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: LL4Y9

Calculation Name: 7K3N-A-Xray171

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7K3N

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2020-11-02

Reference: Y.Handa, K. Kato, Y. Kawashima, K. Fukuzawa et.al., FMO calculation for SARS Cov-2 related proteins. To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water All crystal waters in PDB.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 227
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1158666.948627
FMO2-HF: Nuclear repulsion 1107242.048904
FMO2-HF: Total energy -51424.899722
FMO2-MP2: Total energy -51573.836596


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:5:VAL )


Summations of interaction energy for fragment #1(A:5:VAL )
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.
-46.224-36.9121.01-4.112-6.209-0.033
Interaction energy analysis for fragmet #1(A:5:VAL )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.897 / q_NPA : 0.939
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].
3A7LEU 0-0.0030.0182.651-8.386-5.7250.270-1.090-1.841-0.006
4A8SER 00.0340.0035.3975.7825.843-0.001-0.006-0.0540.000
5A9LEU 0-0.0030.0057.4520.3410.3410.0000.0000.0000.000
6A10PRO 00.0380.03210.4981.4631.4630.0000.0000.0000.000
7A11VAL 00.005-0.00914.104-0.269-0.2690.0000.0000.0000.000
8A12LEU 00.0110.00516.5280.8020.8020.0000.0000.0000.000
9A13GLN 00.0040.01519.1760.2160.2160.0000.0000.0000.000
10A14VAL 00.0360.00822.5310.0200.0200.0000.0000.0000.000
11A15ARG 10.7840.89123.48110.42710.4270.0000.0000.0000.000
12A16ASP -1-0.761-0.82623.182-11.949-11.9490.0000.0000.0000.000
13A17VAL 0-0.0460.00119.951-0.130-0.1300.0000.0000.0000.000
14A18LEU 00.0100.00421.9470.6080.6080.0000.0000.0000.000
15A19VAL 0-0.022-0.00319.9120.5240.5240.0000.0000.0000.000
16A20ARG 10.8010.90320.03311.48111.4810.0000.0000.0000.000
17A21GLY 00.0450.02319.1720.0250.0250.0000.0000.0000.000
18A22PHE 0-0.008-0.02113.095-0.438-0.4380.0000.0000.0000.000
19A23GLY 00.0510.02918.143-0.284-0.2840.0000.0000.0000.000
20A24ASP -1-0.869-0.90921.117-12.477-12.4770.0000.0000.0000.000
21A25SER 0-0.036-0.02422.1550.3050.3050.0000.0000.0000.000
22A26VAL 00.0290.00119.580-0.823-0.8230.0000.0000.0000.000
23A27GLU -1-0.837-0.88018.530-15.049-15.0490.0000.0000.0000.000
24A28GLU -1-0.741-0.82117.542-15.808-15.8080.0000.0000.0000.000
25A29VAL 00.0000.01416.896-1.275-1.2750.0000.0000.0000.000
26A30LEU 0-0.022-0.01913.968-1.807-1.8070.0000.0000.0000.000
27A31SER 0-0.085-0.04312.565-2.839-2.8390.0000.0000.0000.000
28A32GLU -1-0.738-0.83712.558-20.920-20.9200.0000.0000.0000.000
29A33ALA 00.0070.02711.415-1.619-1.6190.0000.0000.0000.000
30A34ARG 10.8210.8948.21322.35222.3520.0000.0000.0000.000
31A35GLN 0-0.047-0.0077.819-4.453-4.4530.0000.0000.0000.000
32A36HIS 10.9110.9359.43420.40020.4000.0000.0000.0000.000
33A37LEU 0-0.063-0.0315.223-2.175-2.1750.0000.0000.0000.000
34A38LYS 10.8950.9505.03132.76932.7690.0000.0000.0000.000
35A39ASP -1-0.799-0.8696.111-28.601-28.6010.0000.0000.0000.000
36A40GLY 0-0.0520.0007.7141.9431.9430.0000.0000.0000.000
37A41THR 00.0160.0258.8822.1952.1950.0000.0000.0000.000
38A42CYS 0-0.0100.0019.3121.6741.6740.0000.0000.0000.000
39A43GLY 00.0540.03311.204-1.064-1.0640.0000.0000.0000.000
40A44LEU 0-0.090-0.02912.322-0.759-0.7590.0000.0000.0000.000
41A45VAL 00.0140.02014.5170.8510.8510.0000.0000.0000.000
42A46GLU -1-0.791-0.86218.087-16.456-16.4560.0000.0000.0000.000
43A47VAL 00.0110.01219.5790.7280.7280.0000.0000.0000.000
44A48GLU -1-0.768-0.84821.960-12.332-12.3320.0000.0000.0000.000
45A49LYS 10.9290.95525.5169.6519.6510.0000.0000.0000.000
46A50GLY 0-0.006-0.00428.8180.0820.0820.0000.0000.0000.000
47A51VAL 0-0.0140.00822.4020.1420.1420.0000.0000.0000.000
48A52LEU 00.0520.02221.766-0.097-0.0970.0000.0000.0000.000
49A53PRO 0-0.015-0.00625.062-0.017-0.0170.0000.0000.0000.000
50A54GLN 0-0.052-0.00826.3470.3820.3820.0000.0000.0000.000
51A55LEU 00.0010.00920.394-0.220-0.2200.0000.0000.0000.000
52A56GLU -1-0.777-0.82622.920-12.131-12.1310.0000.0000.0000.000
53A57GLN 00.0200.03622.276-0.899-0.8990.0000.0000.0000.000
54A58PRO 00.0470.00820.6380.2510.2510.0000.0000.0000.000
55A59TYR 0-0.0310.00119.614-0.478-0.4780.0000.0000.0000.000
56A60VAL 00.0150.00513.086-0.320-0.3200.0000.0000.0000.000
57A61PHE 0-0.016-0.00515.554-0.280-0.2800.0000.0000.0000.000
58A62ILE 00.0120.0088.794-1.513-1.5130.0000.0000.0000.000
59A63LYS 10.8420.91212.27918.05618.0560.0000.0000.0000.000
60A64ARG 10.9210.96811.93817.73117.7310.0000.0000.0000.000
61A65SER 0-0.059-0.0279.8011.6501.6500.0000.0000.0000.000
62A66ASP -1-0.734-0.86111.815-18.376-18.3760.0000.0000.0000.000
63A67ALA 0-0.013-0.01213.541-0.614-0.6140.0000.0000.0000.000
64A68ARG 10.9000.96413.74716.33316.3330.0000.0000.0000.000
65A69THR 00.0440.02414.503-0.906-0.9060.0000.0000.0000.000
66A70ALA 00.0110.01511.6730.3620.3620.0000.0000.0000.000
67A71PRO 00.0100.02512.0160.1560.1560.0000.0000.0000.000
68A72HIS 00.010-0.0169.896-0.414-0.4140.0000.0000.0000.000
69A73GLY 00.0500.04110.8101.4741.4740.0000.0000.0000.000
70A74HIS 0-0.0320.0116.920-1.679-1.6790.0000.0000.0000.000
71A75VAL 00.0070.0158.7130.6390.6390.0000.0000.0000.000
72A76MET 0-0.0310.0146.477-4.190-4.1900.0000.0000.0000.000
73A77VAL 00.0030.0046.9323.5953.5950.0000.0000.0000.000
74A78GLU -1-0.792-0.8807.576-28.617-28.6170.0000.0000.0000.000
75A79LEU 0-0.0080.0089.1460.3890.3890.0000.0000.0000.000
76A80VAL 0-0.051-0.00911.9070.5980.5980.0000.0000.0000.000
77A81ALA 00.0710.04515.689-0.017-0.0170.0000.0000.0000.000
78A82GLU -1-0.768-0.82318.153-12.775-12.7750.0000.0000.0000.000
79A83LEU 00.0570.03021.734-0.197-0.1970.0000.0000.0000.000
80A84GLU -1-0.891-0.92224.841-10.422-10.4220.0000.0000.0000.000
81A85GLY 0-0.018-0.00727.0120.2920.2920.0000.0000.0000.000
82A86ILE 0-0.048-0.01224.853-0.193-0.1930.0000.0000.0000.000
83A87GLN 0-0.003-0.01720.709-0.898-0.8980.0000.0000.0000.000
84A88TYR 0-0.014-0.00819.6500.2540.2540.0000.0000.0000.000
85A89GLY 00.031-0.00116.823-1.172-1.1720.0000.0000.0000.000
86A90ARG 10.9300.95417.04614.95714.9570.0000.0000.0000.000
87A91SER 0-0.003-0.00213.634-0.771-0.7710.0000.0000.0000.000
88A92GLY 00.0140.01915.4691.3081.3080.0000.0000.0000.000
89A93GLU -1-0.905-0.93117.253-15.550-15.5500.0000.0000.0000.000
90A94THR 00.011-0.00216.137-1.509-1.5090.0000.0000.0000.000
91A95LEU 0-0.024-0.02012.3590.4140.4140.0000.0000.0000.000
92A96GLY 00.0590.02615.9410.3780.3780.0000.0000.0000.000
93A97VAL 0-0.022-0.00215.774-0.721-0.7210.0000.0000.0000.000
94A98LEU 0-0.033-0.02210.282-0.554-0.5540.0000.0000.0000.000
95A99VAL 00.0150.01614.1511.1601.1600.0000.0000.0000.000
96A100PRO 00.0360.02614.404-1.662-1.6620.0000.0000.0000.000
97A101HIS 0-0.047-0.00314.116-0.197-0.1970.0000.0000.0000.000
98A102VAL 00.000-0.00115.892-0.577-0.5770.0000.0000.0000.000
99A103GLY 00.0440.03518.1110.9060.9060.0000.0000.0000.000
100A104GLU -1-0.774-0.84519.296-15.244-15.2440.0000.0000.0000.000
101A105ILE 00.0340.03019.332-0.930-0.9300.0000.0000.0000.000
102A106PRO 0-0.0110.01017.0820.3780.3780.0000.0000.0000.000
103A107VAL 00.0190.02719.3830.6480.6480.0000.0000.0000.000
104A108ALA 0-0.012-0.00518.3580.3790.3790.0000.0000.0000.000
105A109TYR 00.0490.03912.773-0.776-0.7760.0000.0000.0000.000
106A110ARG 10.9230.97012.15621.91721.9170.0000.0000.0000.000
107A111LYS 10.8970.9679.60119.44619.4460.0000.0000.0000.000
108A112VAL 00.0140.0025.9232.6112.6110.0000.0000.0000.000
109A113LEU 0-0.018-0.0372.783-7.267-6.7120.159-0.212-0.501-0.001
110A114LEU 0-0.027-0.0113.0666.3727.6220.113-0.456-0.907-0.001
111A115ARG 10.8820.9362.78714.54817.7080.346-1.694-1.812-0.019
112A116LYS 00.0120.0503.136-3.352-2.6530.028-0.134-0.593-0.001
113A201HOH 0-0.014-0.02111.8060.9350.9350.0000.0000.0000.000
114A202HOH 00.024-0.0058.3900.0230.0230.0000.0000.0000.000
115A203HOH 00.002-0.00915.0160.0460.0460.0000.0000.0000.000
116A204HOH 0-0.021-0.02119.1770.2280.2280.0000.0000.0000.000
117A205HOH 0-0.008-0.01426.4210.0680.0680.0000.0000.0000.000
118A206HOH 0-0.030-0.02016.716-0.357-0.3570.0000.0000.0000.000
119A207HOH 0-0.035-0.02426.336-0.018-0.0180.0000.0000.0000.000
120A208HOH 0-0.046-0.05012.5390.0300.0300.0000.0000.0000.000
121A209HOH 0-0.015-0.02528.354-0.161-0.1610.0000.0000.0000.000
122A210HOH 0-0.029-0.02222.6930.1320.1320.0000.0000.0000.000
123A211HOH 0-0.044-0.03419.646-0.091-0.0910.0000.0000.0000.000
124A212HOH 00.0330.0179.692-1.078-1.0780.0000.0000.0000.000
125A213HOH 0-0.013-0.01825.6780.2220.2220.0000.0000.0000.000
126A214HOH 00.0270.02011.140-0.416-0.4160.0000.0000.0000.000
127A215HOH 0-0.042-0.03812.057-0.622-0.6220.0000.0000.0000.000
128A216HOH 0-0.045-0.03121.5860.3160.3160.0000.0000.0000.000
129A217HOH 0-0.019-0.02920.163-0.364-0.3640.0000.0000.0000.000
130A218HOH 0-0.035-0.04418.7490.2480.2480.0000.0000.0000.000
131A219HOH 0-0.054-0.05022.259-0.165-0.1650.0000.0000.0000.000
132A220HOH 0-0.019-0.02220.874-0.084-0.0840.0000.0000.0000.000
133A221HOH 0-0.033-0.03123.2070.2590.2590.0000.0000.0000.000
134A222HOH 00.000-0.01117.056-0.063-0.0630.0000.0000.0000.000
135A223HOH 00.0070.00821.377-0.164-0.1640.0000.0000.0000.000
136A224HOH 00.0130.00112.262-0.773-0.7730.0000.0000.0000.000
137A225HOH 0-0.048-0.04421.933-0.198-0.1980.0000.0000.0000.000
138A226HOH 0-0.035-0.03315.8500.4840.4840.0000.0000.0000.000
139A227HOH 0-0.049-0.04425.4660.1930.1930.0000.0000.0000.000
140A228HOH 00.005-0.00230.4020.0460.0460.0000.0000.0000.000
141A229HOH 00.003-0.00526.705-0.129-0.1290.0000.0000.0000.000
142A230HOH 0-0.014-0.00723.1140.0880.0880.0000.0000.0000.000
143A231HOH 0-0.042-0.03316.608-0.444-0.4440.0000.0000.0000.000
144A232HOH 0-0.014-0.02222.040-0.174-0.1740.0000.0000.0000.000
145A233HOH 00.0300.02432.222-0.050-0.0500.0000.0000.0000.000
146A234HOH 0-0.022-0.03118.077-0.157-0.1570.0000.0000.0000.000
147A235HOH 00.012-0.00426.0330.1160.1160.0000.0000.0000.000
148A236HOH 00.0090.00620.201-0.028-0.0280.0000.0000.0000.000
149A237HOH 0-0.007-0.00913.671-0.466-0.4660.0000.0000.0000.000
150A238HOH 00.0370.02723.675-0.204-0.2040.0000.0000.0000.000
151A239HOH 00.0420.02936.278-0.113-0.1130.0000.0000.0000.000
152A240HOH 00.0110.00315.182-0.444-0.4440.0000.0000.0000.000
153A241HOH 0-0.038-0.04022.9190.1780.1780.0000.0000.0000.000
154A242HOH 0-0.019-0.03612.977-0.129-0.1290.0000.0000.0000.000
155A243HOH 0-0.016-0.0239.227-0.984-0.9840.0000.0000.0000.000
156A244HOH 0-0.013-0.03422.806-0.067-0.0670.0000.0000.0000.000
157A245HOH 0-0.036-0.02415.796-0.558-0.5580.0000.0000.0000.000
158A246HOH 00.006-0.0017.192-0.012-0.0120.0000.0000.0000.000
159A247HOH 0-0.027-0.02427.2390.0380.0380.0000.0000.0000.000
160A248HOH 0-0.040-0.02618.766-0.006-0.0060.0000.0000.0000.000
161A249HOH 0-0.044-0.03717.602-0.480-0.4800.0000.0000.0000.000
162A250HOH 0-0.009-0.01324.149-0.096-0.0960.0000.0000.0000.000
163A251HOH 00.0360.01920.900-0.260-0.2600.0000.0000.0000.000
164A252HOH 0-0.033-0.02722.9890.2210.2210.0000.0000.0000.000
165A253HOH 0-0.025-0.03427.0570.0780.0780.0000.0000.0000.000
166A254HOH 00.003-0.00228.3590.1100.1100.0000.0000.0000.000
167A255HOH 00.001-0.00323.797-0.173-0.1730.0000.0000.0000.000
168A256HOH 0-0.012-0.01911.346-0.636-0.6360.0000.0000.0000.000
169A257HOH 0-0.040-0.03117.354-0.011-0.0110.0000.0000.0000.000
170A258HOH 00.0200.00723.4040.0850.0850.0000.0000.0000.000
171A259HOH 0-0.012-0.00923.296-0.224-0.2240.0000.0000.0000.000
172A260HOH 00.000-0.01819.451-0.426-0.4260.0000.0000.0000.000
173A261HOH 0-0.0050.00213.948-0.437-0.4370.0000.0000.0000.000
174A262HOH 00.0310.01826.484-0.070-0.0700.0000.0000.0000.000
175A263HOH 0-0.019-0.03118.2770.1320.1320.0000.0000.0000.000
176A264HOH 0-0.040-0.0376.285-1.508-1.5080.0000.0000.0000.000
177A265HOH 0-0.034-0.02727.3160.1150.1150.0000.0000.0000.000
178A266HOH 0-0.010-0.00610.552-0.333-0.3330.0000.0000.0000.000
179A267HOH 0-0.005-0.0137.7030.3170.3170.0000.0000.0000.000
180A268HOH 00.0220.01026.4940.0950.0950.0000.0000.0000.000
181A269HOH 00.003-0.00624.222-0.129-0.1290.0000.0000.0000.000
182A270HOH 0-0.037-0.04416.0740.5230.5230.0000.0000.0000.000
183A271HOH 0-0.009-0.01124.7930.1880.1880.0000.0000.0000.000
184A272HOH 00.0100.0027.168-1.216-1.2160.0000.0000.0000.000
185A273HOH 0-0.045-0.04112.6490.3140.3140.0000.0000.0000.000
186A274HOH 00.007-0.00328.472-0.083-0.0830.0000.0000.0000.000
187A275HOH 0-0.001-0.01116.111-0.182-0.1820.0000.0000.0000.000
188A276HOH 0-0.023-0.02111.8720.2380.2380.0000.0000.0000.000
189A277HOH 0-0.059-0.05326.3830.1020.1020.0000.0000.0000.000
190A278HOH 00.0370.02710.319-0.823-0.8230.0000.0000.0000.000
191A279HOH 00.010-0.01223.2270.0030.0030.0000.0000.0000.000
192A280HOH 0-0.001-0.00318.215-0.172-0.1720.0000.0000.0000.000
193A281HOH 0-0.017-0.0198.4590.6350.6350.0000.0000.0000.000
194A282HOH 0-0.007-0.00327.6350.0290.0290.0000.0000.0000.000
195A283HOH 0-0.001-0.01211.9590.1950.1950.0000.0000.0000.000
196A284HOH 0-0.017-0.01511.8610.6110.6110.0000.0000.0000.000
197A285HOH 0-0.052-0.04027.2650.1010.1010.0000.0000.0000.000
198A286HOH 0-0.011-0.0029.614-0.650-0.6500.0000.0000.0000.000
199A287HOH 0-0.018-0.0168.8920.5690.5690.0000.0000.0000.000
200A288HOH 0-0.051-0.03527.4470.1950.1950.0000.0000.0000.000
201A289HOH 0-0.019-0.01728.0290.1460.1460.0000.0000.0000.000
202A290HOH 0-0.027-0.02619.907-0.046-0.0460.0000.0000.0000.000
203A291HOH 0-0.006-0.00614.026-0.040-0.0400.0000.0000.0000.000
204A292HOH 0-0.012-0.02023.9270.0550.0550.0000.0000.0000.000
205A293HOH 00.0220.01615.864-0.222-0.2220.0000.0000.0000.000
206A294HOH 0-0.0090.00122.157-0.096-0.0960.0000.0000.0000.000
207A295HOH 0-0.033-0.04023.598-0.177-0.1770.0000.0000.0000.000
208A296HOH 0-0.037-0.02714.3280.1680.1680.0000.0000.0000.000
209A297HOH 0-0.040-0.0267.3670.0910.0910.0000.0000.0000.000
210A298HOH 00.005-0.00228.1770.2070.2070.0000.0000.0000.000
211A299HOH 0-0.037-0.02424.8640.0420.0420.0000.0000.0000.000
212A300HOH 00.0100.00429.951-0.035-0.0350.0000.0000.0000.000
213A301HOH 0-0.032-0.01422.241-0.115-0.1150.0000.0000.0000.000
214A302HOH 0-0.018-0.01410.779-0.540-0.5400.0000.0000.0000.000
215A303HOH 00.006-0.00825.0180.0580.0580.0000.0000.0000.000
216A304HOH 00.0290.01927.233-0.162-0.1620.0000.0000.0000.000
217A305HOH 0-0.027-0.02620.4720.1560.1560.0000.0000.0000.000
218A306HOH 0-0.027-0.01518.7990.3420.3420.0000.0000.0000.000
219A307HOH 00.006-0.00317.444-0.507-0.5070.0000.0000.0000.000
220A308HOH 0-0.011-0.0134.6310.7590.779-0.001-0.001-0.0180.000
221A309HOH 0-0.053-0.0553.099-4.556-3.6500.096-0.519-0.483-0.005
222A310HOH 0-0.025-0.02219.210-0.215-0.2150.0000.0000.0000.000
223A311HOH 0-0.026-0.01620.616-0.289-0.2890.0000.0000.0000.000
224A312HOH 0-0.013-0.02223.5010.1240.1240.0000.0000.0000.000
225A313HOH 00.0350.02825.8080.0360.0360.0000.0000.0000.000
226A314HOH 00.0020.00621.750-0.201-0.2010.0000.0000.0000.000
227A315HOH 0-0.020-0.01021.176-0.202-0.2020.0000.0000.0000.000