Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 94652

Calculation Name: 4ALN-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ALN

Chain ID: F

ChEMBL ID:

UniProt ID: A0A0H3

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2352760.438295
FMO2-HF: Nuclear repulsion 2273786.250266
FMO2-HF: Total energy -78974.188029
FMO2-MP2: Total energy -79208.27608


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(F:3:ASN)


Summations of interaction energy for fragment #1(F:3:ASN)
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.
-20.269-31.64834.544-12.993-10.173-0.062
Interaction energy analysis for fragmet #1(F:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.014
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].
3F5GLU-1-0.793-0.8921.791-14.999-28.38233.230-11.974-7.874-0.060
4F6ASN0-0.118-0.0634.8430.7470.808-0.001-0.005-0.0550.000
5F7LYS10.9010.9806.3692.6952.6950.0000.0000.0000.000
6F8THR0-0.008-0.0228.740-0.058-0.0580.0000.0000.0000.000
7F9TYR0-0.0220.0126.890-0.055-0.0550.0000.0000.0000.000
8F10VAL00.0370.02412.3470.0620.0620.0000.0000.0000.000
9F11ILE0-0.044-0.03012.0250.0150.0150.0000.0000.0000.000
10F12MET00.0000.00616.2590.0720.0720.0000.0000.0000.000
11F13GLY00.0490.02319.5870.0000.0000.0000.0000.0000.000
12F14ILE0-0.076-0.03417.2100.0250.0250.0000.0000.0000.000
13F15ALA0-0.052-0.02721.3340.0330.0330.0000.0000.0000.000
14F16ASN00.025-0.00723.8020.0100.0100.0000.0000.0000.000
15F17LYS11.0231.00721.6260.2830.2830.0000.0000.0000.000
16F18ARG10.8870.93920.8690.2740.2740.0000.0000.0000.000
17F19SER00.0800.06620.7310.0110.0110.0000.0000.0000.000
18F20ILE00.1200.06516.905-0.043-0.0430.0000.0000.0000.000
19F21ALA00.0420.02316.490-0.067-0.0670.0000.0000.0000.000
20F22PHE0-0.007-0.00815.645-0.092-0.0920.0000.0000.0000.000
21F23GLY0-0.028-0.02214.995-0.062-0.0620.0000.0000.0000.000
22F24VAL00.016-0.00511.236-0.116-0.1160.0000.0000.0000.000
23F25ALA00.0310.01410.821-0.265-0.2650.0000.0000.0000.000
24F26LYS10.9440.97411.1530.4170.4170.0000.0000.0000.000
25F27VAL0-0.0250.0076.804-0.043-0.0430.0000.0000.0000.000
26F28LEU00.0310.0036.696-0.435-0.4350.0000.0000.0000.000
27F29ASP-1-0.818-0.9107.056-1.875-1.8750.0000.0000.0000.000
28F30GLN0-0.054-0.0207.808-0.287-0.2870.0000.0000.0000.000
29F31LEU0-0.059-0.0312.530-0.9750.1231.293-0.595-1.7960.001
30F32GLY00.0010.0053.336-3.381-2.7260.024-0.396-0.283-0.003
31F33ALA0-0.0140.0105.734-0.215-0.2150.0000.0000.0000.000
32F34LYS10.9170.9617.5541.9021.9020.0000.0000.0000.000
33F35LEU0-0.023-0.01810.1150.0500.0500.0000.0000.0000.000
34F36VAL00.0440.02313.2910.1580.1580.0000.0000.0000.000
35F37PHE0-0.018-0.00115.008-0.024-0.0240.0000.0000.0000.000
36F38THR00.0600.02919.0430.0450.0450.0000.0000.0000.000
37F39TYR0-0.044-0.01522.174-0.011-0.0110.0000.0000.0000.000
38F40ARG11.0241.02224.9320.3360.3360.0000.0000.0000.000
39F41LYS10.9460.95228.2680.2790.2790.0000.0000.0000.000
40F42GLU-1-0.733-0.86829.703-0.350-0.3500.0000.0000.0000.000
41F43ARG10.8810.92630.9380.2350.2350.0000.0000.0000.000
42F44SER0-0.071-0.03927.170-0.002-0.0020.0000.0000.0000.000
43F45ARG11.0001.02326.4360.4130.4130.0000.0000.0000.000
44F46LYS10.9620.96826.1180.2650.2650.0000.0000.0000.000
45F47GLU-1-0.927-0.96724.867-0.380-0.3800.0000.0000.0000.000
46F48LEU00.0360.00920.413-0.016-0.0160.0000.0000.0000.000
47F49GLU-1-0.915-0.94822.006-0.438-0.4380.0000.0000.0000.000
48F50LYS10.9330.95523.0180.3120.3120.0000.0000.0000.000
49F51LEU0-0.044-0.02420.045-0.002-0.0020.0000.0000.0000.000
50F52LEU0-0.023-0.01717.893-0.035-0.0350.0000.0000.0000.000
51F53GLU-1-0.945-0.96218.210-0.428-0.4280.0000.0000.0000.000
52F54GLN0-0.134-0.06618.2380.0040.0040.0000.0000.0000.000
53F55LEU0-0.063-0.01113.917-0.008-0.0080.0000.0000.0000.000
54F56ASN0-0.027-0.00511.5190.2570.2570.0000.0000.0000.000
55F57GLN0-0.005-0.02410.931-0.109-0.1090.0000.0000.0000.000
56F58PRO0-0.0450.00112.7410.1320.1320.0000.0000.0000.000
57F59GLU-1-0.888-0.96015.633-0.619-0.6190.0000.0000.0000.000
58F60ALA0-0.0180.00017.639-0.078-0.0780.0000.0000.0000.000
59F61HIS10.9110.96116.7860.9280.9280.0000.0000.0000.000
60F62LEU0-0.036-0.01719.991-0.034-0.0340.0000.0000.0000.000
61F63TYR00.000-0.02620.8450.0120.0120.0000.0000.0000.000
62F64GLN0-0.049-0.01924.562-0.011-0.0110.0000.0000.0000.000
63F65ILE00.0410.02023.7480.0050.0050.0000.0000.0000.000
64F66ASP-1-0.928-0.96827.129-0.323-0.3230.0000.0000.0000.000
65F67VAL0-0.002-0.00625.2260.0120.0120.0000.0000.0000.000
66F68GLN0-0.109-0.04728.4100.0280.0280.0000.0000.0000.000
67F69SER0-0.044-0.04431.4800.0220.0220.0000.0000.0000.000
68F70ASP-1-0.851-0.91631.445-0.275-0.2750.0000.0000.0000.000
69F71GLU-1-0.971-0.97531.229-0.267-0.2670.0000.0000.0000.000
70F72GLU-1-0.818-0.91629.975-0.344-0.3440.0000.0000.0000.000
71F73VAL0-0.053-0.01725.775-0.031-0.0310.0000.0000.0000.000
72F74ILE00.0120.01026.765-0.027-0.0270.0000.0000.0000.000
73F75ASN0-0.030-0.01727.891-0.009-0.0090.0000.0000.0000.000
74F76GLY0-0.001-0.02226.038-0.018-0.0180.0000.0000.0000.000
75F77PHE00.011-0.00120.016-0.043-0.0430.0000.0000.0000.000
76F78GLU-1-0.877-0.92823.725-0.369-0.3690.0000.0000.0000.000
77F79GLN0-0.094-0.03725.5580.0160.0160.0000.0000.0000.000
78F80ILE0-0.0090.00719.374-0.024-0.0240.0000.0000.0000.000
79F81GLY00.0450.01821.414-0.044-0.0440.0000.0000.0000.000
80F82LYS10.8420.92222.5910.3360.3360.0000.0000.0000.000
81F83ASP-1-0.874-0.94322.687-0.498-0.4980.0000.0000.0000.000
82F84VAL0-0.123-0.05616.980-0.044-0.0440.0000.0000.0000.000
83F85GLY0-0.030-0.00418.235-0.060-0.0600.0000.0000.0000.000
84F86ASN0-0.045-0.04617.7910.0110.0110.0000.0000.0000.000
85F87ILE0-0.037-0.02314.770-0.103-0.1030.0000.0000.0000.000
86F88ASP-1-0.740-0.86510.680-1.653-1.6530.0000.0000.0000.000
87F89GLY00.031-0.06412.5350.0420.0420.0000.0000.0000.000
88F90VAL0-0.018-0.00513.523-0.026-0.0260.0000.0000.0000.000
89F91TYR0-0.002-0.01513.5320.0630.0630.0000.0000.0000.000
90F92HIS00.028-0.01915.4900.0090.0090.0000.0000.0000.000
91F93SER0-0.026-0.00718.5230.0660.0660.0000.0000.0000.000
92F94ILE0-0.020-0.01420.1470.0290.0290.0000.0000.0000.000
93F109THR00.0670.01941.061-0.001-0.0010.0000.0000.0000.000
94F110SER0-0.077-0.02343.0680.0000.0000.0000.0000.0000.000
95F111ARG11.0321.01042.3990.1150.1150.0000.0000.0000.000
96F112GLU-1-0.856-0.94141.440-0.141-0.1410.0000.0000.0000.000
97F113GLY00.0090.00038.979-0.009-0.0090.0000.0000.0000.000
98F114PHE0-0.006-0.00337.429-0.011-0.0110.0000.0000.0000.000
99F115LEU00.015-0.00736.463-0.009-0.0090.0000.0000.0000.000
100F116LEU00.0280.04035.114-0.011-0.0110.0000.0000.0000.000
101F117ALA0-0.001-0.01132.981-0.017-0.0170.0000.0000.0000.000
102F118GLN0-0.0080.00031.645-0.021-0.0210.0000.0000.0000.000
103F119ASP-1-0.874-0.93231.245-0.269-0.2690.0000.0000.0000.000
104F120ILE00.0200.00428.635-0.021-0.0210.0000.0000.0000.000
105F121SER0-0.113-0.01627.354-0.030-0.0300.0000.0000.0000.000
106F122SER0-0.010-0.02026.418-0.025-0.0250.0000.0000.0000.000
107F123TYR00.0500.03027.253-0.015-0.0150.0000.0000.0000.000
108F124SER00.013-0.04126.285-0.021-0.0210.0000.0000.0000.000
109F125LEU0-0.022-0.00220.891-0.027-0.0270.0000.0000.0000.000
110F126THR00.0520.03324.268-0.017-0.0170.0000.0000.0000.000
111F127ILE0-0.0260.01426.524-0.007-0.0070.0000.0000.0000.000
112F128VAL00.0450.01121.310-0.011-0.0110.0000.0000.0000.000
113F129ALA0-0.0220.01022.005-0.029-0.0290.0000.0000.0000.000
114F130HIS0-0.048-0.02023.0680.0030.0030.0000.0000.0000.000
115F131GLU-1-0.851-0.95025.076-0.355-0.3550.0000.0000.0000.000
116F132ALA00.013-0.00419.391-0.014-0.0140.0000.0000.0000.000
117F133LYS10.9400.98920.7870.2760.2760.0000.0000.0000.000
118F134LYS10.8350.92222.1050.3530.3530.0000.0000.0000.000
119F135LEU0-0.095-0.04519.3780.0040.0040.0000.0000.0000.000
120F136MET0-0.0260.04415.340-0.075-0.0750.0000.0000.0000.000
121F137PRO00.0070.01618.7680.0540.0540.0000.0000.0000.000
122F138GLU-1-0.967-0.99017.064-0.426-0.4260.0000.0000.0000.000
123F139GLY00.0130.01317.3530.0380.0380.0000.0000.0000.000
124F140GLY00.010-0.00913.869-0.106-0.1060.0000.0000.0000.000
125F141SER0-0.096-0.02611.9410.1510.1510.0000.0000.0000.000
126F142ILE00.0450.01414.011-0.116-0.1160.0000.0000.0000.000
127F143VAL0-0.008-0.00912.4560.0550.0550.0000.0000.0000.000
128F144ALA00.0160.03315.779-0.024-0.0240.0000.0000.0000.000
129F145THR0-0.045-0.00816.600-0.005-0.0050.0000.0000.0000.000
130F146THR00.0270.02118.8180.0320.0320.0000.0000.0000.000
131F147TYR0-0.033-0.02422.0140.0100.0100.0000.0000.0000.000
132F148LEU00.0520.03321.675-0.001-0.0010.0000.0000.0000.000
133F149GLY0-0.022-0.02823.3730.0230.0230.0000.0000.0000.000
134F150GLY0-0.082-0.05026.613-0.018-0.0180.0000.0000.0000.000
135F151GLU-1-0.870-0.91029.238-0.156-0.1560.0000.0000.0000.000
136F152PHE0-0.060-0.06029.825-0.023-0.0230.0000.0000.0000.000
137F153ALA00.0590.03532.0740.0090.0090.0000.0000.0000.000
138F154VAL0-0.0240.00933.3500.0000.0000.0000.0000.0000.000
139F155GLN00.0070.00035.9980.0130.0130.0000.0000.0000.000
140F156ASN0-0.025-0.02339.741-0.004-0.0040.0000.0000.0000.000
141F157TYR0-0.044-0.01039.583-0.001-0.0010.0000.0000.0000.000
142F158ASN00.0990.04132.917-0.008-0.0080.0000.0000.0000.000
143F159VAL00.0400.01135.668-0.003-0.0030.0000.0000.0000.000
144F160MET00.0540.01931.209-0.010-0.0100.0000.0000.0000.000
145F161GLY00.0030.01431.118-0.013-0.0130.0000.0000.0000.000
146F162VAL00.010-0.00331.414-0.007-0.0070.0000.0000.0000.000
147F163ALA00.0110.00130.901-0.002-0.0020.0000.0000.0000.000
148F164LYS10.9020.95726.3340.2760.2760.0000.0000.0000.000
149F165ALA00.0420.02927.699-0.010-0.0100.0000.0000.0000.000
150F166SER0-0.012-0.00729.075-0.005-0.0050.0000.0000.0000.000
151F167LEU00.0030.01923.099-0.003-0.0030.0000.0000.0000.000
152F168GLU-1-0.931-0.97624.239-0.233-0.2330.0000.0000.0000.000
153F169ALA0-0.045-0.02525.1460.0000.0000.0000.0000.0000.000
154F170ASN0-0.007-0.02925.9510.0070.0070.0000.0000.0000.000
155F171VAL0-0.021-0.01020.588-0.006-0.0060.0000.0000.0000.000
156F172LYS10.9600.98922.9380.1850.1850.0000.0000.0000.000
157F173TYR0-0.006-0.01624.8070.0110.0110.0000.0000.0000.000
158F174LEU00.0100.02523.2700.0020.0020.0000.0000.0000.000
159F175ALA0-0.004-0.00321.248-0.005-0.0050.0000.0000.0000.000
160F176LEU0-0.116-0.06022.1630.0150.0150.0000.0000.0000.000
161F177ASP-1-0.959-0.99325.298-0.223-0.2230.0000.0000.0000.000
162F178LEU0-0.007-0.00621.819-0.003-0.0030.0000.0000.0000.000
163F179GLY00.0280.02921.475-0.015-0.0150.0000.0000.0000.000
164F180PRO0-0.058-0.03622.0070.0040.0040.0000.0000.0000.000
165F181ASP-1-0.910-0.94622.841-0.265-0.2650.0000.0000.0000.000
166F182ASN0-0.071-0.04216.399-0.011-0.0110.0000.0000.0000.000
167F183ILE0-0.0210.00317.619-0.077-0.0770.0000.0000.0000.000
168F184ARG10.8230.93610.5800.6850.6850.0000.0000.0000.000
169F185VAL00.0100.01316.731-0.088-0.0880.0000.0000.0000.000
170F186ASN00.0270.01614.9070.1350.1350.0000.0000.0000.000
171F187ALA0-0.008-0.00617.213-0.057-0.0570.0000.0000.0000.000
172F188ILE0-0.0170.00513.063-0.002-0.0020.0000.0000.0000.000
173F189SER00.011-0.02817.4100.0000.0000.0000.0000.0000.000
174F190ALA0-0.026-0.01219.4220.0080.0080.0000.0000.0000.000
175F191GLY00.0080.00820.3600.0340.0340.0000.0000.0000.000
176F222ASP-1-0.799-0.91817.082-0.384-0.3840.0000.0000.0000.000
177F223GLN0-0.058-0.03516.557-0.046-0.0460.0000.0000.0000.000
178F224VAL00.0020.01111.885-0.116-0.1160.0000.0000.0000.000
179F225GLU-1-0.958-0.96712.081-0.455-0.4550.0000.0000.0000.000
180F226VAL00.0080.00112.459-0.081-0.0810.0000.0000.0000.000
181F227GLY00.0230.00411.059-0.118-0.1180.0000.0000.0000.000
182F228LYS10.9670.9857.8160.0900.0900.0000.0000.0000.000
183F229THR00.0200.0257.751-0.378-0.3780.0000.0000.0000.000
184F230ALA00.007-0.0069.603-0.035-0.0350.0000.0000.0000.000
185F231ALA00.0090.0124.844-0.121-0.1210.0000.0000.0000.000
186F232TYR0-0.011-0.0036.135-0.176-0.1760.0000.0000.0000.000
187F233LEU0-0.0300.0196.9940.2760.2760.0000.0000.0000.000
188F234LEU0-0.017-0.0028.3430.1860.1860.0000.0000.0000.000
189F235SER0-0.047-0.0304.7670.0410.050-0.001-0.007-0.0010.000
190F236ASP-1-0.902-0.9706.6660.8300.8300.0000.0000.0000.000
191F237LEU00.0330.0083.9450.0970.278-0.001-0.016-0.1640.000
192F238SER0-0.051-0.0526.7940.1980.1980.0000.0000.0000.000
193F239SER0-0.003-0.00310.060-0.086-0.0860.0000.0000.0000.000
194F240GLY0-0.0130.00012.0320.0000.0000.0000.0000.0000.000
195F241VAL0-0.087-0.02813.3600.0030.0030.0000.0000.0000.000
196F242THR00.0540.00215.291-0.110-0.1100.0000.0000.0000.000
197F243GLY00.0250.00417.9270.0450.0450.0000.0000.0000.000
198F244GLU-1-0.964-0.96616.968-0.133-0.1330.0000.0000.0000.000
199F245ASN0-0.017-0.02718.485-0.095-0.0950.0000.0000.0000.000
200F246ILE00.007-0.00213.6430.0370.0370.0000.0000.0000.000
201F247HIS0-0.008-0.00317.608-0.054-0.0540.0000.0000.0000.000
202F248VAL0-0.056-0.02114.6330.0080.0080.0000.0000.0000.000
203F249ASP-1-0.736-0.88417.744-0.205-0.2050.0000.0000.0000.000
204F250SER0-0.051-0.03519.9920.0370.0370.0000.0000.0000.000
205F251GLY0-0.004-0.00921.2020.0290.0290.0000.0000.0000.000
206F252PHE0-0.029-0.00122.7340.0230.0230.0000.0000.0000.000
207F253HIS0-0.044-0.02421.3180.0280.0280.0000.0000.0000.000
208F254ALA0-0.0330.00225.2730.0090.0090.0000.0000.0000.000
209F255ILE0-0.076-0.02727.0130.0110.0110.0000.0000.0000.000