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: QY9KY

Calculation Name: 4Q7K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Q7K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WYC3

Base Structure: X-ray

Registration Date: 2023-09-20

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2071730.179697
FMO2-HF: Nuclear repulsion 1997580.103669
FMO2-HF: Total energy -74150.076028
FMO2-MP2: Total energy -74369.049158


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(A:353:ASN)


Summations of interaction energy for fragment #1(A:353:ASN)
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.
-0.0679999999999993.2260.031-1.49-1.8350.004
Interaction energy analysis for fragmet #1(A:353:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : -0.003
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].
3A355SER00.0330.0182.975-1.5701.5390.033-1.453-1.6890.004
4A356VAL00.0410.0204.452-0.845-0.778-0.001-0.020-0.0460.000
5A357LYS10.9360.9777.062-0.062-0.0620.0000.0000.0000.000
6A358PRO00.0270.0208.807-0.007-0.0070.0000.0000.0000.000
7A359GLY0-0.051-0.04412.206-0.011-0.0110.0000.0000.0000.000
8A360SER0-0.041-0.02010.9590.0020.0020.0000.0000.0000.000
9A361LEU00.001-0.00513.404-0.013-0.0130.0000.0000.0000.000
10A362VAL0-0.020-0.01210.8430.0410.0410.0000.0000.0000.000
11A363ALA00.0110.02113.560-0.045-0.0450.0000.0000.0000.000
12A364VAL0-0.030-0.01814.3270.0670.0670.0000.0000.0000.000
13A365LEU00.0150.01215.430-0.030-0.0300.0000.0000.0000.000
14A366GLY00.0430.01816.2530.0200.0200.0000.0000.0000.000
15A367GLU-1-0.857-0.94218.5600.0490.0490.0000.0000.0000.000
16A368THR0-0.040-0.02020.7400.0070.0070.0000.0000.0000.000
17A369GLY00.0120.02720.237-0.018-0.0180.0000.0000.0000.000
18A370SER0-0.021-0.01820.8300.0140.0140.0000.0000.0000.000
19A371GLY00.0280.00019.420-0.010-0.0100.0000.0000.0000.000
20A372LYS10.8650.93120.141-0.077-0.0770.0000.0000.0000.000
21A373SER0-0.075-0.03621.720-0.006-0.0060.0000.0000.0000.000
22A374THR0-0.0270.00417.038-0.022-0.0220.0000.0000.0000.000
23A375LEU0-0.0040.00814.890-0.027-0.0270.0000.0000.0000.000
24A376MET00.0240.00016.012-0.005-0.0050.0000.0000.0000.000
25A377ASN0-0.001-0.00215.7160.0070.0070.0000.0000.0000.000
26A378LEU0-0.014-0.02110.208-0.058-0.0580.0000.0000.0000.000
27A379ILE00.0180.02212.098-0.017-0.0170.0000.0000.0000.000
28A380PRO0-0.023-0.00713.1280.0220.0220.0000.0000.0000.000
29A381ARG10.9150.9708.1320.9270.9270.0000.0000.0000.000
30A382LEU0-0.045-0.0058.5350.0230.0230.0000.0000.0000.000
31A407GLY00.0500.03023.178-0.005-0.0050.0000.0000.0000.000
32A408HIS0-0.041-0.03321.5760.0030.0030.0000.0000.0000.000
33A409ILE00.010-0.00618.8280.0100.0100.0000.0000.0000.000
34A410SER0-0.023-0.00122.058-0.007-0.0070.0000.0000.0000.000
35A411ALA00.0350.01422.9800.0090.0090.0000.0000.0000.000
36A412VAL0-0.028-0.01724.577-0.007-0.0070.0000.0000.0000.000
37A413PRO00.0230.01326.5780.0070.0070.0000.0000.0000.000
38A414GLN00.0380.01928.8530.0050.0050.0000.0000.0000.000
39A415GLU-1-0.938-0.97330.0720.0440.0440.0000.0000.0000.000
40A416THR0-0.049-0.02132.998-0.004-0.0040.0000.0000.0000.000
41A417VAL00.0560.02934.434-0.003-0.0030.0000.0000.0000.000
42A418LEU0-0.0100.00136.4250.0010.0010.0000.0000.0000.000
43A419PHE0-0.007-0.00838.455-0.001-0.0010.0000.0000.0000.000
44A420SER0-0.056-0.04742.0830.0010.0010.0000.0000.0000.000
45A421GLY00.0440.02844.814-0.002-0.0020.0000.0000.0000.000
46A422THR00.0190.02243.9380.0020.0020.0000.0000.0000.000
47A423ILE00.0220.00839.0880.0000.0000.0000.0000.0000.000
48A424LYS10.9680.99139.292-0.021-0.0210.0000.0000.0000.000
49A425GLU-1-0.891-0.94139.0200.0170.0170.0000.0000.0000.000
50A426ASN0-0.031-0.02637.8700.0000.0000.0000.0000.0000.000
51A427LEU0-0.021-0.00434.0740.0010.0010.0000.0000.0000.000
52A428LYS10.9230.97234.174-0.018-0.0180.0000.0000.0000.000
53A429TRP0-0.0170.01335.746-0.002-0.0020.0000.0000.0000.000
54A430GLY0-0.028-0.03033.2040.0020.0020.0000.0000.0000.000
55A431ARG10.7500.87030.260-0.025-0.0250.0000.0000.0000.000
56A432GLU-1-0.889-0.94733.6200.0070.0070.0000.0000.0000.000
57A433ASP-1-0.857-0.92833.8000.0170.0170.0000.0000.0000.000
58A434ALA0-0.048-0.01633.6920.0010.0010.0000.0000.0000.000
59A435THR00.001-0.00135.071-0.001-0.0010.0000.0000.0000.000
60A436ASP-1-0.832-0.93836.4720.0260.0260.0000.0000.0000.000
61A437ASP-1-0.921-0.96935.3940.0400.0400.0000.0000.0000.000
62A438GLU-1-0.842-0.92531.9200.0320.0320.0000.0000.0000.000
63A439ILE0-0.057-0.03232.4150.0030.0030.0000.0000.0000.000
64A440VAL00.0250.02334.1440.0030.0030.0000.0000.0000.000
65A441GLU-1-0.835-0.90830.4770.0580.0580.0000.0000.0000.000
66A442ALA0-0.031-0.00929.4340.0050.0050.0000.0000.0000.000
67A443ALA00.010-0.00630.3060.0050.0050.0000.0000.0000.000
68A444LYS10.8360.89831.977-0.052-0.0520.0000.0000.0000.000
69A445ILE0-0.0270.00625.5380.0050.0050.0000.0000.0000.000
70A446ALA0-0.025-0.01228.2860.0070.0070.0000.0000.0000.000
71A447GLN0-0.014-0.01629.803-0.001-0.0010.0000.0000.0000.000
72A448ILE0-0.020-0.01232.409-0.001-0.0010.0000.0000.0000.000
73A449HIS00.0790.07534.987-0.003-0.0030.0000.0000.0000.000
74A450ASP-1-0.861-0.92636.8530.0500.0500.0000.0000.0000.000
75A451PHE0-0.046-0.02838.631-0.002-0.0020.0000.0000.0000.000
76A452ILE0-0.0100.00537.316-0.002-0.0020.0000.0000.0000.000
77A453ILE0-0.014-0.00840.610-0.002-0.0020.0000.0000.0000.000
78A454SER0-0.093-0.05142.866-0.002-0.0020.0000.0000.0000.000
79A455LEU0-0.033-0.01543.155-0.001-0.0010.0000.0000.0000.000
80A456PRO00.0210.01246.4680.0000.0000.0000.0000.0000.000
81A457GLU-1-0.879-0.93948.3100.0230.0230.0000.0000.0000.000
82A458GLY00.0250.02744.5420.0000.0000.0000.0000.0000.000
83A459TYR0-0.023-0.06637.3410.0010.0010.0000.0000.0000.000
84A460ASP-1-0.929-0.95842.6690.0220.0220.0000.0000.0000.000
85A461SER0-0.026-0.02444.777-0.002-0.0020.0000.0000.0000.000
86A462ARG10.9660.98045.096-0.018-0.0180.0000.0000.0000.000
87A463VAL0-0.0050.00941.2930.0020.0020.0000.0000.0000.000
88A464GLU-1-0.891-0.96244.5080.0210.0210.0000.0000.0000.000
89A465ARG10.9340.97144.243-0.015-0.0150.0000.0000.0000.000
90A466GLY00.0240.00141.3040.0010.0010.0000.0000.0000.000
91A467GLY00.0050.00040.9110.0020.0020.0000.0000.0000.000
92A468ARG10.8780.92741.992-0.020-0.0200.0000.0000.0000.000
93A469ASN00.0310.02944.2690.0010.0010.0000.0000.0000.000
94A470PHE00.0160.01740.4460.0010.0010.0000.0000.0000.000
95A471SER00.0480.01239.6160.0000.0000.0000.0000.0000.000
96A472GLY00.0560.01337.6890.0000.0000.0000.0000.0000.000
97A473GLY00.1010.03834.5810.0010.0010.0000.0000.0000.000
98A474GLN0-0.024-0.00634.5310.0010.0010.0000.0000.0000.000
99A475LYS10.9500.98835.941-0.039-0.0390.0000.0000.0000.000
100A476GLN00.0600.03331.0910.0020.0020.0000.0000.0000.000
101A477ARG10.8970.95231.165-0.063-0.0630.0000.0000.0000.000
102A478LEU00.0150.01231.9270.0000.0000.0000.0000.0000.000
103A479SER0-0.027-0.01831.216-0.004-0.0040.0000.0000.0000.000
104A480ILE00.0120.00626.446-0.002-0.0020.0000.0000.0000.000
105A481ALA00.0140.00828.2960.0000.0000.0000.0000.0000.000
106A482ARG10.8350.90430.427-0.032-0.0320.0000.0000.0000.000
107A483ALA0-0.044-0.01726.031-0.004-0.0040.0000.0000.0000.000
108A484LEU0-0.007-0.01224.257-0.001-0.0010.0000.0000.0000.000
109A485VAL00.0420.03427.032-0.002-0.0020.0000.0000.0000.000
110A486LYS10.8910.94727.468-0.028-0.0280.0000.0000.0000.000
111A487LYS10.8830.96525.360-0.033-0.0330.0000.0000.0000.000
112A488PRO0-0.0130.00621.938-0.004-0.0040.0000.0000.0000.000
113A489LYS10.9630.97118.467-0.033-0.0330.0000.0000.0000.000
114A490VAL0-0.0040.00315.9140.0130.0130.0000.0000.0000.000
115A491LEU00.0210.01818.436-0.013-0.0130.0000.0000.0000.000
116A492ILE0-0.007-0.00618.7570.0150.0150.0000.0000.0000.000
117A493LEU00.017-0.00620.772-0.012-0.0120.0000.0000.0000.000
118A494ASP-1-0.799-0.91122.4470.0840.0840.0000.0000.0000.000
119A495ASP-1-0.872-0.93323.9220.0980.0980.0000.0000.0000.000
120A496CYS0-0.040-0.00325.760-0.006-0.0060.0000.0000.0000.000
121A497THR00.027-0.00225.613-0.006-0.0060.0000.0000.0000.000
122A498SER0-0.0040.01628.6020.0000.0000.0000.0000.0000.000
123A499SER0-0.053-0.02830.637-0.003-0.0030.0000.0000.0000.000
124A500VAL0-0.081-0.03830.390-0.005-0.0050.0000.0000.0000.000
125A501ASP-1-0.793-0.84831.3090.0920.0920.0000.0000.0000.000
126A502PRO00.0810.01429.2010.0020.0020.0000.0000.0000.000
127A503ILE0-0.0100.00828.8620.0080.0080.0000.0000.0000.000
128A504THR0-0.067-0.08329.9510.0010.0010.0000.0000.0000.000
129A505GLU-1-0.850-0.91025.4790.1420.1420.0000.0000.0000.000
130A506LYS10.8920.94823.844-0.150-0.1500.0000.0000.0000.000
131A507ARG10.9250.97025.341-0.081-0.0810.0000.0000.0000.000
132A508ILE00.0010.01225.065-0.002-0.0020.0000.0000.0000.000
133A509LEU0-0.015-0.01121.0200.0000.0000.0000.0000.0000.000
134A510ASP-1-0.865-0.94621.6950.1500.1500.0000.0000.0000.000
135A511GLY00.0010.00123.139-0.004-0.0040.0000.0000.0000.000
136A512LEU0-0.030-0.01020.767-0.005-0.0050.0000.0000.0000.000
137A513LYS10.9170.96817.554-0.196-0.1960.0000.0000.0000.000
138A514ARG10.8740.95519.809-0.093-0.0930.0000.0000.0000.000
139A515TYR00.008-0.01522.604-0.006-0.0060.0000.0000.0000.000
140A516THR00.0070.01921.377-0.009-0.0090.0000.0000.0000.000
141A517LYS10.9881.01415.494-0.086-0.0860.0000.0000.0000.000
142A518GLY0-0.096-0.05718.103-0.008-0.0080.0000.0000.0000.000
143A519CYS0-0.022-0.01218.373-0.006-0.0060.0000.0000.0000.000
144A520THR00.0040.01812.3570.0100.0100.0000.0000.0000.000
145A521THR00.0290.01415.366-0.019-0.0190.0000.0000.0000.000
146A522PHE00.0080.00112.1350.0220.0220.0000.0000.0000.000
147A523ILE00.0020.00416.803-0.023-0.0230.0000.0000.0000.000
148A524ILE0-0.0020.00618.8730.0310.0310.0000.0000.0000.000
149A525THR00.009-0.00719.452-0.018-0.0180.0000.0000.0000.000
150A526GLN00.0380.00320.6660.0240.0240.0000.0000.0000.000
151A527LYS10.9020.97122.956-0.130-0.1300.0000.0000.0000.000
152A528ILE00.0500.02118.9490.0170.0170.0000.0000.0000.000
153A529PRO0-0.005-0.01020.5430.0180.0180.0000.0000.0000.000
154A530THR0-0.007-0.02821.0080.0030.0030.0000.0000.0000.000
155A531ALA0-0.004-0.01517.0870.0060.0060.0000.0000.0000.000
156A532LEU0-0.043-0.02016.7750.0380.0380.0000.0000.0000.000
157A533LEU0-0.050-0.01318.136-0.005-0.0050.0000.0000.0000.000
158A534ALA0-0.064-0.02414.851-0.026-0.0260.0000.0000.0000.000
159A535ASP-1-0.860-0.92911.7720.2520.2520.0000.0000.0000.000
160A536LYS10.8340.9145.462-0.366-0.3660.0000.0000.0000.000
161A537ILE00.0270.01910.515-0.112-0.1120.0000.0000.0000.000
162A538LEU0-0.027-0.0129.7440.2370.2370.0000.0000.0000.000
163A539VAL00.0140.00811.013-0.108-0.1080.0000.0000.0000.000
164A540LEU0-0.058-0.03612.077-0.016-0.0160.0000.0000.0000.000
165A541HIS00.0430.00114.4410.0340.0340.0000.0000.0000.000
166A542GLU-1-0.893-0.94115.958-0.003-0.0030.0000.0000.0000.000
167A543GLY00.0340.03316.744-0.003-0.0030.0000.0000.0000.000
168A544LYS10.9000.93212.2320.1820.1820.0000.0000.0000.000
169A545VAL0-0.023-0.0157.6350.0500.0500.0000.0000.0000.000
170A546ALA00.0270.0089.689-0.089-0.0890.0000.0000.0000.000
171A547GLY00.0330.0218.1750.0870.0870.0000.0000.0000.000
172A548PHE0-0.028-0.0384.910-0.621-0.503-0.001-0.017-0.1000.000
173A549GLY00.0500.0436.0431.1591.1590.0000.0000.0000.000
174A550THR0-0.0030.0017.609-0.506-0.5060.0000.0000.0000.000
175A551HIS00.1180.09510.5850.1370.1370.0000.0000.0000.000
176A552LYS10.9530.96913.123-0.468-0.4680.0000.0000.0000.000
177A553GLU-1-0.834-0.9257.0432.0832.0830.0000.0000.0000.000
178A554LEU0-0.0050.0049.2710.0740.0740.0000.0000.0000.000
179A555LEU0-0.048-0.03011.126-0.133-0.1330.0000.0000.0000.000
180A556GLU-1-0.969-0.98111.2970.8790.8790.0000.0000.0000.000
181A557HIS0-0.064-0.0176.870-0.382-0.3820.0000.0000.0000.000
182A558CYS0-0.048-0.00310.712-0.118-0.1180.0000.0000.0000.000
183A559LYS10.9390.96612.408-0.240-0.2400.0000.0000.0000.000
184A560PRO00.0530.01114.215-0.012-0.0120.0000.0000.0000.000
185A561TYR00.035-0.04013.958-0.031-0.0310.0000.0000.0000.000
186A562ARG10.9180.96214.593-0.505-0.5050.0000.0000.0000.000
187A563GLU-1-0.891-0.94018.0360.1560.1560.0000.0000.0000.000
188A564ILE0-0.0080.00517.644-0.021-0.0210.0000.0000.0000.000
189A565TYR0-0.019-0.01618.866-0.016-0.0160.0000.0000.0000.000
190A566GLU-1-0.915-0.95520.8310.1910.1910.0000.0000.0000.000
191A567SER0-0.108-0.05823.568-0.024-0.0240.0000.0000.0000.000
192A568GLN0-0.016-0.01823.238-0.009-0.0090.0000.0000.0000.000
193A569PHE0-0.076-0.03923.115-0.008-0.0080.0000.0000.0000.000
194A570GLY00.0440.03825.9670.0070.0070.0000.0000.0000.000