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: MV7KZ

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 OptHSide
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 -2355318.125335
FMO2-HF: Nuclear repulsion 2276341.953781
FMO2-HF: Total energy -78976.171554
FMO2-MP2: Total energy -79210.103012


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.
-25.089-21.4714.633-9.004-9.247-0.05
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 : -0.052 / q_NPA : -0.019
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-1-0.781-0.8821.889-18.316-17.84413.120-7.461-6.130-0.045
4F6ASN0-0.142-0.0755.0051.0461.099-0.001-0.006-0.0460.000
5F7LYS10.8840.9546.1712.1332.1330.0000.0000.0000.000
6F8THR0-0.003-0.0108.863-0.170-0.1700.0000.0000.0000.000
7F9TYR0-0.0160.0036.849-0.010-0.0100.0000.0000.0000.000
8F10VAL00.0260.01912.3030.0330.0330.0000.0000.0000.000
9F11ILE0-0.046-0.03011.5710.0280.0280.0000.0000.0000.000
10F12MET0-0.0050.00715.7370.0720.0720.0000.0000.0000.000
11F13GLY00.0540.02218.8790.0040.0040.0000.0000.0000.000
12F14ILE0-0.085-0.03416.4720.0280.0280.0000.0000.0000.000
13F15ALA0-0.054-0.02520.6290.0380.0380.0000.0000.0000.000
14F16ASN0-0.001-0.02023.1870.0140.0140.0000.0000.0000.000
15F17LYS10.9250.95021.0620.3820.3820.0000.0000.0000.000
16F18ARG10.9240.96320.3910.2920.2920.0000.0000.0000.000
17F19SER00.0740.06320.2060.0180.0180.0000.0000.0000.000
18F20ILE00.1210.05216.328-0.057-0.0570.0000.0000.0000.000
19F21ALA00.0350.02115.899-0.079-0.0790.0000.0000.0000.000
20F22PHE00.001-0.00414.998-0.114-0.1140.0000.0000.0000.000
21F23GLY0-0.039-0.02814.531-0.091-0.0910.0000.0000.0000.000
22F24VAL00.0150.00010.481-0.152-0.1520.0000.0000.0000.000
23F25ALA00.0310.01610.197-0.314-0.3140.0000.0000.0000.000
24F26LYS10.9280.97110.7460.5270.5270.0000.0000.0000.000
25F27VAL0-0.0110.0096.410-0.114-0.1140.0000.0000.0000.000
26F28LEU00.0420.0105.750-0.643-0.6430.0000.0000.0000.000
27F29ASP-1-0.779-0.8726.909-2.333-2.3330.0000.0000.0000.000
28F30GLN0-0.071-0.0287.942-0.288-0.2880.0000.0000.0000.000
29F31LEU0-0.043-0.0222.406-1.4090.0421.463-0.757-2.1570.000
30F32GLY0-0.0030.0023.297-3.953-3.0070.030-0.628-0.348-0.005
31F33ALA0-0.0170.0145.7800.0010.0010.0000.0000.0000.000
32F34LYS10.9360.9667.6671.8691.8690.0000.0000.0000.000
33F35LEU0-0.039-0.0349.8420.0830.0830.0000.0000.0000.000
34F36VAL00.0250.02013.3750.1670.1670.0000.0000.0000.000
35F37PHE00.0090.00314.761-0.024-0.0240.0000.0000.0000.000
36F38THR00.0660.03118.8830.0520.0520.0000.0000.0000.000
37F39TYR0-0.075-0.05321.779-0.018-0.0180.0000.0000.0000.000
38F40ARG10.9030.94624.4950.3320.3320.0000.0000.0000.000
39F41LYS10.9680.96927.7230.2860.2860.0000.0000.0000.000
40F42GLU-1-0.720-0.83629.302-0.379-0.3790.0000.0000.0000.000
41F43ARG10.8860.93430.6940.2480.2480.0000.0000.0000.000
42F44SER0-0.075-0.05526.552-0.002-0.0020.0000.0000.0000.000
43F45ARG10.9200.98126.2470.4370.4370.0000.0000.0000.000
44F46LYS10.9620.97526.0240.3000.3000.0000.0000.0000.000
45F47GLU-1-0.829-0.90924.409-0.451-0.4510.0000.0000.0000.000
46F48LEU00.0440.01119.605-0.021-0.0210.0000.0000.0000.000
47F49GLU-1-0.823-0.89521.847-0.505-0.5050.0000.0000.0000.000
48F50LYS10.7700.86322.9020.4060.4060.0000.0000.0000.000
49F51LEU0-0.051-0.02219.656-0.007-0.0070.0000.0000.0000.000
50F52LEU0-0.016-0.00917.312-0.048-0.0480.0000.0000.0000.000
51F53GLU-1-0.816-0.88818.179-0.501-0.5010.0000.0000.0000.000
52F54GLN0-0.114-0.06417.8860.0020.0020.0000.0000.0000.000
53F55LEU0-0.062-0.00813.441-0.016-0.0160.0000.0000.0000.000
54F56ASN0-0.066-0.02811.6910.2850.2850.0000.0000.0000.000
55F57GLN00.004-0.03010.936-0.073-0.0730.0000.0000.0000.000
56F58PRO0-0.0340.01012.8820.1500.1500.0000.0000.0000.000
57F59GLU-1-0.825-0.92515.762-0.781-0.7810.0000.0000.0000.000
58F60ALA0-0.032-0.00317.753-0.081-0.0810.0000.0000.0000.000
59F61HIS10.8540.92217.2460.9630.9630.0000.0000.0000.000
60F62LEU0-0.040-0.02220.058-0.036-0.0360.0000.0000.0000.000
61F63TYR0-0.015-0.04621.0950.0160.0160.0000.0000.0000.000
62F64GLN0-0.054-0.02524.449-0.008-0.0080.0000.0000.0000.000
63F65ILE00.0270.00623.3490.0120.0120.0000.0000.0000.000
64F66ASP-1-0.822-0.90526.606-0.322-0.3220.0000.0000.0000.000
65F67VAL0-0.006-0.00124.3660.0140.0140.0000.0000.0000.000
66F68GLN0-0.104-0.03927.7190.0300.0300.0000.0000.0000.000
67F69SER0-0.071-0.06730.8360.0210.0210.0000.0000.0000.000
68F70ASP-1-0.823-0.92030.923-0.246-0.2460.0000.0000.0000.000
69F71GLU-1-0.965-0.97230.847-0.249-0.2490.0000.0000.0000.000
70F72GLU-1-0.791-0.87729.527-0.327-0.3270.0000.0000.0000.000
71F73VAL0-0.026-0.00825.244-0.032-0.0320.0000.0000.0000.000
72F74ILE00.0160.01426.522-0.025-0.0250.0000.0000.0000.000
73F75ASN0-0.067-0.04227.823-0.013-0.0130.0000.0000.0000.000
74F76GLY0-0.006-0.01925.894-0.019-0.0190.0000.0000.0000.000
75F77PHE00.0150.00019.433-0.045-0.0450.0000.0000.0000.000
76F78GLU-1-0.757-0.84723.881-0.354-0.3540.0000.0000.0000.000
77F79GLN0-0.090-0.03825.9010.0180.0180.0000.0000.0000.000
78F80ILE00.0010.00919.570-0.030-0.0300.0000.0000.0000.000
79F81GLY00.0540.01521.718-0.043-0.0430.0000.0000.0000.000
80F82LYS10.7280.84722.7860.3250.3250.0000.0000.0000.000
81F83ASP-1-0.860-0.91322.982-0.504-0.5040.0000.0000.0000.000
82F84VAL0-0.133-0.06417.105-0.055-0.0550.0000.0000.0000.000
83F85GLY0-0.0190.00118.410-0.057-0.0570.0000.0000.0000.000
84F86ASN0-0.041-0.03517.7850.0000.0000.0000.0000.0000.000
85F87ILE0-0.047-0.03315.138-0.118-0.1180.0000.0000.0000.000
86F88ASP-1-0.741-0.85310.723-1.398-1.3980.0000.0000.0000.000
87F89GLY00.038-0.02712.2390.0880.0880.0000.0000.0000.000
88F90VAL0-0.042-0.01213.156-0.060-0.0600.0000.0000.0000.000
89F91TYR00.012-0.00912.8100.0600.0600.0000.0000.0000.000
90F92HIS00.010-0.03114.796-0.009-0.0090.0000.0000.0000.000
91F93SER00.002-0.00717.7810.0750.0750.0000.0000.0000.000
92F94ILE0-0.050-0.01619.5590.0240.0240.0000.0000.0000.000
93F109THR00.0590.02040.566-0.001-0.0010.0000.0000.0000.000
94F110SER0-0.097-0.07143.1240.0000.0000.0000.0000.0000.000
95F111ARG11.0031.00441.9350.0950.0950.0000.0000.0000.000
96F112GLU-1-0.813-0.90140.927-0.123-0.1230.0000.0000.0000.000
97F113GLY00.0280.01338.459-0.009-0.0090.0000.0000.0000.000
98F114PHE0-0.003-0.00136.930-0.010-0.0100.0000.0000.0000.000
99F115LEU00.009-0.00835.981-0.007-0.0070.0000.0000.0000.000
100F116LEU00.0140.03834.451-0.009-0.0090.0000.0000.0000.000
101F117ALA00.009-0.00532.462-0.016-0.0160.0000.0000.0000.000
102F118GLN0-0.006-0.00531.134-0.020-0.0200.0000.0000.0000.000
103F119ASP-1-0.872-0.93830.712-0.242-0.2420.0000.0000.0000.000
104F120ILE00.0390.00628.172-0.019-0.0190.0000.0000.0000.000
105F121SER0-0.097-0.01526.830-0.029-0.0290.0000.0000.0000.000
106F122SER0-0.013-0.02325.919-0.020-0.0200.0000.0000.0000.000
107F123TYR00.0220.01926.684-0.011-0.0110.0000.0000.0000.000
108F124SER00.037-0.01825.546-0.020-0.0200.0000.0000.0000.000
109F125LEU0-0.028-0.00320.054-0.026-0.0260.0000.0000.0000.000
110F126THR00.0190.00723.650-0.012-0.0120.0000.0000.0000.000
111F127ILE0-0.0100.01925.835-0.005-0.0050.0000.0000.0000.000
112F128VAL00.0450.00920.640-0.011-0.0110.0000.0000.0000.000
113F129ALA0-0.0210.01021.336-0.025-0.0250.0000.0000.0000.000
114F130HIS0-0.043-0.02622.3810.0090.0090.0000.0000.0000.000
115F131GLU-1-0.786-0.89124.647-0.296-0.2960.0000.0000.0000.000
116F132ALA00.015-0.00119.063-0.013-0.0130.0000.0000.0000.000
117F133LYS10.8640.94220.6560.1770.1770.0000.0000.0000.000
118F134LYS10.7550.86621.7660.3140.3140.0000.0000.0000.000
119F135LEU0-0.087-0.03619.5390.0000.0000.0000.0000.0000.000
120F136MET0-0.0270.01615.622-0.070-0.0700.0000.0000.0000.000
121F137PRO00.0090.00818.7800.0580.0580.0000.0000.0000.000
122F138GLU-1-0.969-0.98517.215-0.274-0.2740.0000.0000.0000.000
123F139GLY00.0110.02216.7340.0690.0690.0000.0000.0000.000
124F140GLY00.015-0.00813.205-0.096-0.0960.0000.0000.0000.000
125F141SER0-0.107-0.03810.8710.1370.1370.0000.0000.0000.000
126F142ILE00.0320.01013.097-0.151-0.1510.0000.0000.0000.000
127F143VAL00.005-0.00411.8280.0630.0630.0000.0000.0000.000
128F144ALA00.0140.03515.197-0.047-0.0470.0000.0000.0000.000
129F145THR0-0.040-0.00516.2030.0010.0010.0000.0000.0000.000
130F146THR00.0270.01118.4230.0250.0250.0000.0000.0000.000
131F147TYR0-0.015-0.02021.7470.0100.0100.0000.0000.0000.000
132F148LEU00.0520.03620.962-0.005-0.0050.0000.0000.0000.000
133F149GLY0-0.030-0.02922.6230.0270.0270.0000.0000.0000.000
134F150GLY0-0.078-0.04425.844-0.022-0.0220.0000.0000.0000.000
135F151GLU-1-0.780-0.86728.510-0.152-0.1520.0000.0000.0000.000
136F152PHE0-0.083-0.07329.104-0.019-0.0190.0000.0000.0000.000
137F153ALA0-0.021-0.00531.5960.0070.0070.0000.0000.0000.000
138F154VAL0-0.0220.01033.0390.0020.0020.0000.0000.0000.000
139F155GLN0-0.008-0.01035.7730.0160.0160.0000.0000.0000.000
140F156ASN0-0.012-0.01639.493-0.002-0.0020.0000.0000.0000.000
141F157TYR0-0.034-0.00939.5350.0000.0000.0000.0000.0000.000
142F158ASN00.0980.04232.751-0.012-0.0120.0000.0000.0000.000
143F159VAL00.0350.00935.3440.0000.0000.0000.0000.0000.000
144F160MET00.0520.02130.711-0.011-0.0110.0000.0000.0000.000
145F161GLY00.0240.02430.775-0.010-0.0100.0000.0000.0000.000
146F162VAL0-0.002-0.00630.960-0.004-0.0040.0000.0000.0000.000
147F163ALA0-0.0010.00630.5800.0000.0000.0000.0000.0000.000
148F164LYS10.8830.94126.1990.2400.2400.0000.0000.0000.000
149F165ALA00.0270.02327.130-0.005-0.0050.0000.0000.0000.000
150F166SER00.0030.00728.3890.0010.0010.0000.0000.0000.000
151F167LEU00.0090.01922.5860.0020.0020.0000.0000.0000.000
152F168GLU-1-0.846-0.93323.279-0.139-0.1390.0000.0000.0000.000
153F169ALA0-0.054-0.02624.3340.0080.0080.0000.0000.0000.000
154F170ASN00.006-0.01925.3270.0090.0090.0000.0000.0000.000
155F171VAL0-0.019-0.00919.679-0.001-0.0010.0000.0000.0000.000
156F172LYS10.9100.96621.9940.1160.1160.0000.0000.0000.000
157F173TYR00.000-0.01223.8250.0150.0150.0000.0000.0000.000
158F174LEU00.0050.02222.3620.0040.0040.0000.0000.0000.000
159F175ALA00.0010.00420.0610.0010.0010.0000.0000.0000.000
160F176LEU0-0.111-0.05121.0980.0240.0240.0000.0000.0000.000
161F177ASP-1-0.967-1.00124.159-0.134-0.1340.0000.0000.0000.000
162F178LEU00.008-0.00121.007-0.004-0.0040.0000.0000.0000.000
163F179GLY00.0250.02920.317-0.001-0.0010.0000.0000.0000.000
164F180PRO0-0.056-0.03620.8570.0170.0170.0000.0000.0000.000
165F181ASP-1-0.853-0.91121.717-0.154-0.1540.0000.0000.0000.000
166F182ASN0-0.072-0.04815.6630.0120.0120.0000.0000.0000.000
167F183ILE0-0.0040.00816.539-0.050-0.0500.0000.0000.0000.000
168F184ARG10.8200.9299.4500.2350.2350.0000.0000.0000.000
169F185VAL00.0000.00415.759-0.099-0.0990.0000.0000.0000.000
170F186ASN00.0150.01113.5700.1300.1300.0000.0000.0000.000
171F187ALA0-0.011-0.01216.353-0.075-0.0750.0000.0000.0000.000
172F188ILE0-0.0100.00812.5920.0100.0100.0000.0000.0000.000
173F189SER0-0.022-0.01916.993-0.018-0.0180.0000.0000.0000.000
174F190ALA00.0050.00219.1850.0120.0120.0000.0000.0000.000
175F191GLY0-0.029-0.01720.2130.0400.0400.0000.0000.0000.000
176F222ASP-1-0.761-0.89316.864-0.466-0.4660.0000.0000.0000.000
177F223GLN0-0.102-0.06716.458-0.030-0.0300.0000.0000.0000.000
178F224VAL0-0.0140.00012.001-0.126-0.1260.0000.0000.0000.000
179F225GLU-1-0.850-0.90511.967-0.425-0.4250.0000.0000.0000.000
180F226VAL00.0020.00012.472-0.041-0.0410.0000.0000.0000.000
181F227GLY00.0290.00410.737-0.093-0.0930.0000.0000.0000.000
182F228LYS10.8620.9247.776-0.009-0.0090.0000.0000.0000.000
183F229THR00.0120.0187.709-0.288-0.2880.0000.0000.0000.000
184F230ALA00.006-0.0049.1480.0020.0020.0000.0000.0000.000
185F231ALA00.0120.0114.378-0.127-0.112-0.001-0.003-0.0100.000
186F232TYR0-0.018-0.0165.332-0.299-0.2990.0000.0000.0000.000
187F233LEU0-0.007-0.0046.2720.3510.3510.0000.0000.0000.000
188F234LEU0-0.0200.0007.8180.2390.2390.0000.0000.0000.000
189F235SER0-0.039-0.0133.635-0.0350.1410.005-0.055-0.1260.000
190F236ASP-1-0.887-0.9625.6191.8471.8470.0000.0000.0000.000
191F237LEU00.003-0.0043.184-0.4320.0740.017-0.094-0.4300.000
192F238SER0-0.055-0.0176.3320.0110.0110.0000.0000.0000.000
193F239SER00.0390.0139.355-0.250-0.2500.0000.0000.0000.000
194F240GLY0-0.028-0.00511.299-0.066-0.0660.0000.0000.0000.000
195F241VAL0-0.074-0.02212.835-0.048-0.0480.0000.0000.0000.000
196F242THR00.0590.01414.331-0.105-0.1050.0000.0000.0000.000
197F243GLY00.0200.00016.9400.0340.0340.0000.0000.0000.000
198F244GLU-1-0.935-0.95616.1490.0240.0240.0000.0000.0000.000
199F245ASN0-0.066-0.05117.633-0.105-0.1050.0000.0000.0000.000
200F246ILE00.006-0.00212.9190.0400.0400.0000.0000.0000.000
201F247HIS00.0110.00817.012-0.077-0.0770.0000.0000.0000.000
202F248VAL0-0.037-0.01314.4440.0230.0230.0000.0000.0000.000
203F249ASP-1-0.736-0.86917.613-0.143-0.1430.0000.0000.0000.000
204F250SER0-0.045-0.02720.0010.0260.0260.0000.0000.0000.000
205F251GLY00.006-0.00421.0680.0250.0250.0000.0000.0000.000
206F252PHE0-0.031-0.00422.6950.0180.0180.0000.0000.0000.000
207F253HIS0-0.073-0.06020.8390.0330.0330.0000.0000.0000.000
208F254ALA0-0.0320.00325.2420.0090.0090.0000.0000.0000.000
209F255ILE0-0.074-0.02526.9000.0080.0080.0000.0000.0000.000