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

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FMODB ID: 17VGZ

Calculation Name: 4AEH-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AEH

Chain ID: L

ChEMBL ID:

UniProt ID:

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2142813.050143
FMO2-HF: Nuclear repulsion 2060663.068044
FMO2-HF: Total energy -82149.982099
FMO2-MP2: Total energy -82389.416475


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.
-85.866-79.82712.155-8.811-9.3820.079
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 : -0.842 / q_NPA : -0.908
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].
3L3GLN0-0.071-0.0361.820-38.979-35.84010.502-7.254-6.3860.088
4L4MET0-0.026-0.0104.874-6.222-6.215-0.001-0.0110.0040.000
5L5THR00.007-0.0018.600-2.004-2.0040.0000.0000.0000.000
6L6GLN00.009-0.02311.273-0.347-0.3470.0000.0000.0000.000
7L7SER0-0.059-0.01014.323-0.509-0.5090.0000.0000.0000.000
8L8PRO00.0580.02917.857-0.163-0.1630.0000.0000.0000.000
9L9ALA00.0690.03418.6970.2530.2530.0000.0000.0000.000
10L10SER0-0.021-0.01419.721-0.105-0.1050.0000.0000.0000.000
11L11LEU0-0.029-0.01823.419-0.019-0.0190.0000.0000.0000.000
12L12SER00.0270.00526.4550.0100.0100.0000.0000.0000.000
13L13VAL0-0.061-0.03828.730-0.078-0.0780.0000.0000.0000.000
14L14SER00.013-0.02831.673-0.197-0.1970.0000.0000.0000.000
15L15VAL0-0.008-0.00734.4650.1700.1700.0000.0000.0000.000
16L16GLY00.0000.01236.017-0.216-0.2160.0000.0000.0000.000
17L17GLU-1-0.776-0.85133.0489.4269.4260.0000.0000.0000.000
18L18THR0-0.024-0.01830.3480.0540.0540.0000.0000.0000.000
19L19VAL0-0.0090.00725.9030.0470.0470.0000.0000.0000.000
20L20THR0-0.010-0.02023.250-0.066-0.0660.0000.0000.0000.000
21L21ILE00.0060.02319.0190.0350.0350.0000.0000.0000.000
22L22THR0-0.017-0.00917.2640.1550.1550.0000.0000.0000.000
23L23CYS0-0.0010.01213.2170.2000.2000.0000.0000.0000.000
24L24ARG10.8820.94612.597-19.819-19.8190.0000.0000.0000.000
25L25ALA00.0350.0228.7351.5191.5190.0000.0000.0000.000
26L26SER00.0200.0144.984-2.699-2.590-0.001-0.014-0.0940.000
27L27GLU-1-0.793-0.8944.30734.86234.973-0.001-0.026-0.0840.000
28L28ASN0-0.047-0.0328.017-1.136-1.1360.0000.0000.0000.000
29L29ILE00.0740.0447.7040.2410.2410.0000.0000.0000.000
30L30TYR0-0.022-0.01410.263-1.768-1.7680.0000.0000.0000.000
31L31ARG10.8690.92713.874-15.158-15.1580.0000.0000.0000.000
32L32ASN0-0.0190.01010.929-1.482-1.4820.0000.0000.0000.000
33L33LEU0-0.018-0.01511.2191.9151.9150.0000.0000.0000.000
34L34ALA0-0.029-0.00613.521-1.575-1.5750.0000.0000.0000.000
35L35TRP00.005-0.00515.4621.1911.1910.0000.0000.0000.000
36L36TYR0-0.020-0.02114.906-1.330-1.3300.0000.0000.0000.000
37L37GLN00.0140.00619.7850.0170.0170.0000.0000.0000.000
38L38GLN00.006-0.00820.9370.7350.7350.0000.0000.0000.000
39L39LYS10.8460.92523.377-10.637-10.6370.0000.0000.0000.000
40L40GLN00.0750.02926.4930.4520.4520.0000.0000.0000.000
41L41GLY00.0020.00527.222-0.359-0.3590.0000.0000.0000.000
42L42LYS10.9090.95926.539-10.368-10.3680.0000.0000.0000.000
43L43SER00.0740.03222.9540.4200.4200.0000.0000.0000.000
44L44PRO00.0030.00518.647-0.434-0.4340.0000.0000.0000.000
45L45GLN0-0.053-0.02321.396-0.652-0.6520.0000.0000.0000.000
46L46LEU00.0010.00419.0210.2460.2460.0000.0000.0000.000
47L47LEU0-0.025-0.00221.270-0.603-0.6030.0000.0000.0000.000
48L48VAL0-0.017-0.01220.535-0.535-0.5350.0000.0000.0000.000
49L49TYR00.0370.01118.2250.9060.9060.0000.0000.0000.000
50L50ALA00.0390.01717.075-0.558-0.5580.0000.0000.0000.000
51L51ALA00.0040.00416.612-0.409-0.4090.0000.0000.0000.000
52L52THR0-0.067-0.04618.202-0.197-0.1970.0000.0000.0000.000
53L53ASN0-0.0360.00021.583-0.645-0.6450.0000.0000.0000.000
54L54LEU00.0140.01122.9890.4550.4550.0000.0000.0000.000
55L55ALA00.0120.00423.583-0.165-0.1650.0000.0000.0000.000
56L56ALA00.004-0.01525.459-0.358-0.3580.0000.0000.0000.000
57L57GLY00.0180.01428.7880.0160.0160.0000.0000.0000.000
58L58VAL0-0.0390.00125.906-0.155-0.1550.0000.0000.0000.000
59L59PRO00.0190.00229.316-0.152-0.1520.0000.0000.0000.000
60L60SER00.0420.00730.2970.3070.3070.0000.0000.0000.000
61L61ARG10.7530.85530.906-9.628-9.6280.0000.0000.0000.000
62L62PHE0-0.017-0.00625.7950.2730.2730.0000.0000.0000.000
63L63SER0-0.005-0.00926.221-0.197-0.1970.0000.0000.0000.000
64L64GLY00.0310.02022.0120.3330.3330.0000.0000.0000.000
65L65SER0-0.033-0.01721.138-0.569-0.5690.0000.0000.0000.000
66L66GLY00.0810.03018.4590.7370.7370.0000.0000.0000.000
67L67SER0-0.047-0.01717.115-0.839-0.8390.0000.0000.0000.000
68L68GLY00.0760.04514.6030.2100.2100.0000.0000.0000.000
69L69THR00.0500.04011.0530.3780.3780.0000.0000.0000.000
70L70GLN00.0010.01713.2071.2561.2560.0000.0000.0000.000
71L71TYR00.013-0.02012.993-1.507-1.5070.0000.0000.0000.000
72L72SER0-0.021-0.03217.3290.3380.3380.0000.0000.0000.000
73L73LEU0-0.0220.01319.900-0.172-0.1720.0000.0000.0000.000
74L74LYS10.8890.93922.085-10.815-10.8150.0000.0000.0000.000
75L75ILE00.0310.02325.789-0.042-0.0420.0000.0000.0000.000
76L76ASN0-0.012-0.01528.7240.0470.0470.0000.0000.0000.000
77L77SER00.0010.00032.118-0.237-0.2370.0000.0000.0000.000
78L78LEU0-0.0130.00629.467-0.042-0.0420.0000.0000.0000.000
79L79GLN00.0390.00632.856-0.398-0.3980.0000.0000.0000.000
80L80SER00.0510.00733.3110.2730.2730.0000.0000.0000.000
81L81GLU-1-0.816-0.89632.2349.2889.2880.0000.0000.0000.000
82L82ASP-1-0.736-0.82529.21110.61510.6150.0000.0000.0000.000
83L83PHE0-0.0080.02428.2020.4710.4710.0000.0000.0000.000
84L84GLY00.001-0.00926.690-0.185-0.1850.0000.0000.0000.000
85L85SER00.0080.01121.045-0.090-0.0900.0000.0000.0000.000
86L86TYR00.000-0.01420.635-0.312-0.3120.0000.0000.0000.000
87L87TYR0-0.008-0.00615.1970.4120.4120.0000.0000.0000.000
88L89GLN00.002-0.00210.543-0.980-0.9800.0000.0000.0000.000
89L90HIS0-0.025-0.0104.672-5.843-5.741-0.001-0.005-0.0960.000
90L91PHE0-0.015-0.0319.1380.6140.6140.0000.0000.0000.000
91L92TRP0-0.066-0.0255.988-2.859-2.8590.0000.0000.0000.000
92L93ASN00.002-0.0042.6872.1533.4320.770-0.906-1.143-0.009
93L94ILE0-0.0100.0165.220-0.686-0.561-0.001-0.014-0.1100.000
94L95PRO00.0530.0202.3472.5303.5090.890-0.565-1.3040.000
95L96PHE00.0480.0314.7672.6252.660-0.001-0.004-0.0290.000
96L97THR0-0.027-0.0284.004-5.536-5.383-0.001-0.012-0.1400.000
97L98PHE00.013-0.0046.896-2.100-2.1000.0000.0000.0000.000
98L99GLY00.0210.0039.6112.5682.5680.0000.0000.0000.000
99L100SER0-0.012-0.02111.789-0.601-0.6010.0000.0000.0000.000
100L101GLY0-0.0090.00013.405-1.056-1.0560.0000.0000.0000.000
101L102THR0-0.046-0.03916.8280.2070.2070.0000.0000.0000.000
102L103LYS10.8140.89920.235-12.012-12.0120.0000.0000.0000.000
103L104LEU0-0.033-0.01323.564-0.155-0.1550.0000.0000.0000.000
104L105GLU-1-0.802-0.84226.73410.14310.1430.0000.0000.0000.000
105L106ILE00.0090.00329.976-0.017-0.0170.0000.0000.0000.000
106L107LYS10.8090.90032.367-9.632-9.6320.0000.0000.0000.000
107L108ARG10.8260.91135.321-8.083-8.0830.0000.0000.0000.000
108L109ALA00.0270.01538.5230.1000.1000.0000.0000.0000.000
109L110ASP-1-0.817-0.88338.7318.3088.3080.0000.0000.0000.000
110L111ALA0-0.018-0.01240.453-0.208-0.2080.0000.0000.0000.000
111L112ALA00.0380.02340.8540.2010.2010.0000.0000.0000.000
112L113PRO0-0.0160.00640.624-0.053-0.0530.0000.0000.0000.000
113L114THR00.0170.00042.523-0.222-0.2220.0000.0000.0000.000
114L115VAL0-0.053-0.03043.4380.0350.0350.0000.0000.0000.000
115L116SER0-0.042-0.01845.539-0.259-0.2590.0000.0000.0000.000
116L117ILE0-0.015-0.01246.1470.1720.1720.0000.0000.0000.000
117L118PHE0-0.003-0.00646.756-0.166-0.1660.0000.0000.0000.000
118L119PRO00.0130.00648.7900.1310.1310.0000.0000.0000.000
119L120PRO00.0130.02149.1580.0360.0360.0000.0000.0000.000
120L121SER0-0.022-0.02850.653-0.097-0.0970.0000.0000.0000.000
121L122SER00.031-0.01253.0620.0020.0020.0000.0000.0000.000
122L123GLU-1-0.812-0.85853.3455.9525.9520.0000.0000.0000.000
123L124GLN00.0370.02546.152-0.037-0.0370.0000.0000.0000.000
124L125LEU00.0340.02451.6540.0220.0220.0000.0000.0000.000
125L126THR0-0.070-0.05053.848-0.084-0.0840.0000.0000.0000.000
126L127SER0-0.104-0.05951.2580.0130.0130.0000.0000.0000.000
127L128GLY00.0410.02552.1050.0590.0590.0000.0000.0000.000
128L129GLY0-0.038-0.01548.5770.0920.0920.0000.0000.0000.000
129L130ALA00.002-0.01947.903-0.132-0.1320.0000.0000.0000.000
130L131SER0-0.020-0.01943.9260.0890.0890.0000.0000.0000.000
131L132VAL0-0.0030.01345.918-0.129-0.1290.0000.0000.0000.000
132L133VAL00.0040.00143.2220.2210.2210.0000.0000.0000.000
133L134CYS0-0.073-0.02642.6370.0210.0210.0000.0000.0000.000
134L135PHE0-0.0220.00041.9250.2040.2040.0000.0000.0000.000
135L136LEU00.0430.00338.753-0.179-0.1790.0000.0000.0000.000
136L137ASN00.024-0.00739.9520.3910.3910.0000.0000.0000.000
137L138ASN0-0.001-0.01440.824-0.224-0.2240.0000.0000.0000.000
138L139PHE00.0190.02734.833-0.135-0.1350.0000.0000.0000.000
139L140TYR00.008-0.03233.0600.1080.1080.0000.0000.0000.000
140L141PRO00.0160.00433.070-0.228-0.2280.0000.0000.0000.000
141L142LYS10.9210.94026.891-11.456-11.4560.0000.0000.0000.000
142L143ASP-1-0.909-0.92829.15910.98010.9800.0000.0000.0000.000
143L144ILE0-0.0060.00032.128-0.319-0.3190.0000.0000.0000.000
144L145ASN0-0.047-0.02131.9690.3500.3500.0000.0000.0000.000
145L146VAL00.0180.01035.422-0.264-0.2640.0000.0000.0000.000
146L147LYS10.8040.89937.415-8.004-8.0040.0000.0000.0000.000
147L148TRP00.0440.00339.999-0.279-0.2790.0000.0000.0000.000
148L149LYS10.8050.87842.817-7.089-7.0890.0000.0000.0000.000
149L150ILE00.0190.00145.906-0.055-0.0550.0000.0000.0000.000
150L151ASP-1-0.750-0.86848.7816.1146.1140.0000.0000.0000.000
151L152GLY0-0.0050.00549.881-0.039-0.0390.0000.0000.0000.000
152L153SER0-0.013-0.00247.1830.1210.1210.0000.0000.0000.000
153L154GLU-1-0.805-0.88339.3658.1688.1680.0000.0000.0000.000
154L155ARG10.8290.90642.495-7.285-7.2850.0000.0000.0000.000
155L156GLN0-0.005-0.00936.2620.2080.2080.0000.0000.0000.000
156L157ASN00.014-0.00838.0430.1950.1950.0000.0000.0000.000
157L158GLY00.0650.02638.409-0.263-0.2630.0000.0000.0000.000
158L159VAL0-0.045-0.00336.902-0.118-0.1180.0000.0000.0000.000
159L160LEU0-0.0090.01634.8620.2820.2820.0000.0000.0000.000
160L161ASN00.0270.01033.379-0.490-0.4900.0000.0000.0000.000
161L162SER0-0.011-0.00533.1980.3160.3160.0000.0000.0000.000
162L163TRP00.0550.01030.825-0.158-0.1580.0000.0000.0000.000
163L164THR0-0.020-0.00833.0290.0600.0600.0000.0000.0000.000
164L165ASP-1-0.816-0.90329.20211.16611.1660.0000.0000.0000.000
165L166GLN0-0.048-0.01731.974-0.084-0.0840.0000.0000.0000.000
166L167ASP-1-0.776-0.87233.9217.8537.8530.0000.0000.0000.000
167L168SER0-0.030-0.03037.441-0.043-0.0430.0000.0000.0000.000
168L169LYS10.7970.87838.380-7.588-7.5880.0000.0000.0000.000
169L170ASP-1-0.798-0.85940.9107.5577.5570.0000.0000.0000.000
170L171SER0-0.021-0.00936.7260.0490.0490.0000.0000.0000.000
171L172THR0-0.090-0.04936.8100.2010.2010.0000.0000.0000.000
172L173TYR0-0.048-0.05130.7080.2700.2700.0000.0000.0000.000
173L174SER00.0150.01436.437-0.364-0.3640.0000.0000.0000.000
174L175MET0-0.0410.00434.5850.2700.2700.0000.0000.0000.000
175L176SER0-0.018-0.00437.068-0.335-0.3350.0000.0000.0000.000
176L177SER00.0480.01437.2990.2230.2230.0000.0000.0000.000
177L178THR0-0.030-0.03239.252-0.275-0.2750.0000.0000.0000.000
178L179LEU00.0050.03140.1650.1940.1940.0000.0000.0000.000
179L180THR0-0.015-0.00441.837-0.252-0.2520.0000.0000.0000.000
180L181LEU0-0.065-0.01943.4520.1100.1100.0000.0000.0000.000
181L182THR00.024-0.01446.3530.0380.0380.0000.0000.0000.000
182L183LYS10.8410.89849.032-5.741-5.7410.0000.0000.0000.000
183L184ASP-1-0.751-0.85252.4436.2156.2150.0000.0000.0000.000
184L185GLU-1-0.788-0.88347.7786.5956.5950.0000.0000.0000.000
185L186TYR00.013-0.01150.459-0.007-0.0070.0000.0000.0000.000
186L187GLU-1-0.830-0.92051.7565.6725.6720.0000.0000.0000.000
187L188ARG10.7900.90150.745-6.349-6.3490.0000.0000.0000.000
188L189HIS10.7880.91349.823-6.442-6.4420.0000.0000.0000.000
189L190ASN0-0.006-0.00654.084-0.120-0.1200.0000.0000.0000.000
190L191SER0-0.066-0.02653.642-0.039-0.0390.0000.0000.0000.000
191L192TYR00.0110.00548.2990.1640.1640.0000.0000.0000.000
192L193THR0-0.004-0.01946.757-0.127-0.1270.0000.0000.0000.000
193L195GLU-1-0.822-0.89942.5307.1197.1190.0000.0000.0000.000
194L196ALA00.0270.01240.3570.2280.2280.0000.0000.0000.000
195L197THR0-0.013-0.00437.582-0.183-0.1830.0000.0000.0000.000
196L198HIS00.0350.02036.5820.0680.0680.0000.0000.0000.000
197L199LYS10.8500.90636.349-8.570-8.5700.0000.0000.0000.000
198L200THR0-0.033-0.04438.128-0.181-0.1810.0000.0000.0000.000
199L201SER0-0.037-0.01640.923-0.182-0.1820.0000.0000.0000.000
200L202THR00.0370.01538.8020.0600.0600.0000.0000.0000.000
201L203SER00.0320.02440.9620.0270.0270.0000.0000.0000.000
202L204PRO0-0.030-0.01341.991-0.045-0.0450.0000.0000.0000.000
203L205ILE00.0110.00643.559-0.217-0.2170.0000.0000.0000.000
204L206VAL0-0.008-0.00344.9800.1350.1350.0000.0000.0000.000
205L207LYS10.8870.95047.437-6.647-6.6470.0000.0000.0000.000
206L208SER00.0590.01748.5620.1740.1740.0000.0000.0000.000
207L209PHE0-0.0100.00949.663-0.093-0.0930.0000.0000.0000.000
208L210ASN00.0180.00853.7930.0550.0550.0000.0000.0000.000
209L211ARG10.8600.93554.892-5.815-5.8150.0000.0000.0000.000