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: 5N9MZ

Calculation Name: 2C2Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C2Y

Chain ID: A

ChEMBL ID:

UniProt ID: P9WG81

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptHSide
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 280
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3457084.318276
FMO2-HF: Nuclear repulsion 3354755.774821
FMO2-HF: Total energy -102328.543456
FMO2-MP2: Total energy -102629.728983


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
-5.34-1.1332.435-3.421-3.22-0.021
Interaction energy analysis for fragmet #1(A:2:GLY)
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 : 0.011
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].
3A4ILE0-0.022-0.0183.8030.4621.962-0.007-0.843-0.6490.005
4A5MET0-0.036-0.0086.6640.3740.3740.0000.0000.0000.000
5A6LEU0-0.017-0.0058.6310.1700.1700.0000.0000.0000.000
6A7ASP-1-0.734-0.87812.159-0.158-0.1580.0000.0000.0000.000
7A8GLY00.0610.02814.2000.0310.0310.0000.0000.0000.000
8A9LYS10.7750.87415.3840.2570.2570.0000.0000.0000.000
9A10ALA00.0420.02217.1700.0240.0240.0000.0000.0000.000
10A11THR00.005-0.01317.5170.0030.0030.0000.0000.0000.000
11A12ARG10.8050.87920.1170.1660.1660.0000.0000.0000.000
12A13ASP-1-0.861-0.90822.371-0.127-0.1270.0000.0000.0000.000
13A14GLU-1-0.823-0.87122.122-0.282-0.2820.0000.0000.0000.000
14A15ILE0-0.0010.00123.8150.0120.0120.0000.0000.0000.000
15A16PHE0-0.022-0.02126.5540.0150.0150.0000.0000.0000.000
16A17GLY00.0240.01827.8270.0120.0120.0000.0000.0000.000
17A18ASP-1-0.833-0.90428.899-0.146-0.1460.0000.0000.0000.000
18A19LEU0-0.005-0.02130.0830.0100.0100.0000.0000.0000.000
19A20LYS10.8840.95032.3990.0840.0840.0000.0000.0000.000
20A21GLN0-0.069-0.03631.7130.0110.0110.0000.0000.0000.000
21A22ARG10.7770.85031.8780.1480.1480.0000.0000.0000.000
22A23VAL0-0.020-0.00536.4310.0040.0040.0000.0000.0000.000
23A24ALA00.0020.00438.2880.0060.0060.0000.0000.0000.000
24A25ALA0-0.010-0.00639.7130.0040.0040.0000.0000.0000.000
25A26LEU0-0.058-0.02739.4500.0030.0030.0000.0000.0000.000
26A27ASP-1-0.887-0.91542.430-0.056-0.0560.0000.0000.0000.000
27A28ALA0-0.0060.00844.2010.0040.0040.0000.0000.0000.000
28A29ALA0-0.089-0.04445.7490.0030.0030.0000.0000.0000.000
29A30GLY0-0.0100.00047.5830.0010.0010.0000.0000.0000.000
30A31ARG10.8440.91943.9120.0790.0790.0000.0000.0000.000
31A32THR00.030-0.01342.681-0.004-0.0040.0000.0000.0000.000
32A33PRO0-0.007-0.00439.1700.0010.0010.0000.0000.0000.000
33A34GLY00.0400.01241.6680.0030.0030.0000.0000.0000.000
34A35LEU0-0.042-0.01635.820-0.004-0.0040.0000.0000.0000.000
35A36GLY00.0460.00439.9720.0050.0050.0000.0000.0000.000
36A37THR0-0.044-0.02437.965-0.005-0.0050.0000.0000.0000.000
37A38ILE00.0090.01240.7890.0040.0040.0000.0000.0000.000
38A39LEU0-0.016-0.00439.193-0.004-0.0040.0000.0000.0000.000
39A40VAL00.0050.00642.0910.0030.0030.0000.0000.0000.000
40A41GLY00.004-0.00343.0720.0000.0000.0000.0000.0000.000
41A42ASP-1-0.926-0.96242.377-0.026-0.0260.0000.0000.0000.000
42A43ASP-1-0.750-0.84736.531-0.040-0.0400.0000.0000.0000.000
43A44PRO00.0210.00136.396-0.003-0.0030.0000.0000.0000.000
44A45GLY0-0.0050.00233.471-0.001-0.0010.0000.0000.0000.000
45A46SER0-0.001-0.03633.834-0.008-0.0080.0000.0000.0000.000
46A47GLN0-0.067-0.04536.043-0.003-0.0030.0000.0000.0000.000
47A48ALA0-0.064-0.03132.546-0.001-0.0010.0000.0000.0000.000
48A49TYR0-0.020-0.00828.580-0.007-0.0070.0000.0000.0000.000
49A50VAL00.0230.01132.837-0.006-0.0060.0000.0000.0000.000
50A51ARG10.9550.97834.8360.0330.0330.0000.0000.0000.000
51A52GLY0-0.013-0.00131.4770.0000.0000.0000.0000.0000.000
52A53LYS10.8970.95432.0540.0880.0880.0000.0000.0000.000
53A54HIS00.0600.03233.353-0.004-0.0040.0000.0000.0000.000
54A55ALA0-0.0030.00832.9580.0010.0010.0000.0000.0000.000
55A56ASP-1-0.818-0.90029.155-0.099-0.0990.0000.0000.0000.000
56A57CYS0-0.0040.01032.202-0.004-0.0040.0000.0000.0000.000
57A58ALA00.0320.01835.3560.0000.0000.0000.0000.0000.000
58A59LYS10.8020.89429.4410.0790.0790.0000.0000.0000.000
59A60VAL0-0.028-0.02431.7780.0000.0000.0000.0000.0000.000
60A61GLY00.0160.01934.699-0.001-0.0010.0000.0000.0000.000
61A62ILE0-0.038-0.00835.1730.0010.0010.0000.0000.0000.000
62A63THR00.0440.01738.9680.0040.0040.0000.0000.0000.000
63A64SER0-0.031-0.02839.360-0.003-0.0030.0000.0000.0000.000
64A65ILE0-0.0020.00741.6940.0050.0050.0000.0000.0000.000
65A66ARG10.8390.90839.3120.0430.0430.0000.0000.0000.000
66A67ARG10.8230.88144.1170.0500.0500.0000.0000.0000.000
67A68ASP-1-0.816-0.90143.195-0.046-0.0460.0000.0000.0000.000
68A69LEU00.002-0.00345.8920.0020.0020.0000.0000.0000.000
69A70PRO00.0570.03546.8350.0000.0000.0000.0000.0000.000
70A71ALA00.036-0.01546.611-0.002-0.0020.0000.0000.0000.000
71A72ASP-1-0.928-0.96147.852-0.027-0.0270.0000.0000.0000.000
72A73ILE0-0.0140.01848.0650.0010.0010.0000.0000.0000.000
73A74SER00.0320.01151.683-0.001-0.0010.0000.0000.0000.000
74A75THR00.061-0.00350.765-0.001-0.0010.0000.0000.0000.000
75A76ALA0-0.015-0.00652.190-0.002-0.0020.0000.0000.0000.000
76A77THR00.0720.05052.4360.0000.0000.0000.0000.0000.000
77A78LEU00.0250.02245.811-0.001-0.0010.0000.0000.0000.000
78A79ASN0-0.010-0.02749.420-0.004-0.0040.0000.0000.0000.000
79A80GLU-1-0.892-0.93651.357-0.038-0.0380.0000.0000.0000.000
80A81THR0-0.037-0.02147.7630.0000.0000.0000.0000.0000.000
81A82ILE0-0.018-0.00845.963-0.002-0.0020.0000.0000.0000.000
82A83ASP-1-0.809-0.86648.315-0.053-0.0530.0000.0000.0000.000
83A84GLU-1-0.787-0.85550.227-0.049-0.0490.0000.0000.0000.000
84A85LEU0-0.010-0.01944.562-0.001-0.0010.0000.0000.0000.000
85A86ASN00.0170.02146.914-0.005-0.0050.0000.0000.0000.000
86A87ALA0-0.018-0.00448.659-0.002-0.0020.0000.0000.0000.000
87A88ASN0-0.048-0.02948.5250.0000.0000.0000.0000.0000.000
88A89PRO0-0.027-0.01948.531-0.003-0.0030.0000.0000.0000.000
89A90ASP-1-0.856-0.91547.227-0.054-0.0540.0000.0000.0000.000
90A91CYS0-0.133-0.04644.409-0.004-0.0040.0000.0000.0000.000
91A92THR00.0120.02541.452-0.002-0.0020.0000.0000.0000.000
92A93GLY00.016-0.00339.952-0.004-0.0040.0000.0000.0000.000
93A94TYR0-0.014-0.03839.9220.0030.0030.0000.0000.0000.000
94A95ILE0-0.0350.00435.303-0.004-0.0040.0000.0000.0000.000
95A96VAL00.0370.00938.5880.0060.0060.0000.0000.0000.000
96A97GLN0-0.057-0.03433.766-0.009-0.0090.0000.0000.0000.000
97A98LEU00.0110.03036.0080.0040.0040.0000.0000.0000.000
98A99PRO0-0.026-0.02235.875-0.002-0.0020.0000.0000.0000.000
99A100LEU00.0470.01638.4710.0030.0030.0000.0000.0000.000
100A101PRO00.008-0.00442.1980.0010.0010.0000.0000.0000.000
101A102LYS10.8890.93041.0150.0480.0480.0000.0000.0000.000
102A103HIS0-0.064-0.01445.743-0.001-0.0010.0000.0000.0000.000
103A104LEU0-0.042-0.01646.2860.0000.0000.0000.0000.0000.000
104A105ASP-1-0.861-0.93245.849-0.058-0.0580.0000.0000.0000.000
105A106GLU-1-0.843-0.94339.546-0.064-0.0640.0000.0000.0000.000
106A107ASN0-0.054-0.03541.764-0.006-0.0060.0000.0000.0000.000
107A108ALA00.0190.01143.169-0.002-0.0020.0000.0000.0000.000
108A109ALA0-0.016-0.00844.2250.0000.0000.0000.0000.0000.000
109A110LEU0-0.017-0.02038.876-0.002-0.0020.0000.0000.0000.000
110A111GLU-1-0.907-0.95342.544-0.076-0.0760.0000.0000.0000.000
111A112ARG10.7610.87044.7690.0510.0510.0000.0000.0000.000
112A113VAL0-0.029-0.00241.8450.0010.0010.0000.0000.0000.000
113A114ASP-1-0.817-0.90845.014-0.076-0.0760.0000.0000.0000.000
114A115PRO0-0.028-0.01742.169-0.004-0.0040.0000.0000.0000.000
115A116ALA0-0.034-0.02041.576-0.007-0.0070.0000.0000.0000.000
116A117LYS10.8110.91442.1070.0650.0650.0000.0000.0000.000
117A118ASP-1-0.763-0.86937.698-0.110-0.1100.0000.0000.0000.000
118A119ALA0-0.008-0.00336.141-0.008-0.0080.0000.0000.0000.000
119A120ASP-1-0.846-0.96033.109-0.123-0.1230.0000.0000.0000.000
120A121GLY0-0.039-0.00832.909-0.011-0.0110.0000.0000.0000.000
121A122LEU0-0.067-0.05531.715-0.008-0.0080.0000.0000.0000.000
122A123HIS00.0560.06135.634-0.001-0.0010.0000.0000.0000.000
123A124PRO00.0530.01338.784-0.007-0.0070.0000.0000.0000.000
124A125THR0-0.012-0.01940.275-0.002-0.0020.0000.0000.0000.000
125A126ASN0-0.072-0.06637.6480.0000.0000.0000.0000.0000.000
126A127LEU0-0.0010.01233.761-0.009-0.0090.0000.0000.0000.000
127A128GLY00.0130.00536.852-0.005-0.0050.0000.0000.0000.000
128A129ARG10.9000.94539.4180.0970.0970.0000.0000.0000.000
129A130LEU0-0.0140.01131.488-0.003-0.0030.0000.0000.0000.000
130A131VAL0-0.048-0.02735.704-0.006-0.0060.0000.0000.0000.000
131A132LEU0-0.046-0.02237.101-0.001-0.0010.0000.0000.0000.000
132A133GLY0-0.0090.01337.2370.0010.0010.0000.0000.0000.000
133A134THR0-0.051-0.03638.2900.0040.0040.0000.0000.0000.000
134A135PRO0-0.030-0.02337.732-0.003-0.0030.0000.0000.0000.000
135A136ALA00.0050.00337.2270.0090.0090.0000.0000.0000.000
136A137PRO0-0.025-0.00335.729-0.010-0.0100.0000.0000.0000.000
137A138LEU00.0400.02530.130-0.001-0.0010.0000.0000.0000.000
138A139PRO00.0080.01929.8790.0010.0010.0000.0000.0000.000
139A140CYS0-0.0090.00928.487-0.015-0.0150.0000.0000.0000.000
140A141THR00.0200.01623.409-0.012-0.0120.0000.0000.0000.000
141A142PRO0-0.0150.00223.809-0.027-0.0270.0000.0000.0000.000
142A143ARG10.8190.88224.2520.1610.1610.0000.0000.0000.000
143A144GLY00.0250.00423.385-0.013-0.0130.0000.0000.0000.000
144A145ILE0-0.018-0.01319.090-0.031-0.0310.0000.0000.0000.000
145A146VAL00.0050.00019.615-0.048-0.0480.0000.0000.0000.000
146A147HIS00.0010.00721.151-0.023-0.0230.0000.0000.0000.000
147A148LEU00.002-0.00215.577-0.011-0.0110.0000.0000.0000.000
148A149LEU00.000-0.00315.281-0.062-0.0620.0000.0000.0000.000
149A150ARG10.8880.91817.1020.2850.2850.0000.0000.0000.000
150A151ARG10.7580.87618.0010.3810.3810.0000.0000.0000.000
151A152TYR0-0.004-0.01812.284-0.004-0.0040.0000.0000.0000.000
152A153ASP-1-0.931-0.94614.884-0.607-0.6070.0000.0000.0000.000
153A154ILE0-0.045-0.00812.783-0.019-0.0190.0000.0000.0000.000
154A155SER0-0.026-0.01016.4560.0700.0700.0000.0000.0000.000
155A156ILE0-0.013-0.02019.285-0.017-0.0170.0000.0000.0000.000
156A157ALA00.013-0.00121.8330.0160.0160.0000.0000.0000.000
157A158GLY0-0.041-0.02223.430-0.018-0.0180.0000.0000.0000.000
158A159ALA0-0.0110.01819.727-0.004-0.0040.0000.0000.0000.000
159A160HIS00.0040.00120.5230.0620.0620.0000.0000.0000.000
160A161VAL0-0.012-0.02119.451-0.047-0.0470.0000.0000.0000.000
161A162VAL00.0280.02319.1670.0490.0490.0000.0000.0000.000
162A163VAL0-0.020-0.01219.670-0.029-0.0290.0000.0000.0000.000
163A164ILE0-0.0030.00818.2290.0330.0330.0000.0000.0000.000
164A165GLY00.0510.02222.1580.0020.0020.0000.0000.0000.000
165A166ARG10.8960.93725.0630.1120.1120.0000.0000.0000.000
166A167GLY00.0350.01927.4300.0130.0130.0000.0000.0000.000
167A168VAL00.030-0.01629.105-0.011-0.0110.0000.0000.0000.000
168A169THR00.0460.03229.218-0.005-0.0050.0000.0000.0000.000
169A170VAL00.002-0.01023.272-0.010-0.0100.0000.0000.0000.000
170A171GLY00.0580.02725.293-0.008-0.0080.0000.0000.0000.000
171A172ARG10.9230.95626.2530.1280.1280.0000.0000.0000.000
172A173PRO00.0200.02028.837-0.002-0.0020.0000.0000.0000.000
173A174LEU00.0200.01422.419-0.002-0.0020.0000.0000.0000.000
174A175GLY00.0460.02226.668-0.012-0.0120.0000.0000.0000.000
175A176LEU0-0.0240.00427.7990.0000.0000.0000.0000.0000.000
176A177LEU0-0.037-0.01126.2780.0020.0020.0000.0000.0000.000
177A178LEU00.020-0.01222.379-0.004-0.0040.0000.0000.0000.000
178A179THR0-0.0110.00026.531-0.004-0.0040.0000.0000.0000.000
179A180ARG10.8610.93329.4940.2220.2220.0000.0000.0000.000
180A181ARG10.9900.97230.2490.1460.1460.0000.0000.0000.000
181A182SER0-0.040-0.03030.476-0.001-0.0010.0000.0000.0000.000
182A183GLU-1-0.832-0.85725.905-0.260-0.2600.0000.0000.0000.000
183A184ASN0-0.018-0.01626.400-0.007-0.0070.0000.0000.0000.000
184A185ALA00.0350.03523.450-0.007-0.0070.0000.0000.0000.000
185A186THR0-0.010-0.00424.6470.0380.0380.0000.0000.0000.000
186A187VAL0-0.011-0.01224.042-0.026-0.0260.0000.0000.0000.000
187A188THR0-0.013-0.00423.6300.0270.0270.0000.0000.0000.000
188A189LEU0-0.026-0.01224.311-0.013-0.0130.0000.0000.0000.000
189A190CYS0-0.0110.00323.6110.0200.0200.0000.0000.0000.000
190A191HIS00.015-0.01325.7620.0060.0060.0000.0000.0000.000
191A192THR00.0680.02026.992-0.001-0.0010.0000.0000.0000.000
192A193GLY0-0.028-0.00128.6410.0090.0090.0000.0000.0000.000
193A194THR0-0.042-0.01425.6530.0030.0030.0000.0000.0000.000
194A195ARG10.9850.98927.8260.1190.1190.0000.0000.0000.000
195A196ASP-1-0.907-0.96724.200-0.159-0.1590.0000.0000.0000.000
196A197LEU00.0660.02520.792-0.010-0.0100.0000.0000.0000.000
197A198PRO00.0600.03119.258-0.026-0.0260.0000.0000.0000.000
198A199ALA0-0.0070.01019.628-0.034-0.0340.0000.0000.0000.000
199A200LEU0-0.028-0.01222.031-0.011-0.0110.0000.0000.0000.000
200A201THR00.001-0.02716.774-0.006-0.0060.0000.0000.0000.000
201A202ARG10.8290.91616.3740.1660.1660.0000.0000.0000.000
202A203GLN0-0.092-0.05617.085-0.031-0.0310.0000.0000.0000.000
203A204ALA0-0.040-0.00216.6420.0010.0010.0000.0000.0000.000
204A205ASP-1-0.803-0.87615.603-0.640-0.6400.0000.0000.0000.000
205A206ILE0-0.026-0.01114.684-0.118-0.1180.0000.0000.0000.000
206A207VAL00.0220.01214.5120.1000.1000.0000.0000.0000.000
207A208VAL0-0.020-0.00815.500-0.044-0.0440.0000.0000.0000.000
208A209ALA00.0100.01116.5020.0480.0480.0000.0000.0000.000
209A210ALA0-0.011-0.01818.2750.0060.0060.0000.0000.0000.000
210A211VAL0-0.072-0.05521.1250.0200.0200.0000.0000.0000.000
211A212GLY0-0.048-0.01022.0070.0190.0190.0000.0000.0000.000
212A213VAL0-0.073-0.04721.4590.0200.0200.0000.0000.0000.000
213A214ALA00.0270.01319.666-0.019-0.0190.0000.0000.0000.000
214A215HIS0-0.046-0.03814.9720.0330.0330.0000.0000.0000.000
215A216LEU0-0.0100.01216.7440.0040.0040.0000.0000.0000.000
216A217LEU0-0.032-0.02513.3430.0000.0000.0000.0000.0000.000
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