Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 66ZRZ

Calculation Name: 1AZ4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AZ4

Chain ID: A

ChEMBL ID:

UniProt ID: P04390

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2364519.306905
FMO2-HF: Nuclear repulsion 2284062.467178
FMO2-HF: Total energy -80456.839727
FMO2-MP2: Total energy -80698.650414


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-11.681-7.9269.374-6.278-6.850.021
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.012
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].
3A4ARG10.8610.9183.233-4.203-1.5100.113-1.238-1.5680.006
4A5SER0-0.004-0.0121.838-4.705-5.7838.694-4.141-3.4750.007
5A6ASP-1-0.861-0.9273.908-2.396-1.3860.028-0.311-0.7260.001
6A7LEU0-0.033-0.0055.6810.1200.1200.0000.0000.0000.000
7A8ILE00.0370.0186.396-0.235-0.2350.0000.0000.0000.000
8A9ASN00.009-0.0046.8790.0280.0280.0000.0000.0000.000
9A10ALA00.002-0.0059.3460.0070.0070.0000.0000.0000.000
10A11LEU0-0.0170.00111.1350.0270.0270.0000.0000.0000.000
11A12TYR0-0.077-0.05511.424-0.004-0.0040.0000.0000.0000.000
12A13ASP-1-0.891-0.93013.595-0.152-0.1520.0000.0000.0000.000
13A14GLU-1-0.856-0.92615.3520.0200.0200.0000.0000.0000.000
14A15ASN0-0.060-0.02917.2220.0270.0270.0000.0000.0000.000
15A16GLN0-0.009-0.01418.8550.0070.0070.0000.0000.0000.000
16A17LYS10.7820.87718.2960.0600.0600.0000.0000.0000.000
17A18TYR0-0.001-0.00916.5320.0290.0290.0000.0000.0000.000
18A19ASP-1-0.909-0.91323.2830.0070.0070.0000.0000.0000.000
19A20VAL00.0520.02226.7550.0030.0030.0000.0000.0000.000
20A21CYS0-0.037-0.02429.376-0.002-0.0020.0000.0000.0000.000
21A22GLY00.0500.02132.892-0.002-0.0020.0000.0000.0000.000
22A23ILE0-0.0200.01033.2980.0030.0030.0000.0000.0000.000
23A24ILE0-0.006-0.00634.062-0.004-0.0040.0000.0000.0000.000
24A25SER0-0.067-0.03236.6180.0040.0040.0000.0000.0000.000
25A26ALA00.0580.01339.363-0.002-0.0020.0000.0000.0000.000
26A27GLU-1-0.963-0.97540.2910.0250.0250.0000.0000.0000.000
27A28GLY00.0240.00340.118-0.003-0.0030.0000.0000.0000.000
28A29LYS10.8970.96240.764-0.030-0.0300.0000.0000.0000.000
29A30ILE00.0400.03037.0210.0030.0030.0000.0000.0000.000
30A31TYR0-0.012-0.02238.583-0.003-0.0030.0000.0000.0000.000
31A32PRO00.0300.04037.3270.0020.0020.0000.0000.0000.000
32A33LEU0-0.019-0.01030.8810.0030.0030.0000.0000.0000.000
33A41SER0-0.003-0.01526.028-0.006-0.0060.0000.0000.0000.000
34A42THR00.0690.04525.5710.0080.0080.0000.0000.0000.000
35A43ILE00.015-0.00225.4990.0130.0130.0000.0000.0000.000
36A44PHE00.0390.00921.5250.0030.0030.0000.0000.0000.000
37A45GLU-1-0.874-0.93621.0140.2070.2070.0000.0000.0000.000
38A46LEU0-0.076-0.05021.2500.0220.0220.0000.0000.0000.000
39A47PHE00.0120.02620.2580.0040.0040.0000.0000.0000.000
40A48SER00.0370.02716.5890.0050.0050.0000.0000.0000.000
41A49ARG10.9180.98216.716-0.195-0.1950.0000.0000.0000.000
42A50PRO0-0.0100.02117.2500.0400.0400.0000.0000.0000.000
43A51ILE00.0050.00413.0080.0150.0150.0000.0000.0000.000
44A52ILE0-0.023-0.02412.5910.0410.0410.0000.0000.0000.000
45A53ASN0-0.037-0.05112.3930.1180.1180.0000.0000.0000.000
46A54LYS10.9871.01111.526-0.021-0.0210.0000.0000.0000.000
47A55ILE0-0.029-0.0187.374-0.040-0.0400.0000.0000.0000.000
48A56ALA00.0730.0318.9510.1780.1780.0000.0000.0000.000
49A57GLU-1-0.919-0.94510.5570.4560.4560.0000.0000.0000.000
50A58LYS10.8730.9546.7820.1790.1790.0000.0000.0000.000
51A59HIS0-0.096-0.0682.824-1.271-0.1410.539-0.588-1.0810.007
52A60GLY0-0.021-0.0098.4450.0870.0870.0000.0000.0000.000
53A61TYR0-0.069-0.0376.9050.1520.1520.0000.0000.0000.000
54A62ILE00.0120.01712.195-0.073-0.0730.0000.0000.0000.000
55A63VAL00.001-0.01013.9610.0590.0590.0000.0000.0000.000
56A64GLU-1-0.802-0.87516.3360.3070.3070.0000.0000.0000.000
57A65GLU-1-0.807-0.89319.3020.2810.2810.0000.0000.0000.000
58A66PRO00.0020.00221.647-0.011-0.0110.0000.0000.0000.000
59A67LYS10.7990.87623.544-0.296-0.2960.0000.0000.0000.000
60A68GLN00.0180.01527.819-0.021-0.0210.0000.0000.0000.000
61A69GLN0-0.021-0.00528.2310.0080.0080.0000.0000.0000.000
62A70ASN0-0.029-0.02728.0210.0080.0080.0000.0000.0000.000
63A71HIS0-0.036-0.02325.413-0.006-0.0060.0000.0000.0000.000
64A72TYR0-0.0410.00817.3280.0070.0070.0000.0000.0000.000
65A73PRO00.014-0.01617.562-0.003-0.0030.0000.0000.0000.000
66A74ASP-1-0.768-0.89018.9930.2850.2850.0000.0000.0000.000
67A75PHE0-0.005-0.01915.769-0.013-0.0130.0000.0000.0000.000
68A76THR0-0.027-0.01215.8570.0380.0380.0000.0000.0000.000
69A77LEU0-0.018-0.01710.189-0.013-0.0130.0000.0000.0000.000
70A78TYR00.003-0.00112.6030.0610.0610.0000.0000.0000.000
71A79LYS10.9781.0199.207-1.439-1.4390.0000.0000.0000.000
72A80PRO00.024-0.01013.581-0.037-0.0370.0000.0000.0000.000
73A81SER0-0.0010.00115.779-0.028-0.0280.0000.0000.0000.000
74A82GLU-1-0.878-0.91813.1730.5500.5500.0000.0000.0000.000
75A83PRO00.0270.01515.1410.0600.0600.0000.0000.0000.000
76A84ASN0-0.004-0.01217.444-0.004-0.0040.0000.0000.0000.000
77A85LYS10.8700.91411.965-0.620-0.6200.0000.0000.0000.000
78A86LYS10.8060.94712.250-0.342-0.3420.0000.0000.0000.000
79A87ILE0-0.0200.0077.8640.0000.0000.0000.0000.0000.000
80A88ALA00.0050.00212.241-0.086-0.0860.0000.0000.0000.000
81A89ILE0-0.0140.00211.1280.0590.0590.0000.0000.0000.000
82A90ASP-1-0.844-0.95014.8250.2410.2410.0000.0000.0000.000
83A91ILE0-0.0160.00516.6390.0120.0120.0000.0000.0000.000
84A92LYS10.8730.94918.747-0.254-0.2540.0000.0000.0000.000
85A93ALA00.029-0.00520.229-0.008-0.0080.0000.0000.0000.000
86A94THR0-0.0270.00122.921-0.007-0.0070.0000.0000.0000.000
87A95TYR00.005-0.01225.669-0.008-0.0080.0000.0000.0000.000
88A96THR0-0.032-0.00526.824-0.004-0.0040.0000.0000.0000.000
89A97ASN00.001-0.00129.361-0.004-0.0040.0000.0000.0000.000
90A98LYS10.8400.92232.539-0.012-0.0120.0000.0000.0000.000
91A99GLU-1-0.814-0.90230.956-0.015-0.0150.0000.0000.0000.000
92A100ASN00.0070.03426.986-0.003-0.0030.0000.0000.0000.000
93A101GLU-1-0.740-0.89228.1490.0130.0130.0000.0000.0000.000
94A102LYS10.9680.99327.8470.0000.0000.0000.0000.0000.000
95A103ILE00.012-0.02123.3800.0040.0040.0000.0000.0000.000
96A104LYS10.9060.98524.951-0.057-0.0570.0000.0000.0000.000
97A105PHE00.0180.01520.9900.0020.0020.0000.0000.0000.000
98A106THR0-0.0120.00924.250-0.013-0.0130.0000.0000.0000.000
99A107LEU0-0.056-0.05019.7330.0200.0200.0000.0000.0000.000
100A108GLY00.0400.04023.0970.0100.0100.0000.0000.0000.000
101A109GLY00.0610.01424.512-0.019-0.0190.0000.0000.0000.000
102A110TYR00.0100.01526.1570.0140.0140.0000.0000.0000.000
103A111THR0-0.010-0.01327.817-0.006-0.0060.0000.0000.0000.000
104A112SER00.019-0.00128.1760.0000.0000.0000.0000.0000.000
105A113PHE00.0470.02322.078-0.006-0.0060.0000.0000.0000.000
106A114ILE00.0850.06323.9740.0090.0090.0000.0000.0000.000
107A115ARG10.8840.97025.445-0.133-0.1330.0000.0000.0000.000
108A116ASN0-0.049-0.01828.643-0.011-0.0110.0000.0000.0000.000
109A117ASN00.0330.02523.9680.0160.0160.0000.0000.0000.000
110A118THR00.0410.02025.3650.0130.0130.0000.0000.0000.000
111A119LYS10.8600.92727.867-0.177-0.1770.0000.0000.0000.000
112A120ASN00.019-0.01027.4870.0040.0040.0000.0000.0000.000
113A121ILE0-0.0060.02320.7460.0020.0020.0000.0000.0000.000
114A122VAL0-0.0250.00021.440-0.020-0.0200.0000.0000.0000.000
115A123TYR0-0.054-0.05620.034-0.012-0.0120.0000.0000.0000.000
116A124PRO0-0.005-0.02322.312-0.006-0.0060.0000.0000.0000.000
117A125PHE00.0880.02720.7260.0330.0330.0000.0000.0000.000
118A126ASP-1-0.915-0.95219.7150.3230.3230.0000.0000.0000.000
119A127GLN0-0.053-0.04918.4080.0280.0280.0000.0000.0000.000
120A128TYR0-0.049-0.03115.4390.0560.0560.0000.0000.0000.000
121A129ILE00.0050.01910.024-0.035-0.0350.0000.0000.0000.000
122A130ALA00.0260.01210.5630.0550.0550.0000.0000.0000.000
123A131HIS00.0310.03412.515-0.051-0.0510.0000.0000.0000.000
124A132TRP00.004-0.0146.4290.1940.1940.0000.0000.0000.000
125A133ILE0-0.048-0.00812.993-0.063-0.0630.0000.0000.0000.000
126A134ILE00.000-0.00212.3020.0320.0320.0000.0000.0000.000
127A135GLY00.0110.00415.216-0.026-0.0260.0000.0000.0000.000
128A136TYR0-0.017-0.02417.678-0.033-0.0330.0000.0000.0000.000
129A137VAL0-0.018-0.01420.4790.0030.0030.0000.0000.0000.000
130A138TYR0-0.0030.01423.236-0.013-0.0130.0000.0000.0000.000
131A139THR0-0.020-0.01125.958-0.003-0.0030.0000.0000.0000.000
132A140ARG10.8740.94529.438-0.020-0.0200.0000.0000.0000.000
133A141VAL00.0540.03832.382-0.005-0.0050.0000.0000.0000.000
134A149LYS10.8490.91844.614-0.013-0.0130.0000.0000.0000.000
135A150THR0-0.0090.00342.6310.0010.0010.0000.0000.0000.000
136A151TYR00.0180.01641.340-0.001-0.0010.0000.0000.0000.000
137A152ASN00.0610.01142.0560.0020.0020.0000.0000.0000.000
138A153ILE00.0590.01136.504-0.001-0.0010.0000.0000.0000.000
139A154ASN0-0.016-0.00539.714-0.004-0.0040.0000.0000.0000.000
140A155GLU-1-0.856-0.93841.9780.0090.0090.0000.0000.0000.000
141A156LEU0-0.042-0.01935.1310.0000.0000.0000.0000.0000.000
142A157ASN0-0.034-0.00937.860-0.002-0.0020.0000.0000.0000.000
143A158GLU-1-0.903-0.96139.208-0.003-0.0030.0000.0000.0000.000
144A159ILE0-0.073-0.02037.2690.0020.0020.0000.0000.0000.000
145A160PRO0-0.031-0.00537.308-0.002-0.0020.0000.0000.0000.000
146A161LYS10.8780.92531.206-0.001-0.0010.0000.0000.0000.000
147A162PRO0-0.0070.01930.6590.0000.0000.0000.0000.0000.000
148A163TYR0-0.099-0.13126.3530.0030.0030.0000.0000.0000.000
149A164LYS10.8320.90330.0830.0140.0140.0000.0000.0000.000
150A165GLY00.0180.01526.762-0.004-0.0040.0000.0000.0000.000
151A166VAL00.026-0.00821.6730.0110.0110.0000.0000.0000.000
152A167LYS10.8680.96220.0660.0290.0290.0000.0000.0000.000
153A168VAL00.0850.03714.9580.0200.0200.0000.0000.0000.000
154A169PHE00.0090.02013.653-0.063-0.0630.0000.0000.0000.000
155A170LEU00.0280.0368.0280.0420.0420.0000.0000.0000.000
156A171GLN00.0050.01110.9590.0280.0280.0000.0000.0000.000
157A172ASP-1-0.806-0.89910.6170.7420.7420.0000.0000.0000.000
158A173LYS10.9080.93813.089-0.408-0.4080.0000.0000.0000.000
159A174TRP00.0150.01913.634-0.061-0.0610.0000.0000.0000.000
160A175VAL0-0.0210.02213.041-0.034-0.0340.0000.0000.0000.000
161A176ILE0-0.034-0.00816.341-0.042-0.0420.0000.0000.0000.000
162A177ALA0-0.004-0.03018.7180.0150.0150.0000.0000.0000.000
163A178GLY0-0.024-0.01721.795-0.011-0.0110.0000.0000.0000.000
164A179ASP-1-0.866-0.91625.2310.0610.0610.0000.0000.0000.000
165A180LEU00.0420.01028.9580.0070.0070.0000.0000.0000.000
166A181ALA0-0.106-0.02930.130-0.001-0.0010.0000.0000.0000.000
167A182GLY00.0670.02730.971-0.007-0.0070.0000.0000.0000.000
168A183SER0-0.022-0.02133.210-0.001-0.0010.0000.0000.0000.000
169A184GLY0-0.005-0.01132.9800.0050.0050.0000.0000.0000.000
170A185ASN0-0.0270.00627.380-0.003-0.0030.0000.0000.0000.000
171A186THR00.0450.02030.2600.0030.0030.0000.0000.0000.000
172A187THR0-0.008-0.02630.8030.0020.0020.0000.0000.0000.000
173A188ASN0-0.027-0.01827.0900.0200.0200.0000.0000.0000.000
174A189ILE00.0220.03224.240-0.009-0.0090.0000.0000.0000.000
175A190GLY0-0.0100.02025.3080.0140.0140.0000.0000.0000.000
176A191SER0-0.026-0.01621.7390.0000.0000.0000.0000.0000.000
177A192ILE00.0670.04320.583-0.009-0.0090.0000.0000.0000.000
178A193HIS0-0.003-0.03724.1120.0030.0030.0000.0000.0000.000
179A194ALA00.0040.00522.359-0.009-0.0090.0000.0000.0000.000
180A195HIS0-0.036-0.03123.6070.0040.0040.0000.0000.0000.000
181A196TYR00.029-0.00716.382-0.024-0.0240.0000.0000.0000.000
182A197LYS10.7750.85416.0880.2150.2150.0000.0000.0000.000
183A198ASP-1-0.804-0.90419.007-0.061-0.0610.0000.0000.0000.000
184A199PHE00.016-0.01216.996-0.004-0.0040.0000.0000.0000.000
185A200VAL0-0.006-0.00813.6700.0300.0300.0000.0000.0000.000
186A201GLU-1-0.876-0.91912.889-0.299-0.2990.0000.0000.0000.000
187A202GLY0-0.059-0.02814.768-0.017-0.0170.0000.0000.0000.000
188A203LYS10.9050.92815.2890.1760.1760.0000.0000.0000.000
189A204GLY00.0590.05118.9010.0100.0100.0000.0000.0000.000
190A205ILE0-0.087-0.05520.371-0.016-0.0160.0000.0000.0000.000
191A206PHE0-0.0210.01520.7720.0000.0000.0000.0000.0000.000
192A207ASP-1-0.866-0.92520.4100.0130.0130.0000.0000.0000.000
193A208SER0-0.058-0.03818.3230.0010.0010.0000.0000.0000.000
194A209GLU-1-0.942-0.98516.0210.3990.3990.0000.0000.0000.000
195A210ASP-1-0.898-0.96218.7350.1840.1840.0000.0000.0000.000
196A211GLU-1-0.877-0.95121.9640.0560.0560.0000.0000.0000.000
197A212PHE0-0.055-0.00920.0320.0080.0080.0000.0000.0000.000
198A213LEU0-0.044-0.05021.020-0.002-0.0020.0000.0000.0000.000
199A214ASP-1-1.005-0.98823.9720.0890.0890.0000.0000.0000.000
200A215TYR00.0460.01526.374-0.013-0.0130.0000.0000.0000.000
201A216TRP0-0.036-0.01224.536-0.002-0.0020.0000.0000.0000.000
202A217ARG10.8620.92823.920-0.192-0.1920.0000.0000.0000.000