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: JLZ89

Calculation Name: 4ALN-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ALN

Chain ID: L

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-20

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2088958.783684
FMO2-HF: Nuclear repulsion 2015641.892301
FMO2-HF: Total energy -73316.891384
FMO2-MP2: Total energy -73533.799271


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:3:ASN)


Summations of interaction energy for fragment #1(L:3:ASN)
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.
-20.829-17.53711.761-7.585-7.467-0.043
Interaction energy analysis for fragmet #1(L:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.016
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].
3L5GLU-1-0.822-0.9001.869-16.375-14.69510.554-6.847-5.387-0.042
4L6ASN0-0.108-0.0614.7950.5670.619-0.001-0.004-0.0460.000
5L7LYS10.8890.9716.2292.2882.2880.0000.0000.0000.000
6L8THR00.005-0.0088.561-0.047-0.0470.0000.0000.0000.000
7L9TYR0-0.0290.0046.642-0.070-0.0700.0000.0000.0000.000
8L10VAL00.0390.03012.2290.0480.0480.0000.0000.0000.000
9L11ILE0-0.045-0.02112.1950.0120.0120.0000.0000.0000.000
10L12MET00.0190.01216.2310.0630.0630.0000.0000.0000.000
11L13GLY00.0580.02519.634-0.006-0.0060.0000.0000.0000.000
12L14ILE0-0.090-0.03817.2250.0270.0270.0000.0000.0000.000
13L15ALA0-0.039-0.02121.4820.0320.0320.0000.0000.0000.000
14L16ASN00.036-0.00123.8770.0060.0060.0000.0000.0000.000
15L17LYS11.0271.00621.6900.2760.2760.0000.0000.0000.000
16L18ARG10.8940.94920.9140.2720.2720.0000.0000.0000.000
17L19SER00.0620.05720.7780.0090.0090.0000.0000.0000.000
18L20ILE00.1010.03617.082-0.030-0.0300.0000.0000.0000.000
19L21ALA00.0600.03316.475-0.070-0.0700.0000.0000.0000.000
20L22PHE00.0230.00515.756-0.086-0.0860.0000.0000.0000.000
21L23GLY0-0.042-0.02215.066-0.059-0.0590.0000.0000.0000.000
22L24VAL00.012-0.00611.501-0.114-0.1140.0000.0000.0000.000
23L25ALA00.0240.01511.015-0.240-0.2400.0000.0000.0000.000
24L26LYS10.9250.97311.4760.4640.4640.0000.0000.0000.000
25L27VAL0-0.0010.0096.796-0.017-0.0170.0000.0000.0000.000
26L28LEU00.0230.0086.872-0.479-0.4790.0000.0000.0000.000
27L29ASP-1-0.807-0.8927.309-1.610-1.6100.0000.0000.0000.000
28L30GLN0-0.065-0.0357.994-0.279-0.2790.0000.0000.0000.000
29L31LEU0-0.069-0.0322.330-1.342-0.2241.205-0.565-1.7580.000
30L32GLY00.000-0.0013.698-2.097-1.7960.004-0.164-0.142-0.001
31L33ALA0-0.0110.0085.974-0.037-0.0370.0000.0000.0000.000
32L34LYS10.9210.9667.7181.6001.6000.0000.0000.0000.000
33L35LEU0-0.031-0.02510.2460.0420.0420.0000.0000.0000.000
34L36VAL00.0530.03113.4140.1310.1310.0000.0000.0000.000
35L37PHE0-0.014-0.01214.975-0.028-0.0280.0000.0000.0000.000
36L38THR00.0550.02119.0430.0400.0400.0000.0000.0000.000
37L39TYR0-0.068-0.01922.211-0.006-0.0060.0000.0000.0000.000
38L40ARG10.9981.00425.0670.2920.2920.0000.0000.0000.000
39L41LYS10.9520.96128.4230.2480.2480.0000.0000.0000.000
40L42GLU-1-0.731-0.88429.912-0.306-0.3060.0000.0000.0000.000
41L43ARG10.8630.91831.3200.2110.2110.0000.0000.0000.000
42L44SER0-0.041-0.02027.1960.0000.0000.0000.0000.0000.000
43L45ARG11.0011.03026.4700.3660.3660.0000.0000.0000.000
44L46LYS10.9720.96926.3840.2370.2370.0000.0000.0000.000
45L47GLU-1-0.969-0.98625.084-0.350-0.3500.0000.0000.0000.000
46L48LEU00.0370.01120.618-0.015-0.0150.0000.0000.0000.000
47L49GLU-1-0.904-0.94522.167-0.399-0.3990.0000.0000.0000.000
48L50LYS10.9390.97223.4940.2850.2850.0000.0000.0000.000
49L51LEU0-0.078-0.03720.1750.0010.0010.0000.0000.0000.000
50L52LEU0-0.027-0.02418.054-0.032-0.0320.0000.0000.0000.000
51L53GLU-1-0.936-0.95019.035-0.384-0.3840.0000.0000.0000.000
52L54GLN0-0.134-0.07118.494-0.004-0.0040.0000.0000.0000.000
53L55LEU0-0.067-0.02014.318-0.022-0.0220.0000.0000.0000.000
54L56ASN0-0.0040.01711.7750.2160.2160.0000.0000.0000.000
55L57GLN0-0.013-0.04011.201-0.109-0.1090.0000.0000.0000.000
56L58PRO0-0.053-0.01212.8840.1100.1100.0000.0000.0000.000
57L59GLU-1-0.926-0.96115.886-0.549-0.5490.0000.0000.0000.000
58L60ALA0-0.025-0.01917.810-0.068-0.0680.0000.0000.0000.000
59L61HIS00.0510.03517.0840.0960.0960.0000.0000.0000.000
60L62LEU0-0.079-0.04420.154-0.024-0.0240.0000.0000.0000.000
61L63TYR0-0.005-0.04321.0310.0170.0170.0000.0000.0000.000
62L64GLN0-0.098-0.04524.547-0.009-0.0090.0000.0000.0000.000
63L65ILE00.0660.03823.6470.0050.0050.0000.0000.0000.000
64L66ASP-1-0.943-0.97727.002-0.279-0.2790.0000.0000.0000.000
65L67VAL0-0.016-0.02925.1530.0120.0120.0000.0000.0000.000
66L68GLN0-0.089-0.02828.2780.0220.0220.0000.0000.0000.000
67L69SER0-0.034-0.01631.3790.0210.0210.0000.0000.0000.000
68L70ASP-1-0.858-0.93431.419-0.226-0.2260.0000.0000.0000.000
69L71GLU-1-0.973-0.99131.134-0.223-0.2230.0000.0000.0000.000
70L72GLU-1-0.843-0.92029.896-0.294-0.2940.0000.0000.0000.000
71L73VAL0-0.038-0.01925.585-0.027-0.0270.0000.0000.0000.000
72L74ILE00.0090.01826.551-0.022-0.0220.0000.0000.0000.000
73L75ASN0-0.018-0.01127.674-0.010-0.0100.0000.0000.0000.000
74L76GLY00.009-0.00826.090-0.015-0.0150.0000.0000.0000.000
75L77PHE00.010-0.01619.726-0.043-0.0430.0000.0000.0000.000
76L78GLU-1-0.883-0.92523.476-0.302-0.3020.0000.0000.0000.000
77L79GLN0-0.064-0.02325.5780.0170.0170.0000.0000.0000.000
78L80ILE00.0030.02519.207-0.020-0.0200.0000.0000.0000.000
79L81GLY00.0330.00821.483-0.031-0.0310.0000.0000.0000.000
80L82LYS10.8100.90322.6270.2840.2840.0000.0000.0000.000
81L83ASP-1-0.866-0.92022.798-0.424-0.4240.0000.0000.0000.000
82L84VAL0-0.091-0.04216.838-0.037-0.0370.0000.0000.0000.000
83L85GLY0-0.027-0.00718.200-0.049-0.0490.0000.0000.0000.000
84L86ASN0-0.048-0.04617.4270.0090.0090.0000.0000.0000.000
85L87ILE0-0.020-0.01014.593-0.093-0.0930.0000.0000.0000.000
86L88ASP-1-0.773-0.88410.469-1.397-1.3970.0000.0000.0000.000
87L89GLY00.023-0.04512.3030.0780.0780.0000.0000.0000.000
88L90VAL0-0.032-0.01013.167-0.033-0.0330.0000.0000.0000.000
89L91TYR00.020-0.00313.5980.0450.0450.0000.0000.0000.000
90L92HIS00.015-0.01615.5490.0030.0030.0000.0000.0000.000
91L93SER0-0.028-0.00618.7410.0470.0470.0000.0000.0000.000
92L94ILE0-0.011-0.00920.4700.0220.0220.0000.0000.0000.000
93L108GLU-1-0.919-0.97637.145-0.140-0.1400.0000.0000.0000.000
94L109THR0-0.021-0.01940.8200.0010.0010.0000.0000.0000.000
95L110SER00.0030.02643.1660.0030.0030.0000.0000.0000.000
96L111ARG11.0240.99842.5950.0960.0960.0000.0000.0000.000
97L112GLU-1-0.878-0.94741.493-0.120-0.1200.0000.0000.0000.000
98L113GLY00.0230.01339.322-0.008-0.0080.0000.0000.0000.000
99L114PHE0-0.008-0.01237.697-0.010-0.0100.0000.0000.0000.000
100L115LEU00.014-0.00836.657-0.007-0.0070.0000.0000.0000.000
101L116LEU00.0240.02935.349-0.008-0.0080.0000.0000.0000.000
102L117ALA0-0.014-0.00833.367-0.014-0.0140.0000.0000.0000.000
103L118GLN0-0.014-0.00531.914-0.019-0.0190.0000.0000.0000.000
104L119ASP-1-0.862-0.92531.530-0.223-0.2230.0000.0000.0000.000
105L120ILE00.0060.00428.729-0.017-0.0170.0000.0000.0000.000
106L121SER0-0.124-0.03527.669-0.026-0.0260.0000.0000.0000.000
107L122SER00.004-0.00826.693-0.021-0.0210.0000.0000.0000.000
108L123TYR00.0510.02527.537-0.011-0.0110.0000.0000.0000.000
109L124SER00.011-0.03526.271-0.014-0.0140.0000.0000.0000.000
110L125LEU00.0200.02321.194-0.022-0.0220.0000.0000.0000.000
111L126THR00.0400.03624.416-0.011-0.0110.0000.0000.0000.000
112L127ILE0-0.0190.00226.422-0.003-0.0030.0000.0000.0000.000
113L128VAL00.0360.01021.099-0.010-0.0100.0000.0000.0000.000
114L129ALA0-0.026-0.01721.659-0.029-0.0290.0000.0000.0000.000
115L130HIS0-0.057-0.02222.7270.0040.0040.0000.0000.0000.000
116L131GLU-1-0.871-0.95624.863-0.282-0.2820.0000.0000.0000.000
117L132ALA00.0300.00819.166-0.013-0.0130.0000.0000.0000.000
118L133LYS10.9150.97020.5220.2040.2040.0000.0000.0000.000
119L134LYS10.8460.93021.8920.2890.2890.0000.0000.0000.000
120L135LEU0-0.081-0.02619.1400.0090.0090.0000.0000.0000.000
121L136MET0-0.0290.01715.244-0.061-0.0610.0000.0000.0000.000
122L137PRO00.0080.00918.5200.0500.0500.0000.0000.0000.000
123L138GLU-1-0.975-0.98816.919-0.301-0.3010.0000.0000.0000.000
124L139GLY00.0170.01816.6510.0350.0350.0000.0000.0000.000
125L140GLY00.011-0.00513.364-0.091-0.0910.0000.0000.0000.000
126L141SER0-0.122-0.05111.9060.1290.1290.0000.0000.0000.000
127L142ILE00.0310.01113.900-0.101-0.1010.0000.0000.0000.000
128L143VAL00.0110.00412.6800.0510.0510.0000.0000.0000.000
129L144ALA00.0170.02616.031-0.022-0.0220.0000.0000.0000.000
130L145THR0-0.054-0.02116.794-0.009-0.0090.0000.0000.0000.000
131L146THR0-0.040-0.01719.0590.0270.0270.0000.0000.0000.000
132L159VAL00.0320.01735.9560.0000.0000.0000.0000.0000.000
133L160MET00.0710.01631.680-0.007-0.0070.0000.0000.0000.000
134L161GLY00.0130.01631.585-0.009-0.0090.0000.0000.0000.000
135L162VAL00.0020.00231.645-0.004-0.0040.0000.0000.0000.000
136L163ALA00.003-0.00931.0920.0000.0000.0000.0000.0000.000
137L164LYS10.9330.96926.4530.2440.2440.0000.0000.0000.000
138L165ALA00.0440.03527.803-0.007-0.0070.0000.0000.0000.000
139L166SER0-0.020-0.02129.273-0.002-0.0020.0000.0000.0000.000
140L167LEU00.0230.02323.2240.0000.0000.0000.0000.0000.000
141L168GLU-1-0.936-0.96924.491-0.191-0.1910.0000.0000.0000.000
142L169ALA0-0.049-0.02925.3790.0040.0040.0000.0000.0000.000
143L170ASN0-0.011-0.02426.2450.0120.0120.0000.0000.0000.000
144L171VAL0-0.007-0.00320.791-0.002-0.0020.0000.0000.0000.000
145L172LYS10.9520.98923.2850.1430.1430.0000.0000.0000.000
146L173TYR0-0.018-0.02624.9750.0130.0130.0000.0000.0000.000
147L174LEU00.0390.03323.5160.0050.0050.0000.0000.0000.000
148L175ALA0-0.023-0.00721.171-0.001-0.0010.0000.0000.0000.000
149L176LEU0-0.119-0.05922.4150.0190.0190.0000.0000.0000.000
150L177ASP-1-0.965-1.00225.617-0.159-0.1590.0000.0000.0000.000
151L178LEU00.0100.00821.545-0.002-0.0020.0000.0000.0000.000
152L179GLY00.0310.03221.519-0.008-0.0080.0000.0000.0000.000
153L180PRO0-0.066-0.04421.9190.0140.0140.0000.0000.0000.000
154L181ASP-1-0.907-0.94722.477-0.185-0.1850.0000.0000.0000.000
155L182ASN0-0.074-0.03815.9970.0020.0020.0000.0000.0000.000
156L183ILE0-0.0070.00317.289-0.060-0.0600.0000.0000.0000.000
157L184ARG10.8110.93210.9730.4180.4180.0000.0000.0000.000
158L185VAL00.0270.02216.627-0.081-0.0810.0000.0000.0000.000
159L186ASN00.0340.02315.3500.1190.1190.0000.0000.0000.000
160L187ALA0-0.030-0.02117.592-0.052-0.0520.0000.0000.0000.000
161L188ILE0-0.0120.00813.185-0.005-0.0050.0000.0000.0000.000
162L189SER00.0170.00317.6010.0030.0030.0000.0000.0000.000
163L222ASP-1-0.814-0.92717.008-0.421-0.4210.0000.0000.0000.000
164L223GLN0-0.077-0.05416.558-0.044-0.0440.0000.0000.0000.000
165L224VAL00.0120.01311.918-0.101-0.1010.0000.0000.0000.000
166L225GLU-1-0.940-0.96612.023-0.509-0.5090.0000.0000.0000.000
167L226VAL00.0280.01412.152-0.093-0.0930.0000.0000.0000.000
168L227GLY00.0560.02411.162-0.097-0.0970.0000.0000.0000.000
169L228LYS10.9200.9777.8910.3030.3030.0000.0000.0000.000
170L229THR00.0100.0157.841-0.329-0.3290.0000.0000.0000.000
171L230ALA00.011-0.0129.7680.0000.0000.0000.0000.0000.000
172L231ALA00.0210.0115.025-0.063-0.0630.0000.0000.0000.000
173L232TYR0-0.026-0.0046.355-0.025-0.0250.0000.0000.0000.000
174L233LEU0-0.0210.0167.2120.3240.3240.0000.0000.0000.000
175L234LEU0-0.011-0.0028.4110.1940.1940.0000.0000.0000.000
176L235SER0-0.034-0.0105.0680.2050.2050.0000.0000.0000.000
177L236ASP-1-0.900-0.9666.5971.1161.1160.0000.0000.0000.000
178L237LEU00.013-0.0074.418-0.0210.120-0.001-0.005-0.1340.000
179L238SER0-0.053-0.0487.2130.0390.0390.0000.0000.0000.000
180L239SER00.0060.00310.495-0.151-0.1510.0000.0000.0000.000
181L240GLY0-0.015-0.00112.509-0.030-0.0300.0000.0000.0000.000
182L241VAL0-0.090-0.03313.892-0.014-0.0140.0000.0000.0000.000
183L242THR00.0700.00815.653-0.092-0.0920.0000.0000.0000.000
184L243GLY00.008-0.00818.3200.0370.0370.0000.0000.0000.000
185L244GLU-1-0.979-0.98017.270-0.080-0.0800.0000.0000.0000.000
186L245ASN0-0.028-0.02118.507-0.085-0.0850.0000.0000.0000.000
187L246ILE00.0140.01113.9470.0290.0290.0000.0000.0000.000
188L247HIS00.0160.00017.789-0.051-0.0510.0000.0000.0000.000
189L248VAL0-0.025-0.00614.7910.0010.0010.0000.0000.0000.000
190L249ASP-1-0.846-0.94417.820-0.213-0.2130.0000.0000.0000.000
191L250SER0-0.063-0.03919.9610.0270.0270.0000.0000.0000.000
192L251GLY0-0.0090.00921.2410.0280.0280.0000.0000.0000.000
193L252PHE0-0.052-0.01022.7500.0280.0280.0000.0000.0000.000