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: 4J31N

Calculation Name: 1YQF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQF

Chain ID: A

ChEMBL ID:

UniProt ID: Q4Q7K6

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1809308.864768
FMO2-HF: Nuclear repulsion 1736396.074906
FMO2-HF: Total energy -72912.789861
FMO2-MP2: Total energy -73124.11187


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:14:ALA)


Summations of interaction energy for fragment #1(A:14:ALA)
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.
-8.522-2.5212.377-3.659-4.72-0.023
Interaction energy analysis for fragmet #1(A:14:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.015
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].
3A16ASP-1-0.888-0.9502.496-9.481-4.6531.229-2.853-3.205-0.020
4A17ALA00.0460.0272.3880.1721.1041.145-0.764-1.313-0.003
5A18ALA0-0.010-0.0113.9281.0061.2470.003-0.042-0.2020.000
6A19LEU00.0010.0086.3520.7000.7000.0000.0000.0000.000
7A20ALA00.0270.0187.2560.3840.3840.0000.0000.0000.000
8A21ASP-1-0.798-0.8798.210-0.670-0.6700.0000.0000.0000.000
9A22ALA0-0.023-0.00710.1460.2060.2060.0000.0000.0000.000
10A23THR00.0390.01111.5520.1520.1520.0000.0000.0000.000
11A24ARG10.7880.87911.9540.7100.7100.0000.0000.0000.000
12A25ARG10.8480.90110.5430.9390.9390.0000.0000.0000.000
13A26GLU-1-0.881-0.93116.075-0.424-0.4240.0000.0000.0000.000
14A27LEU0-0.023-0.01516.9840.0540.0540.0000.0000.0000.000
15A28GLU-1-0.923-0.95117.049-0.379-0.3790.0000.0000.0000.000
16A29GLU-1-0.967-0.97820.071-0.311-0.3110.0000.0000.0000.000
17A30GLU-1-0.742-0.87521.858-0.240-0.2400.0000.0000.0000.000
18A31MET0-0.093-0.03623.0070.0380.0380.0000.0000.0000.000
19A32GLY0-0.038-0.01124.6670.0220.0220.0000.0000.0000.000
20A33ARG10.7620.86626.4190.2330.2330.0000.0000.0000.000
21A34SER0-0.051-0.03628.5190.0060.0060.0000.0000.0000.000
22A35ASP-1-0.900-0.93130.678-0.174-0.1740.0000.0000.0000.000
23A36LYS10.8150.89526.4420.2190.2190.0000.0000.0000.000
24A37PRO00.010-0.00231.2300.0110.0110.0000.0000.0000.000
25A38GLU-1-0.920-0.95233.911-0.113-0.1130.0000.0000.0000.000
26A39GLN0-0.043-0.02236.3110.0010.0010.0000.0000.0000.000
27A40PRO00.0020.01837.6250.0060.0060.0000.0000.0000.000
28A41THR00.000-0.01241.1210.0000.0000.0000.0000.0000.000
29A42PRO0-0.031-0.00843.4940.0010.0010.0000.0000.0000.000
30A43PRO00.0320.00445.7840.0030.0030.0000.0000.0000.000
31A44ALA00.002-0.00349.4340.0000.0000.0000.0000.0000.000
32A45GLY0-0.046-0.02452.1060.0010.0010.0000.0000.0000.000
33A46TRP0-0.011-0.00247.8660.0010.0010.0000.0000.0000.000
34A47GLN0-0.0110.00043.9460.0000.0000.0000.0000.0000.000
35A48VAL00.0270.02040.1860.0000.0000.0000.0000.0000.000
36A49VAL0-0.013-0.00441.1870.0000.0000.0000.0000.0000.000
37A50ARG10.9080.96130.9110.1520.1520.0000.0000.0000.000
38A51LYS10.9540.98536.6070.1040.1040.0000.0000.0000.000
39A52PRO0-0.003-0.01735.360-0.008-0.0080.0000.0000.0000.000
40A53GLY0-0.006-0.00631.0980.0010.0010.0000.0000.0000.000
41A54THR0-0.059-0.01430.429-0.008-0.0080.0000.0000.0000.000
42A55CYS00.0690.04130.294-0.001-0.0010.0000.0000.0000.000
43A56THR0-0.040-0.01433.0710.0030.0030.0000.0000.0000.000
44A57PHE0-0.018-0.02034.3230.0010.0010.0000.0000.0000.000
45A58ASP-1-0.774-0.85039.394-0.085-0.0850.0000.0000.0000.000
46A59LEU0-0.0100.00443.1370.0000.0000.0000.0000.0000.000
47A60THR0-0.020-0.01745.7020.0040.0040.0000.0000.0000.000
48A61LYS10.9200.95248.7020.0600.0600.0000.0000.0000.000
49A62SER00.0010.00952.2570.0000.0000.0000.0000.0000.000
50A63PHE0-0.032-0.02655.8570.0000.0000.0000.0000.0000.000
51A64GLU-1-0.910-0.95258.623-0.044-0.0440.0000.0000.0000.000
52A65GLY0-0.068-0.03460.9580.0010.0010.0000.0000.0000.000
53A66GLU-1-0.821-0.87257.762-0.049-0.0490.0000.0000.0000.000
54A67ASP-1-0.906-0.95853.382-0.054-0.0540.0000.0000.0000.000
55A68LEU0-0.039-0.02452.555-0.001-0.0010.0000.0000.0000.000
56A69VAL0-0.037-0.03546.414-0.001-0.0010.0000.0000.0000.000
57A70VAL00.0130.02445.5030.0010.0010.0000.0000.0000.000
58A71ARG10.7660.84141.7150.0820.0820.0000.0000.0000.000
59A72TYR00.0440.02238.3900.0030.0030.0000.0000.0000.000
60A73SER0-0.029-0.03334.967-0.004-0.0040.0000.0000.0000.000
61A74THR00.0410.01432.2390.0050.0050.0000.0000.0000.000
62A75ASN0-0.047-0.00630.048-0.019-0.0190.0000.0000.0000.000
63A76GLN0-0.024-0.02630.3610.0120.0120.0000.0000.0000.000
64A77ASP-1-0.918-0.96331.108-0.154-0.1540.0000.0000.0000.000
65A78SER0-0.032-0.01729.414-0.008-0.0080.0000.0000.0000.000
66A79ASP-1-0.871-0.92330.896-0.131-0.1310.0000.0000.0000.000
67A80LYS10.8150.89734.1470.1220.1220.0000.0000.0000.000
68A81ALA00.0270.02032.9480.0000.0000.0000.0000.0000.000
69A82ASN0-0.049-0.04434.9020.0020.0020.0000.0000.0000.000
70A83SER00.0240.03038.4730.0050.0050.0000.0000.0000.000
71A84HIS00.0450.02036.977-0.005-0.0050.0000.0000.0000.000
72A85ASN0-0.022-0.01040.2850.0090.0090.0000.0000.0000.000
73A86ILE0-0.021-0.01341.663-0.003-0.0030.0000.0000.0000.000
74A87PHE0-0.039-0.00941.3630.0020.0020.0000.0000.0000.000
75A88VAL00.0050.00646.3230.0000.0000.0000.0000.0000.000
76A89TYR0-0.005-0.02245.8540.0010.0010.0000.0000.0000.000
77A90ILE0-0.005-0.00251.1760.0000.0000.0000.0000.0000.000
78A91THR0-0.030-0.02253.8140.0000.0000.0000.0000.0000.000
79A92GLN00.0040.00255.9640.0020.0020.0000.0000.0000.000
80A93LYS11.0090.98958.8890.0380.0380.0000.0000.0000.000
81A94ASN0-0.079-0.05260.766-0.001-0.0010.0000.0000.0000.000
82A95GLY00.0460.03457.4950.0010.0010.0000.0000.0000.000
83A96GLN0-0.026-0.00356.745-0.001-0.0010.0000.0000.0000.000
84A97THR0-0.035-0.01552.490-0.001-0.0010.0000.0000.0000.000
85A98MET0-0.0180.01055.2720.0000.0000.0000.0000.0000.000
86A99GLN0-0.015-0.01847.5710.0000.0000.0000.0000.0000.000
87A100ALA0-0.012-0.01251.2820.0020.0020.0000.0000.0000.000
88A101ASP-1-0.792-0.88247.293-0.078-0.0780.0000.0000.0000.000
89A102LEU0-0.015-0.02847.4110.0030.0030.0000.0000.0000.000
90A103SER0-0.017-0.02344.733-0.003-0.0030.0000.0000.0000.000
91A104ILE0-0.068-0.02643.2140.0040.0040.0000.0000.0000.000
92A105GLU-1-0.867-0.92343.702-0.093-0.0930.0000.0000.0000.000
93A106GLU-1-0.926-0.96544.692-0.092-0.0920.0000.0000.0000.000
94A107GLY0-0.061-0.02345.9530.0030.0030.0000.0000.0000.000
95A108GLU-1-0.950-0.96447.495-0.065-0.0650.0000.0000.0000.000
96A109LEU0-0.047-0.02648.574-0.003-0.0030.0000.0000.0000.000
97A110VAL00.0400.03349.1420.0040.0040.0000.0000.0000.000
98A111LEU0-0.043-0.02949.827-0.002-0.0020.0000.0000.0000.000
99A112ASN0-0.002-0.01347.5270.0030.0030.0000.0000.0000.000
100A113ASN0-0.072-0.05250.4280.0010.0010.0000.0000.0000.000
101A114ILE00.0300.02152.276-0.001-0.0010.0000.0000.0000.000
102A115ARG10.8990.97149.6820.0640.0640.0000.0000.0000.000
103A116PHE0-0.005-0.01855.001-0.001-0.0010.0000.0000.0000.000
104A117TYR00.003-0.01749.6890.0000.0000.0000.0000.0000.000
105A118ASP-1-0.872-0.94455.847-0.043-0.0430.0000.0000.0000.000
106A119GLU-1-0.974-0.98753.797-0.048-0.0480.0000.0000.0000.000
107A120ALA00.0230.00052.526-0.002-0.0020.0000.0000.0000.000
108A121ALA00.0150.01449.708-0.003-0.0030.0000.0000.0000.000
109A122LEU00.0200.02248.974-0.003-0.0030.0000.0000.0000.000
110A123ALA00.0000.01149.480-0.002-0.0020.0000.0000.0000.000
111A124LYS10.8950.94646.7610.0600.0600.0000.0000.0000.000
112A125ASP-1-0.880-0.90945.146-0.068-0.0680.0000.0000.0000.000
113A126THR0-0.024-0.02139.814-0.004-0.0040.0000.0000.0000.000
114A127GLY00.012-0.01139.3330.0030.0030.0000.0000.0000.000
115A128ALA00.0190.00338.7160.0010.0010.0000.0000.0000.000
116A129GLU-1-0.860-0.93440.666-0.059-0.0590.0000.0000.0000.000
117A130ALA0-0.022-0.00643.8070.0030.0030.0000.0000.0000.000
118A131GLU-1-0.788-0.86642.308-0.078-0.0780.0000.0000.0000.000
119A132ALA0-0.022-0.01744.5090.0020.0020.0000.0000.0000.000
120A133LYS10.9020.95046.0680.0610.0610.0000.0000.0000.000
121A134ARG10.7740.85744.1720.0760.0760.0000.0000.0000.000
122A135ASN0-0.063-0.03244.4590.0010.0010.0000.0000.0000.000
123A136GLU-1-0.965-0.96348.903-0.050-0.0500.0000.0000.0000.000
124A137LEU0-0.061-0.02152.1810.0030.0030.0000.0000.0000.000
125A138TYR0-0.005-0.01053.822-0.001-0.0010.0000.0000.0000.000
126A139THR00.0390.01051.1560.0000.0000.0000.0000.0000.000
127A140GLY00.0020.02053.910-0.002-0.0020.0000.0000.0000.000
128A141PRO0-0.057-0.02756.4510.0000.0000.0000.0000.0000.000
129A142LEU00.0240.00954.238-0.002-0.0020.0000.0000.0000.000
130A143VAL00.0400.01054.3650.0020.0020.0000.0000.0000.000
131A144HIS0-0.019-0.00755.4880.0000.0000.0000.0000.0000.000
132A145GLU-1-0.958-0.98857.260-0.047-0.0470.0000.0000.0000.000
133A146LEU0-0.075-0.01758.8030.0020.0020.0000.0000.0000.000
134A147ASP-1-0.897-0.94361.801-0.042-0.0420.0000.0000.0000.000
135A148TYR0-0.022-0.03061.572-0.001-0.0010.0000.0000.0000.000
136A149ASP-1-0.898-0.95063.503-0.041-0.0410.0000.0000.0000.000
137A150LEU0-0.010-0.00562.0040.0000.0000.0000.0000.0000.000
138A151LEU00.0640.02656.854-0.001-0.0010.0000.0000.0000.000
139A152ASN00.0440.03459.600-0.003-0.0030.0000.0000.0000.000
140A153CYS0-0.056-0.03461.4100.0000.0000.0000.0000.0000.000
141A154VAL0-0.013-0.00757.1770.0000.0000.0000.0000.0000.000
142A155MET00.0580.03253.542-0.001-0.0010.0000.0000.0000.000
143A156THR0-0.0050.00357.6260.0000.0000.0000.0000.0000.000
144A157TYR0-0.074-0.04558.0860.0000.0000.0000.0000.0000.000
145A158LEU00.007-0.00453.7110.0000.0000.0000.0000.0000.000
146A159GLU-1-0.891-0.93655.840-0.056-0.0560.0000.0000.0000.000
147A160LYS10.8840.93656.9480.0450.0450.0000.0000.0000.000
148A161ARG10.7580.87055.8260.0520.0520.0000.0000.0000.000
149A162GLY0-0.049-0.02553.855-0.001-0.0010.0000.0000.0000.000
150A163VAL0-0.0080.00150.464-0.003-0.0030.0000.0000.0000.000
151A164ASP-1-0.778-0.91051.657-0.067-0.0670.0000.0000.0000.000
152A165GLU-1-0.864-0.94150.112-0.071-0.0710.0000.0000.0000.000
153A166LYS10.8530.93348.7790.0670.0670.0000.0000.0000.000
154A167LEU0-0.049-0.00846.078-0.003-0.0030.0000.0000.0000.000
155A168GLY00.0450.01245.704-0.004-0.0040.0000.0000.0000.000
156A169GLU-1-0.923-0.96044.019-0.091-0.0910.0000.0000.0000.000
157A170PHE00.0170.00441.690-0.005-0.0050.0000.0000.0000.000
158A171VAL00.0220.01140.621-0.006-0.0060.0000.0000.0000.000
159A172VAL00.0100.02539.452-0.007-0.0070.0000.0000.0000.000
160A173LEU00.0160.00338.102-0.009-0.0090.0000.0000.0000.000
161A174TYR0-0.051-0.03836.586-0.008-0.0080.0000.0000.0000.000
162A175SER0-0.010-0.02935.383-0.008-0.0080.0000.0000.0000.000
163A176PHE00.0000.00633.467-0.010-0.0100.0000.0000.0000.000
164A177TRP0-0.0090.00632.228-0.010-0.0100.0000.0000.0000.000
165A178ALA0-0.007-0.01631.581-0.010-0.0100.0000.0000.0000.000
166A179GLU-1-0.882-0.92027.647-0.230-0.2300.0000.0000.0000.000
167A180GLN0-0.056-0.03825.995-0.007-0.0070.0000.0000.0000.000
168A181GLN0-0.066-0.03926.558-0.016-0.0160.0000.0000.0000.000
169A182ASP-1-0.885-0.94726.083-0.208-0.2080.0000.0000.0000.000
170A183TYR0-0.0010.01620.475-0.036-0.0360.0000.0000.0000.000
171A184GLU-1-0.756-0.86721.809-0.276-0.2760.0000.0000.0000.000
172A185ALA0-0.009-0.00121.208-0.027-0.0270.0000.0000.0000.000
173A186TRP0-0.017-0.00917.772-0.039-0.0390.0000.0000.0000.000
174A187LEU00.0240.01917.104-0.058-0.0580.0000.0000.0000.000
175A188THR0-0.024-0.01816.104-0.063-0.0630.0000.0000.0000.000
176A189THR0-0.084-0.04916.249-0.018-0.0180.0000.0000.0000.000
177A190MET0-0.0050.00512.910-0.052-0.0520.0000.0000.0000.000
178A191ASN0-0.040-0.01511.877-0.046-0.0460.0000.0000.0000.000
179A192LYS10.9510.97511.3980.2280.2280.0000.0000.0000.000
180A193PHE0-0.079-0.03911.1200.0320.0320.0000.0000.0000.000
181A194ALA0-0.034-0.0038.007-0.027-0.0270.0000.0000.0000.000
182A195SER0-0.090-0.0377.035-0.039-0.0390.0000.0000.0000.000