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: V5Y11

Calculation Name: 1DLP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DLP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZP48

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2785790.039353
FMO2-HF: Nuclear repulsion 2696022.776048
FMO2-HF: Total energy -89767.263305
FMO2-MP2: Total energy -90028.83012


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(A:1:ASN)


Summations of interaction energy for fragment #1(A:1: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.
-19.678-11.386.209-5.566-8.938-0.008
Interaction energy analysis for fragmet #1(A:1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : -0.003
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].
3A3ILE0-0.010-0.0022.569-6.126-2.0612.009-2.528-3.5460.014
4A4LEU0-0.018-0.0034.547-2.003-1.927-0.001-0.027-0.0480.000
5A5PHE00.0400.0093.6960.3260.5260.000-0.034-0.1660.000
6A6GLY00.0290.0078.699-0.107-0.1070.0000.0000.0000.000
7A7LEU0-0.012-0.01412.237-0.102-0.1020.0000.0000.0000.000
8A8SER0-0.050-0.01214.597-0.057-0.0570.0000.0000.0000.000
9A9HIS00.0460.01013.830-0.013-0.0130.0000.0000.0000.000
10A10GLU-1-0.799-0.87011.509-0.321-0.3210.0000.0000.0000.000
11A11GLY0-0.021-0.00210.951-0.030-0.0300.0000.0000.0000.000
12A12SER0-0.051-0.0496.955-0.260-0.2600.0000.0000.0000.000
13A13HIS0-0.018-0.0015.8520.4320.4320.0000.0000.0000.000
14A14PRO00.030-0.0033.849-2.020-1.6870.002-0.081-0.2540.000
15A15GLN0-0.0010.0156.8440.2590.2590.0000.0000.0000.000
16A16THR0-0.103-0.0669.7990.1590.1590.0000.0000.0000.000
17A17LEU0-0.0110.0197.567-0.136-0.1360.0000.0000.0000.000
18A18HIS00.0740.00410.8340.1120.1120.0000.0000.0000.000
19A19ALA00.0540.00813.3130.0040.0040.0000.0000.0000.000
20A20ALA0-0.063-0.02814.0340.0180.0180.0000.0000.0000.000
21A21GLN0-0.0020.0277.2110.0150.0150.0000.0000.0000.000
22A22SER0-0.051-0.0627.5160.0950.0950.0000.0000.0000.000
23A23LEU0-0.0290.0074.284-0.195-0.009-0.001-0.034-0.1510.000
24A24GLU-1-0.871-0.9293.551-0.2560.1400.000-0.075-0.3200.000
25A25LEU0-0.001-0.0103.493-2.113-1.6970.008-0.284-0.139-0.002
26A26SER0-0.005-0.0036.0960.2800.2800.0000.0000.0000.000
27A27SER0-0.006-0.0038.8310.1510.1510.0000.0000.0000.000
28A28PHE0-0.0020.0059.2450.0080.0080.0000.0000.0000.000
29A29ARG10.9350.9638.062-0.028-0.0280.0000.0000.0000.000
30A30PHE00.0020.0028.5240.1560.1560.0000.0000.0000.000
31A31THR00.014-0.0189.426-0.081-0.0810.0000.0000.0000.000
32A32MET0-0.0450.01911.7420.0520.0520.0000.0000.0000.000
33A33GLN0-0.044-0.05114.042-0.034-0.0340.0000.0000.0000.000
34A34SER00.0350.00516.4920.0090.0090.0000.0000.0000.000
35A35ASP-1-0.859-0.90319.559-0.040-0.0400.0000.0000.0000.000
36A36CYS0-0.103-0.03419.7110.0050.0050.0000.0000.0000.000
37A37ASN00.0580.04819.5530.0340.0340.0000.0000.0000.000
38A38LEU00.0150.00813.241-0.022-0.0220.0000.0000.0000.000
39A39VAL0-0.035-0.01815.1450.0300.0300.0000.0000.0000.000
40A40LEU0-0.0030.01012.182-0.019-0.0190.0000.0000.0000.000
41A41PHE0-0.012-0.01812.933-0.006-0.0060.0000.0000.0000.000
42A42ASP-1-0.756-0.85312.6850.0670.0670.0000.0000.0000.000
43A43SER0-0.009-0.01113.1490.0110.0110.0000.0000.0000.000
44A44ASP-1-0.890-0.91314.728-0.051-0.0510.0000.0000.0000.000
45A45VAL00.006-0.02316.6980.0090.0090.0000.0000.0000.000
46A46ARG10.8750.92517.5340.0250.0250.0000.0000.0000.000
47A47VAL0-0.026-0.00416.3460.0080.0080.0000.0000.0000.000
48A48TRP00.0140.00016.9850.0260.0260.0000.0000.0000.000
49A49ALA0-0.012-0.01117.863-0.022-0.0220.0000.0000.0000.000
50A50SER00.0190.00719.5300.0110.0110.0000.0000.0000.000
51A51ASN0-0.024-0.01521.175-0.010-0.0100.0000.0000.0000.000
52A52THR0-0.051-0.01921.1620.0000.0000.0000.0000.0000.000
53A53ALA00.0230.02223.429-0.010-0.0100.0000.0000.0000.000
54A54GLY00.0040.01724.4580.0040.0040.0000.0000.0000.000
55A55ALA0-0.034-0.01724.7430.0020.0020.0000.0000.0000.000
56A56THR00.016-0.02423.085-0.006-0.0060.0000.0000.0000.000
57A57GLY00.0130.00420.6560.0040.0040.0000.0000.0000.000
58A59ARG10.9300.96415.3680.1170.1170.0000.0000.0000.000
59A60ALA0-0.0060.01112.9500.0260.0260.0000.0000.0000.000
60A61VAL00.006-0.00813.163-0.049-0.0490.0000.0000.0000.000
61A62LEU00.0180.02111.5960.0450.0450.0000.0000.0000.000
62A63GLN0-0.038-0.03614.578-0.075-0.0750.0000.0000.0000.000
63A64SER0-0.031-0.02716.5140.0260.0260.0000.0000.0000.000
64A65ASP-1-0.755-0.86218.1950.1260.1260.0000.0000.0000.000
65A66GLY00.0450.02017.1430.0030.0030.0000.0000.0000.000
66A67LEU0-0.039-0.00217.9500.0310.0310.0000.0000.0000.000
67A68LEU00.0300.02214.094-0.015-0.0150.0000.0000.0000.000
68A69VAL0-0.017-0.01617.176-0.017-0.0170.0000.0000.0000.000
69A70ILE00.0130.01317.360-0.014-0.0140.0000.0000.0000.000
70A71LEU0-0.0180.00218.711-0.002-0.0020.0000.0000.0000.000
71A72THR00.026-0.02920.144-0.013-0.0130.0000.0000.0000.000
72A73ALA00.0240.01822.480-0.007-0.0070.0000.0000.0000.000
73A74GLN0-0.019-0.00823.385-0.010-0.0100.0000.0000.0000.000
74A75ASN00.003-0.00722.6510.0000.0000.0000.0000.0000.000
75A76THR00.0340.03224.3870.0070.0070.0000.0000.0000.000
76A77ILE0-0.0080.00722.643-0.006-0.0060.0000.0000.0000.000
77A78ARG10.8720.93022.7010.0090.0090.0000.0000.0000.000
78A79TRP00.0240.00618.2060.0060.0060.0000.0000.0000.000
79A80SER0-0.010-0.02220.991-0.005-0.0050.0000.0000.0000.000
80A81SER00.0590.04619.045-0.008-0.0080.0000.0000.0000.000
81A82GLY0-0.0230.00621.1790.0080.0080.0000.0000.0000.000
82A83THR0-0.029-0.02021.717-0.009-0.0090.0000.0000.0000.000
83A84LYS10.8260.89321.897-0.112-0.1120.0000.0000.0000.000
84A85GLY00.0220.00921.9860.0050.0050.0000.0000.0000.000
85A86SER0-0.016-0.00822.472-0.033-0.0330.0000.0000.0000.000
86A87ILE00.0160.00321.4320.0080.0080.0000.0000.0000.000
87A88GLY00.0490.03718.7940.0270.0270.0000.0000.0000.000
88A89ASN00.0050.00412.734-0.010-0.0100.0000.0000.0000.000
89A90TYR0-0.007-0.02213.5420.0530.0530.0000.0000.0000.000
90A91VAL0-0.0040.0048.422-0.096-0.0960.0000.0000.0000.000
91A92LEU0-0.0160.0019.233-0.119-0.1190.0000.0000.0000.000
92A93VAL0-0.004-0.0106.0530.3950.3950.0000.0000.0000.000
93A94LEU0-0.0110.0086.991-0.618-0.6180.0000.0000.0000.000
94A95GLN0-0.006-0.0037.8080.8100.8100.0000.0000.0000.000
95A96PRO00.0510.0149.427-0.266-0.2660.0000.0000.0000.000
96A97ASP-1-0.826-0.89612.0080.6760.6760.0000.0000.0000.000
97A98ARG10.8380.91413.302-0.277-0.2770.0000.0000.0000.000
98A99THR00.0110.02413.884-0.123-0.1230.0000.0000.0000.000
99A100VAL00.0220.00611.1550.1790.1790.0000.0000.0000.000
100A101THR0-0.059-0.03711.753-0.147-0.1470.0000.0000.0000.000
101A102ILE0-0.0210.00011.8220.2070.2070.0000.0000.0000.000
102A103TYR0-0.044-0.04511.719-0.131-0.1310.0000.0000.0000.000
103A104GLY00.002-0.01013.7700.0080.0080.0000.0000.0000.000
104A105PRO00.0050.00916.215-0.014-0.0140.0000.0000.0000.000
105A106GLY00.0270.02415.5760.0560.0560.0000.0000.0000.000
106A107LEU0-0.089-0.02816.410-0.036-0.0360.0000.0000.0000.000
107A108TRP00.0280.00115.702-0.026-0.0260.0000.0000.0000.000
108A109ASP-1-0.828-0.91614.6330.1380.1380.0000.0000.0000.000
109A110SER0-0.002-0.00415.3600.0000.0000.0000.0000.0000.000
110A111GLY0-0.0030.02216.922-0.016-0.0160.0000.0000.0000.000
111A112THR0-0.074-0.05114.2830.0070.0070.0000.0000.0000.000
112A113SER0-0.048-0.03413.548-0.026-0.0260.0000.0000.0000.000
113A114ASN0-0.040-0.02713.1830.0680.0680.0000.0000.0000.000
114A115LYS10.8470.92112.7350.2290.2290.0000.0000.0000.000
115A116GLY00.0430.01312.8200.0890.0890.0000.0000.0000.000
116A117SER0-0.0110.00012.343-0.099-0.0990.0000.0000.0000.000
117A118VAL0-0.025-0.0117.218-0.079-0.0790.0000.0000.0000.000
118A119VAL0-0.014-0.0076.350-0.733-0.7330.0000.0000.0000.000
119A120VAL00.0050.0002.306-1.303-0.3580.853-0.505-1.2940.001
120A121ALA00.0060.0095.6550.1390.1390.0000.0000.0000.000
121A122ASN0-0.072-0.0503.7390.2030.3870.001-0.083-0.1020.000
122A123ASN00.0180.0132.102-6.796-6.3733.307-1.673-2.056-0.021
123A124GLY00.0570.0104.5440.0670.226-0.001-0.016-0.1420.000
124A125ASN0-0.0050.0073.7261.1401.3970.001-0.076-0.1820.000
125A126SER0-0.021-0.0076.208-0.706-0.7060.0000.0000.0000.000
126A127ILE0-0.016-0.0028.585-0.196-0.1960.0000.0000.0000.000
127A128LEU0-0.016-0.00510.2630.0200.0200.0000.0000.0000.000
128A129TYR00.0320.02513.662-0.112-0.1120.0000.0000.0000.000
129A130SER00.013-0.00517.246-0.043-0.0430.0000.0000.0000.000
130A131THR0-0.069-0.04220.095-0.019-0.0190.0000.0000.0000.000
131A132GLN00.0560.05221.1950.0360.0360.0000.0000.0000.000
132A133GLY0-0.001-0.00921.833-0.037-0.0370.0000.0000.0000.000
133A134ASN0-0.028-0.03618.8780.0490.0490.0000.0000.0000.000
134A135ASP-1-0.882-0.91818.4350.4300.4300.0000.0000.0000.000
135A136ASN00.010-0.00313.0920.1000.1000.0000.0000.0000.000
136A137HIS00.0230.01614.4630.0780.0780.0000.0000.0000.000
137A138PRO00.0650.01611.5540.0650.0650.0000.0000.0000.000
138A139GLN0-0.006-0.00714.2630.0180.0180.0000.0000.0000.000
139A140THR0-0.053-0.02917.118-0.076-0.0760.0000.0000.0000.000
140A141LEU0-0.0250.00614.9650.0480.0480.0000.0000.0000.000
141A142HIS00.0610.01518.309-0.050-0.0500.0000.0000.0000.000
142A143ALA00.0780.03020.6740.0120.0120.0000.0000.0000.000
143A144THR0-0.080-0.04021.335-0.003-0.0030.0000.0000.0000.000
144A145GLN0-0.0030.02016.9750.0390.0390.0000.0000.0000.000
145A146SER00.003-0.03913.849-0.049-0.0490.0000.0000.0000.000
146A147LEU0-0.0130.01710.0240.0350.0350.0000.0000.0000.000
147A148GLN00.008-0.0219.339-0.303-0.3030.0000.0000.0000.000
148A149LEU00.0020.0103.3390.2480.6830.025-0.105-0.3540.000
149A150SER0-0.037-0.0227.309-0.289-0.2890.0000.0000.0000.000
150A151PRO00.0140.0309.9310.1030.1030.0000.0000.0000.000
151A152TYR00.0270.0128.3000.1660.1660.0000.0000.0000.000
152A153ARG10.8720.93410.785-0.077-0.0770.0000.0000.0000.000
153A154LEU00.0410.02812.603-0.063-0.0630.0000.0000.0000.000
154A155SER0-0.089-0.06314.4370.0070.0070.0000.0000.0000.000
155A156MET0-0.0310.02617.675-0.009-0.0090.0000.0000.0000.000
156A157GLU-1-0.744-0.85120.6900.1660.1660.0000.0000.0000.000
157A158THR00.020-0.00923.6430.0050.0050.0000.0000.0000.000
158A159ASP-1-0.874-0.92926.2240.1100.1100.0000.0000.0000.000
159A160CYS0-0.139-0.04426.0970.0020.0020.0000.0000.0000.000
160A161ASN0-0.002-0.01624.1520.0160.0160.0000.0000.0000.000
161A162LEU00.0300.02117.9370.0120.0120.0000.0000.0000.000
162A163VAL0-0.044-0.02019.116-0.034-0.0340.0000.0000.0000.000
163A164LEU00.0190.00112.9170.0550.0550.0000.0000.0000.000
164A165PHE0-0.037-0.01815.942-0.037-0.0370.0000.0000.0000.000
165A166ASP-1-0.809-0.92014.606-0.309-0.3090.0000.0000.0000.000
166A167ARG10.8320.88115.3530.1770.1770.0000.0000.0000.000
167A168ASP-1-0.834-0.88317.217-0.098-0.0980.0000.0000.0000.000
168A169ASP-1-0.941-0.95319.728-0.081-0.0810.0000.0000.0000.000
169A170ARG10.9130.94219.316-0.056-0.0560.0000.0000.0000.000
170A171VAL00.0000.00816.0330.0030.0030.0000.0000.0000.000
171A172TRP00.0300.01117.5920.0150.0150.0000.0000.0000.000
172A173SER0-0.022-0.01219.6270.0100.0100.0000.0000.0000.000
173A174THR0-0.009-0.00420.916-0.009-0.0090.0000.0000.0000.000
174A175ASN0-0.052-0.02523.293-0.011-0.0110.0000.0000.0000.000
175A176THR00.001-0.01025.155-0.010-0.0100.0000.0000.0000.000
176A177ALA00.0270.02127.6920.0070.0070.0000.0000.0000.000
177A178GLY0-0.024-0.01129.052-0.006-0.0060.0000.0000.0000.000
178A179LYS10.8480.95329.301-0.124-0.1240.0000.0000.0000.000
179A180GLY00.052-0.00630.9660.0090.0090.0000.0000.0000.000
180A181THR0-0.022-0.01130.949-0.009-0.0090.0000.0000.0000.000
181A182GLY00.0280.02428.8330.0060.0060.0000.0000.0000.000
182A184ARG10.9200.96322.383-0.262-0.2620.0000.0000.0000.000
183A185ALA00.0090.00219.037-0.023-0.0230.0000.0000.0000.000
184A186VAL0-0.010-0.00919.0450.0380.0380.0000.0000.0000.000
185A187LEU00.0290.01614.893-0.025-0.0250.0000.0000.0000.000
186A188GLN0-0.0060.00018.684-0.006-0.0060.0000.0000.0000.000
187A189PRO00.0600.01420.9050.0200.0200.0000.0000.0000.000
188A190ASN0-0.0030.00322.3050.0150.0150.0000.0000.0000.000
189A191GLY00.0610.00819.291-0.022-0.0220.0000.0000.0000.000
190A192ARG10.7760.88519.772-0.256-0.2560.0000.0000.0000.000
191A193MET0-0.0060.01215.9590.0430.0430.0000.0000.0000.000
192A194ASP-1-0.751-0.82519.8580.2160.2160.0000.0000.0000.000
193A195VAL00.0120.00422.1330.0320.0320.0000.0000.0000.000
194A196LEU0-0.045-0.01123.735-0.027-0.0270.0000.0000.0000.000
195A197THR00.040-0.01826.5980.0010.0010.0000.0000.0000.000
196A198ASN0-0.035-0.02729.2870.0150.0150.0000.0000.0000.000
197A199GLN00.0120.00930.9260.0000.0000.0000.0000.0000.000
198A200ASN0-0.005-0.00229.5110.0110.0110.0000.0000.0000.000
199A201ILE00.0390.04330.6440.0060.0060.0000.0000.0000.000
200A202ALA00.0330.01527.5570.0060.0060.0000.0000.0000.000
201A203VAL0-0.028-0.02227.379-0.017-0.0170.0000.0000.0000.000
202A204TRP00.011-0.00819.474-0.009-0.0090.0000.0000.0000.000
203A205THR00.010-0.02623.4000.0190.0190.0000.0000.0000.000
204A206SER00.0580.05119.815-0.013-0.0130.0000.0000.0000.000
205A207GLY0-0.0200.00721.879-0.019-0.0190.0000.0000.0000.000
206A208ASN0-0.045-0.05021.801-0.012-0.0120.0000.0000.0000.000
207A209SER0-0.029-0.01822.4160.0230.0230.0000.0000.0000.000
208A210ARG10.8090.88619.256-0.326-0.3260.0000.0000.0000.000
209A211SER00.0180.01724.751-0.003-0.0030.0000.0000.0000.000
210A212ALA0-0.016-0.00424.0990.0270.0270.0000.0000.0000.000
211A213GLY00.001-0.00122.243-0.020-0.0200.0000.0000.0000.000
212A214ARG10.8000.92115.963-0.649-0.6490.0000.0000.0000.000
213A215TYR0-0.030-0.00216.324-0.010-0.0100.0000.0000.0000.000
214A216VAL00.0280.0119.7710.0510.0510.0000.0000.0000.000
215A217PHE00.012-0.00111.502-0.193-0.1930.0000.0000.0000.000
216A218VAL00.005-0.0186.0350.3980.3980.0000.0000.0000.000
217A219LEU00.0080.0268.040-0.385-0.3850.0000.0000.0000.000
218A220GLN0-0.005-0.0165.9920.3940.3940.0000.0000.0000.000
219A221PRO00.0190.0063.415-0.1040.1190.006-0.045-0.1840.000
220A222ASP-1-0.763-0.8456.160-0.377-0.3770.0000.0000.0000.000
221A223ARG10.8760.9269.0990.4010.4010.0000.0000.0000.000
222A224ASN00.0070.00610.4990.1520.1520.0000.0000.0000.000
223A225LEU0-0.0130.00510.3320.0800.0800.0000.0000.0000.000
224A226ALA00.0170.01410.885-0.070-0.0700.0000.0000.0000.000
225A227ILE0-0.037-0.01011.5880.2010.2010.0000.0000.0000.000
226A228TYR0-0.055-0.05710.088-0.142-0.1420.0000.0000.0000.000
227A229GLY00.000-0.02014.5140.0700.0700.0000.0000.0000.000
228A230GLY00.0470.02817.673-0.085-0.0850.0000.0000.0000.000
229A231ALA0-0.013-0.01816.9530.0810.0810.0000.0000.0000.000
230A232LEU0-0.0450.00317.611-0.042-0.0420.0000.0000.0000.000
231A233TRP00.0410.00215.397-0.049-0.0490.0000.0000.0000.000
232A234THR00.0350.00616.4500.1230.1230.0000.0000.0000.000
233A235THR0-0.0350.01216.321-0.048-0.0480.0000.0000.0000.000