FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: MNJ5Z

Calculation Name: 3UAT-A-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 3UAT

Chain ID: A

ChEMBL ID:

UniProt ID: Q62696

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 OptH
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 276
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3826076.137274
FMO2-HF: Nuclear repulsion 3714206.735256
FMO2-HF: Total energy -111869.402018
FMO2-MP2: Total energy -112198.127426


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:582:SER)


Summations of interaction energy for fragment #1(A:582:SER)
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.
-23.188-19.49510.186-5.897-7.982-0.041
Interaction energy analysis for fragmet #1(A:582:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.008
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].
3A584TYR00.0760.0442.362-5.216-3.3484.459-2.444-3.8830.008
4A585VAL0-0.033-0.0225.8280.6890.6890.0000.0000.0000.000
5A586ARG10.9520.9979.5080.6570.6570.0000.0000.0000.000
6A587ALA00.000-0.00212.7080.0510.0510.0000.0000.0000.000
7A588LEU00.0130.00315.2070.0800.0800.0000.0000.0000.000
8A589PHE0-0.046-0.00417.2420.0660.0660.0000.0000.0000.000
9A590ASP-1-0.849-0.93219.298-0.477-0.4770.0000.0000.0000.000
10A591TYR0-0.040-0.02518.7940.0210.0210.0000.0000.0000.000
11A592ASP-1-0.788-0.88720.848-0.361-0.3610.0000.0000.0000.000
12A593LYS10.9300.97520.5130.4540.4540.0000.0000.0000.000
13A594THR0-0.049-0.03523.0040.0260.0260.0000.0000.0000.000
14A595LYS10.8390.91025.9590.3210.3210.0000.0000.0000.000
15A596ASP-1-0.856-0.90922.601-0.370-0.3700.0000.0000.0000.000
16A597SER0-0.0020.00025.2590.0030.0030.0000.0000.0000.000
17A598GLY00.016-0.00525.483-0.001-0.0010.0000.0000.0000.000
18A599LEU0-0.025-0.01119.431-0.009-0.0090.0000.0000.0000.000
19A600PRO0-0.0170.01818.6940.0230.0230.0000.0000.0000.000
20A601SER0-0.011-0.01817.9530.0140.0140.0000.0000.0000.000
21A602GLN00.0330.01619.3420.0430.0430.0000.0000.0000.000
22A603GLY00.0380.00617.886-0.052-0.0520.0000.0000.0000.000
23A604LEU00.0180.01512.7820.0430.0430.0000.0000.0000.000
24A605ASN0-0.095-0.05316.709-0.046-0.0460.0000.0000.0000.000
25A606PHE00.0160.02115.692-0.026-0.0260.0000.0000.0000.000
26A607LYS10.8930.95317.7860.4810.4810.0000.0000.0000.000
27A608PHE0-0.008-0.00517.692-0.075-0.0750.0000.0000.0000.000
28A609GLY0-0.031-0.01317.2370.0340.0340.0000.0000.0000.000
29A610ASP-1-0.781-0.87514.249-0.767-0.7670.0000.0000.0000.000
30A611ILE0-0.005-0.0028.564-0.052-0.0520.0000.0000.0000.000
31A612LEU0-0.030-0.0159.1900.0080.0080.0000.0000.0000.000
32A613HIS00.0070.0012.133-15.473-13.8625.728-3.421-3.918-0.049
33A614VAL0-0.043-0.0284.9510.9140.9140.0000.0000.0000.000
34A615ILE0-0.0130.0034.220-0.935-0.721-0.001-0.032-0.1810.000
35A616ASN00.000-0.0225.9920.6220.6220.0000.0000.0000.000
36A617ALA0-0.0150.0058.112-0.053-0.0530.0000.0000.0000.000
37A618SER0-0.038-0.0189.7620.1920.1920.0000.0000.0000.000
38A619ASP-1-0.758-0.88312.541-0.307-0.3070.0000.0000.0000.000
39A620ASP-1-0.851-0.93814.841-0.318-0.3180.0000.0000.0000.000
40A621GLU-1-0.879-0.91717.124-0.320-0.3200.0000.0000.0000.000
41A622TRP0-0.053-0.04816.101-0.064-0.0640.0000.0000.0000.000
42A623TRP00.006-0.01810.599-0.007-0.0070.0000.0000.0000.000
43A624GLN00.0200.02110.3040.0320.0320.0000.0000.0000.000
44A625ALA0-0.0040.0008.383-0.359-0.3590.0000.0000.0000.000
45A626ARG10.8560.9157.5191.7691.7690.0000.0000.0000.000
46A627GLN0-0.019-0.0189.059-0.378-0.3780.0000.0000.0000.000
47A628VAL0-0.015-0.0127.018-0.105-0.1050.0000.0000.0000.000
48A629THR0-0.041-0.01110.1920.1510.1510.0000.0000.0000.000
49A630PRO00.0200.00112.783-0.041-0.0410.0000.0000.0000.000
50A631ASP-1-0.931-0.94915.122-0.343-0.3430.0000.0000.0000.000
51A632GLY0-0.028-0.01513.6050.0390.0390.0000.0000.0000.000
52A633GLU-1-0.874-0.9446.593-2.975-2.9750.0000.0000.0000.000
53A634SER0-0.068-0.02710.9700.1060.1060.0000.0000.0000.000
54A635ASP-1-0.852-0.91711.698-0.824-0.8240.0000.0000.0000.000
55A636GLU-1-0.883-0.95012.873-0.510-0.5100.0000.0000.0000.000
56A637VAL0-0.098-0.05011.382-0.216-0.2160.0000.0000.0000.000
57A638GLY00.0290.01113.0300.1430.1430.0000.0000.0000.000
58A639VAL0-0.051-0.01913.330-0.111-0.1110.0000.0000.0000.000
59A640ILE00.0330.01611.0280.0560.0560.0000.0000.0000.000
60A641PRO0-0.034-0.00214.7610.0230.0230.0000.0000.0000.000
61A642SER00.0680.04114.161-0.067-0.0670.0000.0000.0000.000
62A643LYS10.9870.98814.2210.5380.5380.0000.0000.0000.000
63A644ARG10.8240.91214.1330.4510.4510.0000.0000.0000.000
64A645ARG10.7850.87818.3120.4650.4650.0000.0000.0000.000
65A646VAL0-0.017-0.00617.3570.0460.0460.0000.0000.0000.000
66A647GLU-1-0.741-0.89019.034-0.358-0.3580.0000.0000.0000.000
67A648LYS10.8160.91321.8620.3170.3170.0000.0000.0000.000
68A649LYS10.9240.96323.2010.3470.3470.0000.0000.0000.000
69A650GLU-1-0.903-0.96222.224-0.364-0.3640.0000.0000.0000.000
70A651ARG10.8740.92021.7650.2980.2980.0000.0000.0000.000
71A652ALA0-0.037-0.00327.8900.0180.0180.0000.0000.0000.000
72A653ARG10.8880.96326.4750.2740.2740.0000.0000.0000.000
73A654LEU0-0.0040.01029.4940.0120.0120.0000.0000.0000.000
74A655LYS11.0081.00633.4870.1170.1170.0000.0000.0000.000
75A707VAL0-0.085-0.04721.3470.0140.0140.0000.0000.0000.000
76A708LEU00.0140.01920.457-0.018-0.0180.0000.0000.0000.000
77A709SER00.004-0.00616.811-0.026-0.0260.0000.0000.0000.000
78A710TYR0-0.001-0.04012.376-0.056-0.0560.0000.0000.0000.000
79A711GLU-1-0.874-0.93913.738-0.522-0.5220.0000.0000.0000.000
80A712PRO0-0.030-0.0108.993-0.136-0.1360.0000.0000.0000.000
81A713VAL0-0.034-0.0158.5920.2930.2930.0000.0000.0000.000
82A714ASN00.017-0.0036.707-0.624-0.6240.0000.0000.0000.000
83A715GLN00.0200.0108.269-0.104-0.1040.0000.0000.0000.000
84A716GLN0-0.039-0.02310.1950.1400.1400.0000.0000.0000.000
85A717GLU-1-0.901-0.94813.2770.0860.0860.0000.0000.0000.000
86A718VAL0-0.091-0.04416.1460.0010.0010.0000.0000.0000.000
87A719ASN00.014-0.00219.668-0.010-0.0100.0000.0000.0000.000
88A720TYR0-0.030-0.00620.666-0.013-0.0130.0000.0000.0000.000
89A721THR00.0270.01023.622-0.012-0.0120.0000.0000.0000.000
90A722ARG10.8070.89817.9730.3040.3040.0000.0000.0000.000
91A723PRO00.0080.01924.3970.0000.0000.0000.0000.0000.000
92A724VAL00.0310.02725.627-0.022-0.0220.0000.0000.0000.000
93A725ILE0-0.012-0.00526.9650.0150.0150.0000.0000.0000.000
94A726ILE00.0490.04027.714-0.022-0.0220.0000.0000.0000.000
95A727LEU0-0.002-0.01328.5330.0140.0140.0000.0000.0000.000
96A728GLY00.0480.03231.141-0.011-0.0110.0000.0000.0000.000
97A729PRO0-0.033-0.03833.4700.0110.0110.0000.0000.0000.000
98A730MET0-0.016-0.00935.096-0.002-0.0020.0000.0000.0000.000
99A731LYS10.8720.94933.6280.1330.1330.0000.0000.0000.000
100A732ASP-1-0.862-0.93034.934-0.116-0.1160.0000.0000.0000.000
101A733ARG10.9110.95537.9480.1150.1150.0000.0000.0000.000
102A734VAL00.0440.02431.7490.0020.0020.0000.0000.0000.000
103A735ASN0-0.012-0.02033.394-0.008-0.0080.0000.0000.0000.000
104A736ASP-1-0.920-0.95735.340-0.096-0.0960.0000.0000.0000.000
105A737ASP-1-0.926-0.95736.142-0.114-0.1140.0000.0000.0000.000
106A738LEU0-0.031-0.00430.6670.0020.0020.0000.0000.0000.000
107A739ILE0-0.025-0.01434.4840.0050.0050.0000.0000.0000.000
108A740SER0-0.071-0.04536.7840.0090.0090.0000.0000.0000.000
109A741GLU-1-0.881-0.92536.021-0.119-0.1190.0000.0000.0000.000
110A742PHE0-0.087-0.03533.4110.0020.0020.0000.0000.0000.000
111A743PRO00.0440.01634.901-0.001-0.0010.0000.0000.0000.000
112A744ASP-1-0.934-0.97434.872-0.062-0.0620.0000.0000.0000.000
113A745LYS10.8820.95825.4610.1610.1610.0000.0000.0000.000
114A746PHE00.0210.01129.083-0.010-0.0100.0000.0000.0000.000
115A747GLY00.0200.00633.1900.0100.0100.0000.0000.0000.000
116A748SER00.0100.01634.499-0.009-0.0090.0000.0000.0000.000
117A749CYS0-0.029-0.00834.6830.0050.0050.0000.0000.0000.000
118A750VAL00.0210.02936.743-0.001-0.0010.0000.0000.0000.000
119A751PRO00.0180.04539.1110.0020.0020.0000.0000.0000.000
120A752HIS00.0370.00139.1340.0040.0040.0000.0000.0000.000
121A753THR00.0010.00242.108-0.003-0.0030.0000.0000.0000.000
122A754THR00.0330.01945.3590.0020.0020.0000.0000.0000.000
123A755ARG10.7250.88348.0960.0450.0450.0000.0000.0000.000
124A756PRO00.004-0.00550.5380.0010.0010.0000.0000.0000.000
125A757LYS10.8400.92951.3410.0250.0250.0000.0000.0000.000
126A758ARG10.9080.96751.6460.0440.0440.0000.0000.0000.000
127A759ASP-1-0.870-0.93654.965-0.024-0.0240.0000.0000.0000.000
128A760TYR0-0.006-0.01153.8110.0000.0000.0000.0000.0000.000
129A761GLU-1-0.780-0.88750.677-0.041-0.0410.0000.0000.0000.000
130A762VAL0-0.023-0.01148.9080.0030.0030.0000.0000.0000.000
131A763ASP-1-0.851-0.94246.879-0.029-0.0290.0000.0000.0000.000
132A764GLY00.0120.01743.9100.0020.0020.0000.0000.0000.000
133A765ARG10.8190.92143.5410.0350.0350.0000.0000.0000.000
134A766ASP-1-0.844-0.93144.328-0.045-0.0450.0000.0000.0000.000
135A767TYR00.033-0.01143.748-0.004-0.0040.0000.0000.0000.000
136A768HIS0-0.0160.01139.6860.0070.0070.0000.0000.0000.000
137A769PHE0-0.028-0.03644.148-0.003-0.0030.0000.0000.0000.000
138A770VAL0-0.020-0.01243.8130.0030.0030.0000.0000.0000.000
139A771THR00.007-0.01146.945-0.001-0.0010.0000.0000.0000.000
140A772SER00.0240.01748.2980.0000.0000.0000.0000.0000.000
141A773ARG10.9460.96347.3500.0370.0370.0000.0000.0000.000
142A774GLU-1-0.848-0.90846.575-0.018-0.0180.0000.0000.0000.000
143A775GLN0-0.043-0.02442.1340.0020.0020.0000.0000.0000.000
144A776MET0-0.001-0.00341.4930.0000.0000.0000.0000.0000.000
145A777GLU-1-0.929-0.97941.794-0.038-0.0380.0000.0000.0000.000
146A778LYS10.9330.96741.2130.0130.0130.0000.0000.0000.000
147A779ASP-1-0.789-0.88838.800-0.028-0.0280.0000.0000.0000.000
148A780ILE0-0.067-0.03537.170-0.004-0.0040.0000.0000.0000.000
149A781GLN0-0.052-0.02336.417-0.002-0.0020.0000.0000.0000.000
150A782GLU-1-0.968-0.97035.459-0.020-0.0200.0000.0000.0000.000
151A783HIS0-0.068-0.02931.335-0.005-0.0050.0000.0000.0000.000
152A784LYS10.8930.95132.1940.0230.0230.0000.0000.0000.000
153A785PHE0-0.073-0.04933.971-0.003-0.0030.0000.0000.0000.000
154A786ILE00.0230.01829.573-0.002-0.0020.0000.0000.0000.000
155A787GLU-1-0.863-0.93932.092-0.125-0.1250.0000.0000.0000.000
156A788ALA00.0260.01535.1600.0070.0070.0000.0000.0000.000
157A789GLY00.0090.01338.846-0.005-0.0050.0000.0000.0000.000
158A790GLN0-0.050-0.03241.9730.0080.0080.0000.0000.0000.000
159A791TYR00.0250.01545.768-0.002-0.0020.0000.0000.0000.000
160A792ASN00.0090.00348.3370.0020.0020.0000.0000.0000.000
161A793ASN0-0.003-0.00250.6190.0020.0020.0000.0000.0000.000
162A794HIS00.0110.01049.0390.0030.0030.0000.0000.0000.000
163A795LEU00.0230.00444.366-0.004-0.0040.0000.0000.0000.000
164A796TYR00.003-0.00442.6240.0030.0030.0000.0000.0000.000
165A797GLY00.0410.01839.106-0.002-0.0020.0000.0000.0000.000
166A798THR00.0140.01134.1760.0060.0060.0000.0000.0000.000
167A799SER00.0130.00234.690-0.004-0.0040.0000.0000.0000.000
168A800VAL00.0900.03829.039-0.005-0.0050.0000.0000.0000.000
169A801GLN00.0160.01131.317-0.001-0.0010.0000.0000.0000.000
170A802SER0-0.037-0.05933.1780.0000.0000.0000.0000.0000.000
171A803VAL00.0260.00029.534-0.001-0.0010.0000.0000.0000.000
172A804ARG10.9510.97226.0340.0370.0370.0000.0000.0000.000
173A805ALA0-0.0110.00530.2190.0050.0050.0000.0000.0000.000
174A806VAL0-0.014-0.01331.5570.0040.0040.0000.0000.0000.000
175A807ALA00.0320.02527.3910.0000.0000.0000.0000.0000.000
176A808GLU-1-0.921-0.96528.496-0.020-0.0200.0000.0000.0000.000
177A809LYS10.8360.93030.0050.0440.0440.0000.0000.0000.000
178A810GLY00.0090.00929.4040.0020.0020.0000.0000.0000.000
179A811LYS10.8700.96130.1410.0620.0620.0000.0000.0000.000
180A812HIS0-0.014-0.03224.354-0.001-0.0010.0000.0000.0000.000
181A813CYS0-0.041-0.02429.1960.0080.0080.0000.0000.0000.000
182A814ILE00.0250.02230.361-0.012-0.0120.0000.0000.0000.000
183A815LEU0-0.078-0.04429.6420.0120.0120.0000.0000.0000.000
184A816ASP-1-0.862-0.92232.823-0.126-0.1260.0000.0000.0000.000
185A817VAL0-0.034-0.01931.3550.0080.0080.0000.0000.0000.000
186A818SER0-0.011-0.00933.199-0.012-0.0120.0000.0000.0000.000
187A819GLY00.0630.01529.288-0.004-0.0040.0000.0000.0000.000
188A820ASN0-0.026-0.02628.131-0.013-0.0130.0000.0000.0000.000
189A821ALA0-0.024-0.00928.8320.0030.0030.0000.0000.0000.000
190A822ILE00.0140.02323.6300.0080.0080.0000.0000.0000.000
191A823LYS10.9820.99521.4870.1980.1980.0000.0000.0000.000
192A824ARG10.9010.93924.1440.1200.1200.0000.0000.0000.000
193A825LEU00.0340.02225.3290.0140.0140.0000.0000.0000.000
194A826GLN00.0300.01020.2650.0130.0130.0000.0000.0000.000
195A827ILE0-0.083-0.03521.2740.0100.0100.0000.0000.0000.000
196A828ALA0-0.043-0.00923.1280.0200.0200.0000.0000.0000.000
197A829GLN0-0.063-0.03918.5370.0220.0220.0000.0000.0000.000
198A830LEU0-0.0170.00321.7960.0110.0110.0000.0000.0000.000
199A831TYR00.0470.00017.022-0.029-0.0290.0000.0000.0000.000
200A832PRO0-0.0020.02121.428-0.001-0.0010.0000.0000.0000.000
201A833ILE00.0070.00721.496-0.035-0.0350.0000.0000.0000.000
202A834SER0-0.017-0.00822.5740.0320.0320.0000.0000.0000.000
203A835ILE00.0310.02123.484-0.034-0.0340.0000.0000.0000.000
204A836PHE00.0120.00525.7370.0280.0280.0000.0000.0000.000
205A837ILE00.0070.00527.707-0.015-0.0150.0000.0000.0000.000
206A838LYS10.8440.91528.1430.2860.2860.0000.0000.0000.000
207A839PRO0-0.048-0.01530.9620.0010.0010.0000.0000.0000.000
208A840LYS10.9090.94432.0180.2060.2060.0000.0000.0000.000
209A841SER0-0.004-0.00834.7070.0030.0030.0000.0000.0000.000
210A842MET00.018-0.01038.1760.0020.0020.0000.0000.0000.000
211A843GLU-1-0.866-0.92541.281-0.115-0.1150.0000.0000.0000.000
212A844ASN00.0050.01435.826-0.005-0.0050.0000.0000.0000.000
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