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: 6YR2Z

Calculation Name: 2D1L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D1L

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R1S4

Base Structure: X-ray

Registration Date: 2023-09-23

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 249
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2479866.34709
FMO2-HF: Nuclear repulsion 2379833.21631
FMO2-HF: Total energy -100033.13078
FMO2-MP2: Total energy -100319.591952


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:-2:ALA)


Summations of interaction energy for fragment #1(A:-2:ALA)
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.
-0.1733.891.415-2.35-3.128-0.003
Interaction energy analysis for fragmet #1(A:-2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.028
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].
3A0HIS00.014-0.0053.810-1.1710.241-0.023-0.733-0.6560.003
4A1MET00.0300.0166.710-0.011-0.0110.0000.0000.0000.000
5A2GLU-1-0.787-0.8942.3981.9642.9121.284-1.090-1.142-0.004
6A3ALA0-0.016-0.0014.451-0.195-0.114-0.001-0.011-0.0690.000
7A4VAL0-0.023-0.0185.9450.0790.0790.0000.0000.0000.000
8A5ILE00.0420.0317.1430.0050.0050.0000.0000.0000.000
9A6GLU-1-0.877-0.9435.443-0.158-0.1580.0000.0000.0000.000
10A7LYS10.8550.9247.9210.3580.3580.0000.0000.0000.000
11A8GLU-1-0.849-0.89711.4130.0480.0480.0000.0000.0000.000
12A9CYS0-0.058-0.02410.9130.0110.0110.0000.0000.0000.000
13A10SER0-0.045-0.01811.479-0.021-0.0210.0000.0000.0000.000
14A11ALA0-0.0020.01114.018-0.006-0.0060.0000.0000.0000.000
15A12LEU0-0.021-0.01215.3730.0010.0010.0000.0000.0000.000
16A13GLY00.0260.01516.615-0.001-0.0010.0000.0000.0000.000
17A14GLY0-0.036-0.02417.852-0.004-0.0040.0000.0000.0000.000
18A15LEU00.0070.00419.7770.0000.0000.0000.0000.0000.000
19A16PHE00.007-0.01121.1650.0020.0020.0000.0000.0000.000
20A17GLN00.0410.00520.5970.0010.0010.0000.0000.0000.000
21A18THR0-0.041-0.00623.606-0.004-0.0040.0000.0000.0000.000
22A19ILE00.0190.02225.3370.0010.0010.0000.0000.0000.000
23A20ILE0-0.0050.00225.7210.0000.0000.0000.0000.0000.000
24A21SER0-0.040-0.02627.509-0.002-0.0020.0000.0000.0000.000
25A22ASP-1-0.901-0.94629.292-0.008-0.0080.0000.0000.0000.000
26A23MET0-0.054-0.02930.2450.0010.0010.0000.0000.0000.000
27A24LYS10.8960.95330.6870.0080.0080.0000.0000.0000.000
28A25GLY00.0070.00833.583-0.001-0.0010.0000.0000.0000.000
29A26SER0-0.036-0.02735.3680.0000.0000.0000.0000.0000.000
30A27TYR00.023-0.00435.2780.0010.0010.0000.0000.0000.000
31A28PRO00.0800.04239.5980.0010.0010.0000.0000.0000.000
32A29VAL00.0160.01741.4430.0000.0000.0000.0000.0000.000
33A30TRP00.002-0.00239.2640.0010.0010.0000.0000.0000.000
34A31GLU-1-0.905-0.96943.505-0.003-0.0030.0000.0000.0000.000
35A32ASP-1-0.869-0.92346.096-0.004-0.0040.0000.0000.0000.000
36A33PHE00.000-0.00247.1380.0000.0000.0000.0000.0000.000
37A34ILE00.0520.02346.3990.0000.0000.0000.0000.0000.000
38A35ASN00.0370.04150.0580.0000.0000.0000.0000.0000.000
39A36LYS10.8200.88751.5440.0040.0040.0000.0000.0000.000
40A37ALA00.0430.03652.6180.0000.0000.0000.0000.0000.000
41A38GLY00.0540.02554.1850.0000.0000.0000.0000.0000.000
42A39LYS10.8070.88454.8170.0030.0030.0000.0000.0000.000
43A40LEU00.0330.01957.4170.0000.0000.0000.0000.0000.000
44A41GLN00.0250.01458.2240.0000.0000.0000.0000.0000.000
45A42SER0-0.022-0.01960.0580.0000.0000.0000.0000.0000.000
46A43GLN0-0.016-0.01962.2540.0000.0000.0000.0000.0000.000
47A44LEU00.0330.02960.9490.0000.0000.0000.0000.0000.000
48A45ARG10.9540.98563.982-0.002-0.0020.0000.0000.0000.000
49A46THR0-0.021-0.02166.1000.0000.0000.0000.0000.0000.000
50A47THR0-0.010-0.00767.1900.0000.0000.0000.0000.0000.000
51A48VAL00.0070.00767.2660.0000.0000.0000.0000.0000.000
52A49VAL0-0.043-0.01270.1940.0000.0000.0000.0000.0000.000
53A50ALA00.0040.00372.3560.0000.0000.0000.0000.0000.000
54A51ALA0-0.001-0.00472.4190.0000.0000.0000.0000.0000.000
55A52ALA00.0160.00874.3430.0000.0000.0000.0000.0000.000
56A53ALA00.0080.00976.2230.0000.0000.0000.0000.0000.000
57A54PHE0-0.008-0.00577.2510.0000.0000.0000.0000.0000.000
58A55LEU00.0100.00075.7470.0000.0000.0000.0000.0000.000
59A56ASP-1-0.855-0.90379.7720.0030.0030.0000.0000.0000.000
60A57ALA0-0.079-0.03982.2870.0000.0000.0000.0000.0000.000
61A58PHE0-0.028-0.01381.8220.0000.0000.0000.0000.0000.000
62A59GLN00.020-0.02983.7410.0000.0000.0000.0000.0000.000
63A60LYS10.9630.98985.432-0.002-0.0020.0000.0000.0000.000
64A61VAL0-0.0140.00487.0600.0000.0000.0000.0000.0000.000
65A62ALA00.0230.01686.7370.0000.0000.0000.0000.0000.000
66A63ASP-1-0.864-0.91988.8560.0030.0030.0000.0000.0000.000
67A64MET0-0.071-0.03491.3150.0000.0000.0000.0000.0000.000
68A65ALA0-0.0050.00791.8630.0000.0000.0000.0000.0000.000
69A66THR00.016-0.01091.4730.0000.0000.0000.0000.0000.000
70A67ASN0-0.080-0.03494.1260.0000.0000.0000.0000.0000.000
71A68THR0-0.064-0.02996.9600.0000.0000.0000.0000.0000.000
72A69ARG10.9610.95599.209-0.002-0.0020.0000.0000.0000.000
73A70GLY00.0410.02799.9180.0000.0000.0000.0000.0000.000
74A71GLY00.0790.04197.4390.0000.0000.0000.0000.0000.000
75A72THR0-0.026-0.01495.2400.0000.0000.0000.0000.0000.000
76A73ARG10.8920.96294.506-0.003-0.0030.0000.0000.0000.000
77A74GLU-1-0.855-0.93993.3660.0030.0030.0000.0000.0000.000
78A75ILE00.0250.02390.1960.0000.0000.0000.0000.0000.000
79A76GLY00.0260.00289.6180.0000.0000.0000.0000.0000.000
80A77SER0-0.028-0.02189.1620.0000.0000.0000.0000.0000.000
81A78ALA00.0160.00786.8440.0000.0000.0000.0000.0000.000
82A79LEU0-0.006-0.00485.2320.0000.0000.0000.0000.0000.000
83A80THR00.0260.01884.3050.0000.0000.0000.0000.0000.000
84A81ARG10.8420.92083.317-0.004-0.0040.0000.0000.0000.000
85A82MET0-0.0040.01679.6580.0000.0000.0000.0000.0000.000
86A83CYS0-0.0190.01379.5370.0000.0000.0000.0000.0000.000
87A84MET0-0.008-0.01979.1470.0000.0000.0000.0000.0000.000
88A85ARG10.8610.93873.997-0.005-0.0050.0000.0000.0000.000
89A86HIS0-0.004-0.03374.7270.0000.0000.0000.0000.0000.000
90A87ARG10.8450.91274.444-0.003-0.0030.0000.0000.0000.000
91A88SER0-0.049-0.01972.2000.0000.0000.0000.0000.0000.000
92A89ILE00.0200.00869.5750.0000.0000.0000.0000.0000.000
93A90GLU-1-0.809-0.92069.5430.0040.0040.0000.0000.0000.000
94A91ALA0-0.012-0.01569.6840.0000.0000.0000.0000.0000.000
95A92LYS10.8920.92966.417-0.007-0.0070.0000.0000.0000.000
96A93LEU00.0160.01365.0610.0000.0000.0000.0000.0000.000
97A94ARG10.8390.91964.937-0.004-0.0040.0000.0000.0000.000
98A95GLN0-0.022-0.00763.7150.0000.0000.0000.0000.0000.000
99A96PHE00.0530.03458.3420.0000.0000.0000.0000.0000.000
100A97SER0-0.041-0.02460.1420.0000.0000.0000.0000.0000.000
101A98SER00.008-0.00660.4280.0000.0000.0000.0000.0000.000
102A99ALA00.0650.04657.6220.0000.0000.0000.0000.0000.000
103A100LEU0-0.022-0.01055.0530.0000.0000.0000.0000.0000.000
104A101ILE0-0.043-0.03555.2440.0000.0000.0000.0000.0000.000
105A102ASP-1-0.886-0.94555.1730.0070.0070.0000.0000.0000.000
106A103CYS0-0.081-0.03953.3390.0010.0010.0000.0000.0000.000
107A104LEU0-0.025-0.01349.4330.0010.0010.0000.0000.0000.000
108A105ILE0-0.047-0.01650.4890.0000.0000.0000.0000.0000.000
109A106ASN00.0450.01450.801-0.001-0.0010.0000.0000.0000.000
110A107PRO00.0280.02149.2570.0000.0000.0000.0000.0000.000
111A108LEU00.0040.00344.6480.0000.0000.0000.0000.0000.000
112A109GLN0-0.025-0.01845.870-0.001-0.0010.0000.0000.0000.000
113A110GLU-1-0.938-0.97546.5170.0060.0060.0000.0000.0000.000
114A111GLN0-0.048-0.00940.8430.0010.0010.0000.0000.0000.000
115A112MET0-0.040-0.01541.7070.0010.0010.0000.0000.0000.000
116A113GLU-1-0.916-0.96739.6730.0030.0030.0000.0000.0000.000
117A114GLU-1-0.793-0.87739.3610.0120.0120.0000.0000.0000.000
118A115TRP0-0.007-0.01237.4200.0010.0010.0000.0000.0000.000
119A116LYS10.9060.97035.6260.0010.0010.0000.0000.0000.000
120A117LYS10.8010.88334.482-0.012-0.0120.0000.0000.0000.000
121A118VAL00.0170.02033.2480.0010.0010.0000.0000.0000.000
122A119ALA00.0170.01131.3050.0020.0020.0000.0000.0000.000
123A120ASN00.008-0.00929.715-0.001-0.0010.0000.0000.0000.000
124A121GLN0-0.102-0.05128.887-0.004-0.0040.0000.0000.0000.000
125A122LEU00.0220.02626.4660.0040.0040.0000.0000.0000.000
126A123ASP-1-0.876-0.94624.5810.0040.0040.0000.0000.0000.000
127A124LYS10.8710.92624.048-0.010-0.0100.0000.0000.0000.000
128A125ASP-1-0.893-0.93824.1260.0350.0350.0000.0000.0000.000
129A126HIS0-0.022-0.01018.2060.0020.0020.0000.0000.0000.000
130A127ALA00.0560.03119.7710.0040.0040.0000.0000.0000.000
131A128LYS10.8570.92619.165-0.036-0.0360.0000.0000.0000.000
132A129GLU-1-0.897-0.96619.2330.0870.0870.0000.0000.0000.000
133A130TYR00.0860.07212.5920.0030.0030.0000.0000.0000.000
134A131LYS10.9240.96214.4360.0220.0220.0000.0000.0000.000
135A132LYS10.9180.95114.654-0.079-0.0790.0000.0000.0000.000
136A133ALA00.0730.05012.9460.0110.0110.0000.0000.0000.000
137A134ARG10.8790.9127.3740.0620.0620.0000.0000.0000.000
138A135GLN0-0.043-0.02110.082-0.033-0.0330.0000.0000.0000.000
139A136GLU-1-0.891-0.96311.6790.1800.1800.0000.0000.0000.000
140A137ILE00.0590.0415.7220.0150.0150.0000.0000.0000.000
141A138LYS10.9120.9626.970-0.001-0.0010.0000.0000.0000.000
142A139LYS10.8450.9108.738-0.202-0.2020.0000.0000.0000.000
143A140LYS11.0021.0087.804-0.458-0.4580.0000.0000.0000.000
144A141SER00.0460.0324.033-0.403-0.236-0.001-0.039-0.1270.000
145A142SER0-0.068-0.0195.736-0.105-0.1050.0000.0000.0000.000
146A143ASP-1-0.923-0.9639.1810.1230.1230.0000.0000.0000.000
147A144THR00.013-0.0165.7820.0740.0740.0000.0000.0000.000
148A145LEU00.0160.0177.858-0.060-0.0600.0000.0000.0000.000
149A146LYS10.9030.9469.0390.0200.0200.0000.0000.0000.000
150A147LEU00.0550.02010.985-0.033-0.0330.0000.0000.0000.000
151A148GLN00.0420.0335.870-0.206-0.2060.0000.0000.0000.000
152A149LYS10.9010.95510.8080.1240.1240.0000.0000.0000.000
153A150LYS10.8700.91713.5380.0110.0110.0000.0000.0000.000
154A151ALA00.0900.05313.4920.0030.0030.0000.0000.0000.000
155A152LYS10.8460.92612.5600.0380.0380.0000.0000.0000.000
156A153LYS10.9430.98116.6360.0110.0110.0000.0000.0000.000
157A154VAL00.0240.01018.7660.0130.0130.0000.0000.0000.000
158A155ASP-1-0.870-0.93921.0760.0020.0020.0000.0000.0000.000
159A156ALA0-0.056-0.02223.3070.0000.0000.0000.0000.0000.000
160A157GLN00.0340.00823.3540.0150.0150.0000.0000.0000.000
161A158GLY00.0570.05119.9770.0130.0130.0000.0000.0000.000
162A159ARG10.8560.89917.268-0.126-0.1260.0000.0000.0000.000
163A160GLY00.0400.01018.9380.0220.0220.0000.0000.0000.000
164A161ASP-1-0.837-0.90420.5140.1370.1370.0000.0000.0000.000
165A162ILE0-0.074-0.03415.3470.0170.0170.0000.0000.0000.000
166A163GLN0-0.088-0.03712.150-0.037-0.0370.0000.0000.0000.000
167A164PRO00.0690.04014.1090.0680.0680.0000.0000.0000.000
168A165GLN00.0210.00914.9460.0470.0470.0000.0000.0000.000
169A166LEU0-0.042-0.0378.8140.0380.0380.0000.0000.0000.000
170A167ASP-1-0.857-0.9319.7720.7000.7000.0000.0000.0000.000
171A168SER00.0140.00610.6970.1710.1710.0000.0000.0000.000
172A169ALA0-0.0220.0009.2520.0630.0630.0000.0000.0000.000
173A170LEU0-0.033-0.0294.7070.0250.117-0.001-0.006-0.0850.000
174A171GLN00.0260.0276.5780.6630.6630.0000.0000.0000.000
175A172ASP-1-0.878-0.9439.2510.6390.6390.0000.0000.0000.000
176A173VAL0-0.080-0.0462.757-0.782-0.3340.109-0.153-0.4040.000
177A174ASN00.0270.0106.175-0.150-0.1500.0000.0000.0000.000
178A175ASP-1-0.880-0.9387.2030.3680.3680.0000.0000.0000.000
179A176LYS10.8160.9078.104-0.603-0.6030.0000.0000.0000.000
180A177TYR0-0.010-0.0153.418-1.224-0.3090.048-0.318-0.645-0.002
181A178LEU00.0540.0378.240-0.162-0.1620.0000.0000.0000.000
182A179LEU0-0.024-0.00711.261-0.104-0.1040.0000.0000.0000.000
183A180LEU0-0.052-0.0239.817-0.070-0.0700.0000.0000.0000.000
184A181GLU-1-0.820-0.93211.9280.1730.1730.0000.0000.0000.000
185A182GLU-1-0.928-0.97413.4770.1790.1790.0000.0000.0000.000
186A183THR0-0.079-0.04015.884-0.037-0.0370.0000.0000.0000.000
187A184GLU-1-0.839-0.92514.9560.0290.0290.0000.0000.0000.000
188A185LYS10.9400.98016.805-0.172-0.1720.0000.0000.0000.000
189A186GLN0-0.008-0.01419.530-0.025-0.0250.0000.0000.0000.000
190A187ALA0-0.035-0.01220.759-0.009-0.0090.0000.0000.0000.000
191A188VAL00.0660.03320.896-0.008-0.0080.0000.0000.0000.000
192A189ARG10.9040.96723.338-0.075-0.0750.0000.0000.0000.000
193A190LYS10.9290.95323.492-0.072-0.0720.0000.0000.0000.000
194A191ALA00.0360.02626.171-0.004-0.0040.0000.0000.0000.000
195A192LEU00.0240.01226.208-0.003-0.0030.0000.0000.0000.000
196A193ILE0-0.073-0.04029.273-0.002-0.0020.0000.0000.0000.000
197A194GLU-1-0.902-0.95431.0210.0200.0200.0000.0000.0000.000
198A195GLU-1-0.918-0.96531.3780.0100.0100.0000.0000.0000.000
199A196ARG10.9560.96833.418-0.029-0.0290.0000.0000.0000.000
200A197GLY00.0180.00235.233-0.001-0.0010.0000.0000.0000.000
201A198ARG10.9360.98435.367-0.010-0.0100.0000.0000.0000.000
202A199PHE00.0380.01137.005-0.001-0.0010.0000.0000.0000.000
203A200CYS0-0.094-0.04638.9430.0000.0000.0000.0000.0000.000
204A201THR0-0.0060.00340.7010.0000.0000.0000.0000.0000.000
205A202PHE00.0450.01942.867-0.001-0.0010.0000.0000.0000.000
206A203ILE00.000-0.00743.194-0.001-0.0010.0000.0000.0000.000
207A204SER0-0.079-0.04545.1550.0000.0000.0000.0000.0000.000
208A205MET0-0.0090.01445.6810.0000.0000.0000.0000.0000.000
209A206LEU00.0140.01148.786-0.001-0.0010.0000.0000.0000.000
210A207ARG10.9100.94547.426-0.016-0.0160.0000.0000.0000.000
211A208PRO00.0350.02651.9610.0000.0000.0000.0000.0000.000
212A209VAL0-0.0060.00854.0510.0000.0000.0000.0000.0000.000
213A210ILE00.011-0.00853.3890.0000.0000.0000.0000.0000.000
214A211GLU-1-0.949-0.97156.2630.0100.0100.0000.0000.0000.000
215A212GLU-1-0.878-0.94058.1230.0080.0080.0000.0000.0000.000
216A213GLU-1-0.966-0.96458.2790.0050.0050.0000.0000.0000.000
217A214ILE00.0090.00256.9700.0000.0000.0000.0000.0000.000
218A215SER0-0.025-0.01761.2900.0000.0000.0000.0000.0000.000
219A216MET0-0.049-0.03963.7510.0000.0000.0000.0000.0000.000
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