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: 5J71Z

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1954076.424133
FMO2-HF: Nuclear repulsion 1881711.808829
FMO2-HF: Total energy -72364.615304
FMO2-MP2: Total energy -72580.068468


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.
-194.585-187.8233.067-3.464-6.365-0.014
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 : 0.969 / q_NPA : 0.984
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].
3A12HIS00.0240.0013.708-8.878-6.184-0.014-1.362-1.3180.004
4A13ILE0-0.0030.0115.142-0.367-0.3670.0000.0000.0000.000
5A14GLU-1-0.953-0.9638.068-17.781-17.7810.0000.0000.0000.000
6A15GLY00.029-0.00511.7890.3650.3650.0000.0000.0000.000
7A16SER0-0.003-0.02613.863-0.031-0.0310.0000.0000.0000.000
8A17PHE0-0.0160.0198.013-1.187-1.1870.0000.0000.0000.000
9A18THR00.018-0.01314.0901.6001.6000.0000.0000.0000.000
10A19ASN0-0.0200.00315.125-0.239-0.2390.0000.0000.0000.000
11A20VAL0-0.0060.00114.694-0.932-0.9320.0000.0000.0000.000
12A21TRP00.0440.01713.0750.7960.7960.0000.0000.0000.000
13A22LYS10.8820.93317.40911.51211.5120.0000.0000.0000.000
14A23ASP-1-0.855-0.92518.088-14.183-14.1830.0000.0000.0000.000
15A24ASP-1-0.917-0.97019.975-12.108-12.1080.0000.0000.0000.000
16A25LYS10.9670.99122.32113.05313.0530.0000.0000.0000.000
17A26THR0-0.106-0.07518.9730.1550.1550.0000.0000.0000.000
18A27LEU0-0.011-0.00121.1930.1030.1030.0000.0000.0000.000
19A28ASP-1-0.872-0.92615.970-16.183-16.1830.0000.0000.0000.000
20A29TRP0-0.005-0.01416.421-0.088-0.0880.0000.0000.0000.000
21A30TYR0-0.015-0.02411.859-1.559-1.5590.0000.0000.0000.000
22A31ALA00.0670.03811.2541.3181.3180.0000.0000.0000.000
23A32ASN0-0.0260.0009.308-3.531-3.5310.0000.0000.0000.000
24A33TYR00.0240.0005.6103.6553.6550.0000.0000.0000.000
25A34GLU-1-0.928-0.9683.441-66.229-65.2040.014-0.481-0.558-0.004
26A35GLY0-0.008-0.0065.423-4.233-4.2330.0000.0000.0000.000
27A36ILE0-0.076-0.0282.533-2.755-1.7890.811-0.368-1.409-0.004
28A37LEU00.0130.0125.7362.3262.3260.0000.0000.0000.000
29A38TRP0-0.026-0.0463.278-5.910-4.4510.105-0.569-0.996-0.005
30A39LYS10.9580.9908.24021.54821.5480.0000.0000.0000.000
31A40ALA00.0070.00810.440-1.330-1.3300.0000.0000.0000.000
32A41THR0-0.070-0.05311.4611.3071.3070.0000.0000.0000.000
33A42GLY00.0530.01413.792-0.092-0.0920.0000.0000.0000.000
34A43VAL0-0.024-0.01615.9520.6440.6440.0000.0000.0000.000
35A44VAL00.0250.02516.176-0.643-0.6430.0000.0000.0000.000
36A45VAL0-0.031-0.01618.5120.9990.9990.0000.0000.0000.000
37A46ILE00.0400.02720.025-0.723-0.7230.0000.0000.0000.000
38A47THR00.0440.01122.1410.4280.4280.0000.0000.0000.000
39A48GLY0-0.012-0.01424.3750.0340.0340.0000.0000.0000.000
40A49ASP-1-0.868-0.89825.205-12.100-12.1000.0000.0000.0000.000
41A50GLU-1-0.931-0.97822.917-12.145-12.1450.0000.0000.0000.000
42A51THR0-0.068-0.04121.537-0.725-0.7250.0000.0000.0000.000
43A52GLN00.010-0.01418.255-1.732-1.7320.0000.0000.0000.000
44A53VAL0-0.0020.01216.2200.6510.6510.0000.0000.0000.000
45A54TYR0-0.038-0.01315.828-0.941-0.9410.0000.0000.0000.000
46A55ALA00.013-0.00213.7150.8940.8940.0000.0000.0000.000
47A56ILE00.0100.01510.348-1.101-1.1010.0000.0000.0000.000
48A57TRP0-0.0240.0148.715-0.241-0.2410.0000.0000.0000.000
49A58VAL00.009-0.0026.218-3.319-3.3190.0000.0000.0000.000
50A59PRO0-0.057-0.0092.0730.6601.2342.152-0.668-2.058-0.005
51A60VAL0-0.022-0.0284.5821.9341.978-0.001-0.016-0.0260.000
52A61GLY00.0050.0046.7422.9512.9510.0000.0000.0000.000
53A62LEU0-0.030-0.0066.830-3.644-3.6440.0000.0000.0000.000
54A63ALA0-0.016-0.0018.7001.3431.3430.0000.0000.0000.000
55A64ILE0-0.012-0.01010.0391.0011.0010.0000.0000.0000.000
56A65PRO0-0.010-0.00113.6930.2920.2920.0000.0000.0000.000
57A66GLU-1-0.897-0.95615.531-16.113-16.1130.0000.0000.0000.000
58A67ASN0-0.066-0.02516.3810.5230.5230.0000.0000.0000.000
59A68GLU-1-0.921-0.94014.665-19.057-19.0570.0000.0000.0000.000
60A92TYR0-0.012-0.02318.8540.2230.2230.0000.0000.0000.000
61A93GLY0-0.0080.00022.2080.0980.0980.0000.0000.0000.000
62A94ASP-1-0.896-0.96521.793-13.828-13.8280.0000.0000.0000.000
63A95THR0-0.0230.00622.8700.0640.0640.0000.0000.0000.000
64A96PRO0-0.038-0.03923.317-0.179-0.1790.0000.0000.0000.000
65A97ILE0-0.0200.01322.2990.6430.6430.0000.0000.0000.000
66A98PRO0-0.002-0.01525.007-0.310-0.3100.0000.0000.0000.000
67A99GLY00.0430.02124.867-0.303-0.3030.0000.0000.0000.000
68A100TYR0-0.049-0.02824.8790.5320.5320.0000.0000.0000.000
69A101ILE0-0.018-0.00623.131-0.527-0.5270.0000.0000.0000.000
70A102TYR0-0.037-0.02120.5110.7230.7230.0000.0000.0000.000
71A103ILE0-0.030-0.02122.851-0.118-0.1180.0000.0000.0000.000
72A104ASN00.0580.03919.7620.7300.7300.0000.0000.0000.000
73A105PRO0-0.036-0.03423.3240.2720.2720.0000.0000.0000.000
74A106LEU00.007-0.01323.7710.5240.5240.0000.0000.0000.000
75A107ASP-1-0.829-0.87822.641-11.750-11.7500.0000.0000.0000.000
76A108GLY00.004-0.01323.696-0.080-0.0800.0000.0000.0000.000
77A109THR0-0.056-0.04825.1020.4280.4280.0000.0000.0000.000
78A110TYR0-0.067-0.03227.5590.3840.3840.0000.0000.0000.000
79A111PRO0-0.0150.00229.4030.0920.0920.0000.0000.0000.000
80A112PRO00.0460.00830.7070.2430.2430.0000.0000.0000.000
81A113GLY0-0.029-0.00233.641-0.108-0.1080.0000.0000.0000.000
82A114THR0-0.064-0.03033.4620.0480.0480.0000.0000.0000.000
83A115GLU-1-0.900-0.96836.780-7.057-7.0570.0000.0000.0000.000
84A116GLN0-0.048-0.01332.3700.0230.0230.0000.0000.0000.000
85A117ASN0-0.028-0.01833.1830.3350.3350.0000.0000.0000.000
86A118PRO00.0290.01936.410-0.112-0.1120.0000.0000.0000.000
87A119ALA0-0.0210.00736.4110.1060.1060.0000.0000.0000.000
88A120ASN00.042-0.00237.213-0.088-0.0880.0000.0000.0000.000
89A121PRO00.006-0.00133.417-0.132-0.1320.0000.0000.0000.000
90A122ASN0-0.061-0.03333.062-0.396-0.3960.0000.0000.0000.000
91A123PRO00.0130.01431.3730.1690.1690.0000.0000.0000.000
92A124SER0-0.083-0.06434.0010.0670.0670.0000.0000.0000.000
93A125LEU0-0.006-0.01333.483-0.256-0.2560.0000.0000.0000.000
94A126GLU-1-0.868-0.89936.694-7.517-7.5170.0000.0000.0000.000
95A127GLU-1-0.912-0.96337.913-7.466-7.4660.0000.0000.0000.000
96A128SER0-0.047-0.02039.1450.0190.0190.0000.0000.0000.000
97A129HIS00.0590.04332.8290.0560.0560.0000.0000.0000.000
98A130PRO0-0.028-0.00537.1270.2100.2100.0000.0000.0000.000
99A131LEU00.0270.00939.800-0.086-0.0860.0000.0000.0000.000
100A132ASN0-0.060-0.03141.7620.0040.0040.0000.0000.0000.000
101A133THR0-0.0320.02136.174-0.119-0.1190.0000.0000.0000.000
102A134PHE00.021-0.00334.4260.1110.1110.0000.0000.0000.000
103A135MET0-0.004-0.00930.334-0.140-0.1400.0000.0000.0000.000
104A136PHE0-0.025-0.02028.8560.1880.1880.0000.0000.0000.000
105A137GLN00.011-0.01325.862-0.446-0.4460.0000.0000.0000.000
106A138GLY00.1270.07525.993-0.394-0.3940.0000.0000.0000.000
107A139ASN0-0.076-0.03324.627-0.186-0.1860.0000.0000.0000.000
108A140ARG10.9560.96528.3639.0379.0370.0000.0000.0000.000
109A141PHE00.0160.00928.735-0.052-0.0520.0000.0000.0000.000
110A142ARG10.9710.99433.9267.9597.9590.0000.0000.0000.000
111A143ASN00.023-0.00336.969-0.138-0.1380.0000.0000.0000.000
112A144ARG10.9050.95539.4087.4507.4500.0000.0000.0000.000
113A145GLN0-0.028-0.02842.123-0.022-0.0220.0000.0000.0000.000
114A146GLY00.0150.01240.8500.0870.0870.0000.0000.0000.000
115A147ALA0-0.0050.01838.463-0.152-0.1520.0000.0000.0000.000
116A148LEU0-0.005-0.01034.4580.0620.0620.0000.0000.0000.000
117A149THR0-0.031-0.01233.480-0.088-0.0880.0000.0000.0000.000
118A150VAL0-0.005-0.02728.4960.1130.1130.0000.0000.0000.000
119A151TYR0-0.039-0.01529.297-0.090-0.0900.0000.0000.0000.000
120A152THR0-0.0070.00126.654-0.141-0.1410.0000.0000.0000.000
121A153GLY00.1340.07227.375-0.170-0.1700.0000.0000.0000.000
122A154THR0-0.082-0.05028.2390.3160.3160.0000.0000.0000.000
123A155VAL00.0100.00629.439-0.269-0.2690.0000.0000.0000.000
124A156THR00.004-0.00931.6930.2390.2390.0000.0000.0000.000
125A157GLN0-0.0120.00731.331-0.102-0.1020.0000.0000.0000.000
126A158GLY00.0370.01034.9940.2350.2350.0000.0000.0000.000
127A159THR0-0.141-0.08637.723-0.063-0.0630.0000.0000.0000.000
128A160ASP-1-0.882-0.92639.952-7.051-7.0510.0000.0000.0000.000
129A161PRO0-0.060-0.03242.0120.1350.1350.0000.0000.0000.000
130A162VAL00.0360.00336.256-0.119-0.1190.0000.0000.0000.000
131A163LYS10.9470.98938.3167.1617.1610.0000.0000.0000.000
132A164THR00.0200.00833.979-0.166-0.1660.0000.0000.0000.000
133A165TYR0-0.0210.01735.2340.1660.1660.0000.0000.0000.000
134A166TYR0-0.006-0.01833.272-0.303-0.3030.0000.0000.0000.000
135A167GLN00.0450.02929.070-0.039-0.0390.0000.0000.0000.000
136A168TYR0-0.049-0.03131.656-0.220-0.2200.0000.0000.0000.000
137A169THR0-0.001-0.02028.4230.2880.2880.0000.0000.0000.000
138A170PRO0-0.043-0.00331.4150.0120.0120.0000.0000.0000.000
139A171VAL0-0.005-0.01129.760-0.285-0.2850.0000.0000.0000.000
140A172SER00.0190.01326.9860.2150.2150.0000.0000.0000.000
141A173SER00.0110.03426.797-0.008-0.0080.0000.0000.0000.000
142A174LYS10.9110.94028.5949.1869.1860.0000.0000.0000.000
143A175ALA00.0360.02327.8730.2810.2810.0000.0000.0000.000
144A176MET0-0.0100.01229.4760.1820.1820.0000.0000.0000.000
145A177TYR00.0290.00331.0310.3780.3780.0000.0000.0000.000
146A178ASP-1-0.840-0.92133.051-8.661-8.6610.0000.0000.0000.000
147A179ALA0-0.066-0.04233.0040.2550.2550.0000.0000.0000.000
148A180TYR00.0220.00534.9130.2840.2840.0000.0000.0000.000
149A181TRP00.0030.00436.2620.2030.2030.0000.0000.0000.000
150A182ASN0-0.114-0.04138.0600.1120.1120.0000.0000.0000.000
151A183GLY00.0350.00639.8530.0970.0970.0000.0000.0000.000
152A184LYS10.8640.94534.5178.8268.8260.0000.0000.0000.000
153A185PHE00.0640.03932.501-0.064-0.0640.0000.0000.0000.000
154A186ARG10.9100.95438.5927.2807.2800.0000.0000.0000.000
155A187ASP-1-0.814-0.91739.878-7.764-7.7640.0000.0000.0000.000
156A188VAL00.0110.01637.4030.0760.0760.0000.0000.0000.000
157A189ALA0-0.0070.00638.885-0.004-0.0040.0000.0000.0000.000
158A190PHE0-0.060-0.02540.6100.0410.0410.0000.0000.0000.000
159A191HIS0-0.0080.00943.4300.2600.2600.0000.0000.0000.000
160A192SER0-0.028-0.01245.2800.0000.0000.0000.0000.0000.000
161A193GLY00.0270.00947.7540.0390.0390.0000.0000.0000.000
162A194PHE0-0.033-0.02546.606-0.092-0.0920.0000.0000.0000.000
163A195ASN0-0.005-0.00743.9590.0830.0830.0000.0000.0000.000
164A196GLU-1-0.901-0.96341.372-7.275-7.2750.0000.0000.0000.000
165A197ASP-1-0.943-0.95938.814-8.036-8.0360.0000.0000.0000.000
166A198PRO0-0.099-0.04534.7520.1010.1010.0000.0000.0000.000
167A199LEU00.0450.02937.671-0.007-0.0070.0000.0000.0000.000
168A200VAL00.0090.00133.684-0.233-0.2330.0000.0000.0000.000
169A201ALA0-0.045-0.01934.3050.1980.1980.0000.0000.0000.000
170A202GLU-1-0.905-0.94935.332-8.445-8.4450.0000.0000.0000.000
171A203TYR0-0.055-0.01532.064-0.261-0.2610.0000.0000.0000.000
172A204GLN00.0800.01330.009-0.421-0.4210.0000.0000.0000.000
173A205GLY00.0410.02628.768-0.434-0.4340.0000.0000.0000.000
174A206GLN0-0.060-0.02327.8560.2320.2320.0000.0000.0000.000
175A207LEU00.0210.01627.804-0.349-0.3490.0000.0000.0000.000
176A208SER0-0.052-0.02523.801-0.042-0.0420.0000.0000.0000.000
177A209TYR0-0.008-0.02224.6360.4700.4700.0000.0000.0000.000
178A210LEU0-0.0090.02019.373-0.386-0.3860.0000.0000.0000.000
179A211PRO00.0120.02317.5420.5990.5990.0000.0000.0000.000
180A212GLN0-0.036-0.01418.985-0.107-0.1070.0000.0000.0000.000
181A213PRO00.0190.00716.7790.3140.3140.0000.0000.0000.000
182A214PRO0-0.017-0.01115.216-0.689-0.6890.0000.0000.0000.000
183A215VAL00.005-0.0119.302-0.115-0.1150.0000.0000.0000.000
184A216ASN0-0.024-0.00710.400-0.147-0.1470.0000.0000.0000.000
185A217ALA0-0.0140.00811.7081.2671.2670.0000.0000.0000.000
186A218PRO0-0.021-0.01014.344-0.500-0.5000.0000.0000.0000.000