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: VQLG1

Calculation Name: 4ANN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ANN

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G185

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptHSide
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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1924139.143676
FMO2-HF: Nuclear repulsion 1853005.202807
FMO2-HF: Total energy -71133.940869
FMO2-MP2: Total energy -71345.037283


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:30:LEU)


Summations of interaction energy for fragment #1(A:30: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.
-7.875-1.4562.975-3.628-5.765-0.018
Interaction energy analysis for fragmet #1(A:30:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.050
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].
3A32MET0-0.075-0.0132.773-2.0821.0450.001-1.489-1.640-0.002
4A33ARG10.8760.9223.889-0.664-0.4200.000-0.128-0.116-0.001
5A34GLU-1-0.825-0.8916.6000.2170.2170.0000.0000.0000.000
6A35ILE0-0.041-0.0119.639-0.027-0.0270.0000.0000.0000.000
7A36PRO00.0420.01512.9250.0450.0450.0000.0000.0000.000
8A37LYS10.8390.92515.8460.0580.0580.0000.0000.0000.000
9A38SER0-0.055-0.01518.981-0.005-0.0050.0000.0000.0000.000
10A39SER0-0.072-0.04917.146-0.005-0.0050.0000.0000.0000.000
11A40ILE00.0000.00917.074-0.011-0.0110.0000.0000.0000.000
12A41LYS10.9090.95220.8290.1180.1180.0000.0000.0000.000
13A42PRO00.0660.01424.254-0.007-0.0070.0000.0000.0000.000
14A43GLU-1-0.857-0.92625.915-0.096-0.0960.0000.0000.0000.000
15A44HIS0-0.011-0.02222.848-0.008-0.0080.0000.0000.0000.000
16A45PHE00.0500.02221.752-0.014-0.0140.0000.0000.0000.000
17A46HIS0-0.068-0.01421.893-0.012-0.0120.0000.0000.0000.000
18A47LEU0-0.004-0.01822.157-0.001-0.0010.0000.0000.0000.000
19A48MET00.0060.01717.590-0.030-0.0300.0000.0000.0000.000
20A49TYR00.0540.03117.717-0.030-0.0300.0000.0000.0000.000
21A50LEU0-0.024-0.00819.099-0.015-0.0150.0000.0000.0000.000
22A51LEU0-0.047-0.03013.570-0.018-0.0180.0000.0000.0000.000
23A52GLU-1-0.849-0.91214.230-0.298-0.2980.0000.0000.0000.000
24A53GLN0-0.083-0.02216.1700.0420.0420.0000.0000.0000.000
25A54HIS0-0.034-0.02517.222-0.010-0.0100.0000.0000.0000.000
26A55SER0-0.004-0.01816.5990.0360.0360.0000.0000.0000.000
27A56PRO0-0.0060.00016.960-0.028-0.0280.0000.0000.0000.000
28A57TYR0-0.004-0.01016.4290.0090.0090.0000.0000.0000.000
29A58PHE0-0.047-0.02911.680-0.004-0.0040.0000.0000.0000.000
30A59ILE00.0070.0217.9880.0680.0680.0000.0000.0000.000
31A60ASP-1-0.871-0.91111.139-0.372-0.3720.0000.0000.0000.000
32A61ALA00.0270.00711.258-0.132-0.1320.0000.0000.0000.000
33A62GLU-1-0.880-0.92912.099-0.282-0.2820.0000.0000.0000.000
34A63LEU0-0.049-0.02812.465-0.048-0.0480.0000.0000.0000.000
35A64THR0-0.053-0.02613.0240.0760.0760.0000.0000.0000.000
36A65GLU-1-0.865-0.94015.075-0.119-0.1190.0000.0000.0000.000
37A66LEU0-0.0150.00813.5380.0310.0310.0000.0000.0000.000
38A67ARG10.8410.90217.612-0.051-0.0510.0000.0000.0000.000
39A68ASP-1-0.834-0.92618.479-0.005-0.0050.0000.0000.0000.000
40A69SER0-0.050-0.04213.624-0.009-0.0090.0000.0000.0000.000
41A70PHE00.0330.02114.5740.0250.0250.0000.0000.0000.000
42A71GLN0-0.038-0.04510.0560.0190.0190.0000.0000.0000.000
43A72ILE0-0.026-0.0108.5640.0580.0580.0000.0000.0000.000
44A73HIS0-0.004-0.0037.779-0.049-0.0490.0000.0000.0000.000
45A74TYR00.0060.0024.9640.2270.2270.0000.0000.0000.000
46A75ASP-1-0.826-0.8988.616-0.215-0.2150.0000.0000.0000.000
47A76ILE0-0.051-0.0244.949-0.075-0.0750.0000.0000.0000.000
48A77ASN0-0.007-0.0129.0730.1350.1350.0000.0000.0000.000
49A78ASP-1-0.854-0.94911.911-0.158-0.1580.0000.0000.0000.000
50A79ASN0-0.191-0.10113.7960.0600.0600.0000.0000.0000.000
51A80HIS00.0150.01911.0700.0240.0240.0000.0000.0000.000
52A81THR0-0.053-0.02410.9840.0080.0080.0000.0000.0000.000
53A82PRO00.0510.0226.735-0.033-0.0330.0000.0000.0000.000
54A83PHE00.0360.0098.6720.1180.1180.0000.0000.0000.000
55A84ASP-1-0.785-0.8958.279-0.079-0.0790.0000.0000.0000.000
56A85ASN0-0.040-0.01910.2960.0380.0380.0000.0000.0000.000
57A86ILE0-0.004-0.00212.5510.0310.0310.0000.0000.0000.000
58A87LYS10.8350.92211.4760.1170.1170.0000.0000.0000.000
59A88SER0-0.034-0.00816.1420.0080.0080.0000.0000.0000.000
60A89PHE0-0.0230.00116.4700.0090.0090.0000.0000.0000.000
61A90THR0-0.001-0.02020.1420.0050.0050.0000.0000.0000.000
62A91LYS10.9130.95422.7430.0590.0590.0000.0000.0000.000
63A92ASN00.0380.00623.985-0.005-0.0050.0000.0000.0000.000
64A93GLU-1-0.749-0.83621.516-0.121-0.1210.0000.0000.0000.000
65A94LYS10.7870.89118.4760.0750.0750.0000.0000.0000.000
66A95LEU0-0.002-0.00619.865-0.014-0.0140.0000.0000.0000.000
67A96ARG10.8060.88322.1000.1300.1300.0000.0000.0000.000
68A97TYR00.0120.00915.820-0.001-0.0010.0000.0000.0000.000
69A98LEU0-0.013-0.01416.656-0.020-0.0200.0000.0000.0000.000
70A99LEU0-0.0050.00718.930-0.012-0.0120.0000.0000.0000.000
71A100ASN0-0.040-0.02619.5630.0080.0080.0000.0000.0000.000
72A101ILE0-0.0120.00215.032-0.017-0.0170.0000.0000.0000.000
73A102LYS10.9360.97617.7770.1200.1200.0000.0000.0000.000
74A103ASN00.003-0.00119.4630.0190.0190.0000.0000.0000.000
75A104LEU00.0170.00713.6290.0010.0010.0000.0000.0000.000
76A105GLU-1-0.910-0.95917.963-0.192-0.1920.0000.0000.0000.000
77A106GLU-1-0.846-0.91020.658-0.172-0.1720.0000.0000.0000.000
78A107VAL0-0.026-0.01516.4670.0100.0100.0000.0000.0000.000
79A108ASN0-0.0060.00919.790-0.007-0.0070.0000.0000.0000.000
80A109ARG10.7900.89821.7660.2050.2050.0000.0000.0000.000
81A110THR0-0.103-0.06120.6250.0050.0050.0000.0000.0000.000
82A111ARG10.9660.97821.5790.1940.1940.0000.0000.0000.000
83A112TYR0-0.073-0.04916.5630.0140.0140.0000.0000.0000.000
84A113THR0-0.034-0.01915.3880.0100.0100.0000.0000.0000.000
85A114PHE00.0520.01912.308-0.049-0.0490.0000.0000.0000.000
86A115VAL00.0130.0128.8150.0730.0730.0000.0000.0000.000
87A116LEU00.0070.02110.102-0.067-0.0670.0000.0000.0000.000
88A117ALA00.0610.0007.3600.0790.0790.0000.0000.0000.000
89A118PRO00.0280.0117.153-0.104-0.1040.0000.0000.0000.000
90A119ASP-1-0.867-0.9392.343-3.920-2.0251.878-1.447-2.325-0.017
91A120GLU-1-0.798-0.8663.921-2.427-2.0710.003-0.107-0.2520.000
92A121LEU0-0.055-0.0046.3790.1110.1110.0000.0000.0000.000
93A122PHE00.0250.0084.8650.0560.0560.0000.0000.0000.000
94A123PHE0-0.003-0.01210.3060.0510.0510.0000.0000.0000.000
95A124THR00.0750.04713.9280.0000.0000.0000.0000.0000.000
96A125ARG10.9350.96316.5840.1810.1810.0000.0000.0000.000
97A126ASP-1-0.907-0.94819.092-0.157-0.1570.0000.0000.0000.000
98A127GLY0-0.014-0.00517.8700.0150.0150.0000.0000.0000.000
99A128LEU0-0.0220.00018.4720.0030.0030.0000.0000.0000.000
100A129PRO0-0.0390.00214.687-0.024-0.0240.0000.0000.0000.000
101A130ILE0-0.017-0.00311.4410.0260.0260.0000.0000.0000.000
102A131ALA00.0180.00810.253-0.066-0.0660.0000.0000.0000.000
103A132LYS10.8430.9192.2671.3972.1941.093-0.457-1.4320.002
104A133THR0-0.076-0.0636.0240.0130.0130.0000.0000.0000.000
105A134ARG10.8340.8978.5970.6990.6990.0000.0000.0000.000
106A135GLY00.0030.02012.334-0.006-0.0060.0000.0000.0000.000
107A136LEU0-0.067-0.04214.7050.0200.0200.0000.0000.0000.000
108A137GLN00.0730.02818.4180.0190.0190.0000.0000.0000.000
109A138ASN0-0.107-0.06521.0800.0110.0110.0000.0000.0000.000
110A139VAL0-0.070-0.04119.6070.0190.0190.0000.0000.0000.000
111A140VAL00.0310.02314.9380.0100.0100.0000.0000.0000.000
112A141ASP-1-0.839-0.89413.947-0.272-0.2720.0000.0000.0000.000
113A142PRO0-0.014-0.02611.176-0.040-0.0400.0000.0000.0000.000
114A143LEU00.0270.03613.6630.0140.0140.0000.0000.0000.000
115A144PRO0-0.0010.01615.867-0.023-0.0230.0000.0000.0000.000
116A145VAL00.0280.00815.2170.0200.0200.0000.0000.0000.000
117A146SER0-0.009-0.01318.2610.0040.0040.0000.0000.0000.000
118A147GLU-1-0.874-0.93420.346-0.138-0.1380.0000.0000.0000.000
119A148ALA0-0.010-0.01421.857-0.003-0.0030.0000.0000.0000.000
120A149GLU-1-0.790-0.88615.657-0.207-0.2070.0000.0000.0000.000
121A150PHE00.0180.00616.358-0.016-0.0160.0000.0000.0000.000
122A151LEU0-0.0030.00417.939-0.008-0.0080.0000.0000.0000.000
123A152THR00.007-0.00117.9060.0080.0080.0000.0000.0000.000
124A153ARG10.8440.91310.7270.2960.2960.0000.0000.0000.000
125A154TYR0-0.029-0.03715.289-0.009-0.0090.0000.0000.0000.000
126A155LYS10.7990.88217.2630.1150.1150.0000.0000.0000.000
127A156ALA00.0290.02615.1500.0110.0110.0000.0000.0000.000
128A157LEU00.0270.01511.1900.0140.0140.0000.0000.0000.000
129A158VAL00.0070.00415.0680.0140.0140.0000.0000.0000.000
130A159ILE0-0.028-0.01818.4400.0150.0150.0000.0000.0000.000
131A160CYS0-0.048-0.02313.7420.0150.0150.0000.0000.0000.000
132A161ALA00.0070.00915.7350.0130.0130.0000.0000.0000.000
133A162PHE0-0.030-0.02416.5370.0150.0150.0000.0000.0000.000
134A163ASN0-0.030-0.00918.3200.0230.0230.0000.0000.0000.000
135A164GLU-1-0.911-0.95615.676-0.011-0.0110.0000.0000.0000.000
136A165LYS10.8780.93615.3800.0200.0200.0000.0000.0000.000
137A166GLN0-0.075-0.03016.7950.0150.0150.0000.0000.0000.000
138A167SER00.0210.01213.505-0.015-0.0150.0000.0000.0000.000
139A168PHE00.0590.00510.169-0.012-0.0120.0000.0000.0000.000
140A169ASP-1-0.844-0.9239.693-0.158-0.1580.0000.0000.0000.000
141A170ALA0-0.019-0.01212.5830.0060.0060.0000.0000.0000.000
142A171LEU0-0.081-0.04415.8310.0010.0010.0000.0000.0000.000
143A172VAL0-0.032-0.02613.5090.0010.0010.0000.0000.0000.000
144A173GLU-1-0.972-0.97113.762-0.079-0.0790.0000.0000.0000.000
145A174GLY0-0.0150.01317.4820.0130.0130.0000.0000.0000.000
146A175ASN0-0.057-0.03420.719-0.010-0.0100.0000.0000.0000.000
147A176LEU00.0700.02420.2240.0060.0060.0000.0000.0000.000
148A177GLU-1-0.890-0.95823.383-0.063-0.0630.0000.0000.0000.000
149A178LEU0-0.115-0.04526.4540.0060.0060.0000.0000.0000.000
150A179HIS0-0.047-0.02122.2320.0070.0070.0000.0000.0000.000
151A180LYS10.8700.93625.3250.0300.0300.0000.0000.0000.000
152A181GLY00.0720.02525.4840.0010.0010.0000.0000.0000.000
153A182THR0-0.068-0.02425.2820.0030.0030.0000.0000.0000.000
154A183PRO00.0520.00527.735-0.003-0.0030.0000.0000.0000.000
155A184PHE00.0090.00522.236-0.001-0.0010.0000.0000.0000.000
156A185GLU-1-0.730-0.85922.248-0.059-0.0590.0000.0000.0000.000
157A186THR00.0080.00024.994-0.004-0.0040.0000.0000.0000.000
158A187LYS10.8570.91927.7870.0540.0540.0000.0000.0000.000
159A188VAL0-0.0080.01121.699-0.004-0.0040.0000.0000.0000.000
160A189ILE0-0.014-0.01822.949-0.007-0.0070.0000.0000.0000.000
161A190GLU-1-0.811-0.88424.908-0.060-0.0600.0000.0000.0000.000
162A191ALA0-0.0490.00425.8560.0010.0010.0000.0000.0000.000
163A192ALA00.006-0.00426.863-0.006-0.0060.0000.0000.0000.000
164A193THR00.0380.00827.079-0.002-0.0020.0000.0000.0000.000
165A194LEU00.0790.04521.9010.0020.0020.0000.0000.0000.000
166A195ASP-1-0.865-0.93325.212-0.118-0.1180.0000.0000.0000.000
167A196LEU0-0.051-0.02328.2290.0040.0040.0000.0000.0000.000
168A197LEU0-0.017-0.00321.2960.0050.0050.0000.0000.0000.000
169A198THR00.010-0.00925.483-0.003-0.0030.0000.0000.0000.000
170A199ALA00.0290.02526.3330.0030.0030.0000.0000.0000.000
171A200PHE00.0200.01525.8800.0050.0050.0000.0000.0000.000
172A201LEU0-0.011-0.01621.9580.0040.0040.0000.0000.0000.000
173A202ASP-1-0.887-0.96226.143-0.102-0.1020.0000.0000.0000.000
174A203GLU-1-0.961-0.97228.793-0.064-0.0640.0000.0000.0000.000
175A204GLN0-0.106-0.04526.5440.0090.0090.0000.0000.0000.000
176A205TYR0-0.086-0.02425.9660.0070.0070.0000.0000.0000.000