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: 2NL1R

Calculation Name: 2YVU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YVU

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YCR6

Base Structure: X-ray

Registration Date: 2023-09-22

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1941729.670587
FMO2-HF: Nuclear repulsion 1871667.933536
FMO2-HF: Total energy -70061.737052
FMO2-MP2: Total energy -70269.833846


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:8:LYS)


Summations of interaction energy for fragment #1(A:8:LYS)
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.
-142.661-133.69327.772-15.171-21.569-0.168
Interaction energy analysis for fragmet #1(A:8:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.891 / q_NPA : 0.959
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].
3A10ILE00.0370.0353.113-4.374-0.1330.004-2.079-2.1670.001
4A11GLU-1-0.891-0.9485.245-18.572-18.536-0.001-0.002-0.0330.000
5A12LYS10.8760.9339.02521.31321.3130.0000.0000.0000.000
6A13GLY0-0.0160.0098.867-2.452-2.4520.0000.0000.0000.000
7A14ILE00.006-0.0149.8491.6421.6420.0000.0000.0000.000
8A15VAL00.0180.01012.303-0.348-0.3480.0000.0000.0000.000
9A16VAL0-0.0140.00212.5650.7850.7850.0000.0000.0000.000
10A17TRP00.0220.00215.5930.2520.2520.0000.0000.0000.000
11A18LEU0-0.005-0.00717.0550.5570.5570.0000.0000.0000.000
12A19THR0-0.0040.00420.6170.7070.7070.0000.0000.0000.000
13A20GLY00.0610.01024.373-0.075-0.0750.0000.0000.0000.000
14A21LEU00.0100.02226.9530.0410.0410.0000.0000.0000.000
15A22PRO00.0090.00628.426-0.428-0.4280.0000.0000.0000.000
16A23GLY00.0530.01728.5030.2800.2800.0000.0000.0000.000
17A24SER0-0.036-0.01726.091-0.072-0.0720.0000.0000.0000.000
18A25GLY00.0500.02324.491-0.172-0.1720.0000.0000.0000.000
19A26LYS10.8220.91221.72211.79611.7960.0000.0000.0000.000
20A27THR00.1070.03520.065-0.769-0.7690.0000.0000.0000.000
21A28THR00.0080.02119.372-0.690-0.6900.0000.0000.0000.000
22A29ILE00.0070.00117.145-0.880-0.8800.0000.0000.0000.000
23A30ALA00.0200.00715.710-1.259-1.2590.0000.0000.0000.000
24A31THR00.0130.00014.383-1.477-1.4770.0000.0000.0000.000
25A32ARG10.8420.91014.26015.79615.7960.0000.0000.0000.000
26A33LEU00.0210.01710.331-1.415-1.4150.0000.0000.0000.000
27A34ALA00.027-0.00110.060-3.077-3.0770.0000.0000.0000.000
28A35ASP-1-0.843-0.8939.586-27.356-27.3560.0000.0000.0000.000
29A36LEU0-0.022-0.0118.923-2.175-2.1750.0000.0000.0000.000
30A37LEU00.0190.0065.356-4.998-4.9980.0000.0000.0000.000
31A38GLN00.0070.0114.700-9.736-9.655-0.001-0.004-0.0760.000
32A39LYS10.8290.9086.08620.66620.6660.0000.0000.0000.000
33A40GLU-1-0.800-0.8682.279-86.500-83.9821.400-1.740-2.178-0.016
34A41GLY0-0.026-0.0201.851-42.317-43.08711.702-5.581-5.350-0.076
35A42TYR0-0.017-0.0122.346-25.465-23.20414.659-5.764-11.157-0.077
36A43ARG10.9650.9873.62142.65143.1570.0100.007-0.5230.000
37A44VAL0-0.036-0.0265.9690.0280.0280.0000.0000.0000.000
38A45GLU-1-0.877-0.9339.194-20.033-20.0330.0000.0000.0000.000
39A46VAL0-0.022-0.00912.855-0.122-0.1220.0000.0000.0000.000
40A47LEU00.0010.00815.7830.9820.9820.0000.0000.0000.000
41A48ASP-1-0.823-0.93318.962-14.366-14.3660.0000.0000.0000.000
42A49GLY0-0.001-0.02022.0760.3200.3200.0000.0000.0000.000
43A50ASP-1-0.814-0.87925.298-10.924-10.9240.0000.0000.0000.000
44A51TRP00.0330.02120.3850.2850.2850.0000.0000.0000.000
45A52ALA00.010-0.00123.8280.3510.3510.0000.0000.0000.000
46A53ARG10.7650.85525.27811.16411.1640.0000.0000.0000.000
47A54THR0-0.0030.00626.7310.2810.2810.0000.0000.0000.000
48A55THR00.006-0.00423.221-0.144-0.1440.0000.0000.0000.000
49A56VAL0-0.027-0.00822.9310.3150.3150.0000.0000.0000.000
50A57SER0-0.102-0.09326.0870.2670.2670.0000.0000.0000.000
51A58GLU-1-0.922-0.95129.013-9.776-9.7760.0000.0000.0000.000
52A59GLY00.0060.02330.8460.2000.2000.0000.0000.0000.000
53A60ALA0-0.084-0.02633.0100.2160.2160.0000.0000.0000.000
54A61GLY00.0330.01834.9300.0490.0490.0000.0000.0000.000
55A62PHE00.006-0.02233.892-0.282-0.2820.0000.0000.0000.000
56A63THR00.008-0.01537.131-0.053-0.0530.0000.0000.0000.000
57A64ARG11.0011.00336.6278.3268.3260.0000.0000.0000.000
58A65GLU-1-0.833-0.91335.773-8.312-8.3120.0000.0000.0000.000
59A66GLU-1-0.900-0.93234.615-8.969-8.9690.0000.0000.0000.000
60A67ARG10.8840.92832.3498.8318.8310.0000.0000.0000.000
61A68LEU00.0010.00630.922-0.447-0.4470.0000.0000.0000.000
62A69ARG10.9350.97630.5548.3238.3230.0000.0000.0000.000
63A70HIS00.0270.04826.094-0.172-0.1720.0000.0000.0000.000
64A71LEU00.0170.00326.307-0.469-0.4690.0000.0000.0000.000
65A72LYS10.9790.98925.6769.7159.7150.0000.0000.0000.000
66A73ARG10.9020.94225.47910.51310.5130.0000.0000.0000.000
67A74ILE0-0.021-0.00821.417-0.441-0.4410.0000.0000.0000.000
68A75ALA00.0200.01021.192-0.733-0.7330.0000.0000.0000.000
69A76TRP00.001-0.00321.074-0.576-0.5760.0000.0000.0000.000
70A77ILE0-0.0130.01018.473-0.417-0.4170.0000.0000.0000.000
71A78ALA00.0230.00116.890-0.856-0.8560.0000.0000.0000.000
72A79ARG10.7380.85016.15212.28312.2830.0000.0000.0000.000
73A80LEU0-0.039-0.02716.697-0.567-0.5670.0000.0000.0000.000
74A81LEU00.0240.02013.151-0.619-0.6190.0000.0000.0000.000
75A82ALA00.0530.03212.118-1.416-1.4160.0000.0000.0000.000
76A83ARG10.8510.92912.29513.73113.7310.0000.0000.0000.000
77A84ASN0-0.112-0.07112.1120.5690.5690.0000.0000.0000.000
78A85GLY00.0650.0438.245-0.882-0.8820.0000.0000.0000.000
79A86VAL0-0.082-0.0297.143-4.102-4.1020.0000.0000.0000.000
80A87ILE00.0110.0075.6392.1222.1220.0000.0000.0000.000
81A88VAL0-0.007-0.0129.5700.5080.5080.0000.0000.0000.000
82A89ILE0-0.0020.00810.7850.8960.8960.0000.0000.0000.000
83A90CYS0-0.029-0.01014.6640.9950.9950.0000.0000.0000.000
84A91SER0-0.0130.00018.4590.3540.3540.0000.0000.0000.000
85A92PHE00.0720.01921.0500.6220.6220.0000.0000.0000.000
86A93VAL0-0.0320.00324.6230.0380.0380.0000.0000.0000.000
87A94SER00.018-0.00926.4850.0040.0040.0000.0000.0000.000
88A95PRO00.0460.02028.721-0.267-0.2670.0000.0000.0000.000
89A96TYR0-0.059-0.05631.2960.0970.0970.0000.0000.0000.000
90A97LYS10.8940.93030.2989.0919.0910.0000.0000.0000.000
91A98GLN00.0140.00830.301-0.293-0.2930.0000.0000.0000.000
92A99ALA00.0070.00030.475-0.163-0.1630.0000.0000.0000.000
93A100ARG10.8130.89125.56911.07811.0780.0000.0000.0000.000
94A101ASN00.0020.00126.085-0.670-0.6700.0000.0000.0000.000
95A102MET0-0.097-0.03627.387-0.203-0.2030.0000.0000.0000.000
96A103VAL00.003-0.00222.639-0.128-0.1280.0000.0000.0000.000
97A104ARG10.8000.88621.75813.43713.4370.0000.0000.0000.000
98A105ARG10.9460.97422.96410.25910.2590.0000.0000.0000.000
99A106ILE0-0.0280.00022.745-0.033-0.0330.0000.0000.0000.000
100A107VAL00.009-0.00717.941-0.189-0.1890.0000.0000.0000.000
101A108GLU-1-0.802-0.91619.838-14.150-14.1500.0000.0000.0000.000
102A109GLU-1-0.874-0.88521.466-11.926-11.9260.0000.0000.0000.000
103A110GLU-1-0.856-0.90818.285-14.440-14.4400.0000.0000.0000.000
104A111GLY00.0110.00218.902-0.458-0.4580.0000.0000.0000.000
105A112ILE0-0.086-0.03314.336-0.946-0.9460.0000.0000.0000.000
106A113PRO00.0340.01613.7080.8880.8880.0000.0000.0000.000
107A114PHE00.0160.00015.863-0.617-0.6170.0000.0000.0000.000
108A115LEU0-0.008-0.00913.8880.7710.7710.0000.0000.0000.000
109A116GLU-1-0.817-0.90017.962-12.781-12.7810.0000.0000.0000.000
110A117ILE00.0010.00016.9140.2150.2150.0000.0000.0000.000
111A118TYR00.019-0.00120.6140.4370.4370.0000.0000.0000.000
112A119VAL0-0.0180.00121.538-0.103-0.1030.0000.0000.0000.000
113A120LYS10.8320.89724.14910.92310.9230.0000.0000.0000.000
114A121ALA00.0200.00327.580-0.106-0.1060.0000.0000.0000.000
115A122SER0-0.0160.00130.3070.1680.1680.0000.0000.0000.000
116A123LEU00.029-0.00933.909-0.118-0.1180.0000.0000.0000.000
117A124GLU-1-0.868-0.93435.848-7.922-7.9220.0000.0000.0000.000
118A125GLU-1-0.795-0.87332.662-9.412-9.4120.0000.0000.0000.000
119A126VAL0-0.053-0.03430.869-0.092-0.0920.0000.0000.0000.000
120A127ILE0-0.034-0.01333.5160.0050.0050.0000.0000.0000.000
121A128ARG10.8220.90236.6148.5978.5970.0000.0000.0000.000
122A129ARG10.8010.89728.39810.71810.7180.0000.0000.0000.000
123A130ASP-1-0.864-0.92633.328-9.452-9.4520.0000.0000.0000.000
124A131PRO00.0520.02835.4430.1210.1210.0000.0000.0000.000
125A132LYS10.9460.96537.2728.6028.6020.0000.0000.0000.000
126A133GLY00.0080.00535.5930.1260.1260.0000.0000.0000.000
127A134LEU0-0.0130.00236.5930.0490.0490.0000.0000.0000.000
128A135TYR00.0270.00038.8190.1150.1150.0000.0000.0000.000
129A136LYS10.9340.97836.7988.7848.7840.0000.0000.0000.000
130A137LYS10.8720.92333.5039.4739.4730.0000.0000.0000.000
131A138ALA00.0310.01239.2970.0990.0990.0000.0000.0000.000
132A139LEU0-0.034-0.01142.7210.1430.1430.0000.0000.0000.000
133A140LYS10.7940.88838.4228.4408.4400.0000.0000.0000.000
134A141GLY00.0400.01942.783-0.032-0.0320.0000.0000.0000.000
135A142GLU-1-0.871-0.88836.294-8.963-8.9630.0000.0000.0000.000
136A143LEU00.0660.02938.076-0.299-0.2990.0000.0000.0000.000
137A144GLU-1-0.903-0.95038.922-7.846-7.8460.0000.0000.0000.000
138A145ASN0-0.048-0.03434.491-0.223-0.2230.0000.0000.0000.000
139A146PHE00.0380.01933.786-0.341-0.3410.0000.0000.0000.000
140A147THR00.018-0.01833.3160.1000.1000.0000.0000.0000.000
141A148GLY0-0.070-0.02435.1770.0430.0430.0000.0000.0000.000
142A149ILE0-0.021-0.01035.8660.1010.1010.0000.0000.0000.000
143A150THR0-0.008-0.02038.3130.0900.0900.0000.0000.0000.000
144A151ASP-1-0.865-0.89235.954-8.586-8.5860.0000.0000.0000.000
145A152PRO00.0170.01735.934-0.285-0.2850.0000.0000.0000.000
146A153TYR0-0.034-0.03027.276-0.096-0.0960.0000.0000.0000.000
147A154GLU-1-0.844-0.91532.891-9.053-9.0530.0000.0000.0000.000
148A155PRO00.004-0.00730.069-0.368-0.3680.0000.0000.0000.000
149A156PRO0-0.022-0.01425.7900.2270.2270.0000.0000.0000.000
150A157GLU-1-0.795-0.87428.631-9.516-9.5160.0000.0000.0000.000
151A158ASN0-0.058-0.04327.256-0.112-0.1120.0000.0000.0000.000
152A159PRO0-0.0240.01323.500-0.322-0.3220.0000.0000.0000.000
153A160GLN00.0620.03919.117-0.165-0.1650.0000.0000.0000.000
154A161LEU00.0150.01117.375-0.422-0.4220.0000.0000.0000.000
155A162VAL0-0.012-0.00421.1580.2590.2590.0000.0000.0000.000
156A163LEU0-0.021-0.01118.413-0.215-0.2150.0000.0000.0000.000
157A164ASP-1-0.717-0.84422.842-10.657-10.6570.0000.0000.0000.000
158A165THR0-0.029-0.02924.151-0.064-0.0640.0000.0000.0000.000
159A166GLU-1-0.845-0.92426.434-9.853-9.8530.0000.0000.0000.000
160A167SER0-0.032-0.01228.3720.3300.3300.0000.0000.0000.000
161A168ASN0-0.053-0.01924.1310.1630.1630.0000.0000.0000.000
162A169THR00.0250.00523.080-0.061-0.0610.0000.0000.0000.000
163A170ILE00.016-0.00619.695-0.442-0.4420.0000.0000.0000.000
164A171GLU-1-0.788-0.87318.753-15.553-15.5530.0000.0000.0000.000
165A172HIS00.0030.00518.284-0.883-0.8830.0000.0000.0000.000
166A173ASN00.018-0.01118.939-0.752-0.7520.0000.0000.0000.000
167A174VAL0-0.006-0.00314.068-0.566-0.5660.0000.0000.0000.000
168A175SER00.0040.00914.281-2.035-2.0350.0000.0000.0000.000
169A176TYR00.0100.00914.657-0.995-0.9950.0000.0000.0000.000
170A177LEU0-0.006-0.01513.749-0.270-0.2700.0000.0000.0000.000
171A178TYR0-0.012-0.0286.4561.4581.4580.0000.0000.0000.000
172A179SER0-0.011-0.00310.565-2.297-2.2970.0000.0000.0000.000
173A180LEU0-0.0220.00612.513-0.441-0.4410.0000.0000.0000.000
174A181VAL00.009-0.0128.244-0.359-0.3590.0000.0000.0000.000
175A182LYS10.8290.8933.89159.59959.694-0.001-0.008-0.0850.000
176A183ALA0-0.030-0.0018.807-0.591-0.5910.0000.0000.0000.000
177A184VAL0-0.040-0.02011.6301.0251.0250.0000.0000.0000.000
178A185ILE0-0.076-0.0305.393-0.064-0.0640.0000.0000.0000.000
179A186GLU-1-0.996-0.9856.866-30.985-30.9850.0000.0000.0000.000