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: N93QQ

Calculation Name: 1SE8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SE8

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RY51

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 OptHSide
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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2590656.10863
FMO2-HF: Nuclear repulsion 2502249.81031
FMO2-HF: Total energy -88406.298321
FMO2-MP2: Total energy -88662.650159


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:3:ARG)


Summations of interaction energy for fragment #1(A:3:ARG)
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.
-89.518-88.59717.655-8.231-10.347-0.07
Interaction energy analysis for fragmet #1(A:3:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.922 / q_NPA : 0.951
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].
3A5MET0-0.051-0.0253.4761.6524.133-0.004-1.224-1.2530.008
4A6ASN00.002-0.0136.5510.2930.2930.0000.0000.0000.000
5A7HIS00.0450.0338.4080.1460.1460.0000.0000.0000.000
6A8VAL0-0.003-0.00812.776-0.126-0.1260.0000.0000.0000.000
7A9TYR0-0.030-0.02514.6680.1120.1120.0000.0000.0000.000
8A10LEU0-0.048-0.01919.2450.1390.1390.0000.0000.0000.000
9A11ILE00.0120.00122.8450.2050.2050.0000.0000.0000.000
10A12GLY00.0380.00626.173-0.004-0.0040.0000.0000.0000.000
11A13ALA00.0110.00928.8910.1110.1110.0000.0000.0000.000
12A14LEU0-0.015-0.00328.901-0.358-0.3580.0000.0000.0000.000
13A15ALA0-0.008-0.00831.7850.3100.3100.0000.0000.0000.000
14A16ARG10.9380.95632.8979.5269.5260.0000.0000.0000.000
15A17ASP-1-0.813-0.90133.944-8.360-8.3600.0000.0000.0000.000
16A18PRO0-0.058-0.02430.397-0.118-0.1180.0000.0000.0000.000
17A19GLU-1-0.840-0.89531.376-8.459-8.4590.0000.0000.0000.000
18A20LEU0-0.015-0.00129.723-0.380-0.3800.0000.0000.0000.000
19A21ARG10.8000.87930.7569.0209.0200.0000.0000.0000.000
20A22TYR0-0.011-0.02330.256-0.173-0.1730.0000.0000.0000.000
21A23THR00.0010.00726.4350.1570.1570.0000.0000.0000.000
22A24GLY00.0410.01529.8890.2480.2480.0000.0000.0000.000
23A25ASN0-0.055-0.03628.2160.1140.1140.0000.0000.0000.000
24A26GLY00.0350.02630.3310.0460.0460.0000.0000.0000.000
25A27MET0-0.068-0.02023.005-0.056-0.0560.0000.0000.0000.000
26A28ALA00.0280.01827.4970.0170.0170.0000.0000.0000.000
27A29VAL0-0.006-0.02125.304-0.553-0.5530.0000.0000.0000.000
28A30PHE00.0480.02526.0670.3670.3670.0000.0000.0000.000
29A31GLU-1-0.852-0.92325.899-11.502-11.5020.0000.0000.0000.000
30A32ALA00.0420.03226.9910.4780.4780.0000.0000.0000.000
31A33THR0-0.053-0.03127.229-0.359-0.3590.0000.0000.0000.000
32A34VAL00.0240.03125.4430.3720.3720.0000.0000.0000.000
33A35ALA00.007-0.00727.859-0.331-0.3310.0000.0000.0000.000
34A36GLY00.0500.02129.6520.2620.2620.0000.0000.0000.000
35A37GLU-1-0.783-0.86629.925-9.270-9.2700.0000.0000.0000.000
36A38ASP-1-0.763-0.85726.443-12.060-12.0600.0000.0000.0000.000
37A39ARG10.9250.95929.4009.4389.4380.0000.0000.0000.000
38A40VAL00.0160.01424.884-0.086-0.0860.0000.0000.0000.000
39A48ARG10.9660.97431.3149.5499.5490.0000.0000.0000.000
40A49ASN0-0.032-0.02731.302-0.369-0.3690.0000.0000.0000.000
41A50LEU0-0.0060.00526.8580.2320.2320.0000.0000.0000.000
42A51PRO0-0.005-0.01329.298-0.270-0.2700.0000.0000.0000.000
43A52TRP0-0.088-0.04526.045-0.366-0.3660.0000.0000.0000.000
44A53TYR0-0.020-0.04127.7180.2170.2170.0000.0000.0000.000
45A54HIS0-0.035-0.03022.958-0.183-0.1830.0000.0000.0000.000
46A55ARG10.8350.91025.63111.01511.0150.0000.0000.0000.000
47A56VAL00.0100.00521.609-0.649-0.6490.0000.0000.0000.000
48A57SER0-0.019-0.01421.9830.4750.4750.0000.0000.0000.000
49A58ILE0-0.0160.00721.207-0.642-0.6420.0000.0000.0000.000
50A59LEU0-0.005-0.00619.6690.4360.4360.0000.0000.0000.000
51A60GLY00.0110.00222.488-0.167-0.1670.0000.0000.0000.000
52A61LYS10.8740.90424.5229.5859.5850.0000.0000.0000.000
53A62PRO00.0300.01321.1770.2860.2860.0000.0000.0000.000
54A63ALA0-0.0010.00724.2530.1240.1240.0000.0000.0000.000
55A64GLU-1-0.757-0.86226.187-9.063-9.0630.0000.0000.0000.000
56A65TRP0-0.0010.00123.323-0.088-0.0880.0000.0000.0000.000
57A66GLN00.0040.01026.055-0.075-0.0750.0000.0000.0000.000
58A67ALA0-0.013-0.01328.1630.2030.2030.0000.0000.0000.000
59A68GLU-1-0.903-0.95131.277-8.516-8.5160.0000.0000.0000.000
60A69ARG10.8460.92125.49810.44210.4420.0000.0000.0000.000
61A70ASN0-0.072-0.02932.6100.1580.1580.0000.0000.0000.000
62A71LEU0-0.027-0.00329.5650.1430.1430.0000.0000.0000.000
63A72LYS10.8700.92133.6708.0798.0790.0000.0000.0000.000
64A73GLY0-0.015-0.02234.898-0.215-0.2150.0000.0000.0000.000
65A74GLY0-0.034-0.02335.2840.2490.2490.0000.0000.0000.000
66A75ASP-1-0.806-0.87533.511-8.426-8.4260.0000.0000.0000.000
67A76ALA00.0260.01231.530-0.266-0.2660.0000.0000.0000.000
68A77VAL0-0.023-0.02527.0080.0970.0970.0000.0000.0000.000
69A78VAL00.0170.00722.719-0.182-0.1820.0000.0000.0000.000
70A79VAL0-0.041-0.03220.5220.1350.1350.0000.0000.0000.000
71A80GLU-1-0.855-0.90515.542-16.588-16.5880.0000.0000.0000.000
72A81GLY0-0.023-0.03016.4760.4950.4950.0000.0000.0000.000
73A82THR0-0.045-0.01311.658-0.542-0.5420.0000.0000.0000.000
74A83LEU00.010-0.00113.6181.4511.4510.0000.0000.0000.000
75A84GLU-1-0.799-0.89313.930-19.977-19.9770.0000.0000.0000.000
76A85TYR0-0.007-0.01214.4981.0321.0320.0000.0000.0000.000
77A86ARG10.9110.94816.38513.49113.4910.0000.0000.0000.000
78A87GLN00.0440.01917.982-0.551-0.5510.0000.0000.0000.000
79A88TRP0-0.024-0.00620.7040.0450.0450.0000.0000.0000.000
80A89GLU-1-0.780-0.88524.330-12.756-12.7560.0000.0000.0000.000
81A90ALA0-0.0160.00127.0880.2750.2750.0000.0000.0000.000
82A91PRO00.0390.00429.931-0.084-0.0840.0000.0000.0000.000
83A92GLU-1-0.831-0.91330.799-9.790-9.7900.0000.0000.0000.000
84A93GLY00.0120.02928.817-0.052-0.0520.0000.0000.0000.000
85A94GLY0-0.015-0.00726.633-0.528-0.5280.0000.0000.0000.000
86A95LYS10.7850.87222.00013.25413.2540.0000.0000.0000.000
87A96ARG10.8640.94123.90911.21011.2100.0000.0000.0000.000
88A97SER00.0100.00119.045-0.038-0.0380.0000.0000.0000.000
89A98ALA0-0.025-0.00920.2800.5340.5340.0000.0000.0000.000
90A99VAL00.0370.02416.105-0.592-0.5920.0000.0000.0000.000
91A100ASN0-0.014-0.00218.8370.9020.9020.0000.0000.0000.000
92A101VAL00.0710.03918.462-0.915-0.9150.0000.0000.0000.000
93A102LYS10.8560.94114.20518.82118.8210.0000.0000.0000.000
94A103ALA00.0700.03017.189-0.663-0.6630.0000.0000.0000.000
95A104LEU0-0.024-0.02515.8310.2420.2420.0000.0000.0000.000
96A105ARG10.9240.96018.34413.61313.6130.0000.0000.0000.000
97A106MET0-0.045-0.01321.923-0.427-0.4270.0000.0000.0000.000
98A107GLU-1-0.862-0.92024.137-10.632-10.6320.0000.0000.0000.000
99A108GLN0-0.007-0.00926.7750.0020.0020.0000.0000.0000.000
100A109LEU0-0.036-0.01828.288-0.013-0.0130.0000.0000.0000.000
101A110GLY00.0250.01031.4360.1870.1870.0000.0000.0000.000
102A111THR0-0.067-0.02333.7140.2220.2220.0000.0000.0000.000
103A112GLN00.0310.00835.492-0.251-0.2510.0000.0000.0000.000
104A113PRO0-0.018-0.00434.3870.0230.0230.0000.0000.0000.000
105A114GLU-1-0.874-0.93436.449-7.505-7.5050.0000.0000.0000.000
106A115LEU0-0.051-0.03335.941-0.294-0.2940.0000.0000.0000.000
107A116ILE0-0.023-0.00936.5150.2330.2330.0000.0000.0000.000
108A117GLN0-0.005-0.00538.336-0.157-0.1570.0000.0000.0000.000
109A118ASP-1-0.844-0.91037.045-8.602-8.6020.0000.0000.0000.000
110A119ALA00.015-0.02140.0640.1270.1270.0000.0000.0000.000
111A120GLY0-0.046-0.00940.1740.1570.1570.0000.0000.0000.000
112A121GLY0-0.042-0.01741.0870.0270.0270.0000.0000.0000.000
113A122GLY0-0.0460.00137.248-0.052-0.0520.0000.0000.0000.000
114A123VAL00.0110.00535.8000.1450.1450.0000.0000.0000.000
115A124ARG10.8120.89732.8998.8778.8770.0000.0000.0000.000
116A125MET00.0080.01530.9620.2390.2390.0000.0000.0000.000
117A126SER0-0.021-0.01232.662-0.263-0.2630.0000.0000.0000.000
118A127GLY0-0.014-0.01732.1640.0330.0330.0000.0000.0000.000
119A128ALA0-0.0380.00528.466-0.061-0.0610.0000.0000.0000.000
120A129MET00.006-0.00620.9270.1500.1500.0000.0000.0000.000
121A130ASN00.001-0.00921.747-0.760-0.7600.0000.0000.0000.000
122A131GLU-1-0.913-0.95117.304-16.763-16.7630.0000.0000.0000.000
123A132VAL0-0.028-0.01213.935-0.270-0.2700.0000.0000.0000.000
124A133LEU00.0140.00811.889-0.262-0.2620.0000.0000.0000.000
125A134VAL0-0.0110.0009.327-0.616-0.6160.0000.0000.0000.000
126A135LEU0-0.014-0.0072.899-2.346-1.3420.313-0.282-1.0350.000
127A136GLY00.0350.0173.561-1.708-1.4650.010-0.089-0.1650.000
128A137ASN0-0.035-0.0241.872-49.240-52.10514.339-5.755-5.718-0.074
129A138VAL00.0620.0514.3045.4745.576-0.001-0.039-0.0630.000
130A139THR0-0.033-0.0267.9370.6310.6310.0000.0000.0000.000
131A140ARG10.8790.92410.34021.28421.2840.0000.0000.0000.000
132A141ASP-1-0.805-0.90313.008-20.863-20.8630.0000.0000.0000.000
133A142PRO0-0.021-0.00313.3580.6580.6580.0000.0000.0000.000
134A143GLU-1-0.859-0.90615.694-12.980-12.9800.0000.0000.0000.000
135A144ILE0-0.0050.00319.318-0.205-0.2050.0000.0000.0000.000
136A145ARG10.7900.87921.26613.47413.4740.0000.0000.0000.000
137A146TYR0-0.014-0.03524.432-0.266-0.2660.0000.0000.0000.000
138A147THR0-0.021-0.00227.2100.3250.3250.0000.0000.0000.000
139A148PRO00.021-0.00729.6230.0530.0530.0000.0000.0000.000
140A149ALA0-0.032-0.01432.6890.1640.1640.0000.0000.0000.000
141A150GLY00.0230.02330.3210.0820.0820.0000.0000.0000.000
142A151ASP-1-0.874-0.91926.823-11.046-11.0460.0000.0000.0000.000
143A152ALA00.0100.00822.848-0.039-0.0390.0000.0000.0000.000
144A153VAL0-0.016-0.01621.557-0.162-0.1620.0000.0000.0000.000
145A154LEU0-0.0050.00815.2830.1040.1040.0000.0000.0000.000
146A155SER0-0.0050.01317.393-0.394-0.3940.0000.0000.0000.000
147A156LEU00.0100.00410.394-0.265-0.2650.0000.0000.0000.000
148A157SER00.003-0.02512.2190.4720.4720.0000.0000.0000.000
149A158ILE0-0.022-0.0096.917-1.503-1.5030.0000.0000.0000.000
150A159ALA0-0.019-0.0126.4803.3043.3040.0000.0000.0000.000
151A160VAL00.006-0.0045.298-8.440-8.4400.0000.0000.0000.000
152A161ASN0-0.070-0.0535.0925.9715.9710.0000.0000.0000.000
153A162GLU-1-0.841-0.9075.438-25.303-25.3030.0000.0000.0000.000
154A163ASN0-0.010-0.0155.4363.9723.9720.0000.0000.0000.000
155A164TYR0-0.025-0.0107.7651.4551.4550.0000.0000.0000.000
156A165GLN00.0290.01211.3490.4750.4750.0000.0000.0000.000
157A166ASP-1-0.763-0.86714.483-14.056-14.0560.0000.0000.0000.000
158A167ARG10.9380.94317.55311.62511.6250.0000.0000.0000.000
159A168GLN0-0.055-0.03220.1490.2720.2720.0000.0000.0000.000
160A169GLY0-0.0100.02017.8580.3040.3040.0000.0000.0000.000
161A170GLN0-0.056-0.02016.435-0.392-0.3920.0000.0000.0000.000
162A171ARG10.8590.8987.44525.68525.6850.0000.0000.0000.000
163A172GLN0-0.040-0.01912.075-0.371-0.3710.0000.0000.0000.000
164A173GLU-1-0.813-0.8747.064-34.171-34.1710.0000.0000.0000.000
165A174LYS10.8270.9239.68222.22122.2210.0000.0000.0000.000
166A175VAL0-0.031-0.0088.506-2.859-2.8590.0000.0000.0000.000
167A176HIS0-0.021-0.0409.8773.9013.9010.0000.0000.0000.000
168A177TYR0-0.029-0.01710.038-3.126-3.1260.0000.0000.0000.000
169A178ILE00.0100.00311.0532.1232.1230.0000.0000.0000.000
170A179ASP-1-0.850-0.89012.096-20.485-20.4850.0000.0000.0000.000
171A180ALA0-0.018-0.01713.1960.3980.3980.0000.0000.0000.000
172A181THR0-0.029-0.03315.0280.0350.0350.0000.0000.0000.000
173A182LEU0-0.006-0.00513.703-0.161-0.1610.0000.0000.0000.000
174A183TRP00.0390.01018.0340.7300.7300.0000.0000.0000.000
175A184ARG10.8840.91821.27711.55111.5510.0000.0000.0000.000
176A185ASP-1-0.837-0.92021.928-13.043-13.0430.0000.0000.0000.000
177A186LEU0-0.023-0.00716.942-0.611-0.6110.0000.0000.0000.000
178A187ALA0-0.024-0.01317.093-1.028-1.0280.0000.0000.0000.000
179A188GLU-1-0.760-0.86918.416-13.595-13.5950.0000.0000.0000.000
180A189ASN0-0.041-0.02216.7270.0940.0940.0000.0000.0000.000
181A190MET0-0.028-0.00510.825-0.762-0.7620.0000.0000.0000.000
182A191LYS10.8360.91414.34713.42613.4260.0000.0000.0000.000
183A192GLU-1-0.869-0.93716.020-15.555-15.5550.0000.0000.0000.000
184A193LEU0-0.064-0.0159.152-1.046-1.0460.0000.0000.0000.000
185A194ARG10.8130.89811.05120.09120.0910.0000.0000.0000.000
186A195LYS10.9350.9719.82819.91319.9130.0000.0000.0000.000
187A196GLY0-0.027-0.0207.2831.0311.0310.0000.0000.0000.000
188A197ASP-1-0.770-0.8515.811-35.398-35.3980.0000.0000.0000.000
189A198PRO0-0.072-0.0272.336-4.814-5.3962.986-0.738-1.666-0.003
190A199VAL00.0210.0073.6528.6918.8520.0050.012-0.1780.000
191A200MET0-0.004-0.0085.446-5.246-5.2460.0000.0000.0000.000
192A201ILE0-0.011-0.0127.5682.9152.9150.0000.0000.0000.000
193A202MET00.0270.01411.035-0.630-0.6300.0000.0000.0000.000
194A203GLY00.0270.01014.1450.5450.5450.0000.0000.0000.000
195A204ARG10.8270.92517.36812.92912.9290.0000.0000.0000.000
196A205LEU00.0070.00717.730-0.439-0.4390.0000.0000.0000.000
197A206VAL00.0120.01920.1811.0121.0120.0000.0000.0000.000
198A207ASN00.000-0.00521.985-0.775-0.7750.0000.0000.0000.000
199A208GLU-1-0.786-0.86221.524-13.981-13.9810.0000.0000.0000.000
200A209GLY0-0.034-0.02525.106-0.063-0.0630.0000.0000.0000.000
201A210TRP00.025-0.01623.7790.2730.2730.0000.0000.0000.000
202A211THR00.0190.00228.5780.1360.1360.0000.0000.0000.000
203A212ASP-1-0.803-0.86328.629-11.079-11.0790.0000.0000.0000.000
204A213LYS10.7970.86830.4329.8469.8460.0000.0000.0000.000
205A214ASP-1-0.877-0.92732.803-9.131-9.1310.0000.0000.0000.000
206A215GLY00.0400.03034.8710.2760.2760.0000.0000.0000.000
207A216ASN0-0.037-0.01530.611-0.267-0.2670.0000.0000.0000.000
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209A218ARG10.8330.89824.46511.90411.9040.0000.0000.0000.000
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