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: VQMR1

Calculation Name: 1Z9S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z9S

Chain ID: A

ChEMBL ID:

UniProt ID: P26926

Base Structure: X-ray

Registration Date: 2023-09-24

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2217450.200392
FMO2-HF: Nuclear repulsion 2138013.937741
FMO2-HF: Total energy -79436.262651
FMO2-MP2: Total energy -79671.411834


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:9:SER)


Summations of interaction energy for fragment #1(A:9: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.
1.0364.197-0.012-1.583-1.5670.006
Interaction energy analysis for fragmet #1(A:9:SER)
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 : 0.017
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].
3A11GLU-1-0.816-0.8943.7381.5824.743-0.012-1.583-1.5670.006
4A12TYR0-0.049-0.0356.178-0.507-0.5070.0000.0000.0000.000
5A13GLY00.0160.0179.4950.1320.1320.0000.0000.0000.000
6A14VAL0-0.010-0.00312.610-0.054-0.0540.0000.0000.0000.000
7A15THR0-0.0060.00216.3220.0330.0330.0000.0000.0000.000
8A16ILE0-0.028-0.00919.102-0.018-0.0180.0000.0000.0000.000
9A17GLY0-0.013-0.02022.6890.0090.0090.0000.0000.0000.000
10A18GLU-1-0.893-0.93825.3790.0060.0060.0000.0000.0000.000
11A19SER00.012-0.01025.112-0.001-0.0010.0000.0000.0000.000
12A20ARG10.8170.90526.056-0.033-0.0330.0000.0000.0000.000
13A21ILE00.0740.04729.114-0.002-0.0020.0000.0000.0000.000
14A22ILE0-0.0060.00731.9860.0010.0010.0000.0000.0000.000
15A23TYR00.003-0.01735.610-0.003-0.0030.0000.0000.0000.000
16A24PRO0-0.010-0.00237.4610.0010.0010.0000.0000.0000.000
17A25LEU0-0.017-0.00941.226-0.002-0.0020.0000.0000.0000.000
18A26ASP-1-0.820-0.89943.000-0.005-0.0050.0000.0000.0000.000
19A27ALA0-0.0380.00241.075-0.001-0.0010.0000.0000.0000.000
20A28ALA00.0120.00142.002-0.001-0.0010.0000.0000.0000.000
21A29GLY0-0.006-0.02238.265-0.002-0.0020.0000.0000.0000.000
22A30VAL0-0.053-0.00833.7460.0010.0010.0000.0000.0000.000
23A31MET0-0.019-0.01032.513-0.002-0.0020.0000.0000.0000.000
24A32VAL00.0600.04427.0670.0030.0030.0000.0000.0000.000
25A33SER0-0.011-0.00225.878-0.005-0.0050.0000.0000.0000.000
26A34VAL00.0350.02221.4430.0070.0070.0000.0000.0000.000
27A35LYS10.9240.95418.1610.0400.0400.0000.0000.0000.000
28A36ASN0-0.012-0.01215.5180.0240.0240.0000.0000.0000.000
29A37THR0-0.055-0.04113.109-0.018-0.0180.0000.0000.0000.000
30A38GLN00.0170.0308.9920.0720.0720.0000.0000.0000.000
31A39ASP-1-0.857-0.94410.093-0.371-0.3710.0000.0000.0000.000
32A40TYR0-0.036-0.0499.454-0.012-0.0120.0000.0000.0000.000
33A41PRO0-0.032-0.00414.2000.0540.0540.0000.0000.0000.000
34A42VAL00.0160.00515.184-0.038-0.0380.0000.0000.0000.000
35A43LEU0-0.007-0.00517.9510.0250.0250.0000.0000.0000.000
36A44ILE00.0020.00519.6250.0000.0000.0000.0000.0000.000
37A45GLN0-0.005-0.01621.7560.0060.0060.0000.0000.0000.000
38A46SER00.0140.00423.2890.0060.0060.0000.0000.0000.000
39A47ARG10.8980.95425.5290.0500.0500.0000.0000.0000.000
40A48ILE00.0390.02227.7110.0040.0040.0000.0000.0000.000
41A49TYR0-0.051-0.02526.150-0.004-0.0040.0000.0000.0000.000
42A50ASP-1-0.704-0.86131.1020.0050.0050.0000.0000.0000.000
43A51GLU-1-0.920-0.95932.1010.0170.0170.0000.0000.0000.000
44A52ASN0-0.030-0.00332.5580.0070.0070.0000.0000.0000.000
45A53LYS10.8210.92225.423-0.020-0.0200.0000.0000.0000.000
46A54GLU-1-0.899-0.96029.9360.0020.0020.0000.0000.0000.000
47A55LYS10.6920.82630.0180.0260.0260.0000.0000.0000.000
48A56GLU-1-0.755-0.86633.059-0.026-0.0260.0000.0000.0000.000
49A57SER0-0.037-0.02136.6960.0020.0020.0000.0000.0000.000
50A58GLU-1-0.894-0.94038.812-0.006-0.0060.0000.0000.0000.000
51A59ASP-1-0.923-0.96639.269-0.023-0.0230.0000.0000.0000.000
52A60PRO0-0.0130.01236.2440.0000.0000.0000.0000.0000.000
53A61PHE0-0.002-0.00734.9320.0010.0010.0000.0000.0000.000
54A62VAL00.0300.01734.776-0.002-0.0020.0000.0000.0000.000
55A63VAL0-0.018-0.01428.7790.0010.0010.0000.0000.0000.000
56A64THR0-0.0610.00032.094-0.004-0.0040.0000.0000.0000.000
57A65PRO00.030-0.01229.0070.0030.0030.0000.0000.0000.000
58A66PRO00.0510.02528.712-0.001-0.0010.0000.0000.0000.000
59A67LEU0-0.008-0.03123.902-0.003-0.0030.0000.0000.0000.000
60A68PHE00.0010.01124.8420.0020.0020.0000.0000.0000.000
61A69ARG10.9060.95621.0560.2060.2060.0000.0000.0000.000
62A70LEU0-0.032-0.00220.5570.0130.0130.0000.0000.0000.000
63A71ASP-1-0.778-0.89819.591-0.216-0.2160.0000.0000.0000.000
64A72ALA00.0480.02315.9140.0180.0180.0000.0000.0000.000
65A73LYS10.8250.91412.5880.1540.1540.0000.0000.0000.000
66A74GLN0-0.0210.00517.9100.0370.0370.0000.0000.0000.000
67A75GLN0-0.011-0.01920.7750.0130.0130.0000.0000.0000.000
68A76ASN00.0130.00923.3910.0020.0020.0000.0000.0000.000
69A77SER0-0.034-0.01826.3390.0080.0080.0000.0000.0000.000
70A78LEU0-0.0120.01125.805-0.005-0.0050.0000.0000.0000.000
71A79ARG10.9930.99029.7720.0290.0290.0000.0000.0000.000
72A80ILE0-0.034-0.01630.041-0.003-0.0030.0000.0000.0000.000
73A81ALA00.023-0.00733.9480.0020.0020.0000.0000.0000.000
74A82GLN00.0330.03237.5650.0000.0000.0000.0000.0000.000
75A83ALA0-0.025-0.01739.790-0.001-0.0010.0000.0000.0000.000
76A84GLY00.0080.02141.5210.0000.0000.0000.0000.0000.000
77A85GLY00.0400.00743.5250.0010.0010.0000.0000.0000.000
78A86VAL0-0.012-0.01244.6320.0000.0000.0000.0000.0000.000
79A87PHE0-0.004-0.00939.6660.0010.0010.0000.0000.0000.000
80A88PRO0-0.0340.00143.4410.0000.0000.0000.0000.0000.000
81A89ARG10.8660.87545.4200.0020.0020.0000.0000.0000.000
82A90ASP-1-0.887-0.93547.7000.0090.0090.0000.0000.0000.000
83A91LYS10.9140.92343.372-0.009-0.0090.0000.0000.0000.000
84A92GLU-1-0.733-0.84738.4300.0140.0140.0000.0000.0000.000
85A93SER0-0.020-0.00739.2060.0000.0000.0000.0000.0000.000
86A94LEU0-0.044-0.01031.5880.0000.0000.0000.0000.0000.000
87A95LYS10.9200.97933.1660.0010.0010.0000.0000.0000.000
88A96TRP0-0.042-0.02425.9570.0070.0070.0000.0000.0000.000
89A97LEU00.0550.03626.233-0.005-0.0050.0000.0000.0000.000
90A98CYS0-0.105-0.04119.614-0.005-0.0050.0000.0000.0000.000
91A99VAL00.0470.01221.027-0.009-0.0090.0000.0000.0000.000
92A100LYS10.9660.97817.9730.1030.1030.0000.0000.0000.000
93A101GLY00.0030.01016.635-0.006-0.0060.0000.0000.0000.000
94A102ILE0-0.066-0.04415.698-0.014-0.0140.0000.0000.0000.000
95A103PRO00.0140.00612.322-0.001-0.0010.0000.0000.0000.000
96A104PRO0-0.0010.01513.4650.0020.0020.0000.0000.0000.000
97A125ASP-1-0.935-0.97717.2060.1200.1200.0000.0000.0000.000
98A126VAL0-0.031-0.01316.135-0.022-0.0220.0000.0000.0000.000
99A127GLY00.0210.02214.1060.0310.0310.0000.0000.0000.000
100A128VAL0-0.002-0.00910.756-0.033-0.0330.0000.0000.0000.000
101A129PHE00.008-0.0068.728-0.051-0.0510.0000.0000.0000.000
102A130VAL00.0360.0268.1410.0210.0210.0000.0000.0000.000
103A131GLN00.0170.0108.557-0.246-0.2460.0000.0000.0000.000
104A132PHE0-0.0010.0037.6590.1170.1170.0000.0000.0000.000
105A133ALA00.019-0.01011.299-0.055-0.0550.0000.0000.0000.000
106A134ILE00.0110.02711.4580.0330.0330.0000.0000.0000.000
107A135ASN00.021-0.01214.665-0.024-0.0240.0000.0000.0000.000
108A136ASN0-0.0150.00318.2960.0190.0190.0000.0000.0000.000
109A138ILE00.0240.01923.1750.0100.0100.0000.0000.0000.000
110A139LYS10.8350.91625.837-0.042-0.0420.0000.0000.0000.000
111A140LEU00.0250.03029.4780.0000.0000.0000.0000.0000.000
112A141LEU0-0.021-0.02632.1650.0010.0010.0000.0000.0000.000
113A142VAL00.0140.01835.277-0.001-0.0010.0000.0000.0000.000
114A143ARG10.7740.83137.643-0.011-0.0110.0000.0000.0000.000
115A144PRO00.0200.02441.095-0.001-0.0010.0000.0000.0000.000
116A145ASN00.0250.01044.8280.0020.0020.0000.0000.0000.000
117A146GLU-1-0.843-0.92646.6340.0020.0020.0000.0000.0000.000
118A147LEU0-0.071-0.01743.1690.0010.0010.0000.0000.0000.000
119A148LYS10.9370.96646.843-0.007-0.0070.0000.0000.0000.000
120A149GLY00.0120.00545.4410.0010.0010.0000.0000.0000.000
121A150THR0-0.0020.00139.8650.0000.0000.0000.0000.0000.000
122A151PRO00.0600.02237.3330.0010.0010.0000.0000.0000.000
123A152ILE00.0450.00337.7410.0010.0010.0000.0000.0000.000
124A153GLN0-0.047-0.01440.1300.0000.0000.0000.0000.0000.000
125A154PHE00.0200.00842.588-0.001-0.0010.0000.0000.0000.000
126A155ALA00.0160.02239.1600.0010.0010.0000.0000.0000.000
127A156GLU-1-0.916-0.95940.8960.0290.0290.0000.0000.0000.000
128A157ASN0-0.073-0.07443.394-0.001-0.0010.0000.0000.0000.000
129A158LEU0-0.0120.02738.513-0.001-0.0010.0000.0000.0000.000
130A159SER0-0.0250.00343.1580.0010.0010.0000.0000.0000.000
131A160TRP00.0680.01036.8880.0020.0020.0000.0000.0000.000
132A161LYS10.9900.99043.378-0.027-0.0270.0000.0000.0000.000
133A162VAL0-0.0070.00542.1420.0020.0020.0000.0000.0000.000
134A163ASP-1-0.920-0.96243.4540.0270.0270.0000.0000.0000.000
135A164GLY00.0670.03843.1240.0010.0010.0000.0000.0000.000
136A165GLY0-0.047-0.01541.7850.0010.0010.0000.0000.0000.000
137A166LYS10.8830.92736.505-0.041-0.0410.0000.0000.0000.000
138A167LEU0-0.0130.01136.892-0.002-0.0020.0000.0000.0000.000
139A168ILE00.0030.00038.6370.0010.0010.0000.0000.0000.000
140A169ALA0-0.0150.00038.6520.0000.0000.0000.0000.0000.000
141A170GLU-1-0.883-0.94840.6910.0220.0220.0000.0000.0000.000
142A171ASN0-0.034-0.01240.0570.0000.0000.0000.0000.0000.000
143A172PRO00.0330.01942.906-0.001-0.0010.0000.0000.0000.000
144A173SER0-0.005-0.01542.529-0.002-0.0020.0000.0000.0000.000
145A174PRO00.010-0.01544.0660.0000.0000.0000.0000.0000.000
146A175PHE00.0240.00039.594-0.001-0.0010.0000.0000.0000.000
147A176TYR0-0.032-0.03435.4550.0020.0020.0000.0000.0000.000
148A177MET0-0.0170.01836.8180.0020.0020.0000.0000.0000.000
149A178ASN00.032-0.01131.2110.0030.0030.0000.0000.0000.000
150A179ILE0-0.0020.00731.8720.0010.0010.0000.0000.0000.000
151A180GLY00.003-0.01928.8700.0020.0020.0000.0000.0000.000
152A181GLU-1-0.904-0.95828.4360.0750.0750.0000.0000.0000.000
153A182LEU00.0150.01330.727-0.006-0.0060.0000.0000.0000.000
154A183THR0-0.021-0.00132.2170.0070.0070.0000.0000.0000.000
155A184PHE00.0250.00834.627-0.004-0.0040.0000.0000.0000.000
156A185GLY00.011-0.01937.0110.0020.0020.0000.0000.0000.000
157A186GLY0-0.013-0.00436.4780.0010.0010.0000.0000.0000.000
158A187LYS10.9100.96833.209-0.067-0.0670.0000.0000.0000.000
159A188SER00.0490.02229.135-0.002-0.0020.0000.0000.0000.000
160A189ILE0-0.038-0.01430.7330.0030.0030.0000.0000.0000.000
161A190PRO0-0.011-0.00226.5950.0010.0010.0000.0000.0000.000
162A191SER00.0220.00728.045-0.005-0.0050.0000.0000.0000.000
163A192HIS10.8870.93828.712-0.039-0.0390.0000.0000.0000.000
164A193TYR0-0.0220.00330.7870.0010.0010.0000.0000.0000.000
165A194ILE0-0.0020.01833.2740.0000.0000.0000.0000.0000.000
166A195PRO00.0220.00537.011-0.001-0.0010.0000.0000.0000.000
167A196PRO0-0.0110.00638.7160.0010.0010.0000.0000.0000.000
168A197LYS10.8590.94541.818-0.013-0.0130.0000.0000.0000.000
169A198SER00.0250.03441.6760.0000.0000.0000.0000.0000.000
170A199THR0-0.011-0.01241.3620.0010.0010.0000.0000.0000.000
171A200TRP00.032-0.00532.869-0.002-0.0020.0000.0000.0000.000
172A201ALA00.0030.00837.5540.0010.0010.0000.0000.0000.000
173A202PHE0-0.033-0.02032.2380.0010.0010.0000.0000.0000.000
174A203ASP-1-0.843-0.92832.7680.0510.0510.0000.0000.0000.000
175A204LEU0-0.016-0.01434.0370.0030.0030.0000.0000.0000.000
176A205PRO0-0.004-0.01234.3470.0040.0040.0000.0000.0000.000
177A206LYS10.9190.99128.551-0.086-0.0860.0000.0000.0000.000
178A207GLY00.004-0.01333.8180.0030.0030.0000.0000.0000.000
179A208LEU0-0.005-0.02136.4110.0020.0020.0000.0000.0000.000
180A209ALA00.009-0.00339.496-0.002-0.0020.0000.0000.0000.000
181A210GLY00.0420.03542.418-0.002-0.0020.0000.0000.0000.000
182A211ALA0-0.0490.01341.168-0.001-0.0010.0000.0000.0000.000
183A212ARG10.9470.95843.121-0.034-0.0340.0000.0000.0000.000
184A213ASN00.0130.02940.285-0.003-0.0030.0000.0000.0000.000
185A214VAL0-0.0060.00338.4190.0030.0030.0000.0000.0000.000
186A215SER00.001-0.00636.995-0.002-0.0020.0000.0000.0000.000
187A216TRP0-0.023-0.02135.2230.0040.0040.0000.0000.0000.000
188A217ARG10.9440.99032.329-0.058-0.0580.0000.0000.0000.000
189A218ILE00.0110.01033.2030.0030.0030.0000.0000.0000.000
190A219ILE0-0.0390.00328.5450.0010.0010.0000.0000.0000.000
191A220ASN00.0400.01831.955-0.004-0.0040.0000.0000.0000.000
192A221ASP-1-0.716-0.85532.5730.0190.0190.0000.0000.0000.000
193A222GLN00.0160.00532.0700.0010.0010.0000.0000.0000.000
194A223GLY0-0.052-0.03128.6540.0020.0020.0000.0000.0000.000
195A224GLY0-0.019-0.00428.3040.0070.0070.0000.0000.0000.000
196A225LEU0-0.023-0.02528.537-0.003-0.0030.0000.0000.0000.000
197A226ASP-1-0.855-0.91331.1920.0330.0330.0000.0000.0000.000
198A227ARG10.9170.94434.801-0.026-0.0260.0000.0000.0000.000
199A228LEU0-0.051-0.02335.5040.0000.0000.0000.0000.0000.000
200A229TYR00.0310.02837.950-0.003-0.0030.0000.0000.0000.000
201A230SER00.017-0.01639.7060.0040.0040.0000.0000.0000.000
202A231LYS10.8720.95942.200-0.030-0.0300.0000.0000.0000.000
203A232ASN00.005-0.01243.6410.0030.0030.0000.0000.0000.000
204A233VAL0-0.0240.00143.186-0.001-0.0010.0000.0000.0000.000
205A234THR0-0.008-0.01545.7840.0000.0000.0000.0000.0000.000