Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4364N

Calculation Name: 2QC7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QC7

Chain ID: A

ChEMBL ID:

UniProt ID: P30040

Base Structure: X-ray

Registration Date: 2023-03-13

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2541997.528528
FMO2-HF: Nuclear repulsion 2454099.32762
FMO2-HF: Total energy -87898.200908
FMO2-MP2: Total energy -88156.128432


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:33:VAL)


Summations of interaction energy for fragment #1(A:33:VAL)
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.
-1.3840.583-0.013-1.006-0.9480.004
Interaction energy analysis for fragmet #1(A:33:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.007
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].
3A35THR0-0.054-0.0313.739-0.2961.671-0.013-1.006-0.9480.004
4A36LYS10.7670.8596.4650.4560.4560.0000.0000.0000.000
5A37GLY00.0320.0168.0540.1500.1500.0000.0000.0000.000
6A38ALA00.0020.0199.3620.0830.0830.0000.0000.0000.000
7A39LEU0-0.006-0.0129.971-0.162-0.1620.0000.0000.0000.000
8A40PRO0-0.022-0.0158.0910.1190.1190.0000.0000.0000.000
9A41LEU0-0.025-0.00410.7270.1480.1480.0000.0000.0000.000
10A42ASP-1-0.746-0.84313.305-0.567-0.5670.0000.0000.0000.000
11A43THR0-0.017-0.03115.4080.0200.0200.0000.0000.0000.000
12A44VAL0-0.031-0.00818.4580.0450.0450.0000.0000.0000.000
13A45THR0-0.067-0.08115.7150.0470.0470.0000.0000.0000.000
14A46PHE00.0220.00417.6710.0110.0110.0000.0000.0000.000
15A47TYR00.0340.01018.9650.0190.0190.0000.0000.0000.000
16A48LYS10.9100.96120.9680.2900.2900.0000.0000.0000.000
17A49VAL0-0.0040.01017.5940.0220.0220.0000.0000.0000.000
18A50ILE00.0400.02319.8440.0120.0120.0000.0000.0000.000
19A51PRO0-0.027-0.01822.8170.0160.0160.0000.0000.0000.000
20A52LYS10.8190.91122.6280.2660.2660.0000.0000.0000.000
21A53SER00.0210.02120.9080.0080.0080.0000.0000.0000.000
22A54LYS10.8210.91824.1360.1580.1580.0000.0000.0000.000
23A55PHE00.0200.00723.6050.0100.0100.0000.0000.0000.000
24A56VAL00.0160.00718.629-0.022-0.0220.0000.0000.0000.000
25A57LEU0-0.0240.00017.5920.0200.0200.0000.0000.0000.000
26A58VAL0-0.0040.00115.958-0.067-0.0670.0000.0000.0000.000
27A59LYS10.7440.8649.5190.9270.9270.0000.0000.0000.000
28A60PHE00.0320.00513.569-0.110-0.1100.0000.0000.0000.000
29A61ASP-1-0.750-0.88711.448-0.441-0.4410.0000.0000.0000.000
30A62THR00.0010.00010.397-0.032-0.0320.0000.0000.0000.000
31A63GLN0-0.034-0.0188.399-0.304-0.3040.0000.0000.0000.000
32A64TYR0-0.007-0.0055.077-0.075-0.0750.0000.0000.0000.000
33A65PRO00.0120.0296.1530.3100.3100.0000.0000.0000.000
34A66TYR0-0.034-0.0367.1610.0170.0170.0000.0000.0000.000
35A67GLY00.0450.0299.399-0.037-0.0370.0000.0000.0000.000
36A68GLU-1-0.851-0.94111.700-0.087-0.0870.0000.0000.0000.000
37A69LYS10.9140.95313.2460.0360.0360.0000.0000.0000.000
38A70GLN00.0410.0456.3370.2020.2020.0000.0000.0000.000
39A71ASP-1-0.857-0.93110.0010.0020.0020.0000.0000.0000.000
40A72GLU-1-0.775-0.88211.136-0.149-0.1490.0000.0000.0000.000
41A73PHE00.0240.0139.4640.0310.0310.0000.0000.0000.000
42A74LYS10.8140.8906.385-0.098-0.0980.0000.0000.0000.000
43A75ARG10.8100.87810.2290.0870.0870.0000.0000.0000.000
44A76LEU0-0.004-0.00913.8690.0260.0260.0000.0000.0000.000
45A77ALA00.0160.01411.2210.0240.0240.0000.0000.0000.000
46A78GLU-1-0.849-0.90610.311-0.201-0.2010.0000.0000.0000.000
47A79ASN0-0.051-0.03513.9540.0530.0530.0000.0000.0000.000
48A80SER0-0.011-0.00915.2170.0160.0160.0000.0000.0000.000
49A81ALA0-0.029-0.00815.4990.0150.0150.0000.0000.0000.000
50A82SER0-0.063-0.04417.5410.0380.0380.0000.0000.0000.000
51A83SER0-0.020-0.01820.9470.0180.0180.0000.0000.0000.000
52A84ASP-1-0.883-0.92821.910-0.204-0.2040.0000.0000.0000.000
53A85ASP-1-0.851-0.91623.080-0.195-0.1950.0000.0000.0000.000
54A86LEU0-0.056-0.03419.726-0.003-0.0030.0000.0000.0000.000
55A87LEU00.0090.01915.791-0.018-0.0180.0000.0000.0000.000
56A88VAL0-0.005-0.01614.0070.0220.0220.0000.0000.0000.000
57A89ALA00.0160.00613.250-0.077-0.0770.0000.0000.0000.000
58A90GLU-1-0.785-0.8727.623-1.747-1.7470.0000.0000.0000.000
59A91VAL0-0.021-0.00611.708-0.071-0.0710.0000.0000.0000.000
60A92GLY00.0480.0319.3630.0720.0720.0000.0000.0000.000
61A93ILE0-0.028-0.01010.3850.0290.0290.0000.0000.0000.000
62A94SER0-0.014-0.02212.784-0.003-0.0030.0000.0000.0000.000
63A95ASP-1-0.813-0.88914.522-0.116-0.1160.0000.0000.0000.000
64A96TYR0-0.019-0.02515.6750.0350.0350.0000.0000.0000.000
65A97GLY0-0.026-0.00216.566-0.019-0.0190.0000.0000.0000.000
66A98ASP-1-0.869-0.93017.494-0.125-0.1250.0000.0000.0000.000
67A99LYS10.8270.90317.5000.1960.1960.0000.0000.0000.000
68A100LEU0-0.0020.00211.851-0.020-0.0200.0000.0000.0000.000
69A101ASN00.035-0.00812.7760.0290.0290.0000.0000.0000.000
70A102MET00.0450.04316.558-0.002-0.0020.0000.0000.0000.000
71A103GLU-1-0.782-0.88119.408-0.243-0.2430.0000.0000.0000.000
72A104LEU0-0.048-0.02116.8330.0110.0110.0000.0000.0000.000
73A105SER0-0.024-0.01719.7000.0030.0030.0000.0000.0000.000
74A106GLU-1-0.881-0.94221.090-0.152-0.1520.0000.0000.0000.000
75A107LYS10.7680.88223.6040.1980.1980.0000.0000.0000.000
76A108TYR0-0.087-0.07521.9600.0020.0020.0000.0000.0000.000
77A109LYS10.8820.95824.5690.1340.1340.0000.0000.0000.000
78A110LEU0-0.0140.00319.4580.0030.0030.0000.0000.0000.000
79A111ASP-1-0.805-0.90621.903-0.120-0.1200.0000.0000.0000.000
80A112LYS10.8100.87417.5770.1030.1030.0000.0000.0000.000
81A113GLU-1-0.965-0.97419.043-0.073-0.0730.0000.0000.0000.000
82A114SER0-0.010-0.01921.1640.0110.0110.0000.0000.0000.000
83A115TYR0-0.074-0.00615.092-0.028-0.0280.0000.0000.0000.000
84A116PRO0-0.068-0.02714.0230.0300.0300.0000.0000.0000.000
85A117VAL00.0300.00015.9910.0350.0350.0000.0000.0000.000
86A118PHE0-0.029-0.02114.735-0.051-0.0510.0000.0000.0000.000
87A119TYR00.0340.01419.1850.0400.0400.0000.0000.0000.000
88A120LEU0-0.037-0.01220.747-0.034-0.0340.0000.0000.0000.000
89A121PHE00.0210.01320.7500.0220.0220.0000.0000.0000.000
90A122ARG10.8900.92424.1540.1440.1440.0000.0000.0000.000
91A123ASP-1-0.827-0.92027.093-0.151-0.1510.0000.0000.0000.000
92A124GLY00.0050.01326.8330.0090.0090.0000.0000.0000.000
93A125ASP-1-0.818-0.88227.847-0.159-0.1590.0000.0000.0000.000
94A126PHE00.0220.00423.461-0.021-0.0210.0000.0000.0000.000
95A127GLU-1-0.811-0.88727.075-0.171-0.1710.0000.0000.0000.000
96A128ASN0-0.123-0.06129.4650.0160.0160.0000.0000.0000.000
97A129PRO0-0.0100.02124.3260.0010.0010.0000.0000.0000.000
98A130VAL00.0160.00126.4130.0080.0080.0000.0000.0000.000
99A131PRO00.0240.02124.101-0.020-0.0200.0000.0000.0000.000
100A132TYR0-0.064-0.06220.9450.0190.0190.0000.0000.0000.000
101A133THR00.009-0.00323.176-0.006-0.0060.0000.0000.0000.000
102A134GLY00.0200.01724.0360.0170.0170.0000.0000.0000.000
103A135ALA00.0060.00022.583-0.008-0.0080.0000.0000.0000.000
104A136VAL00.0300.03016.895-0.006-0.0060.0000.0000.0000.000
105A137LYS10.9590.98517.7750.0670.0670.0000.0000.0000.000
106A138VAL00.0580.03816.664-0.003-0.0030.0000.0000.0000.000
107A139GLY0-0.015-0.01919.3150.0020.0020.0000.0000.0000.000
108A140ALA0-0.088-0.03522.2980.0140.0140.0000.0000.0000.000
109A141ILE00.0940.04717.7660.0050.0050.0000.0000.0000.000
110A142GLN00.0620.02620.473-0.013-0.0130.0000.0000.0000.000
111A143ARG10.8540.92222.9750.0950.0950.0000.0000.0000.000
112A144TRP00.0210.02022.7230.0010.0010.0000.0000.0000.000
113A145LEU00.0390.01820.4870.0020.0020.0000.0000.0000.000
114A146LYS10.8730.93525.2180.1370.1370.0000.0000.0000.000
115A147GLY0-0.033-0.01027.9490.0060.0060.0000.0000.0000.000
116A148GLN0-0.055-0.02927.3910.0070.0070.0000.0000.0000.000
117A149GLY0-0.0030.00629.288-0.001-0.0010.0000.0000.0000.000
118A150VAL0-0.024-0.00523.750-0.003-0.0030.0000.0000.0000.000
119A151TYR0-0.026-0.01926.7850.0160.0160.0000.0000.0000.000
120A152LEU0-0.033-0.02022.010-0.006-0.0060.0000.0000.0000.000
121A153GLY00.0200.01325.0480.0170.0170.0000.0000.0000.000
122A154MET0-0.035-0.02123.740-0.009-0.0090.0000.0000.0000.000
123A155PRO00.0400.01819.6330.0020.0020.0000.0000.0000.000
124A156GLY0-0.009-0.01221.5460.0180.0180.0000.0000.0000.000
125A157CYS0-0.063-0.01022.8050.0120.0120.0000.0000.0000.000
126A158LEU0-0.012-0.00724.571-0.011-0.0110.0000.0000.0000.000
127A159PRO00.0530.02227.9220.0080.0080.0000.0000.0000.000
128A160VAL00.0140.02331.1280.0050.0050.0000.0000.0000.000
129A161TYR0-0.039-0.06030.2530.0080.0080.0000.0000.0000.000
130A162ASP-1-0.790-0.87430.024-0.068-0.0680.0000.0000.0000.000
131A163ALA0-0.024-0.01433.0820.0050.0050.0000.0000.0000.000
132A164LEU00.0140.00335.3980.0040.0040.0000.0000.0000.000
133A165ALA0-0.014-0.00434.5910.0040.0040.0000.0000.0000.000
134A166GLY00.0310.01536.6750.0030.0030.0000.0000.0000.000
135A167GLU-1-0.934-0.98838.963-0.039-0.0390.0000.0000.0000.000
136A168PHE0-0.016-0.01839.4490.0030.0030.0000.0000.0000.000
137A169ILE0-0.052-0.01439.5310.0030.0030.0000.0000.0000.000
138A170ARG10.8820.95240.9190.0390.0390.0000.0000.0000.000
139A171ALA0-0.0180.00445.0400.0000.0000.0000.0000.0000.000
140A172SER00.0410.01947.0380.0020.0020.0000.0000.0000.000
141A173GLY00.0220.00847.721-0.001-0.0010.0000.0000.0000.000
142A174VAL0-0.062-0.03447.9490.0000.0000.0000.0000.0000.000
143A175GLU-1-0.787-0.91247.230-0.020-0.0200.0000.0000.0000.000
144A176ALA00.0560.05243.742-0.002-0.0020.0000.0000.0000.000
145A177ARG10.9930.97842.7950.0130.0130.0000.0000.0000.000
146A178GLN0-0.062-0.03243.459-0.001-0.0010.0000.0000.0000.000
147A179ALA00.0050.00541.084-0.002-0.0020.0000.0000.0000.000
148A180LEU00.014-0.00437.243-0.003-0.0030.0000.0000.0000.000
149A181LEU0-0.010-0.00738.9500.0000.0000.0000.0000.0000.000
150A182LYS10.8420.92438.1710.0410.0410.0000.0000.0000.000
151A183GLN0-0.047-0.02135.200-0.002-0.0020.0000.0000.0000.000
152A184GLY00.0160.00734.565-0.003-0.0030.0000.0000.0000.000
153A185GLN0-0.016-0.01435.068-0.003-0.0030.0000.0000.0000.000
154A186ASP-1-0.809-0.86932.223-0.066-0.0660.0000.0000.0000.000
155A187ASN0-0.028-0.04229.170-0.002-0.0020.0000.0000.0000.000
156A188LEU0-0.068-0.02430.057-0.003-0.0030.0000.0000.0000.000
157A189SER0-0.017-0.01230.500-0.003-0.0030.0000.0000.0000.000
158A190SER0-0.030-0.01126.964-0.005-0.0050.0000.0000.0000.000
159A191VAL00.0270.01923.8680.0000.0000.0000.0000.0000.000
160A192LYS10.9400.96518.0240.1910.1910.0000.0000.0000.000
161A193GLU-1-0.714-0.84320.586-0.059-0.0590.0000.0000.0000.000
162A194THR0-0.125-0.07116.7360.0150.0150.0000.0000.0000.000
163A195GLN00.0520.01419.3110.0040.0040.0000.0000.0000.000
164A196LYS10.8760.94922.2360.0690.0690.0000.0000.0000.000
165A197LYS10.8420.90918.1550.0340.0340.0000.0000.0000.000
166A198TRP0-0.034-0.02517.9340.0010.0010.0000.0000.0000.000
167A199ALA00.0710.04225.0790.0040.0040.0000.0000.0000.000
168A200GLU-1-0.836-0.93427.234-0.032-0.0320.0000.0000.0000.000
169A201GLN0-0.0250.00524.5590.0080.0080.0000.0000.0000.000
170A202TYR00.015-0.02427.8700.0040.0040.0000.0000.0000.000
171A203LEU00.0300.01631.6630.0040.0040.0000.0000.0000.000
172A204LYS10.9110.94630.4620.0170.0170.0000.0000.0000.000
173A205ILE0-0.042-0.00830.3680.0040.0040.0000.0000.0000.000
174A206MET0-0.0160.00334.4080.0010.0010.0000.0000.0000.000
175A207GLY00.0130.00336.9160.0020.0020.0000.0000.0000.000
176A208LYS10.9170.95831.7080.0010.0010.0000.0000.0000.000
177A209ILE0-0.067-0.01437.4180.0010.0010.0000.0000.0000.000
178A210LEU0-0.059-0.02640.4680.0000.0000.0000.0000.0000.000
179A211ASP-1-0.936-0.95140.0290.0000.0000.0000.0000.0000.000
180A212GLN0-0.068-0.04638.4390.0020.0020.0000.0000.0000.000
181A213GLY00.0530.03643.0680.0010.0010.0000.0000.0000.000
182A214GLU-1-0.891-0.96742.112-0.014-0.0140.0000.0000.0000.000
183A215ASP-1-0.872-0.92341.299-0.013-0.0130.0000.0000.0000.000
184A216PHE0-0.0080.02434.4200.0010.0010.0000.0000.0000.000
185A217PRO00.0390.02035.5690.0010.0010.0000.0000.0000.000
186A218ALA00.0530.02735.1960.0010.0010.0000.0000.0000.000
187A219SER0-0.024-0.00936.3660.0020.0020.0000.0000.0000.000
188A220GLU-1-0.749-0.86431.6610.0100.0100.0000.0000.0000.000
189A221MET0-0.0020.00431.3600.0020.0020.0000.0000.0000.000
190A222THR0-0.045-0.03031.5340.0020.0020.0000.0000.0000.000
191A223ARG10.8430.90129.123-0.013-0.0130.0000.0000.0000.000
192A224ILE00.005-0.01026.3240.0070.0070.0000.0000.0000.000
193A225ALA00.0300.01827.5420.0040.0040.0000.0000.0000.000
194A226ARG10.9000.95428.617-0.009-0.0090.0000.0000.0000.000
195A227LEU0-0.005-0.00325.6990.0070.0070.0000.0000.0000.000
196A228ILE00.0120.00722.9660.0120.0120.0000.0000.0000.000
197A229GLU-1-0.900-0.94724.3910.0180.0180.0000.0000.0000.000
198A230LYS10.8010.89827.051-0.033-0.0330.0000.0000.0000.000
199A231ASN00.0250.02420.5410.0030.0030.0000.0000.0000.000
200A232LYS10.9530.99021.742-0.080-0.0800.0000.0000.0000.000
201A233MET0-0.058-0.01919.447-0.002-0.0020.0000.0000.0000.000
202A234SER00.0500.02814.005-0.009-0.0090.0000.0000.0000.000
203A235ASP-1-0.770-0.89313.226-0.027-0.0270.0000.0000.0000.000
204A236GLY00.0380.02613.551-0.034-0.0340.0000.0000.0000.000
205A237LYS10.9410.96514.293-0.174-0.1740.0000.0000.0000.000
206A238LYS10.9160.95317.555-0.049-0.0490.0000.0000.0000.000
207A239GLU-1-0.778-0.87016.015-0.110-0.1100.0000.0000.0000.000
208A240GLU-1-0.838-0.90317.509-0.025-0.0250.0000.0000.0000.000
209A241LEU0-0.027-0.01919.751-0.004-0.0040.0000.0000.0000.000
210A242GLN0-0.033-0.01720.7300.0050.0050.0000.0000.0000.000
211A243LYS10.8760.92517.0750.1240.1240.0000.0000.0000.000
212A244SER0-0.044-0.02222.8430.0010.0010.0000.0000.0000.000
213A245LEU0-0.023-0.02025.5650.0010.0010.0000.0000.0000.000
214A246ASN00.007-0.00323.1710.0060.0060.0000.0000.0000.000
215A247ILE00.0020.02225.1220.0010.0010.0000.0000.0000.000
216A248LEU0-0.024-0.02228.7040.0020.0020.0000.0000.0000.000
217A249THR0-0.077-0.05830.0040.0010.0010.0000.0000.0000.000
218A250ALA0-0.0100.01532.0640.0010.0010.0000.0000.0000.000
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