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: M3Q9Z

Calculation Name: 3QC1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QC1

Chain ID: A

ChEMBL ID:

UniProt ID: Q61249

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2053934.22804
FMO2-HF: Nuclear repulsion 1976935.249165
FMO2-HF: Total energy -76998.978875
FMO2-MP2: Total energy -77224.288028


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:10:LEU)


Summations of interaction energy for fragment #1(A:10:LEU)
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.
0.9062.301-0.002-0.494-0.8990.001
Interaction energy analysis for fragmet #1(A:10:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.015
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].
3A12ARG10.9801.0003.5522.2223.634-0.001-0.486-0.9250.001
4A13LEU00.0870.0515.9070.3600.3600.0000.0000.0000.000
5A14PRO0-0.064-0.0348.4900.1120.1120.0000.0000.0000.000
6A15GLU-1-0.872-0.9385.022-1.703-1.720-0.001-0.0080.0260.000
7A16LEU0-0.0180.0008.2780.2720.2720.0000.0000.0000.000
8A17PHE00.0170.00210.5270.1450.1450.0000.0000.0000.000
9A18GLU-1-0.825-0.92812.458-0.255-0.2550.0000.0000.0000.000
10A19THR0-0.066-0.02910.4950.1110.1110.0000.0000.0000.000
11A20SER00.0090.00113.2780.0870.0870.0000.0000.0000.000
12A21LYS10.8680.94315.7340.2050.2050.0000.0000.0000.000
13A22LYS10.9640.97414.5350.2500.2500.0000.0000.0000.000
14A23LEU0-0.020-0.00915.3870.0340.0340.0000.0000.0000.000
15A24LEU0-0.0060.00018.6930.0190.0190.0000.0000.0000.000
16A25GLU-1-0.849-0.92921.389-0.111-0.1110.0000.0000.0000.000
17A26ASP-1-0.872-0.93020.0580.0110.0110.0000.0000.0000.000
18A27VAL0-0.056-0.03722.5390.0100.0100.0000.0000.0000.000
19A28GLU-1-0.986-1.01224.882-0.041-0.0410.0000.0000.0000.000
20A29VAL0-0.055-0.01125.8310.0000.0000.0000.0000.0000.000
21A30ALA0-0.050-0.01226.5830.0040.0040.0000.0000.0000.000
22A31THR0-0.018-0.00728.506-0.003-0.0030.0000.0000.0000.000
23A32GLU-1-0.936-0.96228.1550.0430.0430.0000.0000.0000.000
24A33PRO00.0400.01331.871-0.003-0.0030.0000.0000.0000.000
25A34THR00.0770.04329.6130.0060.0060.0000.0000.0000.000
26A35GLY00.0010.00729.1330.0040.0040.0000.0000.0000.000
27A36SER0-0.047-0.04328.7480.0080.0080.0000.0000.0000.000
28A37ARG10.8980.94123.919-0.141-0.1410.0000.0000.0000.000
29A38THR00.0300.01823.9560.0060.0060.0000.0000.0000.000
30A39ILE00.0520.03523.1590.0060.0060.0000.0000.0000.000
31A40GLN00.008-0.02023.7450.0000.0000.0000.0000.0000.000
32A41ASP-1-0.850-0.90220.6200.1680.1680.0000.0000.0000.000
33A42LYS10.8440.91319.128-0.044-0.0440.0000.0000.0000.000
34A43VAL00.0010.00919.333-0.011-0.0110.0000.0000.0000.000
35A44SER0-0.013-0.02520.103-0.012-0.0120.0000.0000.0000.000
36A45LYS10.9600.99112.100-0.320-0.3200.0000.0000.0000.000
37A46GLY00.0140.00215.447-0.011-0.0110.0000.0000.0000.000
38A47LEU0-0.004-0.00716.928-0.030-0.0300.0000.0000.0000.000
39A48GLU-1-0.931-0.95312.9630.3120.3120.0000.0000.0000.000
40A49LEU0-0.039-0.03410.831-0.013-0.0130.0000.0000.0000.000
41A50LEU00.0000.00113.009-0.094-0.0940.0000.0000.0000.000
42A51GLU-1-0.945-0.94615.6010.0250.0250.0000.0000.0000.000
43A52LYS10.9320.9737.774-0.119-0.1190.0000.0000.0000.000
44A53ALA00.000-0.01811.795-0.070-0.0700.0000.0000.0000.000
45A54ALA00.0330.01212.738-0.030-0.0300.0000.0000.0000.000
46A55GLY00.0150.00414.081-0.004-0.0040.0000.0000.0000.000
47A56MET0-0.083-0.0566.453-0.045-0.0450.0000.0000.0000.000
48A57LEU0-0.019-0.01312.252-0.022-0.0220.0000.0000.0000.000
49A58SER0-0.027-0.00115.2500.0180.0180.0000.0000.0000.000
50A59GLN0-0.066-0.02412.8730.0260.0260.0000.0000.0000.000
51A60LEU0-0.092-0.04611.987-0.010-0.0100.0000.0000.0000.000
52A61ASP-1-0.863-0.92515.552-0.154-0.1540.0000.0000.0000.000
53A62LEU0-0.020-0.02316.009-0.002-0.0020.0000.0000.0000.000
54A63PHE0-0.041-0.03519.6440.0030.0030.0000.0000.0000.000
55A64SER0-0.0060.03222.8750.0190.0190.0000.0000.0000.000
56A65ARG10.8900.94224.5540.1430.1430.0000.0000.0000.000
57A66ASN0-0.0130.02227.712-0.004-0.0040.0000.0000.0000.000
58A67GLU-1-0.971-1.01329.574-0.082-0.0820.0000.0000.0000.000
59A68ASP-1-0.886-0.94628.554-0.140-0.1400.0000.0000.0000.000
60A69LEU0-0.035-0.02927.4690.0050.0050.0000.0000.0000.000
61A70GLU-1-0.934-0.99727.649-0.129-0.1290.0000.0000.0000.000
62A71GLU-1-0.935-0.96427.616-0.144-0.1440.0000.0000.0000.000
63A72ILE0-0.0430.03022.057-0.014-0.0140.0000.0000.0000.000
64A73ALA00.0470.03419.8130.0050.0050.0000.0000.0000.000
65A74SER00.041-0.03221.475-0.002-0.0020.0000.0000.0000.000
66A75THR0-0.049-0.03216.7680.0020.0020.0000.0000.0000.000
67A76ASP-1-0.883-0.94517.012-0.407-0.4070.0000.0000.0000.000
68A77LEU0-0.0040.00218.7610.0110.0110.0000.0000.0000.000
69A78LYS10.8640.94114.4710.4800.4800.0000.0000.0000.000
70A79TYR00.013-0.01812.632-0.020-0.0200.0000.0000.0000.000
71A80LEU00.0460.03418.5360.0180.0180.0000.0000.0000.000
72A81MET0-0.077-0.01621.6460.0260.0260.0000.0000.0000.000
73A82VAL0-0.0110.00517.0680.0110.0110.0000.0000.0000.000
74A83PRO00.0510.03520.0940.0180.0180.0000.0000.0000.000
75A84ALA00.0350.02022.8460.0170.0170.0000.0000.0000.000
76A85LEU0-0.026-0.00618.9340.0140.0140.0000.0000.0000.000
77A86GLN00.0270.00619.3370.0050.0050.0000.0000.0000.000
78A87GLY00.0240.03922.2970.0190.0190.0000.0000.0000.000
79A88ALA00.011-0.00224.9120.0120.0120.0000.0000.0000.000
80A89LEU0-0.014-0.01019.8000.0120.0120.0000.0000.0000.000
81A90THR0-0.025-0.02324.2040.0170.0170.0000.0000.0000.000
82A91MET0-0.059-0.02225.7880.0120.0120.0000.0000.0000.000
83A92LYS10.9050.96026.0380.0030.0030.0000.0000.0000.000
84A93GLN0-0.029-0.00324.8670.0020.0020.0000.0000.0000.000
85A94VAL0-0.037-0.01227.667-0.006-0.0060.0000.0000.0000.000
86A95ASN00.018-0.00929.6800.0070.0070.0000.0000.0000.000
87A96PRO00.0550.03231.886-0.003-0.0030.0000.0000.0000.000
88A97SER0-0.012-0.01234.763-0.003-0.0030.0000.0000.0000.000
89A98LYS10.8990.95530.823-0.056-0.0560.0000.0000.0000.000
90A99ARG10.8880.93432.450-0.012-0.0120.0000.0000.0000.000
91A100LEU00.0450.01033.520-0.004-0.0040.0000.0000.0000.000
92A101ASP-1-0.872-0.93129.2530.0260.0260.0000.0000.0000.000
93A102HIS00.0240.01428.454-0.001-0.0010.0000.0000.0000.000
94A103LEU00.0170.02829.965-0.006-0.0060.0000.0000.0000.000
95A104GLN0-0.065-0.04432.155-0.002-0.0020.0000.0000.0000.000
96A105ARG10.8530.92026.076-0.011-0.0110.0000.0000.0000.000
97A106ALA00.011-0.00127.762-0.008-0.0080.0000.0000.0000.000
98A107ARG10.8150.88928.8080.0140.0140.0000.0000.0000.000
99A108GLU-1-0.879-0.94028.032-0.019-0.0190.0000.0000.0000.000
100A109HIS00.0310.02722.639-0.017-0.0170.0000.0000.0000.000
101A110PHE00.0570.01926.556-0.011-0.0110.0000.0000.0000.000
102A111VAL0-0.026-0.00729.093-0.006-0.0060.0000.0000.0000.000
103A112HIS00.0260.02122.3040.0020.0020.0000.0000.0000.000
104A113PHE00.008-0.00924.953-0.010-0.0100.0000.0000.0000.000
105A114LEU00.000-0.00326.789-0.008-0.0080.0000.0000.0000.000
106A115THR0-0.081-0.04828.8260.0010.0010.0000.0000.0000.000
107A116GLN0-0.016-0.02124.709-0.008-0.0080.0000.0000.0000.000
108A117CYS0-0.098-0.02626.698-0.004-0.0040.0000.0000.0000.000
109A118HIS00.0480.02725.754-0.002-0.0020.0000.0000.0000.000
110A120TYR0-0.035-0.01331.3150.0040.0040.0000.0000.0000.000
111A121HIS10.9460.97833.8550.0920.0920.0000.0000.0000.000
112A145ALA00.028-0.00469.4700.0000.0000.0000.0000.0000.000
113A146TYR00.0420.01066.981-0.001-0.0010.0000.0000.0000.000
114A147PRO00.0560.04665.1020.0000.0000.0000.0000.0000.000
115A148ASN00.0400.00763.476-0.001-0.0010.0000.0000.0000.000
116A149LEU00.0610.02662.5070.0000.0000.0000.0000.0000.000
117A150VAL00.0220.02660.430-0.001-0.0010.0000.0000.0000.000
118A151ALA00.0350.02558.969-0.001-0.0010.0000.0000.0000.000
119A152MET0-0.032-0.01857.780-0.001-0.0010.0000.0000.0000.000
120A153ALA0-0.026-0.01357.281-0.001-0.0010.0000.0000.0000.000
121A154SER00.017-0.01155.402-0.001-0.0010.0000.0000.0000.000
122A155GLN0-0.015-0.02153.615-0.001-0.0010.0000.0000.0000.000
123A156ARG10.8800.95452.8480.0210.0210.0000.0000.0000.000
124A157GLN0-0.014-0.02751.5510.0000.0000.0000.0000.0000.000
125A158ALA00.1150.08749.383-0.002-0.0020.0000.0000.0000.000
126A159LYS10.9180.94247.1820.0220.0220.0000.0000.0000.000
127A160ILE0-0.0280.00246.4640.0000.0000.0000.0000.0000.000
128A161GLU-1-0.889-0.96745.644-0.038-0.0380.0000.0000.0000.000
129A162ARG10.9931.01242.3520.0320.0320.0000.0000.0000.000
130A163TYR0-0.012-0.00941.554-0.003-0.0030.0000.0000.0000.000
131A164LYS10.9330.97540.9200.0410.0410.0000.0000.0000.000
132A165GLN00.0470.03039.4620.0000.0000.0000.0000.0000.000
133A166LYS10.9440.99035.4130.0440.0440.0000.0000.0000.000
134A167LYS10.9810.98336.1010.0370.0370.0000.0000.0000.000
135A168GLU-1-0.903-0.97036.284-0.056-0.0560.0000.0000.0000.000
136A169VAL0-0.036-0.01732.464-0.005-0.0050.0000.0000.0000.000
137A170GLU-1-0.900-0.97131.700-0.069-0.0690.0000.0000.0000.000
138A171HIS00.0150.02131.522-0.003-0.0030.0000.0000.0000.000
139A172ARG10.8430.90732.0170.0890.0890.0000.0000.0000.000
140A173LEU00.012-0.00227.309-0.006-0.0060.0000.0000.0000.000
141A174SER0-0.059-0.02927.300-0.007-0.0070.0000.0000.0000.000
142A175ALA0-0.032-0.01528.195-0.002-0.0020.0000.0000.0000.000
143A176LEU00.006-0.00526.633-0.004-0.0040.0000.0000.0000.000
144A177LYS10.8750.96821.2110.1330.1330.0000.0000.0000.000
145A178SER00.0270.00422.305-0.021-0.0210.0000.0000.0000.000
146A179ALA00.0430.02121.608-0.020-0.0200.0000.0000.0000.000
147A180VAL0-0.009-0.00521.012-0.020-0.0200.0000.0000.0000.000
148A181GLU-1-0.918-0.97217.858-0.236-0.2360.0000.0000.0000.000
149A182SER0-0.067-0.02417.042-0.040-0.0400.0000.0000.0000.000
150A183GLY0-0.033-0.00218.391-0.023-0.0230.0000.0000.0000.000
151A184GLN0-0.052-0.04319.5050.0110.0110.0000.0000.0000.000
152A185ALA0-0.0420.00122.9850.0190.0190.0000.0000.0000.000
153A186ASP-1-0.768-0.84624.394-0.161-0.1610.0000.0000.0000.000
154A187ASP-1-0.806-0.91424.445-0.211-0.2110.0000.0000.0000.000
155A188GLU-1-0.898-0.94326.110-0.116-0.1160.0000.0000.0000.000
156A189ARG10.8130.86327.5150.1310.1310.0000.0000.0000.000
157A190VAL0-0.0190.00621.8470.0010.0010.0000.0000.0000.000
158A191ARG10.9060.94124.9000.1790.1790.0000.0000.0000.000
159A192GLU-1-0.852-0.91526.432-0.103-0.1030.0000.0000.0000.000
160A193TYR0-0.043-0.03422.2610.0150.0150.0000.0000.0000.000
161A194HIS00.0430.00720.2590.0170.0170.0000.0000.0000.000
162A195LEU00.0250.02425.2290.0090.0090.0000.0000.0000.000
163A196LEU0-0.054-0.02028.4590.0130.0130.0000.0000.0000.000
164A197HIS0-0.009-0.02424.5490.0120.0120.0000.0000.0000.000
165A198LEU00.0500.01825.0560.0100.0100.0000.0000.0000.000
166A199ARG10.9250.96528.0530.0880.0880.0000.0000.0000.000
167A200ARG10.8820.96728.7790.0830.0830.0000.0000.0000.000
168A201TRP00.0920.01824.3970.0090.0090.0000.0000.0000.000
169A202ILE0-0.0220.01129.3110.0060.0060.0000.0000.0000.000
170A203ALA0-0.030-0.01732.2760.0060.0060.0000.0000.0000.000
171A204VAL00.0490.03029.8310.0040.0040.0000.0000.0000.000
172A205SER00.015-0.01229.8110.0050.0050.0000.0000.0000.000
173A206LEU0-0.061-0.02331.9510.0050.0050.0000.0000.0000.000
174A207GLU-1-0.954-0.97635.634-0.037-0.0370.0000.0000.0000.000
175A208GLU-1-0.857-0.93431.260-0.019-0.0190.0000.0000.0000.000
176A209LEU0-0.072-0.03432.7960.0050.0050.0000.0000.0000.000
177A210GLU-1-0.970-0.97235.489-0.021-0.0210.0000.0000.0000.000
178A211SER00.002-0.01336.6040.0040.0040.0000.0000.0000.000
179A212ILE0-0.015-0.01632.0440.0050.0050.0000.0000.0000.000
180A213ASP-1-0.801-0.89236.536-0.016-0.0160.0000.0000.0000.000
181A214GLN0-0.071-0.03339.2970.0020.0020.0000.0000.0000.000
182A215GLU-1-0.799-0.87037.5600.0080.0080.0000.0000.0000.000
183A216ILE0-0.006-0.01535.2700.0040.0040.0000.0000.0000.000
184A217LYS10.8940.94439.4090.0090.0090.0000.0000.0000.000
185A218ILE00.0510.02943.0590.0010.0010.0000.0000.0000.000
186A219LEU0-0.0170.00238.0440.0020.0020.0000.0000.0000.000
187A220LYS10.8520.92538.979-0.002-0.0020.0000.0000.0000.000
188A221GLU-1-0.927-0.95643.0930.0050.0050.0000.0000.0000.000
189A222LYS10.8770.95443.137-0.009-0.0090.0000.0000.0000.000