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: QY7YY

Calculation Name: 3L3P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L3P

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VSC3

Base Structure: X-ray

Registration Date: 2023-06-21

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 266
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3067496.687666
FMO2-HF: Nuclear repulsion 2961192.457344
FMO2-HF: Total energy -106304.230322
FMO2-MP2: Total energy -106615.755815


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:253:SER)


Summations of interaction energy for fragment #1(A:253:SER)
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.
-15.588-5.6710.916-5.279-5.552-0.023
Interaction energy analysis for fragmet #1(A:253:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.004
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].
3A255ALA0-0.021-0.0073.070-1.3261.8500.083-1.637-1.6210.006
4A256ASP-1-0.934-0.9823.358-0.2291.9060.110-1.028-1.2160.000
5A257ALA00.0460.0324.4670.0060.217-0.001-0.034-0.1750.000
6A258VAL0-0.012-0.0105.8970.5850.5850.0000.0000.0000.000
7A259THR00.019-0.0017.8880.2720.2720.0000.0000.0000.000
8A260ALA00.0250.0339.1020.1590.1590.0000.0000.0000.000
9A261TRP0-0.028-0.00310.4250.2190.2190.0000.0000.0000.000
10A262PHE0-0.057-0.03112.9940.0680.0680.0000.0000.0000.000
11A263PRO0-0.044-0.02415.7160.0220.0220.0000.0000.0000.000
12A264GLU-1-0.816-0.92016.827-0.178-0.1780.0000.0000.0000.000
13A265ASN0-0.119-0.05617.056-0.007-0.0070.0000.0000.0000.000
14A266LYS10.9530.97116.7150.2810.2810.0000.0000.0000.000
15A267GLN00.0130.02212.113-0.008-0.0080.0000.0000.0000.000
16A268SER00.008-0.00511.752-0.092-0.0920.0000.0000.0000.000
17A269ASP-1-0.871-0.95211.846-0.471-0.4710.0000.0000.0000.000
18A270VAL00.0060.00110.956-0.061-0.0610.0000.0000.0000.000
19A271SER0-0.023-0.0096.882-0.132-0.1320.0000.0000.0000.000
20A272GLN0-0.068-0.0317.859-0.241-0.2410.0000.0000.0000.000
21A273ILE0-0.054-0.01110.290-0.071-0.0710.0000.0000.0000.000
22A274TRP00.012-0.0097.595-0.022-0.0220.0000.0000.0000.000
23A275HIS00.0280.0223.241-0.1010.1250.003-0.044-0.1860.000
24A276ALA0-0.076-0.0356.9310.0380.0380.0000.0000.0000.000
25A277PHE0-0.049-0.0268.6610.1990.1990.0000.0000.0000.000
26A278GLU-1-0.862-0.9342.688-14.771-10.7640.721-2.501-2.227-0.029
27A279HIS0-0.057-0.0325.7530.3040.3040.0000.0000.0000.000
28A280GLU-1-0.775-0.8488.426-0.568-0.5680.0000.0000.0000.000
29A281GLU-1-0.915-0.9729.994-0.145-0.1450.0000.0000.0000.000
30A282HIS00.0300.00111.000-0.064-0.0640.0000.0000.0000.000
31A283ALA0-0.0050.0136.805-0.024-0.0240.0000.0000.0000.000
32A284ASN0-0.035-0.0235.1960.0360.0360.0000.0000.0000.000
33A285THR00.0560.0315.9440.0770.0770.0000.0000.0000.000
34A286PHE00.0200.0088.648-0.014-0.0140.0000.0000.0000.000
35A287SER0-0.011-0.0254.2130.0600.2220.000-0.035-0.1270.000
36A288ALA00.0540.0376.187-0.069-0.0690.0000.0000.0000.000
37A289PHE0-0.010-0.0057.7570.0700.0700.0000.0000.0000.000
38A290LEU0-0.018-0.0178.1570.0940.0940.0000.0000.0000.000
39A291ASP-1-0.862-0.9375.605-1.085-1.0850.0000.0000.0000.000
40A292ARG10.7480.8209.0710.0820.0820.0000.0000.0000.000
41A293LEU0-0.080-0.02212.1660.0450.0450.0000.0000.0000.000
42A294SER0-0.055-0.03511.4560.0160.0160.0000.0000.0000.000
43A295ASP-1-0.901-0.93713.4090.0310.0310.0000.0000.0000.000
44A296THR0-0.063-0.01415.5760.0360.0360.0000.0000.0000.000
45A297VAL0-0.001-0.01318.727-0.019-0.0190.0000.0000.0000.000
46A298SER0-0.049-0.03020.2330.0100.0100.0000.0000.0000.000
47A299ALA00.0470.03423.234-0.006-0.0060.0000.0000.0000.000
48A300ARG10.8340.88026.3120.0220.0220.0000.0000.0000.000
49A301ASN0-0.0160.01125.0960.0000.0000.0000.0000.0000.000
50A302THR00.0900.04921.1320.0080.0080.0000.0000.0000.000
51A303SER0-0.049-0.04222.9970.0030.0030.0000.0000.0000.000
52A304GLY00.0900.05823.0080.0080.0080.0000.0000.0000.000
53A305PHE0-0.020-0.00518.015-0.011-0.0110.0000.0000.0000.000
54A306ARG10.9460.95214.5780.2470.2470.0000.0000.0000.000
55A307GLU-1-0.910-0.95417.940-0.199-0.1990.0000.0000.0000.000
56A308GLN0-0.038-0.01520.665-0.004-0.0040.0000.0000.0000.000
57A309VAL00.0040.00514.819-0.007-0.0070.0000.0000.0000.000
58A310ALA00.0520.03616.004-0.043-0.0430.0000.0000.0000.000
59A311ALA00.0060.00717.034-0.023-0.0230.0000.0000.0000.000
60A312TRP0-0.079-0.04414.359-0.001-0.0010.0000.0000.0000.000
61A313LEU00.0520.01811.832-0.001-0.0010.0000.0000.0000.000
62A314GLU-1-0.909-0.96415.255-0.400-0.4000.0000.0000.0000.000
63A315LYS10.8480.92117.2050.2830.2830.0000.0000.0000.000
64A316LEU00.0040.00913.8400.0240.0240.0000.0000.0000.000
65A317SER00.0030.01714.492-0.059-0.0590.0000.0000.0000.000
66A318ALA0-0.063-0.01715.5070.0120.0120.0000.0000.0000.000
67A319SER0-0.019-0.00319.0910.0110.0110.0000.0000.0000.000
68A320ALA00.0580.00416.794-0.032-0.0320.0000.0000.0000.000
69A321GLU-1-0.941-0.95817.619-0.223-0.2230.0000.0000.0000.000
70A322LEU0-0.024-0.02418.8130.0130.0130.0000.0000.0000.000
71A323ARG10.8070.87311.8260.7000.7000.0000.0000.0000.000
72A324GLN00.0420.03515.019-0.042-0.0420.0000.0000.0000.000
73A325GLN0-0.023-0.01116.7350.0170.0170.0000.0000.0000.000
74A326SER0-0.030-0.03015.8620.0260.0260.0000.0000.0000.000
75A327PHE00.000-0.0039.263-0.039-0.0390.0000.0000.0000.000
76A328ALA00.0530.03113.4420.0290.0290.0000.0000.0000.000
77A329VAL0-0.044-0.02016.0300.0360.0360.0000.0000.0000.000
78A330ALA0-0.010-0.00613.0390.0270.0270.0000.0000.0000.000
79A331ALA0-0.0120.01013.1200.0350.0350.0000.0000.0000.000
80A332ASP-1-0.878-0.92514.037-0.005-0.0050.0000.0000.0000.000
81A333ALA0-0.021-0.00716.1840.0290.0290.0000.0000.0000.000
82A334THR0-0.064-0.06311.1860.0180.0180.0000.0000.0000.000
83A335GLU-1-0.914-0.95014.5520.0930.0930.0000.0000.0000.000
84A336SER00.0380.02816.6070.0210.0210.0000.0000.0000.000
85A337CYM-1-0.853-0.88316.0910.0600.0600.0000.0000.0000.000
86A338GLU-1-0.971-0.99413.4100.4030.4030.0000.0000.0000.000
87A339ASP-1-0.833-0.90517.3080.1270.1270.0000.0000.0000.000
88A340ARG10.8960.93820.889-0.049-0.0490.0000.0000.0000.000
89A341VAL0-0.0150.02216.9790.0010.0010.0000.0000.0000.000
90A342ALA0-0.0050.00220.3770.0100.0100.0000.0000.0000.000
91A343LEU0-0.033-0.00922.341-0.006-0.0060.0000.0000.0000.000
92A344THR00.003-0.03223.035-0.008-0.0080.0000.0000.0000.000
93A345TRP0-0.013-0.00423.4160.0030.0030.0000.0000.0000.000
94A346ASN00.0300.00725.266-0.001-0.0010.0000.0000.0000.000
95A347ASN0-0.002-0.00328.101-0.005-0.0050.0000.0000.0000.000
96A348LEU00.0210.01424.272-0.007-0.0070.0000.0000.0000.000
97A349ARG10.9040.96328.589-0.140-0.1400.0000.0000.0000.000
98A350LYS10.9480.98430.852-0.088-0.0880.0000.0000.0000.000
99A351THR0-0.042-0.03831.131-0.009-0.0090.0000.0000.0000.000
100A352LEU0-0.017-0.00731.275-0.005-0.0050.0000.0000.0000.000
101A353LEU00.0140.01233.539-0.005-0.0050.0000.0000.0000.000
102A354VAL0-0.007-0.00736.586-0.006-0.0060.0000.0000.0000.000
103A355HIS00.0280.02635.870-0.005-0.0050.0000.0000.0000.000
104A356GLN00.017-0.01135.500-0.005-0.0050.0000.0000.0000.000
105A357ALA0-0.0270.00038.731-0.003-0.0030.0000.0000.0000.000
106A358SER0-0.035-0.02440.801-0.004-0.0040.0000.0000.0000.000
107A359GLU-1-0.986-1.00039.1110.0890.0890.0000.0000.0000.000
108A360GLY0-0.021-0.00542.238-0.002-0.0020.0000.0000.0000.000
109A361LEU0-0.092-0.03738.6330.0000.0000.0000.0000.0000.000
110A362PHE00.045-0.00938.8120.0000.0000.0000.0000.0000.000
111A363ASP-1-0.790-0.82644.5950.0660.0660.0000.0000.0000.000
112A364ASN0-0.046-0.02847.926-0.001-0.0010.0000.0000.0000.000
113A365ASP-1-0.933-0.96444.4320.0800.0800.0000.0000.0000.000
114A366THR00.0430.00145.6500.0020.0020.0000.0000.0000.000
115A367GLY0-0.009-0.00646.6800.0000.0000.0000.0000.0000.000
116A368ALA00.0370.01741.6700.0010.0010.0000.0000.0000.000
117A369LEU00.0070.01141.0540.0030.0030.0000.0000.0000.000
118A370LEU00.0310.01642.4000.0000.0000.0000.0000.0000.000
119A371SER0-0.059-0.02741.274-0.001-0.0010.0000.0000.0000.000
120A372LEU00.008-0.00936.2710.0020.0020.0000.0000.0000.000
121A373GLY00.0250.01038.4170.0020.0020.0000.0000.0000.000
122A374ARG10.8890.93140.427-0.062-0.0620.0000.0000.0000.000
123A375GLU-1-0.812-0.90033.4330.1180.1180.0000.0000.0000.000
124A376MET0-0.039-0.03033.1940.0040.0040.0000.0000.0000.000
125A377PHE00.0590.03836.808-0.002-0.0020.0000.0000.0000.000
126A378ARG10.8000.86837.272-0.078-0.0780.0000.0000.0000.000
127A379LEU0-0.025-0.01331.412-0.002-0.0020.0000.0000.0000.000
128A380GLU-1-0.850-0.92834.3970.0580.0580.0000.0000.0000.000
129A381ILE0-0.0160.00036.630-0.005-0.0050.0000.0000.0000.000
130A382LEU0-0.079-0.04832.417-0.004-0.0040.0000.0000.0000.000
131A383GLU-1-0.950-0.96532.2260.0650.0650.0000.0000.0000.000
132A384ASP-1-0.925-0.97034.3070.0380.0380.0000.0000.0000.000
133A385ILE0-0.100-0.03934.852-0.005-0.0050.0000.0000.0000.000
134A386ALA0-0.001-0.00131.796-0.003-0.0030.0000.0000.0000.000
135A387ARG10.8960.94331.383-0.036-0.0360.0000.0000.0000.000
136A388ASP-1-0.891-0.94335.3800.0210.0210.0000.0000.0000.000
137A389LYS10.8970.95033.982-0.030-0.0300.0000.0000.0000.000
138A390VAL0-0.0300.01131.631-0.006-0.0060.0000.0000.0000.000
139A398GLU-1-0.866-0.94125.0120.0020.0020.0000.0000.0000.000
140A399ILE0-0.074-0.05125.5800.0030.0030.0000.0000.0000.000
141A400GLU-1-0.840-0.90522.7660.0450.0450.0000.0000.0000.000
142A401VAL00.0220.00425.2410.0090.0090.0000.0000.0000.000
143A402TYR0-0.043-0.02427.9470.0020.0020.0000.0000.0000.000
144A403LEU00.0150.01722.3260.0050.0050.0000.0000.0000.000
145A404ALA00.0310.02526.4490.0110.0110.0000.0000.0000.000
146A405PHE0-0.052-0.04527.3290.0020.0020.0000.0000.0000.000
147A406GLN00.017-0.00827.250-0.005-0.0050.0000.0000.0000.000
148A407THR0-0.049-0.03625.0450.0100.0100.0000.0000.0000.000
149A408MET0-0.037-0.01827.1750.0020.0020.0000.0000.0000.000
150A409LEU0-0.072-0.03930.619-0.004-0.0040.0000.0000.0000.000
151A410ALA00.0590.03930.178-0.003-0.0030.0000.0000.0000.000
152A411GLU-1-0.944-0.96032.2970.0960.0960.0000.0000.0000.000
153A412LYS10.8620.93334.647-0.069-0.0690.0000.0000.0000.000
154A413LEU0-0.011-0.01136.284-0.006-0.0060.0000.0000.0000.000
155A414GLN0-0.074-0.02736.115-0.003-0.0030.0000.0000.0000.000
156A415LEU00.0320.01831.878-0.002-0.0020.0000.0000.0000.000
157A416SER0-0.074-0.03430.4510.0060.0060.0000.0000.0000.000
158A417THR0-0.0300.00526.3520.0130.0130.0000.0000.0000.000
159A427VAL0-0.027-0.02527.150-0.003-0.0030.0000.0000.0000.000
160A428SER0-0.028-0.02223.8840.0130.0130.0000.0000.0000.000
161A429GLY00.0850.06025.863-0.009-0.0090.0000.0000.0000.000
162A430VAL00.0080.01427.767-0.009-0.0090.0000.0000.0000.000
163A431THR0-0.042-0.01931.5530.0020.0020.0000.0000.0000.000
164A432ALA00.020-0.00334.4800.0040.0040.0000.0000.0000.000
165A433ASN0-0.065-0.06235.4040.0040.0040.0000.0000.0000.000
166A434ASP-1-0.728-0.86735.4320.0260.0260.0000.0000.0000.000
167A435LEU0-0.025-0.01632.5670.0010.0010.0000.0000.0000.000
168A436ARG10.7750.88036.730-0.048-0.0480.0000.0000.0000.000
169A437THR00.0280.01940.2250.0000.0000.0000.0000.0000.000
170A438ALA00.0750.03537.2990.0000.0000.0000.0000.0000.000
171A439GLU-1-0.815-0.89638.8240.0560.0560.0000.0000.0000.000
172A440ALA0-0.018-0.01440.0650.0000.0000.0000.0000.0000.000
173A441MET0-0.023-0.01440.840-0.003-0.0030.0000.0000.0000.000
174A442VAL00.0130.02738.5190.0000.0000.0000.0000.0000.000
175A443ARG10.8790.93441.819-0.057-0.0570.0000.0000.0000.000
176A444SER0-0.0310.00144.637-0.001-0.0010.0000.0000.0000.000
177A445ARG10.9090.92442.323-0.040-0.0400.0000.0000.0000.000
178A446GLU-1-0.809-0.86042.5390.0630.0630.0000.0000.0000.000
179A447GLU-1-1.039-1.02245.3880.0370.0370.0000.0000.0000.000
180A448ASN0-0.065-0.02448.626-0.002-0.0020.0000.0000.0000.000
181A449GLU-1-0.777-0.87346.1460.0380.0380.0000.0000.0000.000
182A450PHE0-0.028-0.00943.3630.0010.0010.0000.0000.0000.000
183A451THR00.0330.03546.3310.0020.0020.0000.0000.0000.000
184A452ASP-1-0.823-0.92349.4260.0380.0380.0000.0000.0000.000
185A453TRP0-0.043-0.01639.6110.0010.0010.0000.0000.0000.000
186A454PHE0-0.036-0.03343.7290.0030.0030.0000.0000.0000.000
187A455SER0-0.019-0.02545.9660.0010.0010.0000.0000.0000.000
188A456LEU0-0.042-0.02146.140-0.001-0.0010.0000.0000.0000.000
189A457TRP00.0150.02338.0360.0030.0030.0000.0000.0000.000
190A458GLY00.0360.00441.3480.0000.0000.0000.0000.0000.000
191A459PRO0-0.030-0.03039.109-0.001-0.0010.0000.0000.0000.000
192A460TRP00.0410.01441.8500.0020.0020.0000.0000.0000.000
193A461HIS00.0330.01945.2940.0000.0000.0000.0000.0000.000
194A462ALA0-0.092-0.04143.189-0.002-0.0020.0000.0000.0000.000
195A463VAL00.0470.02244.9100.0000.0000.0000.0000.0000.000
196A464LEU0-0.0160.00147.221-0.002-0.0020.0000.0000.0000.000
197A465LYS10.9060.96545.761-0.057-0.0570.0000.0000.0000.000
198A466ARG10.7510.86345.882-0.071-0.0710.0000.0000.0000.000
199A467THR0-0.032-0.01250.124-0.001-0.0010.0000.0000.0000.000
200A468GLU-1-0.905-0.96152.4850.0440.0440.0000.0000.0000.000
201A469ALA00.0370.01654.343-0.001-0.0010.0000.0000.0000.000
202A470ASP-1-0.924-0.96655.3620.0380.0380.0000.0000.0000.000
203A471ARG10.9050.94157.391-0.040-0.0400.0000.0000.0000.000
204A472TRP00.0060.00649.7430.0000.0000.0000.0000.0000.000
205A473ALA0-0.002-0.01055.489-0.001-0.0010.0000.0000.0000.000
206A474GLN00.0060.01858.167-0.002-0.0020.0000.0000.0000.000
207A475ALA00.003-0.00655.595-0.001-0.0010.0000.0000.0000.000
208A476GLU-1-0.873-0.95752.9080.0380.0380.0000.0000.0000.000
209A477GLU-1-0.953-0.97356.5360.0280.0280.0000.0000.0000.000
210A478GLN0-0.006-0.00559.420-0.001-0.0010.0000.0000.0000.000
211A479LYS10.9080.97751.652-0.037-0.0370.0000.0000.0000.000
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