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: 6Y8KZ

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 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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1994754.520403
FMO2-HF: Nuclear repulsion 1923539.944442
FMO2-HF: Total energy -71214.575961
FMO2-MP2: Total energy -71427.592249


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.
100.721104.1122.653-2.528-3.5160.003
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 : -0.941
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-1-0.934-0.9631.87928.72232.0492.652-2.548-3.4300.003
4A187PHE0-0.065-0.0303.635-1.999-1.9350.0010.020-0.0860.000
5A188THR0-0.015-0.0056.724-0.909-0.9090.0000.0000.0000.000
6A189GLU-1-0.878-0.94510.14116.37616.3760.0000.0000.0000.000
7A190GLY00.0120.00613.256-0.824-0.8240.0000.0000.0000.000
8A191ILE0-0.039-0.00313.3900.9390.9390.0000.0000.0000.000
9A192GLY00.0380.01514.152-0.898-0.8980.0000.0000.0000.000
10A193PHE0-0.051-0.05815.2720.4530.4530.0000.0000.0000.000
11A194ASP-1-0.800-0.89216.64915.59215.5920.0000.0000.0000.000
12A195LYS10.7800.87719.504-12.785-12.7850.0000.0000.0000.000
13A196GLY00.0730.07522.9990.2690.2690.0000.0000.0000.000
14A197PHE0-0.066-0.03225.256-0.286-0.2860.0000.0000.0000.000
15A198LEU0-0.028-0.01828.642-0.111-0.1110.0000.0000.0000.000
16A199SER0-0.013-0.01731.515-0.329-0.3290.0000.0000.0000.000
17A200ALA00.0430.02033.0520.1470.1470.0000.0000.0000.000
18A201TYR0-0.046-0.02734.089-0.009-0.0090.0000.0000.0000.000
19A202PHE00.011-0.00231.933-0.108-0.1080.0000.0000.0000.000
20A203VAL0-0.069-0.00530.6710.1890.1890.0000.0000.0000.000
21A204THR0-0.033-0.03330.578-0.196-0.1960.0000.0000.0000.000
22A205ASP-1-0.880-0.91229.3709.8869.8860.0000.0000.0000.000
23A206PHE00.025-0.00930.6030.1700.1700.0000.0000.0000.000
24A207ASP-1-0.934-0.95731.2639.0949.0940.0000.0000.0000.000
25A208ASN0-0.076-0.05126.1680.4810.4810.0000.0000.0000.000
26A209GLN0-0.066-0.03026.7930.4160.4160.0000.0000.0000.000
27A210GLN00.0170.00023.9670.3460.3460.0000.0000.0000.000
28A211ALA0-0.0060.01027.418-0.395-0.3950.0000.0000.0000.000
29A212VAL00.0140.01425.8620.4190.4190.0000.0000.0000.000
30A213LEU0-0.055-0.03626.646-0.567-0.5670.0000.0000.0000.000
31A214GLU-1-0.822-0.90926.02311.87611.8760.0000.0000.0000.000
32A215ASP-1-0.844-0.91727.4099.5039.5030.0000.0000.0000.000
33A216ALA0-0.0190.00726.718-0.395-0.3950.0000.0000.0000.000
34A217LEU00.0290.00828.0480.1880.1880.0000.0000.0000.000
35A218ILE0-0.012-0.01723.9910.0450.0450.0000.0000.0000.000
36A219LEU00.0110.01928.089-0.038-0.0380.0000.0000.0000.000
37A220LEU00.0060.01224.1410.2080.2080.0000.0000.0000.000
38A221HIS0-0.029-0.02528.011-0.368-0.3680.0000.0000.0000.000
39A222GLN00.0440.02127.1680.4370.4370.0000.0000.0000.000
40A223ASP-1-0.811-0.90730.1338.6438.6430.0000.0000.0000.000
41A224LYS10.7750.86932.393-8.160-8.1600.0000.0000.0000.000
42A225ILE00.0060.01032.974-0.222-0.2220.0000.0000.0000.000
43A226SER00.016-0.00736.423-0.030-0.0300.0000.0000.0000.000
44A227SER0-0.012-0.03539.928-0.173-0.1730.0000.0000.0000.000
45A228LEU00.0630.03641.6410.0950.0950.0000.0000.0000.000
46A229PRO0-0.004-0.01643.3420.0400.0400.0000.0000.0000.000
47A230ASP-1-0.823-0.86940.6256.8516.8510.0000.0000.0000.000
48A231LEU00.0470.02036.5180.0860.0860.0000.0000.0000.000
49A232LEU0-0.015-0.00339.9000.1080.1080.0000.0000.0000.000
50A233PRO00.0500.02642.2310.0450.0450.0000.0000.0000.000
51A234LEU0-0.0080.00534.7220.0210.0210.0000.0000.0000.000
52A235LEU0-0.004-0.01136.9990.1290.1290.0000.0000.0000.000
53A236GLU-1-0.925-0.96839.4206.6276.6270.0000.0000.0000.000
54A237LYS10.8310.92539.452-7.255-7.2550.0000.0000.0000.000
55A238VAL00.0400.01835.2220.0490.0490.0000.0000.0000.000
56A239ALA00.0010.01437.8190.0730.0730.0000.0000.0000.000
57A240GLY0-0.025-0.00440.172-0.041-0.0410.0000.0000.0000.000
58A241THR0-0.062-0.05236.7770.0350.0350.0000.0000.0000.000
59A242GLY0-0.040-0.01638.2010.0750.0750.0000.0000.0000.000
60A243LYS10.7950.90030.528-9.419-9.4190.0000.0000.0000.000
61A244PRO0-0.036-0.00830.704-0.144-0.1440.0000.0000.0000.000
62A245LEU0-0.008-0.01131.3570.1450.1450.0000.0000.0000.000
63A246LEU00.0030.00524.518-0.052-0.0520.0000.0000.0000.000
64A247ILE0-0.016-0.01328.975-0.137-0.1370.0000.0000.0000.000
65A248VAL00.0000.00224.0140.1100.1100.0000.0000.0000.000
66A249ALA00.0190.01927.362-0.118-0.1180.0000.0000.0000.000
67A250GLU-1-0.886-0.93128.0559.4349.4340.0000.0000.0000.000
68A251ASP-1-0.794-0.91229.8169.0469.0460.0000.0000.0000.000
69A252VAL00.0120.01632.026-0.112-0.1120.0000.0000.0000.000
70A253GLU-1-0.793-0.90134.5538.0528.0520.0000.0000.0000.000
71A254GLY00.0240.00337.849-0.082-0.0820.0000.0000.0000.000
72A255GLU-1-0.863-0.93941.3766.6606.6600.0000.0000.0000.000
73A256ALA0-0.0210.01538.4510.0080.0080.0000.0000.0000.000
74A257LEU0-0.0010.01035.2050.0790.0790.0000.0000.0000.000
75A258ALA00.0170.01238.3280.0520.0520.0000.0000.0000.000
76A259THR0-0.009-0.02741.5310.0320.0320.0000.0000.0000.000
77A260LEU00.0200.02834.202-0.029-0.0290.0000.0000.0000.000
78A261VAL00.0230.00537.0620.0760.0760.0000.0000.0000.000
79A262VAL00.000-0.00138.789-0.008-0.0080.0000.0000.0000.000
80A263ASN0-0.018-0.00940.169-0.181-0.1810.0000.0000.0000.000
81A264ALA00.0630.05735.9880.0170.0170.0000.0000.0000.000
82A265ILE0-0.009-0.00437.8880.0190.0190.0000.0000.0000.000
83A266ARG10.8290.89240.290-6.729-6.7290.0000.0000.0000.000
84A267LYS10.8420.92636.653-7.920-7.9200.0000.0000.0000.000
85A268THR0-0.015-0.01639.9700.0380.0380.0000.0000.0000.000
86A269LEU00.0260.01335.977-0.041-0.0410.0000.0000.0000.000
87A270LYS10.8450.93231.047-9.378-9.3780.0000.0000.0000.000
88A271ALA00.0280.01532.7490.1570.1570.0000.0000.0000.000
89A272VAL0-0.002-0.00428.393-0.065-0.0650.0000.0000.0000.000
90A273ALA00.0150.01830.4090.0290.0290.0000.0000.0000.000
91A274VAL00.005-0.00124.396-0.045-0.0450.0000.0000.0000.000
92A275LYS10.8320.91426.614-9.482-9.4820.0000.0000.0000.000
93A276GLY00.0720.03624.3420.4070.4070.0000.0000.0000.000
94A277PRO0-0.025-0.00919.807-0.200-0.2000.0000.0000.0000.000
95A278TYR0-0.034-0.03315.122-0.058-0.0580.0000.0000.0000.000
96A279PHE00.0450.01322.186-0.458-0.4580.0000.0000.0000.000
97A280GLY00.0470.01324.0800.2680.2680.0000.0000.0000.000
98A281ASP-1-0.821-0.91024.75710.22010.2200.0000.0000.0000.000
99A282ARG10.8330.89915.359-15.030-15.0300.0000.0000.0000.000
100A283ARG10.7550.88420.843-9.495-9.4950.0000.0000.0000.000
101A284LYS10.8960.93823.228-9.625-9.6250.0000.0000.0000.000
102A285ALA00.0440.01620.3980.0870.0870.0000.0000.0000.000
103A286PHE00.0240.00715.2290.3620.3620.0000.0000.0000.000
104A287LEU00.0100.00519.7900.1890.1890.0000.0000.0000.000
105A288GLU-1-0.831-0.90721.80511.44611.4460.0000.0000.0000.000
106A289ASP-1-0.783-0.85716.66614.84814.8480.0000.0000.0000.000
107A290LEU00.0250.01018.7000.2280.2280.0000.0000.0000.000
108A291ALA0-0.0290.00720.257-0.076-0.0760.0000.0000.0000.000
109A292VAL0-0.023-0.01318.360-0.099-0.0990.0000.0000.0000.000
110A293VAL0-0.022-0.01415.816-0.046-0.0460.0000.0000.0000.000
111A294THR0-0.048-0.04519.109-0.148-0.1480.0000.0000.0000.000
112A295GLY00.0060.02022.434-0.338-0.3380.0000.0000.0000.000
113A296GLY00.0260.02224.796-0.399-0.3990.0000.0000.0000.000
114A297GLN0-0.079-0.04626.4690.0030.0030.0000.0000.0000.000
115A298VAL0-0.020-0.01025.568-0.164-0.1640.0000.0000.0000.000
116A299VAL00.0130.00528.522-0.212-0.2120.0000.0000.0000.000
117A300ASN00.014-0.04230.485-0.039-0.0390.0000.0000.0000.000
118A301PRO00.0160.00632.929-0.120-0.1200.0000.0000.0000.000
119A302ASP-1-0.933-0.94233.5908.0888.0880.0000.0000.0000.000
120A303ALA0-0.071-0.03033.150-0.076-0.0760.0000.0000.0000.000
121A304GLY0-0.009-0.00435.264-0.094-0.0940.0000.0000.0000.000
122A305MET0-0.0410.02232.801-0.064-0.0640.0000.0000.0000.000
123A306VAL00.0350.01037.315-0.004-0.0040.0000.0000.0000.000
124A307LEU0-0.013-0.02035.3880.0130.0130.0000.0000.0000.000
125A308ARG10.8240.89738.416-6.687-6.6870.0000.0000.0000.000
126A309GLU-1-0.970-0.98040.9086.8036.8030.0000.0000.0000.000
127A310VAL0-0.0040.00935.7970.0030.0030.0000.0000.0000.000
128A311GLY0-0.015-0.02837.249-0.144-0.1440.0000.0000.0000.000
129A312LEU00.002-0.01534.9760.1880.1880.0000.0000.0000.000
130A313GLU-1-0.848-0.91133.2728.2558.2550.0000.0000.0000.000
131A314VAL0-0.024-0.01131.9480.1940.1940.0000.0000.0000.000
132A315LEU0-0.062-0.02030.1400.2300.2300.0000.0000.0000.000
133A316GLY00.0710.04126.0470.0570.0570.0000.0000.0000.000
134A317SER0-0.091-0.05525.615-0.297-0.2970.0000.0000.0000.000
135A318ALA00.0520.01022.3890.4710.4710.0000.0000.0000.000
136A319ARG10.7850.90619.142-14.521-14.5210.0000.0000.0000.000
137A320ARG10.8920.93522.050-12.641-12.6410.0000.0000.0000.000
138A321VAL0-0.008-0.00222.2320.4140.4140.0000.0000.0000.000
139A322VAL0-0.016-0.00421.351-0.439-0.4390.0000.0000.0000.000
140A323VAL0-0.0040.00522.2890.3300.3300.0000.0000.0000.000
141A324SER00.022-0.00421.634-0.628-0.6280.0000.0000.0000.000
142A325LYS10.8700.91124.641-10.983-10.9830.0000.0000.0000.000
143A326ASP-1-0.882-0.93522.83711.13911.1390.0000.0000.0000.000
144A327ASP-1-0.904-0.93219.00114.25914.2590.0000.0000.0000.000
145A328THR00.033-0.00119.987-0.794-0.7940.0000.0000.0000.000
146A329VAL00.0000.00416.2820.6690.6690.0000.0000.0000.000
147A330ILE0-0.037-0.01418.254-0.796-0.7960.0000.0000.0000.000
148A331VAL00.0320.01117.4960.7920.7920.0000.0000.0000.000
149A332ASP-1-0.756-0.87918.25414.31714.3170.0000.0000.0000.000
150A333GLY00.0360.02119.414-0.764-0.7640.0000.0000.0000.000
151A334GLY00.018-0.00421.2190.2780.2780.0000.0000.0000.000
152A335GLY00.0050.01620.969-0.402-0.4020.0000.0000.0000.000
153A336THR0-0.019-0.02121.8040.2750.2750.0000.0000.0000.000
154A337ALA00.0570.01319.3560.3300.3300.0000.0000.0000.000
155A338GLU-1-0.908-0.95119.05211.89211.8920.0000.0000.0000.000
156A339ALA00.0110.01720.3790.2290.2290.0000.0000.0000.000
157A340VAL00.0680.02614.9170.2550.2550.0000.0000.0000.000
158A341ALA00.0000.00615.6560.6900.6900.0000.0000.0000.000
159A342ASN0-0.043-0.04716.3660.7030.7030.0000.0000.0000.000
160A343ARG10.7820.88616.668-13.105-13.1050.0000.0000.0000.000
161A344ALA00.0480.01112.3620.3760.3760.0000.0000.0000.000
162A345LYS10.8490.93113.566-12.967-12.9670.0000.0000.0000.000
163A346HIS0-0.050-0.02915.8000.0240.0240.0000.0000.0000.000
164A347LEU00.019-0.00213.125-0.067-0.0670.0000.0000.0000.000
165A348ARG10.9530.9829.936-19.049-19.0490.0000.0000.0000.000
166A349ALA00.0130.01213.387-0.143-0.1430.0000.0000.0000.000
167A350GLU-1-0.848-0.91016.82012.24012.2400.0000.0000.0000.000
168A351ILE0-0.046-0.03010.533-0.113-0.1130.0000.0000.0000.000
169A352ASP-1-0.916-0.96413.95617.39717.3970.0000.0000.0000.000
170A353LYS10.7980.89716.220-13.248-13.2480.0000.0000.0000.000
171A354SER0-0.043-0.00616.933-0.828-0.8280.0000.0000.0000.000
172A355ASP-1-0.915-0.96018.20913.01713.0170.0000.0000.0000.000
173A356SER0-0.041-0.05918.929-0.212-0.2120.0000.0000.0000.000
174A357ASP-1-0.804-0.88315.49117.90317.9030.0000.0000.0000.000
175A358TRP00.0440.02814.7131.2231.2230.0000.0000.0000.000
176A359ASP-1-0.823-0.89415.70714.24414.2440.0000.0000.0000.000
177A360ARG10.8100.89112.790-17.674-17.6740.0000.0000.0000.000
178A361GLU-1-0.840-0.89310.83321.08621.0860.0000.0000.0000.000
179A362LYS10.7080.82811.576-16.740-16.7400.0000.0000.0000.000
180A363LEU0-0.024-0.01213.317-0.343-0.3430.0000.0000.0000.000
181A364GLY00.0350.0219.0680.2540.2540.0000.0000.0000.000
182A365GLU-1-0.762-0.8338.47718.25218.2520.0000.0000.0000.000
183A366ARG10.8200.88710.063-14.999-14.9990.0000.0000.0000.000
184A367LEU0-0.017-0.0048.551-0.377-0.3770.0000.0000.0000.000
185A368ALA00.0110.0036.3010.0950.0950.0000.0000.0000.000
186A369LYS10.8480.9167.899-17.707-17.7070.0000.0000.0000.000
187A370LEU0-0.061-0.02811.349-0.679-0.6790.0000.0000.0000.000
188A371ALA0-0.016-0.0168.879-0.729-0.7290.0000.0000.0000.000
189A372GLY00.0450.03810.9890.0100.0100.0000.0000.0000.000
190A373GLY0-0.026-0.01212.017-0.774-0.7740.0000.0000.0000.000
191A374VAL0-0.049-0.02115.340-0.918-0.9180.0000.0000.0000.000
192A375ALA0-0.023-0.00217.0190.6100.6100.0000.0000.0000.000
193A376VAL00.0000.00915.5520.0280.0280.0000.0000.0000.000
194A377ILE0-0.082-0.03719.006-1.004-1.0040.0000.0000.0000.000