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: V5Z81

Calculation Name: 1IKF-L-Xray372

Preferred Name:

Target Type:

Ligand Name: 4-methyl-4-[(e)-2-butenyl]-4,n-methyl-threonine

ligand 3-letter code: BMT

PDB ID: 1IKF

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2163683.127421
FMO2-HF: Nuclear repulsion 2081006.297365
FMO2-HF: Total energy -82676.830057
FMO2-MP2: Total energy -82917.285261


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.
-45.438-41.4846.002-3.636-6.3180.028
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 : -0.869 / q_NPA : -0.952
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].
3L3GLN00.0010.0073.5543.1644.8600.027-0.861-0.8610.002
4L4MET0-0.032-0.0065.265-3.625-3.587-0.001-0.002-0.0350.000
5L5THR00.014-0.0018.2170.2390.2390.0000.0000.0000.000
6L6GLN0-0.029-0.03611.2790.2670.2670.0000.0000.0000.000
7L7THR0-0.023-0.01514.5540.2710.2710.0000.0000.0000.000
8L8THR00.0210.02617.417-0.427-0.4270.0000.0000.0000.000
9L9SER00.0650.04318.0100.2640.2640.0000.0000.0000.000
10L10SER0-0.023-0.02419.445-0.214-0.2140.0000.0000.0000.000
11L11LEU0-0.027-0.01023.118-0.017-0.0170.0000.0000.0000.000
12L12SER00.0260.00725.7140.0400.0400.0000.0000.0000.000
13L13ALA0-0.031-0.00129.286-0.086-0.0860.0000.0000.0000.000
14L14SER00.024-0.00831.438-0.049-0.0490.0000.0000.0000.000
15L15LEU0-0.019-0.01534.0900.1420.1420.0000.0000.0000.000
16L16GLY0-0.022-0.00535.174-0.216-0.2160.0000.0000.0000.000
17L17ASP-1-0.820-0.89732.4778.9018.9010.0000.0000.0000.000
18L18ARG10.9320.96727.881-10.188-10.1880.0000.0000.0000.000
19L19VAL00.0100.01025.2310.0170.0170.0000.0000.0000.000
20L20THR0-0.009-0.02622.933-0.094-0.0940.0000.0000.0000.000
21L21ILE00.0000.02018.6050.0770.0770.0000.0000.0000.000
22L22SER00.025-0.00918.460-0.199-0.1990.0000.0000.0000.000
23L23CYS0-0.096-0.02212.6730.7800.7800.0000.0000.0000.000
24L24ARG10.8760.92112.851-17.732-17.7320.0000.0000.0000.000
25L25ALA00.0100.0189.5681.5201.5200.0000.0000.0000.000
26L26SER0-0.005-0.0126.856-0.522-0.5220.0000.0000.0000.000
27L27GLN0-0.005-0.0057.146-0.350-0.3500.0000.0000.0000.000
28L28ASP-1-0.842-0.91710.17617.89217.8920.0000.0000.0000.000
29L29ILE0-0.022-0.0328.8981.3491.3490.0000.0000.0000.000
30L30SER0-0.019-0.01811.541-0.191-0.1910.0000.0000.0000.000
31L31THR00.0070.00414.901-0.495-0.4950.0000.0000.0000.000
32L32TYR0-0.025-0.00912.525-0.731-0.7310.0000.0000.0000.000
33L33LEU0-0.044-0.00711.9032.0482.0480.0000.0000.0000.000
34L34ASN0-0.009-0.02213.318-2.294-2.2940.0000.0000.0000.000
35L35TRP00.0370.01614.5061.1081.1080.0000.0000.0000.000
36L36TYR0-0.016-0.02213.678-1.093-1.0930.0000.0000.0000.000
37L37GLN00.0370.01017.899-0.201-0.2010.0000.0000.0000.000
38L38GLN0-0.049-0.02318.9650.2340.2340.0000.0000.0000.000
39L39LYS10.8410.90721.071-11.306-11.3060.0000.0000.0000.000
40L40PRO00.012-0.01624.3980.3440.3440.0000.0000.0000.000
41L41ASP-1-0.870-0.92326.48811.49011.4900.0000.0000.0000.000
42L42GLY00.0150.02122.4670.0470.0470.0000.0000.0000.000
43L43THR0-0.025-0.00521.8680.9070.9070.0000.0000.0000.000
44L44VAL00.0710.03517.4840.1290.1290.0000.0000.0000.000
45L45LYS10.8680.94120.960-12.511-12.5110.0000.0000.0000.000
46L46LEU0-0.031-0.01417.9640.2830.2830.0000.0000.0000.000
47L47LEU00.0090.01419.763-0.756-0.7560.0000.0000.0000.000
48L48ILE00.005-0.01119.732-0.567-0.5670.0000.0000.0000.000
49L49PHE00.015-0.00717.5960.8250.8250.0000.0000.0000.000
50L50TYR0-0.046-0.02617.108-0.993-0.9930.0000.0000.0000.000
51L51THR00.0220.01417.292-0.858-0.8580.0000.0000.0000.000
52L52SER00.0020.00118.709-0.387-0.3870.0000.0000.0000.000
53L53ARG10.8830.96121.733-12.740-12.7400.0000.0000.0000.000
54L54LEU00.0580.04222.3700.5190.5190.0000.0000.0000.000
55L55ARG10.8650.95522.635-12.789-12.7890.0000.0000.0000.000
56L56SER00.006-0.03125.073-0.154-0.1540.0000.0000.0000.000
57L57GLY00.0140.01427.9180.2130.2130.0000.0000.0000.000
58L58VAL0-0.065-0.01324.712-0.083-0.0830.0000.0000.0000.000
59L59PRO00.0320.00828.118-0.145-0.1450.0000.0000.0000.000
60L60SER00.0290.00628.8240.3380.3380.0000.0000.0000.000
61L61ARG10.7600.85630.188-9.658-9.6580.0000.0000.0000.000
62L62PHE0-0.0290.01024.7290.2120.2120.0000.0000.0000.000
63L63SER00.0450.02025.687-0.137-0.1370.0000.0000.0000.000
64L64GLY00.025-0.00321.5870.2730.2730.0000.0000.0000.000
65L65SER0-0.0250.00121.871-0.189-0.1890.0000.0000.0000.000
66L66GLY00.0690.00418.9640.5870.5870.0000.0000.0000.000
67L67SER0-0.054-0.02818.900-0.504-0.5040.0000.0000.0000.000
68L68GLY00.0590.04816.019-0.030-0.0300.0000.0000.0000.000
69L69THR0-0.0050.00812.5861.0071.0070.0000.0000.0000.000
70L70ASP-1-0.825-0.87814.25616.82716.8270.0000.0000.0000.000
71L71TYR00.005-0.01314.039-0.575-0.5750.0000.0000.0000.000
72L72SER0-0.029-0.02517.722-0.075-0.0750.0000.0000.0000.000
73L73LEU00.0090.02720.100-0.062-0.0620.0000.0000.0000.000
74L74THR0-0.039-0.02921.767-0.187-0.1870.0000.0000.0000.000
75L75ILE0-0.0050.01924.6890.1070.1070.0000.0000.0000.000
76L76SER0-0.029-0.03727.672-0.214-0.2140.0000.0000.0000.000
77L77ASN0-0.032-0.02431.077-0.008-0.0080.0000.0000.0000.000
78L78LEU0-0.0080.01828.5880.1570.1570.0000.0000.0000.000
79L79GLU-1-0.814-0.90431.9038.7248.7240.0000.0000.0000.000
80L80GLN0-0.004-0.00932.1520.0000.0000.0000.0000.0000.000
81L81GLU-1-0.832-0.93131.2389.1679.1670.0000.0000.0000.000
82L82ASP-1-0.819-0.87127.72510.73810.7380.0000.0000.0000.000
83L83ILE00.0520.05026.8700.5060.5060.0000.0000.0000.000
84L84ALA0-0.026-0.02823.533-0.060-0.0600.0000.0000.0000.000
85L85THR0-0.0100.00118.437-0.159-0.1590.0000.0000.0000.000
86L86TYR0-0.033-0.01819.0680.2170.2170.0000.0000.0000.000
87L87PHE00.0100.01013.5960.3070.3070.0000.0000.0000.000
88L89GLN00.0460.0169.114-0.626-0.6260.0000.0000.0000.000
89L90GLN00.023-0.0094.641-6.008-5.923-0.001-0.003-0.0810.000
90L91GLY00.0030.0008.1402.2802.2800.0000.0000.0000.000
91L92SER0-0.045-0.0108.473-1.206-1.2060.0000.0000.0000.000
92L93ARG10.9240.9554.839-29.036-29.0360.0000.0000.0000.000
93L94ILE00.0100.0276.039-0.253-0.2530.0000.0000.0000.000
94L95PRO00.0360.0122.501-6.408-4.3823.916-2.118-3.8250.024
95L96PRO0-0.003-0.0024.119-0.1180.1060.000-0.049-0.1750.000
96L97THR0-0.031-0.0072.3410.9770.8122.062-0.602-1.2940.002
97L98PHE00.033-0.0045.344-4.508-4.458-0.001-0.001-0.0470.000
98L99GLY00.0300.0188.0921.9021.9020.0000.0000.0000.000
99L100GLY0-0.009-0.01610.517-0.004-0.0040.0000.0000.0000.000
100L101GLY0-0.0150.00412.781-0.859-0.8590.0000.0000.0000.000
101L102THR0-0.054-0.04816.0250.0440.0440.0000.0000.0000.000
102L103LYS10.8420.90919.242-12.095-12.0950.0000.0000.0000.000
103L104LEU0-0.0010.00622.293-0.053-0.0530.0000.0000.0000.000
104L105GLU-1-0.868-0.88725.3669.8799.8790.0000.0000.0000.000
105L106ILE0-0.015-0.00328.802-0.057-0.0570.0000.0000.0000.000
106L107LEU00.0340.02032.087-0.123-0.1230.0000.0000.0000.000
107L108ARG10.7910.87034.528-7.982-7.9820.0000.0000.0000.000
108L109ALA00.0050.00538.079-0.035-0.0350.0000.0000.0000.000
109L110ASP-1-0.799-0.89540.9887.6727.6720.0000.0000.0000.000
110L111ALA0-0.0240.00241.663-0.178-0.1780.0000.0000.0000.000
111L112ALA00.0390.01542.3330.1590.1590.0000.0000.0000.000
112L113PRO00.0030.01342.240-0.028-0.0280.0000.0000.0000.000
113L114THR0-0.035-0.01444.024-0.245-0.2450.0000.0000.0000.000
114L115VAL0-0.006-0.01145.2450.1160.1160.0000.0000.0000.000
115L116SER0-0.060-0.03046.378-0.217-0.2170.0000.0000.0000.000
116L117ILE0-0.028-0.01246.9160.1560.1560.0000.0000.0000.000
117L118PHE0-0.009-0.01247.000-0.129-0.1290.0000.0000.0000.000
118L119PRO00.0260.01248.9040.1100.1100.0000.0000.0000.000
119L120PRO00.0050.00649.4700.0480.0480.0000.0000.0000.000
120L121SER00.0400.02849.607-0.121-0.1210.0000.0000.0000.000
121L122SER00.023-0.01351.4610.0300.0300.0000.0000.0000.000
122L123GLU-1-0.904-0.94750.5506.4176.4170.0000.0000.0000.000
123L124GLN0-0.006-0.00645.657-0.033-0.0330.0000.0000.0000.000
124L125LEU00.0460.01949.805-0.001-0.0010.0000.0000.0000.000
125L126THR0-0.080-0.03752.637-0.008-0.0080.0000.0000.0000.000
126L127SER00.0120.00649.417-0.043-0.0430.0000.0000.0000.000
127L128GLY0-0.030-0.00650.2530.0720.0720.0000.0000.0000.000
128L129GLY0-0.035-0.01147.365-0.024-0.0240.0000.0000.0000.000
129L130ALA00.0260.00647.999-0.123-0.1230.0000.0000.0000.000
130L131SER0-0.019-0.01843.8820.0830.0830.0000.0000.0000.000
131L132VAL0-0.0240.00346.278-0.106-0.1060.0000.0000.0000.000
132L133VAL00.0220.00842.4740.1690.1690.0000.0000.0000.000
133L134CYS0-0.052-0.00843.362-0.055-0.0550.0000.0000.0000.000
134L135PHE00.0150.01440.3260.2250.2250.0000.0000.0000.000
135L136LEU00.0170.00540.689-0.244-0.2440.0000.0000.0000.000
136L137ASN00.015-0.02740.5580.3590.3590.0000.0000.0000.000
137L138ASN00.012-0.00140.110-0.023-0.0230.0000.0000.0000.000
138L139PHE0-0.0240.00436.841-0.172-0.1720.0000.0000.0000.000
139L140TYR00.034-0.00133.2540.1470.1470.0000.0000.0000.000
140L141PRO00.005-0.01135.506-0.250-0.2500.0000.0000.0000.000
141L142LYS10.9700.98829.310-10.319-10.3190.0000.0000.0000.000
142L143ASP-1-0.928-0.95833.0689.3369.3360.0000.0000.0000.000
143L144ILE0-0.022-0.00135.465-0.288-0.2880.0000.0000.0000.000
144L145ASN0-0.044-0.02437.3250.0400.0400.0000.0000.0000.000
145L146VAL00.0240.00439.700-0.194-0.1940.0000.0000.0000.000
146L147LYS10.8380.91641.673-7.006-7.0060.0000.0000.0000.000
147L148TRP00.0330.01142.518-0.229-0.2290.0000.0000.0000.000
148L149LYS10.8040.88646.523-6.460-6.4600.0000.0000.0000.000
149L150ILE0-0.0060.00348.733-0.044-0.0440.0000.0000.0000.000
150L151ASP-1-0.785-0.89252.3355.7075.7070.0000.0000.0000.000
151L152GLY00.0010.01354.613-0.069-0.0690.0000.0000.0000.000
152L153SER0-0.061-0.02051.8380.0800.0800.0000.0000.0000.000
153L154GLU-1-0.758-0.88144.6537.1397.1390.0000.0000.0000.000
154L155ARG10.8840.94244.650-7.053-7.0530.0000.0000.0000.000
155L156GLN00.006-0.01641.6640.1960.1960.0000.0000.0000.000
156L157ASN0-0.019-0.01140.8380.0730.0730.0000.0000.0000.000
157L158GLY00.0190.01640.093-0.152-0.1520.0000.0000.0000.000
158L159VAL00.0130.00239.017-0.156-0.1560.0000.0000.0000.000
159L160LEU0-0.0150.01134.6750.2540.2540.0000.0000.0000.000
160L161ASN00.0330.01535.073-0.383-0.3830.0000.0000.0000.000
161L162SER00.0000.00532.7820.4100.4100.0000.0000.0000.000
162L163TRP0-0.016-0.01931.572-0.168-0.1680.0000.0000.0000.000
163L164THR0-0.006-0.00631.7270.1780.1780.0000.0000.0000.000
164L165ASP-1-0.801-0.90226.83711.58511.5850.0000.0000.0000.000
165L166GLN0-0.077-0.03030.057-0.082-0.0820.0000.0000.0000.000
166L167ASP-1-0.830-0.90431.8588.7598.7590.0000.0000.0000.000
167L168SER0-0.005-0.01932.2660.0070.0070.0000.0000.0000.000
168L169LYS10.8280.91333.795-8.153-8.1530.0000.0000.0000.000
169L170ASP-1-0.819-0.92437.4417.7447.7440.0000.0000.0000.000
170L171SER0-0.031-0.01033.977-0.130-0.1300.0000.0000.0000.000
171L172THR00.0290.04135.5740.1240.1240.0000.0000.0000.000
172L173TYR0-0.072-0.06730.3350.3720.3720.0000.0000.0000.000
173L174SER00.0380.01735.646-0.412-0.4120.0000.0000.0000.000
174L175MET0-0.0260.00535.8110.2490.2490.0000.0000.0000.000
175L176SER0-0.026-0.00437.176-0.265-0.2650.0000.0000.0000.000
176L177SER00.0240.00137.7850.1730.1730.0000.0000.0000.000
177L178THR0-0.004-0.00439.794-0.253-0.2530.0000.0000.0000.000
178L179LEU00.0070.01841.1350.1320.1320.0000.0000.0000.000
179L180THR0-0.003-0.00242.173-0.114-0.1140.0000.0000.0000.000
180L181LEU0-0.040-0.02144.3250.0180.0180.0000.0000.0000.000
181L182THR00.0360.02547.2780.0480.0480.0000.0000.0000.000
182L183LYS10.9250.96249.586-6.036-6.0360.0000.0000.0000.000
183L184ASP-1-0.870-0.93052.7695.9315.9310.0000.0000.0000.000
184L185GLU-1-0.815-0.89150.0996.1306.1300.0000.0000.0000.000
185L186TYR0-0.012-0.01251.397-0.066-0.0660.0000.0000.0000.000
186L187GLU-1-0.902-0.97953.1105.6075.6070.0000.0000.0000.000
187L188ARG10.8460.94053.399-6.073-6.0730.0000.0000.0000.000
188L189HIS10.7730.86253.134-6.030-6.0300.0000.0000.0000.000
189L190ASN00.0150.01357.0170.0440.0440.0000.0000.0000.000
190L191SER0-0.0060.00056.353-0.037-0.0370.0000.0000.0000.000
191L192TYR0-0.038-0.01450.3300.1180.1180.0000.0000.0000.000
192L193THR0-0.013-0.01650.433-0.073-0.0730.0000.0000.0000.000
193L195GLU-1-0.827-0.91246.5926.4346.4340.0000.0000.0000.000
194L196ALA00.0320.01443.3580.1760.1760.0000.0000.0000.000
195L197THR0-0.0060.00043.018-0.229-0.2290.0000.0000.0000.000
196L198HIS00.0520.01339.2160.0030.0030.0000.0000.0000.000
197L199LYS10.8770.93240.235-7.683-7.6830.0000.0000.0000.000
198L200THR0-0.048-0.03942.838-0.180-0.1800.0000.0000.0000.000
199L201SER0-0.031-0.02845.391-0.210-0.2100.0000.0000.0000.000
200L202THR0-0.0100.00747.2400.0860.0860.0000.0000.0000.000
201L203SER0-0.0070.00149.2450.0610.0610.0000.0000.0000.000
202L204PRO00.0310.02047.8780.0620.0620.0000.0000.0000.000
203L205ILE0-0.0010.01746.331-0.154-0.1540.0000.0000.0000.000
204L206VAL00.012-0.00248.3730.0970.0970.0000.0000.0000.000
205L207LYS10.8870.95849.429-6.342-6.3420.0000.0000.0000.000
206L208SER00.042-0.00351.2380.1090.1090.0000.0000.0000.000
207L209PHE00.0040.02151.384-0.031-0.0310.0000.0000.0000.000
208L210ASN00.0680.02855.5780.0150.0150.0000.0000.0000.000
209L211ARG10.8200.89055.711-5.654-5.6540.0000.0000.0000.000
210L212ALA0-0.0060.02058.380-0.016-0.0160.0000.0000.0000.000
211L213ALA0-0.032-0.01158.509-0.031-0.0310.0000.0000.0000.000