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: LN6N9

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1990839.611746
FMO2-HF: Nuclear repulsion 1916503.581205
FMO2-HF: Total energy -74336.030542
FMO2-MP2: Total energy -74550.224268


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.
-1.665-0.5150.007-0.466-0.690.001
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 : 0.013 / q_NPA : -0.010
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].
313VAL0-0.018-0.0053.462-0.2920.7890.008-0.449-0.6400.001
414CYS00.0030.0074.419-0.862-0.793-0.001-0.017-0.0500.000
515ALA0-0.018-0.0057.0690.3270.3270.0000.0000.0000.000
616GLU-1-0.966-0.9848.690-0.352-0.3520.0000.0000.0000.000
717ALA00.0170.02212.3770.0290.0290.0000.0000.0000.000
818SER0-0.025-0.02414.7580.0450.0450.0000.0000.0000.000
919ASP-1-0.927-0.96218.462-0.242-0.2420.0000.0000.0000.000
10110VAL0-0.013-0.01121.739-0.011-0.0110.0000.0000.0000.000
11111TYR00.0210.00818.9560.0110.0110.0000.0000.0000.000
12112SER0-0.025-0.01123.9450.0010.0010.0000.0000.0000.000
13113PRO00.0610.02926.119-0.001-0.0010.0000.0000.0000.000
14114CYS0-0.063-0.03327.2800.0170.0170.0000.0000.0000.000
15115MET0-0.0050.00528.7380.0160.0160.0000.0000.0000.000
16116ILE0-0.044-0.00426.926-0.014-0.0140.0000.0000.0000.000
17117ALA00.0200.01728.6550.0130.0130.0000.0000.0000.000
18118SER0-0.032-0.03528.500-0.015-0.0150.0000.0000.0000.000
19119THR0-0.0100.00427.8690.0100.0100.0000.0000.0000.000
20120PRO00.0840.04830.6720.0010.0010.0000.0000.0000.000
21121PRO0-0.0260.00033.024-0.003-0.0030.0000.0000.0000.000
22122ALA00.0100.02234.1020.0030.0030.0000.0000.0000.000
23123PRO0-0.031-0.03735.3780.0020.0020.0000.0000.0000.000
24124PHE00.013-0.00332.7400.0010.0010.0000.0000.0000.000
25125SER0-0.039-0.03132.121-0.004-0.0040.0000.0000.0000.000
26126ASP-1-0.853-0.88532.081-0.065-0.0650.0000.0000.0000.000
27127VAL0-0.029-0.02628.683-0.006-0.0060.0000.0000.0000.000
28128THR00.0060.00029.7850.0030.0030.0000.0000.0000.000
29129ALA00.017-0.00129.399-0.011-0.0110.0000.0000.0000.000
30130VAL0-0.0140.00929.0920.0080.0080.0000.0000.0000.000
31131THR0-0.027-0.01230.040-0.011-0.0110.0000.0000.0000.000
32132PHE00.034-0.00427.3190.0050.0050.0000.0000.0000.000
33133ASP-1-0.726-0.85331.539-0.104-0.1040.0000.0000.0000.000
34134LEU0-0.024-0.05127.0020.0010.0010.0000.0000.0000.000
35135ILE0-0.031-0.00631.253-0.001-0.0010.0000.0000.0000.000
36136ASN0-0.061-0.03934.0450.0050.0050.0000.0000.0000.000
37137GLY0-0.031-0.00634.3640.0030.0030.0000.0000.0000.000
38138LYS10.9020.94735.0930.0930.0930.0000.0000.0000.000
39139ILE00.0160.00532.278-0.006-0.0060.0000.0000.0000.000
40140THR0-0.051-0.02134.5210.0080.0080.0000.0000.0000.000
41141PRO00.0330.02834.193-0.005-0.0050.0000.0000.0000.000
42142VAL00.0390.00133.9790.0040.0040.0000.0000.0000.000
43143GLY00.0040.01536.5200.0040.0040.0000.0000.0000.000
44144ASP-1-0.920-0.94235.800-0.082-0.0820.0000.0000.0000.000
45145ASP-1-0.873-0.97136.802-0.078-0.0780.0000.0000.0000.000
46146ASN0-0.106-0.04237.5850.0020.0020.0000.0000.0000.000
47147TRP00.0960.10028.079-0.008-0.0080.0000.0000.0000.000
48148ASN0-0.068-0.06833.7110.0000.0000.0000.0000.0000.000
49149THR0-0.032-0.02933.072-0.008-0.0080.0000.0000.0000.000
50150HIS00.0190.01532.8380.0070.0070.0000.0000.0000.000
51151ILE00.0210.01332.861-0.009-0.0090.0000.0000.0000.000
52152TYR00.0030.03329.7020.0090.0090.0000.0000.0000.000
53153ASN0-0.001-0.02034.1320.0000.0000.0000.0000.0000.000
54154PRO00.0180.02630.6970.0050.0050.0000.0000.0000.000
55155PRO00.027-0.00632.2690.0030.0030.0000.0000.0000.000
56156ILE00.0290.01328.7460.0060.0060.0000.0000.0000.000
57157MET00.0830.05032.4890.0000.0000.0000.0000.0000.000
58158ASN00.0040.00533.9590.0050.0050.0000.0000.0000.000
59159VAL0-0.0100.02035.1780.0050.0050.0000.0000.0000.000
60160LEU0-0.028-0.01731.2590.0050.0050.0000.0000.0000.000
61161ARG10.8860.92535.9060.1040.1040.0000.0000.0000.000
62162THR0-0.030-0.01038.8760.0050.0050.0000.0000.0000.000
63163ALA0-0.0040.00338.4960.0050.0050.0000.0000.0000.000
64164ALA0-0.036-0.00840.259-0.002-0.0020.0000.0000.0000.000
65165TRP0-0.033-0.01140.928-0.001-0.0010.0000.0000.0000.000
66166LYS10.8670.91935.3530.0920.0920.0000.0000.0000.000
67167SER00.0020.00535.2650.0020.0020.0000.0000.0000.000
68168GLY00.0470.02231.8710.0010.0010.0000.0000.0000.000
69169THR00.007-0.01125.2540.0030.0030.0000.0000.0000.000
70170ILE0-0.069-0.02426.2830.0000.0000.0000.0000.0000.000
71171HIS0-0.058-0.04721.601-0.023-0.0230.0000.0000.0000.000
72172VAL0-0.002-0.00422.0730.0090.0090.0000.0000.0000.000
73173GLN00.0380.01616.552-0.068-0.0680.0000.0000.0000.000
74174LEU0-0.040-0.01219.3830.0250.0250.0000.0000.0000.000
75175ASN0-0.008-0.01318.504-0.081-0.0810.0000.0000.0000.000
76176VAL00.002-0.00118.6920.0400.0400.0000.0000.0000.000
77177ARG10.8420.92119.2400.2090.2090.0000.0000.0000.000
78178GLY00.002-0.00120.9210.0190.0190.0000.0000.0000.000
79179ALA0-0.0010.01522.3280.0020.0020.0000.0000.0000.000
80180GLY0-0.019-0.01622.955-0.013-0.0130.0000.0000.0000.000
81181VAL0-0.0030.00222.3110.0170.0170.0000.0000.0000.000
82182LYS10.9140.96321.3340.0300.0300.0000.0000.0000.000
83183ARG11.0110.98912.2250.2480.2480.0000.0000.0000.000
84184ALA0-0.074-0.05319.007-0.003-0.0030.0000.0000.0000.000
85185ASP-1-0.839-0.90420.672-0.044-0.0440.0000.0000.0000.000
86186TRP0-0.071-0.02418.729-0.007-0.0070.0000.0000.0000.000
87187ASP-1-0.898-0.94020.740-0.092-0.0920.0000.0000.0000.000
88188GLY00.0330.01921.727-0.002-0.0020.0000.0000.0000.000
89189GLN0-0.016-0.02419.765-0.009-0.0090.0000.0000.0000.000
90190VAL00.0160.01019.4060.0130.0130.0000.0000.0000.000
91191PHE0-0.021-0.00220.670-0.015-0.0150.0000.0000.0000.000
92192VAL0-0.003-0.01121.3470.0040.0040.0000.0000.0000.000
93193TYR00.0360.02123.612-0.003-0.0030.0000.0000.0000.000
94194LEU0-0.0200.01325.0220.0020.0020.0000.0000.0000.000
95195ARG10.8220.88227.3100.1050.1050.0000.0000.0000.000
96196GLN00.0330.00930.8840.0040.0040.0000.0000.0000.000
97197SER00.0160.01333.9450.0040.0040.0000.0000.0000.000
98198MET00.0240.02232.731-0.005-0.0050.0000.0000.0000.000
99199ASN0-0.0190.01736.9350.0020.0020.0000.0000.0000.000
1001100PRO00.024-0.00337.458-0.004-0.0040.0000.0000.0000.000
1011101GLU-1-0.904-0.96037.740-0.058-0.0580.0000.0000.0000.000
1021102SER0-0.081-0.02035.7350.0000.0000.0000.0000.0000.000
1031103TYR00.0150.00732.4390.0000.0000.0000.0000.0000.000
1041104ASP-1-0.842-0.92428.121-0.118-0.1180.0000.0000.0000.000
1051105ALA0-0.023-0.02028.4650.0030.0030.0000.0000.0000.000
1061106ARG10.9110.94518.9360.2090.2090.0000.0000.0000.000
1071107THR00.0150.01522.8590.0060.0060.0000.0000.0000.000
1081108PHE0-0.058-0.02317.874-0.014-0.0140.0000.0000.0000.000
1091109VAL00.0290.01918.1830.0190.0190.0000.0000.0000.000
1101110ILE00.0000.01414.396-0.029-0.0290.0000.0000.0000.000
1111111SER0-0.034-0.04015.1760.0430.0430.0000.0000.0000.000
1121112GLN0-0.021-0.01010.837-0.067-0.0670.0000.0000.0000.000
1131113PRO0-0.033-0.02113.8930.0060.0060.0000.0000.0000.000
1141114GLY00.0040.01715.820-0.039-0.0390.0000.0000.0000.000
1151115SER0-0.018-0.02016.2000.0250.0250.0000.0000.0000.000
1161116ALA0-0.022-0.00514.274-0.051-0.0510.0000.0000.0000.000
1171117MET0-0.0070.00513.8190.0280.0280.0000.0000.0000.000
1181118LEU0-0.0090.00614.239-0.060-0.0600.0000.0000.0000.000
1191119ASN0-0.017-0.02015.042-0.004-0.0040.0000.0000.0000.000
1201120PHE0-0.034-0.01216.769-0.007-0.0070.0000.0000.0000.000
1211121SER00.0170.01419.4100.0030.0030.0000.0000.0000.000
1221122PHE0-0.019-0.01922.4580.0020.0020.0000.0000.0000.000
1231123ASP-1-0.906-0.95825.852-0.136-0.1360.0000.0000.0000.000
1241124ILE00.0090.03529.0170.0050.0050.0000.0000.0000.000
1251125ILE00.0170.00532.6360.0030.0030.0000.0000.0000.000
1261126GLY0-0.0030.00135.0730.0010.0010.0000.0000.0000.000
1271127PRO0-0.018-0.02338.6820.0020.0020.0000.0000.0000.000
1281128ASN0-0.026-0.00442.1730.0050.0050.0000.0000.0000.000
1291129SER0-0.009-0.01641.7790.0030.0030.0000.0000.0000.000
1301130GLY00.0330.03038.424-0.001-0.0010.0000.0000.0000.000
1311131PHE0-0.065-0.03537.440-0.005-0.0050.0000.0000.0000.000
1321132GLU-1-0.870-0.95636.213-0.086-0.0860.0000.0000.0000.000
1331133PHE0-0.026-0.00939.059-0.003-0.0030.0000.0000.0000.000
1341134ALA0-0.024-0.03537.7560.0020.0020.0000.0000.0000.000
1351135GLU-1-0.883-0.94239.348-0.078-0.0780.0000.0000.0000.000
1361136SER0-0.0350.00241.5540.0050.0050.0000.0000.0000.000
1371137PRO00.029-0.01344.6460.0000.0000.0000.0000.0000.000
1381138TRP00.0040.00346.1110.0020.0020.0000.0000.0000.000
1391139ALA0-0.080-0.02044.1800.0010.0010.0000.0000.0000.000
1401140ASN0-0.023-0.02144.308-0.001-0.0010.0000.0000.0000.000
1411141GLN00.0170.01640.862-0.003-0.0030.0000.0000.0000.000
1421142THR00.0480.02935.8880.0020.0020.0000.0000.0000.000
1431143THR00.0030.01835.553-0.002-0.0020.0000.0000.0000.000
1441144TRP00.0550.00629.045-0.004-0.0040.0000.0000.0000.000
1451145TYR0-0.033-0.02331.608-0.003-0.0030.0000.0000.0000.000
1461146LEU0-0.008-0.01724.293-0.007-0.0070.0000.0000.0000.000
1471147GLU-1-0.908-0.95628.393-0.111-0.1110.0000.0000.0000.000
1481148CYS0-0.077-0.03325.202-0.018-0.0180.0000.0000.0000.000
1491149VAL00.0500.01725.6160.0100.0100.0000.0000.0000.000
1501150ALA0-0.027-0.01624.833-0.016-0.0160.0000.0000.0000.000
1511151THR00.027-0.00723.8180.0130.0130.0000.0000.0000.000
1521152ASN00.0570.02325.0860.0100.0100.0000.0000.0000.000
1531153PRO0-0.0260.00926.278-0.012-0.0120.0000.0000.0000.000
1541154ARG10.8150.87028.3740.0940.0940.0000.0000.0000.000
1551155GLN00.0050.00723.110-0.007-0.0070.0000.0000.0000.000
1561156ILE0-0.0110.00721.674-0.018-0.0180.0000.0000.0000.000
1571157GLN0-0.024-0.01623.9580.0170.0170.0000.0000.0000.000
1581158GLN00.0350.00624.6960.0030.0030.0000.0000.0000.000
1591159PHE00.0070.01322.460-0.023-0.0230.0000.0000.0000.000
1601160GLU-1-0.752-0.87323.142-0.227-0.2270.0000.0000.0000.000
1611161VAL00.0120.00923.336-0.026-0.0260.0000.0000.0000.000
1621162ASN0-0.075-0.03722.1260.0240.0240.0000.0000.0000.000
1631163MET0-0.002-0.01323.549-0.009-0.0090.0000.0000.0000.000
1641164ARG10.9960.99421.8830.2230.2230.0000.0000.0000.000
1651165PHE0-0.0190.00325.904-0.001-0.0010.0000.0000.0000.000
1661166ASP-1-0.785-0.88025.345-0.165-0.1650.0000.0000.0000.000
1671167PRO0-0.016-0.02526.3590.0100.0100.0000.0000.0000.000
1681168ASN0-0.032-0.00928.9270.0070.0070.0000.0000.0000.000
1691169PHE0-0.030-0.00430.7400.0080.0080.0000.0000.0000.000
1701170ARG10.9110.96032.5530.0870.0870.0000.0000.0000.000
1711171VAL0-0.006-0.00836.356-0.002-0.0020.0000.0000.0000.000
1721172ALA00.008-0.00138.8240.0030.0030.0000.0000.0000.000
1731173GLY00.0120.01642.6010.0000.0000.0000.0000.0000.000
1741174ASN00.013-0.00343.729-0.005-0.0050.0000.0000.0000.000
1751175ILE00.0090.01142.4660.0030.0030.0000.0000.0000.000
1761176LEU0-0.049-0.02445.798-0.001-0.0010.0000.0000.0000.000
1771177MET00.0100.02143.072-0.001-0.0010.0000.0000.0000.000
1781178PRO0-0.025-0.00545.6090.0020.0020.0000.0000.0000.000
1791179PRO00.009-0.01145.927-0.002-0.0020.0000.0000.0000.000
1801180PHE00.0080.01040.269-0.001-0.0010.0000.0000.0000.000
1811181PRO00.0000.00441.6990.0010.0010.0000.0000.0000.000
1821182LEU00.0090.00641.010-0.004-0.0040.0000.0000.0000.000
1831183SER0-0.016-0.03636.2770.0010.0010.0000.0000.0000.000
1841184THR0-0.033-0.02136.055-0.003-0.0030.0000.0000.0000.000
1851185GLU-1-0.903-0.95428.141-0.166-0.1660.0000.0000.0000.000
1861186THR0-0.055-0.00831.1300.0060.0060.0000.0000.0000.000
1871187PRO00.033-0.00130.822-0.010-0.0100.0000.0000.0000.000
1881188PRO00.0030.00726.9110.0010.0010.0000.0000.0000.000
1891189LEU0-0.034-0.00928.5730.0010.0010.0000.0000.0000.000