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: N3R8Q

Calculation Name: 4EYY-Q-Xray313

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 191
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1850514.681518
FMO2-HF: Nuclear repulsion 1776401.303282
FMO2-HF: Total energy -74113.378236
FMO2-MP2: Total energy -74334.224229


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.
0.1211.6680.004-0.625-0.9260.003
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 : 0.007 / q_NPA : -0.007
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 -1-0.902-0.9573.8010.9182.4650.004-0.625-0.9260.003
4Q4GLN 0-0.043-0.0135.8610.4480.4480.0000.0000.0000.000
5Q5LEU 0-0.013-0.0177.4020.4810.4810.0000.0000.0000.000
6Q6SER 0-0.024-0.0139.651-0.347-0.3470.0000.0000.0000.000
7Q7ASP -1-0.837-0.93012.0110.5780.5780.0000.0000.0000.000
8Q8GLU -1-0.844-0.93513.0820.6890.6890.0000.0000.0000.000
9Q9GLN 00.0000.0086.413-0.369-0.3690.0000.0000.0000.000
10Q10LYS 10.9190.95911.905-0.714-0.7140.0000.0000.0000.000
11Q11GLU -1-0.891-0.94114.2230.3970.3970.0000.0000.0000.000
12Q12THR 0-0.024-0.01313.355-0.066-0.0660.0000.0000.0000.000
13Q13ILE 0-0.041-0.01710.542-0.055-0.0550.0000.0000.0000.000
14Q14LEU 0-0.009-0.00715.028-0.081-0.0810.0000.0000.0000.000
15Q15LYN 00.0460.03818.421-0.065-0.0650.0000.0000.0000.000
16Q16ALA 0-0.0030.00716.729-0.047-0.0470.0000.0000.0000.000
17Q17LEU 0-0.036-0.02717.132-0.058-0.0580.0000.0000.0000.000
18Q18ASN 0-0.006-0.03120.240-0.050-0.0500.0000.0000.0000.000
19Q19ASP -1-0.795-0.88422.0790.2610.2610.0000.0000.0000.000
20Q20ALA 0-0.018-0.01321.411-0.029-0.0290.0000.0000.0000.000
21Q21ILE 0-0.093-0.06023.391-0.030-0.0300.0000.0000.0000.000
22Q22GLU -1-0.983-0.99425.9340.1810.1810.0000.0000.0000.000
23Q23LYS 10.9360.99323.742-0.280-0.2800.0000.0000.0000.000
24Q24GLY 0-0.042-0.02327.235-0.012-0.0120.0000.0000.0000.000
25Q25PRO 00.0190.01427.865-0.011-0.0110.0000.0000.0000.000
26Q26TRP 0-0.072-0.05224.772-0.015-0.0150.0000.0000.0000.000
27Q27ASP -1-0.864-0.92730.9230.1350.1350.0000.0000.0000.000
28Q28LYS 10.9220.96233.907-0.136-0.1360.0000.0000.0000.000
29Q29SER 00.020-0.00533.955-0.007-0.0070.0000.0000.0000.000
30Q30ASN 0-0.013-0.00834.6380.0110.0110.0000.0000.0000.000
31Q31PHE 00.0600.03727.8950.0070.0070.0000.0000.0000.000
32Q32LEU 00.0350.01428.6510.0100.0100.0000.0000.0000.000
33Q33ARG 11.0071.00229.871-0.110-0.1100.0000.0000.0000.000
34Q34VAL 0-0.039-0.01329.3370.0100.0100.0000.0000.0000.000
35Q35ILE 0-0.041-0.02124.9150.0150.0150.0000.0000.0000.000
36Q36GLY 00.0580.02626.1160.0210.0210.0000.0000.0000.000
37Q37LYS 10.9280.96027.429-0.155-0.1550.0000.0000.0000.000
38Q38LYS 10.9711.00322.693-0.232-0.2320.0000.0000.0000.000
39Q39LEU 00.0580.01821.3480.0250.0250.0000.0000.0000.000
40Q40ILE 0-0.0090.01122.9310.0250.0250.0000.0000.0000.000
41Q41ALA 00.0410.02224.5960.0090.0090.0000.0000.0000.000
42Q42ILE 0-0.050-0.02518.3290.0150.0150.0000.0000.0000.000
43Q43ARG 10.9490.96519.731-0.272-0.2720.0000.0000.0000.000
44Q44ASP -1-0.931-0.96820.9610.2730.2730.0000.0000.0000.000
45Q45ARG 10.9300.96319.221-0.318-0.3180.0000.0000.0000.000
46Q46PHE 0-0.002-0.00613.384-0.003-0.0030.0000.0000.0000.000
47Q47LEU 00.0620.02618.0070.0150.0150.0000.0000.0000.000
48Q48LYS 10.9260.97220.555-0.265-0.2650.0000.0000.0000.000
49Q49ARG 10.9120.95415.450-0.431-0.4310.0000.0000.0000.000
50Q50ILE 00.0040.00515.563-0.013-0.0130.0000.0000.0000.000
51Q51GLY 00.0000.01318.023-0.023-0.0230.0000.0000.0000.000
52Q52ALA 00.0120.00920.597-0.026-0.0260.0000.0000.0000.000
53Q53ALA 0-0.055-0.02017.752-0.020-0.0200.0000.0000.0000.000
54Q54SER 00.0490.01319.239-0.031-0.0310.0000.0000.0000.000
55Q55GLN 00.032-0.04322.204-0.015-0.0150.0000.0000.0000.000
56Q56ALA 0-0.0060.01219.711-0.021-0.0210.0000.0000.0000.000
57Q57GLN 0-0.046-0.01320.076-0.004-0.0040.0000.0000.0000.000
58Q58LEU 00.023-0.00221.418-0.023-0.0230.0000.0000.0000.000
59Q59GLN 0-0.025-0.01324.283-0.022-0.0220.0000.0000.0000.000
60Q60ALA 0-0.032-0.00921.094-0.016-0.0160.0000.0000.0000.000
61Q61GLU -1-0.884-0.94723.0840.0820.0820.0000.0000.0000.000
62Q62SER 0-0.061-0.02125.284-0.013-0.0130.0000.0000.0000.000
63Q63HIS 00.0450.01724.974-0.012-0.0120.0000.0000.0000.000
64Q64LEU 00.0030.00223.962-0.007-0.0070.0000.0000.0000.000
65Q65ALA 00.001-0.01528.339-0.004-0.0040.0000.0000.0000.000
66Q66ASN 0-0.0200.00131.009-0.008-0.0080.0000.0000.0000.000
67Q67GLN 00.0150.00628.778-0.004-0.0040.0000.0000.0000.000
68Q68ILE 00.005-0.00230.053-0.004-0.0040.0000.0000.0000.000
69Q69ALA 0-0.0160.02933.931-0.001-0.0010.0000.0000.0000.000
70Q70LEU 00.0350.01636.165-0.002-0.0020.0000.0000.0000.000
71Q71GLN 0-0.090-0.03634.366-0.002-0.0020.0000.0000.0000.000
72Q72SER 0-0.057-0.06337.3400.0000.0000.0000.0000.0000.000
73Q73GLY 0-0.0200.00639.8440.0020.0020.0000.0000.0000.000
74Q74GLN 0-0.039-0.01737.5750.0080.0080.0000.0000.0000.000
75Q75GLN 00.0240.00439.500-0.004-0.0040.0000.0000.0000.000
76Q76GLU -1-0.843-0.92435.5750.0530.0530.0000.0000.0000.000
77Q77ILE 0-0.047-0.02339.225-0.003-0.0030.0000.0000.0000.000
78Q78TYR 0-0.0040.00137.0890.0050.0050.0000.0000.0000.000
79Q79VAL 00.0200.00742.783-0.003-0.0030.0000.0000.0000.000
80Q80SER 0-0.026-0.00244.5090.0030.0030.0000.0000.0000.000
81Q81LEU 00.000-0.02043.698-0.001-0.0010.0000.0000.0000.000
82Q82TYR 00.008-0.01247.3740.0000.0000.0000.0000.0000.000
83Q83SER 00.0060.01547.951-0.001-0.0010.0000.0000.0000.000
84Q84SER 0-0.007-0.01949.917-0.002-0.0020.0000.0000.0000.000
85Q85ASP -1-0.868-0.94549.1270.0640.0640.0000.0000.0000.000
86Q86GLY 00.0260.01246.8350.0030.0030.0000.0000.0000.000
87Q87SER 00.0350.01345.0610.0020.0020.0000.0000.0000.000
88Q88ASN 00.0090.01843.9900.0090.0090.0000.0000.0000.000
89Q89LEU 0-0.021-0.01138.251-0.001-0.0010.0000.0000.0000.000
90Q90GLN 00.0300.01439.7100.0020.0020.0000.0000.0000.000
91Q91SER 0-0.128-0.07643.197-0.001-0.0010.0000.0000.0000.000
92Q92TRP 00.0280.01242.440-0.004-0.0040.0000.0000.0000.000
93Q93GLU -1-0.856-0.93140.0160.0900.0900.0000.0000.0000.000
94Q94LYS 10.8820.93942.840-0.069-0.0690.0000.0000.0000.000
95Q95ILE 00.0060.01246.076-0.003-0.0030.0000.0000.0000.000
96Q96VAL 00.0140.01241.219-0.003-0.0030.0000.0000.0000.000
97Q97GLY 00.0120.01444.550-0.001-0.0010.0000.0000.0000.000
98Q98SER 0-0.095-0.05945.761-0.002-0.0020.0000.0000.0000.000
99Q99LEU 00.0380.00843.981-0.003-0.0030.0000.0000.0000.000
100Q100PRO 0-0.061-0.07846.893-0.003-0.0030.0000.0000.0000.000
101Q101ARG 10.9891.08049.475-0.041-0.0410.0000.0000.0000.000
102Q102GLN 00.039-0.03449.528-0.001-0.0010.0000.0000.0000.000
103Q103MET 00.0190.00045.4570.0000.0000.0000.0000.0000.000
104Q104ILE 0-0.0450.01949.463-0.001-0.0010.0000.0000.0000.000
105Q105SER 00.0290.02053.039-0.001-0.0010.0000.0000.0000.000
106Q106ARG 10.7830.91449.643-0.042-0.0420.0000.0000.0000.000
107Q107PRO 00.0260.00950.129-0.001-0.0010.0000.0000.0000.000
108Q108ILE 00.0350.01846.4980.0030.0030.0000.0000.0000.000
109Q109TYR 0-0.009-0.02145.150-0.002-0.0020.0000.0000.0000.000
110Q110ALA 00.025-0.01044.2770.0020.0020.0000.0000.0000.000
111Q111ASP -1-0.821-0.89741.6880.0220.0220.0000.0000.0000.000
112Q112GLU -1-0.770-0.86636.8240.0510.0510.0000.0000.0000.000
113Q113GLU -1-0.833-0.93238.8570.0360.0360.0000.0000.0000.000
114Q114ASP -1-0.848-0.94441.7480.0230.0230.0000.0000.0000.000
115Q115ILE 0-0.018-0.00342.5500.0010.0010.0000.0000.0000.000
116Q116LYS 10.8310.93240.474-0.030-0.0300.0000.0000.0000.000
117Q117ALA 0-0.050-0.02643.0870.0010.0010.0000.0000.0000.000
118Q118ILE 00.0060.00345.7270.0000.0000.0000.0000.0000.000
119Q119LEU 0-0.0080.00843.2420.0000.0000.0000.0000.0000.000
120Q120LYS 10.9170.95043.140-0.040-0.0400.0000.0000.0000.000
121Q121THR 0-0.093-0.04946.7220.0000.0000.0000.0000.0000.000
122Q122LYS 10.8870.97249.202-0.040-0.0400.0000.0000.0000.000
123Q123GLU -1-0.883-0.94550.3940.0370.0370.0000.0000.0000.000
124Q124ASN 0-0.035-0.00150.1790.0030.0030.0000.0000.0000.000
125Q125LYS 10.9110.96745.000-0.045-0.0450.0000.0000.0000.000
126Q126GLN 00.0220.00243.8870.0060.0060.0000.0000.0000.000
127Q127ASN 0-0.016-0.02346.1020.0040.0040.0000.0000.0000.000
128Q128GLU -1-0.875-0.94946.3300.0430.0430.0000.0000.0000.000
129Q129ALA 0-0.017-0.00242.0120.0030.0030.0000.0000.0000.000
130Q130TYR 0-0.054-0.04438.140-0.004-0.0040.0000.0000.0000.000
131Q131VAL 0-0.0250.00339.5130.0050.0050.0000.0000.0000.000
132Q132ALA 00.0320.01536.851-0.005-0.0050.0000.0000.0000.000
133Q133ILE 0-0.023-0.01538.4930.0040.0040.0000.0000.0000.000
134Q134TYR 00.0410.04033.228-0.007-0.0070.0000.0000.0000.000
135Q135ILE 0-0.044-0.02139.2370.0010.0010.0000.0000.0000.000
136Q136SER 00.0930.02441.973-0.002-0.0020.0000.0000.0000.000
137Q137GLN 0-0.0040.01742.699-0.004-0.0040.0000.0000.0000.000
138Q138SER 0-0.019-0.01345.889-0.003-0.0030.0000.0000.0000.000
139Q139ASP -1-0.859-0.97447.3130.0270.0270.0000.0000.0000.000
140Q140ILE 0-0.051-0.00846.0930.0010.0010.0000.0000.0000.000
141Q141LEU 0-0.034-0.01450.286-0.002-0.0020.0000.0000.0000.000
142Q142HIS 0-0.001-0.00248.5480.0000.0000.0000.0000.0000.000
143Q143LEU 0-0.0240.00553.832-0.001-0.0010.0000.0000.0000.000
144Q144SER 00.0160.00555.2150.0000.0000.0000.0000.0000.000
145Q145ALA 00.0680.00655.2300.0010.0010.0000.0000.0000.000
146Q146ASP -1-0.913-0.94956.7780.0080.0080.0000.0000.0000.000
147Q147LYS 10.8570.92159.179-0.011-0.0110.0000.0000.0000.000
148Q148ALA 0-0.0400.00554.8380.0010.0010.0000.0000.0000.000
149Q149PRO 00.0160.01555.5020.0000.0000.0000.0000.0000.000
150Q150VAL 00.0210.02354.6500.0000.0000.0000.0000.0000.000
151Q151ASP -1-0.744-0.87650.7220.0270.0270.0000.0000.0000.000
152Q152LYS 10.9330.94854.077-0.030-0.0300.0000.0000.0000.000
153Q153LEU 0-0.073-0.02450.1140.0000.0000.0000.0000.0000.000
154Q154GLY 00.0550.02953.8400.0000.0000.0000.0000.0000.000
155Q155LYS 10.7870.90147.826-0.028-0.0280.0000.0000.0000.000
156Q156PRO 00.0320.00550.6790.0010.0010.0000.0000.0000.000
157Q157LEU 0-0.046-0.00750.3440.0020.0020.0000.0000.0000.000
158Q158LEU 0-0.030-0.01846.549-0.002-0.0020.0000.0000.0000.000
159Q159THR 00.007-0.00750.7970.0010.0010.0000.0000.0000.000
160Q160LEU 0-0.025-0.01347.838-0.001-0.0010.0000.0000.0000.000
161Q161LYS 10.9400.96251.959-0.019-0.0190.0000.0000.0000.000
162Q162ASP -1-0.859-0.93753.0300.0260.0260.0000.0000.0000.000
163Q163LYS 10.8390.91553.360-0.031-0.0310.0000.0000.0000.000
164Q164SER 00.0740.05149.1700.0000.0000.0000.0000.0000.000
165Q165ILE 0-0.030-0.01346.0650.0010.0010.0000.0000.0000.000
166Q166SER 0-0.080-0.03746.5070.0020.0020.0000.0000.0000.000
167Q167LEU 0-0.0020.01239.7370.0020.0020.0000.0000.0000.000
168Q168GLU -1-0.899-0.95239.3610.0540.0540.0000.0000.0000.000
169Q169ASN 0-0.034-0.01234.4740.0110.0110.0000.0000.0000.000
170Q170ILE 0-0.036-0.01736.442-0.002-0.0020.0000.0000.0000.000
171Q171SER 00.1260.04033.046-0.003-0.0030.0000.0000.0000.000
172Q172ARG 10.7540.88632.751-0.054-0.0540.0000.0000.0000.000
173Q173PHE 00.002-0.00134.700-0.005-0.0050.0000.0000.0000.000
174Q174VAL 0-0.0030.00336.0870.0070.0070.0000.0000.0000.000
175Q175HIS 00.0450.06638.003-0.001-0.0010.0000.0000.0000.000
176Q176VAL 00.0110.00438.5350.0020.0020.0000.0000.0000.000
177Q177SER 0-0.071-0.05637.6300.0040.0040.0000.0000.0000.000
178Q178GLY 00.0300.01434.5130.0060.0060.0000.0000.0000.000
179Q179VAL 0-0.0090.00131.781-0.005-0.0050.0000.0000.0000.000
180Q180TYR 0-0.015-0.02532.4050.0140.0140.0000.0000.0000.000
181Q181ARG 10.9260.96226.396-0.151-0.1510.0000.0000.0000.000
182Q182TYR 0-0.005-0.00433.3090.0030.0030.0000.0000.0000.000
183Q183SER 0-0.104-0.10333.2170.0010.0010.0000.0000.0000.000
184Q184ASN 0-0.129-0.22034.235-0.001-0.0010.0000.0000.0000.000
185Q185GLY 00.1770.08336.6210.0000.0000.0000.0000.0000.000
186Q186ARG 10.9511.17037.618-0.076-0.0760.0000.0000.0000.000
187Q187LEU 00.0440.03137.149-0.003-0.0030.0000.0000.0000.000
188Q188ILE 00.0270.03735.5140.0020.0020.0000.0000.0000.000
189Q189LYS 10.9370.94532.496-0.127-0.1270.0000.0000.0000.000
190Q190ASN 0-0.059-0.01928.1870.0120.0120.0000.0000.0000.000
191Q191ALA -1-0.862-0.88326.7460.1680.1680.0000.0000.0000.000