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: K91K3

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2073653.715888
FMO2-HF: Nuclear repulsion 1999502.529831
FMO2-HF: Total energy -74151.186057
FMO2-MP2: Total energy -74370.197874


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.
-1.8461.7340.019-1.647-1.9510.005
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 : 0.014 / q_NPA : -0.012
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].
3A355SER00.0290.0182.920-1.6941.6220.021-1.582-1.7540.005
4A356VAL00.0410.0184.420-0.861-0.791-0.001-0.023-0.0460.000
5A357LYS10.9550.9867.029-0.140-0.1400.0000.0000.0000.000
6A358PRO00.0340.0118.7840.0010.0010.0000.0000.0000.000
7A359GLY0-0.066-0.04612.175-0.022-0.0220.0000.0000.0000.000
8A360SER0-0.054-0.01710.8800.0050.0050.0000.0000.0000.000
9A361LEU0-0.006-0.00713.388-0.010-0.0100.0000.0000.0000.000
10A362VAL0-0.009-0.01110.7430.0500.0500.0000.0000.0000.000
11A363ALA00.0060.02413.545-0.056-0.0560.0000.0000.0000.000
12A364VAL0-0.036-0.02514.2160.0920.0920.0000.0000.0000.000
13A365LEU00.0330.02415.308-0.047-0.0470.0000.0000.0000.000
14A366GLY00.0430.01716.1480.0350.0350.0000.0000.0000.000
15A367GLU-1-0.839-0.93018.5400.1280.1280.0000.0000.0000.000
16A368THR0-0.040-0.01920.993-0.002-0.0020.0000.0000.0000.000
17A369GLY00.0050.02720.553-0.022-0.0220.0000.0000.0000.000
18A370SER00.0260.00620.9470.0180.0180.0000.0000.0000.000
19A371GLY00.0670.03619.413-0.009-0.0090.0000.0000.0000.000
20A372LYS10.8370.90120.353-0.132-0.1320.0000.0000.0000.000
21A373SER0-0.086-0.04022.050-0.011-0.0110.0000.0000.0000.000
22A374THR0-0.082-0.04216.800-0.022-0.0220.0000.0000.0000.000
23A375LEU0-0.022-0.00814.933-0.011-0.0110.0000.0000.0000.000
24A376MET00.0340.00616.3600.0130.0130.0000.0000.0000.000
25A377ASN0-0.019-0.00816.2760.0090.0090.0000.0000.0000.000
26A378LEU00.002-0.00710.511-0.042-0.0420.0000.0000.0000.000
27A379ILE00.0500.04312.4120.0120.0120.0000.0000.0000.000
28A380PRO0-0.0180.01913.0800.0320.0320.0000.0000.0000.000
29A381ARG10.9090.9708.0760.5820.5820.0000.0000.0000.000
30A382LEU0-0.091-0.0608.4440.0940.0940.0000.0000.0000.000
31A407GLY00.0560.03123.128-0.004-0.0040.0000.0000.0000.000
32A408HIS0-0.043-0.03421.5430.0030.0030.0000.0000.0000.000
33A409ILE0-0.004-0.01119.0240.0120.0120.0000.0000.0000.000
34A410SER0-0.0150.00322.014-0.012-0.0120.0000.0000.0000.000
35A411ALA00.0270.01222.9430.0140.0140.0000.0000.0000.000
36A412VAL0-0.010-0.00824.540-0.012-0.0120.0000.0000.0000.000
37A413PRO00.0120.00726.5480.0100.0100.0000.0000.0000.000
38A414GLN00.0080.00328.719-0.001-0.0010.0000.0000.0000.000
39A415GLU-1-0.836-0.91130.0460.0720.0720.0000.0000.0000.000
40A416THR0-0.068-0.03032.892-0.002-0.0020.0000.0000.0000.000
41A417VAL00.0440.01434.404-0.004-0.0040.0000.0000.0000.000
42A418LEU00.0140.02036.4310.0010.0010.0000.0000.0000.000
43A419PHE0-0.014-0.01038.138-0.002-0.0020.0000.0000.0000.000
44A420SER0-0.024-0.02742.0480.0010.0010.0000.0000.0000.000
45A421GLY00.0240.01344.767-0.002-0.0020.0000.0000.0000.000
46A422THR0-0.015-0.01144.0240.0020.0020.0000.0000.0000.000
47A423ILE00.0170.00439.1050.0020.0020.0000.0000.0000.000
48A424LYS10.8920.93839.261-0.038-0.0380.0000.0000.0000.000
49A425GLU-1-0.843-0.90238.9870.0380.0380.0000.0000.0000.000
50A426ASN0-0.024-0.02537.9060.0020.0020.0000.0000.0000.000
51A427LEU0-0.0160.00033.9610.0030.0030.0000.0000.0000.000
52A428LYS10.8580.91634.140-0.039-0.0390.0000.0000.0000.000
53A429TRP0-0.0150.01734.964-0.001-0.0010.0000.0000.0000.000
54A430GLY0-0.029-0.03733.1640.0040.0040.0000.0000.0000.000
55A431ARG10.6720.79230.231-0.053-0.0530.0000.0000.0000.000
56A432GLU-1-0.867-0.93533.5800.0300.0300.0000.0000.0000.000
57A433ASP-1-0.813-0.86933.4750.0440.0440.0000.0000.0000.000
58A434ALA0-0.0250.00133.4760.0010.0010.0000.0000.0000.000
59A435THR00.0280.01535.035-0.002-0.0020.0000.0000.0000.000
60A436ASP-1-0.770-0.89236.4410.0450.0450.0000.0000.0000.000
61A437ASP-1-0.916-0.95935.8110.0580.0580.0000.0000.0000.000
62A438GLU-1-0.723-0.84031.4240.0610.0610.0000.0000.0000.000
63A439ILE0-0.049-0.02432.3870.0050.0050.0000.0000.0000.000
64A440VAL00.0280.02334.1190.0040.0040.0000.0000.0000.000
65A441GLU-1-0.767-0.86130.4830.0810.0810.0000.0000.0000.000
66A442ALA0-0.030-0.00829.4080.0070.0070.0000.0000.0000.000
67A443ALA00.015-0.00230.2840.0070.0070.0000.0000.0000.000
68A444LYS10.7930.86632.075-0.073-0.0730.0000.0000.0000.000
69A445ILE0-0.0300.00025.5650.0060.0060.0000.0000.0000.000
70A446ALA0-0.018-0.00728.2710.0090.0090.0000.0000.0000.000
71A447GLN0-0.020-0.00629.7840.0000.0000.0000.0000.0000.000
72A448ILE0-0.008-0.00732.395-0.002-0.0020.0000.0000.0000.000
73A449HIS00.0840.06534.984-0.004-0.0040.0000.0000.0000.000
74A450ASP-1-0.889-0.94436.7130.0710.0710.0000.0000.0000.000
75A451PHE0-0.012-0.01338.617-0.002-0.0020.0000.0000.0000.000
76A452ILE0-0.0050.00637.200-0.003-0.0030.0000.0000.0000.000
77A453ILE0-0.019-0.01240.538-0.003-0.0030.0000.0000.0000.000
78A454SER0-0.092-0.04742.848-0.002-0.0020.0000.0000.0000.000
79A455LEU0-0.029-0.00643.170-0.002-0.0020.0000.0000.0000.000
80A456PRO00.0270.01246.4490.0000.0000.0000.0000.0000.000
81A457GLU-1-0.869-0.94048.0940.0380.0380.0000.0000.0000.000
82A458GLY00.0260.03044.5200.0000.0000.0000.0000.0000.000
83A459TYR0-0.017-0.04937.2750.0020.0020.0000.0000.0000.000
84A460ASP-1-0.915-0.95842.6430.0400.0400.0000.0000.0000.000
85A461SER0-0.031-0.02244.789-0.002-0.0020.0000.0000.0000.000
86A462ARG10.9520.97845.068-0.034-0.0340.0000.0000.0000.000
87A463VAL0-0.0060.01641.3210.0030.0030.0000.0000.0000.000
88A464GLU-1-0.868-0.95444.4780.0380.0380.0000.0000.0000.000
89A465ARG10.9440.96844.213-0.031-0.0310.0000.0000.0000.000
90A466GLY0-0.003-0.01041.2730.0000.0000.0000.0000.0000.000
91A467GLY00.0030.00140.8820.0030.0030.0000.0000.0000.000
92A468ARG10.8960.94641.964-0.038-0.0380.0000.0000.0000.000
93A469ASN0-0.016-0.00744.2430.0020.0020.0000.0000.0000.000
94A470PHE00.0100.01440.4200.0010.0010.0000.0000.0000.000
95A471SER00.0440.00939.6150.0010.0010.0000.0000.0000.000
96A472GLY00.0690.02337.6710.0010.0010.0000.0000.0000.000
97A473GLY00.0810.02634.5640.0030.0030.0000.0000.0000.000
98A474GLN0-0.040-0.00634.5130.0030.0030.0000.0000.0000.000
99A475LYS10.9220.96735.919-0.067-0.0670.0000.0000.0000.000
100A476GLN00.0340.01531.1260.0030.0030.0000.0000.0000.000
101A477ARG10.8850.94331.141-0.089-0.0890.0000.0000.0000.000
102A478LEU00.0200.01631.9030.0010.0010.0000.0000.0000.000
103A479SER0-0.022-0.01631.229-0.004-0.0040.0000.0000.0000.000
104A480ILE0-0.003-0.00326.3440.0010.0010.0000.0000.0000.000
105A481ALA00.0150.00928.2670.0010.0010.0000.0000.0000.000
106A482ARG10.8090.88430.397-0.064-0.0640.0000.0000.0000.000
107A483ALA0-0.039-0.01726.040-0.003-0.0030.0000.0000.0000.000
108A484LEU0-0.008-0.01224.1880.0010.0010.0000.0000.0000.000
109A485VAL00.0450.03327.001-0.002-0.0020.0000.0000.0000.000
110A486LYS10.8810.95027.481-0.067-0.0670.0000.0000.0000.000
111A487LYS10.7750.89225.306-0.064-0.0640.0000.0000.0000.000
112A488PRO0-0.0110.00821.889-0.003-0.0030.0000.0000.0000.000
113A489LYS10.9620.97418.407-0.083-0.0830.0000.0000.0000.000
114A490VAL0-0.010-0.00315.8810.0190.0190.0000.0000.0000.000
115A491LEU00.0310.02418.396-0.019-0.0190.0000.0000.0000.000
116A492ILE0-0.013-0.01018.6820.0240.0240.0000.0000.0000.000
117A493LEU00.0270.00120.739-0.020-0.0200.0000.0000.0000.000
118A494ASP-1-0.792-0.90422.4230.1570.1570.0000.0000.0000.000
119A495ASP-1-0.846-0.90823.8780.1430.1430.0000.0000.0000.000
120A496CYS0-0.041-0.01125.629-0.009-0.0090.0000.0000.0000.000
121A497THR0-0.007-0.03226.109-0.006-0.0060.0000.0000.0000.000
122A498SER00.0280.02528.586-0.004-0.0040.0000.0000.0000.000
123A499SER0-0.052-0.01630.594-0.006-0.0060.0000.0000.0000.000
124A500VAL0-0.083-0.04330.319-0.008-0.0080.0000.0000.0000.000
125A501ASP-1-0.785-0.85231.2890.1200.1200.0000.0000.0000.000
126A502PRO00.0820.01129.0590.0030.0030.0000.0000.0000.000
127A503ILE0-0.0090.00728.8610.0090.0090.0000.0000.0000.000
128A504THR0-0.032-0.05829.9490.0010.0010.0000.0000.0000.000
129A505GLU-1-0.781-0.83925.4570.1930.1930.0000.0000.0000.000
130A506LYS10.8720.91723.754-0.182-0.1820.0000.0000.0000.000
131A507ARG10.8570.92125.339-0.106-0.1060.0000.0000.0000.000
132A508ILE00.0070.01525.160-0.002-0.0020.0000.0000.0000.000
133A509LEU0-0.010-0.00820.8820.0020.0020.0000.0000.0000.000
134A510ASP-1-0.819-0.91021.6870.1970.1970.0000.0000.0000.000
135A511GLY00.0100.01123.133-0.005-0.0050.0000.0000.0000.000
136A512LEU0-0.028-0.01320.799-0.005-0.0050.0000.0000.0000.000
137A513LYS10.8620.94317.536-0.244-0.2440.0000.0000.0000.000
138A514ARG10.8680.94819.799-0.116-0.1160.0000.0000.0000.000
139A515TYR00.008-0.01222.596-0.009-0.0090.0000.0000.0000.000
140A516THR00.0050.01721.421-0.010-0.0100.0000.0000.0000.000
141A517LYS10.9821.01015.210-0.132-0.1320.0000.0000.0000.000
142A518GLY0-0.058-0.03418.068-0.011-0.0110.0000.0000.0000.000
143A519CYS0-0.030-0.02218.344-0.005-0.0050.0000.0000.0000.000
144A520THR0-0.0160.01012.2160.0050.0050.0000.0000.0000.000
145A521THR00.0270.01115.334-0.021-0.0210.0000.0000.0000.000
146A522PHE00.0170.00311.9290.0300.0300.0000.0000.0000.000
147A523ILE00.0070.00316.776-0.034-0.0340.0000.0000.0000.000
148A524ILE0-0.0090.00318.8380.0390.0390.0000.0000.0000.000
149A525THR0-0.010-0.01919.335-0.031-0.0310.0000.0000.0000.000
150A526GLN00.034-0.00820.5390.0340.0340.0000.0000.0000.000
151A527LYS10.8540.93622.830-0.190-0.1900.0000.0000.0000.000
152A528ILE00.0490.01518.6760.0240.0240.0000.0000.0000.000
153A529PRO00.001-0.00620.5070.0210.0210.0000.0000.0000.000
154A530THR0-0.015-0.02421.1920.0020.0020.0000.0000.0000.000
155A531ALA00.001-0.00916.9600.0100.0100.0000.0000.0000.000
156A532LEU0-0.034-0.01716.7350.0470.0470.0000.0000.0000.000
157A533LEU0-0.041-0.01018.089-0.010-0.0100.0000.0000.0000.000
158A534ALA0-0.056-0.01914.903-0.030-0.0300.0000.0000.0000.000
159A535ASP-1-0.847-0.92011.6800.3250.3250.0000.0000.0000.000
160A536LYS10.7860.8885.515-1.332-1.3320.0000.0000.0000.000
161A537ILE00.0110.01110.472-0.128-0.1280.0000.0000.0000.000
162A538LEU0-0.025-0.0109.4320.3050.3050.0000.0000.0000.000
163A539VAL00.0190.01110.906-0.152-0.1520.0000.0000.0000.000
164A540LEU0-0.048-0.02912.2040.0100.0100.0000.0000.0000.000
165A541HIS00.021-0.00914.6050.0310.0310.0000.0000.0000.000
166A542GLU-1-0.882-0.93016.0880.0540.0540.0000.0000.0000.000
167A543GLY00.0470.03616.942-0.012-0.0120.0000.0000.0000.000
168A544LYS10.8680.91512.520-0.002-0.0020.0000.0000.0000.000
169A545VAL0-0.011-0.0158.1060.0360.0360.0000.0000.0000.000
170A546ALA00.0320.0129.835-0.094-0.0940.0000.0000.0000.000
171A547GLY00.0380.0238.1110.0390.0390.0000.0000.0000.000
172A548PHE0-0.030-0.0344.534-0.665-0.471-0.001-0.042-0.1510.000
173A549GLY00.0110.0195.9171.3141.3140.0000.0000.0000.000
174A550THR0-0.023-0.0377.588-0.520-0.5200.0000.0000.0000.000
175A551HIS00.1150.07310.5560.1650.1650.0000.0000.0000.000
176A552LYS10.8820.92613.037-0.566-0.5660.0000.0000.0000.000
177A553GLU-1-0.748-0.8626.9332.0952.0950.0000.0000.0000.000
178A554LEU00.0110.0139.3980.0670.0670.0000.0000.0000.000
179A555LEU0-0.017-0.00811.034-0.142-0.1420.0000.0000.0000.000
180A556GLU-1-0.883-0.92111.4070.6920.6920.0000.0000.0000.000
181A557HIS0-0.071-0.0266.502-0.512-0.5120.0000.0000.0000.000
182A558CYS0-0.0370.00010.583-0.101-0.1010.0000.0000.0000.000
183A559LYS10.8230.89112.360-0.258-0.2580.0000.0000.0000.000
184A560PRO00.0630.01714.231-0.008-0.0080.0000.0000.0000.000
185A561TYR00.023-0.02013.850-0.022-0.0220.0000.0000.0000.000
186A562ARG10.8780.93014.166-0.545-0.5450.0000.0000.0000.000
187A563GLU-1-0.765-0.85817.9620.1880.1880.0000.0000.0000.000
188A564ILE0-0.0100.00517.515-0.022-0.0220.0000.0000.0000.000
189A565TYR0-0.011-0.00818.725-0.019-0.0190.0000.0000.0000.000
190A566GLU-1-0.916-0.96220.7280.1970.1970.0000.0000.0000.000
191A567SER0-0.099-0.05223.471-0.025-0.0250.0000.0000.0000.000
192A568GLN0-0.029-0.02323.247-0.010-0.0100.0000.0000.0000.000
193A569PHE0-0.047-0.01423.374-0.010-0.0100.0000.0000.0000.000
194A570GLY00.0010.01025.7550.0050.0050.0000.0000.0000.000