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: Q1JLY

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 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 651
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -15319268.08112
FMO2-HF: Nuclear repulsion 15062769.400042
FMO2-HF: Total energy -256498.681078
FMO2-MP2: Total energy -257248.101428


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.
-35.25-17.33119.167-12.122-24.965-0.092
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 : -0.031 / q_NPA : 0.001
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].
3A3ARG10.9640.9793.329-2.1190.0470.017-0.959-1.2250.004
4A4PHE00.0400.0132.678-2.154-0.9370.369-0.392-1.1940.002
5A5VAL00.0370.0164.239-0.966-0.517-0.001-0.145-0.3030.000
6A6THR0-0.066-0.0386.2160.1960.1960.0000.0000.0000.000
7A7LYS10.8870.9527.858-1.059-1.0590.0000.0000.0000.000
8A8ASN0-0.0260.0047.245-0.088-0.0880.0000.0000.0000.000
9A9SER00.0220.01910.686-0.069-0.0690.0000.0000.0000.000
10A10GLN0-0.030-0.02212.956-0.071-0.0710.0000.0000.0000.000
11A11ASP-1-0.889-0.94311.9050.4950.4950.0000.0000.0000.000
12A12LYS10.8960.93813.565-0.185-0.1850.0000.0000.0000.000
13A13SER0-0.069-0.04215.076-0.019-0.0190.0000.0000.0000.000
14A14SER00.0710.04410.274-0.003-0.0030.0000.0000.0000.000
15A15ASP-1-1.003-0.99012.2990.0420.0420.0000.0000.0000.000
16A16LEU00.0110.0058.7070.0170.0170.0000.0000.0000.000
17A17PHE00.005-0.01111.134-0.021-0.0210.0000.0000.0000.000
18A18SER0-0.007-0.00211.3690.0380.0380.0000.0000.0000.000
19A19ILE00.0180.01512.4090.0190.0190.0000.0000.0000.000
20A20CYS0-0.020-0.00114.710-0.033-0.0330.0000.0000.0000.000
21A21SER0-0.041-0.02618.0430.0250.0250.0000.0000.0000.000
22A22ASP-1-0.897-0.94720.4490.0560.0560.0000.0000.0000.000
23A23ARG10.9640.99124.104-0.061-0.0610.0000.0000.0000.000
24A24GLY00.0660.03620.7970.0020.0020.0000.0000.0000.000
25A25THR0-0.066-0.03320.2870.0110.0110.0000.0000.0000.000
26A26PHE00.0250.01714.240-0.014-0.0140.0000.0000.0000.000
27A27VAL0-0.0030.00819.8140.0120.0120.0000.0000.0000.000
28A28ALA00.0210.02717.083-0.009-0.0090.0000.0000.0000.000
29A29HIS0-0.010-0.02019.2210.0010.0010.0000.0000.0000.000
30A30ASN00.030-0.00418.6110.0050.0050.0000.0000.0000.000
31A31ARG10.8980.97121.994-0.074-0.0740.0000.0000.0000.000
32A32VAL00.0370.02523.7450.0020.0020.0000.0000.0000.000
33A33ARG10.8830.92825.586-0.087-0.0870.0000.0000.0000.000
34A34THR00.0140.02427.5100.0070.0070.0000.0000.0000.000
35A35ASP-1-0.840-0.92829.6600.0800.0800.0000.0000.0000.000
36A36PHE0-0.005-0.00432.2830.0050.0050.0000.0000.0000.000
37A37LYS10.9310.96131.543-0.099-0.0990.0000.0000.0000.000
38A38PHE00.0370.02137.0090.0030.0030.0000.0000.0000.000
39A39ASP-1-0.789-0.89040.1870.0550.0550.0000.0000.0000.000
40A40ASN0-0.043-0.02340.604-0.001-0.0010.0000.0000.0000.000
41A41LEU0-0.045-0.00141.244-0.002-0.0020.0000.0000.0000.000
42A42VAL00.0140.00135.2740.0040.0040.0000.0000.0000.000
43A43PHE00.0020.00836.911-0.004-0.0040.0000.0000.0000.000
44A44ASN00.0080.00333.0330.0040.0040.0000.0000.0000.000
45A45ARG10.8730.96932.209-0.086-0.0860.0000.0000.0000.000
46A46VAL0-0.002-0.00729.7090.0060.0060.0000.0000.0000.000
47A47TYR0-0.054-0.05526.960-0.006-0.0060.0000.0000.0000.000
48A48GLY0-0.046-0.04027.0260.0010.0010.0000.0000.0000.000
49A49VAL0-0.0100.01822.008-0.001-0.0010.0000.0000.0000.000
50A50SER0-0.030-0.02722.161-0.003-0.0030.0000.0000.0000.000
51A51GLN00.0380.02618.109-0.009-0.0090.0000.0000.0000.000
52A52LYS10.9790.98419.320-0.103-0.1030.0000.0000.0000.000
53A53PHE0-0.048-0.02713.9300.0120.0120.0000.0000.0000.000
54A54THR00.0310.00317.458-0.021-0.0210.0000.0000.0000.000
55A55LEU00.0150.00814.4370.0200.0200.0000.0000.0000.000
56A56VAL0-0.0290.02116.9740.0030.0030.0000.0000.0000.000
57A57GLY0-0.014-0.00818.6110.0160.0160.0000.0000.0000.000
58A58ASN00.000-0.00419.578-0.006-0.0060.0000.0000.0000.000
59A59PRO0-0.0150.00516.074-0.004-0.0040.0000.0000.0000.000
60A60THR00.0510.02818.551-0.016-0.0160.0000.0000.0000.000
61A61VAL0-0.033-0.03816.2020.0020.0020.0000.0000.0000.000
62A62CYS0-0.0360.00418.888-0.011-0.0110.0000.0000.0000.000
63A63PHE00.012-0.00616.810-0.010-0.0100.0000.0000.0000.000
64A64ASN0-0.023-0.02919.6150.0060.0060.0000.0000.0000.000
65A65GLU-1-1.012-0.99519.864-0.119-0.1190.0000.0000.0000.000
66A66GLY00.0860.05218.3900.0060.0060.0000.0000.0000.000
67A67SER00.0220.00718.0950.0140.0140.0000.0000.0000.000
68A68SER0-0.086-0.06718.306-0.032-0.0320.0000.0000.0000.000
69A69TYR00.0170.01514.907-0.002-0.0020.0000.0000.0000.000
70A70LEU0-0.021-0.02117.184-0.021-0.0210.0000.0000.0000.000
71A71GLU-1-0.894-0.95414.580-0.355-0.3550.0000.0000.0000.000
72A72GLY00.0340.00814.971-0.085-0.0850.0000.0000.0000.000
73A73ILE0-0.103-0.04116.7930.0120.0120.0000.0000.0000.000
74A74ALA00.0060.00420.538-0.006-0.0060.0000.0000.0000.000
75A75LYS10.9360.96422.3700.2430.2430.0000.0000.0000.000
76A76LYS10.8850.96424.2140.1450.1450.0000.0000.0000.000
77A77TYR00.009-0.01026.0610.0130.0130.0000.0000.0000.000
78A78LEU0-0.0200.00021.947-0.002-0.0020.0000.0000.0000.000
79A79THR0-0.056-0.03125.2690.0130.0130.0000.0000.0000.000
80A80LEU0-0.038-0.03124.752-0.012-0.0120.0000.0000.0000.000
81A81ASP-1-0.897-0.93922.374-0.159-0.1590.0000.0000.0000.000
82A82GLY00.0470.02520.9060.0010.0010.0000.0000.0000.000
83A83GLY00.0450.03121.709-0.003-0.0030.0000.0000.0000.000
84A84LEU00.0260.01525.202-0.006-0.0060.0000.0000.0000.000
85A85ALA00.0130.01526.3640.0150.0150.0000.0000.0000.000
86A86ILE00.0390.00329.3110.0010.0010.0000.0000.0000.000
87A87ASP-1-0.837-0.92831.696-0.103-0.1030.0000.0000.0000.000
88A88ASN0-0.068-0.03831.0880.0010.0010.0000.0000.0000.000
89A89VAL00.0090.01029.1760.0000.0000.0000.0000.0000.000
90A90LEU0-0.035-0.02232.0910.0050.0050.0000.0000.0000.000
91A91ASN0-0.042-0.04435.5230.0010.0010.0000.0000.0000.000
92A92GLU-1-0.837-0.91031.967-0.118-0.1180.0000.0000.0000.000
93A93LEU0-0.043-0.02533.1640.0010.0010.0000.0000.0000.000
94A94ARG10.8740.95636.4080.0830.0830.0000.0000.0000.000
95A95SER0-0.083-0.04537.5270.0020.0020.0000.0000.0000.000
96A96THR0-0.0100.01634.3060.0050.0050.0000.0000.0000.000
97A97CYS0-0.032-0.01335.1150.0000.0000.0000.0000.0000.000
98A98GLY00.0430.02838.1700.0040.0040.0000.0000.0000.000
99A99ILE0-0.026-0.01838.2590.0010.0010.0000.0000.0000.000
100A100PRO00.0250.01841.5800.0010.0010.0000.0000.0000.000
101A101GLY00.0680.01243.116-0.003-0.0030.0000.0000.0000.000
102A102ASN00.0460.00644.097-0.001-0.0010.0000.0000.0000.000
103A103ALA00.0160.01142.0270.0000.0000.0000.0000.0000.000
104A104VAL00.0090.01239.010-0.002-0.0020.0000.0000.0000.000
105A105ALA0-0.026-0.01139.666-0.003-0.0030.0000.0000.0000.000
106A106SER00.0060.00741.8100.0000.0000.0000.0000.0000.000
107A107HIS10.8820.95033.5520.0960.0960.0000.0000.0000.000
108A108ALA00.0140.00036.947-0.003-0.0030.0000.0000.0000.000
109A109TYR00.0080.01337.885-0.001-0.0010.0000.0000.0000.000
110A110ASN00.0050.03236.9570.0040.0040.0000.0000.0000.000
111A111ILE0-0.070-0.03432.326-0.002-0.0020.0000.0000.0000.000
112A112THR0-0.038-0.05333.957-0.004-0.0040.0000.0000.0000.000
113A113SER0-0.035-0.01334.455-0.004-0.0040.0000.0000.0000.000
114A114TRP0-0.0010.01130.557-0.006-0.0060.0000.0000.0000.000
115A115ARG10.9320.98427.3450.0850.0850.0000.0000.0000.000
116A116TRP00.020-0.00625.333-0.008-0.0080.0000.0000.0000.000
117A117TYR0-0.013-0.01218.739-0.017-0.0170.0000.0000.0000.000
118A118ASP-1-0.790-0.91317.719-0.303-0.3030.0000.0000.0000.000
119A119ASN00.0880.03015.021-0.039-0.0390.0000.0000.0000.000
120A120HIS10.8520.92413.7290.3500.3500.0000.0000.0000.000
121A121VAL00.0340.0219.997-0.013-0.0130.0000.0000.0000.000
122A122ALA00.0640.04011.7450.0280.0280.0000.0000.0000.000
123A123LEU00.0040.01114.4870.0210.0210.0000.0000.0000.000
124A124LEU0-0.051-0.0459.9010.0090.0090.0000.0000.0000.000
125A125MET00.0150.0199.934-0.023-0.0230.0000.0000.0000.000
126A126ASN00.0230.02511.1480.0780.0780.0000.0000.0000.000
127A127MET0-0.018-0.00412.8200.0240.0240.0000.0000.0000.000
128A128LEU00.0150.0136.5770.0060.0060.0000.0000.0000.000
129A129ARG10.8070.92010.8790.0350.0350.0000.0000.0000.000
130A130ALA00.0400.01512.6760.0160.0160.0000.0000.0000.000
131A131TYR00.005-0.00211.842-0.024-0.0240.0000.0000.0000.000
132A132HIS0-0.053-0.0588.6540.0890.0890.0000.0000.0000.000
133A133LEU00.0410.02014.1080.0050.0050.0000.0000.0000.000
134A134GLN00.0420.04717.4260.0010.0010.0000.0000.0000.000
135A135VAL0-0.015-0.00914.786-0.006-0.0060.0000.0000.0000.000
136A136LEU0-0.024-0.00816.6890.0020.0020.0000.0000.0000.000
137A137THR0-0.043-0.01319.840-0.003-0.0030.0000.0000.0000.000
138A138GLU-1-0.845-0.95020.249-0.050-0.0500.0000.0000.0000.000
139A139GLN0-0.085-0.03918.5820.0050.0050.0000.0000.0000.000
140A140GLY0-0.0050.00723.0370.0020.0020.0000.0000.0000.000
141A141GLN0-0.055-0.04121.0590.0070.0070.0000.0000.0000.000
142A142TYR0-0.0660.00921.0270.0120.0120.0000.0000.0000.000
143A143SER00.010-0.00223.340-0.004-0.0040.0000.0000.0000.000
144A144ALA00.0500.03824.1030.0030.0030.0000.0000.0000.000
145A145GLY0-0.033-0.00323.2890.0070.0070.0000.0000.0000.000
146A146ASP-1-0.845-0.94124.0980.0660.0660.0000.0000.0000.000
147A147ILE0-0.028-0.00922.6540.0120.0120.0000.0000.0000.000
148A148PRO0-0.044-0.02124.052-0.009-0.0090.0000.0000.0000.000
149A149MET0-0.0280.00327.0660.0010.0010.0000.0000.0000.000
150A150TYR00.0270.01628.8070.0000.0000.0000.0000.0000.000
151A151HIS0-0.004-0.02430.558-0.005-0.0050.0000.0000.0000.000
152A152ASP-1-0.814-0.90333.5310.0710.0710.0000.0000.0000.000
153A153GLY0-0.007-0.01935.051-0.002-0.0020.0000.0000.0000.000
154A154HIS10.8810.85337.439-0.063-0.0630.0000.0000.0000.000
155A155VAL00.0250.01735.359-0.002-0.0020.0000.0000.0000.000
156A156LYS10.9440.95634.794-0.055-0.0550.0000.0000.0000.000
157A157ILE0-0.0120.03529.654-0.002-0.0020.0000.0000.0000.000
158A158LYS10.9510.97130.709-0.047-0.0470.0000.0000.0000.000
159A159LEU00.0460.01526.405-0.005-0.0050.0000.0000.0000.000
160A160PRO0-0.0080.00129.062-0.001-0.0010.0000.0000.0000.000
161A161VAL00.0180.01525.3600.0040.0040.0000.0000.0000.000
162A162THR0-0.003-0.01427.290-0.003-0.0030.0000.0000.0000.000
163A163ILE0-0.0400.00026.785-0.006-0.0060.0000.0000.0000.000
164A164ASP-1-0.837-0.93329.0570.0450.0450.0000.0000.0000.000
165A165ASP-1-0.868-0.99026.7600.0570.0570.0000.0000.0000.000
166A166THR0-0.017-0.01129.240-0.002-0.0020.0000.0000.0000.000
167A167ALA0-0.069-0.02232.555-0.003-0.0030.0000.0000.0000.000
168A168GLY0-0.012-0.00229.863-0.003-0.0030.0000.0000.0000.000
169A169PRO00.0100.01126.987-0.002-0.0020.0000.0000.0000.000
170A170THR00.0300.01227.3060.0040.0040.0000.0000.0000.000
171A171GLN00.003-0.03226.2090.0040.0040.0000.0000.0000.000
172A172PHE00.0280.01319.3710.0010.0010.0000.0000.0000.000
173A173ALA0-0.005-0.01223.531-0.009-0.0090.0000.0000.0000.000
174A174TRP00.010-0.01522.054-0.003-0.0030.0000.0000.0000.000
175A175PRO00.0030.01120.4600.0030.0030.0000.0000.0000.000
176A176SER0-0.0020.00623.5220.0020.0020.0000.0000.0000.000
177A177ASP-1-0.908-0.96825.871-0.012-0.0120.0000.0000.0000.000
178A178ARG10.8840.95229.3320.0280.0280.0000.0000.0000.000
179A179SER0-0.075-0.03932.2390.0040.0040.0000.0000.0000.000
180A180THR00.0070.01332.6770.0010.0010.0000.0000.0000.000
181A181ASP-1-0.903-0.95629.288-0.028-0.0280.0000.0000.0000.000
182A182SER00.0220.00931.786-0.001-0.0010.0000.0000.0000.000
183A183TYR0-0.017-0.02727.976-0.003-0.0030.0000.0000.0000.000
184A184PRO0-0.031-0.00525.5760.0010.0010.0000.0000.0000.000
185A185ASP-1-0.923-0.96628.663-0.070-0.0700.0000.0000.0000.000
186A186TRP00.0610.03126.461-0.012-0.0120.0000.0000.0000.000
187A187ALA00.0530.00929.1110.0050.0050.0000.0000.0000.000
188A188GLN0-0.036-0.00529.630-0.014-0.0140.0000.0000.0000.000
189A189PHE0-0.027-0.02429.2410.0050.0050.0000.0000.0000.000
190A190SER00.035-0.00629.926-0.009-0.0090.0000.0000.0000.000
191A191GLU-1-0.894-0.92532.268-0.086-0.0860.0000.0000.0000.000
192A192SER00.014-0.01832.315-0.010-0.0100.0000.0000.0000.000
193A193PHE0-0.039-0.03432.115-0.006-0.0060.0000.0000.0000.000
194A194PRO0-0.0050.02230.0140.0050.0050.0000.0000.0000.000
195A195SER00.008-0.01332.0330.0050.0050.0000.0000.0000.000
196A196ILE0-0.022-0.00932.2220.0060.0060.0000.0000.0000.000
197A197ASP-1-0.788-0.93629.686-0.112-0.1120.0000.0000.0000.000
198A198VAL00.0020.05227.855-0.006-0.0060.0000.0000.0000.000
199A199PRO00.0160.01223.315-0.008-0.0080.0000.0000.0000.000
200A200TYR00.0640.01924.4960.0060.0060.0000.0000.0000.000
201A201LEU0-0.0300.01519.494-0.024-0.0240.0000.0000.0000.000
202A202ASP-1-0.760-0.90120.964-0.188-0.1880.0000.0000.0000.000
203A203VAL00.0400.01019.745-0.030-0.0300.0000.0000.0000.000
204A204ARG10.8470.94622.0700.1930.1930.0000.0000.0000.000
205A205PRO0-0.044-0.01220.9340.0110.0110.0000.0000.0000.000
206A206LEU0-0.050-0.01418.487-0.005-0.0050.0000.0000.0000.000
207A207THR0-0.050-0.00622.3410.0160.0160.0000.0000.0000.000
208A208VAL00.1280.04624.215-0.005-0.0050.0000.0000.0000.000
209A209THR00.0360.00323.9070.0010.0010.0000.0000.0000.000
210A210GLU-1-0.819-0.93120.071-0.196-0.1960.0000.0000.0000.000
211A211VAL00.0080.00320.932-0.008-0.0080.0000.0000.0000.000
212A212ASN00.0730.03023.0070.0000.0000.0000.0000.0000.000
213A213PHE00.0070.00616.0450.0030.0030.0000.0000.0000.000
214A214VAL0-0.013-0.01318.0140.0000.0000.0000.0000.0000.000
215A215LEU0-0.002-0.00519.898-0.002-0.0020.0000.0000.0000.000
216A216MET0-0.0100.01722.3100.0090.0090.0000.0000.0000.000
217A217MET0-0.071-0.02416.4830.0130.0130.0000.0000.0000.000
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