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: XQ87Y

Calculation Name: 5D66-A-Xray13

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D66

Chain ID: A

ChEMBL ID:

UniProt ID: B0VB33

Base Structure: X-ray

Registration Date: 2017-12-04

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20171117
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 200
LigandCharge CL-=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2016474.738078
FMO2-HF: Nuclear repulsion 1941213.828238
FMO2-HF: Total energy -75260.90984
FMO2-MP2: Total energy -75478.189852


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:40:ACE)


Summations of interaction energy for fragment #1(A:40:ACE)
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.
-0.1240.658-0.012-0.329-0.4420
Interaction energy analysis for fragmet #1(A:40:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.039
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].
3A42GLU-1-0.929-0.9593.843-0.3670.349-0.011-0.315-0.3900.000
4A43TYR0-0.018-0.0107.0810.4450.4450.0000.0000.0000.000
5A44PRO00.0510.0353.9660.0420.108-0.001-0.014-0.0520.000
6A45LEU0-0.016-0.0195.9970.1520.1520.0000.0000.0000.000
7A46HIS00.0040.0029.4910.0050.0050.0000.0000.0000.000
8A47MET00.0370.0337.1570.0570.0570.0000.0000.0000.000
9A48ALA0-0.009-0.0138.7150.0800.0800.0000.0000.0000.000
10A49ALA0-0.030-0.01810.1120.0300.0300.0000.0000.0000.000
11A50ALA00.007-0.00112.5490.0230.0230.0000.0000.0000.000
12A51ASN0-0.023-0.01310.272-0.006-0.0060.0000.0000.0000.000
13A52ASP-1-0.838-0.91613.7320.0290.0290.0000.0000.0000.000
14A53ASP-1-0.876-0.93310.6000.2340.2340.0000.0000.0000.000
15A54ILE00.023-0.01612.8210.0430.0430.0000.0000.0000.000
16A55GLN0-0.039-0.03014.0330.0340.0340.0000.0000.0000.000
17A56LEU00.0350.0366.5410.0660.0660.0000.0000.0000.000
18A57ILE00.0340.01210.5730.0480.0480.0000.0000.0000.000
19A58LYS10.9360.96812.386-0.176-0.1760.0000.0000.0000.000
20A59HIS0-0.024-0.0058.628-0.104-0.1040.0000.0000.0000.000
21A60ILE00.0270.0277.0300.0200.0200.0000.0000.0000.000
22A61LEU00.0160.00810.623-0.028-0.0280.0000.0000.0000.000
23A62SER0-0.114-0.06613.408-0.023-0.0230.0000.0000.0000.000
24A63GLN0-0.014-0.0168.458-0.066-0.0660.0000.0000.0000.000
25A64LYS10.8760.94513.917-0.172-0.1720.0000.0000.0000.000
26A65THR0-0.0060.00312.279-0.036-0.0360.0000.0000.0000.000
27A66LEU00.002-0.00515.422-0.002-0.0020.0000.0000.0000.000
28A67ILE00.0460.02615.415-0.014-0.0140.0000.0000.0000.000
29A68ASP-1-0.842-0.90916.139-0.051-0.0510.0000.0000.0000.000
30A69ALA0-0.038-0.02313.658-0.017-0.0170.0000.0000.0000.000
31A70ARG10.7820.87815.2270.0960.0960.0000.0000.0000.000
32A71ASP-1-0.721-0.83512.766-0.320-0.3200.0000.0000.0000.000
33A72GLU-1-0.880-0.95912.892-0.478-0.4780.0000.0000.0000.000
34A73THR0-0.106-0.04915.4090.0560.0560.0000.0000.0000.000
35A74GLY0-0.011-0.01217.4360.0350.0350.0000.0000.0000.000
36A75SER0-0.049-0.02316.8190.0460.0460.0000.0000.0000.000
37A76THR00.0460.02316.279-0.023-0.0230.0000.0000.0000.000
38A77ALA00.0840.03813.415-0.013-0.0130.0000.0000.0000.000
39A78LEU00.0390.02515.1770.0010.0010.0000.0000.0000.000
40A79MET0-0.033-0.00418.5700.0060.0060.0000.0000.0000.000
41A80VAL0-0.008-0.00614.0960.0020.0020.0000.0000.0000.000
42A81ALA00.0110.00417.0180.0020.0020.0000.0000.0000.000
43A82THR0-0.038-0.02818.1280.0120.0120.0000.0000.0000.000
44A83ARG10.8310.89218.3670.1720.1720.0000.0000.0000.000
45A84ALA0-0.019-0.00518.7850.0010.0010.0000.0000.0000.000
46A85ASN0-0.026-0.00820.8220.0120.0120.0000.0000.0000.000
47A86ASN0-0.039-0.01216.7380.0150.0150.0000.0000.0000.000
48A87ILE0-0.011-0.02320.4930.0080.0080.0000.0000.0000.000
49A88HIS0-0.022-0.00220.0360.0090.0090.0000.0000.0000.000
50A89ALA00.0230.00716.4130.0110.0110.0000.0000.0000.000
51A90ALA00.0080.00118.0780.0050.0050.0000.0000.0000.000
52A91HIS00.003-0.01120.6220.0070.0070.0000.0000.0000.000
53A92MET0-0.034-0.00317.1460.0140.0140.0000.0000.0000.000
54A93LEU0-0.027-0.02214.9790.0080.0080.0000.0000.0000.000
55A94ILE00.0090.00119.080-0.001-0.0010.0000.0000.0000.000
56A95GLU-1-0.942-0.97422.8090.0360.0360.0000.0000.0000.000
57A96ALA0-0.084-0.03419.4210.0060.0060.0000.0000.0000.000
58A97GLY0-0.015-0.00621.3780.0030.0030.0000.0000.0000.000
59A98ALA0-0.044-0.01719.549-0.007-0.0070.0000.0000.0000.000
60A99ASP-1-0.873-0.93821.393-0.028-0.0280.0000.0000.0000.000
61A100VAL0-0.019-0.01823.704-0.012-0.0120.0000.0000.0000.000
62A101ASN0-0.051-0.04025.686-0.007-0.0070.0000.0000.0000.000
63A102ALA0-0.0120.00922.827-0.004-0.0040.0000.0000.0000.000
64A103LYS10.8100.89424.6490.0540.0540.0000.0000.0000.000
65A104ASP-1-0.731-0.85122.096-0.125-0.1250.0000.0000.0000.000
66A105ASN0-0.027-0.01322.4390.0190.0190.0000.0000.0000.000
67A106ILE0-0.018-0.00825.0720.0050.0050.0000.0000.0000.000
68A107GLN0-0.044-0.03527.1790.0130.0130.0000.0000.0000.000
69A108ASP-1-0.848-0.91725.585-0.075-0.0750.0000.0000.0000.000
70A109SER00.0330.01325.244-0.005-0.0050.0000.0000.0000.000
71A110PRO00.005-0.00822.3950.0000.0000.0000.0000.0000.000
72A111TYR00.0720.03424.9730.0020.0020.0000.0000.0000.000
73A112LEU0-0.067-0.03228.6350.0010.0010.0000.0000.0000.000
74A113TYR0-0.0010.01525.3310.0010.0010.0000.0000.0000.000
75A114ALA00.002-0.00527.0040.0010.0010.0000.0000.0000.000
76A115GLY0-0.010-0.00728.4740.0030.0030.0000.0000.0000.000
77A116ALA00.002-0.00630.9690.0020.0020.0000.0000.0000.000
78A117GLN0-0.023-0.01527.704-0.002-0.0020.0000.0000.0000.000
79A118GLY00.0210.03430.8200.0010.0010.0000.0000.0000.000
80A119TYR0-0.0260.00524.9870.0040.0040.0000.0000.0000.000
81A120LEU00.0400.00929.3170.0030.0030.0000.0000.0000.000
82A121LYS10.9230.94828.1490.0070.0070.0000.0000.0000.000
83A122ILE00.0830.03623.1640.0050.0050.0000.0000.0000.000
84A123LEU00.0030.01026.9890.0020.0020.0000.0000.0000.000
85A124ARG10.9000.93629.9800.0100.0100.0000.0000.0000.000
86A125MET0-0.0170.02325.5810.0020.0020.0000.0000.0000.000
87A126THR00.005-0.01826.4570.0010.0010.0000.0000.0000.000
88A127LEU0-0.051-0.03728.8740.0010.0010.0000.0000.0000.000
89A128MET0-0.053-0.00731.0100.0010.0010.0000.0000.0000.000
90A129HIS0-0.044-0.01227.7120.0020.0020.0000.0000.0000.000
91A130GLY00.0370.01928.796-0.002-0.0020.0000.0000.0000.000
92A131ALA0-0.026-0.00430.718-0.003-0.0030.0000.0000.0000.000
93A132ASP-1-0.857-0.92531.603-0.023-0.0230.0000.0000.0000.000
94A133LEU0-0.012-0.00733.767-0.004-0.0040.0000.0000.0000.000
95A134LYS10.8850.94136.4370.0160.0160.0000.0000.0000.000
96A135SER0-0.059-0.02432.552-0.003-0.0030.0000.0000.0000.000
97A136THR0-0.016-0.01434.262-0.001-0.0010.0000.0000.0000.000
98A137ASN00.0720.03531.858-0.004-0.0040.0000.0000.0000.000
99A138ARG10.9930.99430.0530.0820.0820.0000.0000.0000.000
100A139TYR0-0.020-0.00933.379-0.002-0.0020.0000.0000.0000.000
101A140GLY00.004-0.00136.0880.0040.0040.0000.0000.0000.000
102A141GLY00.0360.01036.8370.0040.0040.0000.0000.0000.000
103A142THR00.0220.01536.023-0.002-0.0020.0000.0000.0000.000
104A143ALA00.0650.01933.447-0.002-0.0020.0000.0000.0000.000
105A144LEU0-0.032-0.01635.0170.0000.0000.0000.0000.0000.000
106A145ILE0-0.029-0.00638.3800.0010.0010.0000.0000.0000.000
107A146PRO00.0740.04334.5110.0010.0010.0000.0000.0000.000
108A147ALA00.0000.00336.0840.0000.0000.0000.0000.0000.000
109A148ALA0-0.059-0.04437.2050.0010.0010.0000.0000.0000.000
110A149GLU-1-0.893-0.93737.771-0.046-0.0460.0000.0000.0000.000
111A150ARG10.8400.91831.4440.0550.0550.0000.0000.0000.000
112A151GLY0-0.0120.01538.4650.0010.0010.0000.0000.0000.000
113A152HIS00.0280.01133.8680.0050.0050.0000.0000.0000.000
114A153VAL00.005-0.00838.3250.0010.0010.0000.0000.0000.000
115A154GLU-1-0.780-0.86537.858-0.011-0.0110.0000.0000.0000.000
116A155THR0-0.039-0.07134.5570.0020.0020.0000.0000.0000.000
117A156VAL0-0.014-0.00436.9770.0010.0010.0000.0000.0000.000
118A157ARG10.7830.86540.1340.0130.0130.0000.0000.0000.000
119A158THR0-0.025-0.02235.5970.0030.0030.0000.0000.0000.000
120A159LEU00.0130.00634.7200.0010.0010.0000.0000.0000.000
121A160ILE0-0.021-0.00438.6580.0010.0010.0000.0000.0000.000
122A161ALA0-0.067-0.03141.0220.0010.0010.0000.0000.0000.000
123A162ALA0-0.025-0.01237.8030.0010.0010.0000.0000.0000.000
124A163GLY00.0170.02639.7890.0010.0010.0000.0000.0000.000
125A164VAL0-0.037-0.01937.548-0.001-0.0010.0000.0000.0000.000
126A165ASN00.0140.00740.5110.0010.0010.0000.0000.0000.000
127A166VAL00.0360.01143.337-0.002-0.0020.0000.0000.0000.000
128A167ASN0-0.024-0.01745.156-0.001-0.0010.0000.0000.0000.000
129A168HIS0-0.068-0.01640.2840.0020.0020.0000.0000.0000.000
130A169VAL0-0.015-0.01144.2620.0000.0000.0000.0000.0000.000
131A170ASN00.0340.01239.9000.0010.0010.0000.0000.0000.000
132A171ASN0-0.058-0.03638.0780.0020.0020.0000.0000.0000.000
133A172LEU00.003-0.00939.804-0.001-0.0010.0000.0000.0000.000
134A173GLY0-0.078-0.03543.5810.0010.0010.0000.0000.0000.000
135A174TRP0-0.0050.00242.5930.0020.0020.0000.0000.0000.000
136A175THR00.0850.04344.032-0.001-0.0010.0000.0000.0000.000
137A176ALA00.0440.01342.560-0.001-0.0010.0000.0000.0000.000
138A177LEU00.0070.01043.8340.0000.0000.0000.0000.0000.000
139A178LEU0-0.020-0.01547.2300.0000.0000.0000.0000.0000.000
140A179GLU-1-0.751-0.89140.810-0.040-0.0400.0000.0000.0000.000
141A180ALA0-0.021-0.00744.5500.0000.0000.0000.0000.0000.000
142A181ILE0-0.088-0.04345.4170.0010.0010.0000.0000.0000.000
143A182ILE0-0.076-0.05146.6100.0000.0000.0000.0000.0000.000
144A183LEU0-0.0070.00141.5020.0000.0000.0000.0000.0000.000
145A184GLY00.0660.05943.721-0.001-0.0010.0000.0000.0000.000
146A185ASN0-0.048-0.04545.4670.0010.0010.0000.0000.0000.000
147A186GLY00.0250.00847.9620.0010.0010.0000.0000.0000.000
148A187LYS10.9080.96348.4310.0250.0250.0000.0000.0000.000
149A188SER00.0720.02746.335-0.001-0.0010.0000.0000.0000.000
150A189ASN00.0140.00641.4280.0020.0020.0000.0000.0000.000
151A190TYR00.0280.01041.4340.0010.0010.0000.0000.0000.000
152A191GLN0-0.063-0.03046.5860.0010.0010.0000.0000.0000.000
153A192GLN0-0.027-0.01546.0120.0000.0000.0000.0000.0000.000
154A193ILE00.0350.02641.9290.0010.0010.0000.0000.0000.000
155A194VAL00.0190.00145.9080.0000.0000.0000.0000.0000.000
156A195ALA0-0.014-0.00949.0600.0010.0010.0000.0000.0000.000
157A196LEU0-0.056-0.01844.2120.0010.0010.0000.0000.0000.000
158A197LEU00.0170.00044.1140.0010.0010.0000.0000.0000.000
159A198LEU00.0070.01147.8730.0010.0010.0000.0000.0000.000
160A199LYS10.9010.96350.8220.0090.0090.0000.0000.0000.000
161A200ALA0-0.057-0.04747.5700.0010.0010.0000.0000.0000.000
162A201GLY0-0.0040.01249.5550.0000.0000.0000.0000.0000.000
163A202ALA0-0.019-0.00448.5220.0000.0000.0000.0000.0000.000
164A203ASN0-0.010-0.01450.2770.0010.0010.0000.0000.0000.000
165A204PRO00.002-0.00952.414-0.001-0.0010.0000.0000.0000.000
166A205ASN0-0.041-0.02354.382-0.001-0.0010.0000.0000.0000.000
167A206LEU0-0.048-0.01249.9790.0000.0000.0000.0000.0000.000
168A207ALA0-0.003-0.01052.0200.0000.0000.0000.0000.0000.000
169A208ASP-1-0.742-0.85549.893-0.027-0.0270.0000.0000.0000.000
170A209LYS10.9140.94145.3920.0370.0370.0000.0000.0000.000
171A210ASP-1-0.957-0.95751.248-0.029-0.0290.0000.0000.0000.000
172A211GLY0-0.045-0.01754.1930.0010.0010.0000.0000.0000.000
173A212ILE0-0.055-0.02754.2480.0020.0020.0000.0000.0000.000
174A213THR00.0260.01553.942-0.001-0.0010.0000.0000.0000.000
175A214PRO00.0370.00851.9060.0000.0000.0000.0000.0000.000
176A215LEU00.0040.00853.8070.0000.0000.0000.0000.0000.000
177A216GLN0-0.005-0.00757.2450.0000.0000.0000.0000.0000.000
178A217HIS00.0640.02252.1210.0000.0000.0000.0000.0000.000
179A218ALA00.0060.00154.406-0.001-0.0010.0000.0000.0000.000
180A219ARG10.8560.90855.2550.0160.0160.0000.0000.0000.000
181A220THR0-0.038-0.01056.0360.0000.0000.0000.0000.0000.000
182A221ARG10.8530.93150.3950.0260.0260.0000.0000.0000.000
183A222GLY0-0.0250.00755.5940.0000.0000.0000.0000.0000.000
184A223TYR0-0.012-0.00649.7620.0010.0010.0000.0000.0000.000
185A224ARG10.9920.99255.7250.0150.0150.0000.0000.0000.000
186A225GLU-1-0.929-0.96954.722-0.016-0.0160.0000.0000.0000.000
187A226ILE00.0470.01550.3950.0010.0010.0000.0000.0000.000
188A227GLU-1-0.832-0.90454.545-0.015-0.0150.0000.0000.0000.000
189A228LYS10.9110.94757.8480.0120.0120.0000.0000.0000.000
190A229LEU0-0.015-0.00552.8050.0010.0010.0000.0000.0000.000
191A230LEU00.0360.01353.2570.0000.0000.0000.0000.0000.000
192A231LEU0-0.047-0.01856.7300.0000.0000.0000.0000.0000.000
193A232VAL0-0.066-0.02858.6310.0010.0010.0000.0000.0000.000
194A233ALA0-0.0120.00656.0610.0010.0010.0000.0000.0000.000
195A234GLY0-0.015-0.00658.0880.0000.0000.0000.0000.0000.000
196A235ALA0-0.046-0.02357.4940.0000.0000.0000.0000.0000.000
197A236LYS00.0610.02259.169-0.003-0.0030.0000.0000.0000.000
198A301CL--1-0.850-0.90137.676-0.045-0.0450.0000.0000.0000.000
199A302CL--1-0.911-0.95229.742-0.023-0.0230.0000.0000.0000.000
200A303CL--1-0.804-0.84936.478-0.025-0.0250.0000.0000.0000.000