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: YV372

Calculation Name: 2UWM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2UWM

Chain ID: A

ChEMBL ID:

UniProt ID: Q46455

Base Structure: X-ray

Registration Date: 2023-09-24

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2130618.766102
FMO2-HF: Nuclear repulsion 2054346.45736
FMO2-HF: Total energy -76272.308742
FMO2-MP2: Total energy -76502.511281


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:441:GLN)


Summations of interaction energy for fragment #1(A:441:GLN)
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.
-17.187-13.0826.134-0.875-9.3630.023
Interaction energy analysis for fragmet #1(A:441:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.017
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].
3A443TRP0-0.032-0.0292.451-2.105-2.4304.6961.125-5.4960.000
4A444TRP00.1380.0783.053-3.161-1.6570.051-0.461-1.0940.002
5A445GLN00.0360.0164.598-1.060-0.961-0.001-0.012-0.0850.000
6A446ALA0-0.065-0.0206.426-0.370-0.3700.0000.0000.0000.000
7A447VAL0-0.017-0.0157.212-0.395-0.3950.0000.0000.0000.000
8A448THR00.0360.0148.518-0.274-0.2740.0000.0000.0000.000
9A449ARG11.0071.01710.691-1.427-1.4270.0000.0000.0000.000
10A450ALA0-0.046-0.02712.126-0.147-0.1470.0000.0000.0000.000
11A451LEU00.0030.00611.822-0.140-0.1400.0000.0000.0000.000
12A452GLU-1-0.896-0.94813.8010.5660.5660.0000.0000.0000.000
13A453GLU-1-0.842-0.86416.4470.7930.7930.0000.0000.0000.000
14A454PHE0-0.025-0.01917.718-0.082-0.0820.0000.0000.0000.000
15A455HIS00.009-0.00417.1440.0190.0190.0000.0000.0000.000
16A456SER0-0.024-0.02120.427-0.066-0.0660.0000.0000.0000.000
17A457ARG10.9410.98122.217-0.543-0.5430.0000.0000.0000.000
18A458TYR0-0.078-0.05322.171-0.052-0.0520.0000.0000.0000.000
19A459PRO00.0800.04324.2530.0230.0230.0000.0000.0000.000
20A460LEU00.0100.01925.535-0.014-0.0140.0000.0000.0000.000
21A461ARG10.8610.93423.541-0.495-0.4950.0000.0000.0000.000
22A462PRO00.0210.03121.7400.0110.0110.0000.0000.0000.000
23A463GLY00.049-0.00518.4720.0300.0300.0000.0000.0000.000
24A464LEU0-0.0180.01714.732-0.072-0.0720.0000.0000.0000.000
25A465ALA00.0520.01217.0840.0430.0430.0000.0000.0000.000
26A466ARG10.8790.93414.958-0.769-0.7690.0000.0000.0000.000
27A467GLU-1-0.811-0.92214.4811.2511.2510.0000.0000.0000.000
28A468GLU-1-0.895-0.91016.7990.8140.8140.0000.0000.0000.000
29A469LEU0-0.027-0.01910.5100.0440.0440.0000.0000.0000.000
30A470ARG10.8000.90212.147-0.836-0.8360.0000.0000.0000.000
31A471SER0-0.012-0.05113.2890.0990.0990.0000.0000.0000.000
32A472ARG10.8250.88414.058-1.097-1.0970.0000.0000.0000.000
33A473TYR0-0.036-0.0209.635-0.034-0.0340.0000.0000.0000.000
34A474PHE0-0.014-0.0025.608-0.068-0.0680.0000.0000.0000.000
35A475SER00.0150.01210.816-0.167-0.1670.0000.0000.0000.000
36A476ARG10.9270.96111.998-0.960-0.9600.0000.0000.0000.000
37A477LEU0-0.0040.0228.254-0.145-0.1450.0000.0000.0000.000
38A478PRO00.0290.01311.727-0.039-0.0390.0000.0000.0000.000
39A479ALA00.0680.03212.8770.1710.1710.0000.0000.0000.000
40A480ARG10.9480.96213.866-0.380-0.3800.0000.0000.0000.000
41A481VAL00.0580.0278.3360.0520.0520.0000.0000.0000.000
42A482TYR00.0240.0028.8360.3400.3400.0000.0000.0000.000
43A483GLN0-0.003-0.0169.4590.2620.2620.0000.0000.0000.000
44A484ALA0-0.0060.0039.611-0.055-0.0550.0000.0000.0000.000
45A485LEU0-0.0040.0152.762-2.497-1.1820.455-0.629-1.1410.008
46A486LEU0-0.016-0.0106.8900.2740.2740.0000.0000.0000.000
47A487GLU-1-0.851-0.9119.1410.1120.1120.0000.0000.0000.000
48A488GLU-1-0.810-0.8715.503-0.853-0.8530.0000.0000.0000.000
49A489TRP00.016-0.0042.549-2.859-1.3470.933-0.898-1.5470.013
50A490SER0-0.082-0.0408.051-0.294-0.2940.0000.0000.0000.000
51A491ARG10.7620.8299.658-0.017-0.0170.0000.0000.0000.000
52A492GLU-1-0.855-0.8906.484-0.404-0.4040.0000.0000.0000.000
53A493GLY0-0.0060.00210.631-0.036-0.0360.0000.0000.0000.000
54A494ARG10.7950.8657.485-0.045-0.0450.0000.0000.0000.000
55A495LEU0-0.041-0.0249.1030.1880.1880.0000.0000.0000.000
56A496GLN0-0.029-0.00812.587-0.201-0.2010.0000.0000.0000.000
57A497LEU0-0.018-0.02111.9620.0760.0760.0000.0000.0000.000
58A498ALA00.0580.05416.003-0.109-0.1090.0000.0000.0000.000
59A499ALA0-0.0020.00018.5010.0620.0620.0000.0000.0000.000
60A500ASN0-0.061-0.04219.9440.0160.0160.0000.0000.0000.000
61A501THR0-0.022-0.00218.0760.0600.0600.0000.0000.0000.000
62A502VAL0-0.032-0.01811.9460.0080.0080.0000.0000.0000.000
63A503ALA00.0190.01015.412-0.009-0.0090.0000.0000.0000.000
64A504LEU00.0260.01611.9840.1290.1290.0000.0000.0000.000
65A505ALA0-0.0020.00613.991-0.136-0.1360.0000.0000.0000.000
66A506GLY00.0120.00815.901-0.019-0.0190.0000.0000.0000.000
67A507PHE0-0.0190.00118.468-0.036-0.0360.0000.0000.0000.000
68A508THR0-0.002-0.01720.253-0.034-0.0340.0000.0000.0000.000
69A509PRO0-0.0230.01623.765-0.003-0.0030.0000.0000.0000.000
70A510SER0-0.021-0.03025.899-0.029-0.0290.0000.0000.0000.000
71A511PHE00.0030.00528.551-0.010-0.0100.0000.0000.0000.000
72A512SER00.031-0.00431.575-0.009-0.0090.0000.0000.0000.000
73A513GLU-1-0.801-0.91532.4720.1870.1870.0000.0000.0000.000
74A514THR00.0170.00834.885-0.001-0.0010.0000.0000.0000.000
75A515GLN00.0430.03034.0190.0050.0050.0000.0000.0000.000
76A516LYS10.8280.91529.043-0.202-0.2020.0000.0000.0000.000
77A517LYS10.7770.87632.375-0.123-0.1230.0000.0000.0000.000
78A518LEU00.0450.01435.1100.0000.0000.0000.0000.0000.000
79A519LEU0-0.0050.00629.3190.0020.0020.0000.0000.0000.000
80A520LYS10.9480.97728.184-0.204-0.2040.0000.0000.0000.000
81A521ASP-1-0.768-0.85632.7820.1310.1310.0000.0000.0000.000
82A522LEU0-0.004-0.00334.454-0.006-0.0060.0000.0000.0000.000
83A523GLU-1-0.830-0.90029.1520.2310.2310.0000.0000.0000.000
84A524ASP-1-0.822-0.90332.9910.1430.1430.0000.0000.0000.000
85A525LYS10.9280.97335.409-0.134-0.1340.0000.0000.0000.000
86A526TYR0-0.037-0.01434.964-0.005-0.0050.0000.0000.0000.000
87A527ARG10.7560.84831.430-0.170-0.1700.0000.0000.0000.000
88A528VAL0-0.019-0.00634.968-0.006-0.0060.0000.0000.0000.000
89A529SER0-0.050-0.03938.382-0.010-0.0100.0000.0000.0000.000
90A530ARG10.8140.87935.962-0.126-0.1260.0000.0000.0000.000
91A531TRP0-0.013-0.02136.5410.0060.0060.0000.0000.0000.000
92A532GLN00.0020.01740.236-0.001-0.0010.0000.0000.0000.000
93A533PRO00.0040.01538.829-0.004-0.0040.0000.0000.0000.000
94A534PRO0-0.0220.00339.878-0.006-0.0060.0000.0000.0000.000
95A535SER00.002-0.04641.2490.0100.0100.0000.0000.0000.000
96A536PHE00.007-0.00238.485-0.005-0.0050.0000.0000.0000.000
97A537LYS10.8830.91941.806-0.131-0.1310.0000.0000.0000.000
98A538GLU-1-0.829-0.89144.6810.1180.1180.0000.0000.0000.000
99A539VAL0-0.0150.00139.070-0.004-0.0040.0000.0000.0000.000
100A540ALA00.0140.00742.552-0.001-0.0010.0000.0000.0000.000
101A541GLY00.0120.01143.901-0.004-0.0040.0000.0000.0000.000
102A542SER0-0.039-0.03843.236-0.002-0.0020.0000.0000.0000.000
103A543PHE0-0.057-0.03040.005-0.002-0.0020.0000.0000.0000.000
104A544ASN0-0.055-0.01843.637-0.003-0.0030.0000.0000.0000.000
105A545LEU0-0.0160.00439.2680.0020.0020.0000.0000.0000.000
106A546ASP-1-0.839-0.91642.9410.1350.1350.0000.0000.0000.000
107A547PRO0-0.038-0.04141.5900.0090.0090.0000.0000.0000.000
108A548SER00.0020.00439.7030.0080.0080.0000.0000.0000.000
109A549GLU-1-0.788-0.88337.2760.1860.1860.0000.0000.0000.000
110A550LEU0-0.0130.00036.6470.0120.0120.0000.0000.0000.000
111A551GLU-1-0.807-0.89535.6790.2490.2490.0000.0000.0000.000
112A552GLU-1-0.955-0.97032.7910.2690.2690.0000.0000.0000.000
113A553LEU0-0.002-0.00931.9810.0240.0240.0000.0000.0000.000
114A554LEU00.0060.00031.5860.0150.0150.0000.0000.0000.000
115A555HIS00.0230.00930.2550.0420.0420.0000.0000.0000.000
116A556TYR0-0.071-0.05524.3060.0370.0370.0000.0000.0000.000
117A557LEU00.0650.02126.7460.0330.0330.0000.0000.0000.000
118A558VAL0-0.055-0.01327.4460.0140.0140.0000.0000.0000.000
119A559ARG10.8460.91224.387-0.341-0.3410.0000.0000.0000.000
120A560GLU-1-0.813-0.87922.6030.4630.4630.0000.0000.0000.000
121A561GLY0-0.034-0.01722.9760.0240.0240.0000.0000.0000.000
122A562VAL0-0.005-0.00225.071-0.016-0.0160.0000.0000.0000.000
123A563LEU0-0.020-0.00727.098-0.031-0.0310.0000.0000.0000.000
124A564VAL0-0.030-0.02328.9180.0280.0280.0000.0000.0000.000
125A565LYS10.8810.95031.284-0.241-0.2410.0000.0000.0000.000
126A566ILE0-0.066-0.02334.2610.0070.0070.0000.0000.0000.000
127A567ASN00.022-0.00436.695-0.003-0.0030.0000.0000.0000.000
128A568ASP-1-0.842-0.93238.7680.2030.2030.0000.0000.0000.000
129A569GLU-1-0.890-0.90840.5270.1280.1280.0000.0000.0000.000
130A570PHE00.002-0.01440.025-0.004-0.0040.0000.0000.0000.000
131A571TYR00.023-0.01534.0260.0100.0100.0000.0000.0000.000
132A572TRP00.011-0.00634.480-0.015-0.0150.0000.0000.0000.000
133A573HIS00.0530.01529.3990.0150.0150.0000.0000.0000.000
134A574ARG10.9250.96922.248-0.419-0.4190.0000.0000.0000.000
135A575GLN0-0.001-0.01028.153-0.005-0.0050.0000.0000.0000.000
136A576ALA00.0370.03830.447-0.011-0.0110.0000.0000.0000.000
137A577LEU00.0380.01930.732-0.010-0.0100.0000.0000.0000.000
138A578GLY0-0.041-0.02430.223-0.002-0.0020.0000.0000.0000.000
139A579GLU-1-0.786-0.87931.0390.1170.1170.0000.0000.0000.000
140A580ALA00.0020.00934.012-0.011-0.0110.0000.0000.0000.000
141A581ARG10.9210.96329.339-0.251-0.2510.0000.0000.0000.000
142A582GLU-1-0.841-0.88632.1990.1340.1340.0000.0000.0000.000
143A583VAL00.0070.02234.798-0.008-0.0080.0000.0000.0000.000
144A584ILE0-0.019-0.01837.438-0.006-0.0060.0000.0000.0000.000
145A585LYS10.8300.89031.534-0.166-0.1660.0000.0000.0000.000
146A586ASN0-0.021-0.02036.210-0.013-0.0130.0000.0000.0000.000
147A587LEU00.0060.02739.427-0.007-0.0070.0000.0000.0000.000
148A588ALA0-0.018-0.01239.583-0.005-0.0050.0000.0000.0000.000
149A589SER0-0.090-0.04639.704-0.004-0.0040.0000.0000.0000.000
150A590THR0-0.038-0.02341.424-0.006-0.0060.0000.0000.0000.000
151A591GLY00.0310.01944.436-0.005-0.0050.0000.0000.0000.000
152A592PRO0-0.035-0.03244.9500.0050.0050.0000.0000.0000.000
153A593PHE00.0230.02641.093-0.004-0.0040.0000.0000.0000.000
154A594GLY00.0520.01046.4670.0050.0050.0000.0000.0000.000
155A595LEU0-0.033-0.02346.5250.0010.0010.0000.0000.0000.000
156A596ALA0-0.048-0.01448.1200.0010.0010.0000.0000.0000.000
157A597GLU-1-0.699-0.85547.8000.0870.0870.0000.0000.0000.000
158A598ALA00.0300.01243.6920.0010.0010.0000.0000.0000.000
159A599ARG10.7600.85844.610-0.078-0.0780.0000.0000.0000.000
160A600ASP-1-0.818-0.88646.8620.0770.0770.0000.0000.0000.000
161A601ALA0-0.0060.00543.443-0.002-0.0020.0000.0000.0000.000
162A602LEU0-0.044-0.02139.5830.0030.0030.0000.0000.0000.000
163A603GLY00.0010.01443.2690.0010.0010.0000.0000.0000.000
164A604SER0-0.002-0.00544.1570.0010.0010.0000.0000.0000.000
165A605SER0-0.013-0.03346.289-0.005-0.0050.0000.0000.0000.000
166A606ARG10.9850.97046.714-0.086-0.0860.0000.0000.0000.000
167A607LYS10.8970.97646.243-0.112-0.1120.0000.0000.0000.000
168A608TYR00.0280.02342.6730.0020.0020.0000.0000.0000.000
169A609VAL00.0210.00142.4370.0080.0080.0000.0000.0000.000
170A610LEU0-0.0230.00042.9680.0030.0030.0000.0000.0000.000
171A611PRO00.0470.01841.7870.0060.0060.0000.0000.0000.000
172A612LEU00.0050.02236.6620.0110.0110.0000.0000.0000.000
173A613LEU00.003-0.01538.4130.0090.0090.0000.0000.0000.000
174A614GLU-1-0.910-0.96140.1140.1440.1440.0000.0000.0000.000
175A615TYR00.0350.01630.9250.0080.0080.0000.0000.0000.000
176A616LEU0-0.045-0.02834.2000.0150.0150.0000.0000.0000.000
177A617ASP-1-0.736-0.82335.8340.1610.1610.0000.0000.0000.000
178A618GLN00.0370.02535.2990.0040.0040.0000.0000.0000.000
179A619VAL0-0.087-0.04631.1850.0140.0140.0000.0000.0000.000
180A620LYS10.8020.90032.069-0.217-0.2170.0000.0000.0000.000
181A621PHE00.0110.00631.7720.0020.0020.0000.0000.0000.000
182A622THR0-0.026-0.03833.974-0.009-0.0090.0000.0000.0000.000
183A623ARG10.9610.97337.795-0.137-0.1370.0000.0000.0000.000
184A624ARG10.8670.92540.628-0.125-0.1250.0000.0000.0000.000
185A625VAL0-0.028-0.02444.2210.0030.0030.0000.0000.0000.000
186A626GLY00.0340.02847.185-0.005-0.0050.0000.0000.0000.000
187A627ASP-1-0.867-0.92149.1940.1030.1030.0000.0000.0000.000
188A628LYS10.8150.90247.680-0.088-0.0880.0000.0000.0000.000
189A629ARG10.8220.89941.978-0.135-0.1350.0000.0000.0000.000
190A630VAL00.0370.03140.894-0.007-0.0070.0000.0000.0000.000
191A631VAL00.0330.01035.1520.0080.0080.0000.0000.0000.000
192A632VAL0-0.0320.00233.840-0.008-0.0080.0000.0000.0000.000
193A633GLY0-0.032-0.01734.346-0.009-0.0090.0000.0000.0000.000