FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: G6V91

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:


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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2077144.49735
FMO2-HF: Nuclear repulsion 1994590.994459
FMO2-HF: Total energy -82553.502891
FMO2-MP2: Total energy -82789.010815


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.
-18.976-10.4962.551-4.805-6.2260.051
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 : -0.928 / q_NPA : -0.982
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].
3L3GLN0-0.0090.0043.00512.64414.9600.696-1.134-1.8780.006
4L4MET0-0.003-0.0035.453-6.350-6.302-0.001-0.002-0.0440.000
5L5THR0-0.002-0.0097.897-1.181-1.1810.0000.0000.0000.000
6L6GLN0-0.010-0.01711.3010.1980.1980.0000.0000.0000.000
7L7SER0-0.0310.02714.545-0.433-0.4330.0000.0000.0000.000
8L8PRO0-0.003-0.02917.836-0.268-0.2680.0000.0000.0000.000
9L9ALA00.0790.02718.4470.5210.5210.0000.0000.0000.000
10L10ILE00.0170.00219.610-0.068-0.0680.0000.0000.0000.000
11L11MET0-0.024-0.00123.231-0.079-0.0790.0000.0000.0000.000
12L12SER00.0150.00625.877-0.100-0.1000.0000.0000.0000.000
13L13ALA0-0.005-0.00329.198-0.054-0.0540.0000.0000.0000.000
14L14SER00.0320.01531.362-0.039-0.0390.0000.0000.0000.000
15L15PRO0-0.005-0.01134.4460.1130.1130.0000.0000.0000.000
16L16GLY00.0560.04035.224-0.277-0.2770.0000.0000.0000.000
17L17GLU-1-0.921-0.96433.3269.3109.3100.0000.0000.0000.000
18L18LYS10.9250.97228.917-10.722-10.7220.0000.0000.0000.000
19L19VAL00.0120.00625.6390.0760.0760.0000.0000.0000.000
20L20THR0-0.015-0.02623.846-0.240-0.2400.0000.0000.0000.000
21L21MET0-0.0010.02420.1730.1220.1220.0000.0000.0000.000
22L22THR0-0.008-0.01217.242-0.325-0.3250.0000.0000.0000.000
23L23CYS0-0.035-0.00612.4980.2380.2380.0000.0000.0000.000
24L24SER00.006-0.00613.169-0.918-0.9180.0000.0000.0000.000
25L25ALA00.0490.0298.8992.1002.1000.0000.0000.0000.000
26L26SER00.0030.0026.620-1.501-1.5010.0000.0000.0000.000
27L27SER00.0040.0047.589-2.003-2.0030.0000.0000.0000.000
28L29SER0-0.016-0.0259.927-0.507-0.5070.0000.0000.0000.000
29L30VAL00.0050.03410.3491.2791.2790.0000.0000.0000.000
30L31SER0-0.038-0.03011.570-2.676-2.6760.0000.0000.0000.000
31L32TYR0-0.021-0.01912.9151.8371.8370.0000.0000.0000.000
32L33MET0-0.039-0.00711.8922.4812.4810.0000.0000.0000.000
33L34TYR00.0040.02213.759-1.026-1.0260.0000.0000.0000.000
34L35TRP00.007-0.01115.1470.9770.9770.0000.0000.0000.000
35L36TYR0-0.028-0.00314.160-1.049-1.0490.0000.0000.0000.000
36L37GLN00.019-0.00318.687-0.447-0.4470.0000.0000.0000.000
37L38GLN0-0.017-0.01120.4550.5410.5410.0000.0000.0000.000
38L39LYS10.8610.93522.402-11.251-11.2510.0000.0000.0000.000
39L40PRO00.0210.00425.4290.3160.3160.0000.0000.0000.000
40L41GLY00.0550.04526.013-0.466-0.4660.0000.0000.0000.000
41L42SER0-0.070-0.04325.691-0.307-0.3070.0000.0000.0000.000
42L43SER00.0520.01922.8110.5090.5090.0000.0000.0000.000
43L44PRO0-0.036-0.01918.392-0.510-0.5100.0000.0000.0000.000
44L45ARG10.9310.97820.948-12.888-12.8880.0000.0000.0000.000
45L46LEU00.0210.01020.8220.7580.7580.0000.0000.0000.000
46L47LEU00.018-0.01421.865-0.562-0.5620.0000.0000.0000.000
47L48ILE0-0.0150.00521.788-0.538-0.5380.0000.0000.0000.000
48L49TYR0-0.009-0.00620.2060.7930.7930.0000.0000.0000.000
49L50ASP-1-0.849-0.94217.62318.03918.0390.0000.0000.0000.000
50L51SER0-0.003-0.00119.522-0.723-0.7230.0000.0000.0000.000
51L52THR0-0.058-0.02621.226-0.304-0.3040.0000.0000.0000.000
52L53ASN00.011-0.00724.8270.2980.2980.0000.0000.0000.000
53L54LEU00.0050.01325.1870.5640.5640.0000.0000.0000.000
54L55ALA00.0340.01924.679-0.166-0.1660.0000.0000.0000.000
55L56SER0-0.037-0.01426.706-0.585-0.5850.0000.0000.0000.000
56L57GLY0-0.0050.00428.9780.1110.1110.0000.0000.0000.000
57L58VAL0-0.008-0.01526.648-0.002-0.0020.0000.0000.0000.000
58L59PRO00.0150.02229.914-0.261-0.2610.0000.0000.0000.000
59L60VAL00.0680.00431.1050.2910.2910.0000.0000.0000.000
60L61ARG10.8410.94631.543-9.791-9.7910.0000.0000.0000.000
61L62PHE0-0.001-0.00425.4330.1450.1450.0000.0000.0000.000
62L63SER0-0.009-0.01127.069-0.323-0.3230.0000.0000.0000.000
63L64GLY00.0370.02423.5570.3030.3030.0000.0000.0000.000
64L65SER0-0.004-0.00922.452-0.616-0.6160.0000.0000.0000.000
65L66GLY00.0310.01820.0740.7370.7370.0000.0000.0000.000
66L67SER0-0.002-0.00818.7320.2300.2300.0000.0000.0000.000
67L68GLY00.0100.02016.945-0.578-0.5780.0000.0000.0000.000
68L69THR00.0210.01014.1730.9020.9020.0000.0000.0000.000
69L70SER0-0.018-0.01414.3551.1701.1700.0000.0000.0000.000
70L71TYR00.0100.00914.997-1.260-1.2600.0000.0000.0000.000
71L72SER0-0.037-0.02817.3640.3270.3270.0000.0000.0000.000
72L73LEU00.0090.02120.107-0.222-0.2220.0000.0000.0000.000
73L74THR0-0.037-0.02822.263-0.204-0.2040.0000.0000.0000.000
74L75ILE00.0110.02025.843-0.119-0.1190.0000.0000.0000.000
75L76SER0-0.039-0.03228.669-0.279-0.2790.0000.0000.0000.000
76L77ARG10.8780.93332.288-9.122-9.1220.0000.0000.0000.000
77L78MET0-0.0140.01928.9060.2850.2850.0000.0000.0000.000
78L79GLU-1-0.891-0.96332.5168.6538.6530.0000.0000.0000.000
79L80ALA00.005-0.00832.8980.2610.2610.0000.0000.0000.000
80L81GLU-1-0.883-0.93632.4349.3579.3570.0000.0000.0000.000
81L82ASP-1-0.802-0.91128.58710.94610.9460.0000.0000.0000.000
82L83ALA0-0.046-0.01527.1670.5420.5420.0000.0000.0000.000
83L84ALA0-0.037-0.02624.227-0.217-0.2170.0000.0000.0000.000
84L85THR00.0300.01818.537-0.195-0.1950.0000.0000.0000.000
85L86TYR00.0190.00718.882-0.009-0.0090.0000.0000.0000.000
86L87TYR00.0040.00813.7140.4560.4560.0000.0000.0000.000
87L89GLN00.0220.0149.4010.7040.7040.0000.0000.0000.000
88L90GLN00.0940.0177.673-3.069-3.0690.0000.0000.0000.000
89L91TRP00.004-0.0109.0332.3132.3130.0000.0000.0000.000
90L92SER00.0360.04410.035-0.462-0.4620.0000.0000.0000.000
91L93THR0-0.033-0.0106.141-1.491-1.4910.0000.0000.0000.000
92L94TYR0-0.019-0.0272.601-12.894-8.9601.350-2.548-2.7370.034
93L95PRO0-0.037-0.0092.761-10.323-8.4180.505-1.076-1.3330.011
94L96LEU0-0.012-0.0015.514-2.517-2.544-0.001-0.0020.0300.000
95L97THR00.0300.0204.1025.9286.2320.002-0.043-0.2640.000
96L98PHE0-0.043-0.0286.346-2.723-2.7230.0000.0000.0000.000
97L99GLY00.0150.0138.0672.4732.4730.0000.0000.0000.000
98L100ALA0-0.029-0.00710.197-0.351-0.3510.0000.0000.0000.000
99L101GLY00.0400.01212.472-0.848-0.8480.0000.0000.0000.000
100L102THR0-0.073-0.02515.781-0.333-0.3330.0000.0000.0000.000
101L103LYS10.8990.95318.771-13.118-13.1180.0000.0000.0000.000
102L104LEU0-0.027-0.00221.766-0.370-0.3700.0000.0000.0000.000
103L105GLU-1-0.924-0.97224.77711.30111.3010.0000.0000.0000.000
104L106LEU00.015-0.00128.163-0.027-0.0270.0000.0000.0000.000
105L107LYS10.8610.94131.762-9.761-9.7610.0000.0000.0000.000
106L108ARG10.9270.97434.296-8.276-8.2760.0000.0000.0000.000
107L109ALA0-0.007-0.00337.889-0.002-0.0020.0000.0000.0000.000
108L110ASP-1-0.861-0.94839.8798.1718.1710.0000.0000.0000.000
109L111ALA0-0.026-0.00841.052-0.211-0.2110.0000.0000.0000.000
110L112ALA00.023-0.00542.2270.1220.1220.0000.0000.0000.000
111L113PRO0-0.0260.00441.7360.0030.0030.0000.0000.0000.000
112L114THR00.0070.01043.512-0.248-0.2480.0000.0000.0000.000
113L115VAL00.009-0.00244.1520.1140.1140.0000.0000.0000.000
114L116SER0-0.032-0.02545.852-0.249-0.2490.0000.0000.0000.000
115L117ILE0-0.024-0.00546.3230.1580.1580.0000.0000.0000.000
116L118PHE00.003-0.00945.261-0.110-0.1100.0000.0000.0000.000
117L119PRO0-0.028-0.00948.4070.0560.0560.0000.0000.0000.000
118L120PRO00.0050.01348.4550.0470.0470.0000.0000.0000.000
119L121SER00.0430.02048.841-0.133-0.1330.0000.0000.0000.000
120L122SER00.026-0.01051.0700.0380.0380.0000.0000.0000.000
121L123GLU-1-0.917-0.96249.6926.4666.4660.0000.0000.0000.000
122L124GLN00.0300.02744.570-0.025-0.0250.0000.0000.0000.000
123L125LEU00.028-0.00549.376-0.006-0.0060.0000.0000.0000.000
124L126THR0-0.049-0.01652.469-0.051-0.0510.0000.0000.0000.000
125L127SER0-0.0270.00148.599-0.010-0.0100.0000.0000.0000.000
126L128GLY00.0060.00250.424-0.009-0.0090.0000.0000.0000.000
127L129GLY0-0.041-0.01447.2130.0480.0480.0000.0000.0000.000
128L130ALA0-0.034-0.02247.360-0.122-0.1220.0000.0000.0000.000
129L131SER0-0.021-0.01043.3980.1510.1510.0000.0000.0000.000
130L132VAL00.0100.01845.430-0.080-0.0800.0000.0000.0000.000
131L133VAL00.0190.01841.3390.1590.1590.0000.0000.0000.000
132L134CYS0-0.036-0.02242.418-0.054-0.0540.0000.0000.0000.000
133L135PHE0-0.0060.00339.1080.2390.2390.0000.0000.0000.000
134L136LEU00.0040.00839.779-0.208-0.2080.0000.0000.0000.000
135L137ASN00.0420.00439.3440.1390.1390.0000.0000.0000.000
136L138ASN0-0.008-0.01239.363-0.263-0.2630.0000.0000.0000.000
137L139PHE00.0020.01836.222-0.179-0.1790.0000.0000.0000.000
138L140TYR00.0350.01132.9630.2870.2870.0000.0000.0000.000
139L141PRO0-0.013-0.00834.164-0.199-0.1990.0000.0000.0000.000
140L142LYS10.9950.99527.911-11.005-11.0050.0000.0000.0000.000
141L143ASP-1-0.944-0.96633.0249.6659.6650.0000.0000.0000.000
142L144ILE0-0.012-0.00934.995-0.283-0.2830.0000.0000.0000.000
143L145ASN0-0.043-0.01237.119-0.015-0.0150.0000.0000.0000.000
144L146VAL00.0240.00639.199-0.215-0.2150.0000.0000.0000.000
145L147LYS10.8690.95240.989-7.008-7.0080.0000.0000.0000.000
146L148TRP00.0310.00741.523-0.232-0.2320.0000.0000.0000.000
147L149LYS10.9030.95045.672-6.560-6.5600.0000.0000.0000.000
148L150ILE0-0.014-0.00647.673-0.038-0.0380.0000.0000.0000.000
149L151ASP-1-0.781-0.91351.3825.7565.7560.0000.0000.0000.000
150L152GLY00.0110.01753.408-0.120-0.1200.0000.0000.0000.000
151L153SER0-0.043-0.01751.2660.0610.0610.0000.0000.0000.000
152L154GLU-1-0.956-0.98244.9567.0687.0680.0000.0000.0000.000
153L155ARG10.8180.92644.379-6.922-6.9220.0000.0000.0000.000
154L156GLN00.0360.00539.6640.2100.2100.0000.0000.0000.000
155L157ASN0-0.024-0.01239.9580.1620.1620.0000.0000.0000.000
156L158GLY00.0770.02739.302-0.162-0.1620.0000.0000.0000.000
157L159VAL0-0.0150.00038.036-0.074-0.0740.0000.0000.0000.000
158L160LEU0-0.0140.00034.4650.2640.2640.0000.0000.0000.000
159L161ASN00.010-0.00733.524-0.325-0.3250.0000.0000.0000.000
160L162SER00.0070.00931.4300.4390.4390.0000.0000.0000.000
161L163TRP00.004-0.01729.913-0.117-0.1170.0000.0000.0000.000
162L164THR0-0.0040.00629.6310.2480.2480.0000.0000.0000.000
163L165ASP-1-0.941-0.97725.70112.46212.4620.0000.0000.0000.000
164L166GLN00.0230.00428.732-0.290-0.2900.0000.0000.0000.000
165L167ASP-1-0.919-0.94930.3649.4709.4700.0000.0000.0000.000
166L168SER0-0.020-0.02431.8430.0330.0330.0000.0000.0000.000
167L169LYS10.8930.95533.478-8.258-8.2580.0000.0000.0000.000
168L170ASP-1-0.844-0.94437.1608.1968.1960.0000.0000.0000.000
169L171SER0-0.044-0.01033.189-0.068-0.0680.0000.0000.0000.000
170L172THR0-0.060-0.02534.871-0.134-0.1340.0000.0000.0000.000
171L173TYR00.007-0.00529.4400.1590.1590.0000.0000.0000.000
172L174SER00.0130.00334.304-0.426-0.4260.0000.0000.0000.000
173L175MET0-0.055-0.01834.3290.3430.3430.0000.0000.0000.000
174L176SER0-0.0050.00535.291-0.240-0.2400.0000.0000.0000.000
175L177SER00.0450.02336.5970.1340.1340.0000.0000.0000.000
176L178THR00.0150.00138.685-0.260-0.2600.0000.0000.0000.000
177L179LEU0-0.0050.01139.8910.1590.1590.0000.0000.0000.000
178L180THR0-0.023-0.01540.447-0.134-0.1340.0000.0000.0000.000
179L181LEU0-0.035-0.01142.9110.0350.0350.0000.0000.0000.000
180L182THR00.0600.02346.1510.0630.0630.0000.0000.0000.000
181L183LYS10.8680.93748.790-5.901-5.9010.0000.0000.0000.000
182L184ASP-1-0.877-0.95552.1316.1446.1440.0000.0000.0000.000
183L185GLU-1-0.836-0.92048.5586.5446.5440.0000.0000.0000.000
184L186TYR0-0.023-0.02051.134-0.024-0.0240.0000.0000.0000.000
185L187GLU-1-0.955-0.99453.0695.5685.5680.0000.0000.0000.000
186L188ARG10.9010.98152.207-6.112-6.1120.0000.0000.0000.000
187L189HIS0-0.0130.00652.670-0.014-0.0140.0000.0000.0000.000
188L190ASN0-0.006-0.00956.133-0.078-0.0780.0000.0000.0000.000
189L191SER0-0.035-0.01055.3960.0500.0500.0000.0000.0000.000
190L192TYR00.0740.03349.0260.0630.0630.0000.0000.0000.000
191L193THR0-0.030-0.01149.629-0.085-0.0850.0000.0000.0000.000
192L195GLU-1-0.893-0.94645.9116.5806.5800.0000.0000.0000.000
193L196ALA00.016-0.00643.0830.1900.1900.0000.0000.0000.000
194L197THR0-0.0170.00042.426-0.213-0.2130.0000.0000.0000.000
195L198HIS00.037-0.00338.2030.0260.0260.0000.0000.0000.000
196L199LYS10.9510.98338.530-8.233-8.2330.0000.0000.0000.000
197L200THR0-0.024-0.01442.186-0.177-0.1770.0000.0000.0000.000
198L201SER0-0.0140.00444.840-0.126-0.1260.0000.0000.0000.000
199L202THR00.0110.00846.4640.1200.1200.0000.0000.0000.000
200L203SER0-0.0020.00448.639-0.001-0.0010.0000.0000.0000.000
201L204PRO0-0.011-0.01347.0430.0630.0630.0000.0000.0000.000
202L205ILE00.0140.01146.635-0.167-0.1670.0000.0000.0000.000
203L206VAL00.0130.01148.0850.1040.1040.0000.0000.0000.000
204L207LYS10.8960.94249.334-6.486-6.4860.0000.0000.0000.000
205L208SER0-0.012-0.01350.4880.0620.0620.0000.0000.0000.000
206L209PHE00.0080.00750.762-0.074-0.0740.0000.0000.0000.000
207L210ASN00.009-0.00955.216-0.022-0.0220.0000.0000.0000.000
208L211ARG10.8960.97155.660-5.682-5.6820.0000.0000.0000.000