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: M3J4Z

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 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 378
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6131685.198993
FMO2-HF: Nuclear repulsion 5985463.458759
FMO2-HF: Total energy -146221.740234
FMO2-MP2: Total energy -146646.668322


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.
166.944169.3251.37-1.593-2.157-0.001
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 : -0.989
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].
3A77VAL0-0.024-0.0253.1954.5846.4700.194-1.032-1.048-0.002
4A78ASN0-0.049-0.0355.877-0.081-0.0810.0000.0000.0000.000
5A79TYR0-0.009-0.0215.891-2.560-2.5600.0000.0000.0000.000
6A80ASP-1-0.904-0.9484.56440.08240.099-0.001-0.013-0.0020.000
7A81VAL0-0.004-0.0095.426-4.032-4.0320.0000.0000.0000.000
8A82LYS10.9310.9646.616-24.087-24.0870.0000.0000.0000.000
9A83THR00.0280.0099.053-1.255-1.2550.0000.0000.0000.000
10A84PHE0-0.028-0.00612.262-0.233-0.2330.0000.0000.0000.000
11A85GLY0-0.0060.00115.234-0.651-0.6510.0000.0000.0000.000
12A86SER0-0.064-0.03617.3640.6430.6430.0000.0000.0000.000
13A87SER0-0.008-0.01319.1360.3930.3930.0000.0000.0000.000
14A88LEU00.0430.03318.441-0.584-0.5840.0000.0000.0000.000
15A89PRO00.016-0.00621.533-0.241-0.2410.0000.0000.0000.000
16A90VAL00.0210.00924.6370.2500.2500.0000.0000.0000.000
17A91LYS10.9560.97726.363-9.265-9.2650.0000.0000.0000.000
18A92VAL0-0.0090.00622.161-0.074-0.0740.0000.0000.0000.000
19A93MET00.0010.00118.8820.3750.3750.0000.0000.0000.000
20A94GLU-1-0.913-0.96123.09710.81910.8190.0000.0000.0000.000
21A95ALA0-0.015-0.00725.4520.0910.0910.0000.0000.0000.000
22A96LEU0-0.0040.00118.860-0.043-0.0430.0000.0000.0000.000
23A97THR0-0.047-0.02221.7300.3570.3570.0000.0000.0000.000
24A98LEU0-0.089-0.05322.758-0.188-0.1880.0000.0000.0000.000
25A99ALA0-0.058-0.02723.428-0.210-0.2100.0000.0000.0000.000
26A100GLU-1-0.929-0.96723.65611.15611.1560.0000.0000.0000.000
27A101DVA0-0.116-0.05919.941-0.076-0.0760.0000.0000.0000.000
28A102ASP-1-0.933-0.95623.43110.74510.7450.0000.0000.0000.000
29A103ASP-1-0.889-0.93625.73810.65010.6500.0000.0000.0000.000
30A104GLN0-0.016-0.00924.8530.4680.4680.0000.0000.0000.000
31A105LEU0-0.027-0.02722.334-0.258-0.2580.0000.0000.0000.000
32A106THR00.0680.04823.6630.2030.2030.0000.0000.0000.000
33A107ILE0-0.015-0.02621.260-0.144-0.1440.0000.0000.0000.000
34A108ASN0-0.0020.02224.5410.2820.2820.0000.0000.0000.000
35A109ILE0-0.026-0.02219.9210.0260.0260.0000.0000.0000.000
36A110ASP-1-0.780-0.83424.2459.9889.9880.0000.0000.0000.000
37A111GLU-1-0.909-0.94725.56811.73611.7360.0000.0000.0000.000
38A112GLY0-0.044-0.02226.8730.0360.0360.0000.0000.0000.000
39A113GLY0-0.049-0.03325.404-0.064-0.0640.0000.0000.0000.000
40A114TRP0-0.040-0.02026.1560.0880.0880.0000.0000.0000.000
41A115ALA00.0220.01423.6740.1480.1480.0000.0000.0000.000
42A116CYS0-0.028-0.01525.717-0.453-0.4530.0000.0000.0000.000
43A117LEU00.0220.01723.5690.2490.2490.0000.0000.0000.000
44A118VAL00.0120.01126.630-0.363-0.3630.0000.0000.0000.000
45A119CYS0-0.006-0.00527.5850.3960.3960.0000.0000.0000.000
46A120LYS10.9440.96429.069-10.233-10.2330.0000.0000.0000.000
47A121GLU-1-0.898-0.95531.9188.0468.0460.0000.0000.0000.000
48A122LYS10.8810.94630.829-9.821-9.8210.0000.0000.0000.000
49A123LEU00.0150.03030.5070.3540.3540.0000.0000.0000.000
50A124ILE0-0.028-0.00728.055-0.188-0.1880.0000.0000.0000.000
51A125ILE00.0320.00528.5630.3160.3160.0000.0000.0000.000
52A126TRP0-0.010-0.02021.576-0.308-0.3080.0000.0000.0000.000
53A127LYS10.9601.00526.905-10.683-10.6830.0000.0000.0000.000
54A128ILE00.0330.00521.0600.2650.2650.0000.0000.0000.000
55A129ALA0-0.038-0.00822.964-0.252-0.2520.0000.0000.0000.000
56A130LEU00.043-0.00521.0300.5220.5220.0000.0000.0000.000
57A131SER0-0.060-0.02421.7210.3310.3310.0000.0000.0000.000
58A132PRO00.0850.03622.469-0.229-0.2290.0000.0000.0000.000
59A133ILE0-0.063-0.03024.165-0.391-0.3910.0000.0000.0000.000
60A134THR00.0950.02727.939-0.181-0.1810.0000.0000.0000.000
61A135LYS10.9470.98229.855-9.157-9.1570.0000.0000.0000.000
62A136LEU0-0.044-0.02528.826-0.262-0.2620.0000.0000.0000.000
63A137SER0-0.032-0.00428.0480.1560.1560.0000.0000.0000.000
64A138VAL0-0.0040.00329.039-0.408-0.4080.0000.0000.0000.000
65A139CYS0-0.032-0.02127.8100.3200.3200.0000.0000.0000.000
66A140LYS10.8080.92330.385-8.603-8.6030.0000.0000.0000.000
67A141GLU-1-0.880-0.95332.1099.4889.4880.0000.0000.0000.000
68A142LEU0-0.0010.01333.802-0.222-0.2220.0000.0000.0000.000
69A143GLN00.0560.02535.6400.2790.2790.0000.0000.0000.000
70A144LEU0-0.005-0.01033.554-0.128-0.1280.0000.0000.0000.000
71A145PRO0-0.0130.00738.107-0.142-0.1420.0000.0000.0000.000
72A146PRO00.016-0.00239.9760.1560.1560.0000.0000.0000.000
73A147SER0-0.021-0.03238.522-0.076-0.0760.0000.0000.0000.000
74A148ASP-1-0.891-0.93540.0147.2227.2220.0000.0000.0000.000
75A149PHE0-0.128-0.04836.4440.1680.1680.0000.0000.0000.000
76A150HIS00.0200.00230.9450.1640.1640.0000.0000.0000.000
77A151TRP00.0000.00233.179-0.001-0.0010.0000.0000.0000.000
78A152SER00.0230.00030.2000.3650.3650.0000.0000.0000.000
79A153ALA00.002-0.00927.188-0.245-0.2450.0000.0000.0000.000
80A154ASP-1-0.855-0.91328.06810.30210.3020.0000.0000.0000.000
81A155LEU0-0.118-0.06130.347-0.284-0.2840.0000.0000.0000.000
82A156VAL0-0.004-0.00731.355-0.274-0.2740.0000.0000.0000.000
83A157ALA0-0.0120.00232.0800.2430.2430.0000.0000.0000.000
84A158LEU0-0.011-0.02030.210-0.203-0.2030.0000.0000.0000.000
85A159SER00.0230.00634.114-0.057-0.0570.0000.0000.0000.000
86A160TYR0-0.066-0.09130.268-0.059-0.0590.0000.0000.0000.000
87A161SER0-0.0340.00836.931-0.168-0.1680.0000.0000.0000.000
88A162SER0-0.026-0.02736.4700.1150.1150.0000.0000.0000.000
89A170THR00.034-0.00734.354-0.052-0.0520.0000.0000.0000.000
90A171GLN00.0260.01236.109-0.022-0.0220.0000.0000.0000.000
91A172ALA0-0.052-0.02736.531-0.085-0.0850.0000.0000.0000.000
92A173VAL00.0000.01833.6050.0210.0210.0000.0000.0000.000
93A174ALA00.0190.02636.652-0.100-0.1000.0000.0000.0000.000
94A175VAL00.006-0.01935.1770.2490.2490.0000.0000.0000.000
95A176MET0-0.0350.01036.904-0.317-0.3170.0000.0000.0000.000
96A177VAL00.0080.01335.4340.2670.2670.0000.0000.0000.000
97A178ALA00.008-0.00236.902-0.269-0.2690.0000.0000.0000.000
98A179THR00.0060.01437.1210.2090.2090.0000.0000.0000.000
99A180ARG10.9460.96931.487-9.024-9.0240.0000.0000.0000.000
100A181GLU-1-0.733-0.87238.7477.3927.3920.0000.0000.0000.000
101A182GLY0-0.0060.00041.562-0.163-0.1630.0000.0000.0000.000
102A183SER0-0.054-0.01642.506-0.205-0.2050.0000.0000.0000.000
103A184ILE00.010-0.00541.5480.2060.2060.0000.0000.0000.000
104A185ARG10.8070.89240.676-7.426-7.4260.0000.0000.0000.000
105A186TYR00.002-0.01640.6320.1320.1320.0000.0000.0000.000
106A187TRP00.0100.00738.471-0.124-0.1240.0000.0000.0000.000
107A188PRO0-0.018-0.00440.7180.1360.1360.0000.0000.0000.000
108A189SER0-0.015-0.02340.3080.1330.1330.0000.0000.0000.000
109A190LEU00.0330.03133.091-0.051-0.0510.0000.0000.0000.000
110A191ALA0-0.067-0.04237.7860.0970.0970.0000.0000.0000.000
111A192GLY0-0.039-0.00939.574-0.049-0.0490.0000.0000.0000.000
112A193GLU-1-0.794-0.91536.9388.2188.2180.0000.0000.0000.000
113A194ASP-1-0.885-0.93240.4337.3097.3090.0000.0000.0000.000
114A195THR0-0.134-0.06843.367-0.235-0.2350.0000.0000.0000.000
115A196TYR00.004-0.01042.7260.1530.1530.0000.0000.0000.000
116A197THR0-0.038-0.02144.750-0.118-0.1180.0000.0000.0000.000
117A198GLU-1-0.810-0.88645.1456.9686.9680.0000.0000.0000.000
118A199ALA0-0.045-0.02246.364-0.151-0.1510.0000.0000.0000.000
119A200PHE0-0.012-0.00546.3050.0950.0950.0000.0000.0000.000
120A201VAL00.0200.02344.556-0.126-0.1260.0000.0000.0000.000
121A202ASP-1-0.822-0.89247.1096.1616.1610.0000.0000.0000.000
122A203SER0-0.144-0.07649.352-0.133-0.1330.0000.0000.0000.000
123A204GLY00.0030.01150.596-0.100-0.1000.0000.0000.0000.000
124A205GLY0-0.024-0.02148.9240.0170.0170.0000.0000.0000.000
125A206ASP-1-0.898-0.96547.1076.3966.3960.0000.0000.0000.000
126A207LYS10.8940.96544.092-6.496-6.4960.0000.0000.0000.000
127A208THR00.0100.01737.9310.0530.0530.0000.0000.0000.000
128A209TYR0-0.041-0.02538.8320.0300.0300.0000.0000.0000.000
129A210SER00.0300.00834.0460.0680.0680.0000.0000.0000.000
130A211PHE00.0490.02729.9840.1380.1380.0000.0000.0000.000
131A212LEU0-0.013-0.00334.086-0.352-0.3520.0000.0000.0000.000
132A213THR0-0.026-0.00733.4480.3230.3230.0000.0000.0000.000
133A214ALA00.0090.01434.648-0.261-0.2610.0000.0000.0000.000
134A215VAL00.0070.01035.8520.1170.1170.0000.0000.0000.000
135A216GLN0-0.0160.00338.3670.0860.0860.0000.0000.0000.000
136A217GLY00.0620.02440.742-0.115-0.1150.0000.0000.0000.000
137A218GLY0-0.066-0.02240.936-0.115-0.1150.0000.0000.0000.000
138A219SER0-0.0310.00741.570-0.072-0.0720.0000.0000.0000.000
139A220PHE00.031-0.00737.1670.2060.2060.0000.0000.0000.000
140A221ILE0-0.009-0.00438.882-0.232-0.2320.0000.0000.0000.000
141A222LEU0-0.0050.01538.4290.2300.2300.0000.0000.0000.000
142A223SER00.020-0.00337.040-0.196-0.1960.0000.0000.0000.000
143A224SER0-0.050-0.02938.2220.1120.1120.0000.0000.0000.000
144A225SER00.0710.02437.706-0.022-0.0220.0000.0000.0000.000
145A226GLY00.0570.03038.6810.0400.0400.0000.0000.0000.000
146A227SER0-0.028-0.02340.163-0.171-0.1710.0000.0000.0000.000
147A228GLN0-0.022-0.02241.244-0.001-0.0010.0000.0000.0000.000
148A229LEU0-0.036-0.00239.8290.1820.1820.0000.0000.0000.000
149A230ILE0-0.011-0.01242.808-0.213-0.2130.0000.0000.0000.000
150A231ARG10.8230.90743.125-6.773-6.7730.0000.0000.0000.000
151A232LEU0-0.014-0.01341.789-0.168-0.1680.0000.0000.0000.000
152A233ILE00.013-0.02144.1140.1320.1320.0000.0000.0000.000
153A234PRO0-0.0040.00843.906-0.159-0.1590.0000.0000.0000.000
154A235GLU-1-0.894-0.95147.1175.8765.8760.0000.0000.0000.000
155A236SER00.000-0.01550.4480.0170.0170.0000.0000.0000.000
156A237SER0-0.094-0.03951.532-0.014-0.0140.0000.0000.0000.000
157A238GLY00.0200.00450.154-0.046-0.0460.0000.0000.0000.000
158A239LYS10.9380.96650.198-5.490-5.4900.0000.0000.0000.000
159A240ILE00.0420.03345.3080.0770.0770.0000.0000.0000.000
160A241HIS00.0270.05649.026-0.024-0.0240.0000.0000.0000.000
161A242GLN00.033-0.01247.9560.1960.1960.0000.0000.0000.000
162A243HIS10.7220.84248.017-6.505-6.5050.0000.0000.0000.000
163A244ILE00.0340.02147.4100.1360.1360.0000.0000.0000.000
164A245LEU0-0.0140.00542.576-0.088-0.0880.0000.0000.0000.000
165A246PRO00.0190.00747.279-0.074-0.0740.0000.0000.0000.000
166A247GLN0-0.042-0.02847.9920.0150.0150.0000.0000.0000.000
167A248GLY00.0750.04945.8830.1060.1060.0000.0000.0000.000
168A249GLN0-0.022-0.03846.1970.1080.1080.0000.0000.0000.000
169A250GLY00.0130.02544.780-0.002-0.0020.0000.0000.0000.000
170A251MET0-0.0420.00843.867-0.021-0.0210.0000.0000.0000.000
171A270SER0-0.024-0.03946.262-0.010-0.0100.0000.0000.0000.000
172A271ASP-1-0.825-0.89140.6117.2987.2980.0000.0000.0000.000
173A272LEU0-0.037-0.02941.9810.0770.0770.0000.0000.0000.000
174A273THR0-0.007-0.00336.8030.0520.0520.0000.0000.0000.000
175A274LEU0-0.061-0.03035.5400.0660.0660.0000.0000.0000.000
176A275SER0-0.041-0.02131.8170.0090.0090.0000.0000.0000.000
177A276SER0-0.046-0.01630.1510.1540.1540.0000.0000.0000.000
178A277VAL00.006-0.00332.361-0.330-0.3300.0000.0000.0000.000
179A278LEU00.0000.01130.0060.3410.3410.0000.0000.0000.000
180A279TRP00.012-0.00132.575-0.377-0.3770.0000.0000.0000.000
181A280ASP-1-0.790-0.89332.8158.8338.8330.0000.0000.0000.000
182A281ARG10.8730.92331.632-9.293-9.2930.0000.0000.0000.000
183A282GLU-1-0.853-0.93033.7178.5608.5600.0000.0000.0000.000
184A283ARG10.8450.92733.118-8.719-8.7190.0000.0000.0000.000
185A284SER0-0.019-0.01138.760-0.144-0.1440.0000.0000.0000.000
186A285SER0-0.046-0.03237.935-0.256-0.2560.0000.0000.0000.000
187A286PHE00.0020.00136.4780.2250.2250.0000.0000.0000.000
188A287TYR0-0.056-0.07935.371-0.174-0.1740.0000.0000.0000.000
189A288SER0-0.017-0.00136.1310.1480.1480.0000.0000.0000.000
190A289LEU00.0180.03131.751-0.150-0.1500.0000.0000.0000.000
191A290THR00.025-0.00435.5880.1080.1080.0000.0000.0000.000
192A291SER0-0.031-0.02536.4900.0860.0860.0000.0000.0000.000
193A292SER0-0.013-0.00337.5690.0290.0290.0000.0000.0000.000
194A293ASN0-0.073-0.06339.712-0.035-0.0350.0000.0000.0000.000
195A294ILE00.0850.06535.0920.1450.1450.0000.0000.0000.000
196A295SER0-0.0320.00838.865-0.295-0.2950.0000.0000.0000.000
197A296LYS10.9480.98839.375-7.225-7.2250.0000.0000.0000.000
198A297TRP0-0.048-0.01240.945-0.164-0.1640.0000.0000.0000.000
199A298GLU-1-0.939-0.97041.6946.8306.8300.0000.0000.0000.000
200A299LEU0-0.020-0.02241.301-0.156-0.1560.0000.0000.0000.000
201A300ASP-1-0.793-0.86344.3466.3326.3320.0000.0000.0000.000
202A301ASP-1-0.903-0.96744.9796.8756.8750.0000.0000.0000.000
203A302SER0-0.106-0.06046.405-0.033-0.0330.0000.0000.0000.000
204A303SER0-0.073-0.04947.927-0.104-0.1040.0000.0000.0000.000
205A304GLU-1-0.729-0.86744.5836.7136.7130.0000.0000.0000.000
206A305LYS10.9200.96746.708-6.203-6.2030.0000.0000.0000.000
207A306HIS0-0.015-0.00245.3860.0490.0490.0000.0000.0000.000
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