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: NN35Q

Calculation Name: 4N1Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N1Y

Chain ID: A

ChEMBL ID:

UniProt ID: K1QUU5

Base Structure: X-ray

Registration Date: 2023-09-20

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2842500.683828
FMO2-HF: Nuclear repulsion 2752151.09294
FMO2-HF: Total energy -90349.590888
FMO2-MP2: Total energy -90610.789004


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:248:GLN)


Summations of interaction energy for fragment #1(A:248:GLN)
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.
-1.389-0.0749999999999999.307-4.526-6.096-0.01
Interaction energy analysis for fragmet #1(A:248:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.024
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].
3A250VAL00.0180.0042.916-4.882-2.0050.615-1.359-2.1330.010
4A251THR00.0150.0061.971-4.924-7.1568.686-2.974-3.481-0.020
5A252ILE00.0290.0263.6940.5881.2570.006-0.193-0.4820.000
6A253LEU00.0110.0025.8120.5020.5020.0000.0000.0000.000
7A254GLN0-0.061-0.0386.576-0.176-0.1760.0000.0000.0000.000
8A255ALA0-0.030-0.0047.9340.1490.1490.0000.0000.0000.000
9A256LEU00.0310.0229.9000.1570.1570.0000.0000.0000.000
10A257ASN00.0500.02811.3140.1460.1460.0000.0000.0000.000
11A258LYS10.8770.94612.8550.5430.5430.0000.0000.0000.000
12A259ALA0-0.013-0.01414.6470.0100.0100.0000.0000.0000.000
13A260ALA00.0010.01516.0620.0270.0270.0000.0000.0000.000
14A261LEU0-0.024-0.02017.9760.0010.0010.0000.0000.0000.000
15A262PRO0-0.0170.01921.5370.0070.0070.0000.0000.0000.000
16A263VAL00.001-0.00623.5060.0140.0140.0000.0000.0000.000
17A264LEU0-0.058-0.02626.775-0.011-0.0110.0000.0000.0000.000
18A265GLU-1-0.887-0.94229.596-0.021-0.0210.0000.0000.0000.000
19A266SER0-0.095-0.06233.140-0.002-0.0020.0000.0000.0000.000
20A267HIS0-0.014-0.02534.8960.0010.0010.0000.0000.0000.000
21A268HIS00.0290.08138.4190.0000.0000.0000.0000.0000.000
22A269ASN00.0140.00640.547-0.001-0.0010.0000.0000.0000.000
23A270HIS0-0.004-0.03040.1720.0030.0030.0000.0000.0000.000
24A271GLY0-0.0230.00545.3660.0010.0010.0000.0000.0000.000
25A272GLN0-0.064-0.03447.8520.0010.0010.0000.0000.0000.000
26A273PRO00.0310.01048.1210.0010.0010.0000.0000.0000.000
27A274PRO00.0390.03745.773-0.001-0.0010.0000.0000.0000.000
28A275THR0-0.004-0.01746.9960.0030.0030.0000.0000.0000.000
29A276LYS10.9830.98245.542-0.039-0.0390.0000.0000.0000.000
30A277VAL00.0140.00044.8260.0000.0000.0000.0000.0000.000
31A278HIS0-0.046-0.02444.810-0.001-0.0010.0000.0000.0000.000
32A279LEU00.0080.00941.697-0.002-0.0020.0000.0000.0000.000
33A280LEU00.0350.01340.3180.0000.0000.0000.0000.0000.000
34A281ASN00.0360.02340.0930.0000.0000.0000.0000.0000.000
35A282SER0-0.024-0.05438.458-0.004-0.0040.0000.0000.0000.000
36A283LEU0-0.009-0.00935.487-0.002-0.0020.0000.0000.0000.000
37A284VAL00.0100.01535.2800.0000.0000.0000.0000.0000.000
38A285LYS10.8380.91235.7400.0010.0010.0000.0000.0000.000
39A286LEU0-0.034-0.02231.731-0.007-0.0070.0000.0000.0000.000
40A287ALA00.0450.02531.360-0.004-0.0040.0000.0000.0000.000
41A288GLU-1-0.761-0.89030.716-0.004-0.0040.0000.0000.0000.000
42A289ARG10.8370.90630.6150.0170.0170.0000.0000.0000.000
43A290GLU-1-0.893-0.96426.9800.0080.0080.0000.0000.0000.000
44A291LEU00.0300.02126.087-0.006-0.0060.0000.0000.0000.000
45A292VAL0-0.006-0.00226.196-0.006-0.0060.0000.0000.0000.000
46A293HIS0-0.003-0.01023.237-0.021-0.0210.0000.0000.0000.000
47A294LEU00.0090.01521.892-0.019-0.0190.0000.0000.0000.000
48A295ILE00.0160.01321.341-0.011-0.0110.0000.0000.0000.000
49A296ASN0-0.110-0.06321.023-0.024-0.0240.0000.0000.0000.000
50A297TRP0-0.006-0.01315.037-0.009-0.0090.0000.0000.0000.000
51A298ALA00.0620.02616.810-0.038-0.0380.0000.0000.0000.000
52A299LYS10.9030.95316.5950.0980.0980.0000.0000.0000.000
53A300ASN0-0.029-0.01613.677-0.082-0.0820.0000.0000.0000.000
54A301VAL0-0.028-0.00512.151-0.121-0.1210.0000.0000.0000.000
55A302PRO0-0.005-0.0097.9620.0210.0210.0000.0000.0000.000
56A303GLY00.0680.02510.5250.1660.1660.0000.0000.0000.000
57A304TYR00.013-0.01112.8010.0380.0380.0000.0000.0000.000
58A305THR0-0.033-0.02315.6990.0110.0110.0000.0000.0000.000
59A306ASP-1-0.951-0.96314.475-0.142-0.1420.0000.0000.0000.000
60A307LEU0-0.0610.00016.6180.0530.0530.0000.0000.0000.000
61A308SER00.0160.00519.478-0.040-0.0400.0000.0000.0000.000
62A309LEU00.030-0.00123.1200.0030.0030.0000.0000.0000.000
63A310SER00.0330.00825.033-0.001-0.0010.0000.0000.0000.000
64A311ASP-1-0.759-0.88322.2510.1490.1490.0000.0000.0000.000
65A312GLN0-0.082-0.03320.373-0.006-0.0060.0000.0000.0000.000
66A313VAL00.0270.02022.581-0.001-0.0010.0000.0000.0000.000
67A314HIS00.0410.02024.915-0.005-0.0050.0000.0000.0000.000
68A315LEU0-0.010-0.01119.3150.0080.0080.0000.0000.0000.000
69A316ILE0-0.001-0.00321.6380.0050.0050.0000.0000.0000.000
70A317GLU-1-0.877-0.96024.6280.0570.0570.0000.0000.0000.000
71A318CYS0-0.090-0.03325.2470.0050.0050.0000.0000.0000.000
72A319CYS0-0.0090.01422.739-0.001-0.0010.0000.0000.0000.000
73A320TRP00.0200.00625.042-0.006-0.0060.0000.0000.0000.000
74A321MET0-0.0120.01526.345-0.005-0.0050.0000.0000.0000.000
75A322GLU-1-0.819-0.92624.7800.1800.1800.0000.0000.0000.000
76A323LEU0-0.028-0.01320.2920.0010.0010.0000.0000.0000.000
77A324LEU0-0.0110.00323.998-0.005-0.0050.0000.0000.0000.000
78A325LEU0-0.034-0.01226.917-0.003-0.0030.0000.0000.0000.000
79A326LEU00.0250.02420.1680.0020.0020.0000.0000.0000.000
80A327ASN00.0320.00621.9300.0110.0110.0000.0000.0000.000
81A328CYS0-0.065-0.01424.338-0.004-0.0040.0000.0000.0000.000
82A329ALA00.0590.02425.900-0.002-0.0020.0000.0000.0000.000
83A330PHE00.004-0.01320.300-0.002-0.0020.0000.0000.0000.000
84A331ARG10.8840.93524.556-0.031-0.0310.0000.0000.0000.000
85A332SER0-0.044-0.01426.565-0.009-0.0090.0000.0000.0000.000
86A333ILE00.0360.03023.9870.0020.0020.0000.0000.0000.000
87A334GLU-1-0.921-0.96227.9430.0450.0450.0000.0000.0000.000
88A335HIS0-0.106-0.04230.138-0.001-0.0010.0000.0000.0000.000
89A336GLY00.0520.02131.679-0.001-0.0010.0000.0000.0000.000
90A337GLY00.0220.02532.6530.0010.0010.0000.0000.0000.000
91A338LYS10.8640.93734.156-0.055-0.0550.0000.0000.0000.000
92A339SER0-0.024-0.04135.368-0.004-0.0040.0000.0000.0000.000
93A340LEU0-0.014-0.00431.5670.0050.0050.0000.0000.0000.000
94A341ALA0-0.0080.00030.766-0.007-0.0070.0000.0000.0000.000
95A342PHE00.008-0.01130.5750.0000.0000.0000.0000.0000.000
96A343ALA00.0460.02230.933-0.005-0.0050.0000.0000.0000.000
97A344PRO00.0000.00330.6790.0050.0050.0000.0000.0000.000
98A345ASP-1-0.717-0.83233.336-0.002-0.0020.0000.0000.0000.000
99A346LEU0-0.035-0.00835.5280.0010.0010.0000.0000.0000.000
100A347VAL00.0120.00434.6090.0040.0040.0000.0000.0000.000
101A348LEU0-0.017-0.00136.443-0.001-0.0010.0000.0000.0000.000
102A349ASP-1-0.798-0.90637.5970.0470.0470.0000.0000.0000.000
103A350ARG10.9700.97037.713-0.080-0.0800.0000.0000.0000.000
104A351SER00.000-0.00141.6860.0010.0010.0000.0000.0000.000
105A352SER00.0120.00841.348-0.002-0.0020.0000.0000.0000.000
106A353TRP0-0.026-0.02736.6490.0020.0020.0000.0000.0000.000
107A354SER00.0020.00441.5690.0010.0010.0000.0000.0000.000
108A355THR0-0.0240.01645.056-0.002-0.0020.0000.0000.0000.000
109A356VAL0-0.058-0.04640.560-0.002-0.0020.0000.0000.0000.000
110A357GLU-1-0.890-0.93543.0520.0450.0450.0000.0000.0000.000
111A358MET0-0.032-0.00438.3870.0040.0040.0000.0000.0000.000
112A359THR0-0.013-0.00838.8780.0020.0020.0000.0000.0000.000
113A360GLU-1-0.893-0.95238.1620.0960.0960.0000.0000.0000.000
114A361ILE00.0160.01034.1270.0070.0070.0000.0000.0000.000
115A362PHE00.029-0.00734.2400.0060.0060.0000.0000.0000.000
116A363GLU-1-0.912-0.95335.0330.0860.0860.0000.0000.0000.000
117A364GLN0-0.028-0.00931.787-0.001-0.0010.0000.0000.0000.000
118A365VAL0-0.012-0.01229.4510.0100.0100.0000.0000.0000.000
119A366ALA0-0.011-0.00630.4200.0050.0050.0000.0000.0000.000
120A367ALA00.0260.01032.1440.0030.0030.0000.0000.0000.000
121A368VAL0-0.0020.00026.3590.0110.0110.0000.0000.0000.000
122A369SER0-0.044-0.05127.5090.0090.0090.0000.0000.0000.000
123A370GLU-1-0.906-0.95428.1650.1220.1220.0000.0000.0000.000
124A371GLN00.001-0.00426.5790.0080.0080.0000.0000.0000.000
125A372MET0-0.0870.00023.4540.0160.0160.0000.0000.0000.000
126A373MET00.0200.01124.4220.0060.0060.0000.0000.0000.000
127A374GLN0-0.018-0.01026.583-0.002-0.0020.0000.0000.0000.000
128A375ASN0-0.093-0.03822.3390.0200.0200.0000.0000.0000.000
129A376HIS0-0.087-0.04522.1010.0120.0120.0000.0000.0000.000
130A377LEU0-0.033-0.01118.5050.0160.0160.0000.0000.0000.000
131A378HIS00.0600.02714.487-0.017-0.0170.0000.0000.0000.000
132A379LYS10.9940.98515.8840.0620.0620.0000.0000.0000.000
133A380ASP-1-0.851-0.91911.5260.1820.1820.0000.0000.0000.000
134A381GLU-1-0.726-0.84213.0060.3750.3750.0000.0000.0000.000
135A382LEU00.0080.02314.9390.0150.0150.0000.0000.0000.000
136A383LEU0-0.056-0.02512.471-0.009-0.0090.0000.0000.0000.000
137A384LEU0-0.001-0.0029.184-0.035-0.0350.0000.0000.0000.000
138A385LEU00.0100.00213.1320.0350.0350.0000.0000.0000.000
139A386GLN0-0.012-0.00116.7090.0020.0020.0000.0000.0000.000
140A387ALA0-0.0060.00013.250-0.003-0.0030.0000.0000.0000.000
141A388MET00.0040.00012.8380.0120.0120.0000.0000.0000.000
142A389VAL0-0.036-0.02615.6870.0120.0120.0000.0000.0000.000
143A390LEU0-0.006-0.01716.814-0.001-0.0010.0000.0000.0000.000
144A391VAL0-0.056-0.03213.899-0.001-0.0010.0000.0000.0000.000
145A392ASN0-0.024-0.01017.1930.0550.0550.0000.0000.0000.000
146A393ALA0-0.0400.00319.435-0.008-0.0080.0000.0000.0000.000
147A394GLU-1-0.775-0.85522.1490.1770.1770.0000.0000.0000.000
148A395VAL00.0150.01222.4900.0270.0270.0000.0000.0000.000
149A396ARG10.7880.86324.195-0.150-0.1500.0000.0000.0000.000
150A397ARG10.8830.93723.551-0.306-0.3060.0000.0000.0000.000
151A398LEU00.0650.04822.424-0.019-0.0190.0000.0000.0000.000
152A399ALA00.0150.00123.7390.0220.0220.0000.0000.0000.000
153A400SER0-0.031-0.01219.4010.0010.0010.0000.0000.0000.000
154A401TYR0-0.014-0.00518.9390.0460.0460.0000.0000.0000.000
155A402ASN00.015-0.00316.8130.1080.1080.0000.0000.0000.000
156A403GLN0-0.034-0.03714.9680.0960.0960.0000.0000.0000.000
157A404ILE00.0750.03114.0650.0630.0630.0000.0000.0000.000
158A405PHE0-0.0030.00814.0620.0790.0790.0000.0000.0000.000
159A406ASN00.003-0.01210.8700.2720.2720.0000.0000.0000.000
160A407MET0-0.062-0.01510.0030.2560.2560.0000.0000.0000.000
161A408GLN0-0.0070.00310.505-0.054-0.0540.0000.0000.0000.000
162A409GLN00.0320.0089.634-0.181-0.1810.0000.0000.0000.000
163A410SER00.0100.0195.5780.1820.1820.0000.0000.0000.000
164A411LEU00.004-0.0086.659-0.070-0.0700.0000.0000.0000.000
165A412LEU0-0.035-0.0199.139-0.068-0.0680.0000.0000.0000.000
166A413ASP-1-0.898-0.9395.8714.9564.9560.0000.0000.0000.000
167A414ALA0-0.004-0.0056.110-0.298-0.2980.0000.0000.0000.000
168A415ILE0-0.024-0.0147.217-0.159-0.1590.0000.0000.0000.000
169A416VAL0-0.0020.00310.127-0.182-0.1820.0000.0000.0000.000
170A417ASP-1-0.853-0.9235.5152.3572.3570.0000.0000.0000.000
171A418THR0-0.087-0.0688.707-0.208-0.2080.0000.0000.0000.000
172A419ALA0-0.016-0.01910.425-0.135-0.1350.0000.0000.0000.000
173A420GLN00.0070.02211.400-0.058-0.0580.0000.0000.0000.000
174A421LYS10.8470.93010.385-0.598-0.5980.0000.0000.0000.000
175A422TYR0-0.059-0.05912.535-0.085-0.0850.0000.0000.0000.000
176A423HIS10.7630.87615.908-0.404-0.4040.0000.0000.0000.000
177A424PRO00.0450.03216.4500.0330.0330.0000.0000.0000.000
178A425ASP-1-0.885-0.94817.0180.3550.3550.0000.0000.0000.000
179A426ASN0-0.035-0.00818.804-0.020-0.0200.0000.0000.0000.000
180A427VAL00.026-0.00318.9990.0330.0330.0000.0000.0000.000
181A428ARG10.9290.95420.369-0.250-0.2500.0000.0000.0000.000
182A429HIS0-0.042-0.00716.948-0.017-0.0170.0000.0000.0000.000
183A430VAL00.0800.03214.803-0.025-0.0250.0000.0000.0000.000
184A431PRO0-0.017-0.00717.927-0.024-0.0240.0000.0000.0000.000
185A432ALA00.0270.01120.905-0.024-0.0240.0000.0000.0000.000
186A433VAL00.0440.01818.736-0.030-0.0300.0000.0000.0000.000
187A434LEU00.001-0.00416.546-0.026-0.0260.0000.0000.0000.000
188A435LEU0-0.032-0.01120.608-0.025-0.0250.0000.0000.0000.000
189A436LEU0-0.022-0.00523.331-0.030-0.0300.0000.0000.0000.000
190A437LEU00.0130.00219.144-0.025-0.0250.0000.0000.0000.000
191A438THR0-0.054-0.02123.701-0.022-0.0220.0000.0000.0000.000
192A439HIS00.0280.01126.710-0.023-0.0230.0000.0000.0000.000
193A440ILE00.0130.01024.864-0.017-0.0170.0000.0000.0000.000
194A441ARG10.9090.96423.365-0.236-0.2360.0000.0000.0000.000
195A442GLN0-0.034-0.00127.803-0.009-0.0090.0000.0000.0000.000
196A443ALA00.0370.00530.621-0.011-0.0110.0000.0000.0000.000
197A444GLY00.0000.00129.416-0.013-0.0130.0000.0000.0000.000
198A445GLU-1-0.912-0.95430.4220.1150.1150.0000.0000.0000.000
199A446ARG10.8950.94832.624-0.119-0.1190.0000.0000.0000.000
200A447GLY00.0230.00333.849-0.009-0.0090.0000.0000.0000.000
201A448ILE00.0340.01430.457-0.010-0.0100.0000.0000.0000.000
202A449ALA0-0.012-0.00834.766-0.007-0.0070.0000.0000.0000.000
203A450PHE0-0.077-0.04137.863-0.006-0.0060.0000.0000.0000.000
204A451PHE00.053-0.00335.194-0.006-0.0060.0000.0000.0000.000
205A452GLN00.0170.01637.503-0.007-0.0070.0000.0000.0000.000
206A453ARG10.9470.98740.112-0.064-0.0640.0000.0000.0000.000
207A454LEU00.0360.01540.329-0.004-0.0040.0000.0000.0000.000
208A455LYS10.8600.95339.605-0.038-0.0380.0000.0000.0000.000
209A456SER0-0.098-0.05342.820-0.002-0.0020.0000.0000.0000.000
210A457GLU-1-0.960-0.97945.7650.0390.0390.0000.0000.0000.000
211A458GLY0-0.018-0.00946.831-0.002-0.0020.0000.0000.0000.000
212A459VAL0-0.043-0.01247.959-0.003-0.0030.0000.0000.0000.000
213A460VAL0-0.035-0.01442.128-0.002-0.0020.0000.0000.0000.000
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