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: 85Q3Y

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 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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2079731.43754
FMO2-HF: Nuclear repulsion 1997177.019256
FMO2-HF: Total energy -82554.418283
FMO2-MP2: Total energy -82789.974118


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.
-36.876-27.4453.771-5.785-7.4180.059
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 : -0.872 / q_NPA : -0.943
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].
3L3GLN0-0.0040.0053.49910.14613.2500.078-1.598-1.5850.009
4L4MET0-0.014-0.0045.896-5.638-5.6380.0000.0000.0000.000
5L5THR00.003-0.0088.287-0.995-0.9950.0000.0000.0000.000
6L6GLN0-0.024-0.03811.6630.5260.5260.0000.0000.0000.000
7L7SER0-0.0360.02714.882-0.475-0.4750.0000.0000.0000.000
8L8PRO00.009-0.02118.199-0.265-0.2650.0000.0000.0000.000
9L9ALA00.0760.02118.6060.5270.5270.0000.0000.0000.000
10L10ILE00.0220.00219.848-0.086-0.0860.0000.0000.0000.000
11L11MET0-0.0220.00323.443-0.070-0.0700.0000.0000.0000.000
12L12SER00.0430.02526.131-0.005-0.0050.0000.0000.0000.000
13L13ALA0-0.007-0.00529.441-0.067-0.0670.0000.0000.0000.000
14L14SER00.003-0.02631.631-0.041-0.0410.0000.0000.0000.000
15L15PRO00.002-0.00834.7200.1360.1360.0000.0000.0000.000
16L16GLY00.0490.03835.486-0.280-0.2800.0000.0000.0000.000
17L17GLU-1-0.849-0.89833.5639.3159.3150.0000.0000.0000.000
18L18LYS10.9050.95429.039-10.734-10.7340.0000.0000.0000.000
19L19VAL00.0090.00425.9400.0670.0670.0000.0000.0000.000
20L20THR0-0.012-0.01424.321-0.250-0.2500.0000.0000.0000.000
21L21MET0-0.0010.02520.5210.1450.1450.0000.0000.0000.000
22L22THR0-0.008-0.01117.645-0.266-0.2660.0000.0000.0000.000
23L23CYS0-0.0230.00112.7790.2100.2100.0000.0000.0000.000
24L24SER00.0150.00413.635-0.850-0.8500.0000.0000.0000.000
25L25ALA00.0440.0288.8662.0452.0450.0000.0000.0000.000
26L26SER00.0090.0036.543-1.364-1.3640.0000.0000.0000.000
27L27SER00.0000.0017.107-1.828-1.8280.0000.0000.0000.000
28L29SER0-0.004-0.0199.365-0.354-0.3540.0000.0000.0000.000
29L30VAL00.0100.03410.1661.2211.2210.0000.0000.0000.000
30L31SER0-0.023-0.00911.540-2.681-2.6810.0000.0000.0000.000
31L32TYR0-0.014-0.01612.8531.2551.2550.0000.0000.0000.000
32L33MET0-0.0290.00212.1972.4692.4690.0000.0000.0000.000
33L34TYR0-0.0070.01313.445-0.818-0.8180.0000.0000.0000.000
34L35TRP00.008-0.00815.1241.0141.0140.0000.0000.0000.000
35L36TYR0-0.042-0.01413.604-1.153-1.1530.0000.0000.0000.000
36L37GLN00.0180.00718.832-0.468-0.4680.0000.0000.0000.000
37L38GLN0-0.0010.00320.4720.5900.5900.0000.0000.0000.000
38L39LYS10.8530.92722.451-11.281-11.2810.0000.0000.0000.000
39L40PRO00.0170.01025.4230.3410.3410.0000.0000.0000.000
40L41GLY00.0510.03925.964-0.468-0.4680.0000.0000.0000.000
41L42SER0-0.053-0.03425.632-0.301-0.3010.0000.0000.0000.000
42L43SER00.0610.02222.7470.3810.3810.0000.0000.0000.000
43L44PRO0-0.021-0.00418.295-0.554-0.5540.0000.0000.0000.000
44L45ARG10.8840.93120.969-12.932-12.9320.0000.0000.0000.000
45L46LEU00.0290.01220.7880.6870.6870.0000.0000.0000.000
46L47LEU00.008-0.01821.651-0.585-0.5850.0000.0000.0000.000
47L48ILE0-0.0160.00521.530-0.526-0.5260.0000.0000.0000.000
48L49TYR0-0.009-0.01019.7180.7650.7650.0000.0000.0000.000
49L50ASP-1-0.868-0.94817.17417.94017.9400.0000.0000.0000.000
50L51SER0-0.016-0.00619.244-0.613-0.6130.0000.0000.0000.000
51L52THR0-0.064-0.03121.089-0.308-0.3080.0000.0000.0000.000
52L53ASN00.007-0.00224.5460.1260.1260.0000.0000.0000.000
53L54LEU00.0060.01424.7710.5720.5720.0000.0000.0000.000
54L55ALA00.0290.01324.200-0.170-0.1700.0000.0000.0000.000
55L56SER0-0.007-0.00226.268-0.547-0.5470.0000.0000.0000.000
56L57GLY0-0.036-0.00728.6600.1120.1120.0000.0000.0000.000
57L58VAL0-0.003-0.01326.5520.0060.0060.0000.0000.0000.000
58L59PRO00.0300.03029.796-0.270-0.2700.0000.0000.0000.000
59L60VAL00.0680.00331.1260.2890.2890.0000.0000.0000.000
60L61ARG10.7410.87631.748-9.775-9.7750.0000.0000.0000.000
61L62PHE0-0.001-0.00225.5280.1560.1560.0000.0000.0000.000
62L63SER0-0.011-0.01027.297-0.287-0.2870.0000.0000.0000.000
63L64GLY00.0470.02423.5260.2990.2990.0000.0000.0000.000
64L65SER0-0.004-0.00822.557-0.612-0.6120.0000.0000.0000.000
65L66GLY00.0460.02920.0680.7300.7300.0000.0000.0000.000
66L67SER00.000-0.01718.7060.0440.0440.0000.0000.0000.000
67L68GLY00.0050.02216.909-0.606-0.6060.0000.0000.0000.000
68L69THR00.0130.00414.1290.9020.9020.0000.0000.0000.000
69L70SER0-0.021-0.02014.3391.1231.1230.0000.0000.0000.000
70L71TYR0-0.020-0.01914.745-1.356-1.3560.0000.0000.0000.000
71L72SER0-0.037-0.02417.7840.5250.5250.0000.0000.0000.000
72L73LEU00.0180.02220.518-0.226-0.2260.0000.0000.0000.000
73L74THR0-0.017-0.02722.624-0.265-0.2650.0000.0000.0000.000
74L75ILE00.0090.02326.110-0.112-0.1120.0000.0000.0000.000
75L76SER0-0.036-0.03128.998-0.280-0.2800.0000.0000.0000.000
76L77ARG10.8560.91532.632-9.143-9.1430.0000.0000.0000.000
77L78MET0-0.0190.01829.4170.3150.3150.0000.0000.0000.000
78L79GLU-1-0.812-0.91232.7528.7508.7500.0000.0000.0000.000
79L80ALA00.0160.00133.1090.2670.2670.0000.0000.0000.000
80L81GLU-1-0.859-0.93032.5639.3109.3100.0000.0000.0000.000
81L82ASP-1-0.813-0.90528.84110.93810.9380.0000.0000.0000.000
82L83ALA0-0.042-0.01327.3550.5490.5490.0000.0000.0000.000
83L84ALA0-0.023-0.00924.446-0.217-0.2170.0000.0000.0000.000
84L85THR00.0380.01918.646-0.191-0.1910.0000.0000.0000.000
85L86TYR00.0180.01219.0630.0160.0160.0000.0000.0000.000
86L87TYR00.0060.00713.8570.5390.5390.0000.0000.0000.000
87L89GLN00.0330.0098.9230.1720.1720.0000.0000.0000.000
88L90GLN00.0940.0276.973-3.549-3.5490.0000.0000.0000.000
89L91TRP00.019-0.0028.4821.9671.9670.0000.0000.0000.000
90L92SER00.0260.0369.918-0.475-0.4750.0000.0000.0000.000
91L93THR0-0.033-0.0146.091-1.313-1.3130.0000.0000.0000.000
92L94TYR0-0.063-0.0472.511-7.144-4.3922.239-2.020-2.9720.026
93L95PRO0-0.0190.0072.583-15.540-13.0571.447-1.623-2.3070.020
94L96LEU0-0.050-0.0305.282-3.619-3.630-0.001-0.0020.0150.000
95L97THR00.0760.0483.512-8.193-7.0900.008-0.542-0.5690.004
96L98PHE0-0.048-0.0326.364-2.745-2.7450.0000.0000.0000.000
97L99GLY00.0150.0158.1732.4512.4510.0000.0000.0000.000
98L100ALA0-0.034-0.00810.393-0.368-0.3680.0000.0000.0000.000
99L101GLY00.0450.01212.627-0.799-0.7990.0000.0000.0000.000
100L102THR0-0.076-0.02615.939-0.296-0.2960.0000.0000.0000.000
101L103LYS10.8050.88918.993-13.059-13.0590.0000.0000.0000.000
102L104LEU0-0.027-0.00421.933-0.378-0.3780.0000.0000.0000.000
103L105GLU-1-0.871-0.91924.98311.27711.2770.0000.0000.0000.000
104L106LEU00.021-0.00328.343-0.029-0.0290.0000.0000.0000.000
105L107LYS10.8100.91331.956-9.818-9.8180.0000.0000.0000.000
106L108ARG10.8380.92034.513-8.361-8.3610.0000.0000.0000.000
107L109ALA00.0110.00838.0890.0000.0000.0000.0000.0000.000
108L110ASP-1-0.805-0.89839.8548.1578.1570.0000.0000.0000.000
109L111ALA0-0.015-0.00541.200-0.206-0.2060.0000.0000.0000.000
110L112ALA00.033-0.00142.3570.1240.1240.0000.0000.0000.000
111L113PRO0-0.0090.01341.8820.0190.0190.0000.0000.0000.000
112L114THR0-0.0060.00043.556-0.246-0.2460.0000.0000.0000.000
113L115VAL00.010-0.00344.1550.1160.1160.0000.0000.0000.000
114L116SER0-0.030-0.02345.838-0.241-0.2410.0000.0000.0000.000
115L117ILE0-0.026-0.01046.2840.1600.1600.0000.0000.0000.000
116L118PHE0-0.010-0.00845.470-0.103-0.1030.0000.0000.0000.000
117L119PRO0-0.0030.00448.3050.0540.0540.0000.0000.0000.000
118L120PRO00.0030.01248.3720.0600.0600.0000.0000.0000.000
119L121SER00.0320.00748.977-0.138-0.1380.0000.0000.0000.000
120L122SER00.043-0.00450.8890.0030.0030.0000.0000.0000.000
121L123GLU-1-0.938-0.96149.5686.4926.4920.0000.0000.0000.000
122L124GLN00.0260.01744.559-0.021-0.0210.0000.0000.0000.000
123L125LEU00.022-0.00649.1560.0070.0070.0000.0000.0000.000
124L126THR0-0.020-0.00552.255-0.083-0.0830.0000.0000.0000.000
125L127SER0-0.077-0.02648.325-0.018-0.0180.0000.0000.0000.000
126L128GLY00.0050.00250.179-0.008-0.0080.0000.0000.0000.000
127L129GLY0-0.045-0.01646.9970.0470.0470.0000.0000.0000.000
128L130ALA0-0.024-0.01847.150-0.125-0.1250.0000.0000.0000.000
129L131SER0-0.018-0.00442.7580.0480.0480.0000.0000.0000.000
130L132VAL0-0.0040.01145.273-0.076-0.0760.0000.0000.0000.000
131L133VAL00.0120.01341.2390.1570.1570.0000.0000.0000.000
132L134CYS0-0.031-0.02042.342-0.057-0.0570.0000.0000.0000.000
133L135PHE00.0070.00938.8380.2430.2430.0000.0000.0000.000
134L136LEU00.0040.00839.775-0.208-0.2080.0000.0000.0000.000
135L137ASN00.010-0.01338.9200.1320.1320.0000.0000.0000.000
136L138ASN0-0.003-0.01339.422-0.178-0.1780.0000.0000.0000.000
137L139PHE0-0.0010.02036.395-0.183-0.1830.0000.0000.0000.000
138L140TYR00.0110.00833.0250.2860.2860.0000.0000.0000.000
139L141PRO00.003-0.00634.448-0.219-0.2190.0000.0000.0000.000
140L142LYS10.9930.99228.184-10.830-10.8300.0000.0000.0000.000
141L143ASP-1-0.929-0.96233.1209.6299.6290.0000.0000.0000.000
142L144ILE0-0.010-0.00835.120-0.282-0.2820.0000.0000.0000.000
143L145ASN0-0.044-0.01637.190-0.013-0.0130.0000.0000.0000.000
144L146VAL00.0230.01139.390-0.197-0.1970.0000.0000.0000.000
145L147LYS10.8380.93541.000-6.948-6.9480.0000.0000.0000.000
146L148TRP00.0270.00541.335-0.225-0.2250.0000.0000.0000.000
147L149LYS10.8530.90945.645-6.582-6.5820.0000.0000.0000.000
148L150ILE00.0020.00047.722-0.044-0.0440.0000.0000.0000.000
149L151ASP-1-0.731-0.84651.3255.7405.7400.0000.0000.0000.000
150L152GLY00.0120.01753.381-0.120-0.1200.0000.0000.0000.000
151L153SER0-0.037-0.01351.1930.0580.0580.0000.0000.0000.000
152L154GLU-1-0.887-0.93644.7517.0487.0480.0000.0000.0000.000
153L155ARG10.7870.89044.270-6.908-6.9080.0000.0000.0000.000
154L156GLN00.025-0.00339.7670.1980.1980.0000.0000.0000.000
155L157ASN0-0.021-0.00339.8960.1620.1620.0000.0000.0000.000
156L158GLY00.0840.03339.194-0.156-0.1560.0000.0000.0000.000
157L159VAL0-0.016-0.00337.982-0.066-0.0660.0000.0000.0000.000
158L160LEU0-0.019-0.00134.3990.2620.2620.0000.0000.0000.000
159L161ASN00.0210.00433.793-0.299-0.2990.0000.0000.0000.000
160L162SER00.0110.01131.3730.4280.4280.0000.0000.0000.000
161L163TRP00.003-0.01929.843-0.140-0.1400.0000.0000.0000.000
162L164THR00.0160.01829.6030.2000.2000.0000.0000.0000.000
163L165ASP-1-0.874-0.92725.71612.48812.4880.0000.0000.0000.000
164L166GLN0-0.020-0.00528.762-0.266-0.2660.0000.0000.0000.000
165L167ASP-1-0.855-0.91230.4249.2189.2180.0000.0000.0000.000
166L168SER0-0.023-0.01731.9690.0450.0450.0000.0000.0000.000
167L169LYS10.8390.91433.552-8.594-8.5940.0000.0000.0000.000
168L170ASP-1-0.788-0.89537.2278.1818.1810.0000.0000.0000.000
169L171SER0-0.039-0.01333.243-0.080-0.0800.0000.0000.0000.000
170L172THR0-0.022-0.01834.986-0.104-0.1040.0000.0000.0000.000
171L173TYR0-0.023-0.03930.1140.1530.1530.0000.0000.0000.000
172L174SER00.010-0.00334.342-0.430-0.4300.0000.0000.0000.000
173L175MET0-0.055-0.01434.2040.3340.3340.0000.0000.0000.000
174L176SER0-0.0120.00135.291-0.245-0.2450.0000.0000.0000.000
175L177SER00.0430.01136.5430.1360.1360.0000.0000.0000.000
176L178THR00.0060.00138.647-0.264-0.2640.0000.0000.0000.000
177L179LEU0-0.0030.01239.7810.1610.1610.0000.0000.0000.000
178L180THR0-0.011-0.01440.345-0.171-0.1710.0000.0000.0000.000
179L181LEU0-0.026-0.00342.7540.0450.0450.0000.0000.0000.000
180L182THR00.022-0.01345.9880.0680.0680.0000.0000.0000.000
181L183LYS10.8650.92048.599-5.833-5.8330.0000.0000.0000.000
182L184ASP-1-0.847-0.92451.8176.1816.1810.0000.0000.0000.000
183L185GLU-1-0.773-0.85248.6426.4516.4510.0000.0000.0000.000
184L186TYR0-0.016-0.02051.239-0.036-0.0360.0000.0000.0000.000
185L187GLU-1-0.880-0.93652.9205.6145.6140.0000.0000.0000.000
186L188ARG10.8090.90851.776-6.167-6.1670.0000.0000.0000.000
187L189HIS0-0.0280.00353.274-0.021-0.0210.0000.0000.0000.000
188L190ASN0-0.029-0.01856.022-0.074-0.0740.0000.0000.0000.000
189L191SER0-0.049-0.04055.3300.0640.0640.0000.0000.0000.000
190L192TYR00.0600.01948.8070.1380.1380.0000.0000.0000.000
191L193THR0-0.029-0.00349.631-0.081-0.0810.0000.0000.0000.000
192L195GLU-1-0.848-0.92345.8886.6316.6310.0000.0000.0000.000
193L196ALA00.018-0.00843.0990.1860.1860.0000.0000.0000.000
194L197THR0-0.0090.00142.538-0.190-0.1900.0000.0000.0000.000
195L198HIS00.0390.01438.7080.0280.0280.0000.0000.0000.000
196L199LYS10.8710.92839.026-8.171-8.1710.0000.0000.0000.000
197L200THR0-0.046-0.03542.356-0.178-0.1780.0000.0000.0000.000
198L201SER0-0.035-0.01145.005-0.122-0.1220.0000.0000.0000.000
199L202THR00.0180.01246.6140.0610.0610.0000.0000.0000.000
200L203SER00.0030.00948.7800.0000.0000.0000.0000.0000.000
201L204PRO00.0000.00247.1660.0640.0640.0000.0000.0000.000
202L205ILE00.0070.00146.813-0.171-0.1710.0000.0000.0000.000
203L206VAL00.0160.01448.1270.1020.1020.0000.0000.0000.000
204L207LYS10.8800.93349.350-6.465-6.4650.0000.0000.0000.000
205L208SER0-0.019-0.02250.4720.0630.0630.0000.0000.0000.000
206L209PHE00.0120.01150.597-0.072-0.0720.0000.0000.0000.000
207L210ASN00.027-0.00355.161-0.006-0.0060.0000.0000.0000.000
208L211ARG10.8800.95755.368-5.673-5.6730.0000.0000.0000.000