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: N29RQ

Calculation Name: 1D3U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D3U

Chain ID: A

ChEMBL ID:

UniProt ID: P62001

Base Structure: X-ray

Registration Date: 2023-09-27

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1737835.173816
FMO2-HF: Nuclear repulsion 1667248.26752
FMO2-HF: Total energy -70586.906296
FMO2-MP2: Total energy -70792.295941


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-0.6710.712-0.012-0.457-0.9170.002
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.027
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].
3A3ASP-1-0.783-0.8603.832-2.144-0.907-0.010-0.437-0.7910.002
4A4MET0-0.031-0.0164.2990.8370.967-0.001-0.011-0.1190.000
5A5SER0-0.084-0.0737.8980.3700.3700.0000.0000.0000.000
6A6LYS10.8860.93810.2421.2181.2180.0000.0000.0000.000
7A7VAL0-0.0300.00110.6450.1060.1060.0000.0000.0000.000
8A8LYS10.8690.94413.0910.2820.2820.0000.0000.0000.000
9A9LEU0-0.001-0.00516.1160.0300.0300.0000.0000.0000.000
10A10ARG10.9150.96118.6630.1030.1030.0000.0000.0000.000
11A11ILE00.0320.01622.3780.0140.0140.0000.0000.0000.000
12A12GLU-1-0.856-0.91124.578-0.068-0.0680.0000.0000.0000.000
13A13ASN00.0230.00727.439-0.001-0.0010.0000.0000.0000.000
14A14ILE0-0.0090.02527.6700.0060.0060.0000.0000.0000.000
15A15VAL00.010-0.00329.958-0.003-0.0030.0000.0000.0000.000
16A16ALA00.0060.00131.6720.0060.0060.0000.0000.0000.000
17A17SER00.0020.01934.1630.0000.0000.0000.0000.0000.000
18A18VAL0-0.008-0.02036.9790.0000.0000.0000.0000.0000.000
19A19ASP-1-0.794-0.88439.6530.0300.0300.0000.0000.0000.000
20A20LEU00.018-0.00342.569-0.002-0.0020.0000.0000.0000.000
21A21PHE0-0.066-0.02542.419-0.001-0.0010.0000.0000.0000.000
22A22ALA0-0.004-0.03247.552-0.001-0.0010.0000.0000.0000.000
23A23GLN0-0.0020.01650.2660.0010.0010.0000.0000.0000.000
24A24LEU0-0.034-0.02248.927-0.002-0.0020.0000.0000.0000.000
25A25ASP-1-0.879-0.92853.1090.0110.0110.0000.0000.0000.000
26A26LEU00.007-0.02050.053-0.001-0.0010.0000.0000.0000.000
27A27GLU-1-0.794-0.89653.8270.0100.0100.0000.0000.0000.000
28A28LYS10.8860.95957.018-0.007-0.0070.0000.0000.0000.000
29A29VAL0-0.053-0.03650.667-0.001-0.0010.0000.0000.0000.000
30A30LEU0-0.024-0.01352.702-0.001-0.0010.0000.0000.0000.000
31A31ASP-1-0.868-0.90353.932-0.001-0.0010.0000.0000.0000.000
32A32LEU0-0.115-0.06151.706-0.002-0.0020.0000.0000.0000.000
33A33CYS0-0.067-0.03244.968-0.004-0.0040.0000.0000.0000.000
34A34PRO00.0320.02649.9180.0000.0000.0000.0000.0000.000
35A35ASN00.012-0.00247.4390.0020.0020.0000.0000.0000.000
36A36SER0-0.013-0.00948.3730.0010.0010.0000.0000.0000.000
37A37LYS10.8770.91747.571-0.008-0.0080.0000.0000.0000.000
38A38TYR0-0.060-0.05649.6480.0020.0020.0000.0000.0000.000
39A39ASN00.026-0.00251.659-0.001-0.0010.0000.0000.0000.000
40A40PRO00.0000.00052.0610.0010.0010.0000.0000.0000.000
41A41GLU-1-0.972-0.96552.5260.0160.0160.0000.0000.0000.000
42A42GLU-1-0.848-0.88748.8810.0120.0120.0000.0000.0000.000
43A43PHE0-0.024-0.03242.8390.0030.0030.0000.0000.0000.000
44A44PRO00.0100.00147.118-0.002-0.0020.0000.0000.0000.000
45A45GLY0-0.0170.00046.8800.0000.0000.0000.0000.0000.000
46A46ILE0-0.031-0.01447.924-0.001-0.0010.0000.0000.0000.000
47A47ILE0-0.027-0.01043.8940.0010.0010.0000.0000.0000.000
48A49HIS00.0130.00742.3090.0000.0000.0000.0000.0000.000
49A50LEU0-0.0200.00441.751-0.001-0.0010.0000.0000.0000.000
50A51ASP-1-0.836-0.91842.577-0.019-0.0190.0000.0000.0000.000
51A52ASP-1-0.858-0.93341.522-0.028-0.0280.0000.0000.0000.000
52A53PRO0-0.041-0.00138.094-0.002-0.0020.0000.0000.0000.000
53A54LYS10.8840.94633.9950.0290.0290.0000.0000.0000.000
54A55VAL0-0.098-0.05936.1340.0000.0000.0000.0000.0000.000
55A56ALA00.0630.04138.4280.0000.0000.0000.0000.0000.000
56A57LEU0-0.048-0.05239.4710.0020.0020.0000.0000.0000.000
57A58LEU0-0.0070.00840.4320.0000.0000.0000.0000.0000.000
58A59ILE0-0.002-0.01343.3780.0020.0020.0000.0000.0000.000
59A60PHE00.0660.03742.6820.0000.0000.0000.0000.0000.000
60A61SER00.0790.04447.7720.0000.0000.0000.0000.0000.000
61A62SER0-0.029-0.01946.669-0.001-0.0010.0000.0000.0000.000
62A63GLY00.0270.01747.9390.0010.0010.0000.0000.0000.000
63A64LYS10.7990.89042.638-0.036-0.0360.0000.0000.0000.000
64A65LEU00.011-0.00641.472-0.002-0.0020.0000.0000.0000.000
65A66VAL0-0.024-0.00736.9800.0040.0040.0000.0000.0000.000
66A67VAL0-0.0060.01336.547-0.004-0.0040.0000.0000.0000.000
67A68THR0-0.022-0.00834.5110.0030.0030.0000.0000.0000.000
68A69GLY00.0810.03733.656-0.003-0.0030.0000.0000.0000.000
69A70ALA0-0.068-0.02932.821-0.006-0.0060.0000.0000.0000.000
70A71LYS10.8540.91629.0090.0440.0440.0000.0000.0000.000
71A72SER00.013-0.02128.826-0.004-0.0040.0000.0000.0000.000
72A73VAL00.0810.02628.6900.0030.0030.0000.0000.0000.000
73A74GLN00.1060.06731.4280.0040.0040.0000.0000.0000.000
74A75ASP-1-0.802-0.89533.571-0.029-0.0290.0000.0000.0000.000
75A76ILE0-0.007-0.01432.5210.0020.0020.0000.0000.0000.000
76A77GLU-1-0.899-0.94534.588-0.003-0.0030.0000.0000.0000.000
77A78ARG10.8200.89836.6130.0290.0290.0000.0000.0000.000
78A79ALA00.0000.00239.1370.0000.0000.0000.0000.0000.000
79A80VAL00.0190.00939.2640.0010.0010.0000.0000.0000.000
80A81ALA0-0.0160.00541.7980.0010.0010.0000.0000.0000.000
81A82LYS10.8660.92542.6770.0180.0180.0000.0000.0000.000
82A83LEU00.0420.02844.9340.0000.0000.0000.0000.0000.000
83A84ALA00.0710.02745.9090.0010.0010.0000.0000.0000.000
84A85GLN0-0.032-0.02547.6550.0020.0020.0000.0000.0000.000
85A86LYS10.8930.92349.0130.0070.0070.0000.0000.0000.000
86A87LEU00.0590.04748.5940.0010.0010.0000.0000.0000.000
87A88LYS10.8880.94849.9390.0000.0000.0000.0000.0000.000
88A89SER0-0.110-0.05253.7050.0000.0000.0000.0000.0000.000
89A90ILE00.0210.01955.4640.0000.0000.0000.0000.0000.000
90A91GLY0-0.031-0.01457.5400.0010.0010.0000.0000.0000.000
91A92VAL0-0.0070.01652.2720.0010.0010.0000.0000.0000.000
92A93LYS10.9510.95454.011-0.009-0.0090.0000.0000.0000.000
93A94PHE00.0230.01748.8150.0010.0010.0000.0000.0000.000
94A95LYS10.9400.97749.949-0.022-0.0220.0000.0000.0000.000
95A96ARG10.9230.95944.869-0.027-0.0270.0000.0000.0000.000
96A97ALA00.0220.02643.562-0.001-0.0010.0000.0000.0000.000
97A98PRO00.017-0.00941.7430.0020.0020.0000.0000.0000.000
98A99GLN0-0.037-0.00937.476-0.002-0.0020.0000.0000.0000.000
99A100ILE0-0.017-0.01334.6770.0010.0010.0000.0000.0000.000
100A101ASP-1-0.831-0.90033.3210.0470.0470.0000.0000.0000.000
101A102VAL00.0090.00928.058-0.002-0.0020.0000.0000.0000.000
102A103GLN0-0.016-0.03329.9850.0150.0150.0000.0000.0000.000
103A104ASN00.0010.00027.4470.0180.0180.0000.0000.0000.000
104A105MET0-0.0290.02624.447-0.014-0.0140.0000.0000.0000.000
105A106VAL0-0.0010.00024.8430.0110.0110.0000.0000.0000.000
106A107PHE00.0410.01020.861-0.011-0.0110.0000.0000.0000.000
107A108SER0-0.022-0.01822.3950.0060.0060.0000.0000.0000.000
108A109GLY00.039-0.00318.718-0.009-0.0090.0000.0000.0000.000
109A110ASP-1-0.940-0.98517.651-0.225-0.2250.0000.0000.0000.000
110A111ILE00.0410.01512.475-0.029-0.0290.0000.0000.0000.000
111A112GLY0-0.0010.00313.776-0.089-0.0890.0000.0000.0000.000
112A113ARG10.8590.93012.2230.2250.2250.0000.0000.0000.000
113A114GLU-1-0.888-0.93116.468-0.125-0.1250.0000.0000.0000.000
114A115PHE0-0.017-0.02513.470-0.022-0.0220.0000.0000.0000.000
115A116ASN00.0440.03118.7560.0210.0210.0000.0000.0000.000
116A117LEU00.026-0.01120.1360.0190.0190.0000.0000.0000.000
117A118ASP-1-0.807-0.89021.8110.0560.0560.0000.0000.0000.000
118A119VAL0-0.033-0.02017.5610.0200.0200.0000.0000.0000.000
119A120VAL0-0.050-0.02916.2330.0330.0330.0000.0000.0000.000
120A121ALA00.004-0.01918.1790.0470.0470.0000.0000.0000.000
121A122LEU0-0.0270.01319.8300.0140.0140.0000.0000.0000.000
122A123THR00.004-0.00915.4170.0040.0040.0000.0000.0000.000
123A124LEU0-0.055-0.00615.0090.0700.0700.0000.0000.0000.000
124A125PRO00.0480.02915.718-0.039-0.0390.0000.0000.0000.000
125A126ASN0-0.068-0.06318.752-0.028-0.0280.0000.0000.0000.000
126A127CYS0-0.033-0.01120.050-0.018-0.0180.0000.0000.0000.000
127A128GLU-1-0.779-0.84022.1520.1270.1270.0000.0000.0000.000
128A129TYR0-0.018-0.03423.960-0.004-0.0040.0000.0000.0000.000
129A130GLU-1-0.867-0.93225.9890.0590.0590.0000.0000.0000.000
130A131PRO00.0280.01428.134-0.005-0.0050.0000.0000.0000.000
131A132GLU-1-0.935-0.93930.3830.0110.0110.0000.0000.0000.000
132A133GLN0-0.097-0.05732.644-0.003-0.0030.0000.0000.0000.000
133A134PHE0-0.057-0.04426.483-0.006-0.0060.0000.0000.0000.000
134A135PRO00.0200.01128.1570.0040.0040.0000.0000.0000.000
135A136GLY0-0.021-0.00124.722-0.007-0.0070.0000.0000.0000.000
136A137VAL00.005-0.00220.2020.0100.0100.0000.0000.0000.000
137A138ILE0-0.016-0.01022.644-0.005-0.0050.0000.0000.0000.000
138A139TYR00.0240.01114.8480.0270.0270.0000.0000.0000.000
139A140ARG10.8200.87220.798-0.142-0.1420.0000.0000.0000.000
140A141VAL0-0.0040.00317.0060.0440.0440.0000.0000.0000.000
141A142LYS10.8520.91719.675-0.309-0.3090.0000.0000.0000.000
142A143GLU-1-0.946-0.94819.3820.2400.2400.0000.0000.0000.000
143A144PRO00.0580.01317.0020.0460.0460.0000.0000.0000.000
144A145LYS10.9520.97120.137-0.139-0.1390.0000.0000.0000.000
145A146SER0-0.060-0.02419.898-0.021-0.0210.0000.0000.0000.000
146A147VAL0-0.025-0.01721.8590.0210.0210.0000.0000.0000.000
147A148ILE00.010-0.00316.342-0.019-0.0190.0000.0000.0000.000
148A149LEU0-0.0160.00920.4170.0120.0120.0000.0000.0000.000
149A150LEU00.0100.00116.869-0.018-0.0180.0000.0000.0000.000
150A151PHE00.0250.01420.4320.0080.0080.0000.0000.0000.000
151A152SER00.0780.04120.942-0.011-0.0110.0000.0000.0000.000
152A153SER00.0310.01821.474-0.020-0.0200.0000.0000.0000.000
153A154GLY00.0380.02118.311-0.032-0.0320.0000.0000.0000.000
154A155LYS10.8530.94318.0360.1480.1480.0000.0000.0000.000
155A156ILE00.0180.00715.8710.0230.0230.0000.0000.0000.000
156A157VAL00.007-0.00120.107-0.019-0.0190.0000.0000.0000.000
157A158CYS0-0.0470.00619.0730.0260.0260.0000.0000.0000.000
158A159SER00.0160.00021.201-0.022-0.0220.0000.0000.0000.000
159A160GLY00.0280.00923.4750.0200.0200.0000.0000.0000.000
160A161ALA00.0100.02020.8600.0080.0080.0000.0000.0000.000
161A162LYS10.8720.91122.907-0.096-0.0960.0000.0000.0000.000
162A163SER00.009-0.03721.451-0.015-0.0150.0000.0000.0000.000
163A164GLU-1-0.797-0.91218.440-0.061-0.0610.0000.0000.0000.000
164A165ALA0-0.0210.00017.2450.0030.0030.0000.0000.0000.000
165A166ASP-1-0.846-0.89616.3990.1550.1550.0000.0000.0000.000
166A167ALA0-0.010-0.01217.0180.0380.0380.0000.0000.0000.000
167A168TRP0-0.025-0.03212.2620.0220.0220.0000.0000.0000.000
168A169GLU-1-0.865-0.89812.4540.4870.4870.0000.0000.0000.000
169A170ALA0-0.021-0.01512.9130.0960.0960.0000.0000.0000.000
170A171VAL00.0260.00011.9650.0550.0550.0000.0000.0000.000
171A172ARG10.8590.9198.159-0.262-0.2620.0000.0000.0000.000
172A173LYS10.8750.9389.167-0.401-0.4010.0000.0000.0000.000
173A174LEU00.0140.01611.4530.1070.1070.0000.0000.0000.000
174A175LEU0-0.002-0.0108.2130.0060.0060.0000.0000.0000.000
175A176ARG10.9460.9656.384-1.498-1.4980.0000.0000.0000.000
176A177GLU-1-0.891-0.9428.2410.9640.9640.0000.0000.0000.000
177A178LEU0-0.063-0.03410.993-0.059-0.0590.0000.0000.0000.000
178A179ASP-1-0.920-0.9574.6210.2870.303-0.001-0.009-0.0070.000
179A180LYS10.8120.9167.957-1.133-1.1330.0000.0000.0000.000
180A181TYR0-0.0010.0087.646-0.185-0.1850.0000.0000.0000.000