FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: QY85Y

Calculation Name: 5X7V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X7V

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y010

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1914146.951942
FMO2-HF: Nuclear repulsion 1840170.504697
FMO2-HF: Total energy -73976.447246
FMO2-MP2: Total energy -74192.929067


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:29:PHE)


Summations of interaction energy for fragment #1(A:29:PHE)
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.
-21.228-18.55512.133-7.293-7.513-0.056
Interaction energy analysis for fragmet #1(A:29:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.022
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].
3A31GLN0-0.022-0.0163.048-3.248-0.7380.070-1.115-1.4650.003
4A32ASP-1-0.825-0.9141.909-18.675-19.40012.060-5.933-5.403-0.060
5A33PHE0-0.031-0.0174.0230.7281.6160.003-0.245-0.6450.001
6A34GLU-1-0.865-0.9295.9930.3350.3350.0000.0000.0000.000
7A35ASP-1-0.854-0.9037.403-1.156-1.1560.0000.0000.0000.000
8A36ILE0-0.014-0.0087.1640.2280.2280.0000.0000.0000.000
9A37GLN0-0.052-0.0379.9320.1470.1470.0000.0000.0000.000
10A38LYS10.8010.8849.5440.7080.7080.0000.0000.0000.000
11A39ASP-1-0.869-0.94213.089-0.622-0.6220.0000.0000.0000.000
12A40ILE0-0.048-0.01511.5780.0580.0580.0000.0000.0000.000
13A41GLU-1-0.814-0.89315.404-0.149-0.1490.0000.0000.0000.000
14A42GLN0-0.067-0.03816.8510.1030.1030.0000.0000.0000.000
15A43LEU0-0.057-0.01517.1460.0330.0330.0000.0000.0000.000
16A44ASP-1-0.857-0.92618.765-0.216-0.2160.0000.0000.0000.000
17A45ILE0-0.031-0.01921.0810.0300.0300.0000.0000.0000.000
18A46LYS10.8140.90421.6380.3130.3130.0000.0000.0000.000
19A47CYS00.0120.00324.1770.0180.0180.0000.0000.0000.000
20A48ALA00.0390.01625.5380.0170.0170.0000.0000.0000.000
21A49HIS0-0.036-0.01027.3890.0110.0110.0000.0000.0000.000
22A50GLU-1-0.914-0.95728.708-0.151-0.1510.0000.0000.0000.000
23A51GLN00.009-0.00527.3010.0090.0090.0000.0000.0000.000
24A52MET00.0130.01231.3810.0120.0120.0000.0000.0000.000
25A53ASN0-0.052-0.01833.3620.0140.0140.0000.0000.0000.000
26A54ILE0-0.020-0.01934.5600.0080.0080.0000.0000.0000.000
27A55GLN00.0460.01934.8180.0090.0090.0000.0000.0000.000
28A56LYS11.0171.00436.9430.0720.0720.0000.0000.0000.000
29A57GLN00.0060.01839.1550.0070.0070.0000.0000.0000.000
30A58TYR0-0.025-0.03439.6020.0040.0040.0000.0000.0000.000
31A59ASP-1-0.782-0.87240.434-0.049-0.0490.0000.0000.0000.000
32A60GLU-1-0.862-0.92142.948-0.043-0.0430.0000.0000.0000.000
33A61LYS10.8250.92042.5630.0680.0680.0000.0000.0000.000
34A62LYS10.8510.91639.6940.0570.0570.0000.0000.0000.000
35A63LYS10.8560.92346.6890.0450.0450.0000.0000.0000.000
36A64PRO00.0170.00248.9580.0020.0020.0000.0000.0000.000
37A65LEU0-0.0050.00548.0700.0020.0020.0000.0000.0000.000
38A66PHE00.0180.00944.6020.0020.0020.0000.0000.0000.000
39A67GLU-1-0.792-0.88350.828-0.024-0.0240.0000.0000.0000.000
40A68LYS10.8090.89254.1750.0270.0270.0000.0000.0000.000
41A69ARG10.8300.89348.7200.0260.0260.0000.0000.0000.000
42A70ASP-1-0.729-0.84753.607-0.021-0.0210.0000.0000.0000.000
43A71GLU-1-0.803-0.87356.042-0.022-0.0220.0000.0000.0000.000
44A72ILE0-0.046-0.03456.6490.0010.0010.0000.0000.0000.000
45A73ILE00.0100.01653.9180.0010.0010.0000.0000.0000.000
46A74GLN0-0.033-0.01458.5340.0010.0010.0000.0000.0000.000
47A75LYS10.7880.89861.6130.0210.0210.0000.0000.0000.000
48A76ILE0-0.0140.00458.5030.0000.0000.0000.0000.0000.000
49A77PRO0-0.001-0.01361.6830.0000.0000.0000.0000.0000.000
50A78GLY00.0550.03061.9910.0000.0000.0000.0000.0000.000
51A79PHE00.0090.01553.6640.0010.0010.0000.0000.0000.000
52A80TRP00.0880.03651.0080.0000.0000.0000.0000.0000.000
53A81ALA00.0280.02555.3190.0010.0010.0000.0000.0000.000
54A82ASN0-0.030-0.03556.6460.0020.0020.0000.0000.0000.000
55A83THR0-0.014-0.01251.491-0.001-0.0010.0000.0000.0000.000
56A84LEU0-0.005-0.00550.6240.0000.0000.0000.0000.0000.000
57A85ARG10.9120.96251.6150.0050.0050.0000.0000.0000.000
58A86LYS10.8070.88552.6790.0120.0120.0000.0000.0000.000
59A87HIS00.012-0.00743.8180.0000.0000.0000.0000.0000.000
60A88PRO0-0.005-0.01146.7430.0010.0010.0000.0000.0000.000
61A89ALA0-0.0180.00945.1910.0020.0020.0000.0000.0000.000
62A90LEU0-0.027-0.02947.2990.0010.0010.0000.0000.0000.000
63A91SER0-0.031-0.01550.7300.0000.0000.0000.0000.0000.000
64A92ASP-1-0.908-0.93952.6570.0040.0040.0000.0000.0000.000
65A93ILE0-0.0070.01753.2410.0010.0010.0000.0000.0000.000
66A94VAL00.004-0.00255.4860.0000.0000.0000.0000.0000.000
67A95PRO0-0.018-0.02459.172-0.001-0.0010.0000.0000.0000.000
68A96GLU-1-0.821-0.92561.8670.0020.0020.0000.0000.0000.000
69A97ASP-1-0.708-0.83456.9440.0010.0010.0000.0000.0000.000
70A98ILE0-0.040-0.02959.332-0.001-0.0010.0000.0000.0000.000
71A99ASP-1-0.896-0.92961.238-0.003-0.0030.0000.0000.0000.000
72A100ILE0-0.033-0.00660.857-0.001-0.0010.0000.0000.0000.000
73A101LEU00.016-0.00356.182-0.001-0.0010.0000.0000.0000.000
74A102ASN0-0.045-0.02859.826-0.002-0.0020.0000.0000.0000.000
75A103HIS0-0.090-0.04962.595-0.001-0.0010.0000.0000.0000.000
76A104LEU0-0.0230.00255.1460.0000.0000.0000.0000.0000.000
77A105VAL0-0.025-0.01959.225-0.001-0.0010.0000.0000.0000.000
78A106LYS10.7320.82454.3700.0200.0200.0000.0000.0000.000
79A107LEU00.0150.01550.6910.0010.0010.0000.0000.0000.000
80A108ASP-1-0.812-0.88651.117-0.023-0.0230.0000.0000.0000.000
81A109LEU00.0320.02343.1750.0020.0020.0000.0000.0000.000
82A110LYS10.7510.85846.1110.0240.0240.0000.0000.0000.000
83A111ASP-1-0.716-0.86140.096-0.028-0.0280.0000.0000.0000.000
84A112ASN0-0.108-0.06437.917-0.001-0.0010.0000.0000.0000.000
85A113MET0-0.067-0.01039.295-0.003-0.0030.0000.0000.0000.000
86A114ASP-1-0.804-0.85036.694-0.029-0.0290.0000.0000.0000.000
87A115ASN0-0.095-0.06731.191-0.004-0.0040.0000.0000.0000.000
88A116ASN00.017-0.01032.506-0.009-0.0090.0000.0000.0000.000
89A117GLY00.0170.01834.0760.0040.0040.0000.0000.0000.000
90A118SER0-0.031-0.04736.0820.0050.0050.0000.0000.0000.000
91A119TYR0-0.011-0.00439.454-0.004-0.0040.0000.0000.0000.000
92A120LYS10.8450.90542.6670.0190.0190.0000.0000.0000.000
93A121ILE0-0.0150.00345.418-0.002-0.0020.0000.0000.0000.000
94A122THR0-0.030-0.01148.7720.0020.0020.0000.0000.0000.000
95A123PHE00.0220.00750.598-0.001-0.0010.0000.0000.0000.000
96A124ILE0-0.0040.00055.2880.0010.0010.0000.0000.0000.000
97A125PHE00.018-0.00357.5550.0000.0000.0000.0000.0000.000
98A126GLY00.0140.00361.7920.0000.0000.0000.0000.0000.000
99A127GLU-1-0.776-0.88965.278-0.006-0.0060.0000.0000.0000.000
100A128LYS10.9660.98068.2130.0070.0070.0000.0000.0000.000
101A129ALA00.0560.03864.0900.0010.0010.0000.0000.0000.000
102A130LYS10.8190.88766.1790.0070.0070.0000.0000.0000.000
103A131GLU-1-0.919-0.93868.375-0.002-0.0020.0000.0000.0000.000
104A132PHE00.0400.00765.2590.0010.0010.0000.0000.0000.000
105A133MET0-0.026-0.00160.1120.0010.0010.0000.0000.0000.000
106A134GLU-1-0.836-0.89263.537-0.003-0.0030.0000.0000.0000.000
107A135PRO00.0150.00660.3140.0010.0010.0000.0000.0000.000
108A136LEU0-0.018-0.01661.6970.0000.0000.0000.0000.0000.000
109A137THR00.0180.00757.225-0.001-0.0010.0000.0000.0000.000
110A138LEU0-0.026-0.00355.5750.0010.0010.0000.0000.0000.000
111A139VAL00.016-0.00651.806-0.002-0.0020.0000.0000.0000.000
112A140LYS10.9150.96946.4710.0000.0000.0000.0000.0000.000
113A141HIS0-0.118-0.07044.446-0.004-0.0040.0000.0000.0000.000
114A142VAL00.0170.01940.9850.0020.0020.0000.0000.0000.000
115A143THR00.0300.01139.411-0.003-0.0030.0000.0000.0000.000
116A144PHE00.0220.00734.9570.0030.0030.0000.0000.0000.000
117A145ASP-1-0.797-0.85934.3590.0140.0140.0000.0000.0000.000
118A146ASN0-0.067-0.04829.7830.0010.0010.0000.0000.0000.000
119A147ASN0-0.063-0.04828.1660.0000.0000.0000.0000.0000.000
120A148GLN0-0.031-0.00832.4400.0000.0000.0000.0000.0000.000
121A149GLU-1-0.889-0.95335.850-0.002-0.0020.0000.0000.0000.000
122A150LYS10.8100.88337.706-0.013-0.0130.0000.0000.0000.000
123A151VAL00.0260.02141.540-0.004-0.0040.0000.0000.0000.000
124A152VAL0-0.0250.00043.5100.0010.0010.0000.0000.0000.000
125A153GLU-1-0.823-0.89946.294-0.013-0.0130.0000.0000.0000.000
126A154CYS00.0440.01949.2470.0000.0000.0000.0000.0000.000
127A155THR0-0.0590.00051.8300.0000.0000.0000.0000.0000.000
128A156ARG10.8760.93855.102-0.003-0.0030.0000.0000.0000.000
129A157ILE0-0.011-0.00356.5300.0000.0000.0000.0000.0000.000
130A158LYS10.8620.92359.5590.0030.0030.0000.0000.0000.000
131A159TRP00.017-0.00458.730-0.001-0.0010.0000.0000.0000.000
132A160LYS10.8040.91364.4650.0020.0020.0000.0000.0000.000
133A161GLU-1-0.878-0.95967.9370.0040.0040.0000.0000.0000.000
134A162GLY0-0.036-0.01369.6710.0000.0000.0000.0000.0000.000
135A163LYS10.8140.90667.2460.0000.0000.0000.0000.0000.000
136A164ASN00.0340.01161.152-0.001-0.0010.0000.0000.0000.000
137A165PRO00.0140.02259.9480.0010.0010.0000.0000.0000.000
138A166ILE00.019-0.00956.6150.0010.0010.0000.0000.0000.000
139A167ALA0-0.096-0.03059.4570.0010.0010.0000.0000.0000.000
140A168ALA0-0.0100.00960.3580.0000.0000.0000.0000.0000.000
141A181PRO00.005-0.00753.5760.0000.0000.0000.0000.0000.000
142A182LYS10.7620.87954.971-0.005-0.0050.0000.0000.0000.000
143A183TRP00.0250.02649.5180.0010.0010.0000.0000.0000.000
144A184SER0-0.016-0.03854.896-0.001-0.0010.0000.0000.0000.000
145A185ILE00.0340.00551.8630.0000.0000.0000.0000.0000.000
146A186PHE0-0.057-0.04352.782-0.001-0.0010.0000.0000.0000.000
147A187GLU-1-0.818-0.90052.4320.0090.0090.0000.0000.0000.000
148A188TRP0-0.007-0.00345.8340.0000.0000.0000.0000.0000.000
149A189PHE0-0.030-0.02249.8060.0000.0000.0000.0000.0000.000
150A190THR0-0.030-0.05149.6420.0000.0000.0000.0000.0000.000
151A191THR0-0.007-0.02447.419-0.002-0.0020.0000.0000.0000.000
152A192ASP-1-0.902-0.91746.6340.0140.0140.0000.0000.0000.000
153A193GLU-1-0.841-0.91040.7440.0190.0190.0000.0000.0000.000
154A194LEU0-0.035-0.01744.0570.0010.0010.0000.0000.0000.000
155A195GLN0-0.059-0.04540.6620.0010.0010.0000.0000.0000.000
156A196ASP-1-0.925-0.95442.8940.0250.0250.0000.0000.0000.000
157A197LYS10.8490.92044.651-0.013-0.0130.0000.0000.0000.000
158A198PRO0-0.002-0.00244.816-0.001-0.0010.0000.0000.0000.000
159A199ASP-1-0.696-0.83642.255-0.003-0.0030.0000.0000.0000.000
160A200VAL0-0.025-0.03144.275-0.002-0.0020.0000.0000.0000.000
161A201GLY00.0040.00644.477-0.002-0.0020.0000.0000.0000.000
162A202GLU-1-0.763-0.87137.358-0.018-0.0180.0000.0000.0000.000
163A203LEU0-0.0260.00541.509-0.003-0.0030.0000.0000.0000.000
164A204ILE0-0.020-0.02243.587-0.002-0.0020.0000.0000.0000.000
165A205ARG10.7620.85336.3930.0220.0220.0000.0000.0000.000
166A206ARG10.8330.90535.3990.0090.0090.0000.0000.0000.000
167A207GLU-1-0.881-0.91739.973-0.012-0.0120.0000.0000.0000.000
168A208ILE0-0.027-0.01142.610-0.001-0.0010.0000.0000.0000.000
169A209TRP0-0.0040.01344.3810.0000.0000.0000.0000.0000.000
170A210HIS0-0.007-0.01442.610-0.001-0.0010.0000.0000.0000.000
171A211ASN0-0.021-0.02244.8180.0000.0000.0000.0000.0000.000
172A212PRO00.0590.04947.5820.0010.0010.0000.0000.0000.000
173A213LEU00.0070.00150.1930.0020.0020.0000.0000.0000.000
174A214SER00.0080.00447.2530.0010.0010.0000.0000.0000.000
175A215TYR00.0470.05044.6030.0000.0000.0000.0000.0000.000
176A216TYR0-0.0230.00850.7940.0010.0010.0000.0000.0000.000
177A217LEU0-0.078-0.04052.3840.0030.0030.0000.0000.0000.000