FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: J3139

Calculation Name: 4G1L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G1L

Chain ID: A

ChEMBL ID:

UniProt ID: P11206

Base Structure: X-ray

Registration Date: 2023-06-20

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 337
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4994790.597322
FMO2-HF: Nuclear repulsion 4866764.024048
FMO2-HF: Total energy -128026.573274
FMO2-MP2: Total energy -128403.051667


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:14:ALA)


Summations of interaction energy for fragment #1(A:14: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.
8.602-12.56613.77414.985-7.592-0.062
Interaction energy analysis for fragmet #1(A:14:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / 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].
3A16PRO0-0.0340.0002.20019.100-0.2180.54320.453-1.678-0.010
4A17SER00.0630.0144.5770.6750.853-0.001-0.008-0.1690.000
5A18SER00.010-0.0056.6510.1110.1110.0000.0000.0000.000
6A19ASN0-0.036-0.0152.5670.2952.2521.224-1.320-1.860-0.013
7A20LEU00.0360.0236.2520.1320.1320.0000.0000.0000.000
8A21LEU0-0.053-0.0309.093-0.100-0.1000.0000.0000.0000.000
9A22ALA0-0.012-0.0129.724-0.112-0.1120.0000.0000.0000.000
10A23PHE00.0060.04411.442-0.029-0.0290.0000.0000.0000.000
11A24PRO00.028-0.00913.734-0.085-0.0850.0000.0000.0000.000
12A25ILE0-0.014-0.01712.9420.0180.0180.0000.0000.0000.000
13A26VAL00.005-0.0239.3420.2170.2170.0000.0000.0000.000
14A27LEU00.0150.0007.064-0.152-0.1520.0000.0000.0000.000
15A28GLN0-0.027-0.00610.598-0.164-0.1640.0000.0000.0000.000
16A29ASP-1-0.869-0.96012.5860.4750.4750.0000.0000.0000.000
17A30ILE00.0090.03115.220-0.054-0.0540.0000.0000.0000.000
18A31GLY0-0.005-0.00617.448-0.040-0.0400.0000.0000.0000.000
19A32ASP-1-0.769-0.86414.8470.4190.4190.0000.0000.0000.000
20A33GLY00.0410.00815.505-0.055-0.0550.0000.0000.0000.000
21A34LYS10.7650.87317.282-0.350-0.3500.0000.0000.0000.000
22A35LYS10.9340.93118.422-0.221-0.2210.0000.0000.0000.000
23A36GLN00.0400.06317.581-0.016-0.0160.0000.0000.0000.000
24A37ILE00.0320.00211.574-0.037-0.0370.0000.0000.0000.000
25A38ALA00.0060.00213.841-0.008-0.0080.0000.0000.0000.000
26A39PRO00.0310.02714.092-0.006-0.0060.0000.0000.0000.000
27A40GLN0-0.040-0.02610.548-0.036-0.0360.0000.0000.0000.000
28A41TYR00.002-0.00315.1070.0240.0240.0000.0000.0000.000
29A42ARG10.8310.90912.5240.2650.2650.0000.0000.0000.000
30A43ILE00.0370.01716.8400.0340.0340.0000.0000.0000.000
31A44GLN0-0.057-0.01818.601-0.050-0.0500.0000.0000.0000.000
32A45ARG10.8470.89120.4450.1670.1670.0000.0000.0000.000
33A46LEU0-0.051-0.02522.595-0.015-0.0150.0000.0000.0000.000
34A47ASP-1-0.829-0.92324.910-0.135-0.1350.0000.0000.0000.000
35A48SER0-0.020-0.01326.1150.0040.0040.0000.0000.0000.000
36A49TRP0-0.0010.00628.0780.0050.0050.0000.0000.0000.000
37A50THR0-0.050-0.02131.2870.0070.0070.0000.0000.0000.000
38A51ASP-1-0.778-0.84729.657-0.117-0.1170.0000.0000.0000.000
39A52SER00.0410.02632.5790.0070.0070.0000.0000.0000.000
40A53LYS10.9850.98433.9050.0530.0530.0000.0000.0000.000
41A54GLU-1-0.879-0.93435.772-0.048-0.0480.0000.0000.0000.000
42A55ASP-1-0.844-0.91030.993-0.088-0.0880.0000.0000.0000.000
43A56SER0-0.065-0.03330.3620.0080.0080.0000.0000.0000.000
44A57VAL00.0120.00125.736-0.011-0.0110.0000.0000.0000.000
45A58PHE0-0.007-0.02624.7950.0130.0130.0000.0000.0000.000
46A59ILE00.0340.02122.998-0.017-0.0170.0000.0000.0000.000
47A60THR0-0.057-0.04418.9650.0220.0220.0000.0000.0000.000
48A61THR0-0.024-0.01719.468-0.007-0.0070.0000.0000.0000.000
49A62TYR00.020-0.02715.0580.0120.0120.0000.0000.0000.000
50A63GLY00.0260.00116.335-0.018-0.0180.0000.0000.0000.000
51A64PHE0-0.027-0.00412.4490.0190.0190.0000.0000.0000.000
52A65ILE00.0220.00918.283-0.034-0.0340.0000.0000.0000.000
53A66PHE0-0.016-0.03118.5120.0300.0300.0000.0000.0000.000
54A67GLN00.010-0.01822.999-0.031-0.0310.0000.0000.0000.000
55A68VAL0-0.0330.00526.1260.0050.0050.0000.0000.0000.000
56A82PRO0-0.029-0.02324.901-0.005-0.0050.0000.0000.0000.000
57A83LYS11.0191.01127.325-0.102-0.1020.0000.0000.0000.000
58A84HIS10.8050.86323.677-0.153-0.1530.0000.0000.0000.000
59A85GLU-1-0.870-0.92522.7830.2460.2460.0000.0000.0000.000
60A86LEU0-0.0240.02215.320-0.020-0.0200.0000.0000.0000.000
61A87LEU00.0200.02620.0200.0200.0200.0000.0000.0000.000
62A88SER00.009-0.03217.9220.0400.0400.0000.0000.0000.000
63A89ALA00.0190.03414.377-0.038-0.0380.0000.0000.0000.000
64A90ALA0-0.011-0.00516.494-0.015-0.0150.0000.0000.0000.000
65A91MET0-0.0020.00217.750-0.016-0.0160.0000.0000.0000.000
66A92LEU00.0080.01719.368-0.004-0.0040.0000.0000.0000.000
67A93CYS0-0.0490.00322.480-0.015-0.0150.0000.0000.0000.000
68A94LEU00.0900.02823.9990.0070.0070.0000.0000.0000.000
69A95GLY0-0.0050.00326.5530.0040.0040.0000.0000.0000.000
70A96SER0-0.023-0.03027.239-0.005-0.0050.0000.0000.0000.000
71A97VAL00.0460.02529.0670.0070.0070.0000.0000.0000.000
72A98PRO00.0380.01230.775-0.008-0.0080.0000.0000.0000.000
73A99ASN0-0.074-0.02329.830-0.004-0.0040.0000.0000.0000.000
74A100VAL0-0.023-0.02431.889-0.002-0.0020.0000.0000.0000.000
75A101GLY0-0.0060.00131.8650.0010.0010.0000.0000.0000.000
76A102ASP-1-0.807-0.91427.830-0.110-0.1100.0000.0000.0000.000
77A103LEU0-0.022-0.01625.1760.0020.0020.0000.0000.0000.000
78A104VAL00.013-0.00122.4660.0010.0010.0000.0000.0000.000
79A105GLU-1-0.799-0.88824.443-0.058-0.0580.0000.0000.0000.000
80A106LEU00.0000.01526.2490.0120.0120.0000.0000.0000.000
81A107ALA00.005-0.01321.4410.0100.0100.0000.0000.0000.000
82A108ARG10.8590.89923.1440.0810.0810.0000.0000.0000.000
83A109ALA00.0170.01224.5250.0140.0140.0000.0000.0000.000
84A110CYS0-0.076-0.04923.0100.0100.0100.0000.0000.0000.000
85A111LEU0-0.039-0.01919.6020.0140.0140.0000.0000.0000.000
86A112THR0-0.038-0.01923.4440.0100.0100.0000.0000.0000.000
87A113MET0-0.046-0.00824.9690.0010.0010.0000.0000.0000.000
88A114VAL0-0.0190.00326.5850.0090.0090.0000.0000.0000.000
89A115VAL0-0.013-0.00925.919-0.006-0.0060.0000.0000.0000.000
90A116THR00.0410.02227.2820.0100.0100.0000.0000.0000.000
91A117CYS0-0.028-0.01726.319-0.003-0.0030.0000.0000.0000.000
92A118LYS10.9811.01028.941-0.066-0.0660.0000.0000.0000.000
93A119LYS10.8820.94427.663-0.143-0.1430.0000.0000.0000.000
94A120SER0-0.024-0.02530.960-0.009-0.0090.0000.0000.0000.000
95A121ALA00.0260.00732.4720.0070.0070.0000.0000.0000.000
96A122THR0-0.032-0.00634.470-0.003-0.0030.0000.0000.0000.000
97A123ASP-1-0.879-0.91334.6130.0510.0510.0000.0000.0000.000
98A124THR0-0.015-0.02230.6130.0030.0030.0000.0000.0000.000
99A125GLU-1-0.800-0.90428.4420.1280.1280.0000.0000.0000.000
100A126ARG10.7860.87129.373-0.054-0.0540.0000.0000.0000.000
101A127MET00.0160.02325.2590.0060.0060.0000.0000.0000.000
102A128VAL0-0.032-0.02128.282-0.010-0.0100.0000.0000.0000.000
103A129PHE00.018-0.00923.4350.0060.0060.0000.0000.0000.000
104A130SER0-0.008-0.01329.186-0.008-0.0080.0000.0000.0000.000
105A131VAL00.003-0.00229.7650.0050.0050.0000.0000.0000.000
106A132VAL0-0.005-0.00931.150-0.003-0.0030.0000.0000.0000.000
107A133GLN0-0.004-0.01631.597-0.001-0.0010.0000.0000.0000.000
108A134ALA00.0570.02930.5810.0030.0030.0000.0000.0000.000
109A135PRO00.0260.03329.359-0.002-0.0020.0000.0000.0000.000
110A136GLN00.0820.02232.3540.0020.0020.0000.0000.0000.000
111A137VAL00.0070.00430.3340.0000.0000.0000.0000.0000.000
112A138LEU0-0.001-0.01227.402-0.004-0.0040.0000.0000.0000.000
113A139GLN0-0.014-0.00431.4890.0040.0040.0000.0000.0000.000
114A140SER00.0280.03034.2970.0020.0020.0000.0000.0000.000
115A141CYS0-0.087-0.01030.1250.0010.0010.0000.0000.0000.000
116A142ARG10.9330.94631.8680.0070.0070.0000.0000.0000.000
117A143VAL00.0100.01028.1880.0040.0040.0000.0000.0000.000
118A144VAL00.002-0.01629.8300.0050.0050.0000.0000.0000.000
119A145ALA0-0.0220.00432.4310.0030.0030.0000.0000.0000.000
120A146ASN00.0030.00134.511-0.002-0.0020.0000.0000.0000.000
121A147LYS10.9360.98534.224-0.023-0.0230.0000.0000.0000.000
122A148TYR0-0.026-0.00832.3790.0080.0080.0000.0000.0000.000
123A149SER00.0200.01628.234-0.006-0.0060.0000.0000.0000.000
124A150SER00.0280.02830.0810.0110.0110.0000.0000.0000.000
125A151VAL00.0030.02425.343-0.007-0.0070.0000.0000.0000.000
126A152ASN00.0320.00826.1480.0160.0160.0000.0000.0000.000
127A153ALA00.0940.03325.3320.0020.0020.0000.0000.0000.000
128A154VAL00.0250.01622.9230.0160.0160.0000.0000.0000.000
129A155LYS10.8620.92321.629-0.034-0.0340.0000.0000.0000.000
130A156HIS0-0.068-0.03920.755-0.012-0.0120.0000.0000.0000.000
131A157VAL00.0470.03420.1850.0050.0050.0000.0000.0000.000
132A158LYS10.8820.96512.709-0.541-0.5410.0000.0000.0000.000
133A159ALA00.001-0.00617.8790.0070.0070.0000.0000.0000.000
134A160PRO0-0.017-0.00520.503-0.005-0.0050.0000.0000.0000.000
135A161GLU-1-0.855-0.93021.8220.2460.2460.0000.0000.0000.000
136A162LYS10.9020.96818.963-0.387-0.3870.0000.0000.0000.000
137A163ILE0-0.062-0.03222.557-0.002-0.0020.0000.0000.0000.000
138A164PRO00.0390.02226.155-0.011-0.0110.0000.0000.0000.000
139A165GLY0-0.015-0.00829.696-0.004-0.0040.0000.0000.0000.000
140A166SER0-0.038-0.02232.636-0.007-0.0070.0000.0000.0000.000
141A167GLY00.0930.05131.9500.0090.0090.0000.0000.0000.000
142A168THR0-0.035-0.01731.010-0.009-0.0090.0000.0000.0000.000
143A169LEU0-0.011-0.00626.5070.0110.0110.0000.0000.0000.000
144A170GLU-1-0.807-0.89825.6680.1050.1050.0000.0000.0000.000
145A171TYR0-0.053-0.02719.7040.0240.0240.0000.0000.0000.000
146A172LYS10.7900.87917.811-0.132-0.1320.0000.0000.0000.000
147A173VAL00.0480.02219.4310.0210.0210.0000.0000.0000.000
148A174ASN0-0.0090.00313.6060.0010.0010.0000.0000.0000.000
149A175PHE00.0040.01510.575-0.018-0.0180.0000.0000.0000.000
150A176VAL00.0190.01416.0180.0160.0160.0000.0000.0000.000
151A177SER0-0.036-0.03416.431-0.055-0.0550.0000.0000.0000.000
152A178LEU00.0100.01818.3170.0240.0240.0000.0000.0000.000
153A179THR0-0.005-0.03320.634-0.038-0.0380.0000.0000.0000.000
154A180VAL0-0.0030.01622.7470.0170.0170.0000.0000.0000.000
155A181VAL0-0.023-0.02526.099-0.013-0.0130.0000.0000.0000.000
156A182PRO00.0450.02928.0590.0080.0080.0000.0000.0000.000
157A183ARG10.9971.00031.5470.0520.0520.0000.0000.0000.000
158A184LYS10.7520.85629.7310.1060.1060.0000.0000.0000.000
159A185ASP-1-0.893-0.93731.304-0.055-0.0550.0000.0000.0000.000
160A186VAL0-0.054-0.02627.3210.0050.0050.0000.0000.0000.000
161A187TYR0-0.055-0.05429.2460.0030.0030.0000.0000.0000.000
162A188LYS10.9570.98927.7000.0270.0270.0000.0000.0000.000
163A189ILE00.0060.00930.5240.0040.0040.0000.0000.0000.000
164A190PRO00.0160.01832.2520.0040.0040.0000.0000.0000.000
165A191THR00.053-0.01232.060-0.002-0.0020.0000.0000.0000.000
166A192ALA00.0080.00633.8480.0010.0010.0000.0000.0000.000
167A193ALA00.0410.02136.5200.0010.0010.0000.0000.0000.000
168A194LEU0-0.035-0.00930.202-0.002-0.0020.0000.0000.0000.000
169A195LYS10.9250.95934.330-0.013-0.0130.0000.0000.0000.000
170A196VAL0-0.0010.01936.5850.0020.0020.0000.0000.0000.000
171A197SER0-0.033-0.02038.678-0.001-0.0010.0000.0000.0000.000
172A198GLY00.0280.00540.9810.0010.0010.0000.0000.0000.000
173A199SER00.0170.00643.342-0.002-0.0020.0000.0000.0000.000
174A200SER00.0000.00945.688-0.001-0.0010.0000.0000.0000.000
175A201LEU0-0.036-0.01841.279-0.003-0.0030.0000.0000.0000.000
176A202TYR0-0.015-0.00238.6060.0020.0020.0000.0000.0000.000
177A203ASN00.0250.02633.295-0.006-0.0060.0000.0000.0000.000
178A204LEU0-0.020-0.02432.655-0.002-0.0020.0000.0000.0000.000
179A205ALA00.0610.03329.5630.0020.0020.0000.0000.0000.000
180A206LEU0-0.036-0.00925.581-0.007-0.0070.0000.0000.0000.000
181A207ASN00.0360.03024.0030.0080.0080.0000.0000.0000.000
182A208VAL0-0.023-0.01619.126-0.019-0.0190.0000.0000.0000.000
183A209THR00.0160.01818.0810.0090.0090.0000.0000.0000.000
184A210ILE0-0.061-0.05012.975-0.036-0.0360.0000.0000.0000.000
185A211ASP-1-0.799-0.89911.288-0.306-0.3060.0000.0000.0000.000
186A212VAL0-0.052-0.0488.576-0.070-0.0700.0000.0000.0000.000
187A213GLU-1-0.774-0.8531.849-10.523-15.85711.770-3.679-2.758-0.040
188A214VAL0-0.005-0.0133.986-0.1490.1080.004-0.069-0.1930.000
189A215ASP-1-0.774-0.8832.5980.9031.7660.234-0.357-0.7400.001
190A216PRO0-0.007-0.0104.403-0.793-0.7030.001-0.033-0.0580.000
191A217LYS10.9020.9436.221-1.493-1.4930.0000.0000.0000.000
192A218SER0-0.0100.0036.285-0.319-0.3190.0000.0000.0000.000
193A219PRO00.0160.0018.185-0.253-0.2530.0000.0000.0000.000
194A220LEU0-0.024-0.0239.279-0.219-0.2190.0000.0000.0000.000
195A221VAL0-0.0130.0029.633-0.193-0.1930.0000.0000.0000.000
196A222LYS10.9400.97211.222-0.667-0.6670.0000.0000.0000.000
197A223SER0-0.0090.00614.606-0.044-0.0440.0000.0000.0000.000
198A224LEU0-0.081-0.01810.380-0.067-0.0670.0000.0000.0000.000
199A225SER00.0320.01614.7410.0060.0060.0000.0000.0000.000
200A226LYS10.8850.92414.3130.0010.0010.0000.0000.0000.000
201A227SER0-0.050-0.02214.809-0.024-0.0240.0000.0000.0000.000
202A228ASP-1-0.805-0.90715.256-0.053-0.0530.0000.0000.0000.000
203A229SER0-0.042-0.01614.688-0.021-0.0210.0000.0000.0000.000
204A230GLY00.0250.02111.152-0.111-0.1110.0000.0000.0000.000
205A231TYR00.0270.0138.8410.1060.1060.0000.0000.0000.000
206A232TYR0-0.005-0.00411.199-0.112-0.1120.0000.0000.0000.000
207A233ALA00.0030.00913.5080.0710.0710.0000.0000.0000.000
208A234ASN00.008-0.01015.597-0.070-0.0700.0000.0000.0000.000
209A235LEU0-0.011-0.01019.2910.0230.0230.0000.0000.0000.000
210A236PHE00.0200.01521.147-0.016-0.0160.0000.0000.0000.000
211A237LEU0-0.016-0.00823.6100.0090.0090.0000.0000.0000.000
212A238HIS0-0.010-0.00626.347-0.005-0.0050.0000.0000.0000.000
213A239ILE0-0.040-0.04127.185-0.002-0.0020.0000.0000.0000.000
214A240GLY00.0450.01430.752-0.003-0.0030.0000.0000.0000.000
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