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: YZ762

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 OptH
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 -2161754.228112
FMO2-HF: Nuclear repulsion 2079079.394629
FMO2-HF: Total energy -82674.833483
FMO2-MP2: Total energy -82915.303517


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.
-44.856-41.0566.259-3.764-6.2920.026
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 : -0.868 / q_NPA : -0.955
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].
3L3GLN00.0010.0013.3714.1376.0050.053-0.959-0.9610.002
4L4MET0-0.034-0.0085.176-4.298-4.264-0.001-0.002-0.0300.000
5L5THR00.004-0.0068.0720.4770.4770.0000.0000.0000.000
6L6GLN00.008-0.01311.1820.1800.1800.0000.0000.0000.000
7L7THR0-0.034-0.01714.438-0.026-0.0260.0000.0000.0000.000
8L8THR00.0120.01917.327-0.407-0.4070.0000.0000.0000.000
9L9SER00.0700.05117.8910.2580.2580.0000.0000.0000.000
10L10SER0-0.043-0.04519.368-0.186-0.1860.0000.0000.0000.000
11L11LEU0-0.0240.01023.033-0.019-0.0190.0000.0000.0000.000
12L12SER00.0350.01125.6080.0530.0530.0000.0000.0000.000
13L13ALA0-0.0320.00229.173-0.089-0.0890.0000.0000.0000.000
14L14SER00.0340.00831.305-0.050-0.0500.0000.0000.0000.000
15L15LEU00.002-0.00633.9340.1420.1420.0000.0000.0000.000
16L16GLY0-0.028-0.00435.007-0.220-0.2200.0000.0000.0000.000
17L17ASP-1-0.844-0.92832.0839.0719.0710.0000.0000.0000.000
18L18ARG10.9400.97529.273-9.919-9.9190.0000.0000.0000.000
19L19VAL0-0.0010.00825.2710.0110.0110.0000.0000.0000.000
20L20THR00.005-0.01422.899-0.069-0.0690.0000.0000.0000.000
21L21ILE0-0.0080.01818.4230.0870.0870.0000.0000.0000.000
22L22SER00.040-0.00318.2620.0040.0040.0000.0000.0000.000
23L23CYS0-0.083-0.01812.7550.7650.7650.0000.0000.0000.000
24L24ARG10.9280.96612.752-17.883-17.8830.0000.0000.0000.000
25L25ALA00.0160.0279.4021.6271.6270.0000.0000.0000.000
26L26SER0-0.003-0.0136.949-0.477-0.4770.0000.0000.0000.000
27L27GLN0-0.021-0.0186.516-0.429-0.4290.0000.0000.0000.000
28L28ASP-1-0.860-0.93610.11917.65217.6520.0000.0000.0000.000
29L29ILE0-0.011-0.0139.0101.1731.1730.0000.0000.0000.000
30L30SER0-0.023-0.01011.508-0.191-0.1910.0000.0000.0000.000
31L31THR00.0090.00014.869-0.440-0.4400.0000.0000.0000.000
32L32TYR0-0.008-0.00812.498-0.494-0.4940.0000.0000.0000.000
33L33LEU0-0.041-0.00612.1111.9891.9890.0000.0000.0000.000
34L34ASN0-0.017-0.02413.201-2.436-2.4360.0000.0000.0000.000
35L35TRP00.0460.02314.5211.1531.1530.0000.0000.0000.000
36L36TYR0-0.038-0.04413.448-1.183-1.1830.0000.0000.0000.000
37L37GLN00.0250.01217.924-0.336-0.3360.0000.0000.0000.000
38L38GLN0-0.036-0.01018.9510.2290.2290.0000.0000.0000.000
39L39LYS10.8900.94421.114-11.694-11.6940.0000.0000.0000.000
40L40PRO00.013-0.01724.4490.3880.3880.0000.0000.0000.000
41L41ASP-1-0.881-0.92326.46911.43611.4360.0000.0000.0000.000
42L42GLY00.0150.02122.5130.0670.0670.0000.0000.0000.000
43L43THR0-0.047-0.02221.9000.9020.9020.0000.0000.0000.000
44L44VAL00.0860.04117.5500.1200.1200.0000.0000.0000.000
45L45LYS10.9110.96120.979-12.220-12.2200.0000.0000.0000.000
46L46LEU0-0.011-0.00618.0100.3210.3210.0000.0000.0000.000
47L47LEU0-0.039-0.01019.768-0.765-0.7650.0000.0000.0000.000
48L48ILE0-0.005-0.01119.738-0.572-0.5720.0000.0000.0000.000
49L49PHE00.0330.00417.5860.8280.8280.0000.0000.0000.000
50L50TYR0-0.061-0.03317.077-0.653-0.6530.0000.0000.0000.000
51L51THR0-0.0070.00617.287-1.034-1.0340.0000.0000.0000.000
52L52SER00.0180.00518.704-0.375-0.3750.0000.0000.0000.000
53L53ARG10.8810.95321.721-12.609-12.6090.0000.0000.0000.000
54L54LEU00.0680.04622.3550.5250.5250.0000.0000.0000.000
55L55ARG10.8710.97022.886-12.950-12.9500.0000.0000.0000.000
56L56SER00.033-0.03225.053-0.140-0.1400.0000.0000.0000.000
57L57GLY00.0290.02127.9020.2220.2220.0000.0000.0000.000
58L58VAL0-0.057-0.01524.754-0.092-0.0920.0000.0000.0000.000
59L59PRO00.003-0.00528.122-0.125-0.1250.0000.0000.0000.000
60L60SER00.0690.02528.8390.3440.3440.0000.0000.0000.000
61L61ARG10.8600.92130.187-9.826-9.8260.0000.0000.0000.000
62L62PHE0-0.0500.01824.4600.1870.1870.0000.0000.0000.000
63L63SER00.0410.01825.698-0.141-0.1410.0000.0000.0000.000
64L64GLY00.028-0.00321.6040.2860.2860.0000.0000.0000.000
65L65SER0-0.0110.00621.776-0.212-0.2120.0000.0000.0000.000
66L66GLY00.055-0.00518.8610.6020.6020.0000.0000.0000.000
67L67SER0-0.018-0.01318.896-0.432-0.4320.0000.0000.0000.000
68L68GLY00.0110.03015.991-0.012-0.0120.0000.0000.0000.000
69L69THR0-0.0080.00712.4500.9600.9600.0000.0000.0000.000
70L70ASP-1-0.840-0.91914.08416.76416.7640.0000.0000.0000.000
71L71TYR00.001-0.00113.934-0.629-0.6290.0000.0000.0000.000
72L72SER0-0.027-0.02617.521-0.175-0.1750.0000.0000.0000.000
73L73LEU0-0.0020.02820.044-0.061-0.0610.0000.0000.0000.000
74L74THR0-0.043-0.03421.628-0.184-0.1840.0000.0000.0000.000
75L75ILE00.0010.01724.7930.1080.1080.0000.0000.0000.000
76L76SER0-0.051-0.05827.549-0.224-0.2240.0000.0000.0000.000
77L77ASN0-0.023-0.01630.953-0.094-0.0940.0000.0000.0000.000
78L78LEU0-0.0180.00428.6480.1400.1400.0000.0000.0000.000
79L79GLU-1-0.891-0.93431.8038.5798.5790.0000.0000.0000.000
80L80GLN0-0.063-0.04532.0370.0240.0240.0000.0000.0000.000
81L81GLU-1-0.914-0.97131.3739.2609.2600.0000.0000.0000.000
82L82ASP-1-0.820-0.90227.53410.85910.8590.0000.0000.0000.000
83L83ILE00.0110.03026.7440.4690.4690.0000.0000.0000.000
84L84ALA0-0.036-0.04623.564-0.038-0.0380.0000.0000.0000.000
85L85THR0-0.024-0.00418.420-0.173-0.1730.0000.0000.0000.000
86L86TYR00.005-0.00418.9440.2370.2370.0000.0000.0000.000
87L87PHE00.0200.00713.4060.3220.3220.0000.0000.0000.000
88L89GLN00.0610.0469.137-0.928-0.9280.0000.0000.0000.000
89L90GLN00.0410.0184.765-5.923-5.844-0.001-0.002-0.0760.000
90L91GLY0-0.020-0.0218.1092.3132.3130.0000.0000.0000.000
91L92SER0-0.047-0.0108.417-0.858-0.8580.0000.0000.0000.000
92L93ARG10.9420.9594.761-28.741-28.689-0.001-0.003-0.0470.000
93L94ILE0-0.0040.0206.034-0.030-0.0300.0000.0000.0000.000
94L95PRO00.0350.0052.288-6.086-4.3533.768-2.011-3.4910.021
95L96PRO0-0.003-0.0114.039-0.0150.2090.001-0.065-0.1600.000
96L97THR0-0.0320.0022.3310.8910.6522.441-0.720-1.4820.003
97L98PHE00.037-0.0035.374-4.932-4.883-0.001-0.002-0.0450.000
98L99GLY00.0280.0207.9552.1052.1050.0000.0000.0000.000
99L100GLY0-0.016-0.02110.3750.0520.0520.0000.0000.0000.000
100L101GLY0-0.0230.00512.695-0.918-0.9180.0000.0000.0000.000
101L102THR0-0.041-0.04715.9070.0520.0520.0000.0000.0000.000
102L103LYS10.9320.96819.122-12.774-12.7740.0000.0000.0000.000
103L104LEU00.0010.00422.183-0.034-0.0340.0000.0000.0000.000
104L105GLU-1-0.889-0.92125.23910.02010.0200.0000.0000.0000.000
105L106ILE0-0.0100.00828.688-0.063-0.0630.0000.0000.0000.000
106L107LEU00.0340.01631.960-0.126-0.1260.0000.0000.0000.000
107L108ARG10.8210.88134.413-8.061-8.0610.0000.0000.0000.000
108L109ALA00.0020.00637.964-0.034-0.0340.0000.0000.0000.000
109L110ASP-1-0.876-0.94740.8887.7767.7760.0000.0000.0000.000
110L111ALA0-0.0260.00141.556-0.183-0.1830.0000.0000.0000.000
111L112ALA00.0420.01342.2630.1630.1630.0000.0000.0000.000
112L113PRO0-0.0130.00542.162-0.031-0.0310.0000.0000.0000.000
113L114THR0-0.021-0.00843.968-0.249-0.2490.0000.0000.0000.000
114L115VAL0-0.011-0.01845.1960.1130.1130.0000.0000.0000.000
115L116SER0-0.036-0.02246.352-0.231-0.2310.0000.0000.0000.000
116L117ILE0-0.023-0.01246.8190.1570.1570.0000.0000.0000.000
117L118PHE0-0.019-0.01246.377-0.138-0.1380.0000.0000.0000.000
118L119PRO00.0260.00748.5020.1110.1110.0000.0000.0000.000
119L120PRO00.0130.01548.9230.0600.0600.0000.0000.0000.000
120L121SER00.0310.01848.870-0.132-0.1320.0000.0000.0000.000
121L122SER00.027-0.01051.0330.0220.0220.0000.0000.0000.000
122L123GLU-1-0.896-0.94450.1096.4846.4840.0000.0000.0000.000
123L124GLN0-0.0150.00844.773-0.028-0.0280.0000.0000.0000.000
124L125LEU00.0610.01349.395-0.005-0.0050.0000.0000.0000.000
125L126THR0-0.123-0.05152.132-0.016-0.0160.0000.0000.0000.000
126L127SER00.0390.00849.064-0.052-0.0520.0000.0000.0000.000
127L128GLY0-0.0210.00249.7870.0750.0750.0000.0000.0000.000
128L129GLY0-0.039-0.01346.871-0.024-0.0240.0000.0000.0000.000
129L130ALA00.0260.00747.490-0.127-0.1270.0000.0000.0000.000
130L131SER0-0.024-0.01543.2190.0990.0990.0000.0000.0000.000
131L132VAL0-0.0180.00145.712-0.108-0.1080.0000.0000.0000.000
132L133VAL00.0310.01642.1610.1730.1730.0000.0000.0000.000
133L134CYS0-0.051-0.01943.073-0.088-0.0880.0000.0000.0000.000
134L135PHE00.0140.02240.4560.2270.2270.0000.0000.0000.000
135L136LEU00.003-0.00340.714-0.245-0.2450.0000.0000.0000.000
136L137ASN00.009-0.02240.5130.3690.3690.0000.0000.0000.000
137L138ASN00.022-0.00540.088-0.016-0.0160.0000.0000.0000.000
138L139PHE0-0.0340.00136.700-0.172-0.1720.0000.0000.0000.000
139L140TYR00.021-0.00233.2180.1710.1710.0000.0000.0000.000
140L141PRO00.023-0.00235.497-0.245-0.2450.0000.0000.0000.000
141L142LYS10.9780.99229.098-10.583-10.5830.0000.0000.0000.000
142L143ASP-1-0.940-0.96633.1169.4379.4370.0000.0000.0000.000
143L144ILE0-0.0090.00435.435-0.296-0.2960.0000.0000.0000.000
144L145ASN0-0.045-0.02337.3200.0050.0050.0000.0000.0000.000
145L146VAL00.0310.01139.704-0.193-0.1930.0000.0000.0000.000
146L147LYS10.9160.97541.448-6.987-6.9870.0000.0000.0000.000
147L148TRP00.0420.01441.971-0.249-0.2490.0000.0000.0000.000
148L149LYS10.8600.93546.144-6.479-6.4790.0000.0000.0000.000
149L150ILE00.0070.00948.247-0.050-0.0500.0000.0000.0000.000
150L151ASP-1-0.790-0.90851.8025.7255.7250.0000.0000.0000.000
151L152GLY0-0.0040.01154.197-0.068-0.0680.0000.0000.0000.000
152L153SER0-0.063-0.02651.3750.0670.0670.0000.0000.0000.000
153L154GLU-1-0.842-0.95843.9427.2727.2720.0000.0000.0000.000
154L155ARG10.9040.96844.633-7.101-7.1010.0000.0000.0000.000
155L156GLN00.0270.00141.1720.2130.2130.0000.0000.0000.000
156L157ASN0-0.048-0.02840.3910.0290.0290.0000.0000.0000.000
157L158GLY00.0110.00839.580-0.145-0.1450.0000.0000.0000.000
158L159VAL00.0120.00338.599-0.162-0.1620.0000.0000.0000.000
159L160LEU0-0.0140.00834.3660.2620.2620.0000.0000.0000.000
160L161ASN00.0510.03434.742-0.433-0.4330.0000.0000.0000.000
161L162SER0-0.0050.00732.5510.4320.4320.0000.0000.0000.000
162L163TRP0-0.006-0.01431.529-0.165-0.1650.0000.0000.0000.000
163L164THR00.0110.00631.6910.1730.1730.0000.0000.0000.000
164L165ASP-1-0.931-0.97727.26911.78411.7840.0000.0000.0000.000
165L166GLN0-0.083-0.05429.9800.0180.0180.0000.0000.0000.000
166L167ASP-1-0.843-0.91531.7498.8148.8140.0000.0000.0000.000
167L168SER00.003-0.01932.540-0.013-0.0130.0000.0000.0000.000
168L169LYS10.9040.97433.706-8.123-8.1230.0000.0000.0000.000
169L170ASP-1-0.852-0.93537.3547.9017.9010.0000.0000.0000.000
170L171SER0-0.028-0.01934.666-0.050-0.0500.0000.0000.0000.000
171L172THR00.0210.04635.4720.1180.1180.0000.0000.0000.000
172L173TYR0-0.058-0.03530.7030.3850.3850.0000.0000.0000.000
173L174SER00.0450.01535.584-0.429-0.4290.0000.0000.0000.000
174L175MET0-0.0360.00035.7660.2250.2250.0000.0000.0000.000
175L176SER0-0.018-0.00537.069-0.272-0.2720.0000.0000.0000.000
176L177SER00.026-0.01037.5460.1870.1870.0000.0000.0000.000
177L178THR0-0.014-0.00939.357-0.256-0.2560.0000.0000.0000.000
178L179LEU00.0190.02640.5770.1430.1430.0000.0000.0000.000
179L180THR0-0.001-0.00941.468-0.107-0.1070.0000.0000.0000.000
180L181LEU0-0.045-0.03043.7980.0210.0210.0000.0000.0000.000
181L182THR00.0360.02546.7670.0450.0450.0000.0000.0000.000
182L183LYS10.9300.96449.096-6.074-6.0740.0000.0000.0000.000
183L184ASP-1-0.853-0.91852.2695.9205.9200.0000.0000.0000.000
184L185GLU-1-0.851-0.91749.5726.1976.1970.0000.0000.0000.000
185L186TYR0-0.002-0.01650.873-0.064-0.0640.0000.0000.0000.000
186L187GLU-1-0.926-0.98852.5875.6335.6330.0000.0000.0000.000
187L188ARG10.8210.93152.614-6.180-6.1800.0000.0000.0000.000
188L189HIS10.8150.90053.125-6.074-6.0740.0000.0000.0000.000
189L190ASN0-0.0060.01856.4810.0610.0610.0000.0000.0000.000
190L191SER0-0.0240.00355.905-0.036-0.0360.0000.0000.0000.000
191L192TYR0-0.026-0.00549.8700.1180.1180.0000.0000.0000.000
192L193THR0-0.021-0.01750.318-0.066-0.0660.0000.0000.0000.000
193L195GLU-1-0.896-0.97146.4146.5326.5320.0000.0000.0000.000
194L196ALA00.0430.02443.3720.1810.1810.0000.0000.0000.000
195L197THR0-0.0080.00343.019-0.241-0.2410.0000.0000.0000.000
196L198HIS00.025-0.01938.8540.0000.0000.0000.0000.0000.000
197L199LYS10.9520.99240.097-7.661-7.6610.0000.0000.0000.000
198L200THR0-0.039-0.03042.794-0.182-0.1820.0000.0000.0000.000
199L201SER00.0080.00845.335-0.199-0.1990.0000.0000.0000.000
200L202THR0-0.0210.00547.2070.0960.0960.0000.0000.0000.000
201L203SER0-0.038-0.02049.2270.0480.0480.0000.0000.0000.000
202L204PRO00.0290.00147.8410.0460.0460.0000.0000.0000.000
203L205ILE00.0040.02746.075-0.158-0.1580.0000.0000.0000.000
204L206VAL00.0210.00248.3610.1020.1020.0000.0000.0000.000
205L207LYS10.9190.97049.312-6.448-6.4480.0000.0000.0000.000
206L208SER0-0.016-0.02951.0790.0390.0390.0000.0000.0000.000
207L209PHE00.0100.02950.586-0.033-0.0330.0000.0000.0000.000
208L210ASN00.0710.02655.2490.0270.0270.0000.0000.0000.000
209L211ARG10.8640.88955.419-5.687-5.6870.0000.0000.0000.000
210L212ALA0-0.0060.02557.867-0.016-0.0160.0000.0000.0000.000
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