Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: JLZK9

Calculation Name: 3E9N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E9N

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NMW9

Base Structure: X-ray

Registration Date: 2023-09-20

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1970425.988897
FMO2-HF: Nuclear repulsion 1899830.834249
FMO2-HF: Total energy -70595.154648
FMO2-MP2: Total energy -70805.179478


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:4:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-319.473-307.21229.111-18.98-22.392-0.195
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.926
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].
3A6ALA00.0030.0063.751-3.1940.006-0.040-1.658-1.5020.005
4A7VAL0-0.0050.0036.0883.6973.6970.0000.0000.0000.000
5A8VAL00.0090.0019.805-0.325-0.3250.0000.0000.0000.000
6A9THR00.0400.02412.4441.3351.3350.0000.0000.0000.000
7A10GLY00.0310.01116.140-0.230-0.2300.0000.0000.0000.000
8A11ALA0-0.003-0.00515.5630.0410.0410.0000.0000.0000.000
9A12THR00.0450.02717.0530.0010.0010.0000.0000.0000.000
10A13GLY0-0.052-0.01820.0430.8520.8520.0000.0000.0000.000
11A14GLY00.0240.00019.770-0.530-0.5300.0000.0000.0000.000
12A15MET00.012-0.00717.074-0.647-0.6470.0000.0000.0000.000
13A16GLY00.0670.04315.102-1.205-1.2050.0000.0000.0000.000
14A17ILE00.0350.03414.666-1.535-1.5350.0000.0000.0000.000
15A18GLU-1-0.844-0.91915.123-19.566-19.5660.0000.0000.0000.000
16A19ILE0-0.041-0.02710.375-1.602-1.6020.0000.0000.0000.000
17A20VAL0-0.001-0.00210.323-3.184-3.1840.0000.0000.0000.000
18A21LYS10.8800.92810.82116.90416.9040.0000.0000.0000.000
19A22ASP-1-0.886-0.9278.135-34.970-34.9700.0000.0000.0000.000
20A23LEU00.034-0.0055.081-2.919-2.9190.0000.0000.0000.000
21A24SER00.0040.0135.912-5.734-5.7340.0000.0000.0000.000
22A25ARG10.8440.9396.69636.93836.9380.0000.0000.0000.000
23A26ASP-1-0.794-0.8811.731-110.084-112.61512.912-5.853-4.527-0.072
24A27HIS0-0.010-0.0082.054-46.680-42.38314.398-7.734-10.961-0.092
25A28ILE00.0210.0273.5437.2837.8970.019-0.030-0.6030.000
26A29VAL0-0.035-0.0245.606-2.384-2.3840.0000.0000.0000.000
27A30TYR00.0010.0047.5742.6232.6230.0000.0000.0000.000
28A31ALA00.0200.00811.138-0.330-0.3300.0000.0000.0000.000
29A32LEU00.0180.00713.8981.3541.3540.0000.0000.0000.000
30A33GLY0-0.055-0.03816.826-0.250-0.2500.0000.0000.0000.000
31A34ARG10.8770.92520.01212.29712.2970.0000.0000.0000.000
32A35ASN0-0.030-0.01723.3350.4640.4640.0000.0000.0000.000
33A36PRO00.1090.03423.155-0.515-0.5150.0000.0000.0000.000
34A37GLU-1-0.893-0.93723.920-11.802-11.8020.0000.0000.0000.000
35A38HIS0-0.046-0.02521.224-0.488-0.4880.0000.0000.0000.000
36A39LEU0-0.0090.01218.280-0.851-0.8510.0000.0000.0000.000
37A40ALA0-0.0080.00918.985-0.658-0.6580.0000.0000.0000.000
38A41ALA00.012-0.00720.047-0.368-0.3680.0000.0000.0000.000
39A42LEU0-0.067-0.04815.309-0.687-0.6870.0000.0000.0000.000
40A43ALA0-0.022-0.01315.504-1.135-1.1350.0000.0000.0000.000
41A44GLU-1-0.958-0.95816.412-14.073-14.0730.0000.0000.0000.000
42A45ILE0-0.135-0.06511.932-0.266-0.2660.0000.0000.0000.000
43A46GLU-1-0.892-0.94910.675-20.375-20.3750.0000.0000.0000.000
44A47GLY00.0040.0018.428-2.186-2.1860.0000.0000.0000.000
45A48VAL0-0.040-0.0258.703-2.768-2.7680.0000.0000.0000.000
46A49GLU-1-0.800-0.88810.921-16.304-16.3040.0000.0000.0000.000
47A50PRO0-0.0040.01112.698-0.413-0.4130.0000.0000.0000.000
48A51ILE0-0.049-0.03814.1360.7920.7920.0000.0000.0000.000
49A52GLU-1-0.882-0.95617.820-13.229-13.2290.0000.0000.0000.000
50A53SER0-0.075-0.06920.211-0.024-0.0240.0000.0000.0000.000
51A54ASP-1-0.868-0.91122.193-11.407-11.4070.0000.0000.0000.000
52A55ILE00.0510.00518.3830.0990.0990.0000.0000.0000.000
53A56VAL00.0130.00522.476-0.116-0.1160.0000.0000.0000.000
54A57LYS10.8700.95425.18011.49311.4930.0000.0000.0000.000
55A58GLU-1-0.800-0.87922.001-13.287-13.2870.0000.0000.0000.000
56A59VAL0-0.087-0.05319.685-0.033-0.0330.0000.0000.0000.000
57A60LEU0-0.032-0.02522.3910.0470.0470.0000.0000.0000.000
58A61GLU-1-0.964-0.97625.819-9.781-9.7810.0000.0000.0000.000
59A62GLU-1-0.851-0.92925.407-11.098-11.0980.0000.0000.0000.000
60A63GLY0-0.0290.00024.354-0.057-0.0570.0000.0000.0000.000
61A64GLY0-0.004-0.00620.368-0.368-0.3680.0000.0000.0000.000
62A65VAL00.0370.00817.4700.4090.4090.0000.0000.0000.000
63A66ASP-1-0.808-0.89717.585-13.583-13.5830.0000.0000.0000.000
64A67LYS10.7640.85415.67116.46116.4610.0000.0000.0000.000
65A68LEU0-0.019-0.01012.194-1.002-1.0020.0000.0000.0000.000
66A69LYS10.8150.90613.50912.75712.7570.0000.0000.0000.000
67A70ASN0-0.089-0.03012.369-0.439-0.4390.0000.0000.0000.000
68A71LEU0-0.0030.0218.499-0.466-0.4660.0000.0000.0000.000
69A72ASP-1-0.818-0.9029.474-21.640-21.6400.0000.0000.0000.000
70A73HIS10.7940.8775.78125.68625.6860.0000.0000.0000.000
71A74VAL00.0100.0006.305-1.056-1.0560.0000.0000.0000.000
72A75ASP-1-0.808-0.9042.655-59.625-53.7821.818-3.497-4.164-0.036
73A76THR0-0.0130.0083.6613.2713.489-0.001-0.027-0.1900.000
74A77LEU00.0080.0206.4891.9091.9090.0000.0000.0000.000
75A78VAL0-0.014-0.0139.2240.8060.8060.0000.0000.0000.000
76A79HIS00.004-0.00511.8961.1991.1990.0000.0000.0000.000
77A80ALA00.010-0.01115.6470.5490.5490.0000.0000.0000.000
78A81ALA0-0.0420.00017.2221.0831.0830.0000.0000.0000.000
79A92GLY00.0730.03440.8020.1110.1110.0000.0000.0000.000
80A93SER00.016-0.01839.206-0.128-0.1280.0000.0000.0000.000
81A94VAL0-0.0130.01038.108-0.196-0.1960.0000.0000.0000.000
82A95ALA00.0370.01436.985-0.202-0.2020.0000.0000.0000.000
83A96GLU-1-0.857-0.91134.587-9.264-9.2640.0000.0000.0000.000
84A97TRP00.005-0.02833.470-0.363-0.3630.0000.0000.0000.000
85A98HIS00.0220.01332.595-0.420-0.4200.0000.0000.0000.000
86A99ALA00.0520.03730.834-0.328-0.3280.0000.0000.0000.000
87A100HIS0-0.003-0.01728.848-0.658-0.6580.0000.0000.0000.000
88A101LEU0-0.038-0.01227.633-0.465-0.4650.0000.0000.0000.000
89A102ASP-1-0.832-0.92027.248-11.058-11.0580.0000.0000.0000.000
90A103LEU0-0.046-0.02223.354-0.529-0.5290.0000.0000.0000.000
91A104ASN0-0.030-0.02623.215-0.949-0.9490.0000.0000.0000.000
92A105VAL0-0.038-0.02623.036-0.387-0.3870.0000.0000.0000.000
93A106ILE0-0.007-0.00423.415-0.422-0.4220.0000.0000.0000.000
94A107VAL00.0570.04620.057-0.349-0.3490.0000.0000.0000.000
95A108PRO00.0010.00718.576-0.587-0.5870.0000.0000.0000.000
96A109ALA00.0130.01918.594-0.736-0.7360.0000.0000.0000.000
97A110GLU-1-0.755-0.82820.305-13.420-13.4200.0000.0000.0000.000
98A111LEU00.0150.00015.352-0.198-0.1980.0000.0000.0000.000
99A112SER0-0.009-0.03015.292-1.353-1.3530.0000.0000.0000.000
100A113ARG10.7890.85916.23912.92412.9240.0000.0000.0000.000
101A114GLN0-0.110-0.07117.918-0.589-0.5890.0000.0000.0000.000
102A115LEU00.0120.00711.946-0.084-0.0840.0000.0000.0000.000
103A116LEU00.0090.01213.164-1.230-1.2300.0000.0000.0000.000
104A117PRO0-0.043-0.02814.331-0.658-0.6580.0000.0000.0000.000
105A118ALA00.0740.0409.831-0.279-0.2790.0000.0000.0000.000
106A119LEU0-0.0250.0059.234-2.074-2.0740.0000.0000.0000.000
107A120ARG10.8130.86310.49015.01315.0130.0000.0000.0000.000
108A121ALA0-0.061-0.01510.438-0.358-0.3580.0000.0000.0000.000
109A122ALA0-0.031-0.0276.0270.1730.1730.0000.0000.0000.000
110A123SER0-0.054-0.0107.143-2.084-2.0840.0000.0000.0000.000
111A124GLY00.0390.0336.725-2.344-2.3440.0000.0000.0000.000
112A125CYS0-0.089-0.0397.0713.7423.7420.0000.0000.0000.000
113A126VAL00.0290.0109.020-0.977-0.9770.0000.0000.0000.000
114A127ILE0-0.026-0.0229.0311.4041.4040.0000.0000.0000.000
115A128TYR0-0.010-0.01512.7250.3480.3480.0000.0000.0000.000
116A129ILE0-0.0090.00614.783-0.051-0.0510.0000.0000.0000.000
117A130ASN0-0.021-0.02217.8651.1371.1370.0000.0000.0000.000
118A141ASN00.0590.03134.7910.1420.1420.0000.0000.0000.000
119A142THR0-0.026-0.02935.061-0.246-0.2460.0000.0000.0000.000
120A143ILE00.0300.02332.275-0.162-0.1620.0000.0000.0000.000
121A144TYR0-0.046-0.04130.367-0.322-0.3220.0000.0000.0000.000
122A145ALA00.0070.01529.822-0.354-0.3540.0000.0000.0000.000
123A146ALA00.0390.02830.649-0.246-0.2460.0000.0000.0000.000
124A147SER00.0470.02027.520-0.310-0.3100.0000.0000.0000.000
125A148LYS10.9840.99725.69211.34111.3410.0000.0000.0000.000
126A149HIS0-0.079-0.04525.808-0.375-0.3750.0000.0000.0000.000
127A150ALA0-0.017-0.01127.346-0.172-0.1720.0000.0000.0000.000
128A151LEU0-0.0040.01420.144-0.204-0.2040.0000.0000.0000.000
129A152ARG10.8570.91922.28613.32213.3220.0000.0000.0000.000
130A153GLY0-0.002-0.00623.460-0.239-0.2390.0000.0000.0000.000
131A154LEU0-0.0010.00421.2980.0250.0250.0000.0000.0000.000
132A155ALA00.0130.00618.980-0.348-0.3480.0000.0000.0000.000
133A156ASP-1-0.784-0.87819.864-14.838-14.8380.0000.0000.0000.000
134A157ALA0-0.050-0.03722.1690.0720.0720.0000.0000.0000.000
135A158PHE00.1120.06415.4230.0510.0510.0000.0000.0000.000
136A159ARG10.8120.87916.97916.82016.8200.0000.0000.0000.000
137A160LYS10.8380.92618.82312.28612.2860.0000.0000.0000.000
138A161GLU-1-0.958-0.97821.274-13.027-13.0270.0000.0000.0000.000
139A162GLU-1-0.731-0.82116.187-16.615-16.6150.0000.0000.0000.000
140A163ALA0-0.0110.00816.431-0.777-0.7770.0000.0000.0000.000
141A164ASN0-0.053-0.04316.461-0.603-0.6030.0000.0000.0000.000
142A165ASN0-0.087-0.05616.1170.6100.6100.0000.0000.0000.000
143A166GLY00.0280.03212.780-0.661-0.6610.0000.0000.0000.000
144A167ILE0-0.0290.00311.261-2.039-2.0390.0000.0000.0000.000
145A168ARG10.8220.9026.86435.68835.6880.0000.0000.0000.000
146A169VAL0-0.0040.00512.181-0.792-0.7920.0000.0000.0000.000
147A170SER0-0.050-0.03712.8511.1631.1630.0000.0000.0000.000
148A171THR0-0.037-0.01114.7140.1590.1590.0000.0000.0000.000
149A172VAL00.0290.02014.1550.3640.3640.0000.0000.0000.000
150A173SER0-0.017-0.02517.2070.4190.4190.0000.0000.0000.000
151A174PRO00.0250.02419.8730.4150.4150.0000.0000.0000.000
152A175GLY00.0190.00722.5830.3640.3640.0000.0000.0000.000
153A176PRO0-0.035-0.02926.375-0.027-0.0270.0000.0000.0000.000
154A177THR0-0.025-0.02229.3650.3140.3140.0000.0000.0000.000
155A194ARG10.9130.94832.3019.2349.2340.0000.0000.0000.000
156A195PRO00.0340.02131.049-0.175-0.1750.0000.0000.0000.000
157A196GLU-1-0.838-0.95024.918-12.531-12.5310.0000.0000.0000.000
158A197ILE00.0220.01825.833-0.374-0.3740.0000.0000.0000.000
159A198TYR0-0.042-0.02326.7170.0220.0220.0000.0000.0000.000
160A199ILE0-0.071-0.02521.4180.0460.0460.0000.0000.0000.000
161A200GLU-1-0.869-0.93521.040-14.180-14.1800.0000.0000.0000.000
162A201PRO00.0070.00819.018-0.660-0.6600.0000.0000.0000.000
163A202LYS10.9000.93912.11222.60622.6060.0000.0000.0000.000
164A203GLU-1-0.888-0.94415.524-18.346-18.3460.0000.0000.0000.000
165A204ILE0-0.010-0.01015.216-0.626-0.6260.0000.0000.0000.000
166A205ALA00.0180.01912.236-1.392-1.3920.0000.0000.0000.000
167A206ASN0-0.017-0.01111.232-3.651-3.6510.0000.0000.0000.000
168A207ALA0-0.033-0.00311.964-1.205-1.2050.0000.0000.0000.000
169A208ILE00.021-0.0038.498-0.586-0.5860.0000.0000.0000.000
170A209ARG10.7100.8373.07956.00756.3360.002-0.133-0.1990.000
171A210PHE0-0.026-0.0277.974-1.765-1.7650.0000.0000.0000.000
172A211VAL0-0.043-0.0199.7860.1780.1780.0000.0000.0000.000
173A212ILE0-0.036-0.0263.4601.3231.5480.004-0.046-0.1830.000
174A213ASP-1-0.846-0.9234.954-56.657-56.591-0.001-0.002-0.0630.000
175A214ALA0-0.058-0.0056.5253.4403.4400.0000.0000.0000.000
176A215GLY00.0440.0158.669-1.755-1.7550.0000.0000.0000.000
177A216GLU-1-0.861-0.9468.643-30.242-30.2420.0000.0000.0000.000
178A217THR0-0.092-0.03411.4770.7010.7010.0000.0000.0000.000
179A218THR0-0.056-0.02513.0871.8151.8150.0000.0000.0000.000
180A219GLN00.0940.03612.635-1.723-1.7230.0000.0000.0000.000
181A220ILE00.0200.03212.7441.8011.8010.0000.0000.0000.000
182A221THR00.0050.00614.189-0.819-0.8190.0000.0000.0000.000
183A222ASN0-0.024-0.02116.7410.0170.0170.0000.0000.0000.000
184A223VAL00.0290.02915.3850.0890.0890.0000.0000.0000.000
185A224ASP-1-0.832-0.89118.609-13.474-13.4740.0000.0000.0000.000
186A225VAL0-0.007-0.00618.7440.1060.1060.0000.0000.0000.000
187A226ARG10.8180.89122.08913.26013.2600.0000.0000.0000.000
188A227PRO00.0210.02925.085-0.243-0.2430.0000.0000.0000.000
189A228ARG10.9831.01025.87912.09512.0950.0000.0000.0000.000