FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 2289R

Calculation Name: 1XKS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XKS

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WUM0

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:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
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 378
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6134946.279816
FMO2-HF: Nuclear repulsion 5988719.723283
FMO2-HF: Total energy -146226.556533
FMO2-MP2: Total energy -146651.087278


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:75:GLU)


Summations of interaction energy for fragment #1(A:75: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.
169.4841720.957-1.398-2.0760.002
Interaction energy analysis for fragmet #1(A:75:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.976 / q_NPA : -0.995
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].
3A77VAL0-0.021-0.0183.4025.1706.9450.097-0.924-0.9490.000
4A78ASN0-0.049-0.0485.9200.4270.4270.0000.0000.0000.000
5A79TYR0-0.007-0.0315.977-2.285-2.2850.0000.0000.0000.000
6A80ASP-1-0.841-0.8824.18941.57641.6660.000-0.033-0.0570.000
7A81VAL0-0.011-0.0184.810-4.273-4.2730.0000.0000.0000.000
8A82LYS10.8280.9056.222-24.876-24.8760.0000.0000.0000.000
9A83THR00.0480.0208.606-1.261-1.2610.0000.0000.0000.000
10A84PHE0-0.028-0.01312.019-0.179-0.1790.0000.0000.0000.000
11A85GLY0-0.0010.00515.049-0.811-0.8110.0000.0000.0000.000
12A86SER0-0.069-0.05316.9850.6900.6900.0000.0000.0000.000
13A87SER0-0.016-0.02218.8860.3650.3650.0000.0000.0000.000
14A88LEU00.0230.03118.166-0.677-0.6770.0000.0000.0000.000
15A89PRO00.014-0.00121.301-0.196-0.1960.0000.0000.0000.000
16A90VAL00.0120.00824.5960.1850.1850.0000.0000.0000.000
17A91LYS10.9490.96225.897-9.081-9.0810.0000.0000.0000.000
18A92VAL0-0.0050.00921.779-0.045-0.0450.0000.0000.0000.000
19A93MET00.0030.00518.4040.4710.4710.0000.0000.0000.000
20A94GLU-1-0.939-0.96622.60310.71910.7190.0000.0000.0000.000
21A95ALA0-0.018-0.02125.024-0.019-0.0190.0000.0000.0000.000
22A96LEU00.004-0.00518.143-0.093-0.0930.0000.0000.0000.000
23A97THR0-0.076-0.05121.7580.3610.3610.0000.0000.0000.000
24A98LEU0-0.065-0.02822.644-0.189-0.1890.0000.0000.0000.000
25A99ALA0-0.0270.00122.751-0.379-0.3790.0000.0000.0000.000
26A100GLU-1-0.922-0.96123.00411.13711.1370.0000.0000.0000.000
27A101DVA0-0.077-0.05420.1770.2120.2120.0000.0000.0000.000
28A102ASP-1-0.867-0.92123.61610.85710.8570.0000.0000.0000.000
29A103ASP-1-0.851-0.90225.41010.44310.4430.0000.0000.0000.000
30A104GLN0-0.002-0.00624.6960.6390.6390.0000.0000.0000.000
31A105LEU0-0.042-0.01322.044-0.305-0.3050.0000.0000.0000.000
32A106THR00.0450.02523.8250.1070.1070.0000.0000.0000.000
33A107ILE0-0.055-0.03620.908-0.210-0.2100.0000.0000.0000.000
34A108ASN0-0.0050.01324.2150.3730.3730.0000.0000.0000.000
35A109ILE0-0.011-0.01919.6280.0770.0770.0000.0000.0000.000
36A110ASP-1-0.791-0.85723.77110.07510.0750.0000.0000.0000.000
37A111GLU-1-0.783-0.91424.20912.29412.2940.0000.0000.0000.000
38A112GLY0-0.029-0.00326.160-0.022-0.0220.0000.0000.0000.000
39A113GLY0-0.047-0.04124.581-0.084-0.0840.0000.0000.0000.000
40A114TRP0-0.039-0.02425.619-0.081-0.0810.0000.0000.0000.000
41A115ALA00.0290.02523.4520.2110.2110.0000.0000.0000.000
42A116CYS0-0.016-0.00425.475-0.450-0.4500.0000.0000.0000.000
43A117LEU00.0130.01323.1880.1790.1790.0000.0000.0000.000
44A118VAL00.0180.01326.169-0.354-0.3540.0000.0000.0000.000
45A119CYS0-0.032-0.02026.9310.3440.3440.0000.0000.0000.000
46A120LYS10.8860.90828.737-10.643-10.6430.0000.0000.0000.000
47A121GLU-1-0.864-0.91031.5998.0808.0800.0000.0000.0000.000
48A122LYS10.8400.91829.734-9.995-9.9950.0000.0000.0000.000
49A123LEU00.0200.01029.9150.3140.3140.0000.0000.0000.000
50A124ILE0-0.029-0.01327.466-0.204-0.2040.0000.0000.0000.000
51A125ILE00.0300.00928.0640.3210.3210.0000.0000.0000.000
52A126TRP0-0.017-0.02721.390-0.286-0.2860.0000.0000.0000.000
53A127LYS10.8430.93226.872-10.682-10.6820.0000.0000.0000.000
54A128ILE00.0280.01220.7220.2670.2670.0000.0000.0000.000
55A129ALA00.0290.02122.275-0.184-0.1840.0000.0000.0000.000
56A130LEU00.0210.00220.8400.5300.5300.0000.0000.0000.000
57A131SER0-0.029-0.01021.7320.1850.1850.0000.0000.0000.000
58A132PRO00.0520.03122.020-0.264-0.2640.0000.0000.0000.000
59A133ILE0-0.065-0.02923.916-0.418-0.4180.0000.0000.0000.000
60A134THR00.0880.03027.710-0.203-0.2030.0000.0000.0000.000
61A135LYS10.9360.96529.529-9.022-9.0220.0000.0000.0000.000
62A136LEU0-0.036-0.01828.704-0.297-0.2970.0000.0000.0000.000
63A137SER0-0.0240.00627.8020.2190.2190.0000.0000.0000.000
64A138VAL0-0.006-0.00928.718-0.403-0.4030.0000.0000.0000.000
65A139CYS0-0.032-0.01528.1540.3710.3710.0000.0000.0000.000
66A140LYS10.7470.87830.071-8.562-8.5620.0000.0000.0000.000
67A141GLU-1-0.822-0.90431.6019.7479.7470.0000.0000.0000.000
68A142LEU0-0.0180.00133.613-0.264-0.2640.0000.0000.0000.000
69A143GLN00.007-0.00735.3280.3120.3120.0000.0000.0000.000
70A144LEU00.0070.01033.375-0.156-0.1560.0000.0000.0000.000
71A145PRO0-0.0080.00637.834-0.161-0.1610.0000.0000.0000.000
72A146PRO0-0.005-0.01039.8830.1520.1520.0000.0000.0000.000
73A147SER0-0.038-0.05438.843-0.056-0.0560.0000.0000.0000.000
74A148ASP-1-0.918-0.94939.7567.2187.2180.0000.0000.0000.000
75A149PHE0-0.078-0.03736.5860.1530.1530.0000.0000.0000.000
76A150HIS0-0.014-0.00131.3270.2280.2280.0000.0000.0000.000
77A151TRP00.016-0.00233.1550.0930.0930.0000.0000.0000.000
78A152SER0-0.034-0.04029.8390.1630.1630.0000.0000.0000.000
79A153ALA00.0170.00226.893-0.229-0.2290.0000.0000.0000.000
80A154ASP-1-0.765-0.85029.0169.7909.7900.0000.0000.0000.000
81A155LEU0-0.028-0.00430.212-0.308-0.3080.0000.0000.0000.000
82A156VAL0-0.030-0.01630.901-0.274-0.2740.0000.0000.0000.000
83A157ALA00.0070.01031.4560.2730.2730.0000.0000.0000.000
84A158LEU00.0040.00329.805-0.234-0.2340.0000.0000.0000.000
85A159SER00.0290.00533.554-0.041-0.0410.0000.0000.0000.000
86A160TYR0-0.050-0.05329.895-0.088-0.0880.0000.0000.0000.000
87A161SER0-0.0090.00736.710-0.188-0.1880.0000.0000.0000.000
88A162SER0-0.051-0.02836.9760.2980.2980.0000.0000.0000.000
89A170THR00.004-0.01134.727-0.017-0.0170.0000.0000.0000.000
90A171GLN00.0480.03436.0850.0110.0110.0000.0000.0000.000
91A172ALA0-0.027-0.00436.390-0.136-0.1360.0000.0000.0000.000
92A173VAL00.0150.01033.3330.0450.0450.0000.0000.0000.000
93A174ALA00.0110.02636.420-0.089-0.0890.0000.0000.0000.000
94A175VAL0-0.006-0.02234.6120.2750.2750.0000.0000.0000.000
95A176MET0-0.052-0.00436.428-0.352-0.3520.0000.0000.0000.000
96A177VAL00.0030.00534.9600.2800.2800.0000.0000.0000.000
97A178ALA00.0140.01136.673-0.278-0.2780.0000.0000.0000.000
98A179THR0-0.043-0.04636.9000.1990.1990.0000.0000.0000.000
99A180ARG10.8540.91631.354-9.140-9.1400.0000.0000.0000.000
100A181GLU-1-0.709-0.80938.3827.4437.4430.0000.0000.0000.000
101A182GLY00.0160.00841.384-0.167-0.1670.0000.0000.0000.000
102A183SER0-0.035-0.01542.409-0.192-0.1920.0000.0000.0000.000
103A184ILE0-0.015-0.01241.4730.1990.1990.0000.0000.0000.000
104A185ARG10.7960.88140.297-7.524-7.5240.0000.0000.0000.000
105A186TYR00.0430.00740.2190.1470.1470.0000.0000.0000.000
106A187TRP00.013-0.00838.109-0.131-0.1310.0000.0000.0000.000
107A188PRO0-0.010-0.01240.5800.1260.1260.0000.0000.0000.000
108A189SER0-0.027-0.03740.0360.0990.0990.0000.0000.0000.000
109A190LEU00.0390.03232.611-0.061-0.0610.0000.0000.0000.000
110A191ALA0-0.054-0.03937.1210.1320.1320.0000.0000.0000.000
111A192GLY00.0020.00239.240-0.017-0.0170.0000.0000.0000.000
112A193GLU-1-0.745-0.86035.8978.4108.4100.0000.0000.0000.000
113A194ASP-1-0.894-0.93639.7947.2677.2670.0000.0000.0000.000
114A195THR0-0.125-0.06042.902-0.218-0.2180.0000.0000.0000.000
115A196TYR0-0.010-0.00742.3860.1380.1380.0000.0000.0000.000
116A197THR0-0.068-0.03544.396-0.137-0.1370.0000.0000.0000.000
117A198GLU-1-0.785-0.89044.3547.1127.1120.0000.0000.0000.000
118A199ALA0-0.050-0.01945.901-0.170-0.1700.0000.0000.0000.000
119A200PHE00.0030.00945.9390.0880.0880.0000.0000.0000.000
120A201VAL00.0220.02043.853-0.105-0.1050.0000.0000.0000.000
121A202ASP-1-0.752-0.84846.8686.2236.2230.0000.0000.0000.000
122A203SER0-0.126-0.07149.097-0.152-0.1520.0000.0000.0000.000
123A204GLY0-0.0060.00550.177-0.117-0.1170.0000.0000.0000.000
124A205GLY0-0.009-0.00747.8920.0620.0620.0000.0000.0000.000
125A206ASP-1-0.906-0.93947.2046.3446.3440.0000.0000.0000.000
126A207LYS10.8160.89643.953-6.290-6.2900.0000.0000.0000.000
127A208THR0-0.009-0.01337.8000.0490.0490.0000.0000.0000.000
128A209TYR0-0.041-0.02538.5130.0090.0090.0000.0000.0000.000
129A210SER00.0250.01533.8720.0810.0810.0000.0000.0000.000
130A211PHE00.0360.01229.8960.2390.2390.0000.0000.0000.000
131A212LEU0-0.0220.00033.681-0.356-0.3560.0000.0000.0000.000
132A213THR0-0.052-0.02333.0040.3200.3200.0000.0000.0000.000
133A214ALA00.0280.01534.217-0.272-0.2720.0000.0000.0000.000
134A215VAL0-0.026-0.01535.4400.1360.1360.0000.0000.0000.000
135A216GLN00.0130.00738.1060.0530.0530.0000.0000.0000.000
136A217GLY00.0430.02740.575-0.080-0.0800.0000.0000.0000.000
137A218GLY0-0.067-0.02640.641-0.088-0.0880.0000.0000.0000.000
138A219SER0-0.069-0.02240.953-0.069-0.0690.0000.0000.0000.000
139A220PHE00.0440.00236.4880.2030.2030.0000.0000.0000.000
140A221ILE0-0.0060.00638.372-0.253-0.2530.0000.0000.0000.000
141A222LEU0-0.0030.01337.8150.2480.2480.0000.0000.0000.000
142A223SER00.018-0.00436.686-0.199-0.1990.0000.0000.0000.000
143A224SER0-0.030-0.01337.8040.1440.1440.0000.0000.0000.000
144A225SER00.0590.01637.3860.0220.0220.0000.0000.0000.000
145A226GLY00.0400.01738.4020.0630.0630.0000.0000.0000.000
146A227SER0-0.018-0.02939.957-0.253-0.2530.0000.0000.0000.000
147A228GLN0-0.0170.00041.1060.0160.0160.0000.0000.0000.000
148A229LEU0-0.0180.00039.3130.1960.1960.0000.0000.0000.000
149A230ILE0-0.013-0.01642.211-0.217-0.2170.0000.0000.0000.000
150A231ARG10.7950.89442.573-6.786-6.7860.0000.0000.0000.000
151A232LEU0-0.019-0.02041.253-0.184-0.1840.0000.0000.0000.000
152A233ILE00.023-0.00443.2620.1450.1450.0000.0000.0000.000
153A234PRO00.0080.00943.236-0.169-0.1690.0000.0000.0000.000
154A235GLU-1-0.787-0.85046.4235.7695.7690.0000.0000.0000.000
155A236SER0-0.015-0.02049.5870.0410.0410.0000.0000.0000.000
156A237SER0-0.079-0.06751.050-0.015-0.0150.0000.0000.0000.000
157A238GLY00.0230.01849.498-0.059-0.0590.0000.0000.0000.000
158A239LYS10.8190.90049.375-5.638-5.6380.0000.0000.0000.000
159A240ILE00.0450.01944.5410.0780.0780.0000.0000.0000.000
160A241HIS00.0080.03748.408-0.035-0.0350.0000.0000.0000.000
161A242GLN00.011-0.01547.4440.2090.2090.0000.0000.0000.000
162A243HIS10.7150.83047.321-6.559-6.5590.0000.0000.0000.000
163A244ILE00.0340.02446.9110.1270.1270.0000.0000.0000.000
164A245LEU00.0230.02141.774-0.105-0.1050.0000.0000.0000.000
165A246PRO00.0010.01446.477-0.075-0.0750.0000.0000.0000.000
166A247GLN0-0.015-0.01847.6520.0100.0100.0000.0000.0000.000
167A248GLY00.0190.02445.0690.0720.0720.0000.0000.0000.000
168A249GLN0-0.018-0.04145.6400.0670.0670.0000.0000.0000.000
169A250GLY00.0420.03944.514-0.014-0.0140.0000.0000.0000.000
170A251MET0-0.072-0.00643.182-0.058-0.0580.0000.0000.0000.000
171A270SER0-0.031-0.03445.8490.0040.0040.0000.0000.0000.000
172A271ASP-1-0.758-0.82840.1267.4037.4030.0000.0000.0000.000
173A272LEU0-0.029-0.01241.4170.0220.0220.0000.0000.0000.000
174A273THR00.012-0.00436.5810.0490.0490.0000.0000.0000.000
175A274LEU0-0.084-0.04135.3470.0820.0820.0000.0000.0000.000
176A275SER0-0.039-0.02031.6430.0080.0080.0000.0000.0000.000
177A276SER0-0.049-0.04529.3820.1590.1590.0000.0000.0000.000
178A277VAL00.001-0.00331.672-0.330-0.3300.0000.0000.0000.000
179A278LEU0-0.0090.01129.3780.3390.3390.0000.0000.0000.000
180A279TRP00.0300.00032.091-0.409-0.4090.0000.0000.0000.000
181A280ASP-1-0.745-0.82032.6668.9578.9570.0000.0000.0000.000
182A281ARG10.8340.87131.927-9.361-9.3610.0000.0000.0000.000
183A282GLU-1-0.832-0.89032.9648.8228.8220.0000.0000.0000.000
184A283ARG10.7920.86532.606-8.845-8.8450.0000.0000.0000.000
185A284SER0-0.013-0.00138.351-0.114-0.1140.0000.0000.0000.000
186A285SER0-0.021-0.00937.602-0.254-0.2540.0000.0000.0000.000
187A286PHE00.000-0.00235.9460.2500.2500.0000.0000.0000.000
188A287TYR0-0.024-0.04834.817-0.199-0.1990.0000.0000.0000.000
189A288SER00.007-0.00535.6800.0890.0890.0000.0000.0000.000
190A289LEU0-0.0110.01331.345-0.211-0.2110.0000.0000.0000.000
191A290THR0-0.012-0.01435.106-0.017-0.0170.0000.0000.0000.000
192A291SER0-0.020-0.04036.0650.0920.0920.0000.0000.0000.000
193A292SER0-0.030-0.03037.084-0.007-0.0070.0000.0000.0000.000
194A293ASN0-0.042-0.02739.322-0.049-0.0490.0000.0000.0000.000
195A294ILE00.0650.04834.1080.1660.1660.0000.0000.0000.000
196A295SER0-0.0160.00338.149-0.284-0.2840.0000.0000.0000.000
197A296LYS10.8550.93138.945-7.406-7.4060.0000.0000.0000.000
198A297TRP0-0.040-0.04440.588-0.176-0.1760.0000.0000.0000.000
199A298GLU-1-0.802-0.87141.2656.7646.7640.0000.0000.0000.000
200A299LEU0-0.044-0.02939.818-0.129-0.1290.0000.0000.0000.000
201A300ASP-1-0.748-0.83243.7546.3236.3230.0000.0000.0000.000
202A301ASP-1-0.856-0.92944.2037.0167.0160.0000.0000.0000.000
203A302SER0-0.126-0.07845.669-0.031-0.0310.0000.0000.0000.000
204A303SER0-0.058-0.05747.921-0.077-0.0770.0000.0000.0000.000
205A304GLU-1-0.725-0.85144.1276.7816.7810.0000.0000.0000.000
206A305LYS10.7890.88646.250-6.562-6.5620.0000.0000.0000.000
207A306HIS0-0.0050.00645.1870.0350.0350.0000.0000.0000.000
208A307ALA00.0030.00243.066-0.119-0.1190.0000.0000.0000.000
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