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: YNQ32

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 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 280
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3468123.188979
FMO2-HF: Nuclear repulsion 3365794.372474
FMO2-HF: Total energy -102328.816506
FMO2-MP2: Total energy -102630.046035


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.
-4.984-0.3971.346-3.072-2.862-0.023
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 : 0.036 / q_NPA : 0.020
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].
3A4ILE0-0.020-0.0183.8590.5321.880-0.008-0.728-0.6120.004
4A5MET0-0.028-0.0026.7380.4400.4400.0000.0000.0000.000
5A6LEU0-0.0020.0028.8310.2120.2120.0000.0000.0000.000
6A7ASP-1-0.737-0.87512.251-0.218-0.2180.0000.0000.0000.000
7A8GLY00.0540.02114.5500.0310.0310.0000.0000.0000.000
8A9LYS10.7840.87615.7740.3330.3330.0000.0000.0000.000
9A10ALA00.0430.02417.4710.0260.0260.0000.0000.0000.000
10A11THR00.004-0.00917.8620.0110.0110.0000.0000.0000.000
11A12ARG10.7990.87320.4810.1970.1970.0000.0000.0000.000
12A13ASP-1-0.827-0.88522.757-0.156-0.1560.0000.0000.0000.000
13A14GLU-1-0.836-0.88421.969-0.293-0.2930.0000.0000.0000.000
14A15ILE00.0100.00323.9560.0160.0160.0000.0000.0000.000
15A16PHE0-0.034-0.03126.6990.0150.0150.0000.0000.0000.000
16A17GLY00.0280.02027.8300.0140.0140.0000.0000.0000.000
17A18ASP-1-0.847-0.90228.949-0.151-0.1510.0000.0000.0000.000
18A19LEU0-0.003-0.01530.1770.0120.0120.0000.0000.0000.000
19A20LYS10.8690.94232.4060.0970.0970.0000.0000.0000.000
20A21GLN0-0.069-0.03531.7540.0130.0130.0000.0000.0000.000
21A22ARG10.7460.83231.7160.1550.1550.0000.0000.0000.000
22A23VAL0-0.007-0.00536.4410.0050.0050.0000.0000.0000.000
23A24ALA00.0070.00838.3500.0060.0060.0000.0000.0000.000
24A25ALA0-0.011-0.00939.6910.0050.0050.0000.0000.0000.000
25A26LEU0-0.073-0.03239.4360.0030.0030.0000.0000.0000.000
26A27ASP-1-0.890-0.91642.540-0.062-0.0620.0000.0000.0000.000
27A28ALA0-0.004-0.00144.2390.0040.0040.0000.0000.0000.000
28A29ALA0-0.067-0.03145.6780.0020.0020.0000.0000.0000.000
29A30GLY0-0.018-0.00847.3800.0000.0000.0000.0000.0000.000
30A31ARG10.8390.91943.6020.0820.0820.0000.0000.0000.000
31A32THR00.038-0.01143.307-0.004-0.0040.0000.0000.0000.000
32A33PRO0-0.0090.01639.3510.0010.0010.0000.0000.0000.000
33A34GLY00.0480.00741.3700.0030.0030.0000.0000.0000.000
34A35LEU0-0.040-0.01235.776-0.004-0.0040.0000.0000.0000.000
35A36GLY00.0460.00839.9530.0040.0040.0000.0000.0000.000
36A37THR0-0.031-0.02938.021-0.005-0.0050.0000.0000.0000.000
37A38ILE00.0080.01840.8170.0050.0050.0000.0000.0000.000
38A39LEU0-0.027-0.01139.154-0.005-0.0050.0000.0000.0000.000
39A40VAL00.0120.00542.1630.0030.0030.0000.0000.0000.000
40A41GLY00.0220.01143.300-0.001-0.0010.0000.0000.0000.000
41A42ASP-1-0.914-0.95742.497-0.040-0.0400.0000.0000.0000.000
42A43ASP-1-0.752-0.84236.599-0.060-0.0600.0000.0000.0000.000
43A44PRO00.003-0.00936.060-0.004-0.0040.0000.0000.0000.000
44A45GLY0-0.0040.00733.258-0.002-0.0020.0000.0000.0000.000
45A46SER00.010-0.03433.802-0.008-0.0080.0000.0000.0000.000
46A47GLN0-0.017-0.01635.998-0.003-0.0030.0000.0000.0000.000
47A48ALA0-0.059-0.01732.156-0.001-0.0010.0000.0000.0000.000
48A49TYR0-0.021-0.00928.863-0.007-0.0070.0000.0000.0000.000
49A50VAL00.0330.01832.808-0.005-0.0050.0000.0000.0000.000
50A51ARG10.8930.93635.1520.0530.0530.0000.0000.0000.000
51A52GLY0-0.015-0.00731.4630.0000.0000.0000.0000.0000.000
52A53LYS10.8660.93832.2750.1080.1080.0000.0000.0000.000
53A54HIS00.0360.02733.528-0.004-0.0040.0000.0000.0000.000
54A55ALA0-0.003-0.00233.0710.0010.0010.0000.0000.0000.000
55A56ASP-1-0.810-0.87929.130-0.122-0.1220.0000.0000.0000.000
56A57CYS0-0.0190.00332.341-0.004-0.0040.0000.0000.0000.000
57A58ALA00.0430.02135.4930.0010.0010.0000.0000.0000.000
58A59LYS10.7850.88629.5760.1000.1000.0000.0000.0000.000
59A60VAL0-0.017-0.01131.9190.0010.0010.0000.0000.0000.000
60A61GLY00.0170.00634.5700.0010.0010.0000.0000.0000.000
61A62ILE0-0.044-0.00535.1940.0020.0020.0000.0000.0000.000
62A63THR00.0270.00038.9600.0030.0030.0000.0000.0000.000
63A64SER0-0.031-0.03339.398-0.002-0.0020.0000.0000.0000.000
64A65ILE00.0070.01441.4990.0050.0050.0000.0000.0000.000
65A66ARG10.8400.90539.5330.0570.0570.0000.0000.0000.000
66A67ARG10.8320.88044.1360.0590.0590.0000.0000.0000.000
67A68ASP-1-0.802-0.88542.717-0.059-0.0590.0000.0000.0000.000
68A69LEU0-0.0070.00045.4080.0030.0030.0000.0000.0000.000
69A70PRO00.0400.02446.619-0.001-0.0010.0000.0000.0000.000
70A71ALA00.028-0.01546.646-0.002-0.0020.0000.0000.0000.000
71A72ASP-1-0.900-0.95947.829-0.036-0.0360.0000.0000.0000.000
72A73ILE0-0.0220.00948.1610.0010.0010.0000.0000.0000.000
73A74SER00.0350.01351.745-0.001-0.0010.0000.0000.0000.000
74A75THR00.0730.00350.514-0.001-0.0010.0000.0000.0000.000
75A76ALA0-0.0440.00252.282-0.002-0.0020.0000.0000.0000.000
76A77THR00.0950.05152.511-0.001-0.0010.0000.0000.0000.000
77A78LEU00.0080.02145.917-0.002-0.0020.0000.0000.0000.000
78A79ASN0-0.008-0.02149.481-0.005-0.0050.0000.0000.0000.000
79A80GLU-1-0.873-0.94351.400-0.044-0.0440.0000.0000.0000.000
80A81THR0-0.039-0.03147.6260.0000.0000.0000.0000.0000.000
81A82ILE0-0.023-0.01246.001-0.002-0.0020.0000.0000.0000.000
82A83ASP-1-0.817-0.86548.290-0.057-0.0570.0000.0000.0000.000
83A84GLU-1-0.799-0.86449.925-0.056-0.0560.0000.0000.0000.000
84A85LEU00.002-0.01044.329-0.001-0.0010.0000.0000.0000.000
85A86ASN00.0070.02147.060-0.006-0.0060.0000.0000.0000.000
86A87ALA0-0.018-0.01348.741-0.001-0.0010.0000.0000.0000.000
87A88ASN0-0.067-0.03448.722-0.001-0.0010.0000.0000.0000.000
88A89PRO0-0.012-0.01348.744-0.003-0.0030.0000.0000.0000.000
89A90ASP-1-0.859-0.93047.148-0.062-0.0620.0000.0000.0000.000
90A91CYS0-0.099-0.02244.518-0.006-0.0060.0000.0000.0000.000
91A92THR00.0240.00541.287-0.001-0.0010.0000.0000.0000.000
92A93GLY00.0110.00340.093-0.005-0.0050.0000.0000.0000.000
93A94TYR0-0.039-0.04440.0160.0030.0030.0000.0000.0000.000
94A95ILE0-0.050-0.00435.539-0.005-0.0050.0000.0000.0000.000
95A96VAL00.0480.01438.7570.0060.0060.0000.0000.0000.000
96A97GLN0-0.067-0.04433.616-0.009-0.0090.0000.0000.0000.000
97A98LEU00.0160.03336.3100.0050.0050.0000.0000.0000.000
98A99PRO0-0.038-0.02335.802-0.004-0.0040.0000.0000.0000.000
99A100LEU00.0370.00638.5490.0020.0020.0000.0000.0000.000
100A101PRO0-0.002-0.00742.3260.0000.0000.0000.0000.0000.000
101A102LYS10.8290.90741.3070.0610.0610.0000.0000.0000.000
102A103HIS0-0.042-0.00445.6940.0000.0000.0000.0000.0000.000
103A104LEU0-0.047-0.01646.3130.0000.0000.0000.0000.0000.000
104A105ASP-1-0.851-0.92745.821-0.066-0.0660.0000.0000.0000.000
105A106GLU-1-0.785-0.90640.811-0.071-0.0710.0000.0000.0000.000
106A107ASN0-0.073-0.02741.999-0.007-0.0070.0000.0000.0000.000
107A108ALA00.0330.00943.227-0.002-0.0020.0000.0000.0000.000
108A109ALA0-0.025-0.01244.2860.0000.0000.0000.0000.0000.000
109A110LEU0-0.021-0.02038.805-0.002-0.0020.0000.0000.0000.000
110A111GLU-1-0.901-0.95842.470-0.081-0.0810.0000.0000.0000.000
111A112ARG10.7620.86944.6370.0570.0570.0000.0000.0000.000
112A113VAL0-0.0270.00141.5950.0020.0020.0000.0000.0000.000
113A114ASP-1-0.785-0.89544.772-0.081-0.0810.0000.0000.0000.000
114A115PRO0-0.036-0.01942.033-0.005-0.0050.0000.0000.0000.000
115A116ALA0-0.045-0.02941.586-0.007-0.0070.0000.0000.0000.000
116A117LYS10.8050.90941.9300.0710.0710.0000.0000.0000.000
117A118ASP-1-0.768-0.87437.481-0.120-0.1200.0000.0000.0000.000
118A119ALA00.0190.02436.263-0.007-0.0070.0000.0000.0000.000
119A120ASP-1-0.830-0.95832.525-0.138-0.1380.0000.0000.0000.000
120A121GLY0-0.0180.00032.599-0.012-0.0120.0000.0000.0000.000
121A122LEU0-0.060-0.06031.706-0.008-0.0080.0000.0000.0000.000
122A123HIS00.0640.06335.623-0.001-0.0010.0000.0000.0000.000
123A124PRO00.0380.00938.817-0.006-0.0060.0000.0000.0000.000
124A125THR0-0.010-0.01840.2520.0000.0000.0000.0000.0000.000
125A126ASN0-0.069-0.05637.4680.0000.0000.0000.0000.0000.000
126A127LEU00.0020.00333.780-0.008-0.0080.0000.0000.0000.000
127A128GLY00.0210.01236.737-0.004-0.0040.0000.0000.0000.000
128A129ARG10.8790.93039.2210.1000.1000.0000.0000.0000.000
129A130LEU0-0.029-0.00631.450-0.003-0.0030.0000.0000.0000.000
130A131VAL0-0.039-0.02035.517-0.006-0.0060.0000.0000.0000.000
131A132LEU0-0.049-0.02537.1230.0000.0000.0000.0000.0000.000
132A133GLY0-0.0100.01436.8230.0020.0020.0000.0000.0000.000
133A134THR0-0.041-0.02437.8860.0020.0020.0000.0000.0000.000
134A135PRO0-0.032-0.02437.801-0.005-0.0050.0000.0000.0000.000
135A136ALA00.0360.01837.3000.0080.0080.0000.0000.0000.000
136A137PRO00.0070.02635.908-0.008-0.0080.0000.0000.0000.000
137A138LEU00.0140.00030.311-0.002-0.0020.0000.0000.0000.000
138A139PRO00.0040.02329.966-0.002-0.0020.0000.0000.0000.000
139A140CYS0-0.0140.02528.472-0.016-0.0160.0000.0000.0000.000
140A141THR00.0320.02823.375-0.013-0.0130.0000.0000.0000.000
141A142PRO0-0.022-0.00623.971-0.027-0.0270.0000.0000.0000.000
142A143ARG10.8150.88024.5160.1660.1660.0000.0000.0000.000
143A144GLY00.0330.00323.333-0.013-0.0130.0000.0000.0000.000
144A145ILE0-0.022-0.01119.250-0.032-0.0320.0000.0000.0000.000
145A146VAL00.0170.00219.771-0.045-0.0450.0000.0000.0000.000
146A147HIS00.0070.01121.341-0.016-0.0160.0000.0000.0000.000
147A148LEU0-0.010-0.01215.564-0.012-0.0120.0000.0000.0000.000
148A149LEU0-0.012-0.00515.403-0.064-0.0640.0000.0000.0000.000
149A150ARG10.8810.90516.9200.2750.2750.0000.0000.0000.000
150A151ARG10.7580.86017.8640.3920.3920.0000.0000.0000.000
151A152TYR0-0.011-0.00812.549-0.003-0.0030.0000.0000.0000.000
152A153ASP-1-0.906-0.94814.551-0.618-0.6180.0000.0000.0000.000
153A154ILE0-0.051-0.00812.8620.0050.0050.0000.0000.0000.000
154A155SER0-0.031-0.01816.4920.0610.0610.0000.0000.0000.000
155A156ILE0-0.020-0.01619.495-0.009-0.0090.0000.0000.0000.000
156A157ALA00.0150.01021.7550.0140.0140.0000.0000.0000.000
157A158GLY0-0.034-0.02023.080-0.018-0.0180.0000.0000.0000.000
158A159ALA00.0090.01019.1120.0120.0120.0000.0000.0000.000
159A160HIS0-0.013-0.01119.9050.0490.0490.0000.0000.0000.000
160A161VAL00.014-0.00319.048-0.049-0.0490.0000.0000.0000.000
161A162VAL00.0090.00819.0420.0470.0470.0000.0000.0000.000
162A163VAL0-0.016-0.00919.843-0.030-0.0300.0000.0000.0000.000
163A164ILE00.0070.01118.3840.0370.0370.0000.0000.0000.000
164A165GLY00.0760.03422.2200.0020.0020.0000.0000.0000.000
165A166ARG10.8920.93325.1390.1240.1240.0000.0000.0000.000
166A167GLY00.0370.02227.9100.0130.0130.0000.0000.0000.000
167A168VAL00.015-0.02129.380-0.012-0.0120.0000.0000.0000.000
168A169THR00.0390.02829.404-0.004-0.0040.0000.0000.0000.000
169A170VAL00.0150.00023.584-0.009-0.0090.0000.0000.0000.000
170A171GLY00.0520.03125.462-0.006-0.0060.0000.0000.0000.000
171A172ARG10.9260.96526.4200.1350.1350.0000.0000.0000.000
172A173PRO00.0330.01829.162-0.002-0.0020.0000.0000.0000.000
173A174LEU00.0040.00822.438-0.002-0.0020.0000.0000.0000.000
174A175GLY00.0630.02026.517-0.013-0.0130.0000.0000.0000.000
175A176LEU0-0.0200.00827.8370.0000.0000.0000.0000.0000.000
176A177LEU0-0.037-0.01526.2470.0010.0010.0000.0000.0000.000
177A178LEU00.013-0.00322.626-0.005-0.0050.0000.0000.0000.000
178A179THR0-0.009-0.01426.7110.0010.0010.0000.0000.0000.000
179A180ARG10.8610.93429.6540.2190.2190.0000.0000.0000.000
180A181ARG10.9800.97530.2770.1380.1380.0000.0000.0000.000
181A182SER0-0.038-0.02930.5050.0030.0030.0000.0000.0000.000
182A183GLU-1-0.820-0.84125.919-0.253-0.2530.0000.0000.0000.000
183A184ASN0-0.026-0.03026.031-0.005-0.0050.0000.0000.0000.000
184A185ALA00.0600.05623.389-0.004-0.0040.0000.0000.0000.000
185A186THR0-0.031-0.00724.0530.0390.0390.0000.0000.0000.000
186A187VAL0-0.032-0.01723.680-0.026-0.0260.0000.0000.0000.000
187A188THR0-0.008-0.01323.3680.0230.0230.0000.0000.0000.000
188A189LEU0-0.0210.00024.435-0.014-0.0140.0000.0000.0000.000
189A190CYS0-0.034-0.01323.9100.0230.0230.0000.0000.0000.000
190A191HIS00.006-0.02125.9120.0030.0030.0000.0000.0000.000
191A192THR00.0680.02427.2560.0000.0000.0000.0000.0000.000
192A193GLY00.0000.01429.0180.0110.0110.0000.0000.0000.000
193A194THR0-0.048-0.01625.5080.0030.0030.0000.0000.0000.000
194A195ARG10.9680.97727.2280.1110.1110.0000.0000.0000.000
195A196ASP-1-0.863-0.94423.805-0.147-0.1470.0000.0000.0000.000
196A197LEU00.0590.02821.216-0.009-0.0090.0000.0000.0000.000
197A198PRO00.0410.02319.536-0.024-0.0240.0000.0000.0000.000
198A199ALA0-0.0220.00019.609-0.028-0.0280.0000.0000.0000.000
199A200LEU0-0.038-0.00821.894-0.007-0.0070.0000.0000.0000.000
200A201THR0-0.009-0.03316.940-0.005-0.0050.0000.0000.0000.000
201A202ARG10.8480.91215.9570.1400.1400.0000.0000.0000.000
202A203GLN0-0.082-0.04716.794-0.015-0.0150.0000.0000.0000.000
203A204ALA0-0.0250.00715.8170.0100.0100.0000.0000.0000.000
204A205ASP-1-0.807-0.88215.265-0.562-0.5620.0000.0000.0000.000
205A206ILE0-0.033-0.01714.492-0.115-0.1150.0000.0000.0000.000
206A207VAL00.0190.01514.6560.0980.0980.0000.0000.0000.000
207A208VAL0-0.017-0.01815.806-0.049-0.0490.0000.0000.0000.000
208A209ALA0-0.0040.01117.0160.0530.0530.0000.0000.0000.000
209A210ALA0-0.004-0.02118.7410.0000.0000.0000.0000.0000.000
210A211VAL0-0.078-0.05221.5950.0240.0240.0000.0000.0000.000
211A212GLY0-0.034-0.00722.3540.0190.0190.0000.0000.0000.000
212A213VAL0-0.084-0.05621.7780.0230.0230.0000.0000.0000.000
213A214ALA00.0330.01519.651-0.021-0.0210.0000.0000.0000.000
214A215HIS0-0.044-0.02814.9690.0440.0440.0000.0000.0000.000
215A216LEU0-0.0150.01016.8190.0050.0050.0000.0000.0000.000
216A217LEU0-0.020-0.01913.5830.0100.0100.0000.0000.0000.000
217A218THR00.064-0.00813.770-0.045-0.0450.0000.0000.0000.000
218A219ALA00.0520.0119.809-0.072-0.0720.0000.0000.0000.000
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