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: 17V2Z

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166316.954984
FMO2-HF: Nuclear repulsion 2083639.112494
FMO2-HF: Total energy -82677.84249
FMO2-MP2: Total energy -82918.390683


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.
-51.144-45.8761.933-2.776-4.4220.024
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 : -0.899 / q_NPA : -0.958
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].
3L3GLN00.0120.0233.8591.9213.7150.004-0.785-1.0130.004
4L4MET0-0.0340.0035.100-3.977-3.915-0.001-0.003-0.0570.000
5L5THR0-0.005-0.0137.9480.1980.1980.0000.0000.0000.000
6L6GLN00.034-0.00911.0550.4310.4310.0000.0000.0000.000
7L7THR0-0.017-0.00614.5270.2370.2370.0000.0000.0000.000
8L8THR00.0020.00217.464-0.843-0.8430.0000.0000.0000.000
9L9SER00.0690.05517.8240.1080.1080.0000.0000.0000.000
10L10SER0-0.045-0.03219.079-0.142-0.1420.0000.0000.0000.000
11L11LEU0-0.0120.00622.785-0.111-0.1110.0000.0000.0000.000
12L12SER00.0130.00025.6600.0430.0430.0000.0000.0000.000
13L13ALA0-0.0130.00429.086-0.052-0.0520.0000.0000.0000.000
14L14SER00.0340.00331.592-0.054-0.0540.0000.0000.0000.000
15L15LEU0-0.007-0.01133.8810.2020.2020.0000.0000.0000.000
16L16GLY0-0.010-0.01035.005-0.215-0.2150.0000.0000.0000.000
17L17ASP-1-0.803-0.87832.1938.8888.8880.0000.0000.0000.000
18L18ARG10.8620.92327.358-10.267-10.2670.0000.0000.0000.000
19L19VAL00.0340.02525.2890.1450.1450.0000.0000.0000.000
20L20THR0-0.016-0.02022.821-0.166-0.1660.0000.0000.0000.000
21L21ILE0-0.0010.02018.5160.0880.0880.0000.0000.0000.000
22L22SER00.013-0.01718.731-0.195-0.1950.0000.0000.0000.000
23L23CYS0-0.102-0.04712.6200.5850.5850.0000.0000.0000.000
24L24ARG10.8610.91312.435-18.104-18.1040.0000.0000.0000.000
25L25ALA00.0280.0169.3011.5241.5240.0000.0000.0000.000
26L26SER0-0.003-0.0076.538-0.739-0.7390.0000.0000.0000.000
27L27GLN00.011-0.0017.142-0.593-0.5930.0000.0000.0000.000
28L28ASP-1-0.825-0.8979.69118.47118.4710.0000.0000.0000.000
29L29ILE0-0.035-0.0288.6921.6051.6050.0000.0000.0000.000
30L30SER0-0.016-0.03411.352-0.234-0.2340.0000.0000.0000.000
31L31THR0-0.002-0.00414.979-0.585-0.5850.0000.0000.0000.000
32L32TYR0-0.0180.00612.470-0.774-0.7740.0000.0000.0000.000
33L33LEU0-0.049-0.01512.1872.0862.0860.0000.0000.0000.000
34L34ASN0-0.025-0.02713.964-2.459-2.4590.0000.0000.0000.000
35L35TRP00.0490.02114.9151.1521.1520.0000.0000.0000.000
36L36TYR0-0.012-0.02014.632-1.079-1.0790.0000.0000.0000.000
37L37GLN00.0460.02118.458-0.107-0.1070.0000.0000.0000.000
38L38GLN0-0.048-0.02419.0660.2360.2360.0000.0000.0000.000
39L39LYS10.8350.90521.396-11.233-11.2330.0000.0000.0000.000
40L40PRO00.0300.00324.4110.3550.3550.0000.0000.0000.000
41L41ASP-1-0.860-0.92026.36011.68711.6870.0000.0000.0000.000
42L42GLY00.0260.01923.0520.0400.0400.0000.0000.0000.000
43L43THR0-0.037-0.00722.2480.9530.9530.0000.0000.0000.000
44L44VAL00.019-0.00518.1450.1240.1240.0000.0000.0000.000
45L45LYS10.8420.92221.433-12.893-12.8930.0000.0000.0000.000
46L46LEU00.0090.00918.3860.2360.2360.0000.0000.0000.000
47L47LEU0-0.039-0.00920.271-0.781-0.7810.0000.0000.0000.000
48L48ILE00.0200.00120.437-0.650-0.6500.0000.0000.0000.000
49L49PHE00.005-0.00818.4170.8880.8880.0000.0000.0000.000
50L50TYR0-0.007-0.00317.414-1.119-1.1190.0000.0000.0000.000
51L51THR00.0190.00917.677-0.812-0.8120.0000.0000.0000.000
52L52SER0-0.045-0.02018.995-0.420-0.4200.0000.0000.0000.000
53L53ARG10.9150.97622.150-13.038-13.0380.0000.0000.0000.000
54L54LEU00.0520.03323.1840.5300.5300.0000.0000.0000.000
55L55ARG10.8400.93323.525-12.705-12.7050.0000.0000.0000.000
56L56SER00.019-0.01525.994-0.177-0.1770.0000.0000.0000.000
57L57GLY00.0200.00728.7780.2300.2300.0000.0000.0000.000
58L58VAL0-0.048-0.00425.327-0.068-0.0680.0000.0000.0000.000
59L59PRO00.0420.02028.705-0.144-0.1440.0000.0000.0000.000
60L60SER00.006-0.00929.5430.3200.3200.0000.0000.0000.000
61L61ARG10.7590.85630.236-9.755-9.7550.0000.0000.0000.000
62L62PHE0-0.0160.00325.0240.2260.2260.0000.0000.0000.000
63L63SER00.0220.00725.777-0.122-0.1220.0000.0000.0000.000
64L64GLY00.0070.00421.9980.2940.2940.0000.0000.0000.000
65L65SER0-0.031-0.01621.272-0.537-0.5370.0000.0000.0000.000
66L66GLY00.0760.02018.8850.5550.5550.0000.0000.0000.000
67L67SER0-0.035-0.02818.384-0.656-0.6560.0000.0000.0000.000
68L68GLY00.0690.05115.6420.0390.0390.0000.0000.0000.000
69L69THR0-0.017-0.00612.3681.2031.2030.0000.0000.0000.000
70L70ASP-1-0.818-0.85714.02917.24717.2470.0000.0000.0000.000
71L71TYR00.033-0.01113.814-0.752-0.7520.0000.0000.0000.000
72L72SER0-0.038-0.02517.479-0.193-0.1930.0000.0000.0000.000
73L73LEU00.0010.01419.8980.0080.0080.0000.0000.0000.000
74L74THR0-0.025-0.00621.677-0.133-0.1330.0000.0000.0000.000
75L75ILE0-0.0030.00524.3510.0100.0100.0000.0000.0000.000
76L76SER0-0.029-0.03227.472-0.259-0.2590.0000.0000.0000.000
77L77ASN0-0.014-0.00330.896-0.170-0.1700.0000.0000.0000.000
78L78LEU0-0.036-0.00428.5550.1740.1740.0000.0000.0000.000
79L79GLU-1-0.810-0.89731.8848.8198.8190.0000.0000.0000.000
80L80GLN00.019-0.01032.1420.0720.0720.0000.0000.0000.000
81L81GLU-1-0.865-0.94531.7129.1429.1420.0000.0000.0000.000
82L82ASP-1-0.784-0.85127.90910.79610.7960.0000.0000.0000.000
83L83ILE00.0230.02726.8510.5410.5410.0000.0000.0000.000
84L84ALA0-0.025-0.01423.460-0.001-0.0010.0000.0000.0000.000
85L85THR00.0010.01018.262-0.125-0.1250.0000.0000.0000.000
86L86TYR0-0.021-0.00919.1560.2420.2420.0000.0000.0000.000
87L87PHE00.0280.02213.6290.3150.3150.0000.0000.0000.000
88L89GLN00.0370.00910.181-0.694-0.6940.0000.0000.0000.000
89L90GLN00.0270.0055.271-6.222-6.2220.0000.0000.0000.000
90L91GLY00.000-0.0048.9572.2602.2600.0000.0000.0000.000
91L92SER0-0.0100.0128.835-1.550-1.5500.0000.0000.0000.000
92L93ARG10.8450.9175.102-30.162-30.1620.0000.0000.0000.000
93L94ILE00.0030.0286.632-0.897-0.8970.0000.0000.0000.000
94L95PRO00.0620.0232.690-6.608-4.1991.711-1.639-2.4800.019
95L96PRO0-0.012-0.0014.8321.2371.292-0.001-0.006-0.0470.000
96L97THR0-0.011-0.0162.649-0.4970.4510.220-0.343-0.8250.001
97L98PHE00.0330.0006.134-4.689-4.6890.0000.0000.0000.000
98L99GLY00.0220.0107.9912.0142.0140.0000.0000.0000.000
99L100GLY0-0.027-0.02510.379-0.272-0.2720.0000.0000.0000.000
100L101GLY0-0.0040.00412.297-0.908-0.9080.0000.0000.0000.000
101L102THR0-0.051-0.04415.4410.0370.0370.0000.0000.0000.000
102L103LYS10.8320.91718.869-12.089-12.0890.0000.0000.0000.000
103L104LEU0-0.026-0.01621.933-0.096-0.0960.0000.0000.0000.000
104L105GLU-1-0.855-0.87825.2149.9009.9000.0000.0000.0000.000
105L106ILE0-0.019-0.01928.6710.0020.0020.0000.0000.0000.000
106L107LEU00.0190.01631.932-0.151-0.1510.0000.0000.0000.000
107L108ARG10.7740.86634.388-8.027-8.0270.0000.0000.0000.000
108L109ALA00.0240.01137.989-0.012-0.0120.0000.0000.0000.000
109L110ASP-1-0.800-0.89140.7557.6587.6580.0000.0000.0000.000
110L111ALA0-0.034-0.00641.344-0.139-0.1390.0000.0000.0000.000
111L112ALA00.0390.02042.1740.1390.1390.0000.0000.0000.000
112L113PRO0-0.0180.00642.102-0.016-0.0160.0000.0000.0000.000
113L114THR00.009-0.00143.827-0.232-0.2320.0000.0000.0000.000
114L115VAL0-0.032-0.02145.5170.0730.0730.0000.0000.0000.000
115L116SER0-0.054-0.02946.165-0.225-0.2250.0000.0000.0000.000
116L117ILE0-0.022-0.01546.5660.1620.1620.0000.0000.0000.000
117L118PHE00.0130.00546.741-0.122-0.1220.0000.0000.0000.000
118L119PRO00.0090.01148.7300.1110.1110.0000.0000.0000.000
119L120PRO00.0080.00249.0970.0600.0600.0000.0000.0000.000
120L121SER0-0.003-0.01249.503-0.094-0.0940.0000.0000.0000.000
121L122SER00.0470.00451.2740.0160.0160.0000.0000.0000.000
122L123GLU-1-0.812-0.86950.1946.3086.3080.0000.0000.0000.000
123L124GLN00.0150.01645.441-0.047-0.0470.0000.0000.0000.000
124L125LEU00.0360.01249.656-0.002-0.0020.0000.0000.0000.000
125L126THR0-0.082-0.05952.706-0.038-0.0380.0000.0000.0000.000
126L127SER0-0.031-0.02049.450-0.036-0.0360.0000.0000.0000.000
127L128GLY0-0.0130.00650.5970.0520.0520.0000.0000.0000.000
128L129GLY0-0.034-0.00947.6540.0160.0160.0000.0000.0000.000
129L130ALA00.015-0.00847.864-0.136-0.1360.0000.0000.0000.000
130L131SER0-0.004-0.00943.7560.0930.0930.0000.0000.0000.000
131L132VAL0-0.0180.01046.038-0.080-0.0800.0000.0000.0000.000
132L133VAL00.0240.01042.5580.1740.1740.0000.0000.0000.000
133L134CYS0-0.068-0.02143.337-0.052-0.0520.0000.0000.0000.000
134L135PHE00.0110.00740.1260.2250.2250.0000.0000.0000.000
135L136LEU00.011-0.00640.284-0.232-0.2320.0000.0000.0000.000
136L137ASN00.0390.00240.2920.3670.3670.0000.0000.0000.000
137L138ASN0-0.012-0.02140.042-0.023-0.0230.0000.0000.0000.000
138L139PHE0-0.023-0.00636.673-0.169-0.1690.0000.0000.0000.000
139L140TYR00.028-0.01333.0190.1520.1520.0000.0000.0000.000
140L141PRO00.0450.00735.211-0.260-0.2600.0000.0000.0000.000
141L142LYS10.9460.99329.282-10.319-10.3190.0000.0000.0000.000
142L143ASP-1-0.919-0.95733.1409.2929.2920.0000.0000.0000.000
143L144ILE0-0.020-0.00735.469-0.291-0.2910.0000.0000.0000.000
144L145ASN0-0.057-0.02537.1140.0320.0320.0000.0000.0000.000
145L146VAL00.0190.00339.554-0.210-0.2100.0000.0000.0000.000
146L147LYS10.8240.91141.243-7.035-7.0350.0000.0000.0000.000
147L148TRP00.0280.00042.266-0.186-0.1860.0000.0000.0000.000
148L149LYS10.7960.87746.253-6.490-6.4900.0000.0000.0000.000
149L150ILE00.0230.00048.548-0.021-0.0210.0000.0000.0000.000
150L151ASP-1-0.776-0.87152.3175.6875.6870.0000.0000.0000.000
151L152GLY00.0050.01354.407-0.081-0.0810.0000.0000.0000.000
152L153SER0-0.059-0.02852.0050.0980.0980.0000.0000.0000.000
153L154GLU-1-0.772-0.87744.7617.1087.1080.0000.0000.0000.000
154L155ARG10.8560.92544.969-6.971-6.9710.0000.0000.0000.000
155L156GLN00.011-0.01441.4950.1820.1820.0000.0000.0000.000
156L157ASN00.0080.00741.1850.0980.0980.0000.0000.0000.000
157L158GLY00.0580.02640.738-0.156-0.1560.0000.0000.0000.000
158L159VAL0-0.021-0.00138.947-0.081-0.0810.0000.0000.0000.000
159L160LEU0-0.0060.01434.8670.2380.2380.0000.0000.0000.000
160L161ASN00.0170.00834.973-0.401-0.4010.0000.0000.0000.000
161L162SER00.000-0.00232.6020.3940.3940.0000.0000.0000.000
162L163TRP00.004-0.00831.512-0.197-0.1970.0000.0000.0000.000
163L164THR0-0.004-0.00631.5970.1500.1500.0000.0000.0000.000
164L165ASP-1-0.778-0.88026.66811.59111.5910.0000.0000.0000.000
165L166GLN0-0.054-0.01829.802-0.102-0.1020.0000.0000.0000.000
166L167ASP-1-0.804-0.89731.6908.7518.7510.0000.0000.0000.000
167L168SER0-0.039-0.03232.0990.1470.1470.0000.0000.0000.000
168L169LYS10.8200.89733.875-8.166-8.1660.0000.0000.0000.000
169L170ASP-1-0.775-0.89437.5337.7457.7450.0000.0000.0000.000
170L171SER0-0.0170.01433.978-0.105-0.1050.0000.0000.0000.000
171L172THR0-0.0090.01735.4650.1330.1330.0000.0000.0000.000
172L173TYR0-0.056-0.06030.0690.4150.4150.0000.0000.0000.000
173L174SER00.0290.02635.651-0.410-0.4100.0000.0000.0000.000
174L175MET0-0.052-0.00835.6400.2480.2480.0000.0000.0000.000
175L176SER0-0.0270.00037.013-0.262-0.2620.0000.0000.0000.000
176L177SER00.0380.00137.6330.1760.1760.0000.0000.0000.000
177L178THR0-0.012-0.00939.966-0.221-0.2210.0000.0000.0000.000
178L179LEU0-0.0100.01940.9600.1560.1560.0000.0000.0000.000
179L180THR0-0.011-0.00342.309-0.154-0.1540.0000.0000.0000.000
180L181LEU0-0.065-0.03144.5100.0210.0210.0000.0000.0000.000
181L182THR0-0.014-0.02047.4610.0740.0740.0000.0000.0000.000
182L183LYS10.9240.95549.757-5.971-5.9710.0000.0000.0000.000
183L184ASP-1-0.803-0.88852.7375.9745.9740.0000.0000.0000.000
184L185GLU-1-0.818-0.88150.3056.1176.1170.0000.0000.0000.000
185L186TYR0-0.009-0.01251.307-0.039-0.0390.0000.0000.0000.000
186L187GLU-1-0.890-0.96052.9925.5805.5800.0000.0000.0000.000
187L188ARG10.8360.92353.645-6.031-6.0310.0000.0000.0000.000
188L189HIS10.7590.87352.840-6.029-6.0290.0000.0000.0000.000
189L190ASN0-0.009-0.00156.902-0.029-0.0290.0000.0000.0000.000
190L191SER00.008-0.00456.505-0.025-0.0250.0000.0000.0000.000
191L192TYR0-0.033-0.02550.3680.1250.1250.0000.0000.0000.000
192L193THR0-0.015-0.02350.102-0.091-0.0910.0000.0000.0000.000
193L195GLU-1-0.816-0.90046.2276.4296.4290.0000.0000.0000.000
194L196ALA00.0380.01143.2250.1720.1720.0000.0000.0000.000
195L197THR0-0.0070.00142.738-0.199-0.1990.0000.0000.0000.000
196L198HIS00.0400.01238.926-0.004-0.0040.0000.0000.0000.000
197L199LYS10.8600.91739.681-7.720-7.7200.0000.0000.0000.000
198L200THR0-0.024-0.02942.485-0.164-0.1640.0000.0000.0000.000
199L201SER0-0.071-0.04645.248-0.220-0.2200.0000.0000.0000.000
200L202THR00.0010.01147.1140.1000.1000.0000.0000.0000.000
201L203SER00.0090.01049.4460.0210.0210.0000.0000.0000.000
202L204PRO00.0120.02547.3510.0830.0830.0000.0000.0000.000
203L205ILE00.0210.00946.255-0.167-0.1670.0000.0000.0000.000
204L206VAL00.0000.00147.8360.1100.1100.0000.0000.0000.000
205L207LYS10.8610.93649.453-6.332-6.3320.0000.0000.0000.000
206L208SER00.0550.01850.7950.1390.1390.0000.0000.0000.000
207L209PHE0-0.0050.01851.044-0.036-0.0360.0000.0000.0000.000
208L210ASN00.0370.00655.5910.0000.0000.0000.0000.0000.000
209L211ARG10.8470.92055.904-5.599-5.5990.0000.0000.0000.000
210L212ALA0-0.0020.01358.569-0.023-0.0230.0000.0000.0000.000
211L213ALA0-0.031-0.01159.0460.0020.0020.0000.0000.0000.000