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: LN839

Calculation Name: 4ML1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ML1

Chain ID: A

ChEMBL ID:

UniProt ID: A6GV51

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptHSide
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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2068549.935255
FMO2-HF: Nuclear repulsion 1988829.411633
FMO2-HF: Total energy -79720.523622
FMO2-MP2: Total energy -79947.302794


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:11:ALA)


Summations of interaction energy for fragment #1(A:11:ALA)
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.
-0.6170.744-0.018-0.561-0.7810.003
Interaction energy analysis for fragmet #1(A:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.024
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].
3A13LYS10.8470.9023.790-0.3081.053-0.018-0.561-0.7810.003
4A14ILE0-0.009-0.0076.0610.4040.4040.0000.0000.0000.000
5A15GLU-1-0.841-0.9098.936-0.615-0.6150.0000.0000.0000.000
6A16ASP-1-0.894-0.95211.935-0.081-0.0810.0000.0000.0000.000
7A17ILE0-0.069-0.03212.2070.0390.0390.0000.0000.0000.000
8A18VAL00.0060.00615.759-0.011-0.0110.0000.0000.0000.000
9A19GLU-1-0.962-0.96719.3920.0300.0300.0000.0000.0000.000
10A20LEU00.0210.00521.182-0.004-0.0040.0000.0000.0000.000
11A21PRO0-0.034-0.01023.6780.0010.0010.0000.0000.0000.000
12A22ILE0-0.048-0.03924.0270.0030.0030.0000.0000.0000.000
13A23LYS10.9450.96926.216-0.030-0.0300.0000.0000.0000.000
14A24GLY00.0090.00627.9590.0000.0000.0000.0000.0000.000
15A25VAL0-0.013-0.01224.3590.0000.0000.0000.0000.0000.000
16A26ARG10.8830.94327.711-0.065-0.0650.0000.0000.0000.000
17A27ALA00.0410.02827.8310.0030.0030.0000.0000.0000.000
18A28VAL0-0.029-0.02529.314-0.008-0.0080.0000.0000.0000.000
19A29GLN00.009-0.00531.6290.0030.0030.0000.0000.0000.000
20A30SER0-0.007-0.01433.573-0.009-0.0090.0000.0000.0000.000
21A31ASP-1-0.930-0.95334.5130.0850.0850.0000.0000.0000.000
22A32GLY00.0110.00934.2830.0030.0030.0000.0000.0000.000
23A33GLN0-0.051-0.01630.1880.0130.0130.0000.0000.0000.000
24A34ILE0-0.021-0.02427.906-0.010-0.0100.0000.0000.0000.000
25A35MET0-0.0150.00427.3580.0110.0110.0000.0000.0000.000
26A36PHE00.0180.00124.207-0.004-0.0040.0000.0000.0000.000
27A37LEU00.0130.01727.040-0.003-0.0030.0000.0000.0000.000
28A38SER00.0520.02528.0950.0010.0010.0000.0000.0000.000
29A39GLU-1-0.789-0.89629.4410.0490.0490.0000.0000.0000.000
30A40ASN0-0.051-0.03031.3010.0000.0000.0000.0000.0000.000
31A41GLY0-0.010-0.01032.898-0.003-0.0030.0000.0000.0000.000
32A42ARG10.9140.98230.735-0.033-0.0330.0000.0000.0000.000
33A43PHE00.004-0.00926.904-0.001-0.0010.0000.0000.0000.000
34A44VAL00.0180.00528.2280.0010.0010.0000.0000.0000.000
35A45ILE0-0.0100.00221.6440.0000.0000.0000.0000.0000.000
36A46SER00.0340.00624.7670.0040.0040.0000.0000.0000.000
37A47GLY00.009-0.00321.8550.0090.0090.0000.0000.0000.000
38A48GLN0-0.019-0.01119.366-0.022-0.0220.0000.0000.0000.000
39A49ILE00.0130.02319.2790.0190.0190.0000.0000.0000.000
40A50TYR00.020-0.01114.8560.0190.0190.0000.0000.0000.000
41A51ASP-1-0.778-0.85517.6560.2040.2040.0000.0000.0000.000
42A52LEU00.017-0.02512.0520.0180.0180.0000.0000.0000.000
43A53TRP0-0.021-0.00715.5740.0130.0130.0000.0000.0000.000
44A54SER0-0.042-0.04017.871-0.015-0.0150.0000.0000.0000.000
45A55LYS10.8830.95214.735-0.273-0.2730.0000.0000.0000.000
46A56LYS10.8990.96617.194-0.183-0.1830.0000.0000.0000.000
47A57PRO00.0240.01818.870-0.003-0.0030.0000.0000.0000.000
48A58LEU0-0.040-0.02220.343-0.023-0.0230.0000.0000.0000.000
49A59ASN00.0400.01123.2450.0080.0080.0000.0000.0000.000
50A60THR00.0360.01425.864-0.008-0.0080.0000.0000.0000.000
51A61MET00.0570.02228.8460.0050.0050.0000.0000.0000.000
52A62SER0-0.0140.00531.2640.0000.0000.0000.0000.0000.000
53A63GLN00.0460.02424.460-0.003-0.0030.0000.0000.0000.000
54A64MET00.0020.01024.9780.0030.0030.0000.0000.0000.000
55A65ARG10.8530.92428.365-0.084-0.0840.0000.0000.0000.000
56A66ASP-1-0.864-0.92827.8950.1160.1160.0000.0000.0000.000
57A67VAL00.009-0.00224.042-0.003-0.0030.0000.0000.0000.000
58A68ALA0-0.061-0.01627.286-0.005-0.0050.0000.0000.0000.000
59A69GLU-1-0.911-0.95129.9690.0690.0690.0000.0000.0000.000
60A70ARG10.7890.88630.436-0.090-0.0900.0000.0000.0000.000
61A71ILE00.0060.01226.8690.0060.0060.0000.0000.0000.000
62A72HIS0-0.046-0.04126.339-0.008-0.0080.0000.0000.0000.000
63A73PHE00.0390.00025.6310.0100.0100.0000.0000.0000.000
64A74LYS10.9210.95124.810-0.067-0.0670.0000.0000.0000.000
65A75SER0-0.0010.00423.9460.0060.0060.0000.0000.0000.000
66A76MET0-0.039-0.00720.9780.0160.0160.0000.0000.0000.000
67A77GLY0-0.050-0.02220.3320.0070.0070.0000.0000.0000.000
68A78MET0-0.048-0.01421.579-0.012-0.0120.0000.0000.0000.000
69A79ASP-1-0.827-0.92823.8750.0570.0570.0000.0000.0000.000
70A80VAL00.0210.00926.782-0.006-0.0060.0000.0000.0000.000
71A81ASP-1-0.813-0.87929.5390.0390.0390.0000.0000.0000.000
72A82THR0-0.107-0.05725.895-0.006-0.0060.0000.0000.0000.000
73A83LEU0-0.041-0.00926.683-0.005-0.0050.0000.0000.0000.000
74A84ASN0-0.016-0.01330.172-0.003-0.0030.0000.0000.0000.000
75A85THR0-0.016-0.02332.5420.0000.0000.0000.0000.0000.000
76A86VAL0-0.0150.00435.378-0.003-0.0030.0000.0000.0000.000
77A87SER00.0190.00138.3900.0030.0030.0000.0000.0000.000
78A88MET0-0.035-0.00139.978-0.003-0.0030.0000.0000.0000.000
79A89GLY00.0310.01142.7930.0020.0020.0000.0000.0000.000
80A90ARG10.8850.93340.640-0.034-0.0340.0000.0000.0000.000
81A91GLY00.0670.05643.7150.0010.0010.0000.0000.0000.000
82A92ASP-1-0.899-0.93840.8980.0430.0430.0000.0000.0000.000
83A93LYS10.8500.95338.744-0.042-0.0420.0000.0000.0000.000
84A94GLU-1-0.795-0.89232.9480.0590.0590.0000.0000.0000.000
85A95VAL0-0.014-0.00136.4740.0030.0030.0000.0000.0000.000
86A96VAL00.0010.01632.263-0.003-0.0030.0000.0000.0000.000
87A97VAL0-0.006-0.01635.5090.0000.0000.0000.0000.0000.000
88A98PHE00.0170.03330.009-0.002-0.0020.0000.0000.0000.000
89A99VAL00.025-0.01735.836-0.001-0.0010.0000.0000.0000.000
90A100ASP-1-0.705-0.84138.0260.0140.0140.0000.0000.0000.000
91A101PRO00.021-0.00139.3880.0000.0000.0000.0000.0000.000
92A102ARG10.8900.93342.571-0.010-0.0100.0000.0000.0000.000
93A103CYS0-0.045-0.00341.9340.0020.0020.0000.0000.0000.000
94A104ALA00.0650.03244.5370.0010.0010.0000.0000.0000.000
95A105VAL0-0.008-0.00145.0590.0010.0010.0000.0000.0000.000
96A107HIS00.0430.01644.0960.0010.0010.0000.0000.0000.000
97A108GLN0-0.031-0.02247.0470.0010.0010.0000.0000.0000.000
98A109LEU0-0.0330.00441.6520.0000.0000.0000.0000.0000.000
99A110MET00.0000.00443.3190.0010.0010.0000.0000.0000.000
100A111GLY00.0050.00045.7950.0000.0000.0000.0000.0000.000
101A112ASP-1-0.826-0.89847.6860.0260.0260.0000.0000.0000.000
102A113ALA00.0170.00144.8210.0010.0010.0000.0000.0000.000
103A114LYS10.9590.98546.759-0.019-0.0190.0000.0000.0000.000
104A115SER0-0.091-0.03449.1740.0000.0000.0000.0000.0000.000
105A116LEU0-0.033-0.03046.2400.0010.0010.0000.0000.0000.000
106A117VAL0-0.005-0.00545.9710.0020.0020.0000.0000.0000.000
107A118ASP-1-0.901-0.94146.4810.0280.0280.0000.0000.0000.000
108A119ASP-1-0.873-0.91345.4590.0370.0370.0000.0000.0000.000
109A120TYR0-0.112-0.09741.0420.0040.0040.0000.0000.0000.000
110A121THR0-0.050-0.02439.088-0.004-0.0040.0000.0000.0000.000
111A122PHE0-0.009-0.01939.1910.0030.0030.0000.0000.0000.000
112A123LYS10.8000.87333.963-0.050-0.0500.0000.0000.0000.000
113A124PHE00.009-0.01536.6660.0020.0020.0000.0000.0000.000
114A125ILE00.001-0.00731.340-0.002-0.0020.0000.0000.0000.000
115A126VAL0-0.0010.00035.148-0.001-0.0010.0000.0000.0000.000
116A127ILE00.014-0.00432.154-0.001-0.0010.0000.0000.0000.000
117A128PRO0-0.055-0.01934.0710.0000.0000.0000.0000.0000.000
118A129ALA00.015-0.00535.637-0.002-0.0020.0000.0000.0000.000
119A130LEU0-0.050-0.01936.6050.0000.0000.0000.0000.0000.000
120A131GLY00.0040.01538.545-0.002-0.0020.0000.0000.0000.000
121A132ALA00.039-0.00239.4490.0000.0000.0000.0000.0000.000
122A133GLU-1-0.776-0.85941.2210.0020.0020.0000.0000.0000.000
123A134SER0-0.044-0.02840.0140.0000.0000.0000.0000.0000.000
124A135ASN00.0210.00035.5720.0020.0020.0000.0000.0000.000
125A136ARG10.8320.90538.697-0.002-0.0020.0000.0000.0000.000
126A137LEU00.0230.00641.3580.0000.0000.0000.0000.0000.000
127A138ALA00.0490.02336.8590.0010.0010.0000.0000.0000.000
128A139LYS10.8830.93935.7250.0090.0090.0000.0000.0000.000
129A140ASN0-0.005-0.00338.2600.0000.0000.0000.0000.0000.000
130A141LEU00.0390.02638.3440.0000.0000.0000.0000.0000.000
131A142TYR00.0100.00830.658-0.002-0.0020.0000.0000.0000.000
132A143CYS0-0.106-0.07135.9480.0000.0000.0000.0000.0000.000
133A144ALA00.0220.03138.847-0.001-0.0010.0000.0000.0000.000
134A145LYS10.8360.89040.8670.0040.0040.0000.0000.0000.000
135A146ASP-1-0.804-0.87842.1710.0100.0100.0000.0000.0000.000
136A147LYS10.7940.87637.791-0.009-0.0090.0000.0000.0000.000
137A148THR0-0.060-0.05242.5190.0020.0020.0000.0000.0000.000
138A149HIS00.0350.02645.4030.0010.0010.0000.0000.0000.000
139A150ALA0-0.044-0.02742.0160.0000.0000.0000.0000.0000.000
140A151LEU00.0030.00543.3790.0000.0000.0000.0000.0000.000
141A152ASP-1-0.828-0.92344.6560.0160.0160.0000.0000.0000.000
142A153ALA0-0.0180.00145.9700.0000.0000.0000.0000.0000.000
143A154LEU0-0.045-0.03040.9440.0000.0000.0000.0000.0000.000
144A155MET0-0.037-0.03144.8170.0010.0010.0000.0000.0000.000
145A156ASN0-0.073-0.03247.2280.0000.0000.0000.0000.0000.000
146A157ASN0-0.039-0.00547.403-0.001-0.0010.0000.0000.0000.000
147A158THR00.0410.01148.496-0.001-0.0010.0000.0000.0000.000
148A159LEU00.0240.00442.245-0.001-0.0010.0000.0000.0000.000
149A160GLY0-0.058-0.02345.779-0.001-0.0010.0000.0000.0000.000
150A161SER0-0.042-0.00947.242-0.001-0.0010.0000.0000.0000.000
151A162LEU0-0.0050.00643.6660.0000.0000.0000.0000.0000.000
152A163PRO00.0370.01045.862-0.001-0.0010.0000.0000.0000.000
153A164SER0-0.0150.00241.9790.0010.0010.0000.0000.0000.000
154A165LYS10.9240.96135.755-0.003-0.0030.0000.0000.0000.000
155A166GLU-1-0.818-0.89241.277-0.006-0.0060.0000.0000.0000.000
156A167THR0-0.035-0.01936.204-0.002-0.0020.0000.0000.0000.000
157A169ASP-1-0.843-0.91635.281-0.013-0.0130.0000.0000.0000.000
158A170PRO0-0.0040.01332.293-0.002-0.0020.0000.0000.0000.000
159A171GLY00.0650.03331.263-0.001-0.0010.0000.0000.0000.000
160A172GLN0-0.011-0.01532.2600.0040.0040.0000.0000.0000.000
161A173TYR0-0.044-0.02728.6720.0020.0020.0000.0000.0000.000
162A174ASP-1-0.811-0.90429.2860.0140.0140.0000.0000.0000.000
163A175GLN00.0630.01925.2740.0070.0070.0000.0000.0000.000
164A176THR00.0580.04927.3470.0070.0070.0000.0000.0000.000
165A177LEU0-0.031-0.02329.2410.0050.0050.0000.0000.0000.000
166A178LEU0-0.005-0.00324.8010.0030.0030.0000.0000.0000.000
167A179THR0-0.026-0.02324.0120.0060.0060.0000.0000.0000.000
168A180ALA00.011-0.00525.5670.0080.0080.0000.0000.0000.000
169A181HIS0-0.012-0.00726.1300.0040.0040.0000.0000.0000.000
170A182PHE0-0.048-0.01717.8960.0040.0040.0000.0000.0000.000
171A183ILE0-0.055-0.03922.4490.0090.0090.0000.0000.0000.000
172A184GLY00.0310.02524.5120.0060.0060.0000.0000.0000.000
173A185ILE0-0.061-0.01327.383-0.002-0.0020.0000.0000.0000.000
174A186GLU-1-0.827-0.89130.5080.0440.0440.0000.0000.0000.000
175A187GLY0-0.033-0.02133.3100.0000.0000.0000.0000.0000.000
176A188VAL0-0.0280.01036.1880.0020.0020.0000.0000.0000.000
177A189PRO00.008-0.04038.688-0.002-0.0020.0000.0000.0000.000
178A190PHE0-0.0060.00132.0280.0000.0000.0000.0000.0000.000
179A191VAL0-0.031-0.01636.325-0.001-0.0010.0000.0000.0000.000
180A192VAL00.0110.00631.7270.0020.0020.0000.0000.0000.000
181A193ALA0-0.009-0.01035.035-0.003-0.0030.0000.0000.0000.000
182A194PRO00.0510.02435.0540.0040.0040.0000.0000.0000.000
183A195ASP-1-0.801-0.88534.6310.0730.0730.0000.0000.0000.000
184A196GLY00.0390.00832.0680.0060.0060.0000.0000.0000.000
185A197ARG10.8040.90832.616-0.057-0.0570.0000.0000.0000.000
186A198VAL00.0460.03431.815-0.004-0.0040.0000.0000.0000.000
187A199SER0-0.073-0.04835.108-0.002-0.0020.0000.0000.0000.000
188A200LYS10.8020.89634.605-0.047-0.0470.0000.0000.0000.000
189A201GLY00.0650.02737.920-0.002-0.0020.0000.0000.0000.000
190A202ARG10.8160.89441.098-0.024-0.0240.0000.0000.0000.000
191A203PRO00.0090.01342.160-0.001-0.0010.0000.0000.0000.000
192A204LYS10.9440.96944.663-0.033-0.0330.0000.0000.0000.000
193A205ASN00.0500.03647.8320.0000.0000.0000.0000.0000.000
194A206LEU00.0480.03243.0160.0020.0020.0000.0000.0000.000
195A207LYS10.9060.94945.304-0.034-0.0340.0000.0000.0000.000
196A208SER0-0.012-0.03146.5520.0020.0020.0000.0000.0000.000
197A209TRP0-0.018-0.00637.7310.0010.0010.0000.0000.0000.000
198A210LEU00.0390.01040.6460.0030.0030.0000.0000.0000.000
199A211GLU-1-0.866-0.90241.6480.0450.0450.0000.0000.0000.000
200A212SER0-0.058-0.01840.6670.0030.0030.0000.0000.0000.000