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: N295Q

Calculation Name: 5XE7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XE7

Chain ID: A

ChEMBL ID:

UniProt ID: L0TCG5

Base Structure: X-ray

Registration Date: 2023-09-26

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 279
LigandResidueName
LigandFragmentNumber 0
LigandCharge DAS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3479930.042944
FMO2-HF: Nuclear repulsion 3376045.794121
FMO2-HF: Total energy -103884.248824
FMO2-MP2: Total energy -104190.502554


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:2:GLU)


Summations of interaction energy for fragment #1(A:2: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.
90.1997.2362.434-4.492-4.988-0.027
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.923 / q_NPA : -0.965
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].
3A4SER0-0.023-0.0043.493-10.278-7.7500.029-1.187-1.3690.006
4A5GLU-1-0.906-0.9612.47125.47329.6792.405-3.231-3.381-0.033
5A6PHE00.0100.0154.216-3.141-2.8290.000-0.074-0.2380.000
6A7GLU-1-0.794-0.8836.05122.08922.0890.0000.0000.0000.000
7A8ALA0-0.011-0.0128.070-2.906-2.9060.0000.0000.0000.000
8A9LEU0-0.0200.0039.237-2.351-2.3510.0000.0000.0000.000
9A10ARG10.9460.95710.269-24.990-24.9900.0000.0000.0000.000
10A11GLN0-0.044-0.02211.936-2.303-2.3030.0000.0000.0000.000
11A12HIS0-0.0120.00013.724-1.352-1.3520.0000.0000.0000.000
12A13LEU0-0.027-0.02213.122-1.124-1.1240.0000.0000.0000.000
13A14MET0-0.004-0.01415.835-1.138-1.1380.0000.0000.0000.000
14A15SER0-0.037-0.01617.683-1.135-1.1350.0000.0000.0000.000
15A16VAL0-0.019-0.00819.000-0.775-0.7750.0000.0000.0000.000
16A17ALA00.0190.00719.879-0.699-0.6990.0000.0000.0000.000
17A18TYR0-0.024-0.05021.577-0.571-0.5710.0000.0000.0000.000
18A19ARG10.8350.91823.523-12.284-12.2840.0000.0000.0000.000
19A20LEU0-0.032-0.00123.236-0.559-0.5590.0000.0000.0000.000
20A21THR0-0.0080.00525.566-0.586-0.5860.0000.0000.0000.000
21A22GLY00.058-0.00428.126-0.097-0.0970.0000.0000.0000.000
22A23THR0-0.065-0.01826.769-0.317-0.3170.0000.0000.0000.000
23A24VAL0-0.032-0.03821.7750.3030.3030.0000.0000.0000.000
24A25ALA00.0800.03022.4670.5840.5840.0000.0000.0000.000
25A26ASP-1-0.848-0.94923.72411.11311.1130.0000.0000.0000.000
26A27ALA0-0.021-0.01020.7730.1230.1230.0000.0000.0000.000
27A28GLU-1-0.986-1.00518.87715.63915.6390.0000.0000.0000.000
28A29ASP-1-0.900-0.94219.22413.70213.7020.0000.0000.0000.000
29A30ILE0-0.065-0.01920.6180.0960.0960.0000.0000.0000.000
30A31VAL0-0.025-0.03114.6770.3480.3480.0000.0000.0000.000
31A32GLN0-0.016-0.00215.7440.7340.7340.0000.0000.0000.000
32A33GLU-1-0.810-0.90216.90214.07414.0740.0000.0000.0000.000
33A34ALA0-0.029-0.01115.0670.1700.1700.0000.0000.0000.000
34A35TRP00.007-0.0148.7750.9880.9880.0000.0000.0000.000
35A36LEU00.0140.01313.4760.3130.3130.0000.0000.0000.000
36A37ARG10.8140.90416.437-14.145-14.1450.0000.0000.0000.000
37A38TRP0-0.069-0.0458.7340.0220.0220.0000.0000.0000.000
38A39DAS-1-0.936-0.96514.34119.11119.1110.0000.0000.0000.000
39A40SER0-0.0080.00315.996-1.157-1.1570.0000.0000.0000.000
40A41PRO0-0.114-0.08915.598-0.479-0.4790.0000.0000.0000.000
41A42ASP-1-0.829-0.8969.59227.20727.2070.0000.0000.0000.000
42A43THR0-0.025-0.00211.6700.0390.0390.0000.0000.0000.000
43A44VAL0-0.031-0.00612.8950.7440.7440.0000.0000.0000.000
44A45ILE0-0.014-0.00214.1590.4820.4820.0000.0000.0000.000
45A46ALA00.005-0.01613.274-0.484-0.4840.0000.0000.0000.000
46A47ASP-1-0.850-0.93013.47917.19417.1940.0000.0000.0000.000
47A48PRO00.0270.0079.877-0.840-0.8400.0000.0000.0000.000
48A49ARG10.9720.98810.618-19.137-19.1370.0000.0000.0000.000
49A50ALA00.0240.01013.749-0.498-0.4980.0000.0000.0000.000
50A51TRP00.0130.01815.282-1.201-1.2010.0000.0000.0000.000
51A52LEU00.0770.04412.321-0.741-0.7410.0000.0000.0000.000
52A53THR0-0.0120.01216.612-0.669-0.6690.0000.0000.0000.000
53A54THR0-0.018-0.01019.006-0.656-0.6560.0000.0000.0000.000
54A55VAL00.0120.01918.561-0.622-0.6220.0000.0000.0000.000
55A56VAL00.0430.01517.596-0.430-0.4300.0000.0000.0000.000
56A57SER0-0.055-0.06320.648-0.593-0.5930.0000.0000.0000.000
57A58ARG10.8930.93523.768-12.140-12.1400.0000.0000.0000.000
58A59LEU00.0030.01220.783-0.459-0.4590.0000.0000.0000.000
59A60GLY0-0.012-0.01324.399-0.204-0.2040.0000.0000.0000.000
60A61LEU0-0.072-0.05525.689-0.390-0.3900.0000.0000.0000.000
61A62ASP-1-0.978-0.98127.50410.19010.1900.0000.0000.0000.000
62A63LYS10.8480.96327.373-11.168-11.1680.0000.0000.0000.000
63A64LEU0-0.077-0.03329.649-0.558-0.5580.0000.0000.0000.000
64A72GLU-1-0.865-0.93835.5148.5878.5870.0000.0000.0000.000
65A73THR0-0.103-0.06137.782-0.123-0.1230.0000.0000.0000.000
66A74TYR00.0230.01440.221-0.077-0.0770.0000.0000.0000.000
67A75THR0-0.097-0.06642.698-0.169-0.1690.0000.0000.0000.000
68A76GLY00.0200.00143.662-0.026-0.0260.0000.0000.0000.000
69A77THR0-0.118-0.07242.2850.0050.0050.0000.0000.0000.000
70A78TRP00.0540.03132.242-0.065-0.0650.0000.0000.0000.000
71A79LEU0-0.053-0.04336.181-0.130-0.1300.0000.0000.0000.000
72A80PRO0-0.0170.00831.4270.1000.1000.0000.0000.0000.000
73A81GLU-1-0.656-0.76327.02911.25211.2520.0000.0000.0000.000
74A82PRO0-0.062-0.00328.8710.2200.2200.0000.0000.0000.000
75A83VAL00.0280.00623.1680.2600.2600.0000.0000.0000.000
76A84VAL0-0.075-0.04526.098-0.355-0.3550.0000.0000.0000.000
77A85THR00.0030.02422.6280.2760.2760.0000.0000.0000.000
78A86GLY00.0160.00124.930-0.589-0.5890.0000.0000.0000.000
79A87LEU0-0.037-0.04525.9740.1110.1110.0000.0000.0000.000
80A88ASP-1-0.884-0.93223.26413.17013.1700.0000.0000.0000.000
81A89ALA0-0.028-0.01222.4610.2790.2790.0000.0000.0000.000
82A90THR0-0.064-0.03419.0390.6480.6480.0000.0000.0000.000
83A91ASP-1-0.837-0.91818.20615.05215.0520.0000.0000.0000.000
84A92PRO00.014-0.00515.3280.1500.1500.0000.0000.0000.000
85A93LEU0-0.018-0.01416.8480.1950.1950.0000.0000.0000.000
86A94ALA00.0300.01619.617-0.684-0.6840.0000.0000.0000.000
87A95ALA00.024-0.00116.476-0.538-0.5380.0000.0000.0000.000
88A96VAL0-0.042-0.01018.377-0.206-0.2060.0000.0000.0000.000
89A97VAL0-0.039-0.02620.306-0.473-0.4730.0000.0000.0000.000
90A98ALA00.0150.02020.612-0.477-0.4770.0000.0000.0000.000
91A99ALA0-0.035-0.00422.587-0.349-0.3490.0000.0000.0000.000
92A100GLU-1-0.769-0.87524.1779.1239.1230.0000.0000.0000.000
93A101ASP-1-0.840-0.91926.26810.71310.7130.0000.0000.0000.000
94A102ALA0-0.010-0.00725.448-0.059-0.0590.0000.0000.0000.000
95A103ARG10.7870.88127.563-9.250-9.2500.0000.0000.0000.000
96A104PHE00.0630.00930.613-0.170-0.1700.0000.0000.0000.000
97A105ALA0-0.013-0.00632.865-0.146-0.1460.0000.0000.0000.000
98A106ALA00.0290.00731.568-0.199-0.1990.0000.0000.0000.000
99A107MET0-0.0040.01728.245-0.044-0.0440.0000.0000.0000.000
100A108VAL00.015-0.00532.200-0.089-0.0890.0000.0000.0000.000
101A109VAL0-0.082-0.01935.582-0.233-0.2330.0000.0000.0000.000
102A110LEU0-0.048-0.02730.017-0.222-0.2220.0000.0000.0000.000
103A111GLU-1-0.725-0.84631.9719.3119.3110.0000.0000.0000.000
104A112ARG10.7930.91434.674-8.129-8.1290.0000.0000.0000.000
105A113LEU0-0.090-0.04337.257-0.302-0.3020.0000.0000.0000.000
106A114ARG10.9040.95533.560-9.000-9.0000.0000.0000.0000.000
107A115PRO00.0070.02134.1000.2870.2870.0000.0000.0000.000
108A116ASP-1-0.848-0.92735.1338.1258.1250.0000.0000.0000.000
109A117GLN00.002-0.01634.5110.2880.2880.0000.0000.0000.000
110A118ARG10.7460.87230.180-9.579-9.5790.0000.0000.0000.000
111A119VAL00.0980.04927.4130.1050.1050.0000.0000.0000.000
112A120ALA00.0190.00528.6750.1810.1810.0000.0000.0000.000
113A121PHE0-0.024-0.02030.707-0.065-0.0650.0000.0000.0000.000
114A122VAL00.0460.01725.7790.0560.0560.0000.0000.0000.000
115A123LEU00.0190.02023.4060.2140.2140.0000.0000.0000.000
116A124HIS0-0.089-0.04425.588-0.134-0.1340.0000.0000.0000.000
117A125ASP-1-0.975-1.00627.7799.5969.5960.0000.0000.0000.000
118A126GLY00.0430.03926.4860.0630.0630.0000.0000.0000.000
119A127PHE0-0.117-0.05720.5380.2070.2070.0000.0000.0000.000
120A128ALA0-0.0230.00722.5680.3350.3350.0000.0000.0000.000
121A129VAL00.000-0.01322.4800.1810.1810.0000.0000.0000.000
122A130PRO0-0.0260.00824.360-0.519-0.5190.0000.0000.0000.000
123A131PHE00.0840.00027.467-0.011-0.0110.0000.0000.0000.000
124A132ALA00.0090.01428.706-0.110-0.1100.0000.0000.0000.000
125A133GLU-1-0.766-0.90523.73710.67010.6700.0000.0000.0000.000
126A134VAL0-0.061-0.02826.2490.1080.1080.0000.0000.0000.000
127A135ALA0-0.027-0.03827.897-0.097-0.0970.0000.0000.0000.000
128A136GLU-1-0.949-0.93325.55410.75110.7510.0000.0000.0000.000
129A137VAL0-0.063-0.02824.741-0.002-0.0020.0000.0000.0000.000
130A138LEU0-0.089-0.01727.654-0.215-0.2150.0000.0000.0000.000
131A139GLY00.0330.01431.193-0.139-0.1390.0000.0000.0000.000
132A140THR0-0.066-0.03433.029-0.343-0.3430.0000.0000.0000.000
133A141SER00.000-0.01734.1640.1710.1710.0000.0000.0000.000
134A142GLU-1-0.795-0.89233.9428.2398.2390.0000.0000.0000.000
135A143ALA0-0.061-0.04534.9910.0690.0690.0000.0000.0000.000
136A144ALA0-0.032-0.02237.132-0.137-0.1370.0000.0000.0000.000
137A145ALA00.0900.05532.2930.0070.0070.0000.0000.0000.000
138A146ARG10.9420.97234.427-7.951-7.9510.0000.0000.0000.000
139A147GLN0-0.079-0.04135.858-0.282-0.2820.0000.0000.0000.000
140A148LEU0-0.0150.00534.368-0.177-0.1770.0000.0000.0000.000
141A149ALA00.0840.04833.6010.0490.0490.0000.0000.0000.000
142A150SER0-0.050-0.03035.443-0.075-0.0750.0000.0000.0000.000
143A151ARG10.9020.93638.652-7.281-7.2810.0000.0000.0000.000
144A152ALA00.0640.04335.715-0.078-0.0780.0000.0000.0000.000
145A153ARG10.9100.96236.489-7.630-7.6300.0000.0000.0000.000
146A154LYS10.9210.96237.927-6.794-6.7940.0000.0000.0000.000
147A155ALA0-0.0190.00139.603-0.146-0.1460.0000.0000.0000.000
148A156VAL00.0210.02837.5030.0110.0110.0000.0000.0000.000
149A157THR0-0.051-0.01840.217-0.086-0.0860.0000.0000.0000.000
150A168ASP-1-0.818-0.90536.8337.5457.5450.0000.0000.0000.000
151A169PRO00.0280.01735.1600.1760.1760.0000.0000.0000.000
152A170ALA00.0310.01236.1900.0530.0530.0000.0000.0000.000
153A171HIS00.0060.00734.733-0.262-0.2620.0000.0000.0000.000
154A172ASN00.1060.03033.1670.0130.0130.0000.0000.0000.000
155A173GLU-1-0.852-0.89036.7027.1357.1350.0000.0000.0000.000
156A174VAL0-0.061-0.04139.989-0.204-0.2040.0000.0000.0000.000
157A175VAL00.0120.00137.219-0.175-0.1750.0000.0000.0000.000
158A176GLY0-0.016-0.01039.445-0.065-0.0650.0000.0000.0000.000
159A177ARG10.8200.89440.429-7.050-7.0500.0000.0000.0000.000
160A178LEU0-0.015-0.01042.663-0.151-0.1510.0000.0000.0000.000
161A179MET0-0.037-0.02338.690-0.140-0.1400.0000.0000.0000.000
162A180ALA0-0.0030.00942.759-0.025-0.0250.0000.0000.0000.000
163A181ALA00.0470.02345.451-0.130-0.1300.0000.0000.0000.000
164A182MET00.0010.00946.505-0.141-0.1410.0000.0000.0000.000
165A183ALA0-0.020-0.01247.803-0.109-0.1090.0000.0000.0000.000
166A184ALA0-0.055-0.02849.773-0.087-0.0870.0000.0000.0000.000
167A185GLY0-0.039-0.01752.254-0.130-0.1300.0000.0000.0000.000
168A186ASP-1-0.890-0.94052.5845.7125.7120.0000.0000.0000.000
169A187LEU0-0.014-0.01953.1700.0970.0970.0000.0000.0000.000
170A188ASP-1-0.905-0.94254.8395.4555.4550.0000.0000.0000.000
171A189THR0-0.069-0.05551.1480.0870.0870.0000.0000.0000.000
172A190VAL00.001-0.00949.2280.0990.0990.0000.0000.0000.000
173A191VAL0-0.0080.00050.3460.0970.0970.0000.0000.0000.000
174A192SER0-0.037-0.01252.2300.0140.0140.0000.0000.0000.000
175A193LEU0-0.023-0.01946.2450.0650.0650.0000.0000.0000.000
176A194LEU00.0230.02446.8270.1810.1810.0000.0000.0000.000
177A195HIS00.0760.04646.953-0.090-0.0900.0000.0000.0000.000
178A196PRO00.0400.00948.952-0.025-0.0250.0000.0000.0000.000
179A197ASP-1-0.909-0.95749.4355.9645.9640.0000.0000.0000.000
180A198VAL0-0.0200.01945.7520.1360.1360.0000.0000.0000.000
181A199THR0-0.041-0.03744.639-0.162-0.1620.0000.0000.0000.000
182A200PHE00.0180.00943.8380.0940.0940.0000.0000.0000.000
183A201THR0-0.003-0.01541.391-0.221-0.2210.0000.0000.0000.000
184A202GLY00.0330.00941.1940.1610.1610.0000.0000.0000.000
185A203ASP-1-0.819-0.90536.4428.3358.3350.0000.0000.0000.000
186A204SER0-0.028-0.00239.771-0.049-0.0490.0000.0000.0000.000
187A205ASN00.0160.03138.296-0.189-0.1890.0000.0000.0000.000
188A206GLY00.0090.00739.5220.0120.0120.0000.0000.0000.000
189A207LYS10.9190.96638.811-8.280-8.2800.0000.0000.0000.000
190A208ALA00.021-0.00642.045-0.012-0.0120.0000.0000.0000.000
191A209PRO0-0.079-0.04743.896-0.042-0.0420.0000.0000.0000.000
192A210THR00.0650.04542.1290.0250.0250.0000.0000.0000.000
193A211ALA0-0.019-0.00345.103-0.187-0.1870.0000.0000.0000.000
194A212VAL00.0200.00545.3370.0640.0640.0000.0000.0000.000
195A213ARG10.8880.95346.467-6.230-6.2300.0000.0000.0000.000
196A214ALA00.0670.03645.7680.0000.0000.0000.0000.0000.000
197A215VAL0-0.040-0.00547.191-0.207-0.2070.0000.0000.0000.000
198A216ARG10.8920.92547.854-6.380-6.3800.0000.0000.0000.000
199A217GLY00.0320.01750.443-0.142-0.1420.0000.0000.0000.000
200A218SER00.0110.00351.3290.0340.0340.0000.0000.0000.000
201A219ASP-1-0.866-0.93752.3505.6175.6170.0000.0000.0000.000
202A220LYS10.8790.92354.045-5.696-5.6960.0000.0000.0000.000
203A221VAL00.0290.02848.0690.0210.0210.0000.0000.0000.000
204A222VAL00.0550.02450.8500.0550.0550.0000.0000.0000.000
205A223ARG10.8850.95052.495-5.593-5.5930.0000.0000.0000.000
206A224PHE00.0190.01046.544-0.046-0.0460.0000.0000.0000.000
207A225ILE00.0380.00747.8680.0450.0450.0000.0000.0000.000
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