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: R9NR8

Calculation Name: 4UID-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UID

Chain ID: A

ChEMBL ID:

UniProt ID: O68840

Base Structure: X-ray

Registration Date: 2023-06-21

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1708316.292024
FMO2-HF: Nuclear repulsion 1636431.763109
FMO2-HF: Total energy -71884.528915
FMO2-MP2: Total energy -72099.244925


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:447:ALA)


Summations of interaction energy for fragment #1(A:447: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.
-2.1632.2635.826-4.369-5.883-0.023
Interaction energy analysis for fragmet #1(A:447:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.010
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].
3A449VAL0-0.024-0.0073.9960.3881.900-0.002-0.847-0.6620.003
4A450SER00.0450.0246.1710.1650.1650.0000.0000.0000.000
5A451GLU-1-0.872-0.9268.496-0.071-0.0710.0000.0000.0000.000
6A452LEU0-0.005-0.00910.336-0.011-0.0110.0000.0000.0000.000
7A453LYS10.8680.94112.8770.2500.2500.0000.0000.0000.000
8A454LEU00.0480.03216.3480.0180.0180.0000.0000.0000.000
9A455THR0-0.048-0.04618.0650.0010.0010.0000.0000.0000.000
10A456LYS10.9150.95920.6610.0410.0410.0000.0000.0000.000
11A457ASP-1-0.845-0.93623.276-0.026-0.0260.0000.0000.0000.000
12A458ASN0-0.043-0.02920.356-0.001-0.0010.0000.0000.0000.000
13A459LYS10.8840.97121.5100.0300.0300.0000.0000.0000.000
14A460GLU-1-0.800-0.89719.790-0.208-0.2080.0000.0000.0000.000
15A461VAL0-0.048-0.02222.0950.0090.0090.0000.0000.0000.000
16A462VAL0-0.0140.00123.726-0.016-0.0160.0000.0000.0000.000
17A463THR0-0.050-0.02426.282-0.002-0.0020.0000.0000.0000.000
18A464LEU00.0530.03025.1210.0060.0060.0000.0000.0000.000
19A465TYR0-0.0170.00528.770-0.005-0.0050.0000.0000.0000.000
20A466ALA00.0530.00830.7450.0010.0010.0000.0000.0000.000
21A467ASN0-0.030-0.01332.1540.0000.0000.0000.0000.0000.000
22A468GLY00.0310.01629.5700.0050.0050.0000.0000.0000.000
23A469ASN0-0.081-0.02929.5370.0020.0020.0000.0000.0000.000
24A470ALA00.0400.01027.037-0.007-0.0070.0000.0000.0000.000
25A471PHE0-0.040-0.02228.5770.0070.0070.0000.0000.0000.000
26A472ASP-1-0.755-0.88327.064-0.082-0.0820.0000.0000.0000.000
27A473LYS10.8560.89522.7720.1430.1430.0000.0000.0000.000
28A474ASP-1-0.917-0.93629.051-0.077-0.0770.0000.0000.0000.000
29A475GLY0-0.038-0.00631.6370.0030.0030.0000.0000.0000.000
30A476ASN0-0.033-0.01432.5370.0100.0100.0000.0000.0000.000
31A477GLN0-0.024-0.01731.442-0.005-0.0050.0000.0000.0000.000
32A478ILE0-0.0020.01225.9340.0050.0050.0000.0000.0000.000
33A479SER00.001-0.01229.984-0.001-0.0010.0000.0000.0000.000
34A480SER00.0190.02228.7000.0050.0050.0000.0000.0000.000
35A481GLY00.0250.01125.570-0.007-0.0070.0000.0000.0000.000
36A482THR00.0080.00323.045-0.003-0.0030.0000.0000.0000.000
37A483LEU0-0.041-0.02523.155-0.004-0.0040.0000.0000.0000.000
38A484THR00.0450.01717.4210.0150.0150.0000.0000.0000.000
39A485LEU00.0130.02215.377-0.026-0.0260.0000.0000.0000.000
40A486THR0-0.057-0.02213.3380.0440.0440.0000.0000.0000.000
41A487ALA00.018-0.0119.175-0.053-0.0530.0000.0000.0000.000
42A488LYS10.8130.9128.3000.2850.2850.0000.0000.0000.000
43A489PHE00.032-0.0032.849-0.556-0.1040.095-0.109-0.4380.000
44A490LYS10.8240.9183.9831.0731.3010.000-0.053-0.1750.000
45A491ASP-1-0.743-0.8742.015-2.614-1.7594.875-3.465-2.266-0.025
46A492GLN0-0.018-0.0183.043-0.181-0.7300.0050.844-0.301-0.001
47A493TYR0-0.070-0.0334.858-0.101-0.057-0.001-0.007-0.0360.000
48A494GLY0-0.0060.0106.1930.0660.0660.0000.0000.0000.000
49A495ASN0-0.078-0.0526.738-0.045-0.0450.0000.0000.0000.000
50A496GLU-1-0.819-0.9156.510-0.311-0.3110.0000.0000.0000.000
51A497LEU00.0010.0082.914-0.3520.0580.297-0.151-0.555-0.001
52A498THR0-0.011-0.0057.012-0.131-0.1310.0000.0000.0000.000
53A499GLY0-0.014-0.01210.4410.1020.1020.0000.0000.0000.000
54A500LYS10.7870.8956.835-0.942-0.9420.0000.0000.0000.000
55A501VAL00.020-0.00310.647-0.108-0.1080.0000.0000.0000.000
56A502ALA00.0080.00711.9460.0460.0460.0000.0000.0000.000
57A503GLY00.009-0.00112.692-0.026-0.0260.0000.0000.0000.000
58A504THR0-0.081-0.04512.791-0.006-0.0060.0000.0000.0000.000
59A505ASP-1-0.810-0.8787.7441.0111.0110.0000.0000.0000.000
60A506TYR0-0.008-0.0067.2890.0750.0750.0000.0000.0000.000
61A507THR0-0.0280.0009.182-0.031-0.0310.0000.0000.0000.000
62A508PHE0-0.031-0.02311.469-0.086-0.0860.0000.0000.0000.000
63A509GLU-1-0.788-0.88613.764-0.031-0.0310.0000.0000.0000.000
64A510SER0-0.026-0.02116.493-0.037-0.0370.0000.0000.0000.000
65A511LEU0-0.030-0.02317.0020.0090.0090.0000.0000.0000.000
66A512ASN00.0140.00820.613-0.010-0.0100.0000.0000.0000.000
67A513PRO00.0560.02423.4460.0030.0030.0000.0000.0000.000
68A514GLU-1-0.918-0.95125.017-0.053-0.0530.0000.0000.0000.000
69A515VAL0-0.072-0.02326.4430.0030.0030.0000.0000.0000.000
70A516LEU0-0.001-0.01721.8260.0010.0010.0000.0000.0000.000
71A517VAL00.0310.03323.809-0.004-0.0040.0000.0000.0000.000
72A518VAL0-0.025-0.02417.468-0.004-0.0040.0000.0000.0000.000
73A519ALA0-0.0060.01119.9190.0040.0040.0000.0000.0000.000
74A520PRO00.0560.02016.416-0.009-0.0090.0000.0000.0000.000
75A521ASP-1-0.794-0.92014.9410.0580.0580.0000.0000.0000.000
76A522GLY0-0.022-0.00716.092-0.002-0.0020.0000.0000.0000.000
77A523SER0-0.031-0.01316.726-0.025-0.0250.0000.0000.0000.000
78A524VAL0-0.046-0.01920.117-0.009-0.0090.0000.0000.0000.000
79A525THR0-0.004-0.00722.5390.0080.0080.0000.0000.0000.000
80A526PRO0-0.037-0.01326.175-0.004-0.0040.0000.0000.0000.000
81A527ILE0-0.0060.01427.8910.0080.0080.0000.0000.0000.000
82A528VAL0-0.0010.00230.5370.0040.0040.0000.0000.0000.000
83A529PRO0-0.050-0.03930.618-0.005-0.0050.0000.0000.0000.000
84A530GLY00.0270.02230.1270.0030.0030.0000.0000.0000.000
85A531THR0-0.049-0.02824.629-0.001-0.0010.0000.0000.0000.000
86A532ALA00.0100.00822.8640.0040.0040.0000.0000.0000.000
87A533LEU0-0.034-0.01819.142-0.019-0.0190.0000.0000.0000.000
88A534VAL00.0480.02015.6470.0170.0170.0000.0000.0000.000
89A535LYS10.9450.96212.0600.3230.3230.0000.0000.0000.000
90A536VAL00.0130.0248.3190.0590.0590.0000.0000.0000.000
91A537LYS10.8200.8778.259-0.153-0.1530.0000.0000.0000.000
92A538TYR00.0500.0123.637-0.0320.4330.008-0.078-0.3950.000
93A539GLY00.0100.0134.485-0.199-0.140-0.001-0.008-0.0500.000
94A540GLU-1-0.908-0.9555.733-0.219-0.2190.0000.0000.0000.000
95A541VAL0-0.066-0.0162.382-1.157-0.2070.550-0.495-1.0050.001
96A542THR0-0.035-0.0265.5330.5610.5610.0000.0000.0000.000
97A543LYS10.8910.9468.3720.8370.8370.0000.0000.0000.000
98A544THR00.002-0.00410.5840.1000.1000.0000.0000.0000.000
99A545ILE0-0.0280.00214.377-0.036-0.0360.0000.0000.0000.000
100A546PRO00.0180.00317.0140.0270.0270.0000.0000.0000.000
101A547VAL00.0080.01420.025-0.001-0.0010.0000.0000.0000.000
102A548THR0-0.011-0.00922.6750.0030.0030.0000.0000.0000.000
103A549VAL00.0030.03126.4420.0040.0040.0000.0000.0000.000
104A550LYS10.9070.94228.8780.0940.0940.0000.0000.0000.000
105A551ALA00.0530.01232.3000.0050.0050.0000.0000.0000.000
106A552ASN00.0640.02735.417-0.004-0.0040.0000.0000.0000.000
107A553PRO00.0100.01436.6130.0000.0000.0000.0000.0000.000
108A554VAL0-0.0140.00139.7480.0030.0030.0000.0000.0000.000
109A555LEU0-0.027-0.00243.304-0.002-0.0020.0000.0000.0000.000
110A556GLU-1-0.849-0.92945.149-0.045-0.0450.0000.0000.0000.000
111A557THR0-0.030-0.02047.1290.0010.0010.0000.0000.0000.000
112A558ILE00.0070.01449.3850.0000.0000.0000.0000.0000.000
113A559ALA0-0.024-0.01850.5970.0000.0000.0000.0000.0000.000
114A560VAL00.000-0.01452.4750.0010.0010.0000.0000.0000.000
115A561ASP-1-0.864-0.92355.815-0.028-0.0280.0000.0000.0000.000
116A562SER00.0050.00956.8610.0000.0000.0000.0000.0000.000
117A563THR00.0260.00660.029-0.001-0.0010.0000.0000.0000.000
118A564GLY0-0.030-0.01462.4990.0000.0000.0000.0000.0000.000
119A565VAL0-0.042-0.00664.7810.0000.0000.0000.0000.0000.000
120A566SER00.0010.00167.2290.0010.0010.0000.0000.0000.000
121A567VAL0-0.0150.00269.8790.0000.0000.0000.0000.0000.000
122A568ALA00.0160.02271.7020.0000.0000.0000.0000.0000.000
123A569LYS10.8820.90674.5810.0120.0120.0000.0000.0000.000
124A570GLY0-0.024-0.00976.0630.0000.0000.0000.0000.0000.000
125A571GLN0-0.0380.00272.2080.0000.0000.0000.0000.0000.000
126A572LYS10.9810.98764.9760.0140.0140.0000.0000.0000.000
127A573ALA0-0.017-0.00466.4530.0000.0000.0000.0000.0000.000
128A574THR0-0.019-0.01960.5250.0010.0010.0000.0000.0000.000
129A575PHE00.0060.01958.6950.0000.0000.0000.0000.0000.000
130A576LYS10.9160.95054.2320.0250.0250.0000.0000.0000.000
131A577VAL00.0250.01553.468-0.001-0.0010.0000.0000.0000.000
132A578THR0-0.033-0.02848.0600.0000.0000.0000.0000.0000.000
133A579LEU0-0.0170.01748.089-0.001-0.0010.0000.0000.0000.000
134A580LYS10.9420.96345.1240.0420.0420.0000.0000.0000.000
135A581ASP-1-0.742-0.87439.791-0.053-0.0530.0000.0000.0000.000
136A582GLN00.0430.00239.1210.0020.0020.0000.0000.0000.000
137A583TYR0-0.131-0.07236.257-0.005-0.0050.0000.0000.0000.000
138A584GLY0-0.0130.00839.845-0.002-0.0020.0000.0000.0000.000
139A585ASN0-0.036-0.02037.7190.0000.0000.0000.0000.0000.000
140A586LYS10.8600.90341.4090.0390.0390.0000.0000.0000.000
141A587PHE00.0080.01541.997-0.001-0.0010.0000.0000.0000.000
142A588THR0-0.014-0.01443.6620.0010.0010.0000.0000.0000.000
143A589GLY00.0300.01445.5540.0000.0000.0000.0000.0000.000
144A590ASN0-0.0160.00748.4420.0000.0000.0000.0000.0000.000
145A591VAL0-0.0050.01052.095-0.001-0.0010.0000.0000.0000.000
146A592ASN0-0.036-0.01955.0640.0020.0020.0000.0000.0000.000
147A593VAL00.0140.01958.814-0.001-0.0010.0000.0000.0000.000
148A594THR0-0.006-0.00161.6790.0010.0010.0000.0000.0000.000
149A595SER0-0.019-0.03665.286-0.001-0.0010.0000.0000.0000.000
150A596ASP-1-0.871-0.93268.318-0.018-0.0180.0000.0000.0000.000
151A597LYS10.8540.91470.8030.0150.0150.0000.0000.0000.000
152A598THR00.0140.00671.2200.0000.0000.0000.0000.0000.000
153A599GLU-1-0.846-0.91673.565-0.013-0.0130.0000.0000.0000.000
154A600THR0-0.036-0.00174.6060.0000.0000.0000.0000.0000.000
155A601ALA00.0350.00970.9360.0000.0000.0000.0000.0000.000
156A602THR00.0340.03469.8880.0000.0000.0000.0000.0000.000
157A603VAL0-0.020-0.00963.6270.0000.0000.0000.0000.0000.000
158A604SER0-0.012-0.00363.5290.0000.0000.0000.0000.0000.000
159A605VAL00.0230.01157.086-0.001-0.0010.0000.0000.0000.000
160A606SER00.0140.00955.2690.0010.0010.0000.0000.0000.000
161A607ASN00.025-0.01053.638-0.001-0.0010.0000.0000.0000.000
162A608SER00.0330.02055.1140.0000.0000.0000.0000.0000.000
163A609GLY00.0080.01755.3190.0000.0000.0000.0000.0000.000
164A610ILE0-0.025-0.01351.676-0.001-0.0010.0000.0000.0000.000
165A611GLY00.0270.01848.2880.0010.0010.0000.0000.0000.000
166A612GLN0-0.023-0.01347.5320.0000.0000.0000.0000.0000.000
167A613SER00.0490.02545.6250.0000.0000.0000.0000.0000.000
168A614GLU-1-0.886-0.93447.106-0.035-0.0350.0000.0000.0000.000
169A615TYR0-0.0080.00050.4620.0020.0020.0000.0000.0000.000
170A616THR0-0.020-0.02854.049-0.001-0.0010.0000.0000.0000.000
171A617VAL0-0.0060.00457.3590.0010.0010.0000.0000.0000.000
172A618THR0-0.033-0.02060.3870.0000.0000.0000.0000.0000.000
173A619VAL00.004-0.00763.8610.0000.0000.0000.0000.0000.000
174A620ASN0-0.021-0.02066.9680.0000.0000.0000.0000.0000.000
175A621GLY00.0540.01570.3550.0000.0000.0000.0000.0000.000
176A622VAL0-0.057-0.01873.3990.0010.0010.0000.0000.0000.000
177A623ALA0-0.008-0.01476.0730.0010.0010.0000.0000.0000.000
178A624GLU-1-0.841-0.91277.481-0.013-0.0130.0000.0000.0000.000
179A625GLY00.0060.01078.0240.0000.0000.0000.0000.0000.000
180A626SER0-0.034-0.01973.7470.0000.0000.0000.0000.0000.000
181A627THR0-0.010-0.01170.7080.0000.0000.0000.0000.0000.000
182A628THR00.0100.00866.401-0.001-0.0010.0000.0000.0000.000
183A629ILE00.0040.01862.9800.0010.0010.0000.0000.0000.000
184A630THR0-0.0220.00062.626-0.001-0.0010.0000.0000.0000.000
185A631ILE0-0.003-0.00856.7810.0010.0010.0000.0000.0000.000
186A632LYS10.8780.91457.5100.0200.0200.0000.0000.0000.000
187A633SER00.002-0.02351.9790.0000.0000.0000.0000.0000.000
188A634GLY00.0180.01251.683-0.001-0.0010.0000.0000.0000.000
189A635THR0-0.014-0.00951.9120.0010.0010.0000.0000.0000.000
190A636LYS10.8030.90948.6200.0400.0400.0000.0000.0000.000
191A637GLU-1-0.773-0.88854.650-0.021-0.0210.0000.0000.0000.000
192A638VAL0-0.0190.01156.130-0.001-0.0010.0000.0000.0000.000
193A639LYS10.8900.92558.9170.0240.0240.0000.0000.0000.000
194A640VAL00.0020.00161.331-0.001-0.0010.0000.0000.0000.000
195A641PRO00.0360.03664.0860.0010.0010.0000.0000.0000.000
196A642VAL0-0.006-0.01967.1560.0000.0000.0000.0000.0000.000
197A643ASN0-0.009-0.01469.6750.0010.0010.0000.0000.0000.000
198A644VAL0-0.017-0.00272.9460.0000.0000.0000.0000.0000.000
199A645VAL00.0060.00174.9860.0000.0000.0000.0000.0000.000
200A646ALA00.0460.02277.3750.0000.0000.0000.0000.0000.000