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: LNK19

Calculation Name: 1P74-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P74

Chain ID: A

ChEMBL ID:

UniProt ID: P43876

Base Structure: X-ray

Registration Date: 2023-09-24

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 272
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3599321.826142
FMO2-HF: Nuclear repulsion 3494641.875183
FMO2-HF: Total energy -104679.950958
FMO2-MP2: Total energy -104984.405479


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-11.047-6.848.702-3.476-9.432-0.02
Interaction energy analysis for fragmet #1(A:1: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 : -0.004
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].
3A3LEU00.0370.0163.8050.1271.882-0.008-0.769-0.9780.005
4A4TYR00.0160.0085.4680.7150.7150.0000.0000.0000.000
5A5ALA00.0270.0048.660-0.134-0.1340.0000.0000.0000.000
6A6VAL0-0.0660.01011.4500.1430.1430.0000.0000.0000.000
7A7TRP00.0640.01314.169-0.013-0.0130.0000.0000.0000.000
8A8GLY0-0.009-0.02017.4970.0600.0600.0000.0000.0000.000
9A9ASN0-0.0680.00120.811-0.017-0.0170.0000.0000.0000.000
10A10PRO00.0870.02323.4310.0210.0210.0000.0000.0000.000
11A11ILE00.0240.00117.3830.0090.0090.0000.0000.0000.000
12A12ALA00.0120.01418.703-0.010-0.0100.0000.0000.0000.000
13A13GLN0-0.005-0.00919.7400.0020.0020.0000.0000.0000.000
14A14SER0-0.023-0.01117.2380.0430.0430.0000.0000.0000.000
15A15LYS10.9400.96316.8990.1200.1200.0000.0000.0000.000
16A16SER00.0180.01014.7310.0350.0350.0000.0000.0000.000
17A17PRO00.0520.02711.0950.0490.0490.0000.0000.0000.000
18A18LEU0-0.0140.00410.6090.0040.0040.0000.0000.0000.000
19A19ILE0-0.008-0.01112.3970.0690.0690.0000.0000.0000.000
20A20GLN00.0330.00410.2060.1450.1450.0000.0000.0000.000
21A21ASN0-0.001-0.0046.0580.0130.0130.0000.0000.0000.000
22A22LYS10.8780.9408.2220.0870.0870.0000.0000.0000.000
23A23LEU0-0.016-0.00210.9580.1230.1230.0000.0000.0000.000
24A24ALA00.0360.0136.3650.0900.0900.0000.0000.0000.000
25A25ALA0-0.0100.0058.0950.3410.3410.0000.0000.0000.000
26A26GLN0-0.036-0.0178.8100.1100.1100.0000.0000.0000.000
27A27THR0-0.019-0.01311.1060.0230.0230.0000.0000.0000.000
28A28HIS0-0.020-0.0059.0510.0730.0730.0000.0000.0000.000
29A29GLN0-0.021-0.0017.5900.3250.3250.0000.0000.0000.000
30A30THR0-0.006-0.0072.421-0.977-2.2234.927-0.877-2.8040.002
31A31MET0-0.0180.0002.931-2.022-0.2952.140-1.317-2.550-0.014
32A32GLU-1-0.916-0.9472.228-9.502-7.6201.640-0.493-3.029-0.013
33A33TYR0-0.017-0.0394.1030.1090.1980.003-0.020-0.0710.000
34A34ILE00.0310.0107.3330.1650.1650.0000.0000.0000.000
35A35ALA0-0.033-0.0159.8400.1010.1010.0000.0000.0000.000
36A36LYS10.9160.97311.3211.2091.2090.0000.0000.0000.000
37A37LEU0-0.037-0.02615.3760.0630.0630.0000.0000.0000.000
38A38GLY00.0150.01919.113-0.019-0.0190.0000.0000.0000.000
39A39ASP-1-0.823-0.91620.761-0.307-0.3070.0000.0000.0000.000
40A40LEU0-0.018-0.03323.922-0.001-0.0010.0000.0000.0000.000
41A41ASP-1-0.905-0.93626.934-0.238-0.2380.0000.0000.0000.000
42A42ALA0-0.046-0.02924.4100.0000.0000.0000.0000.0000.000
43A43PHE0-0.0020.00719.310-0.040-0.0400.0000.0000.0000.000
44A44GLU-1-0.727-0.83720.830-0.384-0.3840.0000.0000.0000.000
45A45GLN00.0300.01121.482-0.037-0.0370.0000.0000.0000.000
46A46GLN0-0.007-0.00618.464-0.047-0.0470.0000.0000.0000.000
47A47LEU0-0.047-0.01816.288-0.095-0.0950.0000.0000.0000.000
48A48LEU00.0420.00716.472-0.083-0.0830.0000.0000.0000.000
49A49ALA00.0410.03617.161-0.046-0.0460.0000.0000.0000.000
50A50PHE00.014-0.00110.138-0.111-0.1110.0000.0000.0000.000
51A51PHE0-0.026-0.02612.306-0.186-0.1860.0000.0000.0000.000
52A52GLU-1-0.936-0.96213.016-0.761-0.7610.0000.0000.0000.000
53A53GLU-1-0.967-0.97710.946-1.395-1.3950.0000.0000.0000.000
54A54GLY0-0.006-0.0178.494-0.300-0.3000.0000.0000.0000.000
55A55ALA0-0.0360.0028.331-0.320-0.3200.0000.0000.0000.000
56A56LYS10.9450.9727.6011.1981.1980.0000.0000.0000.000
57A57GLY00.0100.0049.9740.3130.3130.0000.0000.0000.000
58A58CYS0-0.030-0.00711.298-0.160-0.1600.0000.0000.0000.000
59A59ASN0-0.040-0.03213.6030.1000.1000.0000.0000.0000.000
60A60ILE0-0.0110.01216.569-0.053-0.0530.0000.0000.0000.000
61A61THR0-0.044-0.02719.6730.0510.0510.0000.0000.0000.000
62A62SER0-0.0260.03622.438-0.002-0.0020.0000.0000.0000.000
63A63PRO00.003-0.02224.487-0.013-0.0130.0000.0000.0000.000
64A64PHE00.057-0.01721.7110.0070.0070.0000.0000.0000.000
65A65LYS10.8650.94823.8000.1880.1880.0000.0000.0000.000
66A66GLU-1-0.923-0.96724.910-0.185-0.1850.0000.0000.0000.000
67A67ARG10.7820.84125.5460.2980.2980.0000.0000.0000.000
68A68ALA00.0110.00021.241-0.009-0.0090.0000.0000.0000.000
69A69TYR0-0.012-0.02423.116-0.001-0.0010.0000.0000.0000.000
70A70GLN0-0.033-0.01725.1900.0130.0130.0000.0000.0000.000
71A71LEU0-0.0180.00122.0290.0010.0010.0000.0000.0000.000
72A72ALA0-0.100-0.03622.538-0.017-0.0170.0000.0000.0000.000
73A73ASP-1-0.827-0.88922.089-0.306-0.3060.0000.0000.0000.000
74A74GLU-1-0.846-0.90722.775-0.140-0.1400.0000.0000.0000.000
75A75TYR00.037-0.00523.966-0.001-0.0010.0000.0000.0000.000
76A76SER0-0.043-0.02824.5030.0200.0200.0000.0000.0000.000
77A77GLN00.0520.01126.414-0.002-0.0020.0000.0000.0000.000
78A78ARG10.8560.89724.0300.0710.0710.0000.0000.0000.000
79A79ALA0-0.0200.00725.345-0.004-0.0040.0000.0000.0000.000
80A80LYS10.9580.98427.4400.1280.1280.0000.0000.0000.000
81A81LEU0-0.019-0.00530.6640.0010.0010.0000.0000.0000.000
82A82ALA0-0.0150.00429.2790.0040.0040.0000.0000.0000.000
83A83GLU-1-0.870-0.92430.915-0.126-0.1260.0000.0000.0000.000
84A84ALA00.0370.01027.253-0.013-0.0130.0000.0000.0000.000
85A85CYS0-0.077-0.00322.7590.0060.0060.0000.0000.0000.000
86A86ASN00.0210.02121.581-0.023-0.0230.0000.0000.0000.000
87A87THR0-0.011-0.01116.840-0.027-0.0270.0000.0000.0000.000
88A88LEU00.0590.03516.9350.0330.0330.0000.0000.0000.000
89A89LYS10.8660.92413.5720.0970.0970.0000.0000.0000.000
90A90LYS10.8910.95011.1201.2471.2470.0000.0000.0000.000
91A91LEU0-0.066-0.03613.591-0.007-0.0070.0000.0000.0000.000
92A92ASP-1-0.910-0.97212.694-0.385-0.3850.0000.0000.0000.000
93A93ASP-1-0.868-0.93515.115-0.294-0.2940.0000.0000.0000.000
94A94GLY00.0210.00316.585-0.022-0.0220.0000.0000.0000.000
95A95LYS10.7890.92217.6200.1720.1720.0000.0000.0000.000
96A96LEU00.005-0.00617.064-0.038-0.0380.0000.0000.0000.000
97A97TYR0-0.036-0.02418.6660.0610.0610.0000.0000.0000.000
98A98ALA00.0190.01119.382-0.031-0.0310.0000.0000.0000.000
99A99ASP-1-0.754-0.84821.349-0.073-0.0730.0000.0000.0000.000
100A100ASN0-0.034-0.04622.481-0.045-0.0450.0000.0000.0000.000
101A101THR00.0230.00020.2440.0150.0150.0000.0000.0000.000
102A102ASP-1-0.784-0.89523.391-0.121-0.1210.0000.0000.0000.000
103A103GLY00.0870.04625.2290.0140.0140.0000.0000.0000.000
104A104ILE0-0.0170.00823.2320.0090.0090.0000.0000.0000.000
105A105GLY00.0240.02924.1070.0190.0190.0000.0000.0000.000
106A106LEU0-0.017-0.01524.7200.0120.0120.0000.0000.0000.000
107A107VAL00.001-0.00728.2220.0090.0090.0000.0000.0000.000
108A108THR00.017-0.00224.0010.0150.0150.0000.0000.0000.000
109A109ASP-1-0.762-0.84426.4720.0180.0180.0000.0000.0000.000
110A110LEU00.0260.01327.8020.0060.0060.0000.0000.0000.000
111A111GLN0-0.022-0.01029.3390.0100.0100.0000.0000.0000.000
112A112ARG10.8390.91726.230-0.025-0.0250.0000.0000.0000.000
113A113LEU0-0.046-0.03129.7620.0050.0050.0000.0000.0000.000
114A114ASN0-0.057-0.02332.677-0.002-0.0020.0000.0000.0000.000
115A115TRP0-0.036-0.00934.592-0.005-0.0050.0000.0000.0000.000
116A116LEU0-0.0030.00932.510-0.006-0.0060.0000.0000.0000.000
117A117ARG10.9140.95936.152-0.027-0.0270.0000.0000.0000.000
118A118PRO00.0310.01738.910-0.005-0.0050.0000.0000.0000.000
119A119ASN0-0.033-0.02440.620-0.001-0.0010.0000.0000.0000.000
120A120GLN0-0.0080.00138.2140.0030.0030.0000.0000.0000.000
121A121HIS00.0010.01042.646-0.006-0.0060.0000.0000.0000.000
122A122VAL0-0.016-0.02237.8900.0010.0010.0000.0000.0000.000
123A123LEU00.0040.01741.328-0.004-0.0040.0000.0000.0000.000
124A124ILE0-0.031-0.01536.386-0.001-0.0010.0000.0000.0000.000
125A125LEU00.0200.00339.374-0.002-0.0020.0000.0000.0000.000
126A126GLY00.0090.00438.451-0.003-0.0030.0000.0000.0000.000
127A127ALA0-0.0120.00436.846-0.007-0.0070.0000.0000.0000.000
128A128GLY00.0510.00736.1510.0020.0020.0000.0000.0000.000
129A129GLY0-0.016-0.00934.794-0.001-0.0010.0000.0000.0000.000
130A130ALA00.006-0.00130.965-0.006-0.0060.0000.0000.0000.000
131A131THR00.0330.00630.269-0.006-0.0060.0000.0000.0000.000
132A132LYS10.8860.95432.1500.1410.1410.0000.0000.0000.000
133A133GLY0-0.0100.00029.4080.0040.0040.0000.0000.0000.000
134A134VAL00.001-0.02129.3610.0060.0060.0000.0000.0000.000
135A135LEU0-0.0050.01231.4070.0090.0090.0000.0000.0000.000
136A136LEU00.0370.03030.9760.0060.0060.0000.0000.0000.000
137A137PRO0-0.015-0.00629.2980.0070.0070.0000.0000.0000.000
138A138LEU00.0240.01732.0710.0090.0090.0000.0000.0000.000
139A139LEU0-0.018-0.00134.7350.0060.0060.0000.0000.0000.000
140A140GLN0-0.020-0.03032.0410.0040.0040.0000.0000.0000.000
141A141ALA0-0.053-0.00433.9070.0070.0070.0000.0000.0000.000
142A142GLN0-0.017-0.01235.9420.0070.0070.0000.0000.0000.000
143A143GLN0-0.043-0.02436.7300.0010.0010.0000.0000.0000.000
144A144ASN0-0.0110.00639.769-0.005-0.0050.0000.0000.0000.000
145A145ILE0-0.007-0.01337.780-0.001-0.0010.0000.0000.0000.000
146A146VAL00.0380.03142.061-0.002-0.0020.0000.0000.0000.000
147A147LEU0-0.021-0.01839.333-0.002-0.0020.0000.0000.0000.000
148A148ALA00.0700.04542.7310.0010.0010.0000.0000.0000.000
149A149ASN0-0.012-0.02140.437-0.003-0.0030.0000.0000.0000.000
150A150ARG10.9410.97843.8380.0570.0570.0000.0000.0000.000
151A151THR0-0.018-0.03043.843-0.002-0.0020.0000.0000.0000.000
152A152PHE00.0420.02845.7630.0020.0020.0000.0000.0000.000
153A153SER0-0.010-0.01546.1480.0000.0000.0000.0000.0000.000
154A154LYS10.9360.94140.7150.0930.0930.0000.0000.0000.000
155A155THR00.0280.00641.153-0.002-0.0020.0000.0000.0000.000
156A156LYS10.9550.98442.8650.0580.0580.0000.0000.0000.000
157A157GLU-1-0.797-0.87642.259-0.086-0.0860.0000.0000.0000.000
158A158LEU0-0.038-0.02037.326-0.001-0.0010.0000.0000.0000.000
159A159ALA00.008-0.00740.6350.0010.0010.0000.0000.0000.000
160A160GLU-1-0.906-0.94843.084-0.053-0.0530.0000.0000.0000.000
161A161ARG10.7880.89734.4270.1080.1080.0000.0000.0000.000
162A162PHE0-0.031-0.05034.323-0.001-0.0010.0000.0000.0000.000
163A163GLN0-0.0040.00339.8580.0080.0080.0000.0000.0000.000
164A164PRO0-0.030-0.01740.6210.0040.0040.0000.0000.0000.000
165A165TYR0-0.059-0.03336.8010.0020.0020.0000.0000.0000.000
166A166GLY00.0290.01939.5310.0040.0040.0000.0000.0000.000
167A167ASN0-0.032-0.00341.921-0.004-0.0040.0000.0000.0000.000
168A168ILE00.0280.01339.7910.0000.0000.0000.0000.0000.000
169A169GLN00.0130.02643.7520.0010.0010.0000.0000.0000.000
170A170ALA0-0.036-0.01444.722-0.001-0.0010.0000.0000.0000.000
171A171VAL0-0.021-0.01146.0580.0020.0020.0000.0000.0000.000
172A172SER0-0.021-0.04147.323-0.005-0.0050.0000.0000.0000.000
173A173MET0-0.058-0.02444.0010.0020.0020.0000.0000.0000.000
174A174ASP-1-0.834-0.89148.672-0.040-0.0400.0000.0000.0000.000
175A175SER0-0.050-0.03751.2300.0020.0020.0000.0000.0000.000
176A176ILE0-0.043-0.02146.7950.0000.0000.0000.0000.0000.000
177A177PRO00.0290.02148.9750.0020.0020.0000.0000.0000.000
178A178LEU00.0320.01850.6800.0000.0000.0000.0000.0000.000
179A179GLN0-0.053-0.03248.1660.0010.0010.0000.0000.0000.000
180A180THR00.0410.02247.324-0.001-0.0010.0000.0000.0000.000
181A181TYR0-0.035-0.03643.898-0.001-0.0010.0000.0000.0000.000
182A182ASP-1-0.845-0.92642.155-0.001-0.0010.0000.0000.0000.000
183A183LEU0-0.032-0.01935.6720.0010.0010.0000.0000.0000.000
184A184VAL00.0220.02739.882-0.004-0.0040.0000.0000.0000.000
185A185ILE0-0.006-0.01834.3580.0000.0000.0000.0000.0000.000
186A186ASN0-0.031-0.01335.350-0.003-0.0030.0000.0000.0000.000
187A187ALA0-0.018-0.03934.173-0.003-0.0030.0000.0000.0000.000
188A188THR0-0.045-0.01734.622-0.009-0.0090.0000.0000.0000.000
189A189SER0-0.014-0.00532.289-0.003-0.0030.0000.0000.0000.000
190A190ALA0-0.031-0.02133.4360.0040.0040.0000.0000.0000.000
191A191GLY00.0480.01734.263-0.010-0.0100.0000.0000.0000.000
192A192LEU00.0030.01836.4020.0060.0060.0000.0000.0000.000
193A193SER00.000-0.00639.5780.0040.0040.0000.0000.0000.000
194A194GLY0-0.0110.00040.9030.0050.0050.0000.0000.0000.000
195A195GLY0-0.003-0.02037.537-0.004-0.0040.0000.0000.0000.000
196A196THR0-0.021-0.00236.737-0.003-0.0030.0000.0000.0000.000
197A197ALA0-0.007-0.00639.3790.0020.0020.0000.0000.0000.000
198A198SER0-0.003-0.00442.1990.0000.0000.0000.0000.0000.000
199A199VAL0-0.033-0.01543.097-0.002-0.0020.0000.0000.0000.000
200A200ASP-1-0.824-0.91446.013-0.029-0.0290.0000.0000.0000.000
201A201ALA00.0440.00748.3270.0000.0000.0000.0000.0000.000
202A202GLU-1-0.923-0.96849.401-0.017-0.0170.0000.0000.0000.000
203A203ILE0-0.058-0.01546.1040.0010.0010.0000.0000.0000.000
204A204LEU0-0.020-0.01843.1230.0010.0010.0000.0000.0000.000
205A205LYS10.9000.93646.1410.0150.0150.0000.0000.0000.000
206A206LEU0-0.0060.02047.8850.0030.0030.0000.0000.0000.000
207A207GLY0-0.0120.01044.2840.0010.0010.0000.0000.0000.000
208A208SER0-0.014-0.00343.6110.0020.0020.0000.0000.0000.000
209A209ALA00.0000.00238.5600.0040.0040.0000.0000.0000.000
210A210PHE0-0.0310.00138.581-0.004-0.0040.0000.0000.0000.000
211A211TYR00.018-0.03128.601-0.003-0.0030.0000.0000.0000.000
212A212ASP-1-0.795-0.87033.324-0.069-0.0690.0000.0000.0000.000
213A213MET00.0130.01230.1280.0000.0000.0000.0000.0000.000
214A214GLN0-0.0230.00528.397-0.013-0.0130.0000.0000.0000.000
215A215TYR00.0270.00823.1150.0080.0080.0000.0000.0000.000
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