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: 98282

Calculation Name: 1NY7-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NY7

Chain ID: 1

ChEMBL ID:

UniProt ID: P03599

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 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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1991036.084896
FMO2-HF: Nuclear repulsion 1916698.945292
FMO2-HF: Total energy -74337.139604
FMO2-MP2: Total energy -74551.214289


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:GLY)


Summations of interaction energy for fragment #1(1:1:GLY)
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.
-1.735-0.5560.007-0.483-0.7020.001
Interaction energy analysis for fragmet #1(1:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.009
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].
313VAL0-0.030-0.0123.463-0.3640.7450.008-0.465-0.6510.001
414CYS00.0110.0104.419-0.878-0.808-0.001-0.018-0.0510.000
515ALA0-0.025-0.0067.0690.3160.3160.0000.0000.0000.000
616GLU-1-0.968-0.9868.690-0.348-0.3480.0000.0000.0000.000
717ALA00.0170.02312.3770.0270.0270.0000.0000.0000.000
818SER0-0.012-0.03214.7580.0260.0260.0000.0000.0000.000
919ASP-1-0.874-0.90918.462-0.230-0.2300.0000.0000.0000.000
10110VAL00.0040.00021.739-0.011-0.0110.0000.0000.0000.000
11111TYR00.0300.01419.1120.0110.0110.0000.0000.0000.000
12112SER0-0.024-0.00823.9450.0010.0010.0000.0000.0000.000
13113PRO00.0610.03026.203-0.001-0.0010.0000.0000.0000.000
14114CYS0-0.079-0.03727.2800.0170.0170.0000.0000.0000.000
15115MET00.0070.01028.7410.0150.0150.0000.0000.0000.000
16116ILE0-0.036-0.00227.213-0.014-0.0140.0000.0000.0000.000
17117ALA00.0160.01428.6490.0130.0130.0000.0000.0000.000
18118SER0-0.021-0.02428.496-0.015-0.0150.0000.0000.0000.000
19119THR00.0080.00627.8950.0100.0100.0000.0000.0000.000
20120PRO00.0800.04530.6710.0010.0010.0000.0000.0000.000
21121PRO0-0.031-0.00433.029-0.003-0.0030.0000.0000.0000.000
22122ALA00.0010.02134.0430.0030.0030.0000.0000.0000.000
23123PRO0-0.030-0.03835.3890.0010.0010.0000.0000.0000.000
24124PHE00.0240.00333.1440.0010.0010.0000.0000.0000.000
25125SER0-0.041-0.04332.123-0.003-0.0030.0000.0000.0000.000
26126ASP-1-0.873-0.89532.080-0.061-0.0610.0000.0000.0000.000
27127VAL0-0.035-0.02728.658-0.006-0.0060.0000.0000.0000.000
28128THR0-0.016-0.02629.7770.0020.0020.0000.0000.0000.000
29129ALA00.0160.00129.385-0.010-0.0100.0000.0000.0000.000
30130VAL0-0.0210.00529.1490.0080.0080.0000.0000.0000.000
31131THR0-0.001-0.00530.018-0.011-0.0110.0000.0000.0000.000
32132PHE00.019-0.00727.5240.0050.0050.0000.0000.0000.000
33133ASP-1-0.709-0.83131.539-0.100-0.1000.0000.0000.0000.000
34134LEU0-0.020-0.04826.7070.0010.0010.0000.0000.0000.000
35135ILE0-0.030-0.00931.253-0.001-0.0010.0000.0000.0000.000
36136ASN0-0.069-0.04834.0450.0040.0040.0000.0000.0000.000
37137GLY0-0.033-0.00834.3650.0030.0030.0000.0000.0000.000
38138LYS10.8730.92335.0940.0900.0900.0000.0000.0000.000
39139ILE0-0.0030.00232.537-0.006-0.0060.0000.0000.0000.000
40140THR0-0.040-0.01934.4880.0070.0070.0000.0000.0000.000
41141PRO00.0320.02534.182-0.005-0.0050.0000.0000.0000.000
42142VAL00.0250.00233.9500.0040.0040.0000.0000.0000.000
43143GLY00.0100.01736.5020.0040.0040.0000.0000.0000.000
44144ASP-1-0.885-0.90335.414-0.078-0.0780.0000.0000.0000.000
45145ASP-1-0.888-0.97836.794-0.075-0.0750.0000.0000.0000.000
46146ASN0-0.101-0.04337.5830.0030.0030.0000.0000.0000.000
47147TRP00.0910.09127.901-0.008-0.0080.0000.0000.0000.000
48148ASN0-0.068-0.06433.7250.0000.0000.0000.0000.0000.000
49149THR0-0.011-0.01933.070-0.007-0.0070.0000.0000.0000.000
50150HIS0-0.021-0.01032.9690.0070.0070.0000.0000.0000.000
51151ILE00.0300.01932.861-0.008-0.0080.0000.0000.0000.000
52152TYR00.0000.02829.5660.0100.0100.0000.0000.0000.000
53153ASN00.023-0.00334.132-0.001-0.0010.0000.0000.0000.000
54154PRO00.0300.03530.6000.0050.0050.0000.0000.0000.000
55155PRO00.013-0.01532.4600.0030.0030.0000.0000.0000.000
56156ILE00.0230.01828.5660.0060.0060.0000.0000.0000.000
57157MET00.0760.04032.4890.0010.0010.0000.0000.0000.000
58158ASN0-0.012-0.00633.9590.0060.0060.0000.0000.0000.000
59159VAL0-0.0060.02135.1770.0050.0050.0000.0000.0000.000
60160LEU0-0.022-0.01131.2020.0050.0050.0000.0000.0000.000
61161ARG10.8860.92235.9060.1010.1010.0000.0000.0000.000
62162THR0-0.034-0.01438.8760.0050.0050.0000.0000.0000.000
63163ALA00.0060.01038.4580.0040.0040.0000.0000.0000.000
64164ALA0-0.042-0.01140.259-0.002-0.0020.0000.0000.0000.000
65165TRP0-0.024-0.01240.934-0.001-0.0010.0000.0000.0000.000
66166LYS10.8640.91735.4730.0890.0890.0000.0000.0000.000
67167SER0-0.0010.00235.2780.0020.0020.0000.0000.0000.000
68168GLY00.0470.02531.8690.0010.0010.0000.0000.0000.000
69169THR0-0.034-0.04825.2600.0030.0030.0000.0000.0000.000
70170ILE0-0.051-0.01926.3470.0000.0000.0000.0000.0000.000
71171HIS0-0.057-0.05521.627-0.025-0.0250.0000.0000.0000.000
72172VAL0-0.008-0.01322.0760.0090.0090.0000.0000.0000.000
73173GLN0-0.002-0.01117.167-0.040-0.0400.0000.0000.0000.000
74174LEU0-0.043-0.01019.3960.0240.0240.0000.0000.0000.000
75175ASN00.0020.00018.695-0.080-0.0800.0000.0000.0000.000
76176VAL00.0130.00418.7800.0370.0370.0000.0000.0000.000
77177ARG10.8270.88519.2440.1990.1990.0000.0000.0000.000
78178GLY0-0.0020.00020.9360.0180.0180.0000.0000.0000.000
79179ALA0-0.0050.01222.3410.0020.0020.0000.0000.0000.000
80180GLY0-0.013-0.01522.977-0.012-0.0120.0000.0000.0000.000
81181VAL0-0.021-0.00922.4160.0160.0160.0000.0000.0000.000
82182LYS10.8390.90321.3640.0260.0260.0000.0000.0000.000
83183ARG11.0150.99012.2210.2430.2430.0000.0000.0000.000
84184ALA0-0.060-0.04019.036-0.004-0.0040.0000.0000.0000.000
85185ASP-1-0.788-0.86520.700-0.034-0.0340.0000.0000.0000.000
86186TRP0-0.032-0.00618.678-0.006-0.0060.0000.0000.0000.000
87187ASP-1-0.897-0.92920.751-0.084-0.0840.0000.0000.0000.000
88188GLY00.0440.02321.714-0.001-0.0010.0000.0000.0000.000
89189GLN0-0.022-0.02219.905-0.009-0.0090.0000.0000.0000.000
90190VAL00.0030.00719.1580.0120.0120.0000.0000.0000.000
91191PHE0-0.0060.00720.647-0.016-0.0160.0000.0000.0000.000
92192VAL0-0.013-0.02021.3320.0040.0040.0000.0000.0000.000
93193TYR00.0310.01923.581-0.005-0.0050.0000.0000.0000.000
94194LEU0-0.0210.01524.9980.0020.0020.0000.0000.0000.000
95195ARG10.8480.89727.3100.1020.1020.0000.0000.0000.000
96196GLN00.0370.01230.8840.0020.0020.0000.0000.0000.000
97197SER00.0300.01733.9450.0040.0040.0000.0000.0000.000
98198MET00.0170.01432.966-0.006-0.0060.0000.0000.0000.000
99199ASN0-0.0250.01336.8980.0020.0020.0000.0000.0000.000
1001100PRO00.0270.00637.412-0.004-0.0040.0000.0000.0000.000
1011101GLU-1-0.902-0.96337.698-0.058-0.0580.0000.0000.0000.000
1021102SER0-0.083-0.02235.8910.0000.0000.0000.0000.0000.000
1031103TYR00.0230.00732.4390.0000.0000.0000.0000.0000.000
1041104ASP-1-0.863-0.92728.157-0.113-0.1130.0000.0000.0000.000
1051105ALA0-0.023-0.01628.5140.0030.0030.0000.0000.0000.000
1061106ARG10.9210.94918.5920.2140.2140.0000.0000.0000.000
1071107THR00.0140.01823.0040.0070.0070.0000.0000.0000.000
1081108PHE0-0.058-0.03118.000-0.014-0.0140.0000.0000.0000.000
1091109VAL00.0430.02618.3440.0200.0200.0000.0000.0000.000
1101110ILE0-0.0040.00714.480-0.030-0.0300.0000.0000.0000.000
1111111SER0-0.042-0.04515.1590.0430.0430.0000.0000.0000.000
1121112GLN0-0.043-0.02811.424-0.066-0.0660.0000.0000.0000.000
1131113PRO0-0.034-0.02214.0920.0020.0020.0000.0000.0000.000
1141114GLY0-0.0020.01715.838-0.036-0.0360.0000.0000.0000.000
1151115SER00.000-0.01016.4550.0210.0210.0000.0000.0000.000
1161116ALA0-0.0080.00714.255-0.053-0.0530.0000.0000.0000.000
1171117MET0-0.017-0.00213.8400.0300.0300.0000.0000.0000.000
1181118LEU0-0.0030.01114.239-0.060-0.0600.0000.0000.0000.000
1191119ASN0-0.009-0.02015.083-0.001-0.0010.0000.0000.0000.000
1201120PHE0-0.025-0.00816.769-0.008-0.0080.0000.0000.0000.000
1211121SER00.0270.01719.4100.0000.0000.0000.0000.0000.000
1221122PHE0-0.022-0.01622.4580.0020.0020.0000.0000.0000.000
1231123ASP-1-0.848-0.90825.852-0.144-0.1440.0000.0000.0000.000
1241124ILE0-0.0110.02329.0170.0050.0050.0000.0000.0000.000
1251125ILE00.001-0.00432.6360.0030.0030.0000.0000.0000.000
1261126GLY0-0.0030.00435.0730.0010.0010.0000.0000.0000.000
1271127PRO0-0.017-0.01738.6820.0020.0020.0000.0000.0000.000
1281128ASN0-0.040-0.00842.1730.0050.0050.0000.0000.0000.000
1291129SER0-0.005-0.01841.7750.0030.0030.0000.0000.0000.000
1301130GLY00.0470.03038.423-0.001-0.0010.0000.0000.0000.000
1311131PHE0-0.066-0.02837.440-0.005-0.0050.0000.0000.0000.000
1321132GLU-1-0.810-0.92436.325-0.082-0.0820.0000.0000.0000.000
1331133PHE0-0.049-0.01739.059-0.002-0.0020.0000.0000.0000.000
1341134ALA0-0.020-0.03237.7620.0020.0020.0000.0000.0000.000
1351135GLU-1-0.842-0.90339.191-0.078-0.0780.0000.0000.0000.000
1361136SER0-0.0280.00441.5540.0040.0040.0000.0000.0000.000
1371137PRO00.040-0.01244.6460.0000.0000.0000.0000.0000.000
1381138TRP0-0.013-0.00545.9970.0020.0020.0000.0000.0000.000
1391139ALA0-0.074-0.01344.1030.0010.0010.0000.0000.0000.000
1401140ASN0-0.035-0.03244.4140.0000.0000.0000.0000.0000.000
1411141GLN00.0270.02440.882-0.004-0.0040.0000.0000.0000.000
1421142THR00.0170.01335.8280.0030.0030.0000.0000.0000.000
1431143THR0-0.0100.00535.482-0.002-0.0020.0000.0000.0000.000
1441144TRP00.022-0.00328.503-0.005-0.0050.0000.0000.0000.000
1451145TYR0-0.036-0.04831.608-0.003-0.0030.0000.0000.0000.000
1461146LEU0-0.037-0.02324.323-0.007-0.0070.0000.0000.0000.000
1471147GLU-1-0.889-0.94828.393-0.106-0.1060.0000.0000.0000.000
1481148CYS0-0.060-0.02725.253-0.018-0.0180.0000.0000.0000.000
1491149VAL00.0430.00825.5870.0100.0100.0000.0000.0000.000
1501150ALA0-0.025-0.01324.816-0.016-0.0160.0000.0000.0000.000
1511151THR00.014-0.01223.9350.0130.0130.0000.0000.0000.000
1521152ASN00.047-0.00425.1920.0100.0100.0000.0000.0000.000
1531153PRO0-0.0170.01026.281-0.011-0.0110.0000.0000.0000.000
1541154ARG10.8250.89528.4270.0890.0890.0000.0000.0000.000
1551155GLN00.0230.02122.987-0.012-0.0120.0000.0000.0000.000
1561156ILE0-0.0190.00421.705-0.017-0.0170.0000.0000.0000.000
1571157GLN0-0.029-0.01923.9620.0160.0160.0000.0000.0000.000
1581158GLN00.0280.01224.7030.0010.0010.0000.0000.0000.000
1591159PHE00.0280.01722.181-0.022-0.0220.0000.0000.0000.000
1601160GLU-1-0.731-0.83823.207-0.217-0.2170.0000.0000.0000.000
1611161VAL00.0080.01123.336-0.025-0.0250.0000.0000.0000.000
1621162ASN0-0.048-0.03222.1420.0270.0270.0000.0000.0000.000
1631163MET0-0.013-0.00923.549-0.010-0.0100.0000.0000.0000.000
1641164ARG10.8970.93422.5710.2160.2160.0000.0000.0000.000
1651165PHE0-0.022-0.00625.904-0.001-0.0010.0000.0000.0000.000
1661166ASP-1-0.784-0.87525.246-0.165-0.1650.0000.0000.0000.000
1671167PRO0-0.007-0.02126.3310.0100.0100.0000.0000.0000.000
1681168ASN0-0.045-0.00728.6350.0100.0100.0000.0000.0000.000
1691169PHE0-0.0020.00530.7790.0080.0080.0000.0000.0000.000
1701170ARG10.8810.93932.5530.0860.0860.0000.0000.0000.000
1711171VAL0-0.010-0.01136.356-0.002-0.0020.0000.0000.0000.000
1721172ALA00.0040.00038.8240.0030.0030.0000.0000.0000.000
1731173GLY00.0110.01442.6010.0000.0000.0000.0000.0000.000
1741174ASN00.004-0.00843.729-0.005-0.0050.0000.0000.0000.000
1751175ILE0-0.0030.00842.1530.0030.0030.0000.0000.0000.000
1761176LEU0-0.043-0.02245.798-0.001-0.0010.0000.0000.0000.000
1771177MET00.0110.02243.073-0.001-0.0010.0000.0000.0000.000
1781178PRO0-0.0140.00045.3020.0020.0020.0000.0000.0000.000
1791179PRO00.002-0.01745.927-0.002-0.0020.0000.0000.0000.000
1801180PHE00.0180.01640.624-0.001-0.0010.0000.0000.0000.000
1811181PRO0-0.0030.00141.8800.0010.0010.0000.0000.0000.000
1821182LEU0-0.007-0.00141.034-0.004-0.0040.0000.0000.0000.000
1831183SER0-0.010-0.02936.5550.0020.0020.0000.0000.0000.000
1841184THR0-0.034-0.01836.055-0.003-0.0030.0000.0000.0000.000
1851185GLU-1-0.890-0.95228.509-0.159-0.1590.0000.0000.0000.000
1861186THR00.0050.01231.0960.0070.0070.0000.0000.0000.000
1871187PRO0-0.020-0.01530.822-0.010-0.0100.0000.0000.0000.000
1881188PRO00.0010.00126.8190.0020.0020.0000.0000.0000.000
1891189LEU0-0.033-0.00728.4900.0010.0010.0000.0000.0000.000