0-0.044-0.00650.142-0.001-0.0010.0000.0000.0000.000
154Q154GLY00.0430.01853.8790.0000.0000.0000.0000.0000.000
155Q155LYS10.7190.84047.969-0.034-0.0340.0000.0000.0000.000
156Q156PRO00.0360.01150.8050.0010.0010.0000.0000.0000.000
157Q157LEU0-0.051-0.00950.3560.0020.0020.0000.0000.0000.000
158Q158LEU0-0.026-0.01846.623-0.002-0.0020.0000.0000.0000.000
159Q159THR0-0.007-0.00950.8010.0020.0020.0000.0000.0000.000
160Q160LEU0-0.030-0.02047.791-0.001-0.0010.0000.0000.0000.000
161Q161LYS10.8890.93851.421-0.027-0.0270.0000.0000.0000.000
162Q162ASP-1-0.837-0.93253.0390.0320.0320.0000.0000.0000.000
163Q163LYS10.8410.92653.407-0.036-0.0360.0000.0000.0000.000
164Q164SER00.0530.03049.2080.0000.0000.0000.0000.0000.000
165Q165ILE0-0.009-0.00346.2130.0010.0010.0000.0000.0000.000
166Q166SER0-0.084-0.04046.5140.0020.0020.0000.0000.0000.000
167Q167LEU0-0.024-0.00740.0750.0020.0020.0000.0000.0000.000
168Q168GLU-1-0.866-0.93539.3980.0630.0630.0000.0000.0000.000
169Q169ASN0-0.036-0.00934.7560.0120.0120.0000.0000.0000.000
170Q170ILE0-0.041-0.02336.615-0.002-0.0020.0000.0000.0000.000
171Q171SER00.0180.01732.969-0.001-0.0010.0000.0000.0000.000
172Q172ARG10.8220.86032.760-0.063-0.0630.0000.0000.0000.000
173Q173PHE00.008-0.00334.709-0.006-0.0060.0000.0000.0000.000
174Q174VAL00.0020.00736.0710.0080.0080.0000.0000.0000.000
175Q175HIS00.0430.04338.0130.0000.0000.0000.0000.0000.000
176Q176VAL0-0.0090.00338.5450.0020.0020.0000.0000.0000.000
177Q177SER0-0.050-0.03437.8910.0050.0050.0000.0000.0000.000
178Q178GLY00.0390.01934.5230.0070.0070.0000.0000.0000.000
179Q179VAL0-0.0100.00431.802-0.005-0.0050.0000.0000.0000.000
180Q180TYR0-0.052-0.04432.4130.0160.0160.0000.0000.0000.000
181Q181ARG10.9380.94327.670-0.161-0.1610.0000.0000.0000.000
182Q182TYR00.0060.00133.3140.0030.0030.0000.0000.0000.000
183Q183SER0-0.081-0.08033.2370.0010.0010.0000.0000.0000.000
184Q184ASN0-0.124-0.16134.2350.0010.0010.0000.0000.0000.000
185Q185GLY00.1970.05236.6220.0000.0000.0000.0000.0000.000
186Q186ARG10.9111.13337.617-0.083-0.0830.0000.0000.0000.000
187Q187LEU00.0240.01937.185-0.003-0.0030.0000.0000.0000.000
188Q188ILE00.0290.02635.5200.0030.0030.0000.0000.0000.000
189Q189LYS10.9410.95932.355-0.129-0.1290.0000.0000.0000.000
190Q190ASN0-0.030-0.00828.2520.0170.0170.0000.0000.0000.000
191Q191ALA00.0030.02525.800-0.005-0.0050.0000.0000.0000.000