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

tag_button

FMODB ID: 765QK

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 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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1986328.647001
FMO2-HF: Nuclear repulsion 1915115.847153
FMO2-HF: Total energy -71212.799848
FMO2-MP2: Total energy -71425.841639


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.
112.509112.72711.527-5.194-6.5520.018
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 : -0.924 / q_NPA : -0.966
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-1-0.941-0.9631.55938.82039.60411.536-5.877-6.4430.020
4A187PHE0-0.060-0.0303.168-3.131-3.697-0.0090.683-0.109-0.002
5A188THR0-0.032-0.0106.092-0.849-0.8490.0000.0000.0000.000
6A189GLU-1-0.942-0.9869.53816.99516.9950.0000.0000.0000.000
7A190GLY00.0140.00912.403-0.818-0.8180.0000.0000.0000.000
8A191ILE0-0.0200.00413.1980.9250.9250.0000.0000.0000.000
9A192GLY00.0680.02214.310-0.930-0.9300.0000.0000.0000.000
10A193PHE0-0.070-0.04115.4070.6060.6060.0000.0000.0000.000
11A194ASP-1-0.845-0.90517.15915.31115.3110.0000.0000.0000.000
12A195LYS10.8200.91919.581-12.231-12.2310.0000.0000.0000.000
13A196GLY00.0860.07322.9170.2850.2850.0000.0000.0000.000
14A197PHE0-0.084-0.03825.230-0.312-0.3120.0000.0000.0000.000
15A198LEU0-0.006-0.00628.563-0.088-0.0880.0000.0000.0000.000
16A199SER0-0.005-0.01331.458-0.314-0.3140.0000.0000.0000.000
17A200ALA00.0390.01832.9590.1720.1720.0000.0000.0000.000
18A201TYR0-0.042-0.02734.287-0.004-0.0040.0000.0000.0000.000
19A202PHE00.000-0.00332.021-0.080-0.0800.0000.0000.0000.000
20A203VAL0-0.0510.00030.9470.2170.2170.0000.0000.0000.000
21A204THR0-0.028-0.02630.484-0.166-0.1660.0000.0000.0000.000
22A205ASP-1-0.829-0.90728.9609.9049.9040.0000.0000.0000.000
23A206PHE0-0.010-0.02830.4320.2310.2310.0000.0000.0000.000
24A207ASP-1-0.958-0.94730.7339.1489.1480.0000.0000.0000.000
25A208ASN0-0.103-0.06925.8390.5730.5730.0000.0000.0000.000
26A209GLN0-0.072-0.03126.8450.4600.4600.0000.0000.0000.000
27A210GLN00.0460.01823.3930.1780.1780.0000.0000.0000.000
28A211ALA0-0.023-0.00527.245-0.395-0.3950.0000.0000.0000.000
29A212VAL00.0070.01325.3660.3920.3920.0000.0000.0000.000
30A213LEU0-0.112-0.07326.459-0.552-0.5520.0000.0000.0000.000
31A214GLU-1-0.928-0.97226.08711.65811.6580.0000.0000.0000.000
32A215ASP-1-0.886-0.94626.8129.8209.8200.0000.0000.0000.000
33A216ALA0-0.021-0.01127.268-0.426-0.4260.0000.0000.0000.000
34A217LEU00.0110.00728.1730.1950.1950.0000.0000.0000.000
35A218ILE0-0.014-0.02524.1300.0330.0330.0000.0000.0000.000
36A219LEU00.0330.02428.305-0.085-0.0850.0000.0000.0000.000
37A220LEU0-0.0070.00824.7480.1510.1510.0000.0000.0000.000
38A221HIS0-0.015-0.01428.300-0.300-0.3000.0000.0000.0000.000
39A222GLN00.0450.01227.8510.3600.3600.0000.0000.0000.000
40A223ASP-1-0.797-0.90130.3528.6038.6030.0000.0000.0000.000
41A224LYS10.8840.94732.735-8.064-8.0640.0000.0000.0000.000
42A225ILE00.0140.01633.636-0.201-0.2010.0000.0000.0000.000
43A226SER00.0250.00136.685-0.045-0.0450.0000.0000.0000.000
44A227SER00.003-0.00539.999-0.164-0.1640.0000.0000.0000.000
45A228LEU00.0730.03741.7110.1120.1120.0000.0000.0000.000
46A229PRO0-0.025-0.02943.4960.0440.0440.0000.0000.0000.000
47A230ASP-1-0.890-0.96240.7217.1977.1970.0000.0000.0000.000
48A231LEU00.0580.03336.7590.0960.0960.0000.0000.0000.000
49A232LEU0-0.028-0.01640.3210.1070.1070.0000.0000.0000.000
50A233PRO00.0520.03042.6390.0370.0370.0000.0000.0000.000
51A234LEU00.0310.02635.0100.0140.0140.0000.0000.0000.000
52A235LEU0-0.003-0.01036.9340.1250.1250.0000.0000.0000.000
53A236GLU-1-0.948-0.96939.5616.6266.6260.0000.0000.0000.000
54A237LYS10.9270.95939.756-7.229-7.2290.0000.0000.0000.000
55A238VAL00.0300.01635.2550.0520.0520.0000.0000.0000.000
56A239ALA0-0.0190.02037.8590.0850.0850.0000.0000.0000.000
57A240GLY0-0.034-0.00740.087-0.046-0.0460.0000.0000.0000.000
58A241THR0-0.093-0.08536.6960.0500.0500.0000.0000.0000.000
59A242GLY0-0.025-0.00537.9240.0640.0640.0000.0000.0000.000
60A243LYS10.8290.91930.914-9.432-9.4320.0000.0000.0000.000
61A244PRO0-0.045-0.01330.439-0.165-0.1650.0000.0000.0000.000
62A245LEU00.0100.00030.9740.1340.1340.0000.0000.0000.000
63A246LEU00.0100.01224.332-0.054-0.0540.0000.0000.0000.000
64A247ILE0-0.009-0.01428.792-0.060-0.0600.0000.0000.0000.000
65A248VAL00.0030.00924.2140.1210.1210.0000.0000.0000.000
66A249ALA00.0360.01627.464-0.076-0.0760.0000.0000.0000.000
67A250GLU-1-0.940-0.97128.6599.1089.1080.0000.0000.0000.000
68A251ASP-1-0.901-0.98930.2378.9488.9480.0000.0000.0000.000
69A252VAL00.0050.02032.131-0.135-0.1350.0000.0000.0000.000
70A253GLU-1-0.914-0.97534.6397.7207.7200.0000.0000.0000.000
71A254GLY00.0220.00638.019-0.078-0.0780.0000.0000.0000.000
72A255GLU-1-0.868-0.95241.6026.6686.6680.0000.0000.0000.000
73A256ALA0-0.034-0.00438.9220.0040.0040.0000.0000.0000.000
74A257LEU00.0180.01235.4930.0850.0850.0000.0000.0000.000
75A258ALA00.0180.02038.4900.0710.0710.0000.0000.0000.000
76A259THR0-0.0080.00041.4250.0220.0220.0000.0000.0000.000
77A260LEU00.0500.03634.8360.0080.0080.0000.0000.0000.000
78A261VAL0-0.006-0.00637.3960.0860.0860.0000.0000.0000.000
79A262VAL00.010-0.00138.9240.0000.0000.0000.0000.0000.000
80A263ASN0-0.016-0.03240.503-0.192-0.1920.0000.0000.0000.000
81A264ALA00.0300.03936.3080.0360.0360.0000.0000.0000.000
82A265ILE0-0.049-0.02238.2270.0490.0490.0000.0000.0000.000
83A266ARG10.8260.91040.541-6.735-6.7350.0000.0000.0000.000
84A267LYS10.9390.97735.931-8.217-8.2170.0000.0000.0000.000
85A268THR0-0.041-0.02240.2530.0180.0180.0000.0000.0000.000
86A269LEU00.0350.00936.139-0.012-0.0120.0000.0000.0000.000
87A270LYS10.8770.96231.287-9.397-9.3970.0000.0000.0000.000
88A271ALA00.0400.01932.5420.1460.1460.0000.0000.0000.000
89A272VAL00.0040.00328.447-0.072-0.0720.0000.0000.0000.000
90A273ALA00.0040.02330.1860.0980.0980.0000.0000.0000.000
91A274VAL00.012-0.00524.344-0.036-0.0360.0000.0000.0000.000
92A275LYS10.8780.96226.956-9.709-9.7090.0000.0000.0000.000
93A276GLY00.0370.00824.3870.4320.4320.0000.0000.0000.000
94A277PRO0-0.030-0.01019.957-0.259-0.2590.0000.0000.0000.000
95A278TYR0-0.019-0.01615.814-0.243-0.2430.0000.0000.0000.000
96A279PHE00.051-0.00922.532-0.461-0.4610.0000.0000.0000.000
97A280GLY00.0300.01124.4840.2350.2350.0000.0000.0000.000
98A281ASP-1-0.849-0.92824.45710.39210.3920.0000.0000.0000.000
99A282ARG10.9240.96715.720-14.740-14.7400.0000.0000.0000.000
100A283ARG10.8070.94121.245-9.585-9.5850.0000.0000.0000.000
101A284LYS10.9460.97523.542-9.722-9.7220.0000.0000.0000.000
102A285ALA00.0260.01220.4560.0610.0610.0000.0000.0000.000
103A286PHE00.015-0.00116.0530.2470.2470.0000.0000.0000.000
104A287LEU00.0070.01120.2400.2160.2160.0000.0000.0000.000
105A288GLU-1-0.857-0.93522.04911.24911.2490.0000.0000.0000.000
106A289ASP-1-0.764-0.85516.82814.88114.8810.0000.0000.0000.000
107A290LEU0-0.005-0.00519.1500.2050.2050.0000.0000.0000.000
108A291ALA00.0020.02320.754-0.057-0.0570.0000.0000.0000.000
109A292VAL0-0.028-0.00818.808-0.118-0.1180.0000.0000.0000.000
110A293VAL0-0.013-0.01616.238-0.069-0.0690.0000.0000.0000.000
111A294THR0-0.069-0.06119.440-0.176-0.1760.0000.0000.0000.000
112A295GLY00.0170.01622.743-0.341-0.3410.0000.0000.0000.000
113A296GLY00.0170.02524.938-0.396-0.3960.0000.0000.0000.000
114A297GLN0-0.087-0.05126.697-0.003-0.0030.0000.0000.0000.000
115A298VAL0-0.017-0.00825.823-0.112-0.1120.0000.0000.0000.000
116A299VAL00.0310.00528.693-0.223-0.2230.0000.0000.0000.000
117A300ASN00.007-0.04331.155-0.002-0.0020.0000.0000.0000.000
118A301PRO00.0330.00933.099-0.106-0.1060.0000.0000.0000.000
119A302ASP-1-0.877-0.92434.1797.9637.9630.0000.0000.0000.000
120A303ALA0-0.149-0.06833.440-0.062-0.0620.0000.0000.0000.000
121A304GLY0-0.016-0.01135.562-0.107-0.1070.0000.0000.0000.000
122A305MET0-0.0370.03133.272-0.063-0.0630.0000.0000.0000.000
123A306VAL00.0310.01137.702-0.035-0.0350.0000.0000.0000.000
124A307LEU00.0030.00335.9910.0450.0450.0000.0000.0000.000
125A308ARG10.9450.96938.703-6.640-6.6400.0000.0000.0000.000
126A309GLU-1-1.033-1.01540.8766.8516.8510.0000.0000.0000.000
127A310VAL0-0.0260.01636.0160.0430.0430.0000.0000.0000.000
128A311GLY0-0.051-0.05237.752-0.133-0.1330.0000.0000.0000.000
129A312LEU0-0.022-0.03835.4390.1580.1580.0000.0000.0000.000
130A313GLU-1-0.846-0.90033.5738.2428.2420.0000.0000.0000.000
131A314VAL0-0.026-0.00331.5850.2430.2430.0000.0000.0000.000
132A315LEU0-0.048-0.02030.2500.2380.2380.0000.0000.0000.000
133A316GLY00.0640.04226.3320.0510.0510.0000.0000.0000.000
134A317SER0-0.084-0.04025.819-0.261-0.2610.0000.0000.0000.000
135A318ALA00.0570.01322.5950.4700.4700.0000.0000.0000.000
136A319ARG10.8780.95419.631-14.133-14.1330.0000.0000.0000.000
137A320ARG10.9830.99720.802-13.132-13.1320.0000.0000.0000.000
138A321VAL0-0.0030.00822.0570.4600.4600.0000.0000.0000.000
139A322VAL0-0.007-0.00121.277-0.480-0.4800.0000.0000.0000.000
140A323VAL0-0.0250.00022.1090.3620.3620.0000.0000.0000.000
141A324SER00.0580.02521.896-0.612-0.6120.0000.0000.0000.000
142A325LYS10.9680.96224.603-10.125-10.1250.0000.0000.0000.000
143A326ASP-1-1.002-1.00822.22512.11912.1190.0000.0000.0000.000
144A327ASP-1-0.870-0.92118.94814.35714.3570.0000.0000.0000.000
145A328THR00.014-0.02019.910-0.738-0.7380.0000.0000.0000.000
146A329VAL00.0250.02016.4680.6590.6590.0000.0000.0000.000
147A330ILE0-0.055-0.03618.024-0.830-0.8300.0000.0000.0000.000
148A331VAL00.0330.00917.1640.7730.7730.0000.0000.0000.000
149A332ASP-1-0.784-0.90017.90614.49014.4900.0000.0000.0000.000
150A333GLY00.0070.00119.439-0.761-0.7610.0000.0000.0000.000
151A334GLY0-0.003-0.01421.4410.2200.2200.0000.0000.0000.000
152A335GLY0-0.0090.01121.458-0.428-0.4280.0000.0000.0000.000
153A336THR0-0.012-0.01222.0240.3080.3080.0000.0000.0000.000
154A337ALA00.0620.01219.4280.4080.4080.0000.0000.0000.000
155A338GLU-1-0.924-0.96319.13811.92211.9220.0000.0000.0000.000
156A339ALA00.0100.02020.5940.1590.1590.0000.0000.0000.000
157A340VAL00.0660.02715.1580.2650.2650.0000.0000.0000.000
158A341ALA0-0.009-0.00515.7490.6770.6770.0000.0000.0000.000
159A342ASN0-0.022-0.02316.4830.6790.6790.0000.0000.0000.000
160A343ARG10.8150.91716.624-13.085-13.0850.0000.0000.0000.000
161A344ALA00.0520.01812.3550.3350.3350.0000.0000.0000.000
162A345LYS10.8920.94113.689-13.669-13.6690.0000.0000.0000.000
163A346HIS0-0.017-0.00615.827-0.149-0.1490.0000.0000.0000.000
164A347LEU00.0320.00613.093-0.191-0.1910.0000.0000.0000.000
165A348ARG10.9440.97110.515-19.098-19.0980.0000.0000.0000.000
166A349ALA0-0.0150.00813.403-0.065-0.0650.0000.0000.0000.000
167A350GLU-1-0.947-0.98016.53412.59912.5990.0000.0000.0000.000
168A351ILE0-0.079-0.04310.600-0.043-0.0430.0000.0000.0000.000
169A352ASP-1-0.931-0.96914.28617.45617.4560.0000.0000.0000.000
170A353LYS10.8850.94616.468-12.316-12.3160.0000.0000.0000.000
171A354SER0-0.0160.01017.022-0.721-0.7210.0000.0000.0000.000
172A355ASP-1-0.937-0.97218.54312.79212.7920.0000.0000.0000.000
173A356SER00.0240.01719.089-0.161-0.1610.0000.0000.0000.000
174A357ASP-1-0.845-0.94215.66117.04517.0450.0000.0000.0000.000
175A358TRP0-0.0030.00114.9940.9520.9520.0000.0000.0000.000
176A359ASP-1-0.870-0.95216.05513.72413.7240.0000.0000.0000.000
177A360ARG10.8830.94311.628-17.872-17.8720.0000.0000.0000.000
178A361GLU-1-0.851-0.90810.95720.28520.2850.0000.0000.0000.000
179A362LYS10.7520.88011.800-16.193-16.1930.0000.0000.0000.000
180A363LEU0-0.025-0.02113.5270.2040.2040.0000.0000.0000.000
181A364GLY00.0260.0129.4750.3760.3760.0000.0000.0000.000
182A365GLU-1-0.875-0.9458.77519.28419.2840.0000.0000.0000.000
183A366ARG10.8130.88810.309-14.793-14.7930.0000.0000.0000.000
184A367LEU0-0.035-0.0118.400-0.371-0.3710.0000.0000.0000.000
185A368ALA00.0050.0006.5460.2460.2460.0000.0000.0000.000
186A369LYS10.8390.9007.902-17.857-17.8570.0000.0000.0000.000
187A370LEU0-0.045-0.02111.288-0.451-0.4510.0000.0000.0000.000
188A371ALA0-0.017-0.0179.190-0.789-0.7890.0000.0000.0000.000
189A372GLY00.0540.03711.020-0.265-0.2650.0000.0000.0000.000
190A373GLY0-0.0210.00911.989-0.732-0.7320.0000.0000.0000.000
191A374VAL0-0.046-0.01615.217-1.060-1.0600.0000.0000.0000.000
192A375ALA00.0190.02616.6280.6640.6640.0000.0000.0000.000
193A376VAL0-0.021-0.01215.223-0.072-0.0720.0000.0000.0000.000
194A377ILE0-0.037-0.01018.640-0.595-0.5950.0000.0000.0000.000