FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 2N89R

Calculation Name: 3M6C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M6C

Chain ID: A

ChEMBL ID:

UniProt ID: P9WPE9

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1987018.944819
FMO2-HF: Nuclear repulsion 1915804.980298
FMO2-HF: Total energy -71213.964521
FMO2-MP2: Total energy -71426.96014


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:184:GLU)


Summations of interaction energy for fragment #1(A:184:GLU)
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.
103.768108.33.818-3.73-4.6210.012
Interaction energy analysis for fragmet #1(A:184:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.911 / q_NPA : -0.939
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].
3A186GLU-1-0.942-0.9631.79030.68535.2553.819-3.848-4.5420.013
4A187PHE0-0.059-0.0333.488-2.489-2.527-0.0010.118-0.079-0.001
5A188THR0-0.031-0.0106.416-0.934-0.9340.0000.0000.0000.000
6A189GLU-1-0.931-0.9809.79116.73816.7380.0000.0000.0000.000
7A190GLY00.0200.01012.723-0.738-0.7380.0000.0000.0000.000
8A191ILE0-0.0340.00113.2550.9320.9320.0000.0000.0000.000
9A192GLY00.0570.01614.366-0.926-0.9260.0000.0000.0000.000
10A193PHE0-0.076-0.06615.4470.5470.5470.0000.0000.0000.000
11A194ASP-1-0.846-0.90817.04415.63515.6350.0000.0000.0000.000
12A195LYS10.8090.91119.600-12.529-12.5290.0000.0000.0000.000
13A196GLY00.0780.06622.9460.2760.2760.0000.0000.0000.000
14A197PHE0-0.073-0.03525.256-0.326-0.3260.0000.0000.0000.000
15A198LEU0-0.014-0.00928.593-0.095-0.0950.0000.0000.0000.000
16A199SER0-0.013-0.01531.487-0.318-0.3180.0000.0000.0000.000
17A200ALA00.0460.02032.9880.1700.1700.0000.0000.0000.000
18A201TYR0-0.040-0.02634.311-0.006-0.0060.0000.0000.0000.000
19A202PHE00.002-0.00432.073-0.083-0.0830.0000.0000.0000.000
20A203VAL0-0.056-0.00130.7430.2090.2090.0000.0000.0000.000
21A204THR0-0.026-0.02230.637-0.189-0.1890.0000.0000.0000.000
22A205ASP-1-0.849-0.91529.5099.8289.8280.0000.0000.0000.000
23A206PHE00.003-0.02230.5700.2340.2340.0000.0000.0000.000
24A207ASP-1-0.949-0.94730.9549.1319.1310.0000.0000.0000.000
25A208ASN0-0.096-0.06525.9970.4870.4870.0000.0000.0000.000
26A209GLN0-0.079-0.03327.0000.3760.3760.0000.0000.0000.000
27A210GLN00.0490.01823.5590.3030.3030.0000.0000.0000.000
28A211ALA0-0.029-0.00527.281-0.392-0.3920.0000.0000.0000.000
29A212VAL00.0190.02025.6410.3830.3830.0000.0000.0000.000
30A213LEU0-0.083-0.05126.635-0.582-0.5820.0000.0000.0000.000
31A214GLU-1-0.852-0.92326.13611.87911.8790.0000.0000.0000.000
32A215ASP-1-0.844-0.91927.1499.6139.6130.0000.0000.0000.000
33A216ALA0-0.021-0.00827.200-0.427-0.4270.0000.0000.0000.000
34A217LEU00.0190.01028.2380.1890.1890.0000.0000.0000.000
35A218ILE0-0.017-0.02724.2000.0380.0380.0000.0000.0000.000
36A219LEU00.0240.02628.368-0.095-0.0950.0000.0000.0000.000
37A220LEU00.0020.01124.4330.1470.1470.0000.0000.0000.000
38A221HIS0-0.026-0.02428.257-0.334-0.3340.0000.0000.0000.000
39A222GLN00.0480.02227.5090.3830.3830.0000.0000.0000.000
40A223ASP-1-0.789-0.89930.2728.6628.6620.0000.0000.0000.000
41A224LYS10.8250.90932.622-8.223-8.2230.0000.0000.0000.000
42A225ILE00.0070.00733.381-0.206-0.2060.0000.0000.0000.000
43A226SER00.022-0.00536.732-0.035-0.0350.0000.0000.0000.000
44A227SER00.0060.00040.042-0.164-0.1640.0000.0000.0000.000
45A228LEU00.0620.03241.7610.1090.1090.0000.0000.0000.000
46A229PRO0-0.003-0.01843.5470.0520.0520.0000.0000.0000.000
47A230ASP-1-0.812-0.90641.1877.0027.0020.0000.0000.0000.000
48A231LEU00.0390.02036.7950.0990.0990.0000.0000.0000.000
49A232LEU0-0.030-0.01240.3780.1080.1080.0000.0000.0000.000
50A233PRO00.0640.03742.6220.0360.0360.0000.0000.0000.000
51A234LEU0-0.0020.00635.0880.0120.0120.0000.0000.0000.000
52A235LEU00.012-0.00137.0280.1210.1210.0000.0000.0000.000
53A236GLU-1-0.931-0.96539.6206.6176.6170.0000.0000.0000.000
54A237LYS10.8630.93139.779-7.278-7.2780.0000.0000.0000.000
55A238VAL00.0270.00735.1020.0480.0480.0000.0000.0000.000
56A239ALA0-0.0150.00837.9230.0780.0780.0000.0000.0000.000
57A240GLY0-0.031-0.00540.147-0.047-0.0470.0000.0000.0000.000
58A241THR0-0.080-0.06536.6640.0450.0450.0000.0000.0000.000
59A242GLY0-0.027-0.00638.0680.0590.0590.0000.0000.0000.000
60A243LYS10.7810.89430.517-9.451-9.4510.0000.0000.0000.000
61A244PRO0-0.041-0.01430.423-0.158-0.1580.0000.0000.0000.000
62A245LEU00.003-0.00431.2140.1290.1290.0000.0000.0000.000
63A246LEU00.0090.00924.316-0.057-0.0570.0000.0000.0000.000
64A247ILE0-0.022-0.02028.845-0.074-0.0740.0000.0000.0000.000
65A248VAL00.0120.01224.1920.1210.1210.0000.0000.0000.000
66A249ALA00.0250.01327.513-0.095-0.0950.0000.0000.0000.000
67A250GLU-1-0.893-0.92528.7009.3109.3100.0000.0000.0000.000
68A251ASP-1-0.782-0.91230.2719.0979.0970.0000.0000.0000.000
69A252VAL0-0.0140.01432.165-0.145-0.1450.0000.0000.0000.000
70A253GLU-1-0.877-0.95434.6797.9127.9120.0000.0000.0000.000
71A254GLY00.0380.01638.055-0.077-0.0770.0000.0000.0000.000
72A255GLU-1-0.878-0.95541.6406.6756.6750.0000.0000.0000.000
73A256ALA0-0.034-0.00338.9540.0020.0020.0000.0000.0000.000
74A257LEU00.0020.00735.3790.0800.0800.0000.0000.0000.000
75A258ALA00.0290.02438.5300.0690.0690.0000.0000.0000.000
76A259THR0-0.001-0.00241.6740.0350.0350.0000.0000.0000.000
77A260LEU00.0360.03334.2840.0000.0000.0000.0000.0000.000
78A261VAL00.010-0.00837.3030.0810.0810.0000.0000.0000.000
79A262VAL00.0150.00138.963-0.003-0.0030.0000.0000.0000.000
80A263ASN0-0.015-0.01440.522-0.192-0.1920.0000.0000.0000.000
81A264ALA00.0340.04036.3140.0300.0300.0000.0000.0000.000
82A265ILE0-0.052-0.02438.2710.0480.0480.0000.0000.0000.000
83A266ARG10.8320.90740.579-6.737-6.7370.0000.0000.0000.000
84A267LYS10.9350.97436.287-8.091-8.0910.0000.0000.0000.000
85A268THR0-0.030-0.02040.315-0.001-0.0010.0000.0000.0000.000
86A269LEU00.0240.00336.132-0.017-0.0170.0000.0000.0000.000
87A270LYS10.8380.93531.008-9.444-9.4440.0000.0000.0000.000
88A271ALA00.0340.01732.5960.1430.1430.0000.0000.0000.000
89A272VAL00.0010.00228.473-0.070-0.0700.0000.0000.0000.000
90A273ALA00.0020.01930.2330.0900.0900.0000.0000.0000.000
91A274VAL0-0.007-0.01424.317-0.034-0.0340.0000.0000.0000.000
92A275LYS10.8320.91626.990-9.606-9.6060.0000.0000.0000.000
93A276GLY00.0510.01524.4260.4340.4340.0000.0000.0000.000
94A277PRO0-0.035-0.00919.962-0.235-0.2350.0000.0000.0000.000
95A278TYR0-0.036-0.04215.446-0.323-0.3230.0000.0000.0000.000
96A279PHE00.0490.00222.443-0.458-0.4580.0000.0000.0000.000
97A280GLY00.0540.02424.3040.2550.2550.0000.0000.0000.000
98A281ASP-1-0.815-0.90724.65610.31110.3110.0000.0000.0000.000
99A282ARG10.8530.92415.265-15.379-15.3790.0000.0000.0000.000
100A283ARG10.7570.88921.117-9.597-9.5970.0000.0000.0000.000
101A284LYS10.9070.94323.429-9.781-9.7810.0000.0000.0000.000
102A285ALA00.0100.00120.4920.0530.0530.0000.0000.0000.000
103A286PHE00.0280.00315.7320.2550.2550.0000.0000.0000.000
104A287LEU00.0020.00720.1590.1970.1970.0000.0000.0000.000
105A288GLU-1-0.825-0.90422.12511.37511.3750.0000.0000.0000.000
106A289ASP-1-0.777-0.84817.10714.70914.7090.0000.0000.0000.000
107A290LEU0-0.0020.00218.9530.1670.1670.0000.0000.0000.000
108A291ALA0-0.0070.01420.748-0.076-0.0760.0000.0000.0000.000
109A292VAL0-0.016-0.00718.745-0.117-0.1170.0000.0000.0000.000
110A293VAL0-0.011-0.01716.214-0.088-0.0880.0000.0000.0000.000
111A294THR0-0.077-0.05219.535-0.186-0.1860.0000.0000.0000.000
112A295GLY00.0200.01722.815-0.342-0.3420.0000.0000.0000.000
113A296GLY00.0160.02625.054-0.392-0.3920.0000.0000.0000.000
114A297GLN0-0.090-0.05326.782-0.011-0.0110.0000.0000.0000.000
115A298VAL0-0.017-0.00625.817-0.111-0.1110.0000.0000.0000.000
116A299VAL00.014-0.00128.701-0.239-0.2390.0000.0000.0000.000
117A300ASN00.004-0.04730.985-0.015-0.0150.0000.0000.0000.000
118A301PRO00.0190.00033.073-0.108-0.1080.0000.0000.0000.000
119A302ASP-1-0.906-0.93734.2417.9487.9480.0000.0000.0000.000
120A303ALA0-0.104-0.04233.420-0.063-0.0630.0000.0000.0000.000
121A304GLY0-0.012-0.00735.560-0.113-0.1130.0000.0000.0000.000
122A305MET0-0.0400.02733.014-0.063-0.0630.0000.0000.0000.000
123A306VAL00.0500.01437.712-0.035-0.0350.0000.0000.0000.000
124A307LEU0-0.0070.00135.8200.0260.0260.0000.0000.0000.000
125A308ARG10.8390.90738.681-6.682-6.6820.0000.0000.0000.000
126A309GLU-1-1.015-1.00641.2006.7826.7820.0000.0000.0000.000
127A310VAL0-0.0020.02635.9140.0370.0370.0000.0000.0000.000
128A311GLY0-0.039-0.04237.764-0.152-0.1520.0000.0000.0000.000
129A312LEU0-0.011-0.03035.4860.1630.1630.0000.0000.0000.000
130A313GLU-1-0.840-0.90333.6448.2318.2310.0000.0000.0000.000
131A314VAL0-0.025-0.00731.8850.2420.2420.0000.0000.0000.000
132A315LEU0-0.051-0.02030.2940.2380.2380.0000.0000.0000.000
133A316GLY00.0670.04326.3790.0420.0420.0000.0000.0000.000
134A317SER0-0.075-0.04025.884-0.264-0.2640.0000.0000.0000.000
135A318ALA00.0460.01222.6240.4610.4610.0000.0000.0000.000
136A319ARG10.8540.93719.779-14.195-14.1950.0000.0000.0000.000
137A320ARG10.9100.95021.749-12.775-12.7750.0000.0000.0000.000
138A321VAL0-0.0040.00722.1900.4430.4430.0000.0000.0000.000
139A322VAL0-0.0060.00021.424-0.491-0.4910.0000.0000.0000.000
140A323VAL0-0.027-0.00122.1460.3540.3540.0000.0000.0000.000
141A324SER00.036-0.00521.613-0.607-0.6070.0000.0000.0000.000
142A325LYS10.9640.96524.626-10.434-10.4340.0000.0000.0000.000
143A326ASP-1-0.971-1.00323.23011.80111.8010.0000.0000.0000.000
144A327ASP-1-0.867-0.90718.97114.65514.6550.0000.0000.0000.000
145A328THR00.006-0.00919.940-0.751-0.7510.0000.0000.0000.000
146A329VAL00.0280.02216.3120.6660.6660.0000.0000.0000.000
147A330ILE0-0.056-0.03518.072-0.855-0.8550.0000.0000.0000.000
148A331VAL00.0240.00617.3740.7710.7710.0000.0000.0000.000
149A332ASP-1-0.770-0.88618.13414.29414.2940.0000.0000.0000.000
150A333GLY00.0140.00619.511-0.739-0.7390.0000.0000.0000.000
151A334GLY00.004-0.01021.5150.2100.2100.0000.0000.0000.000
152A335GLY0-0.0050.01221.607-0.419-0.4190.0000.0000.0000.000
153A336THR0-0.021-0.01922.2150.2840.2840.0000.0000.0000.000
154A337ALA00.0600.01319.6890.4050.4050.0000.0000.0000.000
155A338GLU-1-0.915-0.96119.40911.66911.6690.0000.0000.0000.000
156A339ALA00.0130.02120.8440.1640.1640.0000.0000.0000.000
157A340VAL00.0640.02615.3690.2840.2840.0000.0000.0000.000
158A341ALA0-0.015-0.00516.0210.6550.6550.0000.0000.0000.000
159A342ASN0-0.035-0.03016.7410.6690.6690.0000.0000.0000.000
160A343ARG10.7890.88816.846-12.940-12.9400.0000.0000.0000.000
161A344ALA00.0480.01412.5420.3960.3960.0000.0000.0000.000
162A345LYS10.8900.94413.878-13.185-13.1850.0000.0000.0000.000
163A346HIS0-0.064-0.03416.059-0.102-0.1020.0000.0000.0000.000
164A347LEU00.022-0.00113.232-0.128-0.1280.0000.0000.0000.000
165A348ARG10.9440.97210.212-18.688-18.6880.0000.0000.0000.000
166A349ALA0-0.0180.00313.552-0.058-0.0580.0000.0000.0000.000
167A350GLU-1-0.893-0.94616.58212.52212.5220.0000.0000.0000.000
168A351ILE0-0.080-0.04610.568-0.050-0.0500.0000.0000.0000.000
169A352ASP-1-0.915-0.95914.03117.29317.2930.0000.0000.0000.000
170A353LYS10.8770.94416.417-12.507-12.5070.0000.0000.0000.000
171A354SER0-0.034-0.00217.023-0.516-0.5160.0000.0000.0000.000
172A355ASP-1-0.936-0.97018.63312.83312.8330.0000.0000.0000.000
173A356SER0-0.028-0.03619.220-0.149-0.1490.0000.0000.0000.000
174A357ASP-1-0.783-0.87415.59517.85017.8500.0000.0000.0000.000
175A358TRP00.0280.01715.2711.0771.0770.0000.0000.0000.000
176A359ASP-1-0.828-0.90216.12813.98013.9800.0000.0000.0000.000
177A360ARG10.8440.89712.999-17.706-17.7060.0000.0000.0000.000
178A361GLU-1-0.846-0.89611.25620.81120.8110.0000.0000.0000.000
179A362LYS10.7110.84211.637-16.516-16.5160.0000.0000.0000.000
180A363LEU0-0.014-0.01813.3570.1830.1830.0000.0000.0000.000
181A364GLY00.0350.0159.3340.3130.3130.0000.0000.0000.000
182A365GLU-1-0.763-0.8568.66518.69818.6980.0000.0000.0000.000
183A366ARG10.8070.87610.110-14.948-14.9480.0000.0000.0000.000
184A367LEU0-0.032-0.0118.651-0.442-0.4420.0000.0000.0000.000
185A368ALA00.0030.0006.4310.1170.1170.0000.0000.0000.000
186A369LYS10.8770.9347.863-17.999-17.9990.0000.0000.0000.000
187A370LEU0-0.045-0.02111.215-0.513-0.5130.0000.0000.0000.000
188A371ALA0-0.012-0.0159.302-0.809-0.8090.0000.0000.0000.000
189A372GLY00.0580.03711.063-0.315-0.3150.0000.0000.0000.000
190A373GLY0-0.0190.00912.061-0.707-0.7070.0000.0000.0000.000
191A374VAL0-0.045-0.02015.188-1.024-1.0240.0000.0000.0000.000
192A375ALA00.0260.03616.8510.6470.6470.0000.0000.0000.000
193A376VAL00.0040.00315.678-0.131-0.1310.0000.0000.0000.000
194A377ILE0-0.078-0.03819.069-1.058-1.0580.0000.0000.0000.000