Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6N5KZ

Calculation Name: 3EOT-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EOT

Chain ID: L

ChEMBL ID:

UniProt ID: P01837

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2093912.83266
FMO2-HF: Nuclear repulsion 2011629.773604
FMO2-HF: Total energy -82283.059056
FMO2-MP2: Total energy -82523.516497


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:GLN)


Summations of interaction energy for fragment #1(L:1:GLN)
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.
-18.02-16.01611.481-5.936-7.546-0.045
Interaction energy analysis for fragmet #1(L:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.034
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].
3L3GLN00.0290.0361.843-12.060-13.7148.338-3.231-3.453-0.030
4L4LEU00.0150.0035.1801.3491.456-0.001-0.007-0.0990.000
5L5THR0-0.023-0.0148.573-0.190-0.1900.0000.0000.0000.000
6L6GLN00.006-0.01411.2560.1410.1410.0000.0000.0000.000
7L7SER0-0.0160.01814.681-0.003-0.0030.0000.0000.0000.000
8L8PRO00.0610.02117.9900.0440.0440.0000.0000.0000.000
9L9SER00.0640.02717.016-0.059-0.0590.0000.0000.0000.000
10L10SER0-0.035-0.01318.5570.0240.0240.0000.0000.0000.000
11L11LEU0-0.021-0.00622.149-0.007-0.0070.0000.0000.0000.000
12L12SER00.0180.01825.4220.0210.0210.0000.0000.0000.000
13L13ALA00.000-0.01029.138-0.004-0.0040.0000.0000.0000.000
14L14SER0-0.009-0.01531.2390.0080.0080.0000.0000.0000.000
15L15VAL0-0.020-0.00634.037-0.004-0.0040.0000.0000.0000.000
16L16GLY00.0150.01635.4010.0060.0060.0000.0000.0000.000
17L17ASP-1-0.809-0.87932.249-0.201-0.2010.0000.0000.0000.000
18L18ARG10.9490.98428.4010.2250.2250.0000.0000.0000.000
19L19VAL0-0.016-0.01025.707-0.015-0.0150.0000.0000.0000.000
20L20THR0-0.047-0.03923.5490.0180.0180.0000.0000.0000.000
21L21ILE0-0.023-0.00918.989-0.015-0.0150.0000.0000.0000.000
22L22THR00.0240.01017.4730.0600.0600.0000.0000.0000.000
23L23CYS0-0.019-0.02313.479-0.089-0.0890.0000.0000.0000.000
24L24SER0-0.0020.01013.8010.0940.0940.0000.0000.0000.000
25L25ALA0-0.029-0.0228.995-0.231-0.2310.0000.0000.0000.000
26L26SER0-0.001-0.0046.172-0.315-0.3150.0000.0000.0000.000
27L27SER00.006-0.0056.306-0.222-0.2220.0000.0000.0000.000
28L28SER0-0.045-0.0258.7370.0370.0370.0000.0000.0000.000
29L29VAL00.0130.0238.4810.1690.1690.0000.0000.0000.000
30L30ASN00.0280.01110.662-0.092-0.0920.0000.0000.0000.000
31L31SER00.0810.02813.6230.0270.0270.0000.0000.0000.000
32L32SER0-0.063-0.03916.538-0.021-0.0210.0000.0000.0000.000
33L33ALA0-0.053-0.01811.7700.0540.0540.0000.0000.0000.000
34L34LEU00.0100.00911.8520.0630.0630.0000.0000.0000.000
35L35PHE0-0.044-0.01913.9380.0110.0110.0000.0000.0000.000
36L36TRP00.011-0.00515.408-0.118-0.1180.0000.0000.0000.000
37L37TYR0-0.028-0.02815.1540.0670.0670.0000.0000.0000.000
38L38GLN0-0.0030.00219.467-0.038-0.0380.0000.0000.0000.000
39L39GLN0-0.018-0.00519.464-0.008-0.0080.0000.0000.0000.000
40L40LYS10.8140.89322.4370.1230.1230.0000.0000.0000.000
41L41PRO00.0540.01324.8240.0080.0080.0000.0000.0000.000
42L42GLY00.0240.01824.7710.0190.0190.0000.0000.0000.000
43L43LYS10.8510.93124.6520.0860.0860.0000.0000.0000.000
44L44ALA00.0630.03621.683-0.020-0.0200.0000.0000.0000.000
45L45PRO0-0.007-0.01317.730-0.006-0.0060.0000.0000.0000.000
46L46LYS10.9560.99320.8490.1010.1010.0000.0000.0000.000
47L47PRO00.0300.01020.259-0.036-0.0360.0000.0000.0000.000
48L48TRP0-0.033-0.02520.8600.0060.0060.0000.0000.0000.000
49L49ILE00.0070.00220.7890.0030.0030.0000.0000.0000.000
50L50TYR00.0000.00819.055-0.004-0.0040.0000.0000.0000.000
51L51LEU00.0180.01518.325-0.017-0.0170.0000.0000.0000.000
52L52THR0-0.012-0.02919.7970.0480.0480.0000.0000.0000.000
53L53SER00.0390.04621.869-0.024-0.0240.0000.0000.0000.000
54L54ASN0-0.032-0.01823.8350.0010.0010.0000.0000.0000.000
55L55LEU0-0.019-0.00627.615-0.003-0.0030.0000.0000.0000.000
56L56ALA00.0380.02430.452-0.003-0.0030.0000.0000.0000.000
57L57SER00.023-0.00534.0790.0090.0090.0000.0000.0000.000
58L58GLY00.0240.01437.184-0.003-0.0030.0000.0000.0000.000
59L59VAL0-0.023-0.00431.3300.0040.0040.0000.0000.0000.000
60L60PRO0-0.020-0.00132.6180.0050.0050.0000.0000.0000.000
61L61SER00.053-0.00428.633-0.004-0.0040.0000.0000.0000.000
62L62ARG10.9340.98427.319-0.046-0.0460.0000.0000.0000.000
63L63PHE0-0.022-0.00926.6780.0020.0020.0000.0000.0000.000
64L64SER0-0.005-0.00922.5980.0080.0080.0000.0000.0000.000
65L65GLY00.0310.01322.926-0.007-0.0070.0000.0000.0000.000
66L66SER0-0.032-0.00718.2200.0160.0160.0000.0000.0000.000
67L67GLY00.0500.03218.698-0.013-0.0130.0000.0000.0000.000
68L68SER0-0.015-0.02513.6530.0270.0270.0000.0000.0000.000
69L69GLY00.0260.01813.891-0.007-0.0070.0000.0000.0000.000
70L70THR00.0200.01211.5240.0680.0680.0000.0000.0000.000
71L71ASP-1-0.870-0.92413.501-0.839-0.8390.0000.0000.0000.000
72L72TYR0-0.004-0.01413.7260.1410.1410.0000.0000.0000.000
73L73THR0-0.003-0.01017.533-0.046-0.0460.0000.0000.0000.000
74L74LEU00.0070.03120.1480.0470.0470.0000.0000.0000.000
75L75THR0-0.040-0.03922.071-0.021-0.0210.0000.0000.0000.000
76L76ILE00.0320.05025.8260.0220.0220.0000.0000.0000.000
77L77SER0-0.019-0.02728.543-0.009-0.0090.0000.0000.0000.000
78L78SER0-0.031-0.03131.7360.0030.0030.0000.0000.0000.000
79L79LEU0-0.0230.00229.4100.0070.0070.0000.0000.0000.000
80L80GLN00.0180.00532.3050.0190.0190.0000.0000.0000.000
81L81PRO00.0230.00332.647-0.011-0.0110.0000.0000.0000.000
82L82GLU-1-0.949-0.97332.526-0.100-0.1000.0000.0000.0000.000
83L83ASP-1-0.808-0.89628.614-0.166-0.1660.0000.0000.0000.000
84L84PHE0-0.0390.00627.438-0.023-0.0230.0000.0000.0000.000
85L85ALA0-0.0110.00024.1320.0230.0230.0000.0000.0000.000
86L86THR0-0.008-0.00118.723-0.020-0.0200.0000.0000.0000.000
87L87TYR00.010-0.00519.8000.0410.0410.0000.0000.0000.000
88L88TYR0-0.016-0.01514.474-0.071-0.0710.0000.0000.0000.000
89L89CYS0-0.0010.02812.0500.0500.0500.0000.0000.0000.000
90L90GLN00.0250.01210.754-0.202-0.2020.0000.0000.0000.000
91L91GLN00.0210.0025.212-0.165-0.099-0.001-0.002-0.0620.000
92L92ILE0-0.016-0.0108.7020.2110.2110.0000.0000.0000.000
93L93SER00.0170.0108.474-0.099-0.0990.0000.0000.0000.000
94L94GLY0-0.013-0.0024.609-0.479-0.435-0.001-0.011-0.0320.000
95L95ASN0-0.034-0.0044.0440.0200.2310.002-0.089-0.1230.000
96L96PRO00.0550.0092.093-6.440-3.7103.138-2.498-3.370-0.015
97L97TRP00.0010.0044.2470.8180.9860.001-0.036-0.1330.000
98L98THR0-0.042-0.0263.7710.1090.4410.005-0.062-0.2740.000
99L99PHE00.013-0.0066.7780.3810.3810.0000.0000.0000.000
100L100GLY00.0210.0188.394-0.590-0.5900.0000.0000.0000.000
101L101GLN0-0.037-0.03210.847-0.018-0.0180.0000.0000.0000.000
102L102GLY00.0020.00712.3660.1570.1570.0000.0000.0000.000
103L103THR0-0.033-0.03215.726-0.064-0.0640.0000.0000.0000.000
104L104LYS10.7840.90119.0390.3230.3230.0000.0000.0000.000
105L105VAL00.0110.00522.247-0.018-0.0180.0000.0000.0000.000
106L106GLU-1-0.775-0.87125.427-0.216-0.2160.0000.0000.0000.000
107L107ILE00.011-0.00128.775-0.008-0.0080.0000.0000.0000.000
108L108LYS10.8480.92531.7420.2360.2360.0000.0000.0000.000
109L109ARG10.8440.90334.8900.1220.1220.0000.0000.0000.000
110L110ALA00.0350.02938.258-0.002-0.0020.0000.0000.0000.000
111L111ASP-1-0.777-0.87241.334-0.130-0.1300.0000.0000.0000.000
112L112ALA0-0.025-0.01841.9970.0060.0060.0000.0000.0000.000
113L113ALA00.0460.02742.908-0.005-0.0050.0000.0000.0000.000
114L114PRO0-0.0070.00842.8710.0020.0020.0000.0000.0000.000
115L115THR00.0130.00044.5410.0060.0060.0000.0000.0000.000
116L116VAL0-0.024-0.00845.7120.0010.0010.0000.0000.0000.000
117L117SER0-0.047-0.01146.3180.0050.0050.0000.0000.0000.000
118L118ILE00.016-0.00147.087-0.003-0.0030.0000.0000.0000.000
119L119PHE00.0000.00046.4930.0030.0030.0000.0000.0000.000
120L120PRO00.0220.00949.157-0.002-0.0020.0000.0000.0000.000
121L121PRO0-0.0050.01349.0730.0000.0000.0000.0000.0000.000
122L122SER0-0.018-0.02549.4330.0010.0010.0000.0000.0000.000
123L123SER0-0.021-0.03051.2090.0010.0010.0000.0000.0000.000
124L124GLU-1-0.756-0.85250.008-0.013-0.0130.0000.0000.0000.000
125L125GLN00.0460.03645.2000.0000.0000.0000.0000.0000.000
126L126LEU00.0330.02849.4790.0010.0010.0000.0000.0000.000
127L127THR0-0.093-0.06052.6300.0020.0020.0000.0000.0000.000
128L128SER0-0.091-0.05348.7600.0010.0010.0000.0000.0000.000
129L129GLY00.0390.02249.9640.0010.0010.0000.0000.0000.000
130L130GLY0-0.036-0.01147.617-0.002-0.0020.0000.0000.0000.000
131L131ALA0-0.004-0.02347.8950.0010.0010.0000.0000.0000.000
132L132SER0-0.028-0.01943.686-0.001-0.0010.0000.0000.0000.000
133L133VAL0-0.0070.00946.0940.0020.0020.0000.0000.0000.000
134L134VAL0-0.017-0.00542.783-0.004-0.0040.0000.0000.0000.000
135L135CYS0-0.043-0.02743.7900.0000.0000.0000.0000.0000.000
136L136PHE0-0.016-0.00141.116-0.004-0.0040.0000.0000.0000.000
137L137LEU00.022-0.00341.1740.0030.0030.0000.0000.0000.000
138L138ASN00.027-0.00640.891-0.010-0.0100.0000.0000.0000.000
139L139ASN0-0.026-0.03240.1850.0050.0050.0000.0000.0000.000
140L140PHE0-0.0010.01637.4180.0020.0020.0000.0000.0000.000
141L141TYR00.030-0.00934.315-0.007-0.0070.0000.0000.0000.000
142L142PRO00.001-0.01036.0890.0070.0070.0000.0000.0000.000
143L143LYS10.8580.92228.6140.2250.2250.0000.0000.0000.000
144L144ASP-1-0.916-0.95034.572-0.183-0.1830.0000.0000.0000.000
145L145ILE0-0.044-0.02236.5610.0090.0090.0000.0000.0000.000
146L146ASN0-0.008-0.00438.480-0.006-0.0060.0000.0000.0000.000
147L147VAL00.0110.00341.0530.0050.0050.0000.0000.0000.000
148L148LYS10.7860.88542.8830.0800.0800.0000.0000.0000.000
149L149TRP00.023-0.00743.3950.0060.0060.0000.0000.0000.000
150L150LYS10.7790.88347.3510.0650.0650.0000.0000.0000.000
151L151ILE00.0070.00350.2730.0020.0020.0000.0000.0000.000
152L152ASP-1-0.745-0.84453.501-0.039-0.0390.0000.0000.0000.000
153L153GLY00.0060.01455.8690.0000.0000.0000.0000.0000.000
154L154SER0-0.010-0.00153.946-0.004-0.0040.0000.0000.0000.000
155L155GLU-1-0.828-0.89447.819-0.077-0.0770.0000.0000.0000.000
156L156ARG10.8130.89747.3960.0510.0510.0000.0000.0000.000
157L157GLN00.0970.03242.2360.0040.0040.0000.0000.0000.000
158L158ASN0-0.042-0.02742.733-0.002-0.0020.0000.0000.0000.000
159L159GLY00.0920.04242.4400.0050.0050.0000.0000.0000.000
160L160VAL0-0.0590.00040.3200.0030.0030.0000.0000.0000.000
161L161LEU0-0.0080.00836.125-0.006-0.0060.0000.0000.0000.000
162L162ASN00.0230.01536.1920.0100.0100.0000.0000.0000.000
163L163SER0-0.008-0.00132.974-0.010-0.0100.0000.0000.0000.000
164L164TRP00.0260.01332.2580.0090.0090.0000.0000.0000.000
165L165THR0-0.015-0.01432.0250.0010.0010.0000.0000.0000.000
166L166ASP-1-0.785-0.90826.631-0.232-0.2320.0000.0000.0000.000
167L167GLN00.0020.01629.9770.0010.0010.0000.0000.0000.000
168L168ASP-1-0.770-0.86231.680-0.094-0.0940.0000.0000.0000.000
169L169SER0-0.056-0.03831.577-0.010-0.0100.0000.0000.0000.000
170L170LYS10.8670.91433.6430.0850.0850.0000.0000.0000.000
171L171ASP-1-0.761-0.84537.360-0.101-0.1010.0000.0000.0000.000
172L172SER0-0.033-0.00934.352-0.002-0.0020.0000.0000.0000.000
173L173THR0-0.080-0.04835.898-0.009-0.0090.0000.0000.0000.000
174L174TYR0-0.032-0.04231.113-0.006-0.0060.0000.0000.0000.000
175L175SER00.0260.02136.0260.0110.0110.0000.0000.0000.000
176L176MET0-0.060-0.00836.177-0.009-0.0090.0000.0000.0000.000
177L177SER0-0.0230.00036.9270.0090.0090.0000.0000.0000.000
178L178SER00.008-0.01738.367-0.006-0.0060.0000.0000.0000.000
179L179THR00.0220.00139.9660.0070.0070.0000.0000.0000.000
180L180LEU00.0150.03141.834-0.002-0.0020.0000.0000.0000.000
181L181THR0-0.011-0.00542.4440.0060.0060.0000.0000.0000.000
182L182LEU0-0.051-0.01944.710-0.002-0.0020.0000.0000.0000.000
183L183THR00.0390.00547.6900.0010.0010.0000.0000.0000.000
184L184LYS10.8390.90249.7870.0140.0140.0000.0000.0000.000
185L185ASP-1-0.775-0.88152.810-0.023-0.0230.0000.0000.0000.000
186L186GLU-1-0.811-0.88850.363-0.038-0.0380.0000.0000.0000.000
187L187TYR00.019-0.00251.702-0.002-0.0020.0000.0000.0000.000
188L188GLU-1-0.834-0.90053.418-0.019-0.0190.0000.0000.0000.000
189L189ARG10.7920.90153.4270.0270.0270.0000.0000.0000.000
190L190HIS10.8330.91253.5750.0370.0370.0000.0000.0000.000
191L191ASN0-0.024-0.01357.5530.0030.0030.0000.0000.0000.000
192L192SER0-0.012-0.01357.1040.0000.0000.0000.0000.0000.000
193L193TYR0-0.038-0.05051.244-0.002-0.0020.0000.0000.0000.000
194L194THR0-0.024-0.02751.8180.0010.0010.0000.0000.0000.000
195L195CYS0-0.0030.00746.654-0.001-0.0010.0000.0000.0000.000
196L196GLU-1-0.798-0.90947.766-0.071-0.0710.0000.0000.0000.000
197L197ALA00.0240.00844.835-0.005-0.0050.0000.0000.0000.000
198L198THR0-0.024-0.00844.3870.0020.0020.0000.0000.0000.000
199L199HIS00.0480.02139.9700.0000.0000.0000.0000.0000.000
200L200LYS10.8260.90340.6150.1390.1390.0000.0000.0000.000
201L201THR0-0.025-0.03043.7680.0020.0020.0000.0000.0000.000
202L202SER0-0.021-0.01646.3300.0050.0050.0000.0000.0000.000
203L203THR00.0000.00847.929-0.003-0.0030.0000.0000.0000.000
204L204SER0-0.025-0.00450.0440.0010.0010.0000.0000.0000.000
205L205PRO0-0.009-0.00748.682-0.001-0.0010.0000.0000.0000.000
206L206ILE00.0180.01547.1660.0050.0050.0000.0000.0000.000
207L207VAL0-0.010-0.00149.103-0.001-0.0010.0000.0000.0000.000
208L208LYS10.8350.90750.2870.0600.0600.0000.0000.0000.000
209L209SER00.0450.01451.817-0.002-0.0020.0000.0000.0000.000
210L210PHE00.0190.02551.5260.0010.0010.0000.0000.0000.000
211L211ASN0-0.011-0.03156.365-0.002-0.0020.0000.0000.0000.000
212L212ARG10.8520.93156.2350.0290.0290.0000.0000.0000.000
213L213ASN00.0200.01758.3480.0010.0010.0000.0000.0000.000
214L214GLU-1-0.944-0.94561.053-0.031-0.0310.0000.0000.0000.000