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

tag_button

FMODB ID: 1N3NZ

Calculation Name: 1PGL-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PGL

Chain ID: 1

ChEMBL ID:

UniProt ID: P23009

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1924989.790542
FMO2-HF: Nuclear repulsion 1851729.188287
FMO2-HF: Total energy -73260.602255
FMO2-MP2: Total energy -73471.283785


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(1:1:SER)


Summations of interaction energy for fragment #1(1:1:SER)
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.
-5.646-7.1137.854-2.652-3.7340.022
Interaction energy analysis for fragmet #1(1:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.004
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].
313SER0-0.0030.0063.8051.3902.744-0.016-0.560-0.7780.002
414GLN00.0280.0076.238-0.218-0.2180.0000.0000.0000.000
515GLN00.008-0.0019.8540.1010.1010.0000.0000.0000.000
616THR0-0.021-0.01612.1500.0090.0090.0000.0000.0000.000
717VAL00.0030.01812.526-0.004-0.0040.0000.0000.0000.000
818TRP00.0280.03113.2890.0600.0600.0000.0000.0000.000
919ASN0-0.040-0.03415.450-0.003-0.0030.0000.0000.0000.000
10110GLN00.0260.01317.8660.0050.0050.0000.0000.0000.000
11111MET0-0.0360.02521.1040.0060.0060.0000.0000.0000.000
12112ALA00.0680.01522.721-0.003-0.0030.0000.0000.0000.000
13113THR0-0.0070.00626.3930.0000.0000.0000.0000.0000.000
14114VAL0-0.047-0.01529.348-0.001-0.0010.0000.0000.0000.000
15115ARG10.8800.93432.385-0.029-0.0290.0000.0000.0000.000
16116THR00.006-0.00335.5760.0010.0010.0000.0000.0000.000
17117PRO0-0.0160.02638.381-0.002-0.0020.0000.0000.0000.000
18118LEU00.018-0.01441.625-0.001-0.0010.0000.0000.0000.000
19119ASN0-0.047-0.01243.882-0.001-0.0010.0000.0000.0000.000
20120PHE00.0000.00744.0360.0000.0000.0000.0000.0000.000
21121ASP-1-0.830-0.95146.1110.0170.0170.0000.0000.0000.000
22122SER0-0.035-0.04448.5600.0010.0010.0000.0000.0000.000
23123SER0-0.083-0.03949.5190.0000.0000.0000.0000.0000.000
24124LYN0-0.0030.06147.1160.0000.0000.0000.0000.0000.000
25125GLN0-0.037-0.03544.2180.0000.0000.0000.0000.0000.000
26126SER00.0230.01045.8570.0000.0000.0000.0000.0000.000
27127PHE00.0050.00941.6280.0000.0000.0000.0000.0000.000
28128CYS0-0.066-0.00540.1670.0000.0000.0000.0000.0000.000
29129GLN00.023-0.00737.610-0.001-0.0010.0000.0000.0000.000
30130PHE00.0060.01030.6360.0000.0000.0000.0000.0000.000
31131SER0-0.0090.00231.6820.0020.0020.0000.0000.0000.000
32132VAL00.0220.00626.152-0.001-0.0010.0000.0000.0000.000
33133ASP-1-0.775-0.88026.4350.1190.1190.0000.0000.0000.000
34134LEU0-0.012-0.02821.8620.0050.0050.0000.0000.0000.000
35135LEU0-0.029-0.01019.6910.0190.0190.0000.0000.0000.000
36136GLY00.0110.01922.5200.0070.0070.0000.0000.0000.000
37137GLY0-0.039-0.02324.891-0.005-0.0050.0000.0000.0000.000
38138GLY00.0070.00725.447-0.009-0.0090.0000.0000.0000.000
39139ILE0-0.007-0.01428.9440.0030.0030.0000.0000.0000.000
40140SER0-0.035-0.01231.312-0.004-0.0040.0000.0000.0000.000
41141VAL0-0.011-0.01934.6320.0000.0000.0000.0000.0000.000
42142ASP-1-0.755-0.85137.4720.0350.0350.0000.0000.0000.000
43143LYS10.8890.93140.947-0.033-0.0330.0000.0000.0000.000
44144THR00.007-0.01342.286-0.002-0.0020.0000.0000.0000.000
45145GLY00.0460.02144.104-0.002-0.0020.0000.0000.0000.000
46146ASP-1-0.941-0.96642.8380.0290.0290.0000.0000.0000.000
47147TRP0-0.017-0.02736.2560.0000.0000.0000.0000.0000.000
48148ILE0-0.011-0.00435.8250.0000.0000.0000.0000.0000.000
49149THR0-0.017-0.01132.6580.0000.0000.0000.0000.0000.000
50150LEU00.0090.00628.939-0.002-0.0020.0000.0000.0000.000
51151VAL00.0340.02725.2270.0020.0020.0000.0000.0000.000
52152GLN00.0020.00323.8520.0050.0050.0000.0000.0000.000
53153ASN00.0150.01323.2380.0170.0170.0000.0000.0000.000
54154SER0-0.032-0.04619.0830.0000.0000.0000.0000.0000.000
55155PRO00.015-0.01515.0960.0070.0070.0000.0000.0000.000
56156ILE00.0270.01213.9120.0160.0160.0000.0000.0000.000
57157SER00.0350.02216.3300.0110.0110.0000.0000.0000.000
58158ASN0-0.024-0.01218.895-0.008-0.0080.0000.0000.0000.000
59159LEU0-0.0100.00913.054-0.004-0.0040.0000.0000.0000.000
60160LEU0-0.003-0.00916.7680.0050.0050.0000.0000.0000.000
61161ARG10.8490.91818.887-0.119-0.1190.0000.0000.0000.000
62162VAL00.0160.01618.926-0.012-0.0120.0000.0000.0000.000
63163ALA0-0.0060.01617.014-0.004-0.0040.0000.0000.0000.000
64164ALA0-0.043-0.01418.9730.0000.0000.0000.0000.0000.000
65165TRP0-0.0140.00019.386-0.011-0.0110.0000.0000.0000.000
66166LYS10.8720.92716.725-0.181-0.1810.0000.0000.0000.000
67167LYS11.0061.00414.648-0.413-0.4130.0000.0000.0000.000
68168GLY00.0380.05112.9230.1000.1000.0000.0000.0000.000
69169CYS0-0.038-0.02112.264-0.076-0.0760.0000.0000.0000.000
70170LEU00.0080.03012.5690.1140.1140.0000.0000.0000.000
71171MET0-0.036-0.00513.882-0.043-0.0430.0000.0000.0000.000
72172VAL00.0420.00915.8220.0060.0060.0000.0000.0000.000
73173LYS10.9080.96619.408-0.056-0.0560.0000.0000.0000.000
74174VAL0-0.021-0.00321.4110.0030.0030.0000.0000.0000.000
75175VAL00.002-0.00924.717-0.006-0.0060.0000.0000.0000.000
76176MET0-0.0350.02327.2700.0010.0010.0000.0000.0000.000
77177SER00.022-0.00330.836-0.005-0.0050.0000.0000.0000.000
78178GLY00.021-0.01333.0570.0020.0020.0000.0000.0000.000
79179ASN0-0.078-0.03636.710-0.002-0.0020.0000.0000.0000.000
80180ALA00.025-0.00739.063-0.001-0.0010.0000.0000.0000.000
81181ALA0-0.018-0.00240.685-0.001-0.0010.0000.0000.0000.000
82182VAL0-0.0180.01643.148-0.001-0.0010.0000.0000.0000.000
83183LYS11.0071.00643.842-0.006-0.0060.0000.0000.0000.000
84184ARG11.0190.99537.710-0.006-0.0060.0000.0000.0000.000
85185SER0-0.063-0.04543.7230.0000.0000.0000.0000.0000.000
86186ASP-1-0.895-0.93146.5000.0080.0080.0000.0000.0000.000
87187TRP0-0.082-0.03338.1510.0000.0000.0000.0000.0000.000
88188ALA00.006-0.00543.8540.0000.0000.0000.0000.0000.000
89189SER0-0.033-0.00140.0730.0010.0010.0000.0000.0000.000
90190LEU0-0.0050.00537.913-0.001-0.0010.0000.0000.0000.000
91191VAL00.0010.00133.2380.0010.0010.0000.0000.0000.000
92192GLN0-0.026-0.00634.6500.0000.0000.0000.0000.0000.000
93193VAL00.001-0.00428.3540.0020.0020.0000.0000.0000.000
94194PHE00.025-0.00130.909-0.003-0.0030.0000.0000.0000.000
95195LEU0-0.0080.01123.8330.0040.0040.0000.0000.0000.000
96196THR00.0790.03628.083-0.003-0.0030.0000.0000.0000.000
97197ASN00.0210.02427.295-0.001-0.0010.0000.0000.0000.000
98198SER00.0920.01928.4080.0030.0030.0000.0000.0000.000
99199ASN00.0230.00231.436-0.005-0.0050.0000.0000.0000.000
1001100SER0-0.0480.01134.017-0.006-0.0060.0000.0000.0000.000
1011101THR00.023-0.00736.1890.0010.0010.0000.0000.0000.000
1021102GLU-1-0.987-0.99738.5030.0430.0430.0000.0000.0000.000
1031103HIS0-0.084-0.02632.238-0.002-0.0020.0000.0000.0000.000
1041104PHE00.005-0.00234.314-0.002-0.0020.0000.0000.0000.000
1051105ASP-1-0.819-0.89431.6960.0610.0610.0000.0000.0000.000
1061106ALA0-0.031-0.01426.653-0.002-0.0020.0000.0000.0000.000
1071107CYS0-0.057-0.02726.278-0.005-0.0050.0000.0000.0000.000
1081108ARG10.8430.89928.799-0.045-0.0450.0000.0000.0000.000
1091109TRP00.0320.01924.854-0.003-0.0030.0000.0000.0000.000
1101110THR0-0.014-0.02131.3460.0000.0000.0000.0000.0000.000
1111111LYS10.8660.96228.827-0.031-0.0310.0000.0000.0000.000
1121112SER00.0290.00333.7010.0000.0000.0000.0000.0000.000
1131113GLU-1-0.884-0.93631.9730.0190.0190.0000.0000.0000.000
1141114PRO0-0.030-0.02735.9060.0010.0010.0000.0000.0000.000
1151115HIS0-0.046-0.01936.546-0.001-0.0010.0000.0000.0000.000
1161116SER0-0.026-0.01331.8280.0010.0010.0000.0000.0000.000
1171117TRP00.0120.01628.454-0.001-0.0010.0000.0000.0000.000
1181118GLU-1-0.868-0.94923.8380.0280.0280.0000.0000.0000.000
1191119LEU0-0.056-0.02625.137-0.005-0.0050.0000.0000.0000.000
1201120ILE00.017-0.00318.7340.0090.0090.0000.0000.0000.000
1211121PHE0-0.017-0.00320.247-0.011-0.0110.0000.0000.0000.000
1221122PRO00.0200.00716.3450.0140.0140.0000.0000.0000.000
1231123ILE0-0.0060.00317.363-0.023-0.0230.0000.0000.0000.000
1241124GLU-1-0.913-0.97916.3330.2680.2680.0000.0000.0000.000
1251125VAL0-0.046-0.00717.112-0.028-0.0280.0000.0000.0000.000
1261126CYS00.008-0.00418.0250.0340.0340.0000.0000.0000.000
1271127GLY00.023-0.00720.622-0.016-0.0160.0000.0000.0000.000
1281128PRO0-0.031-0.02022.8170.0010.0010.0000.0000.0000.000
1291129ASN0-0.055-0.00522.436-0.012-0.0120.0000.0000.0000.000
1301130ASN00.0350.00119.587-0.020-0.0200.0000.0000.0000.000
1311131GLY00.0330.02019.4500.0240.0240.0000.0000.0000.000
1321132PHE0-0.070-0.02615.2290.0110.0110.0000.0000.0000.000
1331133GLU-1-0.867-0.94720.0840.1330.1330.0000.0000.0000.000
1341134MET0-0.072-0.01421.6210.0160.0160.0000.0000.0000.000
1351135TRP0-0.065-0.05223.889-0.010-0.0100.0000.0000.0000.000
1361136SER0-0.011-0.00625.433-0.009-0.0090.0000.0000.0000.000
1371137SER0-0.024-0.00527.942-0.011-0.0110.0000.0000.0000.000
1381138GLU-1-0.867-0.94529.6740.0630.0630.0000.0000.0000.000
1391139TRP0-0.007-0.00728.355-0.004-0.0040.0000.0000.0000.000
1401140ALA0-0.088-0.02429.511-0.004-0.0040.0000.0000.0000.000
1411141ASN0-0.049-0.03831.379-0.001-0.0010.0000.0000.0000.000
1421142GLN00.0160.02025.6880.0140.0140.0000.0000.0000.000
1431143THR0-0.0120.00626.396-0.011-0.0110.0000.0000.0000.000
1441144SER0-0.008-0.00824.9470.0150.0150.0000.0000.0000.000
1451145TRP0-0.003-0.01721.449-0.011-0.0110.0000.0000.0000.000
1461146HIS0-0.001-0.00125.1150.0050.0050.0000.0000.0000.000
1471147LEU0-0.014-0.00124.864-0.002-0.0020.0000.0000.0000.000
1481148SER00.007-0.00527.990-0.002-0.0020.0000.0000.0000.000
1491149PHE0-0.006-0.01028.038-0.001-0.0010.0000.0000.0000.000
1501150LEU0-0.0020.01433.622-0.001-0.0010.0000.0000.0000.000
1511151VAL0-0.023-0.02935.818-0.001-0.0010.0000.0000.0000.000
1521152ASP-1-0.841-0.92338.2120.0230.0230.0000.0000.0000.000
1531153ASN00.0110.00441.359-0.001-0.0010.0000.0000.0000.000
1541154PRO00.003-0.00940.1130.0000.0000.0000.0000.0000.000
1551155LYS10.9230.95340.778-0.019-0.0190.0000.0000.0000.000
1561156GLN0-0.0050.01141.251-0.001-0.0010.0000.0000.0000.000
1571157SER00.029-0.00636.356-0.001-0.0010.0000.0000.0000.000
1581158THR0-0.044-0.03237.5280.0020.0020.0000.0000.0000.000
1591159THR00.0510.02531.9860.0010.0010.0000.0000.0000.000
1601160PHE0-0.003-0.00129.936-0.001-0.0010.0000.0000.0000.000
1611161ASP-1-0.845-0.90025.9310.0490.0490.0000.0000.0000.000
1621162VAL0-0.003-0.00522.6910.0000.0000.0000.0000.0000.000
1631163LEU0-0.018-0.01819.5430.0030.0030.0000.0000.0000.000
1641164LEU00.0250.00416.9770.0030.0030.0000.0000.0000.000
1651165GLY0-0.004-0.00213.877-0.014-0.0140.0000.0000.0000.000
1661166ILE00.0030.0099.126-0.044-0.0440.0000.0000.0000.000
1671167SER0-0.012-0.0288.6500.0570.0570.0000.0000.0000.000
1681168GLN0-0.031-0.0521.963-7.880-10.7647.871-2.092-2.8940.020
1691169ASN00.0060.0035.6800.5170.580-0.0010.000-0.0620.000
1701170PHE0-0.0410.0048.471-0.261-0.2610.0000.0000.0000.000
1711171GLU-1-0.891-0.9539.6540.7410.7410.0000.0000.0000.000
1721172ILE0-0.033-0.02811.910-0.112-0.1120.0000.0000.0000.000
1731173ALA00.0190.00014.4890.0020.0020.0000.0000.0000.000
1741174GLY00.0030.00517.137-0.016-0.0160.0000.0000.0000.000
1751175ASN0-0.011-0.01719.4160.0200.0200.0000.0000.0000.000
1761176THR00.0200.01421.628-0.013-0.0130.0000.0000.0000.000
1771177LEU0-0.039-0.02124.386-0.001-0.0010.0000.0000.0000.000
1781178MET00.0270.02024.917-0.003-0.0030.0000.0000.0000.000
1791179PRO0-0.015-0.00527.653-0.004-0.0040.0000.0000.0000.000
1801180ALA00.006-0.00528.4820.0040.0040.0000.0000.0000.000
1811181PHE00.0070.00622.847-0.001-0.0010.0000.0000.0000.000
1821182SER00.000-0.00928.051-0.005-0.0050.0000.0000.0000.000
1831183VAL0-0.0080.00127.5490.0040.0040.0000.0000.0000.000
1841184PRO00.0180.00929.277-0.003-0.0030.0000.0000.0000.000
1851185GLN0-0.0050.00632.1560.0000.0000.0000.0000.0000.000