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: 3JYVL

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2064760.816029
FMO2-HF: Nuclear repulsion 1985041.424953
FMO2-HF: Total energy -79719.391076
FMO2-MP2: Total energy -79946.13216


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.
-0.2861.08-0.019-0.567-0.7810.003
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 : -0.014 / q_NPA : -0.019
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].
3A13LYS10.9340.9743.7900.0261.392-0.019-0.567-0.7810.003
4A14ILE00.000-0.0095.9700.3990.3990.0000.0000.0000.000
5A15GLU-1-0.942-0.9868.917-0.556-0.5560.0000.0000.0000.000
6A16ASP-1-0.877-0.93811.842-0.093-0.0930.0000.0000.0000.000
7A17ILE0-0.080-0.03912.3890.0410.0410.0000.0000.0000.000
8A18VAL0-0.0010.00415.741-0.010-0.0100.0000.0000.0000.000
9A19GLU-1-0.961-0.96619.3750.0310.0310.0000.0000.0000.000
10A20LEU00.008-0.00521.234-0.005-0.0050.0000.0000.0000.000
11A21PRO0-0.034-0.00723.6650.0010.0010.0000.0000.0000.000
12A22ILE0-0.036-0.03223.9320.0030.0030.0000.0000.0000.000
13A23LYS10.9460.97526.205-0.030-0.0300.0000.0000.0000.000
14A24GLY00.0100.00627.9560.0000.0000.0000.0000.0000.000
15A25VAL0-0.005-0.01124.4140.0000.0000.0000.0000.0000.000
16A26ARG10.9040.96227.707-0.067-0.0670.0000.0000.0000.000
17A27ALA00.0390.02927.8700.0030.0030.0000.0000.0000.000
18A28VAL0-0.032-0.02829.315-0.008-0.0080.0000.0000.0000.000
19A29GLN00.012-0.00731.6320.0020.0020.0000.0000.0000.000
20A30SER0-0.042-0.02733.577-0.008-0.0080.0000.0000.0000.000
21A31ASP-1-0.902-0.94034.5180.0850.0850.0000.0000.0000.000
22A32GLY00.0070.00334.2900.0030.0030.0000.0000.0000.000
23A33GLN0-0.041-0.01030.0340.0170.0170.0000.0000.0000.000
24A34ILE0-0.026-0.02627.656-0.010-0.0100.0000.0000.0000.000
25A35MET0-0.0190.00227.3610.0100.0100.0000.0000.0000.000
26A36PHE00.0130.00123.914-0.005-0.0050.0000.0000.0000.000
27A37LEU00.0050.01327.039-0.003-0.0030.0000.0000.0000.000
28A38SER00.0560.02328.0030.0010.0010.0000.0000.0000.000
29A39GLU-1-0.835-0.93129.4350.0480.0480.0000.0000.0000.000
30A40ASN0-0.009-0.00832.1520.0020.0020.0000.0000.0000.000
31A41GLY0-0.025-0.01432.913-0.003-0.0030.0000.0000.0000.000
32A42ARG10.9160.98030.484-0.033-0.0330.0000.0000.0000.000
33A43PHE00.012-0.00526.874-0.002-0.0020.0000.0000.0000.000
34A44VAL00.0200.00728.2580.0010.0010.0000.0000.0000.000
35A45ILE0-0.0080.00021.6130.0000.0000.0000.0000.0000.000
36A46SER00.0260.00624.7460.0040.0040.0000.0000.0000.000
37A47GLY00.011-0.00621.8580.0090.0090.0000.0000.0000.000
38A48GLN0-0.022-0.01019.266-0.021-0.0210.0000.0000.0000.000
39A49ILE00.0170.02419.2840.0190.0190.0000.0000.0000.000
40A50TYR00.001-0.01514.7100.0210.0210.0000.0000.0000.000
41A51ASP-1-0.820-0.90217.6600.2110.2110.0000.0000.0000.000
42A52LEU00.004-0.03212.0440.0220.0220.0000.0000.0000.000
43A53TRP0-0.0190.00115.5800.0130.0130.0000.0000.0000.000
44A54SER0-0.027-0.00617.876-0.013-0.0130.0000.0000.0000.000
45A55LYS10.8900.95714.401-0.321-0.3210.0000.0000.0000.000
46A56LYS10.9560.97617.206-0.192-0.1920.0000.0000.0000.000
47A57PRO00.0110.01619.015-0.002-0.0020.0000.0000.0000.000
48A58LEU0-0.047-0.02020.353-0.023-0.0230.0000.0000.0000.000
49A59ASN00.0690.02323.4110.0060.0060.0000.0000.0000.000
50A60THR00.0190.00425.874-0.009-0.0090.0000.0000.0000.000
51A61MET00.0410.01528.8540.0050.0050.0000.0000.0000.000
52A62SER0-0.025-0.00131.271-0.001-0.0010.0000.0000.0000.000
53A63GLN00.0600.02624.914-0.001-0.0010.0000.0000.0000.000
54A64MET00.0080.01724.9000.0020.0020.0000.0000.0000.000
55A65ARG10.9150.96128.370-0.088-0.0880.0000.0000.0000.000
56A66ASP-1-0.861-0.92427.9580.1190.1190.0000.0000.0000.000
57A67VAL00.0330.01024.145-0.003-0.0030.0000.0000.0000.000
58A68ALA0-0.068-0.01927.290-0.005-0.0050.0000.0000.0000.000
59A69GLU-1-0.976-0.99129.9710.0710.0710.0000.0000.0000.000
60A70ARG10.8270.91430.444-0.093-0.0930.0000.0000.0000.000
61A71ILE00.0230.02626.8840.0060.0060.0000.0000.0000.000
62A72HIS0-0.066-0.05126.324-0.009-0.0090.0000.0000.0000.000
63A73PHE00.0540.00125.6380.0100.0100.0000.0000.0000.000
64A74LYS10.9860.99524.817-0.074-0.0740.0000.0000.0000.000
65A75SER0-0.030-0.01123.9560.0080.0080.0000.0000.0000.000
66A76MET0-0.0280.00320.9880.0160.0160.0000.0000.0000.000
67A77GLY0-0.036-0.01520.3380.0080.0080.0000.0000.0000.000
68A78MET0-0.050-0.01621.587-0.012-0.0120.0000.0000.0000.000
69A79ASP-1-0.830-0.92323.8790.0620.0620.0000.0000.0000.000
70A80VAL00.0330.00626.787-0.006-0.0060.0000.0000.0000.000
71A81ASP-1-0.840-0.88729.5420.0440.0440.0000.0000.0000.000
72A82THR0-0.114-0.05425.948-0.006-0.0060.0000.0000.0000.000
73A83LEU0-0.031-0.00826.700-0.005-0.0050.0000.0000.0000.000
74A84ASN0-0.032-0.02130.167-0.003-0.0030.0000.0000.0000.000
75A85THR0-0.029-0.03632.494-0.001-0.0010.0000.0000.0000.000
76A86VAL0-0.0230.00235.379-0.003-0.0030.0000.0000.0000.000
77A87SER00.018-0.00338.3300.0030.0030.0000.0000.0000.000
78A88MET0-0.040-0.00439.981-0.003-0.0030.0000.0000.0000.000
79A89GLY00.0270.01142.7980.0020.0020.0000.0000.0000.000
80A90ARG10.8800.92740.818-0.035-0.0350.0000.0000.0000.000
81A91GLY00.0800.06743.7240.0000.0000.0000.0000.0000.000
82A92ASP-1-0.886-0.92540.9180.0460.0460.0000.0000.0000.000
83A93LYS10.8850.95838.728-0.046-0.0460.0000.0000.0000.000
84A94GLU-1-0.858-0.92733.2040.0610.0610.0000.0000.0000.000
85A95VAL0-0.0160.00336.4810.0030.0030.0000.0000.0000.000
86A96VAL00.0080.02132.253-0.003-0.0030.0000.0000.0000.000
87A97VAL0-0.017-0.02335.5120.0000.0000.0000.0000.0000.000
88A98PHE00.0210.03630.119-0.002-0.0020.0000.0000.0000.000
89A99VAL00.018-0.02335.835-0.001-0.0010.0000.0000.0000.000
90A100ASP-1-0.688-0.81238.0220.0160.0160.0000.0000.0000.000
91A101PRO00.023-0.00239.3600.0000.0000.0000.0000.0000.000
92A102ARG10.9140.96742.566-0.011-0.0110.0000.0000.0000.000
93A103CYS0-0.0460.00441.9080.0020.0020.0000.0000.0000.000
94A104ALA00.0560.03044.5320.0010.0010.0000.0000.0000.000
95A105VAL00.0080.00744.7820.0010.0010.0000.0000.0000.000
96A107HIS00.0260.00044.0940.0010.0010.0000.0000.0000.000
97A108GLN0-0.023-0.02047.0450.0000.0000.0000.0000.0000.000
98A109LEU0-0.0450.00141.8750.0000.0000.0000.0000.0000.000
99A110MET00.0060.00143.3520.0010.0010.0000.0000.0000.000
100A111GLY0-0.007-0.00645.7950.0000.0000.0000.0000.0000.000
101A112ASP-1-0.830-0.89247.8680.0270.0270.0000.0000.0000.000
102A113ALA00.005-0.00544.8360.0010.0010.0000.0000.0000.000
103A114LYS10.9600.98546.762-0.021-0.0210.0000.0000.0000.000
104A115SER0-0.092-0.03149.1780.0000.0000.0000.0000.0000.000
105A116LEU0-0.040-0.03346.0640.0010.0010.0000.0000.0000.000
106A117VAL0-0.009-0.00845.9790.0020.0020.0000.0000.0000.000
107A118ASP-1-0.904-0.94046.4880.0300.0300.0000.0000.0000.000
108A119ASP-1-0.926-0.94545.6040.0390.0390.0000.0000.0000.000
109A120TYR0-0.123-0.08541.0670.0040.0040.0000.0000.0000.000
110A121THR0-0.052-0.03739.190-0.004-0.0040.0000.0000.0000.000
111A122PHE0-0.012-0.01739.1970.0040.0040.0000.0000.0000.000
112A123LYS10.8170.87834.202-0.054-0.0540.0000.0000.0000.000
113A124PHE00.018-0.00636.6680.0020.0020.0000.0000.0000.000
114A125ILE00.003-0.00431.235-0.002-0.0020.0000.0000.0000.000
115A126VAL0-0.008-0.00235.147-0.001-0.0010.0000.0000.0000.000
116A127ILE00.022-0.00332.1740.0000.0000.0000.0000.0000.000
117A128PRO0-0.050-0.02433.968-0.001-0.0010.0000.0000.0000.000
118A129ALA00.0200.00135.623-0.002-0.0020.0000.0000.0000.000
119A130LEU0-0.062-0.02636.598-0.001-0.0010.0000.0000.0000.000
120A131GLY0-0.0010.01338.533-0.002-0.0020.0000.0000.0000.000
121A132ALA00.0370.00239.4330.0000.0000.0000.0000.0000.000
122A133GLU-1-0.804-0.87841.2110.0030.0030.0000.0000.0000.000
123A134SER0-0.057-0.07039.8720.0000.0000.0000.0000.0000.000
124A135ASN00.0300.00135.6540.0010.0010.0000.0000.0000.000
125A136ARG10.8480.91238.694-0.003-0.0030.0000.0000.0000.000
126A137LEU00.0230.00841.3590.0000.0000.0000.0000.0000.000
127A138ALA00.0500.02236.8280.0010.0010.0000.0000.0000.000
128A139LYS10.9510.97735.5650.0050.0050.0000.0000.0000.000
129A140ASN00.0070.00638.2310.0000.0000.0000.0000.0000.000
130A141LEU00.0430.02838.3330.0000.0000.0000.0000.0000.000
131A142TYR00.0120.00830.677-0.001-0.0010.0000.0000.0000.000
132A143CYS0-0.114-0.07135.9190.0010.0010.0000.0000.0000.000
133A144ALA00.0150.01638.828-0.001-0.0010.0000.0000.0000.000
134A145LYS10.9530.96440.857-0.001-0.0010.0000.0000.0000.000
135A146ASP-1-0.862-0.93042.1680.0120.0120.0000.0000.0000.000
136A147LYS10.7960.88837.869-0.012-0.0120.0000.0000.0000.000
137A148THR0-0.040-0.02242.5200.0020.0020.0000.0000.0000.000
138A149HIS00.0620.03645.4090.0010.0010.0000.0000.0000.000
139A150ALA0-0.042-0.02642.0540.0000.0000.0000.0000.0000.000
140A151LEU0-0.0030.00343.2280.0000.0000.0000.0000.0000.000
141A152ASP-1-0.830-0.92244.6560.0180.0180.0000.0000.0000.000
142A153ALA0-0.020-0.01045.9500.0000.0000.0000.0000.0000.000
143A154LEU0-0.052-0.03440.921-0.001-0.0010.0000.0000.0000.000
144A155MET0-0.043-0.03644.8150.0010.0010.0000.0000.0000.000
145A156ASN0-0.0290.00047.2270.0010.0010.0000.0000.0000.000
146A157ASN0-0.039-0.00547.419-0.001-0.0010.0000.0000.0000.000
147A158THR00.0350.00748.492-0.001-0.0010.0000.0000.0000.000
148A159LEU00.019-0.00242.181-0.001-0.0010.0000.0000.0000.000
149A160GLY0-0.039-0.01445.757-0.001-0.0010.0000.0000.0000.000
150A161SER0-0.051-0.01147.215-0.001-0.0010.0000.0000.0000.000
151A162LEU00.0020.00343.6620.0000.0000.0000.0000.0000.000
152A163PRO00.0090.00345.841-0.001-0.0010.0000.0000.0000.000
153A164SER0-0.0040.00641.9750.0010.0010.0000.0000.0000.000
154A165LYS10.9090.95036.003-0.006-0.0060.0000.0000.0000.000
155A166GLU-1-0.929-0.95941.258-0.008-0.0080.0000.0000.0000.000
156A167THR0-0.022-0.00936.239-0.002-0.0020.0000.0000.0000.000
157A169ASP-1-0.909-0.94435.250-0.012-0.0120.0000.0000.0000.000
158A170PRO00.0000.00832.357-0.002-0.0020.0000.0000.0000.000
159A171GLY00.0620.03431.263-0.002-0.0020.0000.0000.0000.000
160A172GLN0-0.049-0.04532.2600.0040.0040.0000.0000.0000.000
161A173TYR0-0.024-0.00928.6310.0020.0020.0000.0000.0000.000
162A174ASP-1-0.796-0.89629.2830.0180.0180.0000.0000.0000.000
163A175GLN00.0740.02625.3300.0080.0080.0000.0000.0000.000
164A176THR00.0500.04727.3410.0070.0070.0000.0000.0000.000
165A177LEU0-0.025-0.02829.2360.0040.0040.0000.0000.0000.000
166A178LEU0-0.031-0.01724.9070.0030.0030.0000.0000.0000.000
167A179THR0-0.008-0.01124.0980.0060.0060.0000.0000.0000.000
168A180ALA00.010-0.00125.5620.0080.0080.0000.0000.0000.000
169A181HIS0-0.015-0.01126.4210.0050.0050.0000.0000.0000.000
170A182PHE0-0.047-0.01717.8840.0040.0040.0000.0000.0000.000
171A183ILE0-0.059-0.03922.7130.0090.0090.0000.0000.0000.000
172A184GLY00.0390.02924.5100.0060.0060.0000.0000.0000.000
173A185ILE0-0.053-0.01527.379-0.002-0.0020.0000.0000.0000.000
174A186GLU-1-0.881-0.91830.5040.0480.0480.0000.0000.0000.000
175A187GLY0-0.043-0.02533.3050.0000.0000.0000.0000.0000.000
176A188VAL0-0.0280.01336.1840.0020.0020.0000.0000.0000.000
177A189PRO0-0.002-0.04938.685-0.002-0.0020.0000.0000.0000.000
178A190PHE0-0.0020.00832.1440.0000.0000.0000.0000.0000.000
179A191VAL0-0.033-0.01736.3250.0000.0000.0000.0000.0000.000
180A192VAL00.0240.01031.7870.0020.0020.0000.0000.0000.000
181A193ALA0-0.009-0.01135.038-0.003-0.0030.0000.0000.0000.000
182A194PRO00.0390.01635.0600.0040.0040.0000.0000.0000.000
183A195ASP-1-0.825-0.90134.6400.0750.0750.0000.0000.0000.000
184A196GLY00.0520.00832.0750.0060.0060.0000.0000.0000.000
185A197ARG10.7930.89332.621-0.060-0.0600.0000.0000.0000.000
186A198VAL00.0500.04131.835-0.004-0.0040.0000.0000.0000.000
187A199SER0-0.073-0.05735.110-0.002-0.0020.0000.0000.0000.000
188A200LYS10.8550.92334.935-0.048-0.0480.0000.0000.0000.000
189A201GLY00.0670.02937.919-0.003-0.0030.0000.0000.0000.000
190A202ARG10.8400.89541.096-0.026-0.0260.0000.0000.0000.000
191A203PRO0-0.0020.01242.025-0.001-0.0010.0000.0000.0000.000
192A204LYS10.9500.97244.664-0.035-0.0350.0000.0000.0000.000
193A205ASN00.0580.03347.8160.0000.0000.0000.0000.0000.000
194A206LEU00.0470.02842.9330.0020.0020.0000.0000.0000.000
195A207LYS11.0181.01145.308-0.032-0.0320.0000.0000.0000.000
196A208SER0-0.008-0.02446.5580.0020.0020.0000.0000.0000.000
197A209TRP0-0.009-0.00237.7540.0010.0010.0000.0000.0000.000
198A210LEU00.0170.00940.7990.0030.0030.0000.0000.0000.000
199A211GLU-1-0.931-0.93741.6550.0470.0470.0000.0000.0000.000
200A212SER0-0.081-0.03640.6630.0030.0030.0000.0000.0000.000