FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: N9L5Q

Calculation Name: 1BGX-L-Xray372

Preferred Name: Taq polymerase 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1BGX

Chain ID: L

ChEMBL ID: CHEMBL3564

UniProt ID: P19821

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2096748.479328
FMO2-HF: Nuclear repulsion 2014193.451945
FMO2-HF: Total energy -82555.027382
FMO2-MP2: Total energy -82790.85293


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(L:1:ASP)


Summations of interaction energy for fragment #1(L:1:ASP)
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.
-68.324-63.16714.82-8.894-11.0850.111
Interaction energy analysis for fragmet #1(L:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.770 / q_NPA : -0.892
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].
3L3GLN0-0.016-0.0023.8945.4427.702-0.003-1.128-1.1290.005
4L4MET0-0.003-0.0026.294-4.659-4.6590.0000.0000.0000.000
5L5THR0-0.002-0.0108.246-1.138-1.1380.0000.0000.0000.000
6L6GLN00.013-0.00911.7600.9010.9010.0000.0000.0000.000
7L7SER0-0.0380.00514.905-0.410-0.4100.0000.0000.0000.000
8L8PRO00.027-0.00118.511-0.207-0.2070.0000.0000.0000.000
9L9ALA00.0870.03818.4640.5170.5170.0000.0000.0000.000
10L10ILE0-0.001-0.00519.5430.0070.0070.0000.0000.0000.000
11L11MET0-0.0310.00523.160-0.029-0.0290.0000.0000.0000.000
12L12SER00.0290.01626.014-0.049-0.0490.0000.0000.0000.000
13L13ALA0-0.0010.00229.202-0.090-0.0900.0000.0000.0000.000
14L14SER00.015-0.01131.517-0.041-0.0410.0000.0000.0000.000
15L15PRO0-0.012-0.01534.5630.1420.1420.0000.0000.0000.000
16L16GLY00.0270.02335.522-0.289-0.2890.0000.0000.0000.000
17L17GLU-1-0.816-0.89233.0229.5149.5140.0000.0000.0000.000
18L18LYS10.8870.93328.702-10.989-10.9890.0000.0000.0000.000
19L19VAL00.0340.02425.6050.1000.1000.0000.0000.0000.000
20L20THR0-0.006-0.01924.142-0.327-0.3270.0000.0000.0000.000
21L21MET0-0.0310.01020.2440.0970.0970.0000.0000.0000.000
22L22THR00.013-0.00617.853-0.184-0.1840.0000.0000.0000.000
23L23CYS0-0.0280.00912.5590.4030.4030.0000.0000.0000.000
24L24SER00.019-0.00513.372-1.513-1.5130.0000.0000.0000.000
25L25ALA00.0130.0108.3781.9261.9260.0000.0000.0000.000
26L26SER0-0.0060.0027.045-1.034-1.0340.0000.0000.0000.000
27L27SER0-0.014-0.0097.618-1.012-1.0120.0000.0000.0000.000
28L29SER00.0210.01010.250-0.210-0.2100.0000.0000.0000.000
29L30VAL0-0.0010.0239.9480.4100.4100.0000.0000.0000.000
30L31SER00.0010.01511.347-3.012-3.0120.0000.0000.0000.000
31L32TYR0-0.039-0.02512.3281.0751.0750.0000.0000.0000.000
32L33MET0-0.051-0.01911.4932.4422.4420.0000.0000.0000.000
33L34TYR0-0.0180.00613.188-1.143-1.1430.0000.0000.0000.000
34L35TRP00.002-0.00814.6901.3641.3640.0000.0000.0000.000
35L36TYR0-0.038-0.03013.162-1.720-1.7200.0000.0000.0000.000
36L37GLN00.0060.00218.113-0.227-0.2270.0000.0000.0000.000
37L38GLN00.0120.00719.8770.6730.6730.0000.0000.0000.000
38L39LYS10.8480.91121.824-11.503-11.5030.0000.0000.0000.000
39L40PRO00.0400.03024.7540.3360.3360.0000.0000.0000.000
40L41GLY00.0400.02125.851-0.405-0.4050.0000.0000.0000.000
41L42SER0-0.048-0.02625.162-0.246-0.2460.0000.0000.0000.000
42L43SER00.0650.02321.9280.3840.3840.0000.0000.0000.000
43L44PRO0-0.0040.00417.449-0.568-0.5680.0000.0000.0000.000
44L45ARG10.8360.91120.050-13.533-13.5330.0000.0000.0000.000
45L46LEU00.0460.01919.8960.5570.5570.0000.0000.0000.000
46L47LEU0-0.011-0.00620.897-0.676-0.6760.0000.0000.0000.000
47L48ILE0-0.017-0.00920.803-0.653-0.6530.0000.0000.0000.000
48L49TYR00.0070.00118.9410.8630.8630.0000.0000.0000.000
49L50ASP-1-0.801-0.91316.31218.91718.9170.0000.0000.0000.000
50L51SER0-0.022-0.02418.456-0.650-0.6500.0000.0000.0000.000
51L52THR0-0.099-0.04120.270-0.466-0.4660.0000.0000.0000.000
52L53ASN00.0230.01423.681-0.250-0.2500.0000.0000.0000.000
53L54LEU00.0090.01023.9240.6010.6010.0000.0000.0000.000
54L55ALA00.0100.00423.579-0.140-0.1400.0000.0000.0000.000
55L56SER0-0.003-0.01025.595-0.556-0.5560.0000.0000.0000.000
56L57GLY0-0.014-0.01228.3740.0080.0080.0000.0000.0000.000
57L58VAL0-0.035-0.00826.091-0.121-0.1210.0000.0000.0000.000
58L59PRO00.0410.04229.225-0.214-0.2140.0000.0000.0000.000
59L60VAL00.061-0.00230.7620.2840.2840.0000.0000.0000.000
60L61ARG10.7420.87731.025-10.032-10.0320.0000.0000.0000.000
61L62PHE0-0.013-0.00525.1600.1870.1870.0000.0000.0000.000
62L63SER0-0.012-0.01126.696-0.297-0.2970.0000.0000.0000.000
63L64GLY00.0410.02322.7060.3730.3730.0000.0000.0000.000
64L65SER00.002-0.00421.978-0.539-0.5390.0000.0000.0000.000
65L66GLY00.0500.03119.6240.6720.6720.0000.0000.0000.000
66L67SER00.0370.01018.152-0.040-0.0400.0000.0000.0000.000
67L68GLY00.0190.03016.647-0.274-0.2740.0000.0000.0000.000
68L69THR00.005-0.01014.0881.0321.0320.0000.0000.0000.000
69L70SER0-0.029-0.00414.5090.9040.9040.0000.0000.0000.000
70L71TYR0-0.050-0.04114.232-1.361-1.3610.0000.0000.0000.000
71L72SER0-0.051-0.03317.4130.1820.1820.0000.0000.0000.000
72L73LEU00.0290.02320.070-0.179-0.1790.0000.0000.0000.000
73L74THR00.002-0.00222.240-0.294-0.2940.0000.0000.0000.000
74L75ILE00.0010.01925.901-0.061-0.0610.0000.0000.0000.000
75L76SER0-0.049-0.03828.688-0.343-0.3430.0000.0000.0000.000
76L77ARG10.8340.90032.179-9.379-9.3790.0000.0000.0000.000
77L78MET0-0.0110.02529.0260.3400.3400.0000.0000.0000.000
78L79GLU-1-0.820-0.92032.0598.8138.8130.0000.0000.0000.000
79L80ALA00.0240.00732.2790.2940.2940.0000.0000.0000.000
80L81GLU-1-0.849-0.93531.8809.5359.5350.0000.0000.0000.000
81L82ASP-1-0.774-0.86328.39611.19011.1900.0000.0000.0000.000
82L83ALA0-0.0130.01526.9810.5900.5900.0000.0000.0000.000
83L84ALA0-0.049-0.01424.136-0.187-0.1870.0000.0000.0000.000
84L85THR00.0110.00718.561-0.190-0.1900.0000.0000.0000.000
85L86TYR00.000-0.01518.947-0.058-0.0580.0000.0000.0000.000
86L87TYR00.001-0.00513.5580.4290.4290.0000.0000.0000.000
87L89GLN00.0440.0188.892-0.300-0.3000.0000.0000.0000.000
88L90GLN00.0950.0366.762-3.923-3.9230.0000.0000.0000.000
89L91TRP00.0140.0058.3572.1532.1530.0000.0000.0000.000
90L92SER0-0.0030.0129.102-1.277-1.2770.0000.0000.0000.000
91L93THR0-0.036-0.0326.463-3.557-3.5570.0000.0000.0000.000
92L94TYR0-0.053-0.0172.453-4.752-3.0814.232-1.943-3.9600.033
93L95PRO0-0.0020.0092.413-16.371-14.3932.616-1.856-2.7390.025
94L96LEU0-0.040-0.0275.325-3.591-3.585-0.001-0.002-0.0030.000
95L97THR00.0000.0141.826-27.787-28.5627.977-3.958-3.2440.048
96L98PHE0-0.023-0.0254.915-6.238-6.221-0.001-0.007-0.0100.000
97L99GLY00.0060.0047.5932.0942.0940.0000.0000.0000.000
98L100ALA0-0.030-0.0249.956-1.216-1.2160.0000.0000.0000.000
99L101GLY00.0090.01312.249-1.247-1.2470.0000.0000.0000.000
100L102THR0-0.066-0.04015.3800.0330.0330.0000.0000.0000.000
101L103LYS10.7980.87918.792-12.990-12.9900.0000.0000.0000.000
102L104LEU0-0.020-0.00822.010-0.370-0.3700.0000.0000.0000.000
103L105GLU-1-0.789-0.87724.89211.22811.2280.0000.0000.0000.000
104L106LEU00.008-0.00428.074-0.082-0.0820.0000.0000.0000.000
105L107LYS10.7990.91031.652-9.877-9.8770.0000.0000.0000.000
106L108ARG10.8200.89434.181-8.414-8.4140.0000.0000.0000.000
107L109ALA00.0300.01637.7190.0070.0070.0000.0000.0000.000
108L110ASP-1-0.806-0.88639.8008.1318.1310.0000.0000.0000.000
109L111ALA0-0.040-0.01841.013-0.175-0.1750.0000.0000.0000.000
110L112ALA00.0490.01741.8990.1430.1430.0000.0000.0000.000
111L113PRO0-0.0250.00741.6230.0090.0090.0000.0000.0000.000
112L114THR00.0250.00443.265-0.238-0.2380.0000.0000.0000.000
113L115VAL0-0.005-0.00744.0540.1170.1170.0000.0000.0000.000
114L116SER0-0.053-0.03045.320-0.254-0.2540.0000.0000.0000.000
115L117ILE0-0.022-0.01245.7490.1720.1720.0000.0000.0000.000
116L118PHE0-0.003-0.00645.398-0.119-0.1190.0000.0000.0000.000
117L119PRO00.0090.00147.8660.0930.0930.0000.0000.0000.000
118L120PRO00.0030.02348.1060.0790.0790.0000.0000.0000.000
119L121SER0-0.020-0.03348.678-0.101-0.1010.0000.0000.0000.000
120L122SER00.012-0.00750.478-0.035-0.0350.0000.0000.0000.000
121L123GLU-1-0.797-0.88249.2126.3836.3830.0000.0000.0000.000
122L124GLN00.0190.02344.564-0.037-0.0370.0000.0000.0000.000
123L125LEU00.0330.00848.928-0.015-0.0150.0000.0000.0000.000
124L126THR0-0.057-0.03452.210-0.078-0.0780.0000.0000.0000.000
125L127SER0-0.068-0.04048.363-0.020-0.0200.0000.0000.0000.000
126L128GLY0-0.0060.01149.8750.0390.0390.0000.0000.0000.000
127L129GLY0-0.052-0.03047.3130.0310.0310.0000.0000.0000.000
128L130ALA0-0.006-0.01547.445-0.103-0.1030.0000.0000.0000.000
129L131SER0-0.021-0.01842.7040.0490.0490.0000.0000.0000.000
130L132VAL0-0.0090.01745.149-0.062-0.0620.0000.0000.0000.000
131L133VAL00.0100.01041.5520.1880.1880.0000.0000.0000.000
132L134CYS0-0.068-0.03142.417-0.051-0.0510.0000.0000.0000.000
133L135PHE00.0130.01238.8280.2730.2730.0000.0000.0000.000
134L136LEU00.0160.00539.569-0.210-0.2100.0000.0000.0000.000
135L137ASN00.016-0.00538.9010.1380.1380.0000.0000.0000.000
136L138ASN0-0.012-0.01739.509-0.138-0.1380.0000.0000.0000.000
137L139PHE00.0100.03236.337-0.170-0.1700.0000.0000.0000.000
138L140TYR00.0070.00432.9780.2540.2540.0000.0000.0000.000
139L141PRO00.0330.00234.593-0.249-0.2490.0000.0000.0000.000
140L142LYS10.9700.99428.642-10.717-10.7170.0000.0000.0000.000
141L143ASP-1-0.935-0.96233.0179.6629.6620.0000.0000.0000.000
142L144ILE0-0.017-0.01035.219-0.293-0.2930.0000.0000.0000.000
143L145ASN00.0080.00437.304-0.017-0.0170.0000.0000.0000.000
144L146VAL00.0220.01739.444-0.209-0.2090.0000.0000.0000.000
145L147LYS10.8070.91941.146-6.972-6.9720.0000.0000.0000.000
146L148TRP00.0400.00841.572-0.197-0.1970.0000.0000.0000.000
147L149LYS10.8390.90445.888-6.560-6.5600.0000.0000.0000.000
148L150ILE00.0100.00248.384-0.014-0.0140.0000.0000.0000.000
149L151ASP-1-0.740-0.83651.9095.6945.6940.0000.0000.0000.000
150L152GLY00.0050.01354.051-0.091-0.0910.0000.0000.0000.000
151L153SER0-0.024-0.01051.5340.0580.0580.0000.0000.0000.000
152L154GLU-1-0.856-0.92044.9927.0517.0510.0000.0000.0000.000
153L155ARG10.7900.88044.899-6.904-6.9040.0000.0000.0000.000
154L156GLN0-0.010-0.01740.3240.2060.2060.0000.0000.0000.000
155L157ASN0-0.020-0.00340.3190.1660.1660.0000.0000.0000.000
156L158GLY00.0910.03140.046-0.163-0.1630.0000.0000.0000.000
157L159VAL0-0.041-0.01238.596-0.016-0.0160.0000.0000.0000.000
158L160LEU00.0020.01234.7370.2540.2540.0000.0000.0000.000
159L161ASN00.0240.00734.426-0.375-0.3750.0000.0000.0000.000
160L162SER00.0020.00731.4990.4120.4120.0000.0000.0000.000
161L163TRP00.023-0.00630.315-0.170-0.1700.0000.0000.0000.000
162L164THR0-0.016-0.01430.1150.1700.1700.0000.0000.0000.000
163L165ASP-1-0.827-0.91425.80112.59012.5900.0000.0000.0000.000
164L166GLN0-0.059-0.00728.607-0.166-0.1660.0000.0000.0000.000
165L167ASP-1-0.789-0.87730.2229.2119.2110.0000.0000.0000.000
166L168SER0-0.016-0.02031.5260.0910.0910.0000.0000.0000.000
167L169LYS10.8050.89433.291-8.546-8.5460.0000.0000.0000.000
168L170ASP-1-0.785-0.89836.8568.1378.1370.0000.0000.0000.000
169L171SER0-0.043-0.01132.814-0.096-0.0960.0000.0000.0000.000
170L172THR0-0.046-0.00534.583-0.006-0.0060.0000.0000.0000.000
171L173TYR0-0.014-0.04130.1030.1490.1490.0000.0000.0000.000
172L174SER0-0.016-0.01834.282-0.439-0.4390.0000.0000.0000.000
173L175MET0-0.056-0.02234.3790.3460.3460.0000.0000.0000.000
174L176SER0-0.0200.00635.352-0.249-0.2490.0000.0000.0000.000
175L177SER00.0550.00836.7100.1420.1420.0000.0000.0000.000
176L178THR0-0.034-0.02739.144-0.173-0.1730.0000.0000.0000.000
177L179LEU00.0060.02540.2090.1660.1660.0000.0000.0000.000
178L180THR00.0030.00440.534-0.203-0.2030.0000.0000.0000.000
179L181LEU0-0.038-0.00543.2450.0520.0520.0000.0000.0000.000
180L182THR00.019-0.01746.4460.0650.0650.0000.0000.0000.000
181L183LYS10.8300.90249.054-5.775-5.7750.0000.0000.0000.000
182L184ASP-1-0.810-0.89252.2586.1196.1190.0000.0000.0000.000
183L185GLU-1-0.775-0.85648.8396.4276.4270.0000.0000.0000.000
184L186TYR0-0.002-0.01951.098-0.057-0.0570.0000.0000.0000.000
185L187GLU-1-0.849-0.91752.8665.5945.5940.0000.0000.0000.000
186L188ARG10.7910.88651.856-6.154-6.1540.0000.0000.0000.000
187L189HIS0-0.0310.00153.331-0.005-0.0050.0000.0000.0000.000
188L190ASN0-0.040-0.02456.153-0.039-0.0390.0000.0000.0000.000
189L191SER0-0.063-0.04955.7430.0320.0320.0000.0000.0000.000
190L192TYR00.0610.02049.2840.1370.1370.0000.0000.0000.000
191L193THR0-0.019-0.00149.946-0.093-0.0930.0000.0000.0000.000
192L195GLU-1-0.834-0.92045.7616.6206.6200.0000.0000.0000.000
193L196ALA00.0390.00242.8270.1940.1940.0000.0000.0000.000
194L197THR0-0.009-0.00342.832-0.224-0.2240.0000.0000.0000.000
195L198HIS00.0280.01638.6680.0190.0190.0000.0000.0000.000
196L199LYS10.8710.92038.978-8.212-8.2120.0000.0000.0000.000
197L200THR0-0.038-0.03342.218-0.167-0.1670.0000.0000.0000.000
198L201SER0-0.026-0.01444.973-0.128-0.1280.0000.0000.0000.000
199L202THR00.0010.00246.9860.0510.0510.0000.0000.0000.000
200L203SER00.0000.01649.094-0.058-0.0580.0000.0000.0000.000
201L204PRO00.0040.00447.1350.0770.0770.0000.0000.0000.000
202L205ILE00.013-0.00346.682-0.176-0.1760.0000.0000.0000.000
203L206VAL0-0.017-0.00348.0820.0930.0930.0000.0000.0000.000
204L207LYS10.8680.93249.116-6.520-6.5200.0000.0000.0000.000
205L208SER0-0.019-0.01750.3570.0480.0480.0000.0000.0000.000
206L209PHE00.0130.01050.321-0.056-0.0560.0000.0000.0000.000
207L210ASN00.0410.00454.979-0.010-0.0100.0000.0000.0000.000
208L211ARG10.8710.95755.295-5.680-5.6800.0000.0000.0000.000