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: 49GGN

Calculation Name: 2J88-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J88

Chain ID: L

ChEMBL ID:

UniProt ID: Q08169

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 178
LigandCharge DLY=1,DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1712926.340353
FMO2-HF: Nuclear repulsion 1641559.718134
FMO2-HF: Total energy -71366.622219
FMO2-MP2: Total energy -71573.491538


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.
-43.763-40.8331.197-1.513-2.6130.007
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 : -0.943 / q_NPA : -0.972
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].
3L3GLN0-0.024-0.0182.414-9.353-6.7311.199-1.489-2.3310.007
4L4MET0-0.0020.0145.632-2.866-2.8660.0000.0000.0000.000
5L5THR00.003-0.0029.295-0.190-0.1900.0000.0000.0000.000
6L6GLN0-0.0060.00612.145-0.034-0.0340.0000.0000.0000.000
7L7SER0-0.061-0.00215.521-0.233-0.2330.0000.0000.0000.000
8L8PRO00.0450.00718.710-0.041-0.0410.0000.0000.0000.000
9L9ALA00.0740.02219.6750.2010.2010.0000.0000.0000.000
10L10SER0-0.005-0.00520.7230.1430.1430.0000.0000.0000.000
11L11LEU0-0.028-0.01424.4070.0090.0090.0000.0000.0000.000
12L12SER00.0010.00026.945-0.143-0.1430.0000.0000.0000.000
13L13ALA0-0.0100.00330.690-0.046-0.0460.0000.0000.0000.000
14L14SER00.0600.04033.061-0.111-0.1110.0000.0000.0000.000
15L15VAL0-0.005-0.01235.5930.1580.1580.0000.0000.0000.000
16L16GLY0-0.0070.00136.849-0.205-0.2050.0000.0000.0000.000
17L17GLU-1-0.940-0.96534.1958.6098.6090.0000.0000.0000.000
18L18THR0-0.036-0.01532.4580.2090.2090.0000.0000.0000.000
19L19VAL00.0280.01227.8090.0120.0120.0000.0000.0000.000
20L20THR0-0.019-0.03124.252-0.176-0.1760.0000.0000.0000.000
21L21ILE00.0110.03620.9750.0780.0780.0000.0000.0000.000
22L22THR0-0.015-0.01018.221-0.221-0.2210.0000.0000.0000.000
23L23CYS0-0.056-0.02314.2530.4140.4140.0000.0000.0000.000
24L24ARG10.8950.94414.027-15.853-15.8530.0000.0000.0000.000
25L25ALA00.0290.0169.8640.9170.9170.0000.0000.0000.000
26L26SER0-0.025-0.0176.3970.4090.4090.0000.0000.0000.000
27L27GLU-1-0.875-0.9274.86036.40736.517-0.001-0.007-0.1020.000
28L28ASN0-0.057-0.0388.529-1.364-1.3640.0000.0000.0000.000
29L29ILE00.0380.0249.0511.4811.4810.0000.0000.0000.000
30L30TYR00.006-0.00511.653-0.874-0.8740.0000.0000.0000.000
31L31SER00.005-0.00315.393-0.441-0.4410.0000.0000.0000.000
32L32TYR00.0000.00612.514-0.673-0.6730.0000.0000.0000.000
33L33LEU00.001-0.01112.7881.5851.5850.0000.0000.0000.000
34L34THR0-0.059-0.01414.978-1.336-1.3360.0000.0000.0000.000
35L35TRP00.0200.00316.9100.7860.7860.0000.0000.0000.000
36L36TYR00.023-0.00317.038-0.854-0.8540.0000.0000.0000.000
37L37GLN00.0330.01920.905-0.069-0.0690.0000.0000.0000.000
38L38GLN0-0.014-0.02621.8090.4070.4070.0000.0000.0000.000
39L39LYS10.8760.94524.246-9.995-9.9950.0000.0000.0000.000
40L40GLN00.1030.05427.2930.4250.4250.0000.0000.0000.000
41L42LYS10.9120.95528.237-10.630-10.6300.0000.0000.0000.000
42L43SER0-0.020-0.01724.3610.2300.2300.0000.0000.0000.000
43L44PRO0-0.018-0.02120.303-0.369-0.3690.0000.0000.0000.000
44L45GLN00.0850.05723.030-0.194-0.1940.0000.0000.0000.000
45L46LEU00.0200.01020.7810.2400.2400.0000.0000.0000.000
46L47LEU0-0.035-0.00222.651-0.529-0.5290.0000.0000.0000.000
47L48VAL0-0.003-0.00121.560-0.424-0.4240.0000.0000.0000.000
48L49TYR00.0610.02719.9900.9890.9890.0000.0000.0000.000
49L50ASN00.0260.00119.0710.0990.0990.0000.0000.0000.000
50L51ALA00.0000.01418.179-0.407-0.4070.0000.0000.0000.000
51L52LYS10.8730.92519.631-12.779-12.7790.0000.0000.0000.000
52L53THR0-0.0230.01023.206-0.615-0.6150.0000.0000.0000.000
53L54LEU0-0.021-0.01024.4440.4490.4490.0000.0000.0000.000
54L55ALA0-0.0080.00424.943-0.092-0.0920.0000.0000.0000.000
55L56GLU-1-0.870-0.94826.80510.57110.5710.0000.0000.0000.000
56L57GLY0-0.051-0.01730.1260.0300.0300.0000.0000.0000.000
57L58VAL0-0.002-0.00327.8640.0800.0800.0000.0000.0000.000
58L59PRO0-0.031-0.02031.158-0.147-0.1470.0000.0000.0000.000
59L60SER00.0640.01631.4850.2620.2620.0000.0000.0000.000
60L61ARG10.8880.96531.719-8.980-8.9800.0000.0000.0000.000
61L62PHE00.0050.00527.0100.1340.1340.0000.0000.0000.000
62L63SER00.0190.00827.188-0.163-0.1630.0000.0000.0000.000
63L64GLY00.0360.03423.0870.2510.2510.0000.0000.0000.000
64L65SER0-0.032-0.02222.439-0.339-0.3390.0000.0000.0000.000
65L66GLY00.0240.01220.7580.5480.5480.0000.0000.0000.000
66L67SER0-0.015-0.03418.2870.1670.1670.0000.0000.0000.000
67L68GLY00.0170.01615.189-0.268-0.2680.0000.0000.0000.000
68L69THR00.0520.02112.6480.8570.8570.0000.0000.0000.000
69L70GLN00.0330.02314.2890.6650.6650.0000.0000.0000.000
70L71PHE00.0140.01813.788-0.839-0.8390.0000.0000.0000.000
71L72SER0-0.056-0.03618.5620.0460.0460.0000.0000.0000.000
72L73LEU00.0300.02321.380-0.081-0.0810.0000.0000.0000.000
73L74LYS10.8510.93123.422-10.210-10.2100.0000.0000.0000.000
74L75ILE00.0190.01526.225-0.060-0.0600.0000.0000.0000.000
75L76SER0-0.025-0.02229.495-0.210-0.2100.0000.0000.0000.000
76L77SER0-0.016-0.01233.1790.0200.0200.0000.0000.0000.000
77L78LEU00.0000.00430.2690.0120.0120.0000.0000.0000.000
78L79GLN00.003-0.00834.201-0.455-0.4550.0000.0000.0000.000
79L80PRO00.0400.00734.2870.2540.2540.0000.0000.0000.000
80L81DGL-1-0.950-0.97033.9118.8198.8190.0000.0000.0000.000
81L82ASP-1-0.766-0.87430.2329.8309.8300.0000.0000.0000.000
82L83PHE0-0.0050.02828.9340.4040.4040.0000.0000.0000.000
83L84GLY00.004-0.00327.269-0.139-0.1390.0000.0000.0000.000
84L85ASN00.0130.02621.705-0.284-0.2840.0000.0000.0000.000
85L86TYR0-0.035-0.04121.257-0.067-0.0670.0000.0000.0000.000
86L87TYR00.0030.00816.0010.4390.4390.0000.0000.0000.000
87L89GLN0-0.018-0.02712.172-0.364-0.3640.0000.0000.0000.000
88L90HIS00.0400.0295.800-4.635-4.6350.0000.0000.0000.000
89L91HIS0-0.065-0.05410.2290.0310.0310.0000.0000.0000.000
90L92TYR00.0020.0197.726-1.050-1.0500.0000.0000.0000.000
91L93GLY00.0200.0137.908-0.501-0.5010.0000.0000.0000.000
92L94THR0-0.0160.0104.058-4.112-3.914-0.001-0.017-0.1800.000
93L96ARG10.9770.9626.940-24.049-24.0490.0000.0000.0000.000
94L97THR00.0150.0235.518-3.275-3.2750.0000.0000.0000.000
95L98PHE00.022-0.0038.621-1.398-1.3980.0000.0000.0000.000
96L99GLY00.0530.0399.7701.8501.8500.0000.0000.0000.000
97L100GLY0-0.021-0.02512.154-0.333-0.3330.0000.0000.0000.000
98L101GLY0-0.006-0.01014.196-0.764-0.7640.0000.0000.0000.000
99L102THR0-0.067-0.03917.3450.1820.1820.0000.0000.0000.000
100L103ARG10.8030.88420.749-11.605-11.6050.0000.0000.0000.000
101L104LEU0-0.041-0.03124.162-0.147-0.1470.0000.0000.0000.000
102L105GLU-1-0.839-0.90526.97710.36310.3630.0000.0000.0000.000
103L106ILE00.0310.02629.987-0.101-0.1010.0000.0000.0000.000
104L107LYS10.8980.95433.635-8.332-8.3320.0000.0000.0000.000
105L108ARG10.9100.95735.499-7.820-7.8200.0000.0000.0000.000
106L109ALA0-0.004-0.01038.5060.0480.0480.0000.0000.0000.000
107L110ASP-1-0.883-0.93938.5408.1238.1230.0000.0000.0000.000
108L111ALA0-0.047-0.01940.162-0.227-0.2270.0000.0000.0000.000
109L112ALA00.0290.01340.4510.1880.1880.0000.0000.0000.000
110L113PRO00.0000.01439.657-0.040-0.0400.0000.0000.0000.000
111L114THR0-0.022-0.00541.710-0.171-0.1710.0000.0000.0000.000
112L115VAL00.003-0.00942.7090.1300.1300.0000.0000.0000.000
113L116SER0-0.0140.00044.221-0.227-0.2270.0000.0000.0000.000
114L117ILE00.0140.01444.6430.1020.1020.0000.0000.0000.000
115L132DVA00.0120.00543.804-0.029-0.0290.0000.0000.0000.000
116L133VAL0-0.006-0.00140.6910.2250.2250.0000.0000.0000.000
117L134CYS0-0.039-0.01040.2840.0090.0090.0000.0000.0000.000
118L135PHE0-0.022-0.01639.8040.2530.2530.0000.0000.0000.000
119L136LEU00.0150.00137.567-0.188-0.1880.0000.0000.0000.000
120L137ASN00.031-0.00438.5700.4140.4140.0000.0000.0000.000
121L138ASN0-0.031-0.03639.433-0.152-0.1520.0000.0000.0000.000
122L139PHE0-0.0280.00134.146-0.163-0.1630.0000.0000.0000.000
123L140TYR0-0.015-0.01433.4570.2140.2140.0000.0000.0000.000
124L141PRO00.0360.00333.200-0.204-0.2040.0000.0000.0000.000
125L142LYS10.8930.91227.894-10.660-10.6600.0000.0000.0000.000
126L143ASP-1-0.906-0.94729.63110.17510.1750.0000.0000.0000.000
127L144ILE0-0.037-0.01131.803-0.357-0.3570.0000.0000.0000.000
128L145ASN0-0.021-0.01732.5630.3980.3980.0000.0000.0000.000
129L146VAL00.0350.01234.809-0.278-0.2780.0000.0000.0000.000
130L147LYS10.8440.93236.297-7.759-7.7590.0000.0000.0000.000
131L148TRP00.0430.01738.260-0.276-0.2760.0000.0000.0000.000
132L149LYS10.8880.94141.429-7.025-7.0250.0000.0000.0000.000
133L159VAL0-0.026-0.02534.379-0.055-0.0550.0000.0000.0000.000
134L160LEU0-0.0210.01330.5160.3300.3300.0000.0000.0000.000
135L161ASN00.0130.00530.877-0.566-0.5660.0000.0000.0000.000
136L162SER0-0.0070.00330.3890.4600.4600.0000.0000.0000.000
137L163TRP00.0460.00527.239-0.171-0.1710.0000.0000.0000.000
138L164THR0-0.0010.01130.5520.1130.1130.0000.0000.0000.000
139L165ASP-1-0.843-0.91428.08911.17611.1760.0000.0000.0000.000
140L166GLN0-0.058-0.04230.556-0.112-0.1120.0000.0000.0000.000
141L167ASP-1-0.766-0.85932.6898.1688.1680.0000.0000.0000.000
142L168SER0-0.049-0.01434.771-0.110-0.1100.0000.0000.0000.000
143L169LYS10.8110.88936.600-7.983-7.9830.0000.0000.0000.000
144L170ASP-1-0.769-0.87740.0657.6177.6170.0000.0000.0000.000
145L171SER0-0.050-0.03736.489-0.013-0.0130.0000.0000.0000.000
146L172THR0-0.094-0.05336.1970.2000.2000.0000.0000.0000.000
147L173TYR00.0210.00930.2260.2500.2500.0000.0000.0000.000
148L174SER00.0480.03634.886-0.371-0.3710.0000.0000.0000.000
149L175MET0-0.058-0.00733.7670.3530.3530.0000.0000.0000.000
150L176SER0-0.028-0.00134.965-0.232-0.2320.0000.0000.0000.000
151L177SER00.035-0.01635.1960.2100.2100.0000.0000.0000.000
152L178THR0-0.006-0.00436.767-0.339-0.3390.0000.0000.0000.000
153L179LEU0-0.0090.00437.5420.2280.2280.0000.0000.0000.000
154L180THR0-0.018-0.02438.666-0.229-0.2290.0000.0000.0000.000
155L181LEU00.0080.00740.7070.0830.0830.0000.0000.0000.000
156L182THR0-0.059-0.04443.376-0.165-0.1650.0000.0000.0000.000
157L183LYS10.8010.88945.606-6.108-6.1080.0000.0000.0000.000
158L184ASP-1-0.904-0.95548.7966.3046.3040.0000.0000.0000.000
159L185GLU-1-0.819-0.88843.4527.2967.2960.0000.0000.0000.000
160L186TYR0-0.047-0.01847.217-0.138-0.1380.0000.0000.0000.000
161L187GLU-1-0.819-0.90548.5795.7955.7950.0000.0000.0000.000
162L188ARG10.8970.92652.326-5.896-5.8960.0000.0000.0000.000
163L189HIS0-0.0150.00651.663-0.021-0.0210.0000.0000.0000.000
164L190ASN00.0460.04547.1130.0970.0970.0000.0000.0000.000
165L191SER0-0.033-0.04544.399-0.032-0.0320.0000.0000.0000.000
166L192TYR00.0300.02245.7410.0080.0080.0000.0000.0000.000
167L193THR0-0.028-0.02045.936-0.122-0.1220.0000.0000.0000.000
168L195GLU-1-0.811-0.88041.8227.2787.2780.0000.0000.0000.000
169L196ALA00.0360.00339.3310.2090.2090.0000.0000.0000.000
170L197THR0-0.029-0.01337.540-0.156-0.1560.0000.0000.0000.000
171L198HIS00.0790.03136.5670.0300.0300.0000.0000.0000.000
172L199DLY10.8850.94537.208-7.715-7.7150.0000.0000.0000.000
173L200THR00.0420.03438.415-0.132-0.1320.0000.0000.0000.000
174L201SER0-0.028-0.02141.962-0.207-0.2070.0000.0000.0000.000
175L202THR00.000-0.01242.1760.1460.1460.0000.0000.0000.000
176L203DSN0-0.0040.00842.9240.0570.0570.0000.0000.0000.000
177L204PRO0-0.052-0.02642.0840.0970.0970.0000.0000.0000.000
178L205ILE00.0180.02643.343-0.145-0.1450.0000.0000.0000.000