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

tag_button

FMODB ID: LJQY9

Calculation Name: 1D02-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D02

Chain ID: A

ChEMBL ID:

UniProt ID: P43642

Base Structure: X-ray

Registration Date: 2023-03-13

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2224845.918256
FMO2-HF: Nuclear repulsion 2146382.321505
FMO2-HF: Total energy -78463.596751
FMO2-MP2: Total energy -78698.305692


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:6:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-14.546-8.0456.68-5.47-7.713-0.019
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.025
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].
3A8GLY00.0730.0293.736-2.265-0.385-0.010-0.973-0.8970.006
4A9ARG10.9120.9526.015-0.782-0.7820.0000.0000.0000.000
5A10LEU00.0340.0268.036-0.012-0.0120.0000.0000.0000.000
6A11ASN0-0.008-0.00510.6500.1040.1040.0000.0000.0000.000
7A12TRP00.056-0.00212.780-0.056-0.0560.0000.0000.0000.000
8A13GLN0-0.022-0.00815.657-0.021-0.0210.0000.0000.0000.000
9A14ALA00.0670.04515.655-0.023-0.0230.0000.0000.0000.000
10A15LEU0-0.017-0.00217.091-0.026-0.0260.0000.0000.0000.000
11A16ALA0-0.015-0.01718.874-0.017-0.0170.0000.0000.0000.000
12A17GLY00.0340.01920.750-0.009-0.0090.0000.0000.0000.000
13A18LEU00.0060.01620.991-0.011-0.0110.0000.0000.0000.000
14A19LYS10.9200.97223.026-0.059-0.0590.0000.0000.0000.000
15A20ALA0-0.025-0.01825.012-0.006-0.0060.0000.0000.0000.000
16A21SER0-0.083-0.04725.911-0.005-0.0050.0000.0000.0000.000
17A22GLY0-0.026-0.01727.749-0.006-0.0060.0000.0000.0000.000
18A23ALA0-0.0060.00926.447-0.006-0.0060.0000.0000.0000.000
19A24GLU-1-0.948-0.96427.856-0.007-0.0070.0000.0000.0000.000
20A25GLN00.0440.01623.425-0.008-0.0080.0000.0000.0000.000
21A26ASN00.0110.00324.074-0.012-0.0120.0000.0000.0000.000
22A27LEU00.0600.01419.8990.0040.0040.0000.0000.0000.000
23A28TYR0-0.004-0.03119.985-0.003-0.0030.0000.0000.0000.000
24A29ASN00.0130.00219.316-0.005-0.0050.0000.0000.0000.000
25A30VAL00.0180.02019.0590.0140.0140.0000.0000.0000.000
26A31PHE00.013-0.01714.9760.0110.0110.0000.0000.0000.000
27A32ASN0-0.002-0.00314.863-0.026-0.0260.0000.0000.0000.000
28A33ALA00.0260.02815.1000.0110.0110.0000.0000.0000.000
29A34VAL0-0.036-0.01213.4390.0350.0350.0000.0000.0000.000
30A35PHE00.004-0.01010.7790.0100.0100.0000.0000.0000.000
31A36GLU-1-0.901-0.92910.2060.0810.0810.0000.0000.0000.000
32A37GLY00.0050.0058.3950.0660.0660.0000.0000.0000.000
33A38THR0-0.074-0.0286.2250.1550.1550.0000.0000.0000.000
34A39LYS10.9080.9512.2702.1823.6272.454-1.239-2.6610.001
35A40TYR0-0.014-0.0164.410-0.470-0.334-0.001-0.016-0.1190.000
36A41VAL00.0410.0317.8750.1140.1140.0000.0000.0000.000
37A42LEU0-0.015-0.00210.691-0.034-0.0340.0000.0000.0000.000
38A43TYR0-0.091-0.08612.2410.0420.0420.0000.0000.0000.000
39A44GLU-1-0.900-0.95916.927-0.105-0.1050.0000.0000.0000.000
40A45LYS10.8970.95220.6370.1230.1230.0000.0000.0000.000
41A46PRO0-0.0240.00418.399-0.003-0.0030.0000.0000.0000.000
42A47LYS10.9670.95320.1500.1990.1990.0000.0000.0000.000
43A48HIS00.0580.03015.3170.0490.0490.0000.0000.0000.000
44A49LEU00.0360.03520.5700.0030.0030.0000.0000.0000.000
45A50LYS10.9000.95123.7700.1770.1770.0000.0000.0000.000
46A51ASN0-0.019-0.01326.1330.0240.0240.0000.0000.0000.000
47A52LEU0-0.051-0.03325.768-0.008-0.0080.0000.0000.0000.000
48A53TYR00.023-0.02229.4820.0030.0030.0000.0000.0000.000
49A54ALA00.0190.04533.2430.0050.0050.0000.0000.0000.000
50A55GLN00.0400.01529.5320.0130.0130.0000.0000.0000.000
51A56VAL0-0.061-0.02534.096-0.001-0.0010.0000.0000.0000.000
52A57VAL00.0110.00836.0290.0050.0050.0000.0000.0000.000
53A58LEU0-0.021-0.01039.0120.0000.0000.0000.0000.0000.000
54A59PRO00.0160.00742.1700.0010.0010.0000.0000.0000.000
55A60ASP-1-0.846-0.93945.309-0.077-0.0770.0000.0000.0000.000
56A61ASP-1-0.998-1.00748.066-0.061-0.0610.0000.0000.0000.000
57A62VAL00.0200.01344.8180.0010.0010.0000.0000.0000.000
58A63ILE0-0.018-0.00743.6990.0010.0010.0000.0000.0000.000
59A64LYS10.9130.95647.3750.0650.0650.0000.0000.0000.000
60A65GLU-1-0.898-0.93450.166-0.056-0.0560.0000.0000.0000.000
61A66ILE0-0.087-0.02144.4680.0000.0000.0000.0000.0000.000
62A67PHE0-0.037-0.02546.0300.0010.0010.0000.0000.0000.000
63A68ASN0-0.008-0.01945.795-0.006-0.0060.0000.0000.0000.000
64A69PRO0-0.036-0.01243.0910.0020.0020.0000.0000.0000.000
65A70LEU00.0150.01045.046-0.002-0.0020.0000.0000.0000.000
66A71ILE0-0.031-0.02938.641-0.001-0.0010.0000.0000.0000.000
67A72ASP-1-0.752-0.83938.221-0.109-0.1090.0000.0000.0000.000
68A73LEU0-0.004-0.00437.548-0.005-0.0050.0000.0000.0000.000
69A74SER0-0.074-0.04535.420-0.008-0.0080.0000.0000.0000.000
70A75THR0-0.047-0.03433.346-0.009-0.0090.0000.0000.0000.000
71A76THR0-0.051-0.01833.4480.0000.0000.0000.0000.0000.000
72A77GLN0-0.031-0.01827.198-0.010-0.0100.0000.0000.0000.000
73A78TRP00.0150.00431.2030.0030.0030.0000.0000.0000.000
74A79GLY00.0320.01728.541-0.006-0.0060.0000.0000.0000.000
75A80VAL0-0.055-0.02425.5700.0140.0140.0000.0000.0000.000
76A81SER0-0.060-0.04925.126-0.007-0.0070.0000.0000.0000.000
77A82PRO00.0170.03421.8230.0130.0130.0000.0000.0000.000
78A83ALA00.0310.02723.6200.0020.0020.0000.0000.0000.000
79A84PHE00.0150.01118.0640.0080.0080.0000.0000.0000.000
80A85ALA00.0010.01116.230-0.005-0.0050.0000.0000.0000.000
81A86ILE00.0040.01711.9010.0170.0170.0000.0000.0000.000
82A87GLU-1-0.815-0.8719.191-0.707-0.7070.0000.0000.0000.000
83A88ASN00.0370.0425.556-0.188-0.1880.0000.0000.0000.000
84A89THR0-0.040-0.0614.643-0.226-0.131-0.001-0.009-0.0850.000
85A90GLU-1-0.932-0.9622.006-13.384-10.5664.236-3.191-3.864-0.026
86A91THR0-0.063-0.0534.0120.1050.2320.002-0.042-0.0870.000
87A92HIS10.8460.9237.2501.4551.4550.0000.0000.0000.000
88A93LYS10.9070.9919.4750.9120.9120.0000.0000.0000.000
89A94ILE0-0.041-0.04111.235-0.015-0.0150.0000.0000.0000.000
90A95LEU00.0020.01613.8820.0330.0330.0000.0000.0000.000
91A96PHE0-0.015-0.02216.2900.0170.0170.0000.0000.0000.000
92A97GLY00.0460.01119.2820.0100.0100.0000.0000.0000.000
93A98GLU-1-0.958-0.99121.530-0.146-0.1460.0000.0000.0000.000
94A99ILE00.0460.02523.5610.0030.0030.0000.0000.0000.000
95A100LYS10.8420.92226.8560.1040.1040.0000.0000.0000.000
96A101ARG10.9570.98627.8420.0760.0760.0000.0000.0000.000
97A102GLN0-0.050-0.04132.697-0.005-0.0050.0000.0000.0000.000
98A103ASP-1-0.855-0.91536.270-0.033-0.0330.0000.0000.0000.000
99A104GLY0-0.003-0.03139.112-0.004-0.0040.0000.0000.0000.000
100A105TRP0-0.096-0.03340.6910.0020.0020.0000.0000.0000.000
101A106VAL00.0340.00239.6290.0000.0000.0000.0000.0000.000
102A107GLU-1-0.764-0.86341.976-0.010-0.0100.0000.0000.0000.000
103A108GLY0-0.017-0.01045.2920.0000.0000.0000.0000.0000.000
104A109LYS10.8920.96343.1820.0180.0180.0000.0000.0000.000
105A110ASP-1-0.822-0.90447.800-0.017-0.0170.0000.0000.0000.000
106A111PRO0-0.002-0.02846.944-0.002-0.0020.0000.0000.0000.000
107A112SER0-0.0130.00046.577-0.003-0.0030.0000.0000.0000.000
108A113ALA0-0.005-0.00144.791-0.002-0.0020.0000.0000.0000.000
109A114GLY00.0490.03042.471-0.002-0.0020.0000.0000.0000.000
110A115ARG10.8640.91842.9880.0310.0310.0000.0000.0000.000
111A116GLY0-0.038-0.00241.735-0.001-0.0010.0000.0000.0000.000
112A117ASN00.0630.01240.0540.0000.0000.0000.0000.0000.000
113A118ALA00.0550.03437.592-0.004-0.0040.0000.0000.0000.000
114A119HIS0-0.006-0.01034.131-0.007-0.0070.0000.0000.0000.000
115A120GLU-1-0.852-0.92033.971-0.071-0.0710.0000.0000.0000.000
116A121ARG10.9180.95932.2630.0840.0840.0000.0000.0000.000
117A122SER0-0.104-0.06329.633-0.008-0.0080.0000.0000.0000.000
118A123CYS00.0480.01730.189-0.010-0.0100.0000.0000.0000.000
119A124LYS10.9670.99530.0990.1250.1250.0000.0000.0000.000
120A125LEU0-0.018-0.01525.301-0.004-0.0040.0000.0000.0000.000
121A126PHE00.0340.03128.141-0.012-0.0120.0000.0000.0000.000
122A127THR0-0.049-0.01630.5960.0010.0010.0000.0000.0000.000
123A128PRO00.0720.02030.289-0.011-0.0110.0000.0000.0000.000
124A129GLY0-0.019-0.00729.734-0.011-0.0110.0000.0000.0000.000
125A130LEU00.003-0.00627.606-0.012-0.0120.0000.0000.0000.000
126A131LEU00.0300.03125.874-0.019-0.0190.0000.0000.0000.000
127A132LYS10.9800.99224.6770.1490.1490.0000.0000.0000.000
128A133ALA00.0020.00024.364-0.019-0.0190.0000.0000.0000.000
129A134TYR00.026-0.00721.893-0.019-0.0190.0000.0000.0000.000
130A135ARG10.8550.92720.1650.2230.2230.0000.0000.0000.000
131A136THR0-0.056-0.01919.420-0.035-0.0350.0000.0000.0000.000
132A137ILE0-0.056-0.03718.668-0.029-0.0290.0000.0000.0000.000
133A138GLY00.0050.01616.308-0.033-0.0330.0000.0000.0000.000
134A139GLY00.0530.03214.872-0.079-0.0790.0000.0000.0000.000
135A140ILE0-0.032-0.01115.422-0.024-0.0240.0000.0000.0000.000
136A141ASN0-0.009-0.03117.1960.0730.0730.0000.0000.0000.000
137A142ASP-1-0.864-0.91518.105-0.252-0.2520.0000.0000.0000.000
138A143GLU-1-0.922-0.98220.104-0.197-0.1970.0000.0000.0000.000
139A144GLU-1-0.903-0.88020.511-0.161-0.1610.0000.0000.0000.000
140A145ILE0-0.066-0.01218.6810.0180.0180.0000.0000.0000.000
141A146LEU0-0.031-0.01322.079-0.011-0.0110.0000.0000.0000.000
142A147PRO0-0.006-0.01020.082-0.012-0.0120.0000.0000.0000.000
143A148PHE0-0.007-0.00420.139-0.019-0.0190.0000.0000.0000.000
144A149TRP00.0120.00418.2930.0020.0020.0000.0000.0000.000
145A150VAL0-0.036-0.01222.3250.0000.0000.0000.0000.0000.000
146A151VAL00.0260.02122.7510.0080.0080.0000.0000.0000.000
147A152PHE0-0.002-0.01425.8380.0020.0020.0000.0000.0000.000
148A153GLU-1-0.833-0.94126.937-0.061-0.0610.0000.0000.0000.000
149A154GLY00.0550.02330.852-0.002-0.0020.0000.0000.0000.000
150A155ASP-1-0.848-0.92834.392-0.024-0.0240.0000.0000.0000.000
151A156ILE0-0.0230.00233.9720.0010.0010.0000.0000.0000.000
152A157THR0-0.046-0.03831.0920.0020.0020.0000.0000.0000.000
153A158ARG10.7880.85834.0600.0150.0150.0000.0000.0000.000
154A159ASP-1-0.745-0.83036.913-0.031-0.0310.0000.0000.0000.000
155A160PRO00.001-0.00938.723-0.003-0.0030.0000.0000.0000.000
156A161LYS10.9550.97740.6570.0330.0330.0000.0000.0000.000
157A162ARG10.8650.92837.2840.0450.0450.0000.0000.0000.000
158A163VAL00.0340.02934.330-0.004-0.0040.0000.0000.0000.000
159A164ARG10.9000.95135.5570.0240.0240.0000.0000.0000.000
160A165GLU-1-0.800-0.87937.552-0.059-0.0590.0000.0000.0000.000
161A166ILE00.0070.00231.792-0.004-0.0040.0000.0000.0000.000
162A167THR0-0.047-0.03032.850-0.005-0.0050.0000.0000.0000.000
163A168PHE0-0.021-0.02233.743-0.004-0.0040.0000.0000.0000.000
164A169TRP0-0.019-0.02133.738-0.005-0.0050.0000.0000.0000.000
165A170TYR0-0.015-0.00827.209-0.009-0.0090.0000.0000.0000.000
166A171ASP-1-0.843-0.89330.570-0.086-0.0860.0000.0000.0000.000
167A172HIS10.8700.93828.0530.1140.1140.0000.0000.0000.000
168A173TYR00.0000.00325.2450.0000.0000.0000.0000.0000.000
169A174GLN0-0.025-0.03326.9450.0000.0000.0000.0000.0000.000
170A175ASP-1-0.819-0.90021.962-0.096-0.0960.0000.0000.0000.000
171A176ASN0-0.025-0.02321.812-0.003-0.0030.0000.0000.0000.000
172A177TYR0-0.039-0.03424.055-0.003-0.0030.0000.0000.0000.000
173A178PHE0-0.0020.01023.7020.0040.0040.0000.0000.0000.000
174A179MET0-0.045-0.01125.801-0.001-0.0010.0000.0000.0000.000
175A180TRP0-0.001-0.00224.6060.0020.0020.0000.0000.0000.000
176A181ARG10.8770.92527.8160.0300.0300.0000.0000.0000.000
177A182PRO00.0350.00230.5640.0030.0030.0000.0000.0000.000
178A183ASN0-0.013-0.01032.0610.0020.0020.0000.0000.0000.000
179A184GLU-1-0.815-0.87627.5780.0170.0170.0000.0000.0000.000
180A185SER0-0.032-0.00624.898-0.005-0.0050.0000.0000.0000.000
181A186GLY00.0780.02222.409-0.008-0.0080.0000.0000.0000.000
182A187GLU-1-0.987-0.99220.1280.0790.0790.0000.0000.0000.000
183A188LYS10.8800.92320.479-0.024-0.0240.0000.0000.0000.000
184A189LEU0-0.0070.01520.314-0.011-0.0110.0000.0000.0000.000
185A190VAL00.003-0.01415.486-0.021-0.0210.0000.0000.0000.000
186A191GLN00.011-0.00816.970-0.032-0.0320.0000.0000.0000.000
187A192HIS00.0150.02718.5880.0070.0070.0000.0000.0000.000
188A193PHE00.0450.01311.610-0.013-0.0130.0000.0000.0000.000
189A194ASN00.0250.00912.677-0.088-0.0880.0000.0000.0000.000
190A195GLU-1-0.977-0.98614.606-0.001-0.0010.0000.0000.0000.000
191A196LYS10.8910.95217.3760.0580.0580.0000.0000.0000.000
192A197LEU0-0.010-0.01016.376-0.019-0.0190.0000.0000.0000.000
193A198LYS10.8090.9089.3600.1060.1060.0000.0000.0000.000
194A199LYS10.9400.98211.2100.0830.0830.0000.0000.0000.000
195A200TYR0-0.092-0.08812.189-0.076-0.0760.0000.0000.0000.000
196A201LEU0-0.045-0.02710.274-0.016-0.0160.0000.0000.0000.000
197A202ASP-1-0.925-0.9547.599-1.314-1.3140.0000.0000.0000.000