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: 9G7L2

Calculation Name: 2AZO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AZO

Chain ID: A

ChEMBL ID:

UniProt ID: P06722

Base Structure: X-ray

Registration Date: 2023-03-13

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646111.085231
FMO2-HF: Nuclear repulsion 2558921.541302
FMO2-HF: Total energy -87189.543928
FMO2-MP2: Total energy -87449.131881


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:3:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-15.146-12.8619.689-5.245-6.7290.013
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / 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].
3A5ARG10.9500.9643.226-0.6012.0230.065-1.418-1.272-0.001
4A6PRO00.0310.0275.8600.7930.7930.0000.0000.0000.000
5A7LEU0-0.0090.0169.645-0.111-0.1110.0000.0000.0000.000
6A8LEU0-0.027-0.02411.5740.0920.0920.0000.0000.0000.000
7A9SER0-0.038-0.01614.6340.1100.1100.0000.0000.0000.000
8A10PRO00.0320.02516.704-0.118-0.1180.0000.0000.0000.000
9A11PRO0-0.0100.00416.220-0.017-0.0170.0000.0000.0000.000
10A12GLU-1-0.898-0.95318.016-0.484-0.4840.0000.0000.0000.000
11A13THR0-0.049-0.05019.4910.0420.0420.0000.0000.0000.000
12A14GLU-1-0.736-0.84918.866-0.258-0.2580.0000.0000.0000.000
13A15GLU-1-0.827-0.90517.375-0.307-0.3070.0000.0000.0000.000
14A16GLN0-0.037-0.01414.582-0.100-0.1000.0000.0000.0000.000
15A17LEU00.0260.02213.788-0.122-0.1220.0000.0000.0000.000
16A18LEU0-0.016-0.00914.413-0.049-0.0490.0000.0000.0000.000
17A19ALA00.0140.00611.2210.0440.0440.0000.0000.0000.000
18A20GLN0-0.030-0.0289.249-0.087-0.0870.0000.0000.0000.000
19A21ALA00.000-0.0179.892-0.088-0.0880.0000.0000.0000.000
20A22GLN0-0.057-0.04110.3100.0820.0820.0000.0000.0000.000
21A23GLN0-0.077-0.0224.999-0.146-0.110-0.001-0.005-0.0300.000
22A24LEU0-0.013-0.0116.4220.4830.4830.0000.0000.0000.000
23A25SER0-0.019-0.0248.8960.1670.1670.0000.0000.0000.000
24A26GLY0-0.057-0.0208.6350.5430.5430.0000.0000.0000.000
25A27TYR0-0.004-0.0091.878-11.602-11.8166.753-3.128-3.4100.017
26A28THR0-0.072-0.0757.964-0.580-0.5800.0000.0000.0000.000
27A29LEU0-0.016-0.0178.764-0.347-0.3470.0000.0000.0000.000
28A30GLY00.0260.01110.593-0.247-0.2470.0000.0000.0000.000
29A31GLU-1-0.847-0.8885.0531.4331.4330.0000.0000.0000.000
30A32LEU00.0240.0075.832-1.146-1.1460.0000.0000.0000.000
31A33ALA00.0060.0127.263-0.298-0.2980.0000.0000.0000.000
32A34ALA00.0230.0137.483-0.161-0.1610.0000.0000.0000.000
33A35LEU0-0.064-0.0372.198-1.295-1.4562.872-0.694-2.017-0.003
34A36VAL0-0.031-0.0115.812-0.285-0.2850.0000.0000.0000.000
35A37GLY0-0.026-0.0049.1550.4000.4000.0000.0000.0000.000
36A38LEU0-0.037-0.00311.3220.3220.3220.0000.0000.0000.000
37A39VAL00.018-0.00512.454-0.028-0.0280.0000.0000.0000.000
38A40THR0-0.018-0.01513.5830.0190.0190.0000.0000.0000.000
39A41PRO0-0.0430.00215.6990.0600.0600.0000.0000.0000.000
40A42GLU-1-0.744-0.86119.085-0.206-0.2060.0000.0000.0000.000
41A43ASN0-0.031-0.02820.7320.0420.0420.0000.0000.0000.000
42A44LEU00.0740.04119.984-0.018-0.0180.0000.0000.0000.000
43A45LYS10.8960.92822.5900.0890.0890.0000.0000.0000.000
44A46ARG10.7920.87422.4990.2530.2530.0000.0000.0000.000
45A47ASP-1-0.797-0.90021.189-0.468-0.4680.0000.0000.0000.000
46A48LYS10.9050.94822.3440.1990.1990.0000.0000.0000.000
47A49GLY00.0130.00422.6770.0260.0260.0000.0000.0000.000
48A50TRP00.0160.02712.8750.0030.0030.0000.0000.0000.000
49A51ILE00.008-0.00716.117-0.065-0.0650.0000.0000.0000.000
50A52GLY0-0.0010.01616.663-0.043-0.0430.0000.0000.0000.000
51A53VAL00.0750.03217.474-0.056-0.0560.0000.0000.0000.000
52A54LEU0-0.035-0.00710.714-0.085-0.0850.0000.0000.0000.000
53A55LEU00.008-0.00913.196-0.158-0.1580.0000.0000.0000.000
54A56GLU-1-0.948-0.97914.859-0.668-0.6680.0000.0000.0000.000
55A57ILE0-0.024-0.01312.255-0.060-0.0600.0000.0000.0000.000
56A58TRP0-0.052-0.0334.823-0.252-0.2520.0000.0000.0000.000
57A59LEU0-0.023-0.01911.883-0.150-0.1500.0000.0000.0000.000
58A60GLY00.0330.00214.7170.1040.1040.0000.0000.0000.000
59A61ALA0-0.0020.02315.671-0.062-0.0620.0000.0000.0000.000
60A62SER0-0.003-0.01416.7620.1030.1030.0000.0000.0000.000
61A63ALA00.0090.01318.3510.0840.0840.0000.0000.0000.000
62A64GLY0-0.030-0.00721.6410.0400.0400.0000.0000.0000.000
63A65SER0-0.018-0.01523.2600.0280.0280.0000.0000.0000.000
64A66LYS10.9080.94626.5870.4670.4670.0000.0000.0000.000
65A67PRO0-0.0080.01624.8230.0350.0350.0000.0000.0000.000
66A68GLU-1-0.902-0.96226.960-0.346-0.3460.0000.0000.0000.000
67A69GLN0-0.057-0.02524.1410.0190.0190.0000.0000.0000.000
68A70ASP-1-0.799-0.89121.559-0.573-0.5730.0000.0000.0000.000
69A71PHE0-0.033-0.03618.0290.0450.0450.0000.0000.0000.000
70A72ALA0-0.015-0.01423.1710.0420.0420.0000.0000.0000.000
71A73ALA0-0.010-0.00525.1440.0320.0320.0000.0000.0000.000
72A74LEU0-0.0200.00420.4500.0240.0240.0000.0000.0000.000
73A75GLY0-0.0060.00624.9910.0300.0300.0000.0000.0000.000
74A76VAL0-0.025-0.00522.0210.0340.0340.0000.0000.0000.000
75A77GLU-1-0.773-0.86724.323-0.254-0.2540.0000.0000.0000.000
76A78LEU00.0290.01518.7070.0350.0350.0000.0000.0000.000
77A79LYS10.8160.90222.1210.1940.1940.0000.0000.0000.000
78A80THR00.0520.02818.2540.0250.0250.0000.0000.0000.000
79A81ILE0-0.047-0.02020.4690.0110.0110.0000.0000.0000.000
80A82PRO00.0000.01521.0080.0300.0300.0000.0000.0000.000
81A83VAL00.0000.00119.7720.0080.0080.0000.0000.0000.000
82A84ASP-1-0.729-0.86221.6870.2710.2710.0000.0000.0000.000
83A85SER0-0.010-0.00919.7500.0040.0040.0000.0000.0000.000
84A86LEU0-0.061-0.03220.3400.0730.0730.0000.0000.0000.000
85A87GLY00.0130.01820.7670.0060.0060.0000.0000.0000.000
86A88ARG10.8680.91421.507-0.316-0.3160.0000.0000.0000.000
87A89PRO00.0330.02124.956-0.002-0.0020.0000.0000.0000.000
88A90LEU0-0.021-0.00623.8310.0070.0070.0000.0000.0000.000
89A91GLU-1-0.973-0.99127.274-0.028-0.0280.0000.0000.0000.000
90A92THR0-0.099-0.05029.6230.0010.0010.0000.0000.0000.000
91A93THR00.0400.01126.975-0.005-0.0050.0000.0000.0000.000
92A94PHE0-0.014-0.00229.356-0.002-0.0020.0000.0000.0000.000
93A95VAL00.0020.01429.435-0.010-0.0100.0000.0000.0000.000
94A96CYS0-0.012-0.01931.412-0.019-0.0190.0000.0000.0000.000
95A97VAL0-0.018-0.01533.8130.0130.0130.0000.0000.0000.000
96A98ALA00.0460.03336.769-0.001-0.0010.0000.0000.0000.000
97A99PRO0-0.0130.00140.1940.0030.0030.0000.0000.0000.000
98A100LEU00.027-0.00242.8580.0050.0050.0000.0000.0000.000
99A101THR00.0060.00946.2650.0030.0030.0000.0000.0000.000
100A102GLY00.000-0.00546.668-0.004-0.0040.0000.0000.0000.000
101A103ASN0-0.033-0.02145.551-0.003-0.0030.0000.0000.0000.000
102A104SER00.0340.02246.8630.0020.0020.0000.0000.0000.000
103A105GLY0-0.011-0.01049.418-0.004-0.0040.0000.0000.0000.000
104A106VAL0-0.036-0.00342.799-0.002-0.0020.0000.0000.0000.000
105A107THR00.004-0.01644.3000.0040.0040.0000.0000.0000.000
106A108TRP00.0310.00136.454-0.010-0.0100.0000.0000.0000.000
107A109GLU-1-0.806-0.87739.968-0.079-0.0790.0000.0000.0000.000
108A110THR00.006-0.00239.491-0.009-0.0090.0000.0000.0000.000
109A111SER0-0.0180.01538.995-0.008-0.0080.0000.0000.0000.000
110A112HIS00.026-0.01035.666-0.010-0.0100.0000.0000.0000.000
111A113VAL0-0.021-0.01234.673-0.009-0.0090.0000.0000.0000.000
112A114ARG10.9801.01034.0640.0960.0960.0000.0000.0000.000
113A115HIS00.0220.01531.502-0.008-0.0080.0000.0000.0000.000
114A116LYS10.7740.87129.9210.2020.2020.0000.0000.0000.000
115A117LEU0-0.019-0.02029.463-0.001-0.0010.0000.0000.0000.000
116A118LYS10.8260.91729.2610.2090.2090.0000.0000.0000.000
117A119ARG10.8290.88023.3650.1450.1450.0000.0000.0000.000
118A120VAL0-0.045-0.00824.077-0.021-0.0210.0000.0000.0000.000
119A121LEU00.0360.02116.9070.0180.0180.0000.0000.0000.000
120A122TRP00.0020.00521.046-0.032-0.0320.0000.0000.0000.000
121A123ILE00.0460.00815.5610.0180.0180.0000.0000.0000.000
122A124PRO00.0050.00117.794-0.024-0.0240.0000.0000.0000.000
123A125VAL00.0380.02515.2740.0140.0140.0000.0000.0000.000
124A126GLU-1-0.779-0.84516.1450.4880.4880.0000.0000.0000.000
125A127GLY00.0330.00318.581-0.058-0.0580.0000.0000.0000.000
126A128GLU-1-0.777-0.85621.6950.0790.0790.0000.0000.0000.000
127A129ARG10.8920.96522.526-0.037-0.0370.0000.0000.0000.000
128A130SER0-0.110-0.11024.101-0.014-0.0140.0000.0000.0000.000
129A131ILE00.0430.03917.882-0.001-0.0010.0000.0000.0000.000
130A132PRO00.0480.02118.174-0.054-0.0540.0000.0000.0000.000
131A133LEU0-0.024-0.01016.9180.0370.0370.0000.0000.0000.000
132A134ALA00.0540.00913.540-0.012-0.0120.0000.0000.0000.000
133A135GLN00.003-0.01012.530-0.055-0.0550.0000.0000.0000.000
134A136ARG10.7070.87114.2890.1040.1040.0000.0000.0000.000
135A137ARG10.8670.90111.871-0.924-0.9240.0000.0000.0000.000
136A138VAL00.0130.02211.312-0.144-0.1440.0000.0000.0000.000
137A139GLY0-0.009-0.00613.2290.2400.2400.0000.0000.0000.000
138A140SER00.0130.01313.9950.0040.0040.0000.0000.0000.000
139A141PRO0-0.038-0.01013.570-0.034-0.0340.0000.0000.0000.000
140A142LEU0-0.014-0.01716.4480.0530.0530.0000.0000.0000.000
141A143LEU0-0.0120.00919.034-0.029-0.0290.0000.0000.0000.000
142A144TRP0-0.031-0.02821.2030.0340.0340.0000.0000.0000.000
143A145SER00.039-0.00124.930-0.035-0.0350.0000.0000.0000.000
144A146PRO0-0.062-0.00228.4990.0170.0170.0000.0000.0000.000
145A147ASN00.0230.01931.797-0.013-0.0130.0000.0000.0000.000
146A148GLU-1-0.894-0.95333.713-0.030-0.0300.0000.0000.0000.000
147A149GLU-1-0.885-0.95736.3630.0130.0130.0000.0000.0000.000
148A150GLU-1-0.851-0.92731.8450.0190.0190.0000.0000.0000.000
149A151ASP-1-0.873-0.93735.611-0.068-0.0680.0000.0000.0000.000
150A152ARG10.8380.91736.8740.0000.0000.0000.0000.0000.000
151A153GLN00.0000.00538.3000.0040.0040.0000.0000.0000.000
152A154LEU0-0.039-0.03233.646-0.003-0.0030.0000.0000.0000.000
153A155ARG10.7740.84838.2380.0490.0490.0000.0000.0000.000
154A156GLU-1-0.811-0.89941.189-0.013-0.0130.0000.0000.0000.000
155A157ASP-1-0.729-0.84939.330-0.013-0.0130.0000.0000.0000.000
156A158TRP0-0.034-0.02539.619-0.004-0.0040.0000.0000.0000.000
157A159GLU-1-0.804-0.89741.955-0.055-0.0550.0000.0000.0000.000
158A160GLU-1-0.834-0.91545.503-0.016-0.0160.0000.0000.0000.000
159A161LEU0-0.060-0.04741.137-0.002-0.0020.0000.0000.0000.000
160A162MET0-0.040-0.02343.806-0.005-0.0050.0000.0000.0000.000
161A163ASP-1-0.859-0.92146.242-0.045-0.0450.0000.0000.0000.000
162A164MET0-0.072-0.04248.0210.0010.0010.0000.0000.0000.000
163A165ILE0-0.078-0.03943.936-0.001-0.0010.0000.0000.0000.000
164A166VAL0-0.0120.00048.5510.0000.0000.0000.0000.0000.000
165A167LEU0-0.0170.00051.1880.0010.0010.0000.0000.0000.000
166A168GLY00.0010.01452.8430.0040.0040.0000.0000.0000.000
167A169GLN0-0.061-0.03851.7870.0060.0060.0000.0000.0000.000
168A170VAL00.1020.04045.9350.0030.0030.0000.0000.0000.000
169A171GLU-1-0.771-0.83247.393-0.044-0.0440.0000.0000.0000.000
170A172ARG10.8180.88849.6930.0260.0260.0000.0000.0000.000
171A173ILE00.0240.04544.1170.0040.0040.0000.0000.0000.000
172A174THR0-0.063-0.03644.5770.0030.0030.0000.0000.0000.000
173A175ALA0-0.011-0.02641.006-0.001-0.0010.0000.0000.0000.000
174A176ARG10.8680.91642.323-0.004-0.0040.0000.0000.0000.000
175A177HIS00.0740.07244.3850.0020.0020.0000.0000.0000.000
176A178GLY00.0410.03041.620-0.003-0.0030.0000.0000.0000.000
177A179GLU-1-0.881-0.96840.2900.0310.0310.0000.0000.0000.000
178A180TYR0-0.064-0.02735.2100.0120.0120.0000.0000.0000.000
179A181LEU0-0.032-0.02335.329-0.004-0.0040.0000.0000.0000.000
180A182GLN00.0400.03737.4930.0090.0090.0000.0000.0000.000
181A183ILE00.0360.01938.190-0.010-0.0100.0000.0000.0000.000
182A184ARG10.8570.93136.0300.0200.0200.0000.0000.0000.000
183A185PRO00.0400.00938.873-0.009-0.0090.0000.0000.0000.000
184A186LYS10.9430.98834.4910.1390.1390.0000.0000.0000.000
185A187ALA0-0.063-0.04535.069-0.010-0.0100.0000.0000.0000.000
186A188ALA0-0.0230.00235.9760.0050.0050.0000.0000.0000.000
187A189ASN0-0.0070.00036.1500.0020.0020.0000.0000.0000.000
188A190ALA00.0670.03539.834-0.005-0.0050.0000.0000.0000.000
189A191LYS10.8690.91338.0860.0760.0760.0000.0000.0000.000
190A192ALA00.0180.03140.811-0.002-0.0020.0000.0000.0000.000
191A193LEU0-0.014-0.02142.7700.0060.0060.0000.0000.0000.000
192A194THR0-0.035-0.01343.677-0.010-0.0100.0000.0000.0000.000
193A195GLU-1-0.837-0.90245.659-0.070-0.0700.0000.0000.0000.000
194A196ALA0-0.002-0.01047.684-0.003-0.0030.0000.0000.0000.000
195A197ILE00.0350.02149.8640.0010.0010.0000.0000.0000.000
196A198GLY0-0.0110.00552.5130.0010.0010.0000.0000.0000.000
197A199ALA00.0380.00755.1330.0000.0000.0000.0000.0000.000
198A200ARG10.8220.89557.4920.0370.0370.0000.0000.0000.000
199A201GLY00.0330.02457.5530.0000.0000.0000.0000.0000.000
200A202GLU-1-0.855-0.90357.220-0.042-0.0420.0000.0000.0000.000
201A203ARG10.9140.93752.8900.0660.0660.0000.0000.0000.000
202A204ILE0-0.029-0.01151.2070.0030.0030.0000.0000.0000.000
203A205LEU0-0.007-0.01149.631-0.005-0.0050.0000.0000.0000.000
204A206THR0-0.022-0.03845.9480.0040.0040.0000.0000.0000.000
205A207LEU00.0290.01242.160-0.007-0.0070.0000.0000.0000.000
206A208PRO00.0120.00139.6400.0020.0020.0000.0000.0000.000
207A209ARG10.8210.90939.9380.0550.0550.0000.0000.0000.000
208A210GLY0-0.013-0.01536.336-0.012-0.0120.0000.0000.0000.000
209A211PHE00.0740.03336.1930.0110.0110.0000.0000.0000.000
210A212TYR0-0.042-0.03732.099-0.016-0.0160.0000.0000.0000.000
211A213LEU00.0620.03730.0770.0050.0050.0000.0000.0000.000
212A214LYS10.8030.92132.908-0.012-0.0120.0000.0000.0000.000
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214A216ASN00.0090.00930.9880.0070.0070.0000.0000.0000.000
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