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: 438YN

Calculation Name: 1M1C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M1C

Chain ID: A

ChEMBL ID:

UniProt ID: P32503

Base Structure: X-ray

Registration Date: 2023-06-19

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 OptAll
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 651
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -15311857.20409
FMO2-HF: Nuclear repulsion 15055347.485833
FMO2-HF: Total energy -256509.718256
FMO2-MP2: Total energy -257257.713061


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.
-38.914-23.03823.021-13.159-25.739-0.101
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 : -0.022 / q_NPA : -0.008
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].
3A3ARG10.8920.9563.414-1.9700.1080.022-0.924-1.1750.005
4A4PHE0-0.0080.0143.026-0.989-0.0700.080-0.251-0.7480.001
5A5VAL00.0200.0004.109-0.464-0.0520.000-0.116-0.2970.000
6A6THR0-0.063-0.0446.4040.4070.4070.0000.0000.0000.000
7A7LYS10.8520.9078.124-0.328-0.3280.0000.0000.0000.000
8A8ASN00.0160.0127.3900.0870.0870.0000.0000.0000.000
9A9SER0-0.007-0.00910.647-0.009-0.0090.0000.0000.0000.000
10A10GLN0-0.048-0.03813.074-0.027-0.0270.0000.0000.0000.000
11A11ASP-1-0.808-0.87711.5050.1600.1600.0000.0000.0000.000
12A12LYS10.9180.97913.743-0.070-0.0700.0000.0000.0000.000
13A13SER0-0.082-0.04114.5360.0040.0040.0000.0000.0000.000
14A14SER00.0570.01710.178-0.013-0.0130.0000.0000.0000.000
15A15ASP-1-0.942-0.95312.2240.0190.0190.0000.0000.0000.000
16A16LEU0-0.027-0.0098.430-0.002-0.0020.0000.0000.0000.000
17A17PHE00.024-0.00111.089-0.038-0.0380.0000.0000.0000.000
18A18SER0-0.020-0.01111.5190.0860.0860.0000.0000.0000.000
19A19ILE00.0320.02212.078-0.002-0.0020.0000.0000.0000.000
20A20CYS0-0.051-0.00214.107-0.065-0.0650.0000.0000.0000.000
21A21SER0-0.051-0.02817.6430.0260.0260.0000.0000.0000.000
22A22ASP-1-0.847-0.92920.3510.1020.1020.0000.0000.0000.000
23A23ARG10.8580.92823.894-0.108-0.1080.0000.0000.0000.000
24A24GLY00.0830.04920.3310.0010.0010.0000.0000.0000.000
25A25THR0-0.090-0.05120.2460.0170.0170.0000.0000.0000.000
26A26PHE00.0240.00614.083-0.011-0.0110.0000.0000.0000.000
27A27VAL0-0.025-0.01919.8040.0030.0030.0000.0000.0000.000
28A28ALA00.0500.03616.481-0.006-0.0060.0000.0000.0000.000
29A29HIS0-0.014-0.01918.575-0.012-0.0120.0000.0000.0000.000
30A30ASN00.021-0.00618.524-0.001-0.0010.0000.0000.0000.000
31A31ARG10.9210.97421.554-0.067-0.0670.0000.0000.0000.000
32A32VAL00.0200.00723.678-0.002-0.0020.0000.0000.0000.000
33A33ARG10.8190.89525.357-0.052-0.0520.0000.0000.0000.000
34A34THR00.0100.00927.3260.0040.0040.0000.0000.0000.000
35A35ASP-1-0.815-0.90529.6950.0480.0480.0000.0000.0000.000
36A36PHE00.007-0.01232.0320.0030.0030.0000.0000.0000.000
37A37LYS10.8250.90831.028-0.059-0.0590.0000.0000.0000.000
38A38PHE00.0360.00536.7930.0020.0020.0000.0000.0000.000
39A39ASP-1-0.798-0.87040.0000.0340.0340.0000.0000.0000.000
40A40ASN0-0.042-0.02440.561-0.001-0.0010.0000.0000.0000.000
41A41LEU0-0.0140.01441.245-0.001-0.0010.0000.0000.0000.000
42A42VAL00.005-0.01335.6610.0020.0020.0000.0000.0000.000
43A43PHE0-0.0050.00937.147-0.002-0.0020.0000.0000.0000.000
44A44ASN0-0.032-0.02433.1350.0020.0020.0000.0000.0000.000
45A45ARG10.8840.96730.834-0.068-0.0680.0000.0000.0000.000
46A46VAL00.0220.01029.8610.0040.0040.0000.0000.0000.000
47A47TYR0-0.054-0.05427.039-0.001-0.0010.0000.0000.0000.000
48A48GLY0-0.051-0.02126.329-0.001-0.0010.0000.0000.0000.000
49A49VAL0-0.0150.01321.919-0.001-0.0010.0000.0000.0000.000
50A50SER0-0.039-0.02421.7500.0020.0020.0000.0000.0000.000
51A51GLN00.0380.02017.670-0.012-0.0120.0000.0000.0000.000
52A52LYS10.8530.93219.218-0.132-0.1320.0000.0000.0000.000
53A53PHE00.0360.01814.1300.0030.0030.0000.0000.0000.000
54A54THR00.0310.02117.895-0.022-0.0220.0000.0000.0000.000
55A55LEU00.0140.01114.5370.0310.0310.0000.0000.0000.000
56A56VAL0-0.037-0.00517.0770.0080.0080.0000.0000.0000.000
57A57GLY0-0.014-0.00619.1650.0100.0100.0000.0000.0000.000
58A58ASN0-0.007-0.01720.0040.0070.0070.0000.0000.0000.000
59A59PRO00.0130.01816.119-0.014-0.0140.0000.0000.0000.000
60A60THR00.0170.00618.912-0.012-0.0120.0000.0000.0000.000
61A61VAL0-0.023-0.02016.742-0.002-0.0020.0000.0000.0000.000
62A62CYS0-0.0330.00319.241-0.018-0.0180.0000.0000.0000.000
63A63PHE00.021-0.01117.321-0.001-0.0010.0000.0000.0000.000
64A64ASN0-0.015-0.00919.990-0.006-0.0060.0000.0000.0000.000
65A65GLU-1-0.904-0.93720.457-0.072-0.0720.0000.0000.0000.000
66A66GLY00.0720.04018.9570.0060.0060.0000.0000.0000.000
67A67SER0-0.025-0.01317.7860.0090.0090.0000.0000.0000.000
68A68SER0-0.026-0.02118.122-0.023-0.0230.0000.0000.0000.000
69A69TYR0-0.025-0.00714.879-0.004-0.0040.0000.0000.0000.000
70A70LEU00.0210.01416.654-0.030-0.0300.0000.0000.0000.000
71A71GLU-1-0.865-0.93814.253-0.368-0.3680.0000.0000.0000.000
72A72GLY00.0100.01715.367-0.060-0.0600.0000.0000.0000.000
73A73ILE0-0.034-0.01816.8160.0240.0240.0000.0000.0000.000
74A74ALA0-0.018-0.00820.475-0.013-0.0130.0000.0000.0000.000
75A75LYS10.8080.85821.4870.2730.2730.0000.0000.0000.000
76A76LYS10.8020.90724.3880.1310.1310.0000.0000.0000.000
77A77TYR0-0.020-0.06025.5340.0120.0120.0000.0000.0000.000
78A78LEU0-0.0420.00021.8340.0000.0000.0000.0000.0000.000
79A79THR0-0.033-0.01025.3880.0140.0140.0000.0000.0000.000
80A80LEU0-0.023-0.02625.038-0.011-0.0110.0000.0000.0000.000
81A81ASP-1-0.866-0.92622.230-0.163-0.1630.0000.0000.0000.000
82A82GLY00.0370.01120.888-0.001-0.0010.0000.0000.0000.000
83A83GLY00.0240.01921.6490.0000.0000.0000.0000.0000.000
84A84LEU0-0.007-0.00624.985-0.008-0.0080.0000.0000.0000.000
85A85ALA00.0300.02826.6060.0140.0140.0000.0000.0000.000
86A86ILE00.008-0.01929.5770.0020.0020.0000.0000.0000.000
87A87ASP-1-0.814-0.89431.679-0.095-0.0950.0000.0000.0000.000
88A88ASN0-0.055-0.04831.2720.0040.0040.0000.0000.0000.000
89A89VAL0-0.014-0.00228.9360.0010.0010.0000.0000.0000.000
90A90LEU0-0.023-0.02231.9620.0050.0050.0000.0000.0000.000
91A91ASN0-0.076-0.03135.5450.0060.0060.0000.0000.0000.000
92A92GLU-1-0.695-0.79131.699-0.113-0.1130.0000.0000.0000.000
93A93LEU0-0.038-0.02533.8580.0030.0030.0000.0000.0000.000
94A94ARG10.9160.95836.0820.0730.0730.0000.0000.0000.000
95A95SER0-0.060-0.02038.0880.0030.0030.0000.0000.0000.000
96A96THR0-0.014-0.02033.7570.0020.0020.0000.0000.0000.000
97A97CYS0-0.053-0.02035.095-0.001-0.0010.0000.0000.0000.000
98A98GLY00.0330.02537.8450.0030.0030.0000.0000.0000.000
99A99ILE0-0.037-0.01937.8110.0030.0030.0000.0000.0000.000
100A100PRO00.0310.01441.1770.0000.0000.0000.0000.0000.000
101A101GLY00.0390.01543.181-0.002-0.0020.0000.0000.0000.000
102A102ASN00.0370.00443.781-0.003-0.0030.0000.0000.0000.000
103A103ALA00.0230.02642.4190.0000.0000.0000.0000.0000.000
104A104VAL00.0270.00038.824-0.001-0.0010.0000.0000.0000.000
105A105ALA0-0.0110.00539.504-0.002-0.0020.0000.0000.0000.000
106A106SER0-0.013-0.00241.5480.0000.0000.0000.0000.0000.000
107A107HIS10.8900.94133.7660.0780.0780.0000.0000.0000.000
108A108ALA00.011-0.00336.944-0.002-0.0020.0000.0000.0000.000
109A109TYR0-0.008-0.00337.819-0.001-0.0010.0000.0000.0000.000
110A110ASN0-0.014-0.00437.2600.0010.0010.0000.0000.0000.000
111A111ILE0-0.001-0.00332.534-0.001-0.0010.0000.0000.0000.000
112A112THR0-0.070-0.03334.198-0.003-0.0030.0000.0000.0000.000
113A113SER00.0120.01335.119-0.001-0.0010.0000.0000.0000.000
114A114TRP0-0.062-0.01230.501-0.002-0.0020.0000.0000.0000.000
115A115ARG10.8730.91627.4130.0630.0630.0000.0000.0000.000
116A116TRP00.0390.00925.469-0.006-0.0060.0000.0000.0000.000
117A117TYR0-0.033-0.03219.128-0.020-0.0200.0000.0000.0000.000
118A118ASP-1-0.732-0.86417.778-0.254-0.2540.0000.0000.0000.000
119A119ASN00.006-0.02114.871-0.045-0.0450.0000.0000.0000.000
120A120HIS10.8610.90413.7420.2840.2840.0000.0000.0000.000
121A121VAL00.0240.02010.0000.0210.0210.0000.0000.0000.000
122A122ALA00.0740.03911.6690.0460.0460.0000.0000.0000.000
123A123LEU00.0130.02214.3070.0340.0340.0000.0000.0000.000
124A124LEU0-0.049-0.0339.5430.0140.0140.0000.0000.0000.000
125A125MET00.0280.0209.8530.0230.0230.0000.0000.0000.000
126A126ASN00.0310.02110.8190.1040.1040.0000.0000.0000.000
127A127MET0-0.029-0.00812.6360.0180.0180.0000.0000.0000.000
128A128LEU00.004-0.0016.0710.0160.0160.0000.0000.0000.000
129A129ARG10.8050.90110.482-0.084-0.0840.0000.0000.0000.000
130A130ALA00.0380.02712.701-0.002-0.0020.0000.0000.0000.000
131A131TYR00.003-0.01610.980-0.009-0.0090.0000.0000.0000.000
132A132HIS0-0.043-0.0478.4390.1580.1580.0000.0000.0000.000
133A133LEU00.0360.02513.750-0.016-0.0160.0000.0000.0000.000
134A134GLN00.004-0.00117.165-0.021-0.0210.0000.0000.0000.000
135A135VAL0-0.044-0.03014.567-0.021-0.0210.0000.0000.0000.000
136A136LEU00.0050.00016.208-0.014-0.0140.0000.0000.0000.000
137A137THR0-0.0080.00019.291-0.022-0.0220.0000.0000.0000.000
138A138GLU-1-0.789-0.85320.1750.0560.0560.0000.0000.0000.000
139A139GLN0-0.079-0.05417.4710.0000.0000.0000.0000.0000.000
140A140GLY0-0.028-0.00122.389-0.004-0.0040.0000.0000.0000.000
141A141GLN0-0.021-0.02120.8340.0180.0180.0000.0000.0000.000
142A142TYR0-0.037-0.00420.4760.0110.0110.0000.0000.0000.000
143A143SER0-0.018-0.01222.754-0.012-0.0120.0000.0000.0000.000
144A144ALA00.0610.03223.4770.0110.0110.0000.0000.0000.000
145A145GLY0-0.021-0.00223.1090.0110.0110.0000.0000.0000.000
146A146ASP-1-0.820-0.90823.9130.1030.1030.0000.0000.0000.000
147A147ILE0-0.014-0.01023.7860.0170.0170.0000.0000.0000.000
148A148PRO0-0.025-0.01323.913-0.012-0.0120.0000.0000.0000.000
149A149MET00.0070.06326.901-0.002-0.0020.0000.0000.0000.000
150A150TYR00.0090.00728.776-0.001-0.0010.0000.0000.0000.000
151A151HIS00.014-0.02930.743-0.006-0.0060.0000.0000.0000.000
152A152ASP-1-0.761-0.87333.7240.0740.0740.0000.0000.0000.000
153A153GLY0-0.036-0.00835.451-0.003-0.0030.0000.0000.0000.000
154A154HIS10.8010.87737.364-0.064-0.0640.0000.0000.0000.000
155A155VAL00.0170.01234.859-0.002-0.0020.0000.0000.0000.000
156A156LYS10.8630.90535.136-0.070-0.0700.0000.0000.0000.000
157A157ILE00.0330.02929.444-0.002-0.0020.0000.0000.0000.000
158A158LYS10.9640.96430.734-0.071-0.0710.0000.0000.0000.000
159A159LEU00.0460.02826.488-0.005-0.0050.0000.0000.0000.000
160A160PRO0-0.026-0.01429.4010.0010.0010.0000.0000.0000.000
161A161VAL0-0.0020.00225.5960.0070.0070.0000.0000.0000.000
162A162THR0-0.014-0.00827.123-0.006-0.0060.0000.0000.0000.000
163A163ILE0-0.0220.00926.328-0.009-0.0090.0000.0000.0000.000
164A164ASP-1-0.775-0.86828.9430.0850.0850.0000.0000.0000.000
165A165ASP-1-0.830-0.93526.6820.1180.1180.0000.0000.0000.000
166A166THR0-0.105-0.07629.361-0.004-0.0040.0000.0000.0000.000
167A167ALA0-0.024-0.01332.661-0.004-0.0040.0000.0000.0000.000
168A168GLY00.0100.01829.494-0.003-0.0030.0000.0000.0000.000
169A169PRO0-0.033-0.01326.336-0.004-0.0040.0000.0000.0000.000
170A170THR00.019-0.00326.6930.0070.0070.0000.0000.0000.000
171A171GLN0-0.056-0.02425.7410.0030.0030.0000.0000.0000.000
172A172PHE0-0.0090.00218.8720.0010.0010.0000.0000.0000.000
173A173ALA00.009-0.01123.319-0.013-0.0130.0000.0000.0000.000
174A174TRP0-0.007-0.01821.4770.0100.0100.0000.0000.0000.000
175A175PRO00.0080.02420.345-0.001-0.0010.0000.0000.0000.000
176A176SER00.0440.03623.4610.0000.0000.0000.0000.0000.000
177A177ASP-1-0.789-0.87325.8210.0410.0410.0000.0000.0000.000
178A178ARG10.7820.89429.366-0.015-0.0150.0000.0000.0000.000
179A179SER0-0.025-0.02932.1650.0000.0000.0000.0000.0000.000
180A180THR0-0.049-0.03532.212-0.002-0.0020.0000.0000.0000.000
181A181ASP-1-0.857-0.93328.6030.0230.0230.0000.0000.0000.000
182A182SER00.0030.01731.746-0.001-0.0010.0000.0000.0000.000
183A183TYR00.025-0.01527.3630.0010.0010.0000.0000.0000.000
184A184PRO0-0.019-0.00925.599-0.002-0.0020.0000.0000.0000.000
185A185ASP-1-0.808-0.86928.865-0.037-0.0370.0000.0000.0000.000
186A186TRP00.0610.01526.842-0.009-0.0090.0000.0000.0000.000
187A187ALA00.0210.00529.3200.0030.0030.0000.0000.0000.000
188A188GLN00.004-0.00629.201-0.012-0.0120.0000.0000.0000.000
189A189PHE0-0.043-0.03229.2160.0030.0030.0000.0000.0000.000
190A190SER00.0760.01429.718-0.008-0.0080.0000.0000.0000.000
191A191GLU-1-0.899-0.90932.190-0.071-0.0710.0000.0000.0000.000
192A192SER00.004-0.01032.243-0.008-0.0080.0000.0000.0000.000
193A193PHE0-0.022-0.02332.196-0.006-0.0060.0000.0000.0000.000
194A194PRO00.0040.03430.0170.0040.0040.0000.0000.0000.000
195A195SER0-0.022-0.04232.1330.0040.0040.0000.0000.0000.000
196A196ILE00.0180.00732.2880.0050.0050.0000.0000.0000.000
197A197ASP-1-0.743-0.85229.494-0.087-0.0870.0000.0000.0000.000
198A198VAL00.0190.02928.418-0.004-0.0040.0000.0000.0000.000
199A199PRO00.0220.01723.385-0.009-0.0090.0000.0000.0000.000
200A200TYR00.0370.00924.4900.0090.0090.0000.0000.0000.000
201A201LEU00.0130.03719.942-0.023-0.0230.0000.0000.0000.000
202A202ASP-1-0.762-0.87220.769-0.146-0.1460.0000.0000.0000.000
203A203VAL00.0360.01119.841-0.021-0.0210.0000.0000.0000.000
204A204ARG10.8280.90221.8070.1500.1500.0000.0000.0000.000
205A205PRO0-0.0080.01220.3270.0100.0100.0000.0000.0000.000
206A206LEU0-0.050-0.01718.241-0.002-0.0020.0000.0000.0000.000
207A207THR0-0.003-0.00621.9630.0090.0090.0000.0000.0000.000
208A208VAL00.1130.04423.987-0.001-0.0010.0000.0000.0000.000
209A209THR00.0340.01623.7290.0000.0000.0000.0000.0000.000
210A210GLU-1-0.758-0.82519.632-0.111-0.1110.0000.0000.0000.000
211A211VAL00.009-0.00320.583-0.002-0.0020.0000.0000.0000.000
212A212ASN00.0370.00422.6410.0040.0040.0000.0000.0000.000
213A213PHE00.0310.01415.4020.0020.0020.0000.0000.0000.000
214A214VAL0-0.019-0.01617.7280.0040.0040.0000.0000.0000.000
215A215LEU0-0.005-0.00119.7620.0010.0010.0000.0000.0000.000
216A216MET0-0.0070.02922.0780.0070.0070.0000.0000.0000.000
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