FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 49G6N

Calculation Name: 2C7Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C7Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q56WD9

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 390
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6320250.874745
FMO2-HF: Nuclear repulsion 6174884.711081
FMO2-HF: Total energy -145366.163664
FMO2-MP2: Total energy -145784.04402


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:38:ASP)


Summations of interaction energy for fragment #1(A:38:ASP)
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.
-99.012-102.3643.4674.755-4.870.018
Interaction energy analysis for fragmet #1(A:38:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.843 / q_NPA : -0.889
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].
3A40ALA0-0.060-0.0452.995-6.979-13.9210.3627.590-1.0100.014
4A41ALA0-0.021-0.0014.940-0.137-0.052-0.001-0.003-0.0810.000
5A42TYR00.010-0.0078.402-2.094-2.0940.0000.0000.0000.000
6A43GLN00.0370.0136.555-0.141-0.1410.0000.0000.0000.000
7A44ARG10.7910.9069.600-18.517-18.5170.0000.0000.0000.000
8A45THR00.046-0.00810.5450.7240.7240.0000.0000.0000.000
9A46SER0-0.086-0.04213.113-1.655-1.6550.0000.0000.0000.000
10A47LEU00.0770.03414.1120.5690.5690.0000.0000.0000.000
11A48TYR0-0.014-0.02217.794-0.345-0.3450.0000.0000.0000.000
12A49GLY00.0080.01119.805-0.754-0.7540.0000.0000.0000.000
13A50ASP-1-0.750-0.86621.30213.14713.1470.0000.0000.0000.000
14A51ASP-1-0.861-0.90524.19010.46510.4650.0000.0000.0000.000
15A52VAL0-0.0210.00623.679-0.414-0.4140.0000.0000.0000.000
16A53VAL00.001-0.00224.8250.3710.3710.0000.0000.0000.000
17A54ILE0-0.041-0.01323.347-0.081-0.0810.0000.0000.0000.000
18A55VAL00.0220.00327.592-0.052-0.0520.0000.0000.0000.000
19A56ALA00.0310.02030.367-0.262-0.2620.0000.0000.0000.000
20A57ALA00.0080.00426.4860.2710.2710.0000.0000.0000.000
21A58HIS0-0.051-0.01228.597-0.296-0.2960.0000.0000.0000.000
22A59ARG10.7760.83627.140-9.736-9.7360.0000.0000.0000.000
23A60THR00.0300.01929.972-0.217-0.2170.0000.0000.0000.000
24A61PRO0-0.0250.00130.9770.2830.2830.0000.0000.0000.000
25A62LEU0-0.041-0.00626.5040.0390.0390.0000.0000.0000.000
26A63CYS0-0.0090.00331.099-0.241-0.2410.0000.0000.0000.000
27A64LYS10.8540.95528.798-9.652-9.6520.0000.0000.0000.000
28A65SER00.041-0.02031.655-0.165-0.1650.0000.0000.0000.000
29A66LYS10.8060.92333.562-8.796-8.7960.0000.0000.0000.000
30A67ARG10.9100.93735.625-7.636-7.6360.0000.0000.0000.000
31A68GLY00.0680.05236.306-0.167-0.1670.0000.0000.0000.000
32A69ASN0-0.048-0.07537.343-0.265-0.2650.0000.0000.0000.000
33A70PHE00.0580.01033.525-0.128-0.1280.0000.0000.0000.000
34A71LYS10.7380.85738.168-6.915-6.9150.0000.0000.0000.000
35A72ASP-1-0.740-0.84339.6756.8266.8260.0000.0000.0000.000
36A73THR00.0000.03039.022-0.165-0.1650.0000.0000.0000.000
37A74TYR00.0200.04039.1180.1240.1240.0000.0000.0000.000
38A75PRO0-0.004-0.01634.5780.0960.0960.0000.0000.0000.000
39A76ASP-1-0.795-0.90135.5197.7607.7600.0000.0000.0000.000
40A77ASP-1-0.838-0.92737.7617.2347.2340.0000.0000.0000.000
41A78LEU0-0.080-0.03033.9280.0400.0400.0000.0000.0000.000
42A79LEU0-0.003-0.01431.1170.1470.1470.0000.0000.0000.000
43A80ALA00.0190.02634.3390.0730.0730.0000.0000.0000.000
44A81PRO0-0.017-0.00636.679-0.044-0.0440.0000.0000.0000.000
45A82VAL0-0.019-0.01131.0040.0180.0180.0000.0000.0000.000
46A83LEU0-0.012-0.01431.9690.1340.1340.0000.0000.0000.000
47A84ARG10.8830.95734.752-7.369-7.3690.0000.0000.0000.000
48A85ALA00.0400.02335.314-0.054-0.0540.0000.0000.0000.000
49A86LEU0-0.074-0.03530.8980.0420.0420.0000.0000.0000.000
50A87ILE00.0160.03335.0080.0200.0200.0000.0000.0000.000
51A88GLU-1-0.888-0.96838.3987.3367.3360.0000.0000.0000.000
52A89LYS10.8410.92634.804-8.586-8.5860.0000.0000.0000.000
53A90THR0-0.040-0.04135.3350.0750.0750.0000.0000.0000.000
54A91ASN0-0.051-0.02338.654-0.183-0.1830.0000.0000.0000.000
55A92LEU0-0.0150.01936.005-0.098-0.0980.0000.0000.0000.000
56A93ASN00.0700.04740.183-0.030-0.0300.0000.0000.0000.000
57A94PRO00.0380.00339.1750.1830.1830.0000.0000.0000.000
58A95SER0-0.042-0.04838.6770.1620.1620.0000.0000.0000.000
59A96GLU-1-0.838-0.92638.0797.7697.7690.0000.0000.0000.000
60A97VAL0-0.072-0.02033.0580.2670.2670.0000.0000.0000.000
61A98GLY00.0430.01733.808-0.138-0.1380.0000.0000.0000.000
62A99ASP-1-0.778-0.83528.52310.54410.5440.0000.0000.0000.000
63A100ILE00.0180.01930.2990.1030.1030.0000.0000.0000.000
64A101VAL0-0.0210.01424.488-0.044-0.0440.0000.0000.0000.000
65A102VAL00.0100.00026.8790.2010.2010.0000.0000.0000.000
66A103GLY00.007-0.02123.9850.1250.1250.0000.0000.0000.000
67A104THR0-0.075-0.03024.784-0.265-0.2650.0000.0000.0000.000
68A105VAL0-0.051-0.04423.1920.1950.1950.0000.0000.0000.000
69A106LEU0-0.015-0.02426.503-0.135-0.1350.0000.0000.0000.000
70A107ALA00.0340.03329.613-0.237-0.2370.0000.0000.0000.000
71A108PRO00.0090.01530.8380.3510.3510.0000.0000.0000.000
72A109GLY00.0460.00731.540-0.198-0.1980.0000.0000.0000.000
73A110SER00.0240.00532.3230.1830.1830.0000.0000.0000.000
74A111GLN0-0.007-0.01234.879-0.042-0.0420.0000.0000.0000.000
75A112ARG10.8030.89925.250-10.845-10.8450.0000.0000.0000.000
76A113ALA00.0520.02532.1070.0340.0340.0000.0000.0000.000
77A114SER00.0260.00833.596-0.075-0.0750.0000.0000.0000.000
78A115GLU-1-0.772-0.86334.3998.4138.4130.0000.0000.0000.000
79A116CYS0-0.012-0.01031.4660.0430.0430.0000.0000.0000.000
80A117ARG10.8760.93133.708-8.684-8.6840.0000.0000.0000.000
81A118MET0-0.0030.01636.950-0.111-0.1110.0000.0000.0000.000
82A119ALA00.021-0.00235.561-0.132-0.1320.0000.0000.0000.000
83A120ALA0-0.005-0.00835.687-0.067-0.0670.0000.0000.0000.000
84A121PHE00.0250.02237.490-0.098-0.0980.0000.0000.0000.000
85A122TYR00.0220.00941.022-0.177-0.1770.0000.0000.0000.000
86A123ALA0-0.059-0.02838.019-0.069-0.0690.0000.0000.0000.000
87A124GLY0-0.0030.00839.980-0.004-0.0040.0000.0000.0000.000
88A125PHE0-0.047-0.02836.183-0.019-0.0190.0000.0000.0000.000
89A126PRO00.0160.01340.307-0.074-0.0740.0000.0000.0000.000
90A127GLU-1-0.919-0.97840.4917.0137.0130.0000.0000.0000.000
91A128THR0-0.031-0.01540.1880.0730.0730.0000.0000.0000.000
92A129VAL0-0.0370.00535.5820.1600.1600.0000.0000.0000.000
93A130ALA00.0150.00633.5840.0120.0120.0000.0000.0000.000
94A131VAL00.0110.01932.5950.2990.2990.0000.0000.0000.000
95A132ARG10.7940.85425.758-11.001-11.0010.0000.0000.0000.000
96A133THR00.0400.01427.587-0.087-0.0870.0000.0000.0000.000
97A134VAL0-0.038-0.01821.0090.1730.1730.0000.0000.0000.000
98A135ASN0-0.0160.00723.400-0.273-0.2730.0000.0000.0000.000
99A136ARG10.8780.91315.303-15.778-15.7780.0000.0000.0000.000
100A137GLN00.0510.04622.101-0.002-0.0020.0000.0000.0000.000
101A138CYS0-0.017-0.00520.558-0.086-0.0860.0000.0000.0000.000
102A139SER0-0.039-0.01818.3400.7020.7020.0000.0000.0000.000
103A140SER00.0390.01717.435-0.579-0.5790.0000.0000.0000.000
104A141GLY00.0320.01319.388-0.170-0.1700.0000.0000.0000.000
105A142LEU00.0330.00214.835-0.274-0.2740.0000.0000.0000.000
106A143GLN0-0.063-0.03916.8950.6640.6640.0000.0000.0000.000
107A144ALA00.0230.01518.604-0.159-0.1590.0000.0000.0000.000
108A145VAL00.0060.00420.449-0.388-0.3880.0000.0000.0000.000
109A146ALA00.0290.02217.495-0.182-0.1820.0000.0000.0000.000
110A147ASP-1-0.769-0.86019.45014.66714.6670.0000.0000.0000.000
111A148VAL00.0060.02121.628-0.253-0.2530.0000.0000.0000.000
112A149ALA00.0190.01621.239-0.294-0.2940.0000.0000.0000.000
113A150ALA0-0.032-0.01620.354-0.052-0.0520.0000.0000.0000.000
114A151ALA00.0110.00522.302-0.187-0.1870.0000.0000.0000.000
115A152ILE0-0.0010.01325.949-0.275-0.2750.0000.0000.0000.000
116A153LYS10.7650.86622.489-12.085-12.0850.0000.0000.0000.000
117A154ALA0-0.023-0.00325.126-0.106-0.1060.0000.0000.0000.000
118A155GLY0-0.0040.00826.649-0.301-0.3010.0000.0000.0000.000
119A156PHE0-0.056-0.03326.357-0.241-0.2410.0000.0000.0000.000
120A157TYR00.001-0.04327.922-0.190-0.1900.0000.0000.0000.000
121A158ASP-1-0.788-0.88430.8139.4739.4730.0000.0000.0000.000
122A159ILE0-0.007-0.01031.5610.1870.1870.0000.0000.0000.000
123A160GLY00.0200.01829.690-0.146-0.1460.0000.0000.0000.000
124A161ILE0-0.020-0.01029.1710.0740.0740.0000.0000.0000.000
125A162GLY00.0230.02625.1280.0950.0950.0000.0000.0000.000
126A163ALA0-0.017-0.02426.057-0.055-0.0550.0000.0000.0000.000
127A164GLY00.018-0.00425.5680.4330.4330.0000.0000.0000.000
128A165LEU0-0.004-0.00826.881-0.250-0.2500.0000.0000.0000.000
129A166GLU-1-0.717-0.84326.30910.98410.9840.0000.0000.0000.000
130A167SER00.033-0.02029.775-0.224-0.2240.0000.0000.0000.000
131A168MET0-0.035-0.02030.7410.0160.0160.0000.0000.0000.000
132A169THR0-0.0080.01034.637-0.117-0.1170.0000.0000.0000.000
133A170THR00.007-0.02336.9820.2800.2800.0000.0000.0000.000
134A171ASN0-0.017-0.02239.440-0.283-0.2830.0000.0000.0000.000
135A172PRO0-0.0130.01541.9760.0350.0350.0000.0000.0000.000
136A185LYS10.8080.89432.818-8.639-8.6390.0000.0000.0000.000
137A186PHE00.033-0.00931.0420.2920.2920.0000.0000.0000.000
138A187ALA00.0230.00730.8810.2490.2490.0000.0000.0000.000
139A188GLN0-0.018-0.00727.7440.4290.4290.0000.0000.0000.000
140A189ALA00.0510.01826.7840.4190.4190.0000.0000.0000.000
141A190GLN0-0.005-0.00625.9150.5930.5930.0000.0000.0000.000
142A191ASN0-0.005-0.01224.5970.1840.1840.0000.0000.0000.000
143A193LEU0-0.022-0.00621.3890.6510.6510.0000.0000.0000.000
144A194LEU00.0010.00522.2350.2990.2990.0000.0000.0000.000
145A195PRO00.0300.01420.9170.2550.2550.0000.0000.0000.000
146A196MET0-0.0100.01416.0260.9190.9190.0000.0000.0000.000
147A197GLY00.0150.02017.9720.6860.6860.0000.0000.0000.000
148A198VAL00.0110.00319.9270.2590.2590.0000.0000.0000.000
149A199THR0-0.026-0.02115.3130.1030.1030.0000.0000.0000.000
150A200SER0-0.015-0.02515.2650.9420.9420.0000.0000.0000.000
151A201GLU-1-0.796-0.88916.33812.52812.5280.0000.0000.0000.000
152A202ASN00.011-0.00318.269-0.497-0.4970.0000.0000.0000.000
153A203VAL0-0.045-0.00511.8290.3150.3150.0000.0000.0000.000
154A204ALA00.014-0.00314.9640.3370.3370.0000.0000.0000.000
155A205GLN0-0.010-0.01816.618-0.025-0.0250.0000.0000.0000.000
156A206ARG10.8430.91814.265-20.188-20.1880.0000.0000.0000.000
157A207PHE0-0.019-0.01911.9840.6980.6980.0000.0000.0000.000
158A208GLY00.0250.02915.1340.3180.3180.0000.0000.0000.000
159A209VAL0-0.044-0.00314.582-0.529-0.5290.0000.0000.0000.000
160A210SER00.0540.03217.595-0.622-0.6220.0000.0000.0000.000
161A211ARG10.8500.90521.391-10.247-10.2470.0000.0000.0000.000
162A212GLN00.0290.00724.0490.1780.1780.0000.0000.0000.000
163A213GLU-1-0.770-0.87617.81815.34815.3480.0000.0000.0000.000
164A214GLN00.0260.01919.5070.4910.4910.0000.0000.0000.000
165A215ASP-1-0.809-0.89321.50210.56510.5650.0000.0000.0000.000
166A216GLN0-0.025-0.02623.173-0.557-0.5570.0000.0000.0000.000
167A217ALA00.0350.01919.769-0.097-0.0970.0000.0000.0000.000
168A218ALA00.0270.00921.677-0.041-0.0410.0000.0000.0000.000
169A219VAL0-0.054-0.02924.376-0.340-0.3400.0000.0000.0000.000
170A220ASP-1-0.808-0.88122.65811.57411.5740.0000.0000.0000.000
171A221SER0-0.038-0.04222.532-0.340-0.3400.0000.0000.0000.000
172A222HIS00.0290.00124.207-0.477-0.4770.0000.0000.0000.000
173A223ARG10.8490.92125.320-11.050-11.0500.0000.0000.0000.000
174A224LYS10.8430.92221.188-13.080-13.0800.0000.0000.0000.000
175A225ALA00.0630.03626.979-0.153-0.1530.0000.0000.0000.000
176A226ALA0-0.043-0.01628.352-0.309-0.3090.0000.0000.0000.000
177A227ALA00.0090.00529.866-0.266-0.2660.0000.0000.0000.000
178A228ALA00.0110.00928.419-0.194-0.1940.0000.0000.0000.000
179A229THR0-0.045-0.03330.572-0.197-0.1970.0000.0000.0000.000
180A230ALA0-0.043-0.01933.397-0.225-0.2250.0000.0000.0000.000
181A231ALA0-0.014-0.00832.993-0.205-0.2050.0000.0000.0000.000
182A232GLY0-0.044-0.02635.126-0.063-0.0630.0000.0000.0000.000
183A233LYS10.8590.91627.552-10.444-10.4440.0000.0000.0000.000
184A234PHE00.029-0.00627.0840.0880.0880.0000.0000.0000.000
185A235LYS10.9310.97231.646-7.790-7.7900.0000.0000.0000.000
186A236ASP-1-0.818-0.87331.5338.9468.9460.0000.0000.0000.000
187A237GLU-1-0.811-0.88027.57910.58410.5840.0000.0000.0000.000
188A238ILE0-0.045-0.02430.9690.0740.0740.0000.0000.0000.000
189A239ILE0-0.0200.00033.047-0.185-0.1850.0000.0000.0000.000
190A240PRO0-0.014-0.02235.7660.0460.0460.0000.0000.0000.000
191A241VAL00.0050.01136.255-0.076-0.0760.0000.0000.0000.000
192A242LYS10.9380.97639.299-6.858-6.8580.0000.0000.0000.000
193A243THR0-0.052-0.05940.879-0.030-0.0300.0000.0000.0000.000
194A244LYS10.8110.88543.777-6.764-6.7640.0000.0000.0000.000
195A245LEU0-0.033-0.00842.2540.1570.1570.0000.0000.0000.000
196A246VAL00.0070.01245.487-0.133-0.1330.0000.0000.0000.000
197A247ASP-1-0.770-0.86546.5396.2756.2750.0000.0000.0000.000
198A248PRO0-0.036-0.04144.977-0.085-0.0850.0000.0000.0000.000
199A249LYS10.7750.88247.976-6.045-6.0450.0000.0000.0000.000
200A250THR0-0.058-0.06251.200-0.055-0.0550.0000.0000.0000.000
201A251GLY00.0350.02451.163-0.077-0.0770.0000.0000.0000.000
202A252ASP-1-0.873-0.89952.0035.6105.6100.0000.0000.0000.000
203A253GLU-1-0.826-0.91348.1726.4706.4700.0000.0000.0000.000
204A254LYS10.9500.98548.877-6.145-6.1450.0000.0000.0000.000
205A255PRO00.010-0.00747.8360.1540.1540.0000.0000.0000.000
206A256ILE0-0.034-0.00642.763-0.038-0.0380.0000.0000.0000.000
207A257THR00.0340.00841.7770.0230.0230.0000.0000.0000.000
208A258VAL00.0080.02236.9890.0280.0280.0000.0000.0000.000
209A259SER00.012-0.01937.4810.0780.0780.0000.0000.0000.000
210A260VAL00.002-0.00134.7840.1060.1060.0000.0000.0000.000
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