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

tag_button

FMODB ID: VQML1

Calculation Name: 3DGS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DGS

Chain ID: A

ChEMBL ID:

UniProt ID: P03661

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1953047.103243
FMO2-HF: Nuclear repulsion 1880681.222251
FMO2-HF: Total energy -72365.880992
FMO2-MP2: Total energy -72581.175211


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:10:LYS)


Summations of interaction energy for fragment #1(A:10:LYS)
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.
-261.027-259.7824.164-12.135-13.272-0.129
Interaction energy analysis for fragmet #1(A:10:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.924
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].
3A12HIS00.0310.0013.310-11.299-8.8070.045-1.303-1.2340.001
4A13ILE0-0.0140.0034.384-0.816-0.664-0.001-0.010-0.1400.000
5A14GLU-1-0.895-0.9117.824-18.131-18.1310.0000.0000.0000.000
6A15GLY00.0290.00511.582-0.286-0.2860.0000.0000.0000.000
7A16SER0-0.003-0.03013.0850.1220.1220.0000.0000.0000.000
8A17PHE0-0.038-0.0136.989-1.939-1.9390.0000.0000.0000.000
9A18THR00.0420.00213.3862.2842.2840.0000.0000.0000.000
10A19ASN0-0.053-0.03213.967-0.922-0.9220.0000.0000.0000.000
11A20VAL0-0.0190.00814.116-0.773-0.7730.0000.0000.0000.000
12A21TRP00.0310.02012.4550.9550.9550.0000.0000.0000.000
13A22LYS10.8500.91917.12912.08812.0880.0000.0000.0000.000
14A23ASP-1-0.863-0.91318.195-14.630-14.6300.0000.0000.0000.000
15A24ASP-1-0.883-0.95820.091-12.291-12.2910.0000.0000.0000.000
16A25LYS10.9530.97122.63013.06513.0650.0000.0000.0000.000
17A26THR0-0.079-0.09018.7560.3240.3240.0000.0000.0000.000
18A27LEU0-0.0170.01321.5310.0390.0390.0000.0000.0000.000
19A28ASP-1-0.799-0.84216.522-16.336-16.3360.0000.0000.0000.000
20A29TRP00.006-0.00716.373-0.155-0.1550.0000.0000.0000.000
21A30TYR0-0.003-0.01212.202-1.367-1.3670.0000.0000.0000.000
22A31ALA00.0470.03610.5981.3521.3520.0000.0000.0000.000
23A32ASN0-0.017-0.0258.446-3.559-3.5590.0000.0000.0000.000
24A33TYR00.017-0.0184.0715.2885.449-0.001-0.024-0.1350.000
25A34GLU-1-0.823-0.8811.632-127.894-132.40018.174-8.471-5.197-0.101
26A35GLY00.0030.0084.583-3.141-3.043-0.001-0.008-0.0880.000
27A36ILE0-0.082-0.0322.3590.0100.8201.558-0.476-1.891-0.005
28A37LEU00.0360.0275.2071.5761.601-0.001-0.003-0.0210.000
29A38TRP0-0.036-0.0482.251-8.707-7.5943.273-1.362-3.024-0.020
30A39LYS10.8480.9178.30521.71821.7180.0000.0000.0000.000
31A40ALA00.0110.01510.698-1.345-1.3450.0000.0000.0000.000
32A41THR0-0.059-0.04211.8691.4501.4500.0000.0000.0000.000
33A42GLY00.0370.00914.175-0.274-0.2740.0000.0000.0000.000
34A43VAL0-0.019-0.01916.5440.6340.6340.0000.0000.0000.000
35A44VAL00.0200.02616.322-0.470-0.4700.0000.0000.0000.000
36A45VAL0-0.026-0.01618.4731.1201.1200.0000.0000.0000.000
37A46ILE00.0170.02119.229-0.872-0.8720.0000.0000.0000.000
38A47THR00.018-0.02021.3970.4430.4430.0000.0000.0000.000
39A48GLY0-0.023-0.02023.6240.0500.0500.0000.0000.0000.000
40A49ASP-1-0.850-0.87323.982-12.863-12.8630.0000.0000.0000.000
41A50GLU-1-0.912-0.97022.545-12.698-12.6980.0000.0000.0000.000
42A51THR0-0.043-0.03720.694-0.833-0.8330.0000.0000.0000.000
43A52GLN00.003-0.01017.746-1.794-1.7940.0000.0000.0000.000
44A53VAL00.0000.00715.6120.7780.7780.0000.0000.0000.000
45A54TYR0-0.100-0.06415.199-1.218-1.2180.0000.0000.0000.000
46A55ALA00.0180.00313.2161.0971.0970.0000.0000.0000.000
47A56ILE00.0150.01210.623-1.327-1.3270.0000.0000.0000.000
48A57TRP0-0.0110.0068.1630.3220.3220.0000.0000.0000.000
49A58VAL00.0090.0046.803-4.015-4.0150.0000.0000.0000.000
50A59PRO0-0.0130.0032.2720.7411.6191.119-0.473-1.524-0.004
51A60VAL0-0.044-0.0414.8862.7652.789-0.001-0.005-0.0180.000
52A61GLY00.0110.0096.5593.3843.3840.0000.0000.0000.000
53A62LEU0-0.025-0.0086.368-4.376-4.3760.0000.0000.0000.000
54A63ALA0-0.035-0.0158.0441.5001.5000.0000.0000.0000.000
55A64ILE00.0040.0029.4441.4131.4130.0000.0000.0000.000
56A65PRO00.0040.00612.6420.2720.2720.0000.0000.0000.000
57A66GLU-1-0.899-0.95614.508-16.928-16.9280.0000.0000.0000.000
58A67ASN0-0.050-0.02915.7670.9190.9190.0000.0000.0000.000
59A68GLU-1-0.900-0.90613.180-20.774-20.7740.0000.0000.0000.000
60A92TYR0-0.036-0.03718.1000.1780.1780.0000.0000.0000.000
61A93GLY0-0.0090.00221.1350.0000.0000.0000.0000.0000.000
62A94ASP-1-0.862-0.93820.472-14.058-14.0580.0000.0000.0000.000
63A95THR0-0.056-0.03821.548-0.070-0.0700.0000.0000.0000.000
64A96PRO0-0.020-0.01922.413-0.158-0.1580.0000.0000.0000.000
65A97ILE0-0.0080.01421.7580.7300.7300.0000.0000.0000.000
66A98PRO0-0.029-0.02624.222-0.313-0.3130.0000.0000.0000.000
67A99GLY00.0520.02624.261-0.314-0.3140.0000.0000.0000.000
68A100TYR0-0.038-0.01824.5690.5530.5530.0000.0000.0000.000
69A101ILE0-0.022-0.01523.110-0.576-0.5760.0000.0000.0000.000
70A102TYR0-0.036-0.02120.5670.6720.6720.0000.0000.0000.000
71A103ILE0-0.024-0.01723.272-0.009-0.0090.0000.0000.0000.000
72A104ASN00.0470.01920.1440.8560.8560.0000.0000.0000.000
73A105PRO0-0.018-0.01723.4720.2970.2970.0000.0000.0000.000
74A106LEU00.015-0.00823.8850.5740.5740.0000.0000.0000.000
75A107ASP-1-0.803-0.84122.944-11.677-11.6770.0000.0000.0000.000
76A108GLY00.0260.01323.842-0.149-0.1490.0000.0000.0000.000
77A109THR0-0.076-0.07425.5690.4820.4820.0000.0000.0000.000
78A110TYR0-0.074-0.04127.9980.3580.3580.0000.0000.0000.000
79A111PRO00.0130.02629.3710.1200.1200.0000.0000.0000.000
80A112PRO00.0300.01530.8690.2680.2680.0000.0000.0000.000
81A113GLY0-0.040-0.01133.580-0.118-0.1180.0000.0000.0000.000
82A114THR0-0.057-0.04133.5680.0980.0980.0000.0000.0000.000
83A115GLU-1-0.935-0.97836.825-7.114-7.1140.0000.0000.0000.000
84A116GLN0-0.022-0.00232.5760.1260.1260.0000.0000.0000.000
85A117ASN0-0.017-0.01533.6570.2730.2730.0000.0000.0000.000
86A118PRO00.0420.02336.981-0.097-0.0970.0000.0000.0000.000
87A119ALA0-0.0220.00636.8910.1440.1440.0000.0000.0000.000
88A120ASN00.010-0.01637.293-0.085-0.0850.0000.0000.0000.000
89A121PRO00.0170.01433.376-0.119-0.1190.0000.0000.0000.000
90A122ASN0-0.069-0.03733.120-0.364-0.3640.0000.0000.0000.000
91A123PRO00.0290.01630.9340.1900.1900.0000.0000.0000.000
92A124SER0-0.045-0.04033.7570.0670.0670.0000.0000.0000.000
93A125LEU0-0.001-0.01233.056-0.296-0.2960.0000.0000.0000.000
94A126GLU-1-0.763-0.81736.523-7.738-7.7380.0000.0000.0000.000
95A127GLU-1-0.776-0.86837.793-7.625-7.6250.0000.0000.0000.000
96A128SER0-0.020-0.00939.0360.0460.0460.0000.0000.0000.000
97A129HIS00.0570.03932.7380.0550.0550.0000.0000.0000.000
98A130PRO0-0.049-0.01337.1990.2370.2370.0000.0000.0000.000
99A131LEU00.0220.00939.786-0.107-0.1070.0000.0000.0000.000
100A132ASN0-0.085-0.04841.9690.0290.0290.0000.0000.0000.000
101A133THR0-0.0180.01736.463-0.075-0.0750.0000.0000.0000.000
102A134PHE00.0260.00334.7840.1290.1290.0000.0000.0000.000
103A135MET00.0030.00729.893-0.129-0.1290.0000.0000.0000.000
104A136PHE0-0.017-0.01728.3330.1960.1960.0000.0000.0000.000
105A137GLN0-0.008-0.02825.372-0.470-0.4700.0000.0000.0000.000
106A138GLY00.1450.09025.548-0.383-0.3830.0000.0000.0000.000
107A139ASN0-0.066-0.03124.854-0.203-0.2030.0000.0000.0000.000
108A140ARG10.9380.95228.3499.1369.1360.0000.0000.0000.000
109A141PHE00.006-0.00129.098-0.035-0.0350.0000.0000.0000.000
110A142ARG10.8260.88234.0728.2968.2960.0000.0000.0000.000
111A143ASN00.0170.00537.439-0.102-0.1020.0000.0000.0000.000
112A144ARG10.9370.96539.6257.4917.4910.0000.0000.0000.000
113A145GLN0-0.031-0.02342.248-0.025-0.0250.0000.0000.0000.000
114A146GLY00.0210.01941.2170.1260.1260.0000.0000.0000.000
115A147ALA0-0.0060.00338.841-0.188-0.1880.0000.0000.0000.000
116A148LEU00.0010.01034.8080.0430.0430.0000.0000.0000.000
117A149THR0-0.035-0.02533.872-0.082-0.0820.0000.0000.0000.000
118A150VAL0-0.005-0.01228.9120.0960.0960.0000.0000.0000.000
119A151TYR0-0.020-0.00629.431-0.033-0.0330.0000.0000.0000.000
120A152THR0-0.0020.00326.920-0.176-0.1760.0000.0000.0000.000
121A153GLY00.1240.07727.202-0.130-0.1300.0000.0000.0000.000
122A154THR0-0.096-0.05628.0170.5180.5180.0000.0000.0000.000
123A155VAL0-0.006-0.00629.064-0.274-0.2740.0000.0000.0000.000
124A156THR00.0220.01231.4340.1970.1970.0000.0000.0000.000
125A157GLN0-0.023-0.00731.688-0.076-0.0760.0000.0000.0000.000
126A158GLY00.0360.02634.7090.2420.2420.0000.0000.0000.000
127A159THR0-0.122-0.07637.292-0.062-0.0620.0000.0000.0000.000
128A160ASP-1-0.867-0.91739.481-7.135-7.1350.0000.0000.0000.000
129A161PRO0-0.044-0.01841.3180.0930.0930.0000.0000.0000.000
130A162VAL00.021-0.02135.598-0.145-0.1450.0000.0000.0000.000
131A163LYS10.7790.87537.5357.3757.3750.0000.0000.0000.000
132A164THR00.0160.01233.467-0.104-0.1040.0000.0000.0000.000
133A165TYR0-0.026-0.01235.0460.2170.2170.0000.0000.0000.000
134A166TYR0-0.021-0.01933.130-0.425-0.4250.0000.0000.0000.000
135A167GLN00.0110.02129.102-0.003-0.0030.0000.0000.0000.000
136A168TYR0-0.025-0.04131.995-0.185-0.1850.0000.0000.0000.000
137A169THR0-0.006-0.00928.6130.3360.3360.0000.0000.0000.000
138A170PRO0-0.038-0.01131.741-0.009-0.0090.0000.0000.0000.000
139A171VAL0-0.017-0.01130.165-0.281-0.2810.0000.0000.0000.000
140A172SER00.0190.00227.1230.2430.2430.0000.0000.0000.000
141A173SER0-0.049-0.01626.9360.0950.0950.0000.0000.0000.000
142A174LYS10.8400.88128.6909.4269.4260.0000.0000.0000.000
143A175ALA00.0250.01728.2970.3090.3090.0000.0000.0000.000
144A176MET00.0110.02129.6720.1450.1450.0000.0000.0000.000
145A177TYR00.0260.00831.3840.3990.3990.0000.0000.0000.000
146A178ASP-1-0.796-0.88433.415-8.785-8.7850.0000.0000.0000.000
147A179ALA0-0.066-0.03133.1210.2490.2490.0000.0000.0000.000
148A180TYR00.0310.01835.1150.2670.2670.0000.0000.0000.000
149A181TRP0-0.021-0.01136.4000.1990.1990.0000.0000.0000.000
150A182ASN0-0.095-0.04037.9830.0710.0710.0000.0000.0000.000
151A183GLY00.0280.00939.9590.0900.0900.0000.0000.0000.000
152A184LYS10.8420.92634.0809.2829.2820.0000.0000.0000.000
153A185PHE00.0720.04032.799-0.115-0.1150.0000.0000.0000.000
154A186ARG10.9040.96038.7037.5197.5190.0000.0000.0000.000
155A187ASP-1-0.836-0.91638.917-8.049-8.0490.0000.0000.0000.000
156A188VAL00.0190.00737.3890.0880.0880.0000.0000.0000.000
157A189ALA0-0.018-0.00438.7810.0600.0600.0000.0000.0000.000
158A190PHE0-0.043-0.03240.5200.0560.0560.0000.0000.0000.000
159A191HIS0-0.0200.00943.4350.2740.2740.0000.0000.0000.000
160A192SER0-0.042-0.02545.4920.0210.0210.0000.0000.0000.000
161A193GLY00.0410.02247.7540.0700.0700.0000.0000.0000.000
162A194PHE0-0.035-0.01946.526-0.094-0.0940.0000.0000.0000.000
163A195ASN0-0.005-0.00543.6300.0540.0540.0000.0000.0000.000
164A196GLU-1-0.855-0.94441.424-7.435-7.4350.0000.0000.0000.000
165A197ASP-1-0.909-0.93937.967-8.475-8.4750.0000.0000.0000.000
166A198PRO0-0.118-0.05034.4770.1210.1210.0000.0000.0000.000
167A199LEU00.0310.01437.071-0.070-0.0700.0000.0000.0000.000
168A200VAL00.000-0.00333.524-0.203-0.2030.0000.0000.0000.000
169A201ALA0-0.0140.00134.2540.2320.2320.0000.0000.0000.000
170A202GLU-1-0.884-0.93934.946-8.634-8.6340.0000.0000.0000.000
171A203TYR0-0.027-0.01532.230-0.262-0.2620.0000.0000.0000.000
172A204GLN00.017-0.01329.583-0.476-0.4760.0000.0000.0000.000
173A205GLY00.0590.03028.728-0.484-0.4840.0000.0000.0000.000
174A206GLN0-0.080-0.03828.1700.4430.4430.0000.0000.0000.000
175A207LEU00.0200.01827.692-0.397-0.3970.0000.0000.0000.000
176A208SER0-0.037-0.02623.8810.0420.0420.0000.0000.0000.000
177A209TYR0-0.008-0.01224.0850.4230.4230.0000.0000.0000.000
178A210LEU00.0160.03918.405-0.417-0.4170.0000.0000.0000.000
179A211PRO00.0080.00616.9590.6190.6190.0000.0000.0000.000
180A212GLN0-0.0310.00718.111-0.166-0.1660.0000.0000.0000.000
181A213PRO00.0410.01715.3970.3280.3280.0000.0000.0000.000
182A214PRO0-0.024-0.00614.297-0.777-0.7770.0000.0000.0000.000
183A215VAL0-0.010-0.0188.1590.0060.0060.0000.0000.0000.000
184A216ASN0-0.028-0.0199.445-0.892-0.8920.0000.0000.0000.000
185A217ALA00.0000.01610.7931.3401.3400.0000.0000.0000.000
186A218PRO0-0.035-0.00913.361-0.570-0.5700.0000.0000.0000.000