Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: Q1L7Y

Calculation Name: 2Y2C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y2C

Chain ID: A

ChEMBL ID:

UniProt ID: P82974

Base Structure: X-ray

Registration Date: 2023-03-14

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1941852.333937
FMO2-HF: Nuclear repulsion 1872096.250883
FMO2-HF: Total energy -69756.083054
FMO2-MP2: Total energy -69960.806216


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:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-25.642-26.22122.187-9.556-12.0540.004
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.015
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].
3A4ASP-1-0.795-0.8673.893-1.821-0.146-0.008-0.745-0.9230.000
4A5GLU-1-0.855-0.9266.5981.0471.0470.0000.0000.0000.000
5A6GLY00.0400.0308.5750.0450.0450.0000.0000.0000.000
6A7TRP0-0.018-0.0217.2690.0770.0770.0000.0000.0000.000
7A8LEU00.007-0.0032.703-1.2130.5252.211-1.398-2.5490.011
8A9ALA0-0.014-0.0261.820-6.836-14.92017.582-5.536-3.9630.014
9A10GLU-1-0.921-0.9662.768-13.332-9.7580.505-1.277-2.802-0.022
10A11ALA0-0.0330.0005.103-0.538-0.494-0.001-0.002-0.0410.000
11A12ARG10.7490.8347.500-0.603-0.6030.0000.0000.0000.000
12A13ARG10.7680.8655.626-2.114-2.1140.0000.0000.0000.000
13A14VAL0-0.028-0.02011.595-0.189-0.1890.0000.0000.0000.000
14A15PRO0-0.024-0.02014.406-0.003-0.0030.0000.0000.0000.000
15A16SER00.012-0.00516.184-0.096-0.0960.0000.0000.0000.000
16A17PRO0-0.011-0.01318.9330.0070.0070.0000.0000.0000.000
17A18HIS0-0.072-0.04321.180-0.051-0.0510.0000.0000.0000.000
18A19TYR00.0250.02017.0990.0560.0560.0000.0000.0000.000
19A20ASP-1-0.796-0.84820.4610.2830.2830.0000.0000.0000.000
20A21CYS00.0140.00019.7140.0500.0500.0000.0000.0000.000
21A22ARG10.7730.88314.379-0.552-0.5520.0000.0000.0000.000
22A23PRO0-0.015-0.01520.733-0.016-0.0160.0000.0000.0000.000
23A24ASP-1-0.936-0.96522.5420.1840.1840.0000.0000.0000.000
24A25ASP-1-0.930-0.94919.9070.2270.2270.0000.0000.0000.000
25A26GLU-1-0.832-0.87619.1160.2450.2450.0000.0000.0000.000
26A27ASN0-0.014-0.00915.1410.0440.0440.0000.0000.0000.000
27A28PRO0-0.0240.00012.834-0.038-0.0380.0000.0000.0000.000
28A29SER0-0.008-0.01914.640-0.001-0.0010.0000.0000.0000.000
29A30LEU0-0.040-0.01716.371-0.036-0.0360.0000.0000.0000.000
30A31LEU0-0.0150.00211.9230.0600.0600.0000.0000.0000.000
31A32VAL0-0.028-0.01815.415-0.068-0.0680.0000.0000.0000.000
32A33VAL00.0170.00915.1610.0590.0590.0000.0000.0000.000
33A34HIS10.8130.90217.196-0.414-0.4140.0000.0000.0000.000
34A35ASN0-0.094-0.05518.8350.0040.0040.0000.0000.0000.000
35A36ILE00.0550.03920.221-0.010-0.0100.0000.0000.0000.000
36A37SER00.003-0.00622.405-0.005-0.0050.0000.0000.0000.000
37A38LEU0-0.049-0.00724.354-0.003-0.0030.0000.0000.0000.000
38A39PRO00.0320.00526.5260.0060.0060.0000.0000.0000.000
39A40PRO0-0.0160.00128.4170.0030.0030.0000.0000.0000.000
40A41GLY00.0100.00528.015-0.012-0.0120.0000.0000.0000.000
41A42GLU-1-0.956-0.96927.8640.1090.1090.0000.0000.0000.000
42A43PHE00.001-0.02222.9010.0180.0180.0000.0000.0000.000
43A44GLY0-0.012-0.00421.776-0.016-0.0160.0000.0000.0000.000
44A45GLY00.0100.01022.6110.0060.0060.0000.0000.0000.000
45A46PRO00.0200.00322.2030.0260.0260.0000.0000.0000.000
46A47TRP00.028-0.00522.8700.0260.0260.0000.0000.0000.000
47A48ILE00.0370.03119.4080.0010.0010.0000.0000.0000.000
48A49ASP-1-0.745-0.84617.8840.4710.4710.0000.0000.0000.000
49A50ALA00.0060.02720.1540.0100.0100.0000.0000.0000.000
50A51LEU00.0020.00823.572-0.009-0.0090.0000.0000.0000.000
51A52PHE0-0.022-0.01118.480-0.002-0.0020.0000.0000.0000.000
52A53THR0-0.023-0.00619.7060.0270.0270.0000.0000.0000.000
53A54GLY00.0040.00922.013-0.016-0.0160.0000.0000.0000.000
54A55THR0-0.073-0.05024.116-0.025-0.0250.0000.0000.0000.000
55A56ILE0-0.060-0.01726.692-0.014-0.0140.0000.0000.0000.000
56A57ASP-1-0.757-0.87628.1070.1210.1210.0000.0000.0000.000
57A58PRO0-0.023-0.02131.6870.0000.0000.0000.0000.0000.000
58A59ASN0-0.084-0.06534.093-0.011-0.0110.0000.0000.0000.000
59A60ALA0-0.028-0.00732.141-0.006-0.0060.0000.0000.0000.000
60A61HIS00.0520.02232.748-0.001-0.0010.0000.0000.0000.000
61A62PRO00.004-0.00434.6110.0050.0050.0000.0000.0000.000
62A63TYR00.0110.00629.300-0.003-0.0030.0000.0000.0000.000
63A64PHE00.015-0.00729.1830.0090.0090.0000.0000.0000.000
64A65ALA00.0080.00932.3980.0060.0060.0000.0000.0000.000
65A66GLY0-0.0270.00735.004-0.002-0.0020.0000.0000.0000.000
66A67ILE0-0.009-0.01527.9540.0030.0030.0000.0000.0000.000
67A68ALA00.0240.01430.1730.0130.0130.0000.0000.0000.000
68A69HIS0-0.065-0.02431.2340.0050.0050.0000.0000.0000.000
69A70LEU0-0.044-0.01927.4810.0020.0020.0000.0000.0000.000
70A71ARG10.9400.97826.771-0.222-0.2220.0000.0000.0000.000
71A72VAL0-0.018-0.00323.7320.0020.0020.0000.0000.0000.000
72A73SER00.006-0.02418.7410.0060.0060.0000.0000.0000.000
73A74ALA00.0220.02616.491-0.023-0.0230.0000.0000.0000.000
74A75HIS00.005-0.00211.9370.0000.0000.0000.0000.0000.000
75A76CYS0-0.038-0.02210.0420.2560.2560.0000.0000.0000.000
76A77LEU00.0070.01812.674-0.152-0.1520.0000.0000.0000.000
77A78ILE0-0.0220.01210.5940.0950.0950.0000.0000.0000.000
78A79ARG10.8660.91613.751-0.360-0.3600.0000.0000.0000.000
79A80ARG10.8240.89016.191-0.164-0.1640.0000.0000.0000.000
80A81ASP-1-0.865-0.92416.1520.1450.1450.0000.0000.0000.000
81A82GLY0-0.0030.00513.514-0.065-0.0650.0000.0000.0000.000
82A83GLU-1-0.797-0.87511.5570.4140.4140.0000.0000.0000.000
83A84ILE00.0080.0067.0750.0420.0420.0000.0000.0000.000
84A85VAL0-0.0080.00910.1250.0660.0660.0000.0000.0000.000
85A86GLN0-0.013-0.0277.7490.8190.8190.0000.0000.0000.000
86A87TYR0-0.013-0.03011.323-0.058-0.0580.0000.0000.0000.000
87A88VAL0-0.0170.00113.225-0.107-0.1070.0000.0000.0000.000
88A89PRO00.0020.03010.7640.2090.2090.0000.0000.0000.000
89A90PHE00.013-0.0295.805-0.350-0.3500.0000.0000.0000.000
90A91ASP-1-0.786-0.88311.0440.5560.5560.0000.0000.0000.000
91A92LYS10.7890.89313.405-0.734-0.7340.0000.0000.0000.000
92A93ARG10.7660.84115.706-0.245-0.2450.0000.0000.0000.000
93A94ALA00.0270.02116.343-0.023-0.0230.0000.0000.0000.000
94A95TRP0-0.124-0.07318.330-0.050-0.0500.0000.0000.0000.000
95A96HIS00.1090.06318.033-0.036-0.0360.0000.0000.0000.000
96A97ALA00.0080.01521.110-0.025-0.0250.0000.0000.0000.000
97A98GLY00.0300.01023.181-0.028-0.0280.0000.0000.0000.000
98A99VAL00.0030.00126.4230.0020.0020.0000.0000.0000.000
99A100SER00.0030.00325.6040.0030.0030.0000.0000.0000.000
100A101SER0-0.016-0.02127.3710.0000.0000.0000.0000.0000.000
101A102TYR00.027-0.00821.7680.0010.0010.0000.0000.0000.000
102A103GLN0-0.036-0.01923.964-0.011-0.0110.0000.0000.0000.000
103A104GLY00.0230.02227.911-0.008-0.0080.0000.0000.0000.000
104A105ARG10.7810.86422.950-0.221-0.2210.0000.0000.0000.000
105A106GLU-1-0.893-0.96326.7830.1570.1570.0000.0000.0000.000
106A107ARG10.9380.96426.143-0.162-0.1620.0000.0000.0000.000
107A108CYS00.0560.03621.8050.0110.0110.0000.0000.0000.000
108A109ASN00.0020.03320.3700.0360.0360.0000.0000.0000.000
109A110ASP-1-0.792-0.89619.4780.3000.3000.0000.0000.0000.000
110A111PHE00.0090.02618.9310.0210.0210.0000.0000.0000.000
111A112SER0-0.059-0.05216.5920.0130.0130.0000.0000.0000.000
112A113ILE00.0380.01510.4160.0280.0280.0000.0000.0000.000
113A114GLY00.0050.01614.357-0.067-0.0670.0000.0000.0000.000
114A115ILE0-0.016-0.02210.6570.1100.1100.0000.0000.0000.000
115A116GLU-1-0.844-0.94714.2360.2820.2820.0000.0000.0000.000
116A117LEU0-0.023-0.00314.4750.0410.0410.0000.0000.0000.000
117A118GLU-1-0.733-0.84717.3490.2040.2040.0000.0000.0000.000
118A119GLY00.016-0.00419.812-0.029-0.0290.0000.0000.0000.000
119A120THR00.0410.03022.7270.0030.0030.0000.0000.0000.000
120A121ASP-1-0.733-0.83225.0250.1570.1570.0000.0000.0000.000
121A122THR0-0.040-0.02326.724-0.006-0.0060.0000.0000.0000.000
122A123LEU0-0.031-0.00325.673-0.013-0.0130.0000.0000.0000.000
123A124ALA00.0100.01123.3820.0120.0120.0000.0000.0000.000
124A125TYR0-0.009-0.00918.3410.0080.0080.0000.0000.0000.000
125A126THR0-0.009-0.02117.859-0.022-0.0220.0000.0000.0000.000
126A127ASP-1-0.814-0.89817.141-0.012-0.0120.0000.0000.0000.000
127A128ALA00.0160.01613.897-0.020-0.0200.0000.0000.0000.000
128A129GLN0-0.008-0.01912.804-0.024-0.0240.0000.0000.0000.000
129A130TYR00.0160.01313.1270.0580.0580.0000.0000.0000.000
130A131GLN00.0170.00410.6640.0040.0040.0000.0000.0000.000
131A132GLN0-0.019-0.0088.162-0.189-0.1890.0000.0000.0000.000
132A133LEU00.0160.0068.2160.2000.2000.0000.0000.0000.000
133A134ALA0-0.0190.0089.3120.1460.1460.0000.0000.0000.000
134A135ALA00.0000.0084.6940.0060.065-0.001-0.004-0.0550.000
135A136VAL00.0250.0054.6380.2240.428-0.001-0.011-0.1920.000
136A137THR0-0.008-0.0245.7230.2550.2550.0000.0000.0000.000
137A138ASN0-0.006-0.0115.8090.0130.0130.0000.0000.0000.000
138A139ALA0-0.0010.0152.454-0.576-0.4301.896-0.584-1.4580.001
139A140LEU0-0.009-0.0053.862-0.455-0.3900.0040.001-0.0710.000
140A141ILE0-0.009-0.0047.172-0.221-0.2210.0000.0000.0000.000
141A142THR0-0.042-0.0315.724-0.183-0.1830.0000.0000.0000.000
142A143ARG10.8250.9107.701-0.417-0.4170.0000.0000.0000.000
143A144TYR0-0.018-0.0079.157-0.089-0.0890.0000.0000.0000.000
144A145PRO00.0600.03111.8660.0220.0220.0000.0000.0000.000
145A146ALA0-0.0010.00113.180-0.016-0.0160.0000.0000.0000.000
146A147ILE00.0440.02211.378-0.017-0.0170.0000.0000.0000.000
147A148ALA00.0020.00413.415-0.008-0.0080.0000.0000.0000.000
148A149ASN0-0.072-0.03214.713-0.041-0.0410.0000.0000.0000.000
149A150ASN0-0.065-0.01517.060-0.026-0.0260.0000.0000.0000.000
150A151MET00.0370.03014.3820.0590.0590.0000.0000.0000.000
151A152THR0-0.008-0.01117.343-0.050-0.0500.0000.0000.0000.000
152A153GLY00.0800.02718.8660.0360.0360.0000.0000.0000.000
153A154HIS0-0.011-0.01321.303-0.004-0.0040.0000.0000.0000.000
154A155CYS0-0.058-0.03323.355-0.012-0.0120.0000.0000.0000.000
155A156ASN0-0.044-0.01923.657-0.005-0.0050.0000.0000.0000.000
156A157ILE0-0.026-0.00622.335-0.004-0.0040.0000.0000.0000.000
157A158ALA0-0.021-0.01626.125-0.002-0.0020.0000.0000.0000.000
158A159PRO00.0610.03928.4360.0000.0000.0000.0000.0000.000
159A160GLU-1-0.938-0.98130.6700.1110.1110.0000.0000.0000.000
160A161ARG10.8050.91227.366-0.193-0.1930.0000.0000.0000.000
161A162LYS10.8180.90825.319-0.221-0.2210.0000.0000.0000.000
162A163THR0-0.012-0.03627.836-0.005-0.0050.0000.0000.0000.000
163A164ASP-1-0.733-0.84822.7280.2460.2460.0000.0000.0000.000
164A165PRO0-0.074-0.03019.9520.0040.0040.0000.0000.0000.000
165A166GLY00.1060.06022.237-0.011-0.0110.0000.0000.0000.000
166A167PRO0-0.029-0.03524.6270.0010.0010.0000.0000.0000.000
167A168SER0-0.051-0.01824.328-0.007-0.0070.0000.0000.0000.000
168A169PHE0-0.025-0.01616.381-0.001-0.0010.0000.0000.0000.000
169A170ASP-1-0.806-0.90620.7520.0460.0460.0000.0000.0000.000
170A171TRP00.0420.00117.3710.0040.0040.0000.0000.0000.000
171A172ALA0-0.0280.00119.2130.0020.0020.0000.0000.0000.000
172A173ARG10.8050.88116.9800.0000.0000.0000.0000.0000.000
173A174PHE00.008-0.00711.796-0.022-0.0220.0000.0000.0000.000
174A175ARG10.9120.94614.354-0.157-0.1570.0000.0000.0000.000
175A176ALA0-0.024-0.00115.583-0.011-0.0110.0000.0000.0000.000
176A177LEU0-0.041-0.01011.577-0.041-0.0410.0000.0000.0000.000
177A178VAL0-0.007-0.00910.619-0.015-0.0150.0000.0000.0000.000
178A179THR0-0.041-0.02010.506-0.017-0.0170.0000.0000.0000.000
179A180PRO0-0.0340.0059.710-0.024-0.0240.0000.0000.0000.000