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: 7236K

Calculation Name: 3NWC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NWC

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZY2

Base Structure: X-ray

Registration Date: 2023-06-21

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1769138.881757
FMO2-HF: Nuclear repulsion 1699700.577137
FMO2-HF: Total energy -69438.304619
FMO2-MP2: Total energy -69643.621826


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:487:MET)


Summations of interaction energy for fragment #1(A:487:MET)
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.
-28.977-18.1128.223-13.986-25.102-0.04
Interaction energy analysis for fragmet #1(A:487:MET)
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 : 0.015
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].
3A489LEU0-0.0070.0023.038-1.4221.3540.024-1.395-1.4040.003
4A490GLU-1-0.767-0.8653.665-1.229-0.8490.012-0.152-0.240-0.001
5A491SER0-0.108-0.0666.1500.3940.3940.0000.0000.0000.000
6A492SER00.052-0.0292.1340.777-1.7768.217-2.347-3.3180.004
7A493GLU-1-0.902-0.9442.432-6.049-3.1851.558-1.237-3.185-0.013
8A494ARG10.7550.8453.6271.3191.5100.0120.037-0.2400.000
9A495GLU-1-0.753-0.8515.1330.6490.6490.0000.0000.0000.000
10A496LEU00.0240.0232.804-0.7980.2150.189-0.219-0.9830.000
11A497ILE00.0370.0245.129-0.455-0.395-0.001-0.002-0.0560.000
12A498ALA0-0.048-0.0238.140-0.168-0.1680.0000.0000.0000.000
13A499ALA0-0.022-0.0108.122-0.168-0.1680.0000.0000.0000.000
14A500GLU-1-0.872-0.9458.0152.1192.1190.0000.0000.0000.000
15A501ALA0-0.014-0.00510.969-0.213-0.2130.0000.0000.0000.000
16A502GLN0-0.035-0.02512.924-0.146-0.1460.0000.0000.0000.000
17A503ARG10.7690.85712.336-1.389-1.3890.0000.0000.0000.000
18A504GLU-1-0.833-0.88615.3520.4770.4770.0000.0000.0000.000
19A505VAL0-0.102-0.04417.379-0.085-0.0850.0000.0000.0000.000
20A506ARG10.7650.86716.598-0.582-0.5820.0000.0000.0000.000
21A507GLY00.0710.04520.3970.0130.0130.0000.0000.0000.000
22A508ASN0-0.052-0.06221.475-0.053-0.0530.0000.0000.0000.000
23A509ARG10.9120.93220.541-0.397-0.3970.0000.0000.0000.000
24A510ALA0-0.0010.00224.414-0.014-0.0140.0000.0000.0000.000
25A511ALA00.0230.01124.292-0.021-0.0210.0000.0000.0000.000
26A512GLU-1-0.809-0.90024.1930.3840.3840.0000.0000.0000.000
27A513GLU-1-0.778-0.85227.3620.1810.1810.0000.0000.0000.000
28A514LEU0-0.0050.00228.907-0.017-0.0170.0000.0000.0000.000
29A515LYS10.7950.89723.688-0.429-0.4290.0000.0000.0000.000
30A516ARG10.8800.93430.392-0.205-0.2050.0000.0000.0000.000
31A517SER0-0.039-0.03033.504-0.016-0.0160.0000.0000.0000.000
32A518GLY00.0150.01535.421-0.011-0.0110.0000.0000.0000.000
33A519ILE0-0.092-0.04634.421-0.009-0.0090.0000.0000.0000.000
34A520GLY00.0220.01533.8240.0150.0150.0000.0000.0000.000
35A521GLY00.015-0.00132.961-0.006-0.0060.0000.0000.0000.000
36A522ILE0-0.028-0.02128.0840.0150.0150.0000.0000.0000.000
37A523TYR0-0.059-0.05925.801-0.018-0.0180.0000.0000.0000.000
38A524GLY00.0550.03223.422-0.001-0.0010.0000.0000.0000.000
39A525THR0-0.074-0.06519.8560.0130.0130.0000.0000.0000.000
40A526LEU0-0.009-0.01417.393-0.004-0.0040.0000.0000.0000.000
41A527ALA00.0120.00615.2800.0740.0740.0000.0000.0000.000
42A528GLU-1-0.806-0.85015.8370.5430.5430.0000.0000.0000.000
43A529LEU0-0.076-0.03618.298-0.054-0.0540.0000.0000.0000.000
44A530ILE0-0.019-0.01213.157-0.061-0.0610.0000.0000.0000.000
45A531LYS10.8430.91912.992-0.743-0.7430.0000.0000.0000.000
46A532VAL00.0200.0026.842-0.184-0.1840.0000.0000.0000.000
47A533LYS10.7530.85710.245-0.984-0.9840.0000.0000.0000.000
48A534ASP-1-0.878-0.9476.6010.8160.8160.0000.0000.0000.000
49A535GLU-1-0.892-0.9532.234-7.501-4.7182.010-2.451-2.342-0.023
50A536ALA00.0170.0112.8515.9786.9623.059-1.184-2.859-0.014
51A537TYR0-0.006-0.0172.782-3.942-2.6491.112-0.814-1.591-0.013
52A538ALA0-0.002-0.0013.195-2.695-1.4471.030-0.688-1.5910.000
53A539LEU0-0.007-0.0032.336-6.558-8.1239.142-2.962-4.6150.024
54A540ALA00.0270.0143.638-2.683-2.8560.0100.447-0.2840.003
55A541ILE0-0.010-0.0105.492-1.000-1.0000.0000.0000.0000.000
56A542GLU-1-0.771-0.8457.4011.0301.0300.0000.0000.0000.000
57A543VAL0-0.025-0.0117.608-0.652-0.6520.0000.0000.0000.000
58A544ALA0-0.019-0.0019.473-0.376-0.3760.0000.0000.0000.000
59A545LEU0-0.035-0.00911.418-0.315-0.3150.0000.0000.0000.000
60A546GLY00.0890.04412.811-0.222-0.2220.0000.0000.0000.000
61A547ASN0-0.013-0.02614.4290.0420.0420.0000.0000.0000.000
62A548ARG10.8280.91217.040-0.635-0.6350.0000.0000.0000.000
63A549ALA00.0840.04914.327-0.058-0.0580.0000.0000.0000.000
64A550ASP-1-0.820-0.91116.4370.7290.7290.0000.0000.0000.000
65A551ASN0-0.099-0.04619.673-0.111-0.1110.0000.0000.0000.000
66A552VAL00.0130.00321.6970.0270.0270.0000.0000.0000.000
67A553VAL00.0350.01622.507-0.034-0.0340.0000.0000.0000.000
68A554VAL0-0.028-0.02225.293-0.020-0.0200.0000.0000.0000.000
69A555GLU-1-0.762-0.82629.0990.2810.2810.0000.0000.0000.000
70A556ASP-1-0.845-0.93231.6520.2180.2180.0000.0000.0000.000
71A557GLU-1-0.735-0.87733.4370.2240.2240.0000.0000.0000.000
72A558LEU0-0.0050.00634.971-0.005-0.0050.0000.0000.0000.000
73A559VAL0-0.038-0.01432.508-0.005-0.0050.0000.0000.0000.000
74A560ALA00.0290.01931.9030.0040.0040.0000.0000.0000.000
75A561GLU-1-0.817-0.90033.1950.1830.1830.0000.0000.0000.000
76A562LYS10.9120.95836.660-0.198-0.1980.0000.0000.0000.000
77A563ALA00.0580.03331.930-0.006-0.0060.0000.0000.0000.000
78A564ILE0-0.009-0.01132.616-0.002-0.0020.0000.0000.0000.000
79A565LYS10.7670.86334.650-0.184-0.1840.0000.0000.0000.000
80A566TYR0-0.009-0.02334.084-0.013-0.0130.0000.0000.0000.000
81A567LEU0-0.016-0.00830.256-0.006-0.0060.0000.0000.0000.000
82A568LYS10.9380.97234.328-0.199-0.1990.0000.0000.0000.000
83A569GLU-1-0.870-0.94337.3690.1370.1370.0000.0000.0000.000
84A570HIS10.8340.89735.874-0.189-0.1890.0000.0000.0000.000
85A571LYS10.8110.91636.339-0.153-0.1530.0000.0000.0000.000
86A572LEU0-0.0070.01631.3090.0030.0030.0000.0000.0000.000
87A573GLY00.0250.02330.5770.0220.0220.0000.0000.0000.000
88A574ARG10.9000.93429.235-0.272-0.2720.0000.0000.0000.000
89A575LEU00.0630.04724.9480.0150.0150.0000.0000.0000.000
90A576THR0-0.052-0.01924.421-0.026-0.0260.0000.0000.0000.000
91A577PHE00.0140.00625.4940.0230.0230.0000.0000.0000.000
92A578LEU0-0.003-0.00322.003-0.008-0.0080.0000.0000.0000.000
93A579PRO00.0140.00126.6370.0030.0030.0000.0000.0000.000
94A580LEU00.0320.03825.644-0.001-0.0010.0000.0000.0000.000
95A581ASN0-0.0070.00029.1900.0050.0050.0000.0000.0000.000
96A582LYS10.7800.87831.187-0.234-0.2340.0000.0000.0000.000
97A583ILE0-0.059-0.01225.332-0.010-0.0100.0000.0000.0000.000
98A584LYS10.9130.93826.547-0.277-0.2770.0000.0000.0000.000
99A585PRO00.0150.00523.4530.0240.0240.0000.0000.0000.000
100A586LYS10.8470.93720.140-0.519-0.5190.0000.0000.0000.000
101A587HIS00.022-0.00821.4690.0220.0220.0000.0000.0000.000
102A588VAL00.0090.02416.709-0.014-0.0140.0000.0000.0000.000
103A589ASP-1-0.844-0.88319.9860.2620.2620.0000.0000.0000.000
104A590SER0-0.036-0.02319.933-0.029-0.0290.0000.0000.0000.000
105A591SER00.002-0.00719.4830.0240.0240.0000.0000.0000.000
106A592VAL0-0.036-0.01815.453-0.024-0.0240.0000.0000.0000.000
107A593GLY00.0580.02213.486-0.036-0.0360.0000.0000.0000.000
108A594LEU0-0.0090.0159.692-0.022-0.0220.0000.0000.0000.000
109A595PRO00.0040.00311.9320.0970.0970.0000.0000.0000.000
110A596ALA00.0450.01310.9450.0750.0750.0000.0000.0000.000
111A597VAL0-0.030-0.02911.9550.1340.1340.0000.0000.0000.000
112A598ASP-1-0.858-0.92414.0270.5510.5510.0000.0000.0000.000
113A599VAL0-0.0090.0098.571-0.081-0.0810.0000.0000.0000.000
114A600ILE0-0.0140.01410.6180.3120.3120.0000.0000.0000.000
115A601GLU-1-0.827-0.89212.9820.5650.5650.0000.0000.0000.000
116A602TYR00.0230.00016.1080.0790.0790.0000.0000.0000.000
117A603ASP-1-0.839-0.90918.8800.3280.3280.0000.0000.0000.000
118A604GLN00.011-0.00722.6750.0370.0370.0000.0000.0000.000
119A605LYS10.8380.90624.503-0.299-0.2990.0000.0000.0000.000
120A606ILE0-0.014-0.02220.371-0.019-0.0190.0000.0000.0000.000
121A607GLU-1-0.795-0.88422.3190.4080.4080.0000.0000.0000.000
122A608ASN0-0.046-0.02822.6630.0300.0300.0000.0000.0000.000
123A609ALA0-0.016-0.01022.6950.0050.0050.0000.0000.0000.000
124A610VAL00.0360.02517.2220.0320.0320.0000.0000.0000.000
125A611LYS10.9260.94018.508-0.415-0.4150.0000.0000.0000.000
126A612PHE0-0.051-0.01020.444-0.025-0.0250.0000.0000.0000.000
127A613ALA0-0.049-0.02417.294-0.017-0.0170.0000.0000.0000.000
128A614LEU00.0390.01712.7000.0360.0360.0000.0000.0000.000
129A615GLY0-0.0080.00315.9630.0010.0010.0000.0000.0000.000
130A616ASP-1-0.903-0.97618.3450.4680.4680.0000.0000.0000.000
131A617THR0-0.028-0.00511.994-0.011-0.0110.0000.0000.0000.000
132A618VAL0-0.031-0.00113.2550.0530.0530.0000.0000.0000.000
133A619ILE00.0070.0056.7220.0450.0450.0000.0000.0000.000
134A620VAL0-0.039-0.0219.372-0.094-0.0940.0000.0000.0000.000
135A621ASN00.027-0.0087.9920.0580.0580.0000.0000.0000.000
136A622SER0-0.026-0.0348.864-0.094-0.0940.0000.0000.0000.000
137A623MET00.0350.00111.1210.0700.0700.0000.0000.0000.000
138A624GLU-1-0.868-0.92113.763-0.032-0.0320.0000.0000.0000.000
139A625GLU-1-0.804-0.86612.477-0.052-0.0520.0000.0000.0000.000
140A626ALA00.0310.02313.3380.0280.0280.0000.0000.0000.000
141A627ARG10.8330.88515.3570.0000.0000.0000.0000.0000.000
142A628PRO0-0.043-0.01718.5750.0060.0060.0000.0000.0000.000
143A629HIS00.023-0.03217.4400.0030.0030.0000.0000.0000.000
144A630ILE00.0200.03118.4550.0300.0300.0000.0000.0000.000
145A631GLY00.0010.00320.351-0.022-0.0220.0000.0000.0000.000
146A632LYS10.8270.94821.733-0.173-0.1730.0000.0000.0000.000
147A633VAL0-0.002-0.01116.972-0.001-0.0010.0000.0000.0000.000
148A634ARG10.7570.87914.586-0.785-0.7850.0000.0000.0000.000
149A635MET0-0.052-0.01313.052-0.005-0.0050.0000.0000.0000.000
150A636VAL0-0.013-0.0027.6580.0090.0090.0000.0000.0000.000
151A637THR0-0.037-0.0417.671-0.011-0.0110.0000.0000.0000.000
152A638ILE00.013-0.0022.3380.0780.3621.005-0.246-1.043-0.001
153A639GLU-1-0.781-0.8502.840-3.030-1.8040.845-0.772-1.299-0.009
154A640GLY00.0110.0144.7310.3370.393-0.001-0.001-0.0520.000
155A641GLU-1-0.902-0.9346.8430.1230.1230.0000.0000.0000.000
156A642LEU0-0.017-0.01410.1200.0700.0700.0000.0000.0000.000
157A643TYR00.005-0.01412.338-0.117-0.1170.0000.0000.0000.000
158A644GLU-1-0.792-0.88115.7140.6080.6080.0000.0000.0000.000
159A645ARG10.8130.87518.173-0.358-0.3580.0000.0000.0000.000
160A646SER0-0.043-0.02720.498-0.027-0.0270.0000.0000.0000.000
161A647GLY00.014-0.00121.341-0.028-0.0280.0000.0000.0000.000
162A648ALA0-0.062-0.01520.737-0.017-0.0170.0000.0000.0000.000
163A649ILE00.0150.00016.1900.0250.0250.0000.0000.0000.000
164A650THR0-0.048-0.02013.771-0.022-0.0220.0000.0000.0000.000
165A651GLY00.0730.02912.2710.0490.0490.0000.0000.0000.000
166A652GLY0-0.039-0.01411.911-0.055-0.0550.0000.0000.0000.000
167A653HIS0-0.0220.00010.9930.0830.0830.0000.0000.0000.000
168A654PHE00.0400.0189.032-0.002-0.0020.0000.0000.0000.000
169A655ARG10.8030.8879.269-0.019-0.0190.0000.0000.0000.000
170A656ALA00.001-0.00611.866-0.068-0.0680.0000.0000.0000.000
171A657ARG10.9200.95415.310-0.003-0.0030.0000.0000.0000.000
172A658GLY00.0470.03517.750-0.035-0.0350.0000.0000.0000.000
173A659LEU0-0.024-0.02319.0960.0010.0010.0000.0000.0000.000
174A660ALA0-0.0020.00020.957-0.021-0.0210.0000.0000.0000.000
175A661VAL00.005-0.00520.2690.0090.0090.0000.0000.0000.000
176A662ASP-1-0.813-0.89122.447-0.190-0.1900.0000.0000.0000.000
177A663THR00.0180.01522.006-0.030-0.0300.0000.0000.0000.000
178A664THR0-0.037-0.03723.393-0.027-0.0270.0000.0000.0000.000
179A665LYS10.8800.93821.7330.3330.3330.0000.0000.0000.000
180A666LEU00.0190.00427.3630.0080.0080.0000.0000.0000.000
181A667ARG10.8980.95328.4400.1470.1470.0000.0000.0000.000
182A668LEU00.0360.03427.730-0.003-0.0030.0000.0000.0000.000