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

tag_button

FMODB ID: VQL51

Calculation Name: 3GNL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GNL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2814805.435698
FMO2-HF: Nuclear repulsion 2724057.306052
FMO2-HF: Total energy -90748.129646
FMO2-MP2: Total energy -91017.044298


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:9:GLU)


Summations of interaction energy for fragment #1(A:9:GLU)
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.
-109.33-93.6764.078-9.744-9.9890.11
Interaction energy analysis for fragmet #1(A:9:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.891 / q_NPA : -0.963
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].
3A11GLN0-0.061-0.0333.5230.0551.8220.020-0.818-0.9680.002
4A12LEU00.0060.0125.902-0.619-0.6190.0000.0000.0000.000
5A13SER00.0430.0257.727-1.388-1.3880.0000.0000.0000.000
6A14LYS11.0070.98711.259-18.271-18.2710.0000.0000.0000.000
7A15ARG10.8760.93714.046-18.716-18.7160.0000.0000.0000.000
8A16LEU0-0.035-0.02510.167-0.597-0.5970.0000.0000.0000.000
9A17GLU-1-0.904-0.94310.70722.17422.1740.0000.0000.0000.000
10A18LYS10.9130.95611.570-15.595-15.5950.0000.0000.0000.000
11A19VAL0-0.0010.00514.039-0.646-0.6460.0000.0000.0000.000
12A20ALA00.0390.00710.563-0.546-0.5460.0000.0000.0000.000
13A21SER0-0.066-0.02812.496-0.537-0.5370.0000.0000.0000.000
14A22TYR00.008-0.00614.613-0.963-0.9630.0000.0000.0000.000
15A23ILE0-0.0380.00012.673-0.976-0.9760.0000.0000.0000.000
16A24THR0-0.016-0.02014.6660.5480.5480.0000.0000.0000.000
17A25LYS10.8930.93816.910-13.920-13.9200.0000.0000.0000.000
18A26ASN00.0440.02615.0180.7030.7030.0000.0000.0000.000
19A27GLU-1-0.727-0.82315.97916.27216.2720.0000.0000.0000.000
20A28ARG10.8910.96715.357-15.015-15.0150.0000.0000.0000.000
21A29ILE00.0210.00211.561-1.059-1.0590.0000.0000.0000.000
22A30ALA00.008-0.00115.5720.4930.4930.0000.0000.0000.000
23A31ASP-1-0.813-0.89312.62222.48422.4840.0000.0000.0000.000
24A32ILE00.000-0.01315.2710.2740.2740.0000.0000.0000.000
25A33GLY0-0.026-0.01917.740-0.377-0.3770.0000.0000.0000.000
26A34SER0-0.059-0.02011.8651.2081.2080.0000.0000.0000.000
27A35ASP-1-0.823-0.89311.34723.11023.1100.0000.0000.0000.000
28A36HIS0-0.023-0.0328.8611.5331.5330.0000.0000.0000.000
29A37ALA00.0370.0128.3853.2403.2400.0000.0000.0000.000
30A38TYR00.0310.0165.1014.8914.8910.0000.0000.0000.000
31A39LEU0-0.0020.0066.0384.7714.7710.0000.0000.0000.000
32A40PRO00.000-0.0068.1251.0011.0010.0000.0000.0000.000
33A41CYS0-0.0180.0022.936-4.062-2.6210.180-0.716-0.9060.008
34A42PHE00.0160.0064.3272.6532.895-0.001-0.034-0.2070.000
35A43ALA00.017-0.0045.201-2.376-2.362-0.001-0.001-0.0110.000
36A44VAL0-0.0080.0127.117-2.338-2.3380.0000.0000.0000.000
37A45LYS10.8720.9432.494-103.742-97.7081.006-3.703-3.3380.044
38A46ASN0-0.025-0.0016.314-4.609-4.6090.0000.0000.0000.000
39A47GLN0-0.017-0.0088.756-3.091-3.0910.0000.0000.0000.000
40A48THR0-0.043-0.01010.839-2.389-2.3890.0000.0000.0000.000
41A49ALA0-0.040-0.02111.075-1.909-1.9090.0000.0000.0000.000
42A50SER0-0.021-0.01311.7051.4681.4680.0000.0000.0000.000
43A51PHE0-0.029-0.01913.1200.1260.1260.0000.0000.0000.000
44A52ALA00.0140.01111.060-0.302-0.3020.0000.0000.0000.000
45A53ILE0-0.0010.01713.0510.1910.1910.0000.0000.0000.000
46A54ALA00.014-0.00111.6480.2460.2460.0000.0000.0000.000
47A55GLY0-0.004-0.00113.783-0.609-0.6090.0000.0000.0000.000
48A56GLH0-0.074-0.08014.387-0.162-0.1620.0000.0000.0000.000
49A57VAL00.0460.03318.449-0.542-0.5420.0000.0000.0000.000
50A58VAL0-0.008-0.01121.018-0.604-0.6040.0000.0000.0000.000
51A59ASP-1-0.794-0.91720.21915.09315.0930.0000.0000.0000.000
52A60GLY0-0.0270.01219.0290.7660.7660.0000.0000.0000.000
53A61PRO00.0740.01115.6641.0531.0530.0000.0000.0000.000
54A62PHE00.0230.02415.1081.5481.5480.0000.0000.0000.000
55A63GLN00.005-0.01415.1431.1861.1860.0000.0000.0000.000
56A64SER0-0.038-0.01612.4091.5141.5140.0000.0000.0000.000
57A65ALA00.0370.02810.7402.8042.8040.0000.0000.0000.000
58A66GLN00.016-0.00110.2242.4552.4550.0000.0000.0000.000
59A67LYS10.8690.93310.656-21.171-21.1710.0000.0000.0000.000
60A68GLN00.0680.0573.254-9.980-8.8100.063-0.622-0.6110.004
61A69VAL00.0480.0205.7848.3078.3070.0000.0000.0000.000
62A70ARG10.8480.9057.444-22.848-22.8480.0000.0000.0000.000
63A71SER0-0.028-0.0084.864-3.035-3.047-0.001-0.0040.0170.000
64A72SER0-0.0280.0002.266-15.119-10.5082.811-3.689-3.7330.051
65A73GLY0-0.026-0.0164.326-2.182-1.9940.000-0.101-0.0880.001
66A74LEU0-0.004-0.0074.043-2.018-1.8190.001-0.056-0.1440.000
67A75THR0-0.004-0.0208.010-2.350-2.3500.0000.0000.0000.000
68A76GLU-1-0.972-0.97211.30319.44019.4400.0000.0000.0000.000
69A77GLN0-0.049-0.02610.1010.1750.1750.0000.0000.0000.000
70A78ILE0-0.012-0.0047.380-0.380-0.3800.0000.0000.0000.000
71A79ASP-1-0.824-0.88411.47819.22819.2280.0000.0000.0000.000
72A80VAL0-0.053-0.03212.0150.0950.0950.0000.0000.0000.000
73A81ARG10.7260.83114.638-17.665-17.6650.0000.0000.0000.000
74A82LYS10.8770.93518.237-14.217-14.2170.0000.0000.0000.000
75A83GLY00.001-0.02220.779-0.617-0.6170.0000.0000.0000.000
76A84ASN00.0110.00322.4580.7770.7770.0000.0000.0000.000
77A85GLY00.0670.03323.422-0.299-0.2990.0000.0000.0000.000
78A86LEU00.0510.01522.4960.6320.6320.0000.0000.0000.000
79A87ALA0-0.045-0.02224.108-0.121-0.1210.0000.0000.0000.000
80A88VAL0-0.0220.00719.148-0.052-0.0520.0000.0000.0000.000
81A89ILE00.0240.02820.6560.5580.5580.0000.0000.0000.000
82A90GLU-1-0.899-0.95822.62011.29911.2990.0000.0000.0000.000
83A91LYS10.9100.94824.401-10.359-10.3590.0000.0000.0000.000
84A92LYS10.9490.96824.724-12.074-12.0740.0000.0000.0000.000
85A93ASP-1-0.773-0.85620.50915.24215.2420.0000.0000.0000.000
86A94ALA0-0.026-0.00621.1440.5890.5890.0000.0000.0000.000
87A95ILE0-0.006-0.00418.2000.4100.4100.0000.0000.0000.000
88A96ASP-1-0.831-0.90619.83014.19314.1930.0000.0000.0000.000
89A97THR0-0.042-0.06617.810-0.983-0.9830.0000.0000.0000.000
90A98ILE0-0.0060.00518.4300.7490.7490.0000.0000.0000.000
91A99VAL0-0.018-0.00614.840-0.548-0.5480.0000.0000.0000.000
92A100ILE00.0450.01717.8310.1340.1340.0000.0000.0000.000
93A101ALA00.0180.00116.050-0.645-0.6450.0000.0000.0000.000
94A102GLY0-0.0140.00517.9930.2230.2230.0000.0000.0000.000
95A103MET00.0130.02118.899-0.542-0.5420.0000.0000.0000.000
96A104GLY0-0.013-0.01422.303-0.171-0.1710.0000.0000.0000.000
97A105GLY00.0460.01725.8580.1510.1510.0000.0000.0000.000
98A106THR00.0250.00227.593-0.014-0.0140.0000.0000.0000.000
99A107LEU0-0.0010.01824.631-0.133-0.1330.0000.0000.0000.000
100A108ILE00.0260.00622.4800.0510.0510.0000.0000.0000.000
101A109ARG10.8070.90925.993-9.123-9.1230.0000.0000.0000.000
102A110THR00.000-0.00129.439-0.200-0.2000.0000.0000.0000.000
103A111ILE0-0.024-0.00723.570-0.008-0.0080.0000.0000.0000.000
104A112LEU0-0.035-0.02525.0840.0970.0970.0000.0000.0000.000
105A113GLU-1-0.899-0.94928.1739.2349.2340.0000.0000.0000.000
106A114GLU-1-0.927-0.97430.21010.13110.1310.0000.0000.0000.000
107A115GLY0-0.043-0.01727.841-0.042-0.0420.0000.0000.0000.000
108A116ALA00.0800.04028.4690.2600.2600.0000.0000.0000.000
109A117ALA0-0.011-0.01430.5730.0440.0440.0000.0000.0000.000
110A118LYS10.7570.86425.570-12.104-12.1040.0000.0000.0000.000
111A119LEU00.0520.03925.7150.4780.4780.0000.0000.0000.000
112A120ALA0-0.056-0.02627.588-0.085-0.0850.0000.0000.0000.000
113A121GLY0-0.019-0.01327.3190.3010.3010.0000.0000.0000.000
114A122VAL0-0.0040.02722.8870.2460.2460.0000.0000.0000.000
115A123THR0-0.055-0.04224.002-0.391-0.3910.0000.0000.0000.000
116A124LYS10.7780.87319.254-15.870-15.8700.0000.0000.0000.000
117A125LEU0-0.0060.01621.9070.4580.4580.0000.0000.0000.000
118A126ILE0-0.0080.00316.853-0.400-0.4000.0000.0000.0000.000
119A127LEU00.001-0.00119.6350.5230.5230.0000.0000.0000.000
120A128GLN00.003-0.01018.4370.6030.6030.0000.0000.0000.000
121A129PRO0-0.0050.01820.8010.2740.2740.0000.0000.0000.000
122A130ASN00.000-0.01220.2960.1470.1470.0000.0000.0000.000
123A131ILE00.0150.01323.806-0.321-0.3210.0000.0000.0000.000
124A132ALA0-0.001-0.01127.6470.1560.1560.0000.0000.0000.000
125A133ALA00.1150.05327.3770.0070.0070.0000.0000.0000.000
126A134TRP00.0300.01428.6870.1030.1030.0000.0000.0000.000
127A135GLN00.0030.00730.775-0.170-0.1700.0000.0000.0000.000
128A136LEU00.0210.00325.774-0.086-0.0860.0000.0000.0000.000
129A137ARG10.8100.92428.127-10.310-10.3100.0000.0000.0000.000
130A138GLU-1-0.877-0.93431.8178.2408.2400.0000.0000.0000.000
131A139TRP0-0.017-0.00228.955-0.062-0.0620.0000.0000.0000.000
132A140SER0-0.007-0.02230.541-0.125-0.1250.0000.0000.0000.000
133A141GLU-1-0.867-0.93132.3338.0188.0180.0000.0000.0000.000
134A142GLN00.004-0.00936.0270.0170.0170.0000.0000.0000.000
135A143ASN0-0.066-0.03033.138-0.208-0.2080.0000.0000.0000.000
136A144ASN00.0210.02834.3740.0860.0860.0000.0000.0000.000
137A145TRP00.0450.02026.1280.3350.3350.0000.0000.0000.000
138A146LEU0-0.0030.00830.908-0.128-0.1280.0000.0000.0000.000
139A147ILE00.002-0.00227.3560.4440.4440.0000.0000.0000.000
140A148THR0-0.055-0.03425.917-0.133-0.1330.0000.0000.0000.000
141A149SER0-0.030-0.02623.3830.1010.1010.0000.0000.0000.000
142A150GLU-1-0.763-0.88124.07610.69510.6950.0000.0000.0000.000
143A151ALA0-0.0140.00221.040-0.003-0.0030.0000.0000.0000.000
144A152ILE0-0.0020.00723.146-0.030-0.0300.0000.0000.0000.000
145A153LEU00.0000.00418.074-0.002-0.0020.0000.0000.0000.000
146A154ARG10.9290.95821.908-11.226-11.2260.0000.0000.0000.000
147A155GLU-1-0.796-0.90014.82518.60118.6010.0000.0000.0000.000
148A156ASP-1-0.893-0.94717.66015.40715.4070.0000.0000.0000.000
149A157ASN0-0.085-0.05120.713-0.438-0.4380.0000.0000.0000.000
150A158LYS10.9761.00620.027-14.402-14.4020.0000.0000.0000.000
151A159VAL0-0.034-0.02522.6090.3280.3280.0000.0000.0000.000
152A160TYR0-0.008-0.00419.445-0.006-0.0060.0000.0000.0000.000
153A161GLU-1-0.878-0.95322.39310.91710.9170.0000.0000.0000.000
154A162ILE0-0.016-0.01517.8740.4250.4250.0000.0000.0000.000
155A163MET0-0.022-0.00421.814-0.592-0.5920.0000.0000.0000.000
156A164VAL00.0210.00820.7850.5140.5140.0000.0000.0000.000
157A165LEU0-0.018-0.01223.397-0.601-0.6010.0000.0000.0000.000
158A166ALA00.0200.00525.2400.5240.5240.0000.0000.0000.000
159A167PRO00.0040.01427.554-0.352-0.3520.0000.0000.0000.000
160A168SER0-0.044-0.02530.743-0.012-0.0120.0000.0000.0000.000
161A169GLU-1-0.943-0.97034.1348.1718.1710.0000.0000.0000.000
162A170LYS10.8930.95437.256-8.089-8.0890.0000.0000.0000.000
163A171PRO00.016-0.00837.8590.1990.1990.0000.0000.0000.000
164A172VAL0-0.0330.00034.1960.0110.0110.0000.0000.0000.000
165A173THR0-0.030-0.02337.407-0.135-0.1350.0000.0000.0000.000
166A174TRP0-0.041-0.01232.3850.0400.0400.0000.0000.0000.000
167A175THR00.0310.01338.268-0.203-0.2030.0000.0000.0000.000
168A176LYS10.9440.96538.479-6.857-6.8570.0000.0000.0000.000
169A177GLN00.000-0.01638.1850.2280.2280.0000.0000.0000.000
170A178GLU-1-0.861-0.92535.1228.6528.6520.0000.0000.0000.000
171A179ILE00.0410.01733.7400.3620.3620.0000.0000.0000.000
172A180PHE0-0.088-0.03833.4980.2910.2910.0000.0000.0000.000
173A181PHE0-0.032-0.03732.7480.1990.1990.0000.0000.0000.000
174A182GLY00.0430.02530.2990.3260.3260.0000.0000.0000.000
175A183PRO00.0090.00930.691-0.148-0.1480.0000.0000.0000.000
176A184CYS0-0.063-0.03128.159-0.134-0.1340.0000.0000.0000.000
177A185LEU0-0.001-0.00225.908-0.056-0.0560.0000.0000.0000.000
178A186LEU0-0.030-0.00829.800-0.170-0.1700.0000.0000.0000.000
179A187LYS10.9430.96732.605-9.266-9.2660.0000.0000.0000.000
180A188GLU-1-0.972-0.97526.70511.00111.0010.0000.0000.0000.000
181A189GLN0-0.0430.00031.267-0.094-0.0940.0000.0000.0000.000
182A190SER00.0970.04627.447-0.183-0.1830.0000.0000.0000.000
183A191ALA00.0590.01329.442-0.186-0.1860.0000.0000.0000.000
184A192ILE0-0.036-0.02524.242-0.185-0.1850.0000.0000.0000.000
185A193PHE00.0340.02428.512-0.086-0.0860.0000.0000.0000.000
186A194LYS10.9280.95730.280-8.649-8.6490.0000.0000.0000.000
187A195SER0-0.037-0.02130.545-0.117-0.1170.0000.0000.0000.000
188A196LYS10.9310.97528.492-10.349-10.3490.0000.0000.0000.000
189A197TRP00.0640.01631.364-0.223-0.2230.0000.0000.0000.000
190A198ARG10.9370.97734.560-7.725-7.7250.0000.0000.0000.000
191A199HIS0-0.065-0.02432.999-0.313-0.3130.0000.0000.0000.000
192A200GLU-1-0.910-0.96232.2239.0989.0980.0000.0000.0000.000
193A201ALA00.0280.01036.050-0.194-0.1940.0000.0000.0000.000
194A202ASN0-0.009-0.00538.966-0.343-0.3430.0000.0000.0000.000
195A203THR00.0160.00936.964-0.242-0.2420.0000.0000.0000.000
196A204TRP00.013-0.00336.346-0.130-0.1300.0000.0000.0000.000
197A205GLN00.0740.03341.638-0.140-0.1400.0000.0000.0000.000
198A206ASN00.0230.00741.775-0.278-0.2780.0000.0000.0000.000
199A207ILE0-0.064-0.02140.208-0.126-0.1260.0000.0000.0000.000
200A208ILE00.0380.01444.626-0.117-0.1170.0000.0000.0000.000
201A209GLN0-0.041-0.00347.606-0.065-0.0650.0000.0000.0000.000
202A210THR0-0.020-0.01546.663-0.114-0.1140.0000.0000.0000.000
203A211ILE0-0.054-0.03046.297-0.083-0.0830.0000.0000.0000.000
204A212SER0-0.022-0.01950.040-0.141-0.1410.0000.0000.0000.000
205A213ASN0-0.048-0.03152.416-0.046-0.0460.0000.0000.0000.000
206A214ASN0-0.0060.02150.498-0.123-0.1230.0000.0000.0000.000
207A215GLN0-0.0070.01054.4440.0750.0750.0000.0000.0000.000
208A216PRO0-0.023-0.01757.458-0.046-0.0460.0000.0000.0000.000
209A217VAL00.0310.01252.6720.0800.0800.0000.0000.0000.000
210A218SER00.0140.01152.018-0.056-0.0560.0000.0000.0000.000
211A219THR00.0600.00953.8340.0270.0270.0000.0000.0000.000
212A220GLU-1-0.882-0.94349.3796.0836.0830.0000.0000.0000.000
213A221ASN0-0.003-0.02048.4200.2600.2600.0000.0000.0000.000
214A222GLN00.0420.02449.9140.1290.1290.0000.0000.0000.000
215A223ALA0-0.061-0.02549.2590.0260.0260.0000.0000.0000.000
216A224LYS10.9850.99941.970-7.159-7.1590.0000.0000.0000.000
217A225ILE00.0170.00545.9580.1670.1670.0000.0000.0000.000
218A226ARG11.0121.01747.717-6.050-6.0500.0000.0000.0000.000
219A227GLU-1-0.991-0.98341.9387.5827.5820.0000.0000.0000.000
220A228LEU0-0.043-0.03441.7370.1730.1730.0000.0000.0000.000
221A229GLU-1-0.894-0.95743.9636.3136.3130.0000.0000.0000.000
222A230HIS0-0.0090.00643.153-0.013-0.0130.0000.0000.0000.000
223A231LYS10.9150.95337.985-7.904-7.9040.0000.0000.0000.000
224A232ILE00.0090.00340.9720.1690.1690.0000.0000.0000.000
225A233ALA00.0500.03442.7860.0420.0420.0000.0000.0000.000
226A234LEU0-0.052-0.02839.8600.0280.0280.0000.0000.0000.000
227A235VAL0-0.011-0.01037.4220.1370.1370.0000.0000.0000.000
228A236GLU-1-0.946-0.96739.8376.8496.8490.0000.0000.0000.000
229A237ASP-1-0.905-0.95342.5747.1367.1360.0000.0000.0000.000
230A238VAL0-0.041-0.03136.7310.0300.0300.0000.0000.0000.000
231A239LEU0-0.078-0.03736.0300.1490.1490.0000.0000.0000.000
232A240LYS10.8820.95639.589-7.033-7.0330.0000.0000.0000.000
233A241GLU-1-0.968-0.97241.5027.2367.2360.0000.0000.0000.000
234A242GLY0-0.0130.00043.9010.0580.0580.0000.0000.0000.000