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: N141Q

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 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 337
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4994587.40413
FMO2-HF: Nuclear repulsion 4866563.808674
FMO2-HF: Total energy -128023.595456
FMO2-MP2: Total energy -128400.266197


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.
6.885-7.9923.56117.917-6.6-0.042
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 : 0.018 / q_NPA : 0.026
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].
3A16PRO0-0.033-0.0062.46019.216-0.424-0.19321.471-1.638-0.005
4A17SER00.0560.0164.580-0.0270.154-0.001-0.008-0.1710.000
5A18SER0-0.003-0.0166.7720.0790.0790.0000.0000.0000.000
6A19ASN0-0.024-0.0142.152-5.661-3.7253.389-2.399-2.927-0.035
7A20LEU00.0310.0225.8230.3190.3190.0000.0000.0000.000
8A21LEU0-0.048-0.0329.1070.0870.0870.0000.0000.0000.000
9A22ALA0-0.005-0.0109.000-0.003-0.0030.0000.0000.0000.000
10A23PHE0-0.0250.04010.8390.0530.0530.0000.0000.0000.000
11A24PRO00.0540.00113.350-0.048-0.0480.0000.0000.0000.000
12A25ILE0-0.027-0.02412.4150.0340.0340.0000.0000.0000.000
13A26VAL00.007-0.0249.2110.0620.0620.0000.0000.0000.000
14A27LEU00.014-0.0026.916-0.056-0.0560.0000.0000.0000.000
15A28GLN0-0.013-0.00310.542-0.112-0.1120.0000.0000.0000.000
16A29ASP-1-0.937-0.98612.4820.2090.2090.0000.0000.0000.000
17A30ILE00.0250.04015.140-0.036-0.0360.0000.0000.0000.000
18A31GLY0-0.006-0.00917.288-0.030-0.0300.0000.0000.0000.000
19A32ASP-1-0.772-0.86114.8740.1370.1370.0000.0000.0000.000
20A33GLY00.0340.00615.749-0.021-0.0210.0000.0000.0000.000
21A34LYS10.7690.87317.609-0.120-0.1200.0000.0000.0000.000
22A35LYS10.9280.93318.428-0.056-0.0560.0000.0000.0000.000
23A36GLN0-0.0170.01717.565-0.010-0.0100.0000.0000.0000.000
24A37ILE00.0320.00511.555-0.013-0.0130.0000.0000.0000.000
25A38ALA0-0.021-0.01213.960-0.013-0.0130.0000.0000.0000.000
26A39PRO00.0730.04814.086-0.037-0.0370.0000.0000.0000.000
27A40GLN0-0.062-0.04410.551-0.063-0.0630.0000.0000.0000.000
28A41TYR0-0.007-0.00515.1040.0190.0190.0000.0000.0000.000
29A42ARG10.8720.91512.3640.4440.4440.0000.0000.0000.000
30A43ILE00.0360.01717.1550.0310.0310.0000.0000.0000.000
31A44GLN0-0.074-0.03919.147-0.032-0.0320.0000.0000.0000.000
32A45ARG10.9740.98020.8960.2020.2020.0000.0000.0000.000
33A46LEU0-0.044-0.01822.736-0.010-0.0100.0000.0000.0000.000
34A47ASP-1-0.898-0.96525.294-0.137-0.1370.0000.0000.0000.000
35A48SER0-0.057-0.02826.4310.0020.0020.0000.0000.0000.000
36A49TRP00.0020.00328.3770.0050.0050.0000.0000.0000.000
37A50THR0-0.049-0.01531.6060.0070.0070.0000.0000.0000.000
38A51ASP-1-0.893-0.93630.425-0.134-0.1340.0000.0000.0000.000
39A52SER00.0510.03933.0040.0080.0080.0000.0000.0000.000
40A53LYS10.9970.98934.2990.0760.0760.0000.0000.0000.000
41A54GLU-1-0.964-0.99036.091-0.072-0.0720.0000.0000.0000.000
42A55ASP-1-0.869-0.92631.334-0.112-0.1120.0000.0000.0000.000
43A56SER0-0.090-0.05230.4290.0050.0050.0000.0000.0000.000
44A57VAL00.0120.00825.899-0.011-0.0110.0000.0000.0000.000
45A58PHE0-0.001-0.02724.8180.0090.0090.0000.0000.0000.000
46A59ILE00.0480.03023.078-0.021-0.0210.0000.0000.0000.000
47A60THR0-0.060-0.04118.8230.0270.0270.0000.0000.0000.000
48A61THR0-0.031-0.02619.436-0.019-0.0190.0000.0000.0000.000
49A62TYR00.014-0.01914.892-0.003-0.0030.0000.0000.0000.000
50A63GLY00.023-0.00516.272-0.010-0.0100.0000.0000.0000.000
51A64PHE0-0.031-0.01012.3980.0000.0000.0000.0000.0000.000
52A65ILE00.0190.01118.231-0.007-0.0070.0000.0000.0000.000
53A66PHE0-0.020-0.02818.4590.0140.0140.0000.0000.0000.000
54A67GLN00.0440.00923.010-0.013-0.0130.0000.0000.0000.000
55A68VAL0-0.0260.00426.1370.0050.0050.0000.0000.0000.000
56A82PRO00.003-0.01924.762-0.004-0.0040.0000.0000.0000.000
57A83LYS11.0081.01927.324-0.020-0.0200.0000.0000.0000.000
58A84HIS10.8710.91123.665-0.025-0.0250.0000.0000.0000.000
59A85GLU-1-0.900-0.95222.2670.0970.0970.0000.0000.0000.000
60A86LEU0-0.0250.02515.298-0.017-0.0170.0000.0000.0000.000
61A87LEU00.0270.02520.0300.0140.0140.0000.0000.0000.000
62A88SER00.013-0.01517.5250.0230.0230.0000.0000.0000.000
63A89ALA00.0130.02813.939-0.019-0.0190.0000.0000.0000.000
64A90ALA0-0.009-0.01516.0320.0160.0160.0000.0000.0000.000
65A91MET0-0.024-0.01517.479-0.027-0.0270.0000.0000.0000.000
66A92LEU00.0460.03019.0950.0160.0160.0000.0000.0000.000
67A93CYS0-0.0570.01222.268-0.017-0.0170.0000.0000.0000.000
68A94LEU00.0820.02623.9080.0120.0120.0000.0000.0000.000
69A95GLY0-0.013-0.00226.5560.0110.0110.0000.0000.0000.000
70A96SER0-0.027-0.03327.315-0.009-0.0090.0000.0000.0000.000
71A97VAL00.0420.02429.1030.0080.0080.0000.0000.0000.000
72A98PRO00.0350.00330.988-0.008-0.0080.0000.0000.0000.000
73A99ASN0-0.071-0.01130.424-0.010-0.0100.0000.0000.0000.000
74A100VAL0-0.010-0.01532.2000.0030.0030.0000.0000.0000.000
75A101GLY0-0.015-0.00432.127-0.003-0.0030.0000.0000.0000.000
76A102ASP-1-0.844-0.92428.234-0.146-0.1460.0000.0000.0000.000
77A103LEU00.000-0.01725.621-0.005-0.0050.0000.0000.0000.000
78A104VAL00.003-0.00822.735-0.009-0.0090.0000.0000.0000.000
79A105GLU-1-0.835-0.91824.440-0.126-0.1260.0000.0000.0000.000
80A106LEU0-0.0070.00926.6900.0060.0060.0000.0000.0000.000
81A107ALA0-0.017-0.02421.4650.0010.0010.0000.0000.0000.000
82A108ARG10.9130.95123.1460.1360.1360.0000.0000.0000.000
83A109ALA00.0260.01224.5230.0090.0090.0000.0000.0000.000
84A110CYS0-0.062-0.04123.0830.0090.0090.0000.0000.0000.000
85A111LEU0-0.036-0.02519.6580.0020.0020.0000.0000.0000.000
86A112THR0-0.053-0.01623.4460.0110.0110.0000.0000.0000.000
87A113MET0-0.021-0.00724.7450.0090.0090.0000.0000.0000.000
88A114VAL0-0.0160.00926.5910.0010.0010.0000.0000.0000.000
89A115VAL0-0.021-0.01125.7970.0000.0000.0000.0000.0000.000
90A116THR00.0580.03227.2730.0050.0050.0000.0000.0000.000
91A117CYS0-0.038-0.02424.939-0.004-0.0040.0000.0000.0000.000
92A118LYS11.0041.01728.5960.0110.0110.0000.0000.0000.000
93A119LYS10.8870.94726.630-0.033-0.0330.0000.0000.0000.000
94A120SER0-0.032-0.02130.430-0.001-0.0010.0000.0000.0000.000
95A121ALA00.0270.00631.9860.0020.0020.0000.0000.0000.000
96A122THR0-0.069-0.01434.011-0.002-0.0020.0000.0000.0000.000
97A123ASP-1-0.849-0.91334.541-0.010-0.0100.0000.0000.0000.000
98A124THR0-0.029-0.02629.9820.0020.0020.0000.0000.0000.000
99A125GLU-1-0.846-0.94027.7880.0210.0210.0000.0000.0000.000
100A126ARG10.7630.84928.9520.0200.0200.0000.0000.0000.000
101A127MET00.0200.02024.9190.0060.0060.0000.0000.0000.000
102A128VAL0-0.026-0.01527.846-0.008-0.0080.0000.0000.0000.000
103A129PHE00.008-0.00923.2300.0030.0030.0000.0000.0000.000
104A130SER0-0.022-0.02228.821-0.001-0.0010.0000.0000.0000.000
105A131VAL0-0.016-0.01329.484-0.001-0.0010.0000.0000.0000.000
106A132VAL0-0.025-0.01130.9740.0030.0030.0000.0000.0000.000
107A133GLN00.010-0.00931.6010.0030.0030.0000.0000.0000.000
108A134ALA00.0400.01830.582-0.004-0.0040.0000.0000.0000.000
109A135PRO00.0070.02829.2860.0040.0040.0000.0000.0000.000
110A136GLN00.0870.02632.3570.0010.0010.0000.0000.0000.000
111A137VAL00.0100.00530.4800.0010.0010.0000.0000.0000.000
112A138LEU0-0.005-0.00927.519-0.004-0.0040.0000.0000.0000.000
113A139GLN0-0.015-0.00431.4960.0030.0030.0000.0000.0000.000
114A140SER00.0360.02934.3550.0020.0020.0000.0000.0000.000
115A141CYS0-0.089-0.00530.0840.0000.0000.0000.0000.0000.000
116A142ARG10.9560.96631.8420.0590.0590.0000.0000.0000.000
117A143VAL00.0070.01227.9930.0060.0060.0000.0000.0000.000
118A144VAL00.006-0.01329.8300.0050.0050.0000.0000.0000.000
119A145ALA0-0.0180.00332.3070.0050.0050.0000.0000.0000.000
120A146ASN0-0.010-0.01534.4060.0050.0050.0000.0000.0000.000
121A147LYS10.9741.00034.0410.0410.0410.0000.0000.0000.000
122A148TYR0-0.019-0.00632.1290.0020.0020.0000.0000.0000.000
123A149SER00.0140.01227.894-0.002-0.0020.0000.0000.0000.000
124A150SER00.0390.04529.7640.0040.0040.0000.0000.0000.000
125A151VAL00.0120.03425.042-0.002-0.0020.0000.0000.0000.000
126A152ASN00.0450.01326.0220.0070.0070.0000.0000.0000.000
127A153ALA00.1040.03424.909-0.007-0.0070.0000.0000.0000.000
128A154VAL00.0440.02222.3690.0000.0000.0000.0000.0000.000
129A155LYS10.8650.94421.2460.0420.0420.0000.0000.0000.000
130A156HIS0-0.059-0.02420.476-0.012-0.0120.0000.0000.0000.000
131A157VAL00.0420.03019.713-0.012-0.0120.0000.0000.0000.000
132A158LYS10.8930.95312.484-0.066-0.0660.0000.0000.0000.000
133A159ALA00.000-0.00817.3540.0130.0130.0000.0000.0000.000
134A160PRO0-0.001-0.00219.8940.0000.0000.0000.0000.0000.000
135A161GLU-1-0.848-0.92121.5800.0750.0750.0000.0000.0000.000
136A162LYS10.9570.98519.393-0.138-0.1380.0000.0000.0000.000
137A163ILE0-0.075-0.02722.051-0.003-0.0030.0000.0000.0000.000
138A164PRO00.0490.02625.664-0.002-0.0020.0000.0000.0000.000
139A165GLY0-0.013-0.00629.299-0.005-0.0050.0000.0000.0000.000
140A166SER0-0.037-0.02232.164-0.004-0.0040.0000.0000.0000.000
141A167GLY00.0980.05631.7280.0040.0040.0000.0000.0000.000
142A168THR0-0.027-0.01731.544-0.005-0.0050.0000.0000.0000.000
143A169LEU0-0.020-0.00526.1390.0040.0040.0000.0000.0000.000
144A170GLU-1-0.909-0.96425.757-0.014-0.0140.0000.0000.0000.000
145A171TYR0-0.051-0.02819.3540.0030.0030.0000.0000.0000.000
146A172LYS10.9230.98716.6370.0650.0650.0000.0000.0000.000
147A173VAL00.0240.00919.440-0.008-0.0080.0000.0000.0000.000
148A174ASN0-0.045-0.04713.4270.0370.0370.0000.0000.0000.000
149A175PHE0-0.0030.02410.601-0.020-0.0200.0000.0000.0000.000
150A176VAL00.0260.01816.0110.0230.0230.0000.0000.0000.000
151A177SER00.0270.01916.509-0.056-0.0560.0000.0000.0000.000
152A178LEU0-0.0210.00118.4750.0270.0270.0000.0000.0000.000
153A179THR0-0.036-0.05820.956-0.033-0.0330.0000.0000.0000.000
154A180VAL00.0120.02223.0640.0150.0150.0000.0000.0000.000
155A181VAL0-0.037-0.03226.510-0.009-0.0090.0000.0000.0000.000
156A182PRO00.0760.04828.4320.0070.0070.0000.0000.0000.000
157A183ARG11.0911.04631.9150.0740.0740.0000.0000.0000.000
158A184LYS10.8460.91630.1180.1190.1190.0000.0000.0000.000
159A185ASP-1-0.903-0.94931.620-0.081-0.0810.0000.0000.0000.000
160A186VAL0-0.058-0.02027.3830.0020.0020.0000.0000.0000.000
161A187TYR0-0.049-0.04129.273-0.002-0.0020.0000.0000.0000.000
162A188LYS10.9540.98227.9440.0830.0830.0000.0000.0000.000
163A189ILE00.0110.01430.6720.0050.0050.0000.0000.0000.000
164A190PRO00.0170.01632.3440.0000.0000.0000.0000.0000.000
165A191THR00.047-0.01431.9600.0010.0010.0000.0000.0000.000
166A192ALA00.0010.00233.8510.0020.0020.0000.0000.0000.000
167A193ALA00.0500.02536.6410.0020.0020.0000.0000.0000.000
168A194LEU0-0.020-0.00429.9300.0000.0000.0000.0000.0000.000
169A195LYS10.9200.95434.1190.0290.0290.0000.0000.0000.000
170A196VAL0-0.0170.01536.5950.0030.0030.0000.0000.0000.000
171A197SER0-0.035-0.02038.7490.0000.0000.0000.0000.0000.000
172A198GLY00.0440.00941.0410.0010.0010.0000.0000.0000.000
173A199SER00.004-0.00143.445-0.001-0.0010.0000.0000.0000.000
174A200SER0-0.0160.00045.7820.0000.0000.0000.0000.0000.000
175A201LEU0-0.031-0.01941.458-0.002-0.0020.0000.0000.0000.000
176A202TYR0-0.013-0.00138.6160.0020.0020.0000.0000.0000.000
177A203ASN00.0360.02933.185-0.007-0.0070.0000.0000.0000.000
178A204LEU0-0.014-0.02432.8160.0010.0010.0000.0000.0000.000
179A205ALA00.0600.03029.737-0.002-0.0020.0000.0000.0000.000
180A206LEU0-0.022-0.00525.576-0.002-0.0020.0000.0000.0000.000
181A207ASN00.0300.02923.811-0.002-0.0020.0000.0000.0000.000
182A208VAL0-0.013-0.01219.127-0.010-0.0100.0000.0000.0000.000
183A209THR00.0150.01418.0890.0090.0090.0000.0000.0000.000
184A210ILE0-0.056-0.05012.889-0.029-0.0290.0000.0000.0000.000
185A211ASP-1-0.810-0.90811.063-0.114-0.1140.0000.0000.0000.000
186A212VAL0-0.068-0.0497.729-0.115-0.1150.0000.0000.0000.000
187A213GLU-1-0.859-0.9312.820-6.631-5.4240.260-0.685-0.782-0.003
188A214VAL0-0.005-0.0173.753-0.789-0.5440.005-0.066-0.1830.000
189A215ASP-1-0.803-0.9082.9222.9253.8840.102-0.361-0.7000.001
190A216PRO0-0.017-0.0174.624-1.555-1.4680.000-0.030-0.0570.000
191A217LYS10.9540.9787.103-1.659-1.6590.0000.0000.0000.000
192A218SER0-0.0170.0076.548-0.354-0.3540.0000.0000.0000.000
193A219PRO00.0180.0078.300-0.127-0.1270.0000.0000.0000.000
194A220LEU0-0.015-0.0268.578-0.136-0.1360.0000.0000.0000.000
195A221VAL0-0.026-0.0029.417-0.146-0.1460.0000.0000.0000.000
196A222LYS10.9350.96911.093-0.486-0.4860.0000.0000.0000.000
197A223SER0-0.059-0.01114.157-0.060-0.0600.0000.0000.0000.000
198A224LEU0-0.038-0.00510.334-0.059-0.0590.0000.0000.0000.000
199A225SER00.0290.01314.7180.0120.0120.0000.0000.0000.000
200A226LYS10.9290.96313.893-0.268-0.2680.0000.0000.0000.000
201A227SER0-0.045-0.01314.952-0.041-0.0410.0000.0000.0000.000
202A228ASP-1-0.842-0.94015.6270.1630.1630.0000.0000.0000.000
203A229SER0-0.050-0.02814.875-0.001-0.0010.0000.0000.0000.000
204A230GLY00.0190.02011.383-0.046-0.0460.0000.0000.0000.000
205A231TYR00.0180.0099.1140.0570.0570.0000.0000.0000.000
206A232TYR00.000-0.00111.274-0.101-0.1010.0000.0000.0000.000
207A233ALA00.0100.01113.5450.0430.0430.0000.0000.0000.000
208A234ASN00.002-0.00915.652-0.042-0.0420.0000.0000.0000.000
209A235LEU0-0.005-0.00719.3640.0040.0040.0000.0000.0000.000
210A236PHE00.0150.01521.231-0.006-0.0060.0000.0000.0000.000
211A237LEU0-0.022-0.01223.9580.0010.0010.0000.0000.0000.000
212A238HIS0-0.028-0.01526.4860.0000.0000.0000.0000.0000.000
213A239ILE0-0.038-0.03927.120-0.005-0.0050.0000.0000.0000.000
214A240GLY00.0360.01330.984-0.003-0.0030.0000.0000.0000.000
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