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: G5871

Calculation Name: 3ER6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ER6

Chain ID: A

ChEMBL ID:

UniProt ID: Q87I90

Base Structure: X-ray

Registration Date: 2023-09-22

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2112109.400682
FMO2-HF: Nuclear repulsion 2038117.046643
FMO2-HF: Total energy -73992.354039
FMO2-MP2: Total energy -74210.468447


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:7:LYS)


Summations of interaction energy for fragment #1(A:7: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.
-83.053-80.0080.109-1.29-1.8630.001
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.937 / q_NPA : 0.957
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].
3A9LEU0-0.0240.0103.8185.2447.242-0.017-0.969-1.0120.002
4A10ARG10.8870.9436.51027.49027.4900.0000.0000.0000.000
5A11VAL00.0140.00810.1921.6221.6220.0000.0000.0000.000
6A12VAL00.0060.00613.231-0.277-0.2770.0000.0000.0000.000
7A13ALA0-0.004-0.00616.6500.6650.6650.0000.0000.0000.000
8A14LEU00.0280.01719.6100.2050.2050.0000.0000.0000.000
9A15ALA00.015-0.00122.9830.4130.4130.0000.0000.0000.000
10A16PRO00.006-0.00725.8790.1430.1430.0000.0000.0000.000
11A17THR00.0470.02228.9940.3520.3520.0000.0000.0000.000
12A18GLY00.0290.02430.820-0.166-0.1660.0000.0000.0000.000
13A19ARG10.8230.89632.1758.8878.8870.0000.0000.0000.000
14A20TYR00.008-0.00331.5570.3170.3170.0000.0000.0000.000
15A21PHE00.0780.04026.754-0.076-0.0760.0000.0000.0000.000
16A22ALA00.0260.01626.482-0.401-0.4010.0000.0000.0000.000
17A23SER00.0480.02725.834-0.336-0.3360.0000.0000.0000.000
18A24ILE00.0170.02521.676-0.354-0.3540.0000.0000.0000.000
19A25ILE0-0.009-0.00121.496-0.608-0.6080.0000.0000.0000.000
20A26SER00.0730.03021.762-0.268-0.2680.0000.0000.0000.000
21A27SER0-0.071-0.04719.431-0.204-0.2040.0000.0000.0000.000
22A28LEU00.002-0.00516.274-0.532-0.5320.0000.0000.0000.000
23A29GLU-1-0.882-0.93217.144-13.542-13.5420.0000.0000.0000.000
24A30ILE0-0.058-0.01417.748-0.246-0.2460.0000.0000.0000.000
25A31LEU0-0.010-0.02113.491-0.467-0.4670.0000.0000.0000.000
26A32GLU-1-0.875-0.92613.338-21.361-21.3610.0000.0000.0000.000
27A33THR0-0.007-0.00914.168-0.557-0.5570.0000.0000.0000.000
28A34ALA0-0.0050.00013.878-0.021-0.0210.0000.0000.0000.000
29A35ALA0-0.004-0.0089.890-0.472-0.4720.0000.0000.0000.000
30A36GLU-1-0.939-0.95911.065-18.016-18.0160.0000.0000.0000.000
31A37PHE0-0.060-0.04413.6910.3490.3490.0000.0000.0000.000
32A38ALA0-0.072-0.0329.6720.4720.4720.0000.0000.0000.000
33A39GLU-1-0.961-0.97110.230-20.015-20.0150.0000.0000.0000.000
34A40PHE0-0.070-0.0292.887-4.924-3.9880.127-0.288-0.775-0.001
35A41GLN00.0460.0136.3420.8850.8850.0000.0000.0000.000
36A42GLY0-0.038-0.0164.493-2.344-2.233-0.001-0.033-0.0760.000
37A43PHE00.0220.0075.534-1.615-1.6150.0000.0000.0000.000
38A44MET0-0.041-0.0146.7791.1931.1930.0000.0000.0000.000
39A45THR0-0.010-0.02510.3061.0031.0030.0000.0000.0000.000
40A46HIS00.0090.00111.4421.3511.3510.0000.0000.0000.000
41A47VAL00.0040.01416.4340.5080.5080.0000.0000.0000.000
42A48VAL0-0.031-0.00819.223-0.023-0.0230.0000.0000.0000.000
43A49THR00.012-0.02321.9720.2920.2920.0000.0000.0000.000
44A50PRO00.0630.03825.712-0.185-0.1850.0000.0000.0000.000
45A51ASN00.0170.01727.782-0.239-0.2390.0000.0000.0000.000
46A52ASN0-0.007-0.02324.031-0.231-0.2310.0000.0000.0000.000
47A53ARG10.8830.95726.31310.30410.3040.0000.0000.0000.000
48A54PRO00.0260.01828.234-0.215-0.2150.0000.0000.0000.000
49A55LEU0-0.0050.02227.1850.3660.3660.0000.0000.0000.000
50A56ILE00.0170.00530.4170.0320.0320.0000.0000.0000.000
51A57GLY00.0300.03232.8140.0690.0690.0000.0000.0000.000
52A58ARG10.8280.89233.5738.9038.9030.0000.0000.0000.000
53A59GLY00.0420.01235.607-0.160-0.1600.0000.0000.0000.000
54A60GLY0-0.0090.00937.6700.0020.0020.0000.0000.0000.000
55A61ILE00.0230.02731.132-0.070-0.0700.0000.0000.0000.000
56A62SER0-0.012-0.01531.8770.0150.0150.0000.0000.0000.000
57A63VAL00.009-0.00125.813-0.139-0.1390.0000.0000.0000.000
58A64GLN0-0.011-0.02224.9380.5130.5130.0000.0000.0000.000
59A65PRO00.0190.02822.125-0.387-0.3870.0000.0000.0000.000
60A66THR00.0420.00918.0850.4850.4850.0000.0000.0000.000
61A67ALA0-0.0070.00417.146-0.800-0.8000.0000.0000.0000.000
62A68GLN0-0.020-0.01119.1941.2451.2450.0000.0000.0000.000
63A69TRP00.029-0.00119.354-1.088-1.0880.0000.0000.0000.000
64A70GLN00.0700.04219.661-0.944-0.9440.0000.0000.0000.000
65A71SER0-0.065-0.02216.4760.0350.0350.0000.0000.0000.000
66A72PHE0-0.056-0.02713.295-1.675-1.6750.0000.0000.0000.000
67A73ASP-1-0.843-0.90715.055-16.877-16.8770.0000.0000.0000.000
68A74PHE0-0.046-0.0348.7770.2380.2380.0000.0000.0000.000
69A75THR00.021-0.01212.044-1.622-1.6220.0000.0000.0000.000
70A76ASN00.0170.0447.347-0.473-0.4730.0000.0000.0000.000
71A77ILE00.0250.02111.1681.3841.3840.0000.0000.0000.000
72A78LEU00.0080.02213.870-0.699-0.6990.0000.0000.0000.000
73A79ILE0-0.015-0.01217.0000.6110.6110.0000.0000.0000.000
74A80ILE00.0060.01119.7150.0170.0170.0000.0000.0000.000
75A81GLY00.023-0.01923.3550.2980.2980.0000.0000.0000.000
76A82SER0-0.050-0.05125.5360.2970.2970.0000.0000.0000.000
77A83ILE00.0170.00029.300-0.213-0.2130.0000.0000.0000.000
78A84GLY0-0.058-0.01831.8480.2620.2620.0000.0000.0000.000
79A85ASP-1-0.834-0.92534.678-7.741-7.7410.0000.0000.0000.000
80A86PRO00.0070.00734.954-0.011-0.0110.0000.0000.0000.000
81A87LEU00.0100.01336.800-0.007-0.0070.0000.0000.0000.000
82A88GLU-1-0.880-0.91538.986-7.973-7.9730.0000.0000.0000.000
83A89SER0-0.004-0.03434.956-0.016-0.0160.0000.0000.0000.000
84A90LEU00.0020.00133.175-0.218-0.2180.0000.0000.0000.000
85A91ASP-1-0.859-0.93535.103-8.324-8.3240.0000.0000.0000.000
86A92LYS10.7320.85337.0018.2168.2160.0000.0000.0000.000
87A93ILE0-0.085-0.02430.452-0.201-0.2010.0000.0000.0000.000
88A94ASP-1-0.845-0.92829.725-10.403-10.4030.0000.0000.0000.000
89A95PRO00.0330.00830.813-0.269-0.2690.0000.0000.0000.000
90A96ALA00.0560.02728.129-0.216-0.2160.0000.0000.0000.000
91A97LEU0-0.033-0.00924.924-0.512-0.5120.0000.0000.0000.000
92A98PHE00.004-0.01626.298-0.369-0.3690.0000.0000.0000.000
93A99ASP-1-0.916-0.95027.171-10.763-10.7630.0000.0000.0000.000
94A100TRP0-0.020-0.01418.870-0.193-0.1930.0000.0000.0000.000
95A101ILE0-0.018-0.01522.267-0.577-0.5770.0000.0000.0000.000
96A102ARG10.9800.99622.80110.21510.2150.0000.0000.0000.000
97A103GLU-1-0.884-0.94521.583-13.913-13.9130.0000.0000.0000.000
98A104LEU0-0.019-0.01316.741-0.514-0.5140.0000.0000.0000.000
99A105HIS00.0120.00318.651-0.835-0.8350.0000.0000.0000.000
100A106LEU0-0.054-0.02420.337-0.021-0.0210.0000.0000.0000.000
101A107LYS10.8110.91116.80115.68915.6890.0000.0000.0000.000
102A108GLY0-0.0070.00516.334-0.796-0.7960.0000.0000.0000.000
103A109SER0-0.074-0.04314.526-0.460-0.4600.0000.0000.0000.000
104A110LYS10.7590.87412.78017.10117.1010.0000.0000.0000.000
105A111ILE00.0070.00416.041-0.417-0.4170.0000.0000.0000.000
106A112VAL00.0110.00517.2870.5470.5470.0000.0000.0000.000
107A113ALA0-0.0090.00920.255-0.102-0.1020.0000.0000.0000.000
108A114ILE00.004-0.01122.7900.2600.2600.0000.0000.0000.000
109A115ASP-1-0.805-0.88525.658-9.363-9.3630.0000.0000.0000.000
110A116THR00.014-0.00829.398-0.173-0.1730.0000.0000.0000.000
111A117GLY00.0450.04527.0440.0990.0990.0000.0000.0000.000
112A118ILE0-0.060-0.04727.343-0.151-0.1510.0000.0000.0000.000
113A119PHE00.0290.01328.8320.0430.0430.0000.0000.0000.000
114A120VAL0-0.0050.00727.5660.1220.1220.0000.0000.0000.000
115A121VAL0-0.008-0.01224.397-0.043-0.0430.0000.0000.0000.000
116A122ALA0-0.0270.00127.6080.0420.0420.0000.0000.0000.000
117A123LYS10.9060.95031.0938.7838.7830.0000.0000.0000.000
118A124ALA0-0.064-0.03027.9530.0910.0910.0000.0000.0000.000
119A125GLY00.0040.00829.358-0.113-0.1130.0000.0000.0000.000
120A126LEU0-0.081-0.04423.475-0.117-0.1170.0000.0000.0000.000
121A127LEU0-0.042-0.01125.877-0.250-0.2500.0000.0000.0000.000
122A128GLN00.0430.03026.6620.2700.2700.0000.0000.0000.000
123A129GLN0-0.106-0.07627.5000.5940.5940.0000.0000.0000.000
124A130ASN0-0.040-0.01930.9200.0660.0660.0000.0000.0000.000
125A131LYS10.9220.96231.0368.4888.4880.0000.0000.0000.000
126A132ALA00.0430.01230.171-0.350-0.3500.0000.0000.0000.000
127A133VAL0-0.050-0.01028.9140.2030.2030.0000.0000.0000.000
128A134MET00.0260.02931.531-0.161-0.1610.0000.0000.0000.000
129A135HIS0-0.032-0.02132.4500.4130.4130.0000.0000.0000.000
130A136SER00.025-0.02535.0580.0710.0710.0000.0000.0000.000
131A137TYR0-0.066-0.00837.8230.1870.1870.0000.0000.0000.000
132A138PHE00.0530.00435.5500.0760.0760.0000.0000.0000.000
133A139ALA00.0020.00937.626-0.036-0.0360.0000.0000.0000.000
134A140HIS0-0.033-0.02738.560-0.026-0.0260.0000.0000.0000.000
135A141LEU00.0280.01938.7530.0250.0250.0000.0000.0000.000
136A142PHE00.015-0.01232.546-0.042-0.0420.0000.0000.0000.000
137A143GLY0-0.0080.00137.806-0.041-0.0410.0000.0000.0000.000
138A144GLU-1-0.875-0.92940.521-6.608-6.6080.0000.0000.0000.000
139A145LEU0-0.084-0.05237.9150.0260.0260.0000.0000.0000.000
140A146PHE00.005-0.00134.575-0.153-0.1530.0000.0000.0000.000
141A147PRO0-0.0020.02838.184-0.041-0.0410.0000.0000.0000.000
142A148GLU-1-0.932-0.97737.000-7.846-7.8460.0000.0000.0000.000
143A149ILE0-0.049-0.01232.571-0.185-0.1850.0000.0000.0000.000
144A150MET0-0.0070.00935.8490.1220.1220.0000.0000.0000.000
145A151LEU00.0160.00334.352-0.254-0.2540.0000.0000.0000.000
146A152MET0-0.030-0.01332.2840.2930.2930.0000.0000.0000.000
147A153THR00.004-0.01634.333-0.117-0.1170.0000.0000.0000.000
148A154GLU-1-0.965-0.97135.976-7.333-7.3330.0000.0000.0000.000
149A155GLN0-0.052-0.02129.1690.0490.0490.0000.0000.0000.000
150A156LYS10.9590.96829.7528.6228.6220.0000.0000.0000.000
151A157ALA0-0.012-0.01725.108-0.235-0.2350.0000.0000.0000.000
152A158LEU00.0130.01325.8040.3180.3180.0000.0000.0000.000
153A159ILE00.0040.00320.328-0.283-0.2830.0000.0000.0000.000
154A160ASP-1-0.788-0.87823.362-9.980-9.9800.0000.0000.0000.000
155A161GLY00.0180.01121.856-0.209-0.2090.0000.0000.0000.000
156A162ASN00.0250.00015.331-0.187-0.1870.0000.0000.0000.000
157A163VAL00.0090.01918.958-0.579-0.5790.0000.0000.0000.000
158A164TYR0-0.047-0.05316.3960.4140.4140.0000.0000.0000.000
159A165LEU00.0220.02421.705-0.081-0.0810.0000.0000.0000.000
160A166SER00.017-0.02523.9780.2040.2040.0000.0000.0000.000
161A167SER00.0230.00025.9330.0580.0580.0000.0000.0000.000
162A168GLY0-0.0080.03028.930-0.001-0.0010.0000.0000.0000.000
163A169PRO00.009-0.01529.5390.2900.2900.0000.0000.0000.000
164A170TYR0-0.014-0.03128.486-0.354-0.3540.0000.0000.0000.000
165A171SER0-0.0040.01327.193-0.149-0.1490.0000.0000.0000.000
166A172HIS00.0500.02623.0540.1020.1020.0000.0000.0000.000
167A173SER00.0510.02422.228-0.464-0.4640.0000.0000.0000.000
168A174SER0-0.0060.00621.493-0.409-0.4090.0000.0000.0000.000
169A175VAL00.0630.02619.715-0.285-0.2850.0000.0000.0000.000
170A176MET0-0.0100.00517.784-0.814-0.8140.0000.0000.0000.000
171A177LEU0-0.024-0.01216.521-0.745-0.7450.0000.0000.0000.000
172A178GLU-1-0.803-0.85616.787-12.946-12.9460.0000.0000.0000.000
173A179ILE00.0090.00912.954-0.598-0.5980.0000.0000.0000.000
174A180VAL0-0.010-0.01412.527-1.032-1.0320.0000.0000.0000.000
175A181GLU-1-0.816-0.87712.286-13.997-13.9970.0000.0000.0000.000
176A182GLU-1-0.824-0.88312.148-16.232-16.2320.0000.0000.0000.000
177A183TYR0-0.041-0.0226.906-1.019-1.0190.0000.0000.0000.000
178A184PHE0-0.022-0.0056.501-1.460-1.4600.0000.0000.0000.000
179A185GLY00.0310.0349.8640.3530.3530.0000.0000.0000.000
180A186LYS10.8740.89312.96313.05313.0530.0000.0000.0000.000
181A187HIS00.0350.02016.1110.4480.4480.0000.0000.0000.000
182A188THR00.0730.04212.0990.6720.6720.0000.0000.0000.000
183A189ARG10.7760.86215.09813.06813.0680.0000.0000.0000.000
184A190ASN0-0.050-0.03816.9690.5600.5600.0000.0000.0000.000
185A191LEU00.0200.01216.9090.5560.5560.0000.0000.0000.000
186A192GLY00.0570.02518.1460.2950.2950.0000.0000.0000.000
187A193ASN0-0.005-0.00819.1600.4430.4430.0000.0000.0000.000
188A194GLN0-0.031-0.01022.2780.4710.4710.0000.0000.0000.000
189A195PHE0-0.021-0.01320.8300.3690.3690.0000.0000.0000.000
190A196LEU0-0.036-0.02321.4250.2850.2850.0000.0000.0000.000
191A197SER0-0.068-0.02024.7150.4680.4680.0000.0000.0000.000
192A198THR0-0.078-0.04525.0910.4950.4950.0000.0000.0000.000