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: 1NJGZ

Calculation Name: 4UDS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UDS

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1996019.049282
FMO2-HF: Nuclear repulsion 1921597.047936
FMO2-HF: Total energy -74422.001346
FMO2-MP2: Total energy -74637.005147


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:15:ALA)


Summations of interaction energy for fragment #1(A:15: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.
-3.8830.3281.346-2.354-3.2050
Interaction energy analysis for fragmet #1(A:15:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.006
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].
3A17THR00.028-0.0052.841-3.048-0.6870.117-1.071-1.4080.004
4A18GLU-1-0.894-0.9432.380-3.067-1.8951.224-1.005-1.392-0.005
5A19ASN0-0.060-0.0313.5460.5291.2070.005-0.278-0.4050.001
6A20ILE0-0.024-0.0075.4280.5150.5150.0000.0000.0000.000
7A21LEU00.0140.0126.6050.2050.2050.0000.0000.0000.000
8A22GLY00.0390.0227.6920.1580.1580.0000.0000.0000.000
9A23CYS0-0.028-0.0109.0510.1780.1780.0000.0000.0000.000
10A24ALA00.007-0.00511.2280.0910.0910.0000.0000.0000.000
11A25LEU0-0.0130.00512.3110.0630.0630.0000.0000.0000.000
12A26ASP-1-0.826-0.88713.530-0.326-0.3260.0000.0000.0000.000
13A27LEU0-0.020-0.02915.3540.0430.0430.0000.0000.0000.000
14A28PHE0-0.007-0.01016.2520.0300.0300.0000.0000.0000.000
15A29VAL0-0.015-0.00718.0720.0210.0210.0000.0000.0000.000
16A30LYS10.8150.92718.0080.2360.2360.0000.0000.0000.000
17A31ASN0-0.041-0.02021.0520.0040.0040.0000.0000.0000.000
18A32GLY00.0650.05322.3130.0140.0140.0000.0000.0000.000
19A33TYR0-0.004-0.01919.034-0.006-0.0060.0000.0000.0000.000
20A34ARG10.8920.93122.2300.0600.0600.0000.0000.0000.000
21A35ALA00.0150.01624.3720.0070.0070.0000.0000.0000.000
22A36THR00.0390.03117.689-0.003-0.0030.0000.0000.0000.000
23A37THR00.012-0.01520.0630.0110.0110.0000.0000.0000.000
24A38ILE00.0840.03415.270-0.018-0.0180.0000.0000.0000.000
25A39ASP-1-0.840-0.89116.499-0.025-0.0250.0000.0000.0000.000
26A40MET00.0420.02217.6600.0000.0000.0000.0000.0000.000
27A41ILE0-0.004-0.00812.371-0.013-0.0130.0000.0000.0000.000
28A42ALA00.0040.00313.017-0.035-0.0350.0000.0000.0000.000
29A43ALA0-0.025-0.01413.566-0.003-0.0030.0000.0000.0000.000
30A44ARG10.8470.91512.8940.3030.3030.0000.0000.0000.000
31A45ALA00.0300.0149.216-0.030-0.0300.0000.0000.0000.000
32A46GLY00.0090.0319.485-0.037-0.0370.0000.0000.0000.000
33A47LEU0-0.050-0.0208.6900.0980.0980.0000.0000.0000.000
34A48THR00.0750.02812.767-0.021-0.0210.0000.0000.0000.000
35A49LYS10.8130.87415.0450.0110.0110.0000.0000.0000.000
36A50GLY0-0.013-0.00616.749-0.012-0.0120.0000.0000.0000.000
37A51ALA0-0.016-0.00311.7010.0230.0230.0000.0000.0000.000
38A52ILE00.0380.01611.4300.0540.0540.0000.0000.0000.000
39A53TYR0-0.026-0.01912.472-0.008-0.0080.0000.0000.0000.000
40A54PHE0-0.026-0.01112.248-0.028-0.0280.0000.0000.0000.000
41A55TYR0-0.0490.0065.9930.2180.2180.0000.0000.0000.000
42A56PHE00.0400.0058.143-0.039-0.0390.0000.0000.0000.000
43A57LYS10.9780.99912.862-0.071-0.0710.0000.0000.0000.000
44A58THR0-0.023-0.03916.257-0.004-0.0040.0000.0000.0000.000
45A59LYS10.8620.92516.0870.0740.0740.0000.0000.0000.000
46A60ASP-1-0.822-0.91616.974-0.075-0.0750.0000.0000.0000.000
47A61ALA00.0480.03215.089-0.010-0.0100.0000.0000.0000.000
48A62ILE0-0.0230.00211.990-0.019-0.0190.0000.0000.0000.000
49A63MET00.0050.01113.774-0.049-0.0490.0000.0000.0000.000
50A64LEU0-0.032-0.00916.511-0.015-0.0150.0000.0000.0000.000
51A65MET00.0560.0388.3780.0220.0220.0000.0000.0000.000
52A66LEU0-0.049-0.03311.531-0.030-0.0300.0000.0000.0000.000
53A67LEU0-0.023-0.01613.906-0.004-0.0040.0000.0000.0000.000
54A68GLU-1-0.794-0.87814.340-0.130-0.1300.0000.0000.0000.000
55A69GLU-1-0.862-0.9339.855-0.663-0.6630.0000.0000.0000.000
56A70ALA0-0.027-0.01813.5950.0040.0040.0000.0000.0000.000
57A71GLU-1-0.848-0.91116.836-0.115-0.1150.0000.0000.0000.000
58A72LYS10.9310.97310.5920.5140.5140.0000.0000.0000.000
59A73TYR0-0.063-0.0519.8450.0100.0100.0000.0000.0000.000
60A74ILE0-0.020-0.01216.8600.0120.0120.0000.0000.0000.000
61A75VAL0-0.017-0.02420.2950.0150.0150.0000.0000.0000.000
62A76ASP-1-0.805-0.87418.764-0.144-0.1440.0000.0000.0000.000
63A77PRO0-0.065-0.04219.8560.0130.0130.0000.0000.0000.000
64A78ILE0-0.039-0.00822.6170.0080.0080.0000.0000.0000.000
65A79ASP-1-0.880-0.94225.876-0.071-0.0710.0000.0000.0000.000
66A80GLU-1-0.867-0.92225.385-0.100-0.1000.0000.0000.0000.000
67A81TYR00.0350.00024.0090.0080.0080.0000.0000.0000.000
68A82MET0-0.0100.00127.8760.0030.0030.0000.0000.0000.000
69A83ALA0-0.0120.00430.7490.0060.0060.0000.0000.0000.000
70A84ASN0-0.047-0.04128.8800.0100.0100.0000.0000.0000.000
71A85ALA0-0.065-0.00231.7840.0010.0010.0000.0000.0000.000
72A86GLY00.0090.03533.4330.0030.0030.0000.0000.0000.000
73A87PRO0-0.036-0.04537.168-0.002-0.0020.0000.0000.0000.000
74A88LEU00.0410.02039.9180.0010.0010.0000.0000.0000.000
75A89ALA00.0540.02338.300-0.004-0.0040.0000.0000.0000.000
76A90ASP-1-0.841-0.92537.695-0.058-0.0580.0000.0000.0000.000
77A91ALA0-0.023-0.00836.632-0.004-0.0040.0000.0000.0000.000
78A92LYS10.8380.89733.8100.0580.0580.0000.0000.0000.000
79A93LEU00.0420.03532.918-0.006-0.0060.0000.0000.0000.000
80A94VAL0-0.030-0.01833.076-0.006-0.0060.0000.0000.0000.000
81A95LYS10.8900.96127.2680.0960.0960.0000.0000.0000.000
82A96PHE00.0590.00927.872-0.009-0.0090.0000.0000.0000.000
83A97ILE00.0200.02128.327-0.007-0.0070.0000.0000.0000.000
84A98ASN0-0.055-0.03828.619-0.005-0.0050.0000.0000.0000.000
85A99MET0-0.0230.00022.537-0.007-0.0070.0000.0000.0000.000
86A100GLN00.0430.02023.718-0.023-0.0230.0000.0000.0000.000
87A101ALA00.0060.00924.471-0.007-0.0070.0000.0000.0000.000
88A102LEU0-0.075-0.04420.925-0.005-0.0050.0000.0000.0000.000
89A103LEU00.0240.02618.666-0.018-0.0180.0000.0000.0000.000
90A104GLY00.0370.02720.015-0.014-0.0140.0000.0000.0000.000
91A105VAL0-0.069-0.03820.8570.0010.0010.0000.0000.0000.000
92A106THR0-0.068-0.05416.734-0.015-0.0150.0000.0000.0000.000
93A107LYS10.8990.96812.6580.3530.3530.0000.0000.0000.000
94A108PRO00.0830.05616.7880.0060.0060.0000.0000.0000.000
95A109GLN0-0.002-0.03114.4780.0480.0480.0000.0000.0000.000
96A110HIS00.005-0.01212.0730.0540.0540.0000.0000.0000.000
97A111VAL00.0360.01017.3420.0180.0180.0000.0000.0000.000
98A112LEU0-0.008-0.00120.8440.0150.0150.0000.0000.0000.000
99A113LEU0-0.033-0.01316.8090.0140.0140.0000.0000.0000.000
100A114LEU00.0150.00520.3790.0140.0140.0000.0000.0000.000
101A115ILE0-0.0130.01422.8510.0120.0120.0000.0000.0000.000
102A116LEU0-0.004-0.00624.7570.0100.0100.0000.0000.0000.000
103A117VAL0-0.038-0.01521.2580.0080.0080.0000.0000.0000.000
104A118SER0-0.0110.00024.6730.0110.0110.0000.0000.0000.000
105A119ILE00.0010.00527.1580.0090.0090.0000.0000.0000.000
106A120ASP-1-0.824-0.89128.982-0.060-0.0600.0000.0000.0000.000
107A121PHE0-0.033-0.01130.5440.0000.0000.0000.0000.0000.000
108A122SER0-0.028-0.00525.490-0.001-0.0010.0000.0000.0000.000
109A123GLY00.0010.00426.303-0.004-0.0040.0000.0000.0000.000
110A124THR0-0.003-0.01622.8700.0050.0050.0000.0000.0000.000
111A125GLY00.0280.02125.0230.0040.0040.0000.0000.0000.000
112A126ASP-1-0.809-0.90426.385-0.049-0.0490.0000.0000.0000.000
113A127ASP-1-0.929-0.95723.191-0.053-0.0530.0000.0000.0000.000
114A128ILE00.0330.00520.666-0.007-0.0070.0000.0000.0000.000
115A129GLH0-0.021-0.03923.217-0.007-0.0070.0000.0000.0000.000
116A130LYS10.8180.90126.0030.0430.0430.0000.0000.0000.000
117A131ARG10.8530.91517.3270.1120.1120.0000.0000.0000.000
118A132ALA00.0470.01822.843-0.005-0.0050.0000.0000.0000.000
119A133LYS10.8600.91123.8590.0660.0660.0000.0000.0000.000
120A134ALA0-0.059-0.01925.3500.0020.0020.0000.0000.0000.000
121A135ILE00.0360.02720.1930.0010.0010.0000.0000.0000.000
122A136TYR0-0.055-0.04824.3300.0010.0010.0000.0000.0000.000
123A137ARG10.9480.96526.8490.0600.0600.0000.0000.0000.000
124A138ARG10.8150.88621.7330.1210.1210.0000.0000.0000.000
125A139MET0-0.0010.00925.407-0.002-0.0020.0000.0000.0000.000
126A140TYR0-0.060-0.03627.5930.0030.0030.0000.0000.0000.000
127A141GLY00.0450.01530.9960.0040.0040.0000.0000.0000.000
128A142HIS0-0.0230.00027.861-0.001-0.0010.0000.0000.0000.000
129A143VAL0-0.029-0.01130.7920.0020.0020.0000.0000.0000.000
130A144GLU-1-0.864-0.91733.339-0.049-0.0490.0000.0000.0000.000
131A145GLN00.0180.00033.3690.0040.0040.0000.0000.0000.000
132A146LEU0-0.057-0.01233.6580.0020.0020.0000.0000.0000.000
133A147ILE0-0.036-0.02736.5250.0020.0020.0000.0000.0000.000
134A148ALA00.0670.03339.1910.0020.0020.0000.0000.0000.000
135A149GLN0-0.080-0.04239.2420.0030.0030.0000.0000.0000.000
136A150GLY00.052-0.00440.6990.0020.0020.0000.0000.0000.000
137A151GLN0-0.101-0.06042.3000.0020.0020.0000.0000.0000.000
138A152THR0-0.058-0.02344.3550.0030.0030.0000.0000.0000.000
139A153GLU-1-0.834-0.91241.839-0.047-0.0470.0000.0000.0000.000
140A154GLY0-0.0210.00146.2380.0010.0010.0000.0000.0000.000
141A155VAL0-0.050-0.01642.4710.0000.0000.0000.0000.0000.000
142A156PHE0-0.070-0.03038.751-0.001-0.0010.0000.0000.0000.000
143A157ARG10.8570.91944.6750.0430.0430.0000.0000.0000.000
144A158SER00.0450.00845.999-0.001-0.0010.0000.0000.0000.000
145A159ASP-1-0.878-0.91248.413-0.037-0.0370.0000.0000.0000.000
146A160SER0-0.022-0.03345.0420.0000.0000.0000.0000.0000.000
147A161GLY00.0200.02544.7400.0000.0000.0000.0000.0000.000
148A162SER0-0.007-0.04040.317-0.001-0.0010.0000.0000.0000.000
149A163ASP-1-0.834-0.91839.007-0.047-0.0470.0000.0000.0000.000
150A164GLU-1-0.863-0.91438.951-0.045-0.0450.0000.0000.0000.000
151A165LEU0-0.002-0.01639.954-0.003-0.0030.0000.0000.0000.000
152A166ALA00.0160.01035.451-0.003-0.0030.0000.0000.0000.000
153A167SER0-0.045-0.02635.164-0.005-0.0050.0000.0000.0000.000
154A168ILE0-0.0180.00235.688-0.003-0.0030.0000.0000.0000.000
155A169VAL00.0070.01232.873-0.003-0.0030.0000.0000.0000.000
156A170MET00.0020.01627.951-0.006-0.0060.0000.0000.0000.000
157A171ALA00.0030.00431.400-0.005-0.0050.0000.0000.0000.000
158A172ALA0-0.011-0.00533.067-0.002-0.0020.0000.0000.0000.000
159A173HIS0-0.045-0.05228.672-0.006-0.0060.0000.0000.0000.000
160A174ASP-1-0.805-0.89328.200-0.108-0.1080.0000.0000.0000.000
161A175GLY0-0.005-0.00529.020-0.003-0.0030.0000.0000.0000.000
162A176VAL0-0.023-0.01728.9510.0000.0000.0000.0000.0000.000
163A177LEU0-0.0110.00322.661-0.004-0.0040.0000.0000.0000.000
164A178ILE0-0.011-0.01626.721-0.004-0.0040.0000.0000.0000.000
165A179GLU-1-0.837-0.91028.242-0.081-0.0810.0000.0000.0000.000
166A180TRP0-0.056-0.02021.224-0.004-0.0040.0000.0000.0000.000
167A181TYR0-0.008-0.02720.502-0.008-0.0080.0000.0000.0000.000
168A182ARG10.8260.91526.4510.0850.0850.0000.0000.0000.000
169A183ARG10.8650.92129.8640.0760.0760.0000.0000.0000.000
170A184PRO00.0400.02625.9910.0020.0020.0000.0000.0000.000
171A185ASN0-0.048-0.03327.945-0.007-0.0070.0000.0000.0000.000
172A186GLU-1-0.898-0.92930.158-0.069-0.0690.0000.0000.0000.000
173A187LEU0-0.049-0.00529.3380.0030.0030.0000.0000.0000.000
174A188THR00.0400.00926.492-0.008-0.0080.0000.0000.0000.000
175A189GLY00.0620.01724.9770.0040.0040.0000.0000.0000.000
176A190LYS10.9030.94525.1820.1360.1360.0000.0000.0000.000
177A191THR0-0.0140.01928.4650.0030.0030.0000.0000.0000.000
178A192LEU00.0560.01431.0800.0060.0060.0000.0000.0000.000
179A193THR00.0390.03529.5590.0010.0010.0000.0000.0000.000
180A194LYS10.9540.97732.0870.0640.0640.0000.0000.0000.000
181A195ALA00.0310.02435.4370.0030.0030.0000.0000.0000.000
182A196LEU00.0390.02931.5070.0030.0030.0000.0000.0000.000
183A197ARG10.9480.96232.5180.0830.0830.0000.0000.0000.000
184A198SER0-0.056-0.05236.1750.0030.0030.0000.0000.0000.000
185A199VAL0-0.0070.00339.0550.0030.0030.0000.0000.0000.000
186A200LEU0-0.0020.00634.6690.0020.0020.0000.0000.0000.000
187A201LEU0-0.036-0.01838.1410.0010.0010.0000.0000.0000.000
188A202ASN0-0.032-0.03040.9860.0040.0040.0000.0000.0000.000
189A203GLY00.0020.03342.9350.0020.0020.0000.0000.0000.000
190A204LEU0-0.023-0.03443.035-0.001-0.0010.0000.0000.0000.000
191A205ILE0-0.0290.00346.1070.0010.0010.0000.0000.0000.000
192A206VAL00.0400.02849.3040.0000.0000.0000.0000.0000.000