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: 49M6N

Calculation Name: 4TM5-A-Xray372

Preferred Name:

Target Type:

Ligand Name: (2s)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid

ligand 3-letter code: LLP

PDB ID: 4TM5

Chain ID: A

ChEMBL ID:

UniProt ID: Q2T1L0

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 296
LigandResidueName
LigandFragmentNumber 0
LigandCharge LLP=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4125733.466583
FMO2-HF: Nuclear repulsion 4012692.1355
FMO2-HF: Total energy -113041.331082
FMO2-MP2: Total energy -113374.502414


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:6:ILE)


Summations of interaction energy for fragment #1(A:6:ILE)
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.
1.406-8.3216.4423.82-10.537-0.026
Interaction energy analysis for fragmet #1(A:6:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.002
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].
3A8PRO00.0060.0043.038-3.582-0.7140.220-1.395-1.693-0.004
4A9ILE00.0030.0183.7500.4930.7600.002-0.030-0.2390.000
5A10VAL0-0.016-0.0126.6100.0020.0020.0000.0000.0000.000
6A11TYR0-0.047-0.06210.4010.0900.0900.0000.0000.0000.000
7A12LEU0-0.014-0.01213.4460.0120.0120.0000.0000.0000.000
8A13SER00.0020.00816.3560.0300.0300.0000.0000.0000.000
9A14VAL00.0720.01619.7230.0040.0040.0000.0000.0000.000
10A15ALA0-0.006-0.00222.4560.0100.0100.0000.0000.0000.000
11A16SER00.000-0.00924.4760.0070.0070.0000.0000.0000.000
12A17ARG10.8590.93821.6090.0690.0690.0000.0000.0000.000
13A18GLU-1-0.875-0.91217.941-0.212-0.2120.0000.0000.0000.000
14A19GLU-1-0.924-0.95814.191-0.084-0.0840.0000.0000.0000.000
15A20LEU0-0.048-0.0409.372-0.041-0.0410.0000.0000.0000.000
16A21VAL00.0260.0219.3160.0360.0360.0000.0000.0000.000
17A22PRO00.0430.0266.229-0.262-0.2620.0000.0000.0000.000
18A23LEU00.0130.0097.4470.1450.1450.0000.0000.0000.000
19A24SER0-0.090-0.0568.5200.0820.0820.0000.0000.0000.000
20A25GLU-1-0.969-0.99710.3050.3360.3360.0000.0000.0000.000
21A26ALA0-0.0230.01412.376-0.016-0.0160.0000.0000.0000.000
22A27ARG10.9290.94814.047-0.086-0.0860.0000.0000.0000.000
23A28VAL00.0330.02617.682-0.008-0.0080.0000.0000.0000.000
24A29PRO0-0.003-0.00820.9570.0200.0200.0000.0000.0000.000
25A30VAL00.0570.01824.383-0.010-0.0100.0000.0000.0000.000
26A31LEU0-0.030-0.02326.490-0.003-0.0030.0000.0000.0000.000
27A32ASP-1-0.754-0.83225.111-0.115-0.1150.0000.0000.0000.000
28A33ARG10.8070.86627.2130.0710.0710.0000.0000.0000.000
29A34GLY0-0.001-0.00225.452-0.001-0.0010.0000.0000.0000.000
30A35PHE0-0.037-0.01124.4760.0000.0000.0000.0000.0000.000
31A36ILE0-0.061-0.03026.4640.0080.0080.0000.0000.0000.000
32A37PHE0-0.079-0.05830.0410.0090.0090.0000.0000.0000.000
33A38GLY00.0650.06028.053-0.001-0.0010.0000.0000.0000.000
34A39ASP-1-0.804-0.86429.131-0.096-0.0960.0000.0000.0000.000
35A40GLY00.0620.00326.684-0.002-0.0020.0000.0000.0000.000
36A41VAL0-0.084-0.02226.1630.0070.0070.0000.0000.0000.000
37A42TYR00.005-0.00821.674-0.005-0.0050.0000.0000.0000.000
38A43GLU-1-0.763-0.85121.660-0.233-0.2330.0000.0000.0000.000
39A44VAL0-0.010-0.00818.375-0.026-0.0260.0000.0000.0000.000
40A45VAL0-0.018-0.00118.5360.0330.0330.0000.0000.0000.000
41A46PRO00.0140.01817.527-0.067-0.0670.0000.0000.0000.000
42A47ILE0-0.020-0.02314.2850.0320.0320.0000.0000.0000.000
43A48TYR0-0.020-0.05715.198-0.064-0.0640.0000.0000.0000.000
44A49ALA00.009-0.01513.034-0.008-0.0080.0000.0000.0000.000
45A50GLU-1-0.932-0.95415.100-0.310-0.3100.0000.0000.0000.000
46A51GLY00.001-0.01014.2400.0110.0110.0000.0000.0000.000
47A52ALA00.0440.01611.699-0.091-0.0910.0000.0000.0000.000
48A53ARG10.8980.97412.6920.3360.3360.0000.0000.0000.000
49A54ARG10.8950.9468.6601.2641.2640.0000.0000.0000.000
50A55ALA0-0.014-0.00515.1120.0290.0290.0000.0000.0000.000
51A56PRO0-0.021-0.01418.224-0.010-0.0100.0000.0000.0000.000
52A57PHE00.0290.02119.5910.0280.0280.0000.0000.0000.000
53A58ARG10.7990.88722.6400.2110.2110.0000.0000.0000.000
54A59ILE00.0190.00319.9490.0090.0090.0000.0000.0000.000
55A60ALA00.0130.00423.7190.0080.0080.0000.0000.0000.000
56A61GLN00.0500.01527.102-0.001-0.0010.0000.0000.0000.000
57A62HIS00.0310.00523.6590.0060.0060.0000.0000.0000.000
58A63LEU0-0.0060.00322.3270.0080.0080.0000.0000.0000.000
59A64ALA0-0.0090.00125.9920.0160.0160.0000.0000.0000.000
60A65ARG10.7070.82225.4330.2370.2370.0000.0000.0000.000
61A66LEU00.0450.03223.3890.0130.0130.0000.0000.0000.000
62A67ALA00.0550.03127.2390.0140.0140.0000.0000.0000.000
63A68ARG10.8580.92530.0620.1730.1730.0000.0000.0000.000
64A69SER00.0480.00828.7520.0150.0150.0000.0000.0000.000
65A70LEU00.0440.02026.8920.0100.0100.0000.0000.0000.000
66A71LYS10.9390.97430.7630.1280.1280.0000.0000.0000.000
67A72LYS10.7900.87433.7580.1250.1250.0000.0000.0000.000
68A73ILE0-0.0040.02430.1370.0080.0080.0000.0000.0000.000
69A74GLY0-0.002-0.00534.5920.0050.0050.0000.0000.0000.000
70A75ILE0-0.043-0.01528.8020.0060.0060.0000.0000.0000.000
71A76ALA0-0.034-0.01931.849-0.005-0.0050.0000.0000.0000.000
72A77ASP-1-0.790-0.91027.485-0.186-0.1860.0000.0000.0000.000
73A78PRO0-0.036-0.00424.6860.0050.0050.0000.0000.0000.000
74A79HIS10.8470.92921.6410.2160.2160.0000.0000.0000.000
75A80ASP-1-0.777-0.86726.146-0.176-0.1760.0000.0000.0000.000
76A81GLU-1-0.860-0.95826.026-0.225-0.2250.0000.0000.0000.000
77A82ALA00.0280.00824.923-0.022-0.0220.0000.0000.0000.000
78A83GLY00.0130.00623.211-0.020-0.0200.0000.0000.0000.000
79A84TRP0-0.022-0.04320.508-0.037-0.0370.0000.0000.0000.000
80A85ARG10.8790.94320.2000.2210.2210.0000.0000.0000.000
81A86ALA00.0100.01119.339-0.037-0.0370.0000.0000.0000.000
82A87LEU0-0.062-0.01016.163-0.034-0.0340.0000.0000.0000.000
83A88VAL00.008-0.00815.383-0.059-0.0590.0000.0000.0000.000
84A89ALA00.0160.01414.531-0.082-0.0820.0000.0000.0000.000
85A90ARG10.9810.99812.6970.3010.3010.0000.0000.0000.000
86A91LEU0-0.034-0.00710.271-0.071-0.0710.0000.0000.0000.000
87A92VAL00.0270.0009.757-0.213-0.2130.0000.0000.0000.000
88A93ASP-1-0.927-0.9559.275-0.871-0.8710.0000.0000.0000.000
89A94ALA0-0.076-0.0397.399-0.107-0.1070.0000.0000.0000.000
90A95ASN0-0.057-0.0465.090-0.769-0.7690.0000.0000.0000.000
91A96ALA00.0310.0185.583-0.428-0.4280.0000.0000.0000.000
92A97ALA00.001-0.0072.458-1.018-0.1230.734-0.443-1.1870.002
93A98ALA00.017-0.0072.289-2.149-5.78315.201-5.067-6.500-0.012
94A99LEU0-0.122-0.0552.5319.987-0.1350.28510.755-0.918-0.012
95A100GLY00.0320.0225.4290.2520.2520.0000.0000.0000.000
96A101ASP-1-0.896-0.9656.308-0.722-0.7220.0000.0000.0000.000
97A102GLY0-0.069-0.0419.8760.0180.0180.0000.0000.0000.000
98A103GLN0-0.075-0.0178.1050.0950.0950.0000.0000.0000.000
99A104HIS00.0670.04710.776-0.089-0.0890.0000.0000.0000.000
100A105ALA00.0360.01211.009-0.133-0.1330.0000.0000.0000.000
101A106ILE0-0.022-0.00512.6150.1520.1520.0000.0000.0000.000
102A107VAL00.005-0.00313.258-0.106-0.1060.0000.0000.0000.000
103A108TYR0-0.050-0.03614.7540.0850.0850.0000.0000.0000.000
104A109ILE00.0220.00516.200-0.023-0.0230.0000.0000.0000.000
105A110GLN00.0430.04018.9260.0140.0140.0000.0000.0000.000
106A111VAL0-0.014-0.00421.139-0.001-0.0010.0000.0000.0000.000
107A112THR0-0.015-0.03723.7550.0100.0100.0000.0000.0000.000
108A113ARG10.7780.85826.2800.0930.0930.0000.0000.0000.000
109A114GLY00.0430.03526.8820.0070.0070.0000.0000.0000.000
110A115VAL0-0.043-0.01326.0970.0070.0070.0000.0000.0000.000
111A116ALA0-0.0050.00029.0250.0020.0020.0000.0000.0000.000
112A117LYS10.9420.97332.7050.0240.0240.0000.0000.0000.000
113A118ARG10.9880.99634.5970.0260.0260.0000.0000.0000.000
114A119GLY0-0.002-0.01535.8180.0060.0060.0000.0000.0000.000
115A120HIS00.0650.03537.080-0.002-0.0020.0000.0000.0000.000
116A121ALA00.0030.02237.574-0.005-0.0050.0000.0000.0000.000
117A122PHE00.0160.00136.4390.0000.0000.0000.0000.0000.000
118A123PRO00.0070.00833.5840.0040.0040.0000.0000.0000.000
119A124ALA00.008-0.00436.439-0.004-0.0040.0000.0000.0000.000
120A125ASN0-0.045-0.03035.585-0.001-0.0010.0000.0000.0000.000
121A126ALA00.0010.01731.8420.0000.0000.0000.0000.0000.000
122A127VAL0-0.001-0.00126.798-0.003-0.0030.0000.0000.0000.000
123A128PRO0-0.030-0.01526.4480.0020.0020.0000.0000.0000.000
124A129THR0-0.041-0.02821.5620.0010.0010.0000.0000.0000.000
125A130VAL0-0.025-0.01219.220-0.006-0.0060.0000.0000.0000.000
126A131PHE00.0070.00313.5650.0070.0070.0000.0000.0000.000
127A132ALA00.0000.00015.3200.0110.0110.0000.0000.0000.000
128A133MET00.0210.01410.253-0.027-0.0270.0000.0000.0000.000
129A134ALA00.0260.0169.2820.1080.1080.0000.0000.0000.000
130A135SER0-0.028-0.0118.682-0.216-0.2160.0000.0000.0000.000
131A136PRO00.0600.0217.8430.1360.1360.0000.0000.0000.000
132A137LEU0-0.054-0.00910.2760.1430.1430.0000.0000.0000.000
133A138ALA0-0.022-0.01413.904-0.021-0.0210.0000.0000.0000.000
134A139LEU00.002-0.00115.6490.0380.0380.0000.0000.0000.000
135A140PRO0-0.0050.00819.0480.0110.0110.0000.0000.0000.000
136A141THR00.0230.00520.1840.0010.0010.0000.0000.0000.000
137A142ASP-1-0.848-0.92922.417-0.207-0.2070.0000.0000.0000.000
138A143ALA0-0.021-0.01025.0000.0140.0140.0000.0000.0000.000
139A144GLN00.0450.02023.159-0.008-0.0080.0000.0000.0000.000
140A145ARG10.9110.96223.2670.2370.2370.0000.0000.0000.000
141A146ALA0-0.032-0.00728.3710.0090.0090.0000.0000.0000.000
142A147GLN0-0.036-0.02630.0210.0090.0090.0000.0000.0000.000
143A148GLY00.0370.03430.5600.0090.0090.0000.0000.0000.000
144A149VAL0-0.062-0.03227.3590.0010.0010.0000.0000.0000.000
145A150HIS00.0110.01030.6420.0060.0060.0000.0000.0000.000
146A151CYS0-0.0270.00231.557-0.011-0.0110.0000.0000.0000.000
147A152VAL00.0770.05533.6590.0060.0060.0000.0000.0000.000
148A153THR0-0.058-0.05435.819-0.006-0.0060.0000.0000.0000.000
149A154ALA0-0.005-0.00337.2160.0050.0050.0000.0000.0000.000
150A155GLU-1-0.912-0.96639.110-0.062-0.0620.0000.0000.0000.000
151A156ASP-1-0.776-0.86337.883-0.092-0.0920.0000.0000.0000.000
152A157ARG10.8840.94238.4180.0560.0560.0000.0000.0000.000
153A158ARG10.7960.86933.2130.1090.1090.0000.0000.0000.000
154A159TRP00.004-0.00233.4780.0100.0100.0000.0000.0000.000
155A160LEU00.002-0.01038.216-0.003-0.0030.0000.0000.0000.000
156A161HIS00.0020.00236.6390.0000.0000.0000.0000.0000.000
157A162CYS0-0.051-0.01534.346-0.006-0.0060.0000.0000.0000.000
158A163ASP-1-0.786-0.86633.620-0.114-0.1140.0000.0000.0000.000
159A164ILE0-0.078-0.04130.942-0.008-0.0080.0000.0000.0000.000
160A165LLP-1-0.712-0.79624.467-0.279-0.2790.0000.0000.0000.000
161A166SER00.015-0.00227.465-0.010-0.0100.0000.0000.0000.000
162A167VAL00.0410.01023.620-0.006-0.0060.0000.0000.0000.000
163A168SER0-0.048-0.02926.4870.0120.0120.0000.0000.0000.000
164A169LEU0-0.0090.00424.9380.0060.0060.0000.0000.0000.000
165A170LEU00.0040.01028.708-0.001-0.0010.0000.0000.0000.000
166A171GLY00.0250.00330.4360.0030.0030.0000.0000.0000.000
167A172ASN0-0.002-0.01928.5420.0100.0100.0000.0000.0000.000
168A173VAL00.0060.00725.895-0.003-0.0030.0000.0000.0000.000
169A174LEU0-0.026-0.01128.3120.0040.0040.0000.0000.0000.000
170A175MET0-0.0070.00731.4250.0040.0040.0000.0000.0000.000
171A176ALA00.0220.01526.2550.0010.0010.0000.0000.0000.000
172A177GLN0-0.063-0.03827.060-0.009-0.0090.0000.0000.0000.000
173A178HIS00.0170.01228.7760.0070.0070.0000.0000.0000.000
174A179ALA00.0100.00829.1400.0040.0040.0000.0000.0000.000
175A180ALA00.0020.00226.4480.0030.0030.0000.0000.0000.000
176A181GLU-1-0.951-0.97728.228-0.036-0.0360.0000.0000.0000.000
177A182HIS0-0.082-0.03831.0740.0120.0120.0000.0000.0000.000
178A183ASP-1-0.929-0.95029.579-0.059-0.0590.0000.0000.0000.000
179A184ALA0-0.056-0.02430.140-0.005-0.0050.0000.0000.0000.000
180A185ALA0-0.064-0.04027.035-0.007-0.0070.0000.0000.0000.000
181A186GLU-1-0.771-0.86527.359-0.166-0.1660.0000.0000.0000.000
182A187THR00.006-0.00729.9960.0120.0120.0000.0000.0000.000
183A188ILE0-0.029-0.02633.231-0.007-0.0070.0000.0000.0000.000
184A189GLN0-0.038-0.03433.9490.0120.0120.0000.0000.0000.000
185A190LEU00.0160.01437.698-0.002-0.0020.0000.0000.0000.000
186A191ARG10.9090.94640.4710.0720.0720.0000.0000.0000.000
187A192ASP-1-0.863-0.91743.542-0.059-0.0590.0000.0000.0000.000
188A193GLY00.0100.00846.1490.0010.0010.0000.0000.0000.000
189A194ASN0-0.005-0.01044.5970.0010.0010.0000.0000.0000.000
190A195VAL00.005-0.00338.569-0.001-0.0010.0000.0000.0000.000
191A196THR0-0.045-0.03438.107-0.001-0.0010.0000.0000.0000.000
192A197GLU-1-0.782-0.88432.897-0.141-0.1410.0000.0000.0000.000
193A198GLY00.0290.03131.4900.0080.0080.0000.0000.0000.000
194A199SER0-0.082-0.06228.659-0.004-0.0040.0000.0000.0000.000
195A200SER0-0.056-0.03725.469-0.011-0.0110.0000.0000.0000.000
196A201SER0-0.044-0.02926.597-0.016-0.0160.0000.0000.0000.000
197A202ASN0-0.020-0.01428.9980.0030.0030.0000.0000.0000.000
198A203VAL00.0440.01532.031-0.006-0.0060.0000.0000.0000.000
199A204TRP0-0.015-0.00732.5260.0070.0070.0000.0000.0000.000
200A205ILE0-0.004-0.00336.9740.0010.0010.0000.0000.0000.000
201A206VAL00.0050.01338.943-0.001-0.0010.0000.0000.0000.000
202A207LYS10.8650.92341.6570.0710.0710.0000.0000.0000.000
203A208ASN0-0.031-0.02345.3620.0010.0010.0000.0000.0000.000
204A209GLY0-0.0010.00244.4550.0010.0010.0000.0000.0000.000
205A210GLU-1-0.952-0.96644.259-0.079-0.0790.0000.0000.0000.000
206A211LEU00.0040.01037.2140.0000.0000.0000.0000.0000.000
207A212ILE0-0.020-0.02140.8840.0030.0030.0000.0000.0000.000
208A213ALA00.0170.00938.173-0.004-0.0040.0000.0000.0000.000
209A214PRO00.0460.03438.3950.0050.0050.0000.0000.0000.000
210A215PRO00.0060.00840.230-0.006-0.0060.0000.0000.0000.000
211A216ARG10.8870.95136.9660.1210.1210.0000.0000.0000.000
212A217SER00.016-0.00238.9960.0070.0070.0000.0000.0000.000
213A218ASN00.0190.01538.489-0.005-0.0050.0000.0000.0000.000
214A219ARG10.8450.90638.7280.0710.0710.0000.0000.0000.000
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