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: YNQJ2

Calculation Name: 1QR4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QR4

Chain ID: A

ChEMBL ID:

UniProt ID: P10039

Base Structure: X-ray

Registration Date: 2023-09-26

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1555257.466935
FMO2-HF: Nuclear repulsion 1489174.06346
FMO2-HF: Total energy -66083.403474
FMO2-MP2: Total energy -66280.443483


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
-249.453-257.5440.431-18.022-14.3180.151
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.869 / q_NPA : -0.911
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].
3A3PRO00.0490.0393.8208.08610.596-0.009-1.200-1.3000.003
4A4LYS10.9601.0104.317-57.884-57.584-0.001-0.037-0.2620.000
5A5ASP-1-0.908-0.9697.29127.51827.5180.0000.0000.0000.000
6A6LEU0-0.0120.01110.974-0.674-0.6740.0000.0000.0000.000
7A7GLU-1-0.926-0.96412.74917.78417.7840.0000.0000.0000.000
8A8VAL0-0.034-0.03416.3060.1420.1420.0000.0000.0000.000
9A9SER00.007-0.00319.563-0.373-0.3730.0000.0000.0000.000
10A10ASP-1-0.928-0.97322.17912.98712.9870.0000.0000.0000.000
11A11PRO0-0.015-0.00625.388-0.088-0.0880.0000.0000.0000.000
12A12THR00.0260.03927.132-0.556-0.5560.0000.0000.0000.000
13A13GLU-1-0.864-0.92829.7999.0749.0740.0000.0000.0000.000
14A14THR0-0.028-0.01830.4450.0830.0830.0000.0000.0000.000
15A15THR0-0.035-0.03726.0380.2280.2280.0000.0000.0000.000
16A16LEU00.0710.03522.309-0.023-0.0230.0000.0000.0000.000
17A17SER00.0110.02421.4430.5130.5130.0000.0000.0000.000
18A18LEU0-0.011-0.00316.2770.3940.3940.0000.0000.0000.000
19A19ARG10.9930.99714.632-19.181-19.1810.0000.0000.0000.000
20A20TRP0-0.027-0.0068.788-0.507-0.5070.0000.0000.0000.000
21A21ARG10.9490.9736.964-30.822-30.8220.0000.0000.0000.000
22A22ARG10.9410.9786.673-27.903-27.9030.0000.0000.0000.000
23A23PRO0-0.051-0.0202.6910.4053.0080.963-1.625-1.9420.014
24A24VAL00.0310.0091.765-22.586-27.17413.659-4.752-4.3190.056
25A25ALA0-0.067-0.0272.568-16.222-13.8850.859-1.440-1.7550.010
26A26LYS10.9870.9984.005-28.274-28.1640.0020.002-0.1130.000
27A27PHE0-0.128-0.0846.0652.0352.0350.0000.0000.0000.000
28A28ASP-1-0.851-0.9238.05819.67119.6710.0000.0000.0000.000
29A29ARG10.9140.97010.695-19.658-19.6580.0000.0000.0000.000
30A30TYR0-0.0020.0018.1144.8334.8330.0000.0000.0000.000
31A31ARG10.9411.00011.697-19.416-19.4160.0000.0000.0000.000
32A32LEU0-0.009-0.01013.3661.4291.4290.0000.0000.0000.000
33A33THR0-0.025-0.02615.846-0.804-0.8040.0000.0000.0000.000
34A34TYR00.0290.00817.7310.6640.6640.0000.0000.0000.000
35A35VAL0-0.017-0.02020.441-0.451-0.4510.0000.0000.0000.000
36A36SER00.0520.04023.2580.0880.0880.0000.0000.0000.000
37A37PRO00.0720.02226.6380.0820.0820.0000.0000.0000.000
38A38SER0-0.049-0.01828.773-0.233-0.2330.0000.0000.0000.000
39A39GLY00.006-0.00126.304-0.136-0.1360.0000.0000.0000.000
40A40LYS10.9000.97026.454-10.969-10.9690.0000.0000.0000.000
41A41LYS10.9580.97419.794-14.023-14.0230.0000.0000.0000.000
42A42ASN0-0.0180.00222.516-0.686-0.6860.0000.0000.0000.000
43A43GLU-1-0.911-0.97518.63516.33716.3370.0000.0000.0000.000
44A44MET00.0230.01118.545-0.786-0.7860.0000.0000.0000.000
45A45GLU-1-0.890-0.93216.21018.28618.2860.0000.0000.0000.000
46A46ILE0-0.040-0.02114.344-0.803-0.8030.0000.0000.0000.000
47A47PRO00.0860.03214.0451.3691.3690.0000.0000.0000.000
48A48VAL00.018-0.00110.4131.0051.0050.0000.0000.0000.000
49A49ASP-1-0.980-0.98911.77720.17820.1780.0000.0000.0000.000
50A50SER0-0.0140.00613.866-0.964-0.9640.0000.0000.0000.000
51A51THR0-0.037-0.02410.7761.2801.2800.0000.0000.0000.000
52A52SER00.028-0.00313.009-0.042-0.0420.0000.0000.0000.000
53A53PHE00.0130.00216.347-0.178-0.1780.0000.0000.0000.000
54A54ILE0-0.0020.01718.7290.0840.0840.0000.0000.0000.000
55A55LEU0-0.005-0.00420.437-0.154-0.1540.0000.0000.0000.000
56A56ARG10.9520.95222.739-13.050-13.0500.0000.0000.0000.000
57A57GLY0-0.0100.00426.4370.1770.1770.0000.0000.0000.000
58A58LEU0-0.099-0.02824.6290.0090.0090.0000.0000.0000.000
59A59ASP-1-0.860-0.93128.9879.6849.6840.0000.0000.0000.000
60A60ALA00.0380.03230.8460.2960.2960.0000.0000.0000.000
61A61GLY0-0.0270.00532.294-0.151-0.1510.0000.0000.0000.000
62A62THR0-0.085-0.04028.520-0.216-0.2160.0000.0000.0000.000
63A63GLU-1-0.935-0.96825.06712.82012.8200.0000.0000.0000.000
64A64TYR00.0160.00322.893-0.197-0.1970.0000.0000.0000.000
65A65THR0-0.052-0.01618.6640.4900.4900.0000.0000.0000.000
66A66ILE00.008-0.01116.524-0.083-0.0830.0000.0000.0000.000
67A67SER0-0.008-0.01713.5800.4460.4460.0000.0000.0000.000
68A68LEU00.0210.03110.413-0.741-0.7410.0000.0000.0000.000
69A69VAL0-0.063-0.0318.0542.1422.1420.0000.0000.0000.000
70A70ALA00.0690.0365.371-2.019-2.0190.0000.0000.0000.000
71A71GLU-1-0.885-0.9536.90022.65022.6500.0000.0000.0000.000
72A72LYS10.8950.9001.792-72.631-84.39324.955-8.862-4.3300.068
73A73GLY00.0630.0367.871-0.940-0.9400.0000.0000.0000.000
74A74ARG10.9861.00611.457-17.811-17.8110.0000.0000.0000.000
75A75HIS0-0.083-0.0417.935-0.763-0.7630.0000.0000.0000.000
76A76LYS10.9410.9788.156-19.086-19.0860.0000.0000.0000.000
77A77SER00.0130.0034.026-0.1790.0370.004-0.099-0.1200.000
78A78LYS10.9250.9775.132-35.543-35.356-0.001-0.009-0.1770.000
79A79PRO00.016-0.0077.0472.6042.6040.0000.0000.0000.000
80A80THR0-0.055-0.0638.1000.5540.5540.0000.0000.0000.000
81A81THR0-0.038-0.04010.282-1.333-1.3330.0000.0000.0000.000
82A82ILE00.0330.03414.0200.2950.2950.0000.0000.0000.000
83A83LYS10.9370.96517.148-15.323-15.3230.0000.0000.0000.000
84A84GLY00.0610.04320.8580.2460.2460.0000.0000.0000.000
85A85SER00.010-0.00123.1240.0480.0480.0000.0000.0000.000
86A86THR0-0.066-0.05226.8160.1080.1080.0000.0000.0000.000
87A87VAL00.0680.04428.802-0.156-0.1560.0000.0000.0000.000
88A88VAL0-0.007-0.01331.756-0.073-0.0730.0000.0000.0000.000
89A89GLY00.0260.00535.2680.0220.0220.0000.0000.0000.000
90A90SER00.0540.02237.302-0.221-0.2210.0000.0000.0000.000
91A91PRO0-0.063-0.03439.924-0.046-0.0460.0000.0000.0000.000
92A92LYS10.9330.94640.920-7.792-7.7920.0000.0000.0000.000
93A93GLY00.0200.01344.3300.0080.0080.0000.0000.0000.000
94A94ILE0-0.0190.01747.694-0.093-0.0930.0000.0000.0000.000
95A95SER0-0.028-0.01149.931-0.097-0.0970.0000.0000.0000.000
96A96PHE00.013-0.01552.682-0.015-0.0150.0000.0000.0000.000
97A97SER0-0.011-0.00956.849-0.004-0.0040.0000.0000.0000.000
98A98ASP-1-0.868-0.94160.2875.2705.2700.0000.0000.0000.000
99A99ILE0-0.0270.00059.8990.0140.0140.0000.0000.0000.000
100A100THR0-0.050-0.02363.385-0.104-0.1040.0000.0000.0000.000
101A101GLU-1-0.906-0.95465.2004.6924.6920.0000.0000.0000.000
102A102ASN00.016-0.00965.088-0.021-0.0210.0000.0000.0000.000
103A103SER0-0.042-0.02262.4080.0360.0360.0000.0000.0000.000
104A104ALA00.0220.02059.157-0.037-0.0370.0000.0000.0000.000
105A105THR0-0.039-0.00958.0290.0710.0710.0000.0000.0000.000
106A106VAL00.0100.02452.3610.0170.0170.0000.0000.0000.000
107A107SER0-0.045-0.03253.266-0.010-0.0100.0000.0000.0000.000
108A108TRP00.0300.00847.427-0.022-0.0220.0000.0000.0000.000
109A109THR00.0330.01146.277-0.039-0.0390.0000.0000.0000.000
110A110PRO0-0.012-0.00545.4570.1670.1670.0000.0000.0000.000
111A111PRO00.0230.03840.016-0.020-0.0200.0000.0000.0000.000
112A112ARG10.9220.95439.320-7.937-7.9370.0000.0000.0000.000
113A113SER00.0590.01337.2720.3630.3630.0000.0000.0000.000
114A114ARG10.9320.97837.949-8.541-8.5410.0000.0000.0000.000
115A115VAL0-0.012-0.00739.1910.2080.2080.0000.0000.0000.000
116A116ASP-1-0.859-0.92241.3337.8697.8690.0000.0000.0000.000
117A117SER0-0.051-0.03043.544-0.232-0.2320.0000.0000.0000.000
118A118TYR00.0630.02244.0940.2120.2120.0000.0000.0000.000
119A119ARG10.9190.94841.663-7.776-7.7760.0000.0000.0000.000
120A120VAL0-0.0010.00646.2730.0760.0760.0000.0000.0000.000
121A121SER00.0080.00246.818-0.139-0.1390.0000.0000.0000.000
122A122TYR00.020-0.00749.586-0.002-0.0020.0000.0000.0000.000
123A123VAL00.0130.00750.868-0.053-0.0530.0000.0000.0000.000
124A124PRO00.0200.02853.6270.0390.0390.0000.0000.0000.000
125A125ILE00.0420.01052.8540.0750.0750.0000.0000.0000.000
126A126THR0-0.023-0.00953.7850.0480.0480.0000.0000.0000.000
127A127GLY0-0.037-0.01052.8020.0160.0160.0000.0000.0000.000
128A128GLY00.012-0.00252.589-0.140-0.1400.0000.0000.0000.000
129A129THR0-0.025-0.01451.2740.1180.1180.0000.0000.0000.000
130A130PRO0-0.023-0.02148.135-0.112-0.1120.0000.0000.0000.000
131A131ASN0-0.0010.01551.308-0.100-0.1000.0000.0000.0000.000
132A132VAL0-0.012-0.00647.7480.0290.0290.0000.0000.0000.000
133A133VAL00.0000.00150.785-0.094-0.0940.0000.0000.0000.000
134A134THR0-0.013-0.00947.4780.1560.1560.0000.0000.0000.000
135A135VAL0-0.058-0.03149.388-0.187-0.1870.0000.0000.0000.000
136A136ASP-1-0.868-0.95948.9356.8016.8010.0000.0000.0000.000
137A137GLY00.0790.04046.655-0.062-0.0620.0000.0000.0000.000
138A138SER0-0.057-0.01047.445-0.006-0.0060.0000.0000.0000.000
139A139LYS10.8840.95249.963-6.063-6.0630.0000.0000.0000.000
140A140THR00.0170.01250.1560.0870.0870.0000.0000.0000.000
141A141ARG10.9570.96751.602-5.765-5.7650.0000.0000.0000.000
142A142THR0-0.034-0.02253.792-0.053-0.0530.0000.0000.0000.000
143A143LYS10.9631.00055.817-5.349-5.3490.0000.0000.0000.000
144A144LEU00.0000.01154.6610.0460.0460.0000.0000.0000.000
145A145VAL00.033-0.00658.713-0.110-0.1100.0000.0000.0000.000
146A146LYS10.9290.95160.836-5.118-5.1180.0000.0000.0000.000
147A147LEU0-0.0300.00158.6190.0330.0330.0000.0000.0000.000
148A148VAL00.0160.01662.260-0.096-0.0960.0000.0000.0000.000
149A149PRO00.0680.02063.6130.0670.0670.0000.0000.0000.000
150A150GLY00.0000.00764.779-0.005-0.0050.0000.0000.0000.000
151A151VAL0-0.035-0.02159.4580.0080.0080.0000.0000.0000.000
152A152ASP-1-0.866-0.92456.6655.6125.6120.0000.0000.0000.000
153A153TYR0-0.023-0.03455.4180.0280.0280.0000.0000.0000.000
154A154ASN00.0100.00850.0630.0570.0570.0000.0000.0000.000
155A155VAL0-0.045-0.02950.484-0.007-0.0070.0000.0000.0000.000
156A156ASN00.0210.00845.3140.1470.1470.0000.0000.0000.000
157A157ILE0-0.033-0.01145.719-0.120-0.1200.0000.0000.0000.000
158A158ILE00.0510.04040.4250.0800.0800.0000.0000.0000.000
159A159SER0-0.012-0.01239.980-0.307-0.3070.0000.0000.0000.000
160A160VAL00.0140.00839.8890.1740.1740.0000.0000.0000.000
161A161LYS10.9310.95736.028-8.936-8.9360.0000.0000.0000.000
162A162GLY0-0.060-0.02337.3340.2830.2830.0000.0000.0000.000
163A163PHE0-0.018-0.02235.366-0.221-0.2210.0000.0000.0000.000
164A164GLU-1-0.939-0.94832.04510.21310.2130.0000.0000.0000.000
165A165GLU-1-0.915-0.98635.7647.9527.9520.0000.0000.0000.000
166A166SER0-0.035-0.01536.1420.1170.1170.0000.0000.0000.000
167A167GLU-1-0.889-0.92935.1258.9548.9540.0000.0000.0000.000
168A168PRO0-0.043-0.02537.840-0.187-0.1870.0000.0000.0000.000
169A169ILE0-0.0220.00741.3660.0350.0350.0000.0000.0000.000
170A170SER0-0.010-0.02743.959-0.102-0.1020.0000.0000.0000.000
171A171GLY0-0.001-0.00447.1490.0070.0070.0000.0000.0000.000
172A172ILE00.0170.01950.5640.0050.0050.0000.0000.0000.000
173A173LEU0-0.084-0.03953.693-0.061-0.0610.0000.0000.0000.000
174A174LYS11.0061.01356.641-5.628-5.6280.0000.0000.0000.000
175A175THR0-0.0100.00260.075-0.068-0.0680.0000.0000.0000.000