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: LNY59

Calculation Name: 1UAI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UAI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RB42

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptAll
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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2680293.232256
FMO2-HF: Nuclear repulsion 2594949.235254
FMO2-HF: Total energy -85343.997002
FMO2-MP2: Total energy -85593.508629


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:2:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
8.6216.60923.424-6.121-15.2880.055
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.921 / q_NPA : -0.939
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].
3A4CYS0-0.034-0.0221.741-36.055-43.96618.718-2.524-8.2820.084
4A5ASP-1-0.831-0.8932.52739.45442.9842.442-1.869-4.102-0.023
5A6TYR0-0.017-0.0294.471-7.874-7.697-0.001-0.017-0.1580.000
6A7PRO0-0.045-0.0326.4152.3572.3570.0000.0000.0000.000
7A8ALA00.0410.0288.460-0.286-0.2860.0000.0000.0000.000
8A9GLN0-0.011-0.0022.3312.1594.3512.265-1.711-2.746-0.006
9A10GLN0-0.103-0.0665.692-4.206-4.2060.0000.0000.0000.000
10A11LEU0-0.075-0.0478.532-3.048-3.0480.0000.0000.0000.000
11A12ASP-1-0.821-0.88310.92319.61219.6120.0000.0000.0000.000
12A13LEU0-0.041-0.03612.063-1.371-1.3710.0000.0000.0000.000
13A14THR00.0000.00213.927-0.547-0.5470.0000.0000.0000.000
14A15ASP-1-0.833-0.92415.36313.29813.2980.0000.0000.0000.000
15A16TRP0-0.062-0.03916.798-0.914-0.9140.0000.0000.0000.000
16A17LYS10.8140.90617.997-11.923-11.9230.0000.0000.0000.000
17A18VAL0-0.020-0.01116.138-0.072-0.0720.0000.0000.0000.000
18A19THR0-0.010-0.02519.056-0.373-0.3730.0000.0000.0000.000
19A20LEU0-0.015-0.00717.3930.4860.4860.0000.0000.0000.000
20A21PRO0-0.0040.00520.755-0.613-0.6130.0000.0000.0000.000
21A22ILE00.0170.00619.619-0.389-0.3890.0000.0000.0000.000
22A23GLY00.0380.04024.1130.1980.1980.0000.0000.0000.000
23A24SER00.0170.02025.992-0.105-0.1050.0000.0000.0000.000
24A25SER00.005-0.01629.5480.0640.0640.0000.0000.0000.000
25A26GLY00.0210.01632.554-0.119-0.1190.0000.0000.0000.000
26A27LYS10.9350.96927.588-10.920-10.9200.0000.0000.0000.000
27A28PRO00.0070.01025.8490.2330.2330.0000.0000.0000.000
28A29SER0-0.037-0.04222.094-0.266-0.2660.0000.0000.0000.000
29A30GLU-1-0.856-0.91121.45812.29812.2980.0000.0000.0000.000
30A31ILE0-0.041-0.01015.856-0.209-0.2090.0000.0000.0000.000
31A32GLU-1-0.799-0.90318.54812.59912.5990.0000.0000.0000.000
32A33GLN00.0450.02413.2840.9990.9990.0000.0000.0000.000
33A34PRO00.0270.00715.098-0.682-0.6820.0000.0000.0000.000
34A35ALA0-0.020-0.01813.8561.0591.0590.0000.0000.0000.000
35A36LEU0-0.070-0.04113.3981.0461.0460.0000.0000.0000.000
36A37ASP-1-0.905-0.9458.76826.80626.8060.0000.0000.0000.000
37A38THR0-0.021-0.0088.0832.4402.4400.0000.0000.0000.000
38A39PHE0-0.027-0.0099.547-1.183-1.1830.0000.0000.0000.000
39A40ALA00.030-0.0029.6091.2761.2760.0000.0000.0000.000
40A41THR0-0.065-0.02711.689-1.301-1.3010.0000.0000.0000.000
41A42ALA00.0490.04513.295-0.569-0.5690.0000.0000.0000.000
42A43PRO0-0.043-0.03015.019-0.927-0.9270.0000.0000.0000.000
43A44TRP0-0.006-0.01316.903-0.090-0.0900.0000.0000.0000.000
44A45PHE00.0630.04912.998-0.551-0.5510.0000.0000.0000.000
45A46GLN00.0180.00410.825-1.354-1.3540.0000.0000.0000.000
46A47VAL00.0860.0725.665-2.760-2.7600.0000.0000.0000.000
47A48ASN00.0260.0059.0390.7670.7670.0000.0000.0000.000
48A49ALA00.026-0.0029.3762.7892.7890.0000.0000.0000.000
49A50LYS10.8520.91510.320-22.308-22.3080.0000.0000.0000.000
50A52THR00.0190.0137.454-0.070-0.0700.0000.0000.0000.000
51A53GLY00.0730.02910.436-2.675-2.6750.0000.0000.0000.000
52A54VAL0-0.0230.01810.6361.9281.9280.0000.0000.0000.000
53A55GLN0-0.078-0.03812.390-1.724-1.7240.0000.0000.0000.000
54A56PHE00.0500.02014.7570.3680.3680.0000.0000.0000.000
55A57ARG10.8360.90817.613-16.309-16.3090.0000.0000.0000.000
56A58ALA00.0510.02520.3540.0550.0550.0000.0000.0000.000
57A59ALA00.0260.02223.637-0.308-0.3080.0000.0000.0000.000
58A60VAL00.0010.00426.288-0.130-0.1300.0000.0000.0000.000
59A61ASN0-0.002-0.03228.209-0.094-0.0940.0000.0000.0000.000
60A62GLY0-0.0080.01626.8130.0410.0410.0000.0000.0000.000
61A63VAL0-0.039-0.02226.919-0.432-0.4320.0000.0000.0000.000
62A64THR0-0.008-0.00427.8650.1610.1610.0000.0000.0000.000
63A65THR00.0440.00430.4960.0050.0050.0000.0000.0000.000
64A66SER0-0.015-0.00732.390-0.131-0.1310.0000.0000.0000.000
65A67GLY0-0.033-0.00233.849-0.190-0.1900.0000.0000.0000.000
66A68SER0-0.060-0.02534.914-0.163-0.1630.0000.0000.0000.000
67A69GLY00.0590.02433.485-0.035-0.0350.0000.0000.0000.000
68A70TYR0-0.0370.00330.826-0.101-0.1010.0000.0000.0000.000
69A71PRO00.0060.01626.7780.1410.1410.0000.0000.0000.000
70A72ARG10.8300.88724.131-11.204-11.2040.0000.0000.0000.000
71A73SER0-0.027-0.02618.1390.1030.1030.0000.0000.0000.000
72A74GLU-1-0.786-0.87920.53812.25012.2500.0000.0000.0000.000
73A75LEU00.0540.03815.780-0.228-0.2280.0000.0000.0000.000
74A76ARG10.7840.86819.926-11.824-11.8240.0000.0000.0000.000
75A77GLU-1-0.734-0.84521.71411.82711.8270.0000.0000.0000.000
76A78MET0-0.047-0.01120.914-0.765-0.7650.0000.0000.0000.000
77A79THR0-0.002-0.01422.9120.0310.0310.0000.0000.0000.000
78A80ASP-1-0.941-0.96923.31811.18311.1830.0000.0000.0000.000
79A81GLY00.0260.01619.0380.0330.0330.0000.0000.0000.000
80A82GLY0-0.017-0.01418.4870.6440.6440.0000.0000.0000.000
81A83GLU-1-0.973-0.97020.07012.73212.7320.0000.0000.0000.000
82A84GLU-1-0.957-0.97322.8449.5909.5900.0000.0000.0000.000
83A85LYS10.9190.93824.711-9.896-9.8960.0000.0000.0000.000
84A86ALA00.0200.02925.254-0.355-0.3550.0000.0000.0000.000
85A87SER00.0200.00727.141-0.205-0.2050.0000.0000.0000.000
86A88TRP0-0.013-0.01827.703-0.395-0.3950.0000.0000.0000.000
87A89SER0-0.002-0.00332.449-0.178-0.1780.0000.0000.0000.000
88A90ALA00.0430.02435.0610.1500.1500.0000.0000.0000.000
89A91THR0-0.030-0.02336.791-0.033-0.0330.0000.0000.0000.000
90A92SER0-0.0140.00937.738-0.140-0.1400.0000.0000.0000.000
91A93GLY00.0540.03734.5570.2320.2320.0000.0000.0000.000
92A94THR0-0.040-0.03131.362-0.202-0.2020.0000.0000.0000.000
93A95HIS10.8260.90729.300-9.241-9.2410.0000.0000.0000.000
94A96THR0-0.017-0.01126.011-0.345-0.3450.0000.0000.0000.000
95A97MET00.0280.04122.6240.4560.4560.0000.0000.0000.000
96A98VAL0-0.057-0.03522.250-0.487-0.4870.0000.0000.0000.000
97A99PHE00.0370.02020.2660.6120.6120.0000.0000.0000.000
98A100ARG10.8490.90118.982-15.803-15.8030.0000.0000.0000.000
99A101GLU-1-0.817-0.91218.85614.61214.6120.0000.0000.0000.000
100A102ALA00.0050.00020.297-0.526-0.5260.0000.0000.0000.000
101A103PHE00.0640.03521.1350.5730.5730.0000.0000.0000.000
102A104ASN0-0.0030.00018.4860.0050.0050.0000.0000.0000.000
103A105HIS0-0.006-0.00622.253-0.147-0.1470.0000.0000.0000.000
104A106LEU0-0.023-0.00724.8770.0480.0480.0000.0000.0000.000
105A107PRO0-0.0220.00528.1500.0790.0790.0000.0000.0000.000
106A108GLU-1-0.788-0.92330.1819.4439.4430.0000.0000.0000.000
107A109VAL0-0.0590.01033.300-0.119-0.1190.0000.0000.0000.000
108A110LYS10.7950.88635.139-9.189-9.1890.0000.0000.0000.000
109A111PRO00.0480.03632.1420.2440.2440.0000.0000.0000.000
110A112HIS00.0230.00532.1030.0340.0340.0000.0000.0000.000
111A113LEU0-0.055-0.01224.4140.1530.1530.0000.0000.0000.000
112A114VAL0-0.008-0.00227.183-0.236-0.2360.0000.0000.0000.000
113A115GLY00.0040.02523.8150.3430.3430.0000.0000.0000.000
114A116ALA00.0450.02023.2290.4980.4980.0000.0000.0000.000
115A117GLN0-0.054-0.04925.222-0.810-0.8100.0000.0000.0000.000
116A118ILE0-0.011-0.00227.4790.3100.3100.0000.0000.0000.000
117A119HIS0-0.0140.00330.133-0.093-0.0930.0000.0000.0000.000
118A120ASP-1-0.771-0.87531.7868.5188.5180.0000.0000.0000.000
119A121GLY0-0.027-0.01233.9650.1720.1720.0000.0000.0000.000
120A122ASP-1-0.968-0.96736.1897.6917.6910.0000.0000.0000.000
121A123ASP-1-0.877-0.94534.9328.8528.8520.0000.0000.0000.000
122A124ASP-1-0.928-0.97733.0419.4879.4870.0000.0000.0000.000
123A125VAL0-0.0180.00333.563-0.298-0.2980.0000.0000.0000.000
124A126THR0-0.079-0.07232.720-0.159-0.1590.0000.0000.0000.000
125A127VAL00.0120.00729.5210.4050.4050.0000.0000.0000.000
126A128PHE0-0.034-0.01027.315-0.279-0.2790.0000.0000.0000.000
127A129ARG10.8550.89828.454-8.967-8.9670.0000.0000.0000.000
128A130LEU0-0.0160.01028.098-0.250-0.2500.0000.0000.0000.000
129A131GLU-1-0.797-0.88030.7198.8298.8290.0000.0000.0000.000
130A132GLY00.0220.00632.779-0.253-0.2530.0000.0000.0000.000
131A133THR0-0.017-0.01731.4570.3170.3170.0000.0000.0000.000
132A134SER0-0.046-0.01933.198-0.096-0.0960.0000.0000.0000.000
133A135LEU0-0.0190.00929.0760.1010.1010.0000.0000.0000.000
134A136TYR00.000-0.00932.609-0.389-0.3890.0000.0000.0000.000
135A137ILE0-0.026-0.00231.5570.3450.3450.0000.0000.0000.000
136A138THR00.0010.01333.755-0.234-0.2340.0000.0000.0000.000
137A139LYS10.8980.93035.845-7.576-7.5760.0000.0000.0000.000
138A140GLY00.0900.06936.941-0.311-0.3110.0000.0000.0000.000
139A141ASP-1-0.893-0.95037.9057.7607.7600.0000.0000.0000.000
140A142ASP-1-0.898-0.94440.2547.6927.6920.0000.0000.0000.000
141A143THR0-0.001-0.03536.5600.1850.1850.0000.0000.0000.000
142A144HIS10.7920.86136.974-7.986-7.9860.0000.0000.0000.000
143A145HIS00.0050.06137.8020.0550.0550.0000.0000.0000.000
144A146LYS10.8480.93036.686-8.697-8.6970.0000.0000.0000.000
145A147LEU00.0320.02336.5840.2870.2870.0000.0000.0000.000
146A148VAL0-0.047-0.01831.906-0.156-0.1560.0000.0000.0000.000
147A149THR00.008-0.01032.694-0.168-0.1680.0000.0000.0000.000
148A150SER00.0500.03435.0800.0950.0950.0000.0000.0000.000
149A151ASP-1-0.856-0.91634.5799.4109.4100.0000.0000.0000.000
150A152TYR0-0.028-0.02624.5820.2530.2530.0000.0000.0000.000
151A153LYS10.8560.92728.606-9.949-9.9490.0000.0000.0000.000
152A154LEU00.0560.02825.4350.3560.3560.0000.0000.0000.000
153A155ASN0-0.035-0.02520.9390.7770.7770.0000.0000.0000.000
154A156THR0-0.042-0.01221.9380.5020.5020.0000.0000.0000.000
155A157VAL0-0.0060.00919.136-0.162-0.1620.0000.0000.0000.000
156A158PHE0-0.062-0.01622.334-0.626-0.6260.0000.0000.0000.000
157A159GLU-1-0.781-0.87822.82414.21014.2100.0000.0000.0000.000
158A160GLY00.0040.00824.280-0.671-0.6710.0000.0000.0000.000
159A161LYS10.8800.94825.028-10.159-10.1590.0000.0000.0000.000
160A162PHE00.0580.03626.986-0.452-0.4520.0000.0000.0000.000
161A163VAL0-0.017-0.02328.5850.2610.2610.0000.0000.0000.000
162A164VAL0-0.0090.01131.237-0.285-0.2850.0000.0000.0000.000
163A165SER00.0450.01933.5840.1520.1520.0000.0000.0000.000
164A166GLY00.0020.00636.393-0.110-0.1100.0000.0000.0000.000
165A167GLY00.003-0.00339.430-0.200-0.2000.0000.0000.0000.000
166A168LYS10.8330.90238.922-7.361-7.3610.0000.0000.0000.000
167A169ILE00.0640.04333.4200.1730.1730.0000.0000.0000.000
168A170LYS10.8380.91834.125-8.284-8.2840.0000.0000.0000.000
169A171VAL00.0680.03631.1290.2990.2990.0000.0000.0000.000
170A172TYR0-0.048-0.03730.140-0.310-0.3100.0000.0000.0000.000
171A173TYR00.0650.02128.3170.2540.2540.0000.0000.0000.000
172A174ASN00.0260.00427.1110.1020.1020.0000.0000.0000.000
173A175GLY00.0150.01629.018-0.179-0.1790.0000.0000.0000.000
174A176VAL00.0040.00830.476-0.310-0.3100.0000.0000.0000.000
175A177LEU0-0.038-0.02033.5580.1730.1730.0000.0000.0000.000
176A178GLN0-0.026-0.02433.430-0.342-0.3420.0000.0000.0000.000
177A179THR00.036-0.01436.060-0.303-0.3030.0000.0000.0000.000
178A180THR0-0.026-0.02037.1320.1700.1700.0000.0000.0000.000
179A181ILE00.0470.05536.252-0.274-0.2740.0000.0000.0000.000
180A182SER0-0.044-0.02339.3390.0090.0090.0000.0000.0000.000
181A183HIS00.0220.00836.449-0.217-0.2170.0000.0000.0000.000
182A184THR0-0.022-0.03039.8920.0610.0610.0000.0000.0000.000
183A185SER0-0.004-0.00637.912-0.059-0.0590.0000.0000.0000.000
184A186SER0-0.014-0.03036.5790.1320.1320.0000.0000.0000.000
185A187GLY00.0520.04133.989-0.143-0.1430.0000.0000.0000.000
186A188ASN0-0.103-0.05932.2980.0890.0890.0000.0000.0000.000
187A189TYR0-0.019-0.00926.9260.2940.2940.0000.0000.0000.000
188A190PHE00.018-0.00924.634-0.192-0.1920.0000.0000.0000.000
189A191LYS10.8160.90523.452-12.145-12.1450.0000.0000.0000.000
190A192ALA00.0260.00720.287-0.306-0.3060.0000.0000.0000.000
191A193GLY00.0150.01119.3890.5770.5770.0000.0000.0000.000
192A194ALA0-0.016-0.01020.353-0.301-0.3010.0000.0000.0000.000
193A195TYR00.0590.02322.490-0.127-0.1270.0000.0000.0000.000
194A196THR00.022-0.02625.823-0.306-0.3060.0000.0000.0000.000
195A197GLN0-0.038-0.00327.731-0.600-0.6000.0000.0000.0000.000
196A198ALA00.0200.00831.051-0.397-0.3970.0000.0000.0000.000
197A199ASN00.0560.02631.3480.1670.1670.0000.0000.0000.000
198A200CYS0-0.009-0.01133.1910.2070.2070.0000.0000.0000.000
199A201SER0-0.055-0.02235.518-0.252-0.2520.0000.0000.0000.000
200A202ASN00.002-0.02536.1370.0040.0040.0000.0000.0000.000
201A203SER00.003-0.00933.7790.1370.1370.0000.0000.0000.000
202A204SER0-0.0130.00835.931-0.133-0.1330.0000.0000.0000.000
203A205PRO00.0530.01732.678-0.004-0.0040.0000.0000.0000.000
204A207SER00.019-0.00130.0100.0540.0540.0000.0000.0000.000
205A208SER00.0580.01625.1190.0640.0640.0000.0000.0000.000
206A209SER0-0.033-0.00825.4090.4340.4340.0000.0000.0000.000
207A210ASN0-0.040-0.00927.0840.2300.2300.0000.0000.0000.000
208A211TYR0-0.001-0.02022.6070.2490.2490.0000.0000.0000.000
209A212GLY00.0360.04625.504-0.152-0.1520.0000.0000.0000.000
210A213GLN0-0.031-0.03017.8950.1280.1280.0000.0000.0000.000
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