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: NN7ZQ

Calculation Name: 1SVA-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SVA

Chain ID: 1

ChEMBL ID:

UniProt ID: P03087

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 OptAll
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 348
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4536033.758339
FMO2-HF: Nuclear repulsion 4399614.412149
FMO2-HF: Total energy -136419.346191
FMO2-MP2: Total energy -136812.969073


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(1:14:PRO)


Summations of interaction energy for fragment #1(1:14:PRO)
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.
-0.9531.566-0.005-1.218-1.2960.003
Interaction energy analysis for fragmet #1(1:14:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.086 / q_NPA : 0.046
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].
3116LYS10.8690.9333.787-0.9401.579-0.005-1.218-1.2960.003
4117PRO00.0050.0055.4520.1320.1320.0000.0000.0000.000
5118LYS10.9580.9628.5050.3420.3420.0000.0000.0000.000
6119GLU-1-0.756-0.86211.670-0.526-0.5260.0000.0000.0000.000
7120PRO0-0.029-0.01414.5220.0230.0230.0000.0000.0000.000
8121VAL00.0030.00317.2530.0040.0040.0000.0000.0000.000
9122GLN0-0.0150.00119.9360.0220.0220.0000.0000.0000.000
10123VAL00.0210.01023.1060.0080.0080.0000.0000.0000.000
11124PRO00.0140.00426.043-0.002-0.0020.0000.0000.0000.000
12125LYS10.9190.96328.4740.1080.1080.0000.0000.0000.000
13126LEU00.0360.02629.4910.0060.0060.0000.0000.0000.000
14127VAL0-0.029-0.01831.510-0.005-0.0050.0000.0000.0000.000
15128ILE00.0310.00834.3450.0000.0000.0000.0000.0000.000
16129LYS10.9610.97734.3440.0640.0640.0000.0000.0000.000
17130GLY00.005-0.00837.3770.0000.0000.0000.0000.0000.000
18131GLY00.0260.03040.7000.0000.0000.0000.0000.0000.000
19132ILE00.007-0.00143.843-0.002-0.0020.0000.0000.0000.000
20133GLU-1-0.831-0.93745.069-0.044-0.0440.0000.0000.0000.000
21134VAL0-0.033-0.00640.002-0.001-0.0010.0000.0000.0000.000
22135LEU0-0.014-0.00443.146-0.002-0.0020.0000.0000.0000.000
23136GLY0-0.0010.00745.0440.0000.0000.0000.0000.0000.000
24137VAL0-0.044-0.01740.2950.0000.0000.0000.0000.0000.000
25138LYS10.8580.91043.4320.0440.0440.0000.0000.0000.000
26139THR0-0.019-0.01139.150-0.002-0.0020.0000.0000.0000.000
27140GLY00.0170.00239.6060.0020.0020.0000.0000.0000.000
28141VAL00.0310.00740.7890.0010.0010.0000.0000.0000.000
29142ASP-1-0.886-0.94737.355-0.068-0.0680.0000.0000.0000.000
30143SER0-0.098-0.03337.577-0.002-0.0020.0000.0000.0000.000
31144PHE00.0030.00133.2170.0030.0030.0000.0000.0000.000
32145THR0-0.013-0.02038.107-0.002-0.0020.0000.0000.0000.000
33146GLU-1-0.883-0.93835.806-0.061-0.0610.0000.0000.0000.000
34147VAL00.0070.00639.7300.0000.0000.0000.0000.0000.000
35148GLU-1-0.827-0.88138.140-0.051-0.0510.0000.0000.0000.000
36149CYS0-0.057-0.02042.9350.0010.0010.0000.0000.0000.000
37150PHE0-0.019-0.02046.3240.0000.0000.0000.0000.0000.000
38151LEU0-0.0020.02948.9990.0000.0000.0000.0000.0000.000
39152ASN00.012-0.01352.4900.0000.0000.0000.0000.0000.000
40153PRO00.0110.02254.8870.0000.0000.0000.0000.0000.000
41154GLN00.005-0.00857.4490.0010.0010.0000.0000.0000.000
42155MET0-0.065-0.02159.9820.0000.0000.0000.0000.0000.000
43156GLY00.0410.03062.6260.0010.0010.0000.0000.0000.000
44157ASN0-0.083-0.04662.0530.0000.0000.0000.0000.0000.000
45158PRO0-0.0020.00465.1770.0000.0000.0000.0000.0000.000
46159ASP-1-0.788-0.87866.848-0.013-0.0130.0000.0000.0000.000
47160GLU-1-0.947-0.98864.244-0.015-0.0150.0000.0000.0000.000
48161HIS0-0.052-0.02162.951-0.001-0.0010.0000.0000.0000.000
49162GLN0-0.068-0.03762.8730.0000.0000.0000.0000.0000.000
50163LYS10.9760.97859.7670.0190.0190.0000.0000.0000.000
51164GLY0-0.020-0.00658.6560.0000.0000.0000.0000.0000.000
52165LEU0-0.012-0.01359.6120.0000.0000.0000.0000.0000.000
53166SER00.0360.02462.6970.0000.0000.0000.0000.0000.000
54167LYS10.7980.87365.9810.0120.0120.0000.0000.0000.000
55168SER0-0.012-0.00369.1500.0000.0000.0000.0000.0000.000
56169LEU0-0.021-0.00367.1850.0000.0000.0000.0000.0000.000
57170ALA0-0.026-0.00771.5550.0000.0000.0000.0000.0000.000
58171ALA00.0420.01873.9600.0000.0000.0000.0000.0000.000
59172GLU-1-0.921-0.95276.220-0.009-0.0090.0000.0000.0000.000
60173LYS10.8000.89276.4740.0110.0110.0000.0000.0000.000
61174GLN0-0.0010.00580.6480.0000.0000.0000.0000.0000.000
62175PHE00.0630.02279.0720.0000.0000.0000.0000.0000.000
63176THR0-0.037-0.02282.0650.0000.0000.0000.0000.0000.000
64177ASP-1-0.924-0.96483.532-0.009-0.0090.0000.0000.0000.000
65178ASP-1-0.796-0.87476.986-0.011-0.0110.0000.0000.0000.000
66179SER0-0.006-0.01378.4950.0000.0000.0000.0000.0000.000
67180PRO0-0.0220.00673.4560.0000.0000.0000.0000.0000.000
68181ASP-1-0.781-0.88573.188-0.012-0.0120.0000.0000.0000.000
69182LYS10.8330.90567.5980.0170.0170.0000.0000.0000.000
70183GLU-1-0.809-0.90368.778-0.014-0.0140.0000.0000.0000.000
71184GLN0-0.050-0.03568.3880.0000.0000.0000.0000.0000.000
72185LEU0-0.0240.00668.2240.0000.0000.0000.0000.0000.000
73186PRO00.0350.02362.578-0.001-0.0010.0000.0000.0000.000
74187CYS0-0.089-0.01563.1480.0000.0000.0000.0000.0000.000
75188TYR0-0.033-0.03959.588-0.001-0.0010.0000.0000.0000.000
76189SER0-0.0240.00357.1150.0000.0000.0000.0000.0000.000
77190VAL0-0.037-0.02856.508-0.001-0.0010.0000.0000.0000.000
78191ALA0-0.0060.00153.6460.0000.0000.0000.0000.0000.000
79192ARG10.9180.95354.6830.0290.0290.0000.0000.0000.000
80193ILE00.0010.01248.2770.0000.0000.0000.0000.0000.000
81194PRO0-0.006-0.00651.9090.0000.0000.0000.0000.0000.000
82195LEU0-0.007-0.00347.553-0.002-0.0020.0000.0000.0000.000
83196PRO00.0040.00847.0890.0020.0020.0000.0000.0000.000
84197ASN00.0460.02849.881-0.002-0.0020.0000.0000.0000.000
85198ILE0-0.034-0.00546.096-0.001-0.0010.0000.0000.0000.000
86199ASN0-0.008-0.01249.8160.0000.0000.0000.0000.0000.000
871100GLU-1-0.759-0.86351.633-0.040-0.0400.0000.0000.0000.000
881101ASP-1-0.781-0.85052.463-0.038-0.0380.0000.0000.0000.000
891102LEU0-0.013-0.02054.0710.0000.0000.0000.0000.0000.000
901103THR0-0.051-0.04354.7310.0010.0010.0000.0000.0000.000
911104CYS0-0.072-0.03850.615-0.001-0.0010.0000.0000.0000.000
921105GLY00.0120.02052.202-0.001-0.0010.0000.0000.0000.000
931106ASN0-0.152-0.08949.2120.0010.0010.0000.0000.0000.000
941107ILE00.0510.04552.172-0.001-0.0010.0000.0000.0000.000
951108LEU0-0.033-0.02346.474-0.001-0.0010.0000.0000.0000.000
961109MET00.0070.02149.4960.0020.0020.0000.0000.0000.000
971110TRP0-0.013-0.01743.220-0.003-0.0030.0000.0000.0000.000
981111GLU-1-0.684-0.80045.756-0.043-0.0430.0000.0000.0000.000
991112ALA00.0150.00445.166-0.003-0.0030.0000.0000.0000.000
1001113VAL00.0280.01540.7570.0010.0010.0000.0000.0000.000
1011114THR0-0.029-0.03339.2980.0000.0000.0000.0000.0000.000
1021115VAL00.0040.01142.5960.0000.0000.0000.0000.0000.000
1031116LYS10.8520.92136.2610.0500.0500.0000.0000.0000.000
1041117THR0-0.025-0.00542.2970.0010.0010.0000.0000.0000.000
1051118GLU-1-0.839-0.92041.685-0.033-0.0330.0000.0000.0000.000
1061119VAL00.0320.02545.5180.0000.0000.0000.0000.0000.000
1071120ILE00.000-0.00345.4470.0000.0000.0000.0000.0000.000
1081121GLY00.0380.00846.7910.0010.0010.0000.0000.0000.000
1091122VAL00.0350.01046.7240.0010.0010.0000.0000.0000.000
1101123THR00.0130.00145.4930.0010.0010.0000.0000.0000.000
1111124ALA0-0.0020.00048.7860.0010.0010.0000.0000.0000.000
1121125MET0-0.034-0.01851.8960.0010.0010.0000.0000.0000.000
1131126LEU00.0080.01048.6410.0010.0010.0000.0000.0000.000
1141127ASN0-0.0210.00653.1440.0010.0010.0000.0000.0000.000
1151128LEU0-0.0010.00855.6870.0000.0000.0000.0000.0000.000
1161129HIS00.011-0.01455.0500.0010.0010.0000.0000.0000.000
1171130SER00.0130.01859.4360.0000.0000.0000.0000.0000.000
1181131GLY00.0200.01961.5030.0010.0010.0000.0000.0000.000
1191132THR0-0.006-0.00162.0900.0000.0000.0000.0000.0000.000
1201133GLN00.0160.01864.2010.0000.0000.0000.0000.0000.000
1211134LYS10.8810.94064.9360.0060.0060.0000.0000.0000.000
1221135THR0-0.044-0.02162.2820.0000.0000.0000.0000.0000.000
1231136HIS00.0440.01362.7160.0000.0000.0000.0000.0000.000
1241137GLU-1-0.867-0.93466.777-0.005-0.0050.0000.0000.0000.000
1251138ASN0-0.049-0.02465.4340.0000.0000.0000.0000.0000.000
1261139GLY0-0.0120.00862.4610.0000.0000.0000.0000.0000.000
1271140ALA0-0.006-0.00359.2430.0000.0000.0000.0000.0000.000
1281141GLY00.0580.01760.5830.0000.0000.0000.0000.0000.000
1291142LYS10.8540.93260.7320.0100.0100.0000.0000.0000.000
1301143PRO0-0.005-0.00257.2200.0000.0000.0000.0000.0000.000
1311144ILE0-0.005-0.00756.8660.0000.0000.0000.0000.0000.000
1321145GLN0-0.043-0.02757.9490.0000.0000.0000.0000.0000.000
1331146GLY00.0470.02960.1970.0000.0000.0000.0000.0000.000
1341147SER0-0.057-0.04160.734-0.001-0.0010.0000.0000.0000.000
1351148ASN0-0.0090.01057.069-0.001-0.0010.0000.0000.0000.000
1361149PHE0-0.012-0.01958.2780.0000.0000.0000.0000.0000.000
1371150HIS0-0.023-0.01852.9320.0000.0000.0000.0000.0000.000
1381151PHE00.032-0.00654.2380.0000.0000.0000.0000.0000.000
1391152PHE0-0.016-0.01547.663-0.001-0.0010.0000.0000.0000.000
1401153ALA00.0250.01752.7140.0000.0000.0000.0000.0000.000
1411154VAL0-0.022-0.01248.332-0.001-0.0010.0000.0000.0000.000
1421155GLY00.0500.01451.5690.0000.0000.0000.0000.0000.000
1431156GLY00.0010.01152.819-0.001-0.0010.0000.0000.0000.000
1441157GLU-1-0.774-0.88753.817-0.027-0.0270.0000.0000.0000.000
1451158PRO0-0.006-0.00856.9910.0000.0000.0000.0000.0000.000
1461159LEU00.0120.01257.1310.0000.0000.0000.0000.0000.000
1471160GLU-1-0.753-0.85459.508-0.021-0.0210.0000.0000.0000.000
1481161LEU0-0.043-0.01062.3740.0000.0000.0000.0000.0000.000
1491162GLN00.004-0.00664.9520.0000.0000.0000.0000.0000.000
1501163GLY00.001-0.00967.3800.0000.0000.0000.0000.0000.000
1511164VAL0-0.059-0.04169.3930.0000.0000.0000.0000.0000.000
1521165LEU00.0160.01370.2820.0000.0000.0000.0000.0000.000
1531166ALA00.0220.01172.4010.0000.0000.0000.0000.0000.000
1541167ASN00.038-0.00274.2450.0000.0000.0000.0000.0000.000
1551168TYR00.0240.01677.7020.0000.0000.0000.0000.0000.000
1561169ARG10.8550.92578.6390.0090.0090.0000.0000.0000.000
1571170THR0-0.0140.00075.6150.0000.0000.0000.0000.0000.000
1581171LYS10.8490.92678.4430.0100.0100.0000.0000.0000.000
1591172TYR0-0.015-0.04872.0280.0000.0000.0000.0000.0000.000
1601173PRO0-0.0040.02473.4840.0000.0000.0000.0000.0000.000
1611174ALA00.0210.00374.7400.0000.0000.0000.0000.0000.000
1621175GLN0-0.0110.00571.5520.0000.0000.0000.0000.0000.000
1631176THR0-0.024-0.02170.079-0.001-0.0010.0000.0000.0000.000
1641177VAL0-0.0070.00968.9860.0000.0000.0000.0000.0000.000
1651178THR00.0500.01370.0360.0000.0000.0000.0000.0000.000
1661179PRO0-0.0030.00171.5410.0000.0000.0000.0000.0000.000
1671180LYS10.9140.96273.9980.0150.0150.0000.0000.0000.000
1681181ASN0-0.036-0.03177.5880.0000.0000.0000.0000.0000.000
1691182ALA00.0320.02278.9430.0000.0000.0000.0000.0000.000
1701183THR0-0.028-0.03879.9040.0000.0000.0000.0000.0000.000
1711184VAL00.0370.00979.7940.0000.0000.0000.0000.0000.000
1721185ASP-1-0.812-0.88478.443-0.011-0.0110.0000.0000.0000.000
1731186SER0-0.045-0.03275.619-0.001-0.0010.0000.0000.0000.000
1741187GLN0-0.0210.00074.3950.0000.0000.0000.0000.0000.000
1751188GLN0-0.042-0.01573.0720.0000.0000.0000.0000.0000.000
1761189MET0-0.0010.00470.1480.0000.0000.0000.0000.0000.000
1771190ASN00.0330.02472.9270.0000.0000.0000.0000.0000.000
1781191THR00.045-0.00372.5060.0000.0000.0000.0000.0000.000
1791192ASP-1-0.865-0.90573.544-0.014-0.0140.0000.0000.0000.000
1801193HIS10.7740.88172.4350.0140.0140.0000.0000.0000.000
1811194LYS10.8560.92767.7480.0170.0170.0000.0000.0000.000
1821195ALA00.0020.00167.9720.0000.0000.0000.0000.0000.000
1831196VAL00.0080.00362.813-0.001-0.0010.0000.0000.0000.000
1841197LEU00.0050.01959.2140.0000.0000.0000.0000.0000.000
1851198ASP-1-0.800-0.87161.446-0.021-0.0210.0000.0000.0000.000
1861199LYS10.7870.86063.2850.0200.0200.0000.0000.0000.000
1871200ASP-1-0.730-0.85659.615-0.022-0.0220.0000.0000.0000.000
1881201ASN0-0.070-0.05361.8540.0010.0010.0000.0000.0000.000
1891202ALA00.0280.02663.9110.0010.0010.0000.0000.0000.000
1901203TYR00.026-0.00864.6230.0010.0010.0000.0000.0000.000
1911204PRO00.0430.01165.042-0.001-0.0010.0000.0000.0000.000
1921205VAL0-0.007-0.03761.9230.0000.0000.0000.0000.0000.000
1931206GLU-1-0.861-0.90564.909-0.014-0.0140.0000.0000.0000.000
1941207CYS0-0.064-0.01467.9670.0010.0010.0000.0000.0000.000
1951208TRP0-0.045-0.02965.5970.0000.0000.0000.0000.0000.000
1961209VAL00.0340.04463.1490.0000.0000.0000.0000.0000.000
1971210PRO00.0240.01458.9270.0000.0000.0000.0000.0000.000
1981211ASP-1-0.750-0.84061.697-0.018-0.0180.0000.0000.0000.000
1991212PRO0-0.030-0.01661.158-0.001-0.0010.0000.0000.0000.000
2001213SER0-0.109-0.09162.0670.0000.0000.0000.0000.0000.000
2011214LYS10.8210.89663.0150.0210.0210.0000.0000.0000.000
2021215ASN0-0.012-0.00958.252-0.001-0.0010.0000.0000.0000.000
2031216GLU-1-0.822-0.90957.399-0.024-0.0240.0000.0000.0000.000
2041217ASN0-0.066-0.02154.349-0.002-0.0020.0000.0000.0000.000
2051218THR0-0.055-0.04853.862-0.001-0.0010.0000.0000.0000.000
2061219ARG10.8480.91349.7760.0320.0320.0000.0000.0000.000
2071220TYR00.017-0.00452.6240.0000.0000.0000.0000.0000.000
2081221PHE00.0120.00548.8630.0000.0000.0000.0000.0000.000
2091222GLY00.006-0.00852.9140.0000.0000.0000.0000.0000.000
2101223THR0-0.0190.00253.9510.0000.0000.0000.0000.0000.000
2111224TYR0-0.0100.00556.3700.0000.0000.0000.0000.0000.000
2121225THR0-0.015-0.01556.9700.0000.0000.0000.0000.0000.000
2131226GLY00.0280.00959.6620.0000.0000.0000.0000.0000.000
2141227GLY00.013-0.00963.1510.0000.0000.0000.0000.0000.000
2151228GLU-1-0.896-0.92964.796-0.009-0.0090.0000.0000.0000.000
2161229ASN0-0.043-0.04363.4250.0000.0000.0000.0000.0000.000
2171230VAL00.0020.01759.3560.0000.0000.0000.0000.0000.000
2181231PRO00.0170.01555.3880.0000.0000.0000.0000.0000.000
2191232PRO00.0250.02154.1880.0000.0000.0000.0000.0000.000
2201233VAL0-0.037-0.02549.3040.0000.0000.0000.0000.0000.000
2211234LEU0-0.036-0.01748.790-0.001-0.0010.0000.0000.0000.000
2221235HIS00.002-0.00343.4150.0000.0000.0000.0000.0000.000
2231236ILE0-0.0010.00841.1810.0000.0000.0000.0000.0000.000
2241237THR0-0.071-0.04837.3450.0010.0010.0000.0000.0000.000
2251238ASN00.0760.04333.8650.0000.0000.0000.0000.0000.000
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