Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 1N9LZ

Calculation Name: 3DSH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DSH

Chain ID: A

ChEMBL ID:

UniProt ID: Q13568

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:


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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2807059.163009
FMO2-HF: Nuclear repulsion 2710924.968406
FMO2-HF: Total energy -96134.194603
FMO2-MP2: Total energy -96414.51285


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:222:GLU)


Summations of interaction energy for fragment #1(A:222: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.
-19.721-22.68431.912-14.546-14.4040.146
Interaction energy analysis for fragmet #1(A:222:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.798 / q_NPA : -0.901
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].
3A224LEU00.0200.0153.569-7.748-5.081-0.008-1.235-1.4240.002
4A225LEU00.0150.0172.320-4.390-3.4112.199-1.205-1.974-0.001
5A226PRO00.0240.0014.783-2.922-2.766-0.001-0.023-0.1310.000
6A227ASP-1-0.880-0.9387.91020.97220.9720.0000.0000.0000.000
7A228LEU0-0.086-0.0326.110-1.631-1.6310.0000.0000.0000.000
8A229LEU0-0.002-0.0087.506-1.617-1.6170.0000.0000.0000.000
9A230ILE0-0.053-0.02210.345-1.592-1.5920.0000.0000.0000.000
10A231SER00.039-0.00812.636-0.911-0.9110.0000.0000.0000.000
11A232PRO00.0030.00115.315-0.039-0.0390.0000.0000.0000.000
12A233HIS0-0.0280.00614.589-0.745-0.7450.0000.0000.0000.000
13A234MET0-0.045-0.01112.081-0.310-0.3100.0000.0000.0000.000
14A235LEU0-0.014-0.01112.8060.1030.1030.0000.0000.0000.000
15A236PRO00.0310.02116.975-0.411-0.4110.0000.0000.0000.000
16A237LEU0-0.034-0.02515.755-0.022-0.0220.0000.0000.0000.000
17A238THR0-0.040-0.02719.5860.1070.1070.0000.0000.0000.000
18A239ASP-1-0.896-0.94022.44711.31211.3120.0000.0000.0000.000
19A240LEU0-0.059-0.02822.7440.5550.5550.0000.0000.0000.000
20A241GLU-1-0.822-0.87624.76111.69911.6990.0000.0000.0000.000
21A242ILE0-0.012-0.00926.8410.2220.2220.0000.0000.0000.000
22A243LYS10.8830.93229.677-10.532-10.5320.0000.0000.0000.000
23A244PHE00.0430.01331.6600.0440.0440.0000.0000.0000.000
24A245GLN0-0.060-0.04434.9550.1120.1120.0000.0000.0000.000
25A246TYR00.035-0.01136.7590.0170.0170.0000.0000.0000.000
26A247ARG10.8890.94840.373-7.235-7.2350.0000.0000.0000.000
27A248GLY00.0090.00641.093-0.193-0.1930.0000.0000.0000.000
28A249ARG10.8760.94741.316-7.209-7.2090.0000.0000.0000.000
29A250PRO00.0170.01039.0240.1810.1810.0000.0000.0000.000
30A251PRO00.0060.01034.368-0.078-0.0780.0000.0000.0000.000
31A252ARG10.9470.96836.119-7.762-7.7620.0000.0000.0000.000
32A253ALA0-0.017-0.01131.1660.1090.1090.0000.0000.0000.000
33A254LEU0-0.0100.00831.886-0.280-0.2800.0000.0000.0000.000
34A255THR00.0410.01326.6590.1870.1870.0000.0000.0000.000
35A256ILE0-0.029-0.00127.867-0.356-0.3560.0000.0000.0000.000
36A257SER00.0720.03126.7560.2560.2560.0000.0000.0000.000
37A258ASN0-0.015-0.01727.6300.3180.3180.0000.0000.0000.000
38A259PRO00.0300.00426.2580.2180.2180.0000.0000.0000.000
39A260HIS0-0.0080.00626.8020.2480.2480.0000.0000.0000.000
40A261GLY0-0.0060.00828.1740.1450.1450.0000.0000.0000.000
41A262CYS0-0.050-0.01628.981-0.282-0.2820.0000.0000.0000.000
42A263ARG10.8670.92031.821-7.759-7.7590.0000.0000.0000.000
43A264LEU0-0.0150.01031.714-0.164-0.1640.0000.0000.0000.000
44A265PHE0-0.017-0.01635.636-0.032-0.0320.0000.0000.0000.000
45A266TYR00.002-0.00339.3490.0290.0290.0000.0000.0000.000
46A267SER00.029-0.01642.808-0.095-0.0950.0000.0000.0000.000
47A268GLN00.0240.01845.7220.1150.1150.0000.0000.0000.000
48A269LEU0-0.053-0.01947.134-0.100-0.1000.0000.0000.0000.000
49A270GLU-1-0.792-0.87943.8557.1927.1920.0000.0000.0000.000
50A271ALA0-0.013-0.00341.080-0.069-0.0690.0000.0000.0000.000
51A272THR0-0.004-0.00843.043-0.057-0.0570.0000.0000.0000.000
52A273GLN00.010-0.00141.1880.1780.1780.0000.0000.0000.000
53A274GLU-1-0.886-0.95944.3936.5806.5800.0000.0000.0000.000
54A275GLN0-0.020-0.00545.5850.0060.0060.0000.0000.0000.000
55A276VAL00.0080.00939.2260.1080.1080.0000.0000.0000.000
56A277GLU-1-0.923-0.95440.5887.6987.6980.0000.0000.0000.000
57A278LEU0-0.044-0.00641.9010.0890.0890.0000.0000.0000.000
58A279PHE00.004-0.00841.1580.1100.1100.0000.0000.0000.000
59A280GLY00.0330.02637.6560.1690.1690.0000.0000.0000.000
60A281PRO0-0.008-0.01934.720-0.187-0.1870.0000.0000.0000.000
61A282ILE00.0330.01337.3480.0960.0960.0000.0000.0000.000
62A283SER0-0.044-0.01133.727-0.079-0.0790.0000.0000.0000.000
63A284LEU0-0.046-0.00131.7890.2140.2140.0000.0000.0000.000
64A285GLU-1-0.798-0.91032.3698.6828.6820.0000.0000.0000.000
65A286GLN00.0000.00534.281-0.003-0.0030.0000.0000.0000.000
66A287VAL0-0.0020.00033.266-0.111-0.1110.0000.0000.0000.000
67A288ARG10.7790.85936.657-7.045-7.0450.0000.0000.0000.000
68A289PHE0-0.036-0.02636.4260.1380.1380.0000.0000.0000.000
69A290PRO00.0030.00038.512-0.198-0.1980.0000.0000.0000.000
70A291SER00.028-0.00341.620-0.017-0.0170.0000.0000.0000.000
71A292PRO0-0.005-0.00744.8520.0950.0950.0000.0000.0000.000
72A293GLU-1-0.856-0.90046.2906.2396.2390.0000.0000.0000.000
73A294ASP-1-0.908-0.93946.6356.6016.6010.0000.0000.0000.000
74A295ILE0-0.097-0.05244.6020.0750.0750.0000.0000.0000.000
75A296PRO00.0150.01747.876-0.125-0.1250.0000.0000.0000.000
76A297SER0-0.017-0.00349.747-0.143-0.1430.0000.0000.0000.000
77A298ASP-1-0.740-0.87151.0415.8985.8980.0000.0000.0000.000
78A299LYS10.9140.97151.774-6.026-6.0260.0000.0000.0000.000
79A300GLN0-0.014-0.03344.6140.0130.0130.0000.0000.0000.000
80A301ARG10.8890.94547.903-5.955-5.9550.0000.0000.0000.000
81A302PHE0-0.0120.00749.3880.0380.0380.0000.0000.0000.000
82A303TYR00.026-0.00547.308-0.032-0.0320.0000.0000.0000.000
83A304THR0-0.031-0.03243.7570.1490.1490.0000.0000.0000.000
84A305ASN00.013-0.01345.6970.1350.1350.0000.0000.0000.000
85A306GLN0-0.0060.01348.3090.0420.0420.0000.0000.0000.000
86A307LEU0-0.037-0.01042.0970.0520.0520.0000.0000.0000.000
87A308LEU0-0.042-0.02942.1700.0960.0960.0000.0000.0000.000
88A309ASP-1-0.918-0.95044.7866.3606.3600.0000.0000.0000.000
89A310VAL0-0.0360.00744.303-0.014-0.0140.0000.0000.0000.000
90A311LEU0-0.020-0.04438.5520.2270.2270.0000.0000.0000.000
91A312ASP-1-0.788-0.84741.6116.9596.9590.0000.0000.0000.000
92A313ARG10.7470.83241.187-7.512-7.5120.0000.0000.0000.000
93A314GLY00.0320.01838.2690.1370.1370.0000.0000.0000.000
94A315LEU0-0.060-0.03431.369-0.015-0.0150.0000.0000.0000.000
95A316ILE0-0.0040.00931.1230.0390.0390.0000.0000.0000.000
96A317LEU0-0.026-0.01327.6460.2360.2360.0000.0000.0000.000
97A318GLN00.0440.00727.2980.0220.0220.0000.0000.0000.000
98A319LEU00.0450.02521.2720.3240.3240.0000.0000.0000.000
99A320GLN00.0070.00922.658-0.407-0.4070.0000.0000.0000.000
100A321GLY00.0270.02119.8160.5490.5490.0000.0000.0000.000
101A322GLN00.0450.00915.561-0.914-0.9140.0000.0000.0000.000
102A323ASP-1-0.752-0.83317.70016.92116.9210.0000.0000.0000.000
103A324LEU0-0.0100.00119.617-0.684-0.6840.0000.0000.0000.000
104A325TYR0-0.019-0.01921.613-0.016-0.0160.0000.0000.0000.000
105A326ALA00.0340.01625.689-0.269-0.2690.0000.0000.0000.000
106A327ILE00.0000.00329.0360.0220.0220.0000.0000.0000.000
107A328ARG10.8520.94132.440-8.503-8.5030.0000.0000.0000.000
108A329LEU00.0860.03635.248-0.062-0.0620.0000.0000.0000.000
109A330CYS0-0.092-0.01238.467-0.192-0.1920.0000.0000.0000.000
110A331GLN00.009-0.00540.4270.0870.0870.0000.0000.0000.000
111A332CYS0-0.0040.00539.852-0.005-0.0050.0000.0000.0000.000
112A333LYS10.9640.97438.896-7.501-7.5010.0000.0000.0000.000
113A334VAL00.0470.02533.364-0.061-0.0610.0000.0000.0000.000
114A335PHE00.0050.01233.4150.0030.0030.0000.0000.0000.000
115A336TRP00.0320.01924.0820.0470.0470.0000.0000.0000.000
116A337SER00.0070.01526.508-0.183-0.1830.0000.0000.0000.000
117A338GLY00.0430.01523.450-0.203-0.2030.0000.0000.0000.000
118A339PRO0-0.0040.01718.040-0.069-0.0690.0000.0000.0000.000
119A340CYS0-0.035-0.00418.7230.5820.5820.0000.0000.0000.000
120A341ALA0-0.058-0.00620.923-0.432-0.4320.0000.0000.0000.000
121A342SER00.0200.00122.9370.5410.5410.0000.0000.0000.000
122A343ALA0-0.016-0.00622.540-0.260-0.2600.0000.0000.0000.000
123A344HIS0-0.032-0.01924.6080.6220.6220.0000.0000.0000.000
124A345ASP-1-0.874-0.92227.1029.5539.5530.0000.0000.0000.000
125A346SER0-0.037-0.04029.1840.2770.2770.0000.0000.0000.000
126A347CYS0-0.090-0.02831.584-0.141-0.1410.0000.0000.0000.000
127A348PRO00.0110.00032.4770.2550.2550.0000.0000.0000.000
128A349ASN0-0.010-0.01727.928-0.068-0.0680.0000.0000.0000.000
129A350PRO0-0.042-0.01731.9590.0670.0670.0000.0000.0000.000
130A351ILE00.0240.01030.7640.1660.1660.0000.0000.0000.000
131A352GLN00.008-0.00533.214-0.412-0.4120.0000.0000.0000.000
132A353ARG10.8020.90234.779-7.441-7.4410.0000.0000.0000.000
133A354GLU-1-0.780-0.89836.0187.7857.7850.0000.0000.0000.000
134A355VAL0-0.0220.01131.3450.0310.0310.0000.0000.0000.000
135A356LYS10.8680.94026.104-11.437-11.4370.0000.0000.0000.000
136A357THR0-0.018-0.01427.3680.1540.1540.0000.0000.0000.000
137A358LYS10.8340.90917.631-16.385-16.3850.0000.0000.0000.000
138A359LEU0-0.028-0.02323.291-0.072-0.0720.0000.0000.0000.000
139A360PHE00.030-0.00615.4890.2160.2160.0000.0000.0000.000
140A361SER00.013-0.02415.582-0.183-0.1830.0000.0000.0000.000
141A362LEU00.0100.01612.8820.8560.8560.0000.0000.0000.000
142A363GLU-1-0.924-0.95311.08123.40023.4000.0000.0000.0000.000
143A364HIS0-0.034-0.02510.0252.0672.0670.0000.0000.0000.000
144A365PHE0-0.012-0.01210.8231.8401.8400.0000.0000.0000.000
145A366LEU00.0260.0236.4640.9790.9790.0000.0000.0000.000
146A367ASN00.008-0.0096.2155.8895.8890.0000.0000.0000.000
147A368GLU-1-0.868-0.9436.24633.69833.6980.0000.0000.0000.000
148A369LEU0-0.081-0.0188.3920.5640.5640.0000.0000.0000.000
149A370ILE00.0150.0062.441-1.1710.5131.916-1.122-2.4780.007
150A371LEU0-0.049-0.0213.9685.6186.0260.002-0.076-0.3340.000
151A372PHE00.007-0.0016.315-2.638-2.6380.0000.0000.0000.000
152A373GLN0-0.041-0.0116.612-1.639-1.6390.0000.0000.0000.000
153A374LYS10.7670.8651.771-142.854-151.71127.804-10.885-8.0630.138
154A375GLY00.0150.0217.051-1.882-1.8820.0000.0000.0000.000
155A376GLN0-0.072-0.0326.1603.3993.3990.0000.0000.0000.000
156A377THR0-0.017-0.0149.529-2.404-2.4040.0000.0000.0000.000
157A378ASN00.0440.01311.8620.5540.5540.0000.0000.0000.000
158A379THR0-0.050-0.02614.199-1.405-1.4050.0000.0000.0000.000
159A380PRO00.0060.02013.7031.4001.4000.0000.0000.0000.000
160A381PRO00.0380.03111.617-1.170-1.1700.0000.0000.0000.000
161A382PRO0-0.014-0.01214.308-1.014-1.0140.0000.0000.0000.000
162A383PHE00.049-0.00816.9300.2440.2440.0000.0000.0000.000
163A384GLU-1-0.912-0.93318.66611.64711.6470.0000.0000.0000.000
164A385ILE0-0.031-0.02222.3230.1110.1110.0000.0000.0000.000
165A386PHE0-0.015-0.01324.895-0.445-0.4450.0000.0000.0000.000
166A387PHE00.0330.00627.861-0.013-0.0130.0000.0000.0000.000
167A388CYS0-0.077-0.04231.457-0.229-0.2290.0000.0000.0000.000
168A389PHE00.0420.00133.796-0.011-0.0110.0000.0000.0000.000
169A390GLY00.032-0.00437.751-0.159-0.1590.0000.0000.0000.000
170A391GLU-1-0.880-0.94339.0597.6437.6430.0000.0000.0000.000
171A392GLU-1-0.935-0.95837.4578.2058.2050.0000.0000.0000.000
172A393TRP00.0140.00129.699-0.246-0.2460.0000.0000.0000.000
173A394PRO00.0790.03529.6860.0220.0220.0000.0000.0000.000
174A395ASP-1-0.732-0.84432.5158.0088.0080.0000.0000.0000.000
175A396ARG10.9670.98534.975-7.854-7.8540.0000.0000.0000.000
176A397LYS10.7810.87637.190-7.913-7.9130.0000.0000.0000.000
177A398PRO00.0350.02136.2170.1640.1640.0000.0000.0000.000
178A399ARG11.0391.00828.383-10.861-10.8610.0000.0000.0000.000
179A400GLU-1-0.879-0.93535.3498.9628.9620.0000.0000.0000.000
180A401LYS10.8700.92738.468-7.650-7.6500.0000.0000.0000.000
181A402LYS10.7940.91236.518-8.579-8.5790.0000.0000.0000.000
182A403LEU0-0.022-0.01239.605-0.010-0.0100.0000.0000.0000.000
183A404ILE00.0230.00937.721-0.047-0.0470.0000.0000.0000.000
184A405THR0-0.039-0.01033.6080.1830.1830.0000.0000.0000.000
185A406VAL00.0090.00130.932-0.167-0.1670.0000.0000.0000.000
186A407GLN0-0.036-0.00626.120-0.268-0.2680.0000.0000.0000.000
187A408VAL00.001-0.00525.007-0.249-0.2490.0000.0000.0000.000
188A409VAL00.0170.00521.1880.4490.4490.0000.0000.0000.000
189A410PRO00.0370.02918.698-0.438-0.4380.0000.0000.0000.000
190A411VAL00.0370.01419.2160.7100.7100.0000.0000.0000.000
191A412ALA00.0050.00916.1840.4260.4260.0000.0000.0000.000
192A413ALA00.004-0.00114.7320.9650.9650.0000.0000.0000.000
193A414ARG10.7960.87615.101-12.565-12.5650.0000.0000.0000.000
194A415LEU00.0420.01216.6550.3080.3080.0000.0000.0000.000
195A416LEU0-0.0070.00810.0730.5790.5790.0000.0000.0000.000
196A417LEU00.0220.00512.1611.1611.1610.0000.0000.0000.000
197A418GLU-1-0.911-0.95813.68515.50415.5040.0000.0000.0000.000
198A419MET0-0.018-0.00711.4870.4130.4130.0000.0000.0000.000
199A420PHE00.025-0.0145.3600.7590.7590.0000.0000.0000.000
200A421SER0-0.065-0.04410.9470.6240.6240.0000.0000.0000.000
201A422GLY0-0.070-0.02313.943-0.604-0.6040.0000.0000.0000.000
202A423GLU-1-0.958-0.95610.36022.01722.0170.0000.0000.0000.000
203A424LEU0-0.0090.00211.4051.3851.3850.0000.0000.0000.000
204A425SER00.0020.00010.3920.4080.4080.0000.0000.0000.000
205A426TRP00.007-0.00512.011-2.004-2.0040.0000.0000.0000.000
206A427SER0-0.0050.00512.045-0.643-0.6430.0000.0000.0000.000
207A428ALA0-0.040-0.02411.660-1.180-1.1800.0000.0000.0000.000
208A429ASP-1-0.857-0.92813.60617.69717.6970.0000.0000.0000.000
209A430ASP-1-0.939-0.96915.06018.53718.5370.0000.0000.0000.000
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