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: 9GNM2

Calculation Name: 3QC1-A-Xray318

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 193
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2066992.060108
FMO2-HF: Nuclear repulsion 1989651.743694
FMO2-HF: Total energy -77340.316414
FMO2-MP2: Total energy -77566.724336


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:9:ACE )


Summations of interaction energy for fragment #1(A:9: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.
1.6532.448-0.005-0.32-0.4710
Interaction energy analysis for fragmet #1(A:9:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.004
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].
3A11PRO 00.0420.0243.8251.1331.928-0.005-0.320-0.4710.000
4A12ARG 10.9790.9996.5290.5070.5070.0000.0000.0000.000
5A13LEU 00.0870.0518.8740.1050.1050.0000.0000.0000.000
6A14PRO 0-0.063-0.03311.2430.0360.0360.0000.0000.0000.000
7A15GLU -1-0.872-0.9396.419-0.208-0.2080.0000.0000.0000.000
8A16LEU 0-0.021-0.00210.2310.0260.0260.0000.0000.0000.000
9A17PHE 00.0190.00312.2190.0350.0350.0000.0000.0000.000
10A18GLU -1-0.823-0.92713.6530.0200.0200.0000.0000.0000.000
11A19THR 0-0.071-0.03111.4410.0380.0380.0000.0000.0000.000
12A20SER 00.0070.00114.1030.0090.0090.0000.0000.0000.000
13A21LYS 10.8690.94416.8210.0120.0120.0000.0000.0000.000
14A22LYS 10.9700.97614.907-0.080-0.0800.0000.0000.0000.000
15A23LEU 0-0.023-0.01015.8330.0040.0040.0000.0000.0000.000
16A24LEU 0-0.0050.00019.1920.0010.0010.0000.0000.0000.000
17A25GLU -1-0.848-0.92722.1600.0170.0170.0000.0000.0000.000
18A26ASP -1-0.874-0.93220.0770.0370.0370.0000.0000.0000.000
19A27VAL 0-0.055-0.03722.8660.0010.0010.0000.0000.0000.000
20A28GLU -1-0.987-1.01125.241-0.016-0.0160.0000.0000.0000.000
21A29VAL 0-0.054-0.01126.0660.0010.0010.0000.0000.0000.000
22A30ALA 0-0.053-0.01326.6000.0030.0030.0000.0000.0000.000
23A31THR 0-0.015-0.00628.533-0.002-0.0020.0000.0000.0000.000
24A32GLU -1-0.939-0.96427.8670.0120.0120.0000.0000.0000.000
25A33PRO 00.0410.01331.845-0.003-0.0030.0000.0000.0000.000
26A34THR 00.0840.04729.8460.0000.0000.0000.0000.0000.000
27A35GLY 0-0.0070.00429.319-0.004-0.0040.0000.0000.0000.000
28A36SER 0-0.048-0.04428.5500.0000.0000.0000.0000.0000.000
29A37ARG 10.8980.94023.9160.0260.0260.0000.0000.0000.000
30A38THR 00.0300.01823.501-0.006-0.0060.0000.0000.0000.000
31A39ILE 00.0540.03522.950-0.004-0.0040.0000.0000.0000.000
32A40GLN 00.006-0.02023.904-0.011-0.0110.0000.0000.0000.000
33A41ASP -1-0.850-0.90220.354-0.041-0.0410.0000.0000.0000.000
34A42LYS 10.8450.91219.249-0.034-0.0340.0000.0000.0000.000
35A43VAL 00.0000.01019.785-0.011-0.0110.0000.0000.0000.000
36A44SER 0-0.013-0.02620.965-0.012-0.0120.0000.0000.0000.000
37A45LYS 10.9570.99011.8350.0490.0490.0000.0000.0000.000
38A46GLY 00.0220.00416.604-0.025-0.0250.0000.0000.0000.000
39A47LEU 0-0.007-0.00618.262-0.014-0.0140.0000.0000.0000.000
40A48GLU -1-0.934-0.95415.039-0.263-0.2630.0000.0000.0000.000
41A49LEU 0-0.039-0.03512.075-0.037-0.0370.0000.0000.0000.000
42A50LEU 0-0.0010.00114.981-0.024-0.0240.0000.0000.0000.000
43A51GLU -1-0.941-0.94517.864-0.184-0.1840.0000.0000.0000.000
44A52LYS 10.9280.97211.4830.5660.5660.0000.0000.0000.000
45A53ALA 00.001-0.01915.184-0.018-0.0180.0000.0000.0000.000
46A54ALA 00.0340.01415.9560.0040.0040.0000.0000.0000.000
47A55GLY 00.0180.00518.4250.0070.0070.0000.0000.0000.000
48A56MET 0-0.089-0.05910.891-0.001-0.0010.0000.0000.0000.000
49A57LEU 0-0.017-0.01317.0540.0150.0150.0000.0000.0000.000
50A58SER 0-0.0240.00019.7330.0220.0220.0000.0000.0000.000
51A59GLN 0-0.069-0.02518.3400.0050.0050.0000.0000.0000.000
52A60LEU 0-0.093-0.04716.4360.0070.0070.0000.0000.0000.000
53A61ASP -1-0.865-0.92520.511-0.088-0.0880.0000.0000.0000.000
54A62LEU 0-0.022-0.02419.8590.0060.0060.0000.0000.0000.000
55A63PHE 0-0.038-0.03323.2240.0080.0080.0000.0000.0000.000
56A64SER 0-0.0090.03027.4600.0070.0070.0000.0000.0000.000
57A65ARG 10.8860.93929.2750.0500.0500.0000.0000.0000.000
58A66ASN 0-0.0110.02332.227-0.001-0.0010.0000.0000.0000.000
59A67GLU -1-0.970-1.01233.779-0.037-0.0370.0000.0000.0000.000
60A68ASP -1-0.889-0.94832.358-0.044-0.0440.0000.0000.0000.000
61A69LEU 0-0.019-0.02230.6040.0020.0020.0000.0000.0000.000
62A70GLU -1-0.930-0.99330.837-0.019-0.0190.0000.0000.0000.000
63A71GLU -1-0.940-0.96631.063-0.026-0.0260.0000.0000.0000.000
64A72ILE 0-0.0440.02925.469-0.005-0.0050.0000.0000.0000.000
65A73ALA 00.0440.03223.0270.0090.0090.0000.0000.0000.000
66A74SER 00.043-0.03124.471-0.005-0.0050.0000.0000.0000.000
67A75THR 0-0.050-0.03319.2690.0080.0080.0000.0000.0000.000
68A76ASP -1-0.887-0.94820.316-0.085-0.0850.0000.0000.0000.000
69A77LEU 0-0.0040.00421.834-0.006-0.0060.0000.0000.0000.000
70A78LYS 10.8700.94316.2740.0250.0250.0000.0000.0000.000
71A79TYR 00.008-0.02115.152-0.005-0.0050.0000.0000.0000.000
72A80LEU 00.0500.03721.260-0.007-0.0070.0000.0000.0000.000
73A81MET 0-0.078-0.01523.7220.0040.0040.0000.0000.0000.000
74A82VAL 0-0.0130.00319.6170.0020.0020.0000.0000.0000.000
75A83PRO 00.0520.03622.3950.0000.0000.0000.0000.0000.000
76A84ALA 00.0350.02225.3800.0040.0040.0000.0000.0000.000
77A85LEU 0-0.026-0.00720.4890.0050.0050.0000.0000.0000.000
78A86GLN 00.0300.00721.8630.0050.0050.0000.0000.0000.000
79A87GLY 00.0230.03824.1900.0010.0010.0000.0000.0000.000
80A88ALA 00.0150.00026.2060.0030.0030.0000.0000.0000.000
81A89LEU 0-0.018-0.01220.9170.0050.0050.0000.0000.0000.000
82A90THR 0-0.027-0.02525.333-0.001-0.0010.0000.0000.0000.000
83A91MET 0-0.060-0.02127.3730.0020.0020.0000.0000.0000.000
84A92LYS 10.9090.96126.8440.0220.0220.0000.0000.0000.000
85A93GLN 0-0.028-0.00326.3690.0030.0030.0000.0000.0000.000
86A94VAL 0-0.039-0.01328.7020.0040.0040.0000.0000.0000.000
87A95ASN 00.035-0.00530.9960.0030.0030.0000.0000.0000.000
88A96PRO 00.0580.03533.049-0.002-0.0020.0000.0000.0000.000
89A97SER 0-0.047-0.02935.879-0.001-0.0010.0000.0000.0000.000
90A98LYS 10.9080.95932.6730.0470.0470.0000.0000.0000.000
91A99ARG 10.8880.93533.9030.0280.0280.0000.0000.0000.000
92A100LEU 00.0460.01035.338-0.001-0.0010.0000.0000.0000.000
93A101ASP -1-0.872-0.93231.499-0.067-0.0670.0000.0000.0000.000
94A102HIS 00.0270.01530.2840.0000.0000.0000.0000.0000.000
95A103LEU 00.0160.02732.028-0.002-0.0020.0000.0000.0000.000
96A104GLN 0-0.066-0.04534.3290.0000.0000.0000.0000.0000.000
97A105ARG 10.8510.91928.5390.0670.0670.0000.0000.0000.000
98A106ALA 00.011-0.00129.869-0.003-0.0030.0000.0000.0000.000
99A107ARG 10.8170.89030.9160.0410.0410.0000.0000.0000.000
100A108GLU -1-0.877-0.93931.042-0.070-0.0700.0000.0000.0000.000
101A109HIS 00.0280.02625.387-0.001-0.0010.0000.0000.0000.000
102A110PHE 00.0570.01929.1470.0000.0000.0000.0000.0000.000
103A111VAL 0-0.024-0.00631.4290.0030.0030.0000.0000.0000.000
104A112HIS 00.0210.01926.0090.0050.0050.0000.0000.0000.000
105A113PHE 00.011-0.01027.5590.0000.0000.0000.0000.0000.000
106A114LEU 00.001-0.00129.6730.0020.0020.0000.0000.0000.000
107A115THR 0-0.081-0.04732.6250.0020.0020.0000.0000.0000.000
108A116GLN 0-0.024-0.02628.377-0.005-0.0050.0000.0000.0000.000
109A119CYS 0-0.091-0.02529.7030.0060.0060.0000.0000.0000.000
110A118HIS 00.0360.02029.7080.0020.0020.0000.0000.0000.000
111A120TYR 0-0.010-0.01034.0670.0030.0030.0000.0000.0000.000
112A121HIS 0-0.029-0.01336.5990.0010.0010.0000.0000.0000.000
113A122NME 0-0.0090.00435.3880.0020.0020.0000.0000.0000.000
114A144ACE 00.0330.00875.6110.0000.0000.0000.0000.0000.000
115A145ALA 00.007-0.01470.8220.0000.0000.0000.0000.0000.000
116A146TYR 00.0300.01368.4550.0000.0000.0000.0000.0000.000
117A147PRO 00.0550.04566.6940.0000.0000.0000.0000.0000.000
118A148ASN 00.0430.00865.0280.0000.0000.0000.0000.0000.000
119A149LEU 00.0630.02763.9610.0000.0000.0000.0000.0000.000
120A150VAL 00.0180.02562.0030.0000.0000.0000.0000.0000.000
121A151ALA 00.0370.02660.5230.0000.0000.0000.0000.0000.000
122A152MET 0-0.033-0.01859.2600.0000.0000.0000.0000.0000.000
123A153ALA 0-0.024-0.01258.6410.0000.0000.0000.0000.0000.000
124A154SER 00.017-0.01156.8670.0000.0000.0000.0000.0000.000
125A155GLN 0-0.014-0.02155.0950.0000.0000.0000.0000.0000.000
126A156ARG 10.8790.95354.2440.0000.0000.0000.0000.0000.000
127A157GLN 0-0.016-0.02852.8120.0000.0000.0000.0000.0000.000
128A158ALA 00.1150.08850.8390.0000.0000.0000.0000.0000.000
129A159LYS 10.9200.94448.4240.0030.0030.0000.0000.0000.000
130A160ILE 0-0.0310.00047.7040.0000.0000.0000.0000.0000.000
131A161GLU -1-0.889-0.96746.9310.0010.0010.0000.0000.0000.000
132A162ARG 10.9971.01543.7760.0060.0060.0000.0000.0000.000
133A163TYR 0-0.015-0.01042.5000.0000.0000.0000.0000.0000.000
134A164LYS 10.9320.97442.064-0.003-0.0030.0000.0000.0000.000
135A165GLN 00.0500.03240.9010.0010.0010.0000.0000.0000.000
136A166LYS 10.9490.99336.5520.0030.0030.0000.0000.0000.000
137A167LYS 10.9750.98037.270-0.009-0.0090.0000.0000.0000.000
138A168GLU -1-0.903-0.97137.3240.0110.0110.0000.0000.0000.000
139A169VAL 0-0.030-0.01333.8470.0020.0020.0000.0000.0000.000
140A170GLU -1-0.901-0.97132.8100.0030.0030.0000.0000.0000.000
141A171HIS 00.0120.01832.5030.0030.0030.0000.0000.0000.000
142A172ARG 10.8440.90733.298-0.007-0.0070.0000.0000.0000.000
143A173LEU 00.0160.00128.6170.0030.0030.0000.0000.0000.000
144A174SER 0-0.061-0.03028.3390.0030.0030.0000.0000.0000.000
145A175ALA 0-0.036-0.01728.9260.0060.0060.0000.0000.0000.000
146A176LEU 00.008-0.00527.8450.0040.0040.0000.0000.0000.000
147A177LYS 10.8750.96821.980-0.029-0.0290.0000.0000.0000.000
148A178SER 00.0250.00322.9250.0050.0050.0000.0000.0000.000
149A179ALA 00.0410.02122.3680.0070.0070.0000.0000.0000.000
150A180VAL 0-0.005-0.00322.4170.0030.0030.0000.0000.0000.000
151A181GLU -1-0.922-0.97218.7600.0480.0480.0000.0000.0000.000
152A182SER 0-0.066-0.02518.0230.0190.0190.0000.0000.0000.000
153A183GLY 0-0.035-0.00219.0640.0120.0120.0000.0000.0000.000
154A184GLN 0-0.056-0.04620.423-0.002-0.0020.0000.0000.0000.000
155A185ALA 0-0.0430.00023.716-0.004-0.0040.0000.0000.0000.000
156A186ASP -1-0.769-0.84825.4770.0220.0220.0000.0000.0000.000
157A187ASP -1-0.808-0.91526.650-0.003-0.0030.0000.0000.0000.000
158A188GLU -1-0.893-0.94027.9200.0070.0070.0000.0000.0000.000
159A189ARG 10.8110.86228.883-0.020-0.0200.0000.0000.0000.000
160A190VAL 0-0.0210.00423.721-0.002-0.0020.0000.0000.0000.000
161A191ARG 10.9020.94026.5910.0160.0160.0000.0000.0000.000
162A192GLU -1-0.843-0.91128.5830.0050.0050.0000.0000.0000.000
163A193TYR 0-0.042-0.03423.639-0.001-0.0010.0000.0000.0000.000
164A194HIS 00.0330.00321.939-0.006-0.0060.0000.0000.0000.000
165A195LEU 00.0310.02727.025-0.005-0.0050.0000.0000.0000.000
166A196LEU 0-0.047-0.01630.485-0.001-0.0010.0000.0000.0000.000
167A197HIS 0-0.019-0.02925.926-0.002-0.0020.0000.0000.0000.000
168A198LEU 00.0520.01727.297-0.002-0.0020.0000.0000.0000.000
169A199ARG 10.9400.97729.9200.0090.0090.0000.0000.0000.000
170A200ARG 10.8640.96129.8750.0010.0010.0000.0000.0000.000
171A201TRP 00.0810.01125.917-0.001-0.0010.0000.0000.0000.000
172A202ILE 0-0.0030.01931.000-0.003-0.0030.0000.0000.0000.000
173A203ALA 0-0.028-0.01534.116-0.001-0.0010.0000.0000.0000.000
174A204VAL 00.0440.02831.221-0.001-0.0010.0000.0000.0000.000
175A205SER 00.013-0.01431.648-0.003-0.0030.0000.0000.0000.000
176A206LEU 0-0.055-0.02033.744-0.001-0.0010.0000.0000.0000.000
177A207GLU -1-0.958-0.97737.115-0.015-0.0150.0000.0000.0000.000
178A208GLU -1-0.855-0.93332.666-0.028-0.0280.0000.0000.0000.000
179A209LEU 0-0.076-0.03535.187-0.001-0.0010.0000.0000.0000.000
180A210GLU -1-0.966-0.97137.413-0.019-0.0190.0000.0000.0000.000
181A211SER 00.000-0.01338.0280.0010.0010.0000.0000.0000.000
182A212ILE 0-0.018-0.01833.7850.0000.0000.0000.0000.0000.000
183A213ASP -1-0.801-0.89238.310-0.035-0.0350.0000.0000.0000.000
184A214GLN 0-0.070-0.03341.3200.0010.0010.0000.0000.0000.000
185A215GLU -1-0.796-0.86938.954-0.027-0.0270.0000.0000.0000.000
186A216ILE 0-0.009-0.01737.495-0.001-0.0010.0000.0000.0000.000
187A217LYS 10.8930.94441.4600.0250.0250.0000.0000.0000.000
188A218ILE 00.0500.02944.9680.0000.0000.0000.0000.0000.000
189A219LEU 0-0.0170.00339.9320.0000.0000.0000.0000.0000.000
190A220LYS 10.8520.92541.6350.0370.0370.0000.0000.0000.000
191A221GLU -1-0.924-0.96045.387-0.021-0.0210.0000.0000.0000.000
192A222LYS 10.8250.92045.7470.0320.0320.0000.0000.0000.000
193A223NME 00.0430.03549.7700.0010.0010.0000.0000.0000.000