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: 7659K

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 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 276
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3826239.625988
FMO2-HF: Nuclear repulsion 3714368.564512
FMO2-HF: Total energy -111871.061476
FMO2-MP2: Total energy -112199.748378


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.
-2.6691.9760.82-2.15-3.314-0.009
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 : 0.019 / q_NPA : 0.009
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].
3A584TYR00.0610.0402.631-1.3931.6930.430-1.478-2.038-0.002
4A585VAL0-0.042-0.0245.6810.2590.2590.0000.0000.0000.000
5A586ARG10.9010.9539.3861.1621.1620.0000.0000.0000.000
6A587ALA0-0.007-0.00212.726-0.003-0.0030.0000.0000.0000.000
7A588LEU0-0.006-0.00515.2850.0670.0670.0000.0000.0000.000
8A589PHE0-0.027-0.01417.2590.0720.0720.0000.0000.0000.000
9A590ASP-1-0.796-0.88819.478-0.320-0.3200.0000.0000.0000.000
10A591TYR0-0.103-0.06918.2260.0130.0130.0000.0000.0000.000
11A592ASP-1-0.794-0.87821.123-0.118-0.1180.0000.0000.0000.000
12A593LYS10.8870.94019.9390.0580.0580.0000.0000.0000.000
13A594THR0-0.058-0.04523.2000.0070.0070.0000.0000.0000.000
14A595LYS10.8420.90726.2230.1380.1380.0000.0000.0000.000
15A596ASP-1-0.796-0.85022.236-0.207-0.2070.0000.0000.0000.000
16A597SER00.0110.00525.4590.0190.0190.0000.0000.0000.000
17A598GLY00.000-0.01225.607-0.014-0.0140.0000.0000.0000.000
18A599LEU0-0.022-0.00719.764-0.005-0.0050.0000.0000.0000.000
19A600PRO00.0070.02318.7260.0200.0200.0000.0000.0000.000
20A601SER0-0.027-0.02518.0220.0420.0420.0000.0000.0000.000
21A602GLN00.0450.02819.394-0.059-0.0590.0000.0000.0000.000
22A603GLY00.0830.02818.0160.0050.0050.0000.0000.0000.000
23A604LEU00.0200.02613.0000.0410.0410.0000.0000.0000.000
24A605ASN0-0.092-0.04716.924-0.035-0.0350.0000.0000.0000.000
25A606PHE00.0180.00915.9160.0100.0100.0000.0000.0000.000
26A607LYS10.8450.90518.2460.2740.2740.0000.0000.0000.000
27A608PHE00.003-0.00518.039-0.057-0.0570.0000.0000.0000.000
28A609GLY0-0.017-0.00917.4250.0400.0400.0000.0000.0000.000
29A610ASP-1-0.770-0.85614.693-0.447-0.4470.0000.0000.0000.000
30A611ILE0-0.012-0.0069.030-0.147-0.1470.0000.0000.0000.000
31A612LEU0-0.031-0.0109.6280.1970.1970.0000.0000.0000.000
32A613HIS0-0.030-0.0293.152-1.995-0.6330.391-0.654-1.098-0.007
33A614VAL0-0.042-0.0315.2280.7180.7180.0000.0000.0000.000
34A615ILE0-0.0180.0034.330-0.511-0.314-0.001-0.018-0.1780.000
35A616ASN00.000-0.0205.8820.3470.3470.0000.0000.0000.000
36A617ALA0-0.0150.0038.090-0.152-0.1520.0000.0000.0000.000
37A618SER0-0.030-0.0169.7780.0630.0630.0000.0000.0000.000
38A619ASP-1-0.769-0.89112.553-0.172-0.1720.0000.0000.0000.000
39A620ASP-1-0.857-0.94014.862-0.406-0.4060.0000.0000.0000.000
40A621GLU-1-0.900-0.92317.148-0.285-0.2850.0000.0000.0000.000
41A622TRP0-0.056-0.04416.225-0.070-0.0700.0000.0000.0000.000
42A623TRP00.026-0.00910.756-0.073-0.0730.0000.0000.0000.000
43A624GLN00.0190.02510.3160.0380.0380.0000.0000.0000.000
44A625ALA0-0.0010.0028.514-0.073-0.0730.0000.0000.0000.000
45A626ARG10.8380.9148.360-0.494-0.4940.0000.0000.0000.000
46A627GLN0-0.011-0.0249.765-0.292-0.2920.0000.0000.0000.000
47A628VAL0-0.026-0.0177.7880.1150.1150.0000.0000.0000.000
48A629THR0-0.083-0.05311.011-0.060-0.0600.0000.0000.0000.000
49A630PRO00.0380.01113.623-0.007-0.0070.0000.0000.0000.000
50A631ASP-1-0.897-0.91515.890-0.041-0.0410.0000.0000.0000.000
51A632GLY0-0.016-0.00914.6130.0560.0560.0000.0000.0000.000
52A633GLU-1-0.832-0.9267.4210.6520.6520.0000.0000.0000.000
53A634SER0-0.059-0.02112.0080.0580.0580.0000.0000.0000.000
54A635ASP-1-0.852-0.91612.6810.7070.7070.0000.0000.0000.000
55A636GLU-1-0.870-0.94913.4350.0820.0820.0000.0000.0000.000
56A637VAL0-0.100-0.05211.4110.0690.0690.0000.0000.0000.000
57A638GLY00.0360.01313.117-0.018-0.0180.0000.0000.0000.000
58A639VAL0-0.069-0.02213.439-0.038-0.0380.0000.0000.0000.000
59A640ILE00.0310.01211.277-0.009-0.0090.0000.0000.0000.000
60A641PRO0-0.042-0.00414.9420.0090.0090.0000.0000.0000.000
61A642SER00.0610.05214.392-0.100-0.1000.0000.0000.0000.000
62A643LYS11.0051.00414.3920.8970.8970.0000.0000.0000.000
63A644ARG10.8330.90914.2700.4780.4780.0000.0000.0000.000
64A645ARG10.8160.88518.4440.2870.2870.0000.0000.0000.000
65A646VAL0-0.004-0.00517.9020.0440.0440.0000.0000.0000.000
66A647GLU-1-0.770-0.89319.101-0.536-0.5360.0000.0000.0000.000
67A648LYS10.8060.90221.8770.2960.2960.0000.0000.0000.000
68A649LYS10.9010.95523.4150.2550.2550.0000.0000.0000.000
69A650GLU-1-0.911-0.96423.727-0.370-0.3700.0000.0000.0000.000
70A651ARG10.8350.89221.9590.4120.4120.0000.0000.0000.000
71A652ALA0-0.045-0.00527.9760.0160.0160.0000.0000.0000.000
72A653ARG10.8900.96726.6640.2610.2610.0000.0000.0000.000
73A654LEU00.0060.01229.8860.0130.0130.0000.0000.0000.000
74A655LYS11.0121.00733.6870.1360.1360.0000.0000.0000.000
75A707VAL0-0.058-0.02021.5340.0210.0210.0000.0000.0000.000
76A708LEU0-0.013-0.01020.536-0.053-0.0530.0000.0000.0000.000
77A709SER00.0010.00417.324-0.009-0.0090.0000.0000.0000.000
78A710TYR00.005-0.04012.6390.0130.0130.0000.0000.0000.000
79A711GLU-1-0.833-0.90213.622-1.037-1.0370.0000.0000.0000.000
80A712PRO0-0.031-0.0159.151-0.087-0.0870.0000.0000.0000.000
81A713VAL0-0.034-0.0158.5850.3570.3570.0000.0000.0000.000
82A714ASN00.000-0.0106.536-1.616-1.6160.0000.0000.0000.000
83A715GLN00.0170.0157.8490.4310.4310.0000.0000.0000.000
84A716GLN0-0.043-0.0299.836-0.094-0.0940.0000.0000.0000.000
85A717GLU-1-0.861-0.90312.895-0.199-0.1990.0000.0000.0000.000
86A718VAL0-0.067-0.03515.852-0.022-0.0220.0000.0000.0000.000
87A719ASN00.000-0.00819.3310.0160.0160.0000.0000.0000.000
88A720TYR0-0.038-0.01620.8500.0130.0130.0000.0000.0000.000
89A721THR00.0230.01723.309-0.014-0.0140.0000.0000.0000.000
90A722ARG10.8080.88818.3420.4940.4940.0000.0000.0000.000
91A723PRO00.0050.00124.3040.0220.0220.0000.0000.0000.000
92A724VAL00.0270.02725.740-0.027-0.0270.0000.0000.0000.000
93A725ILE0-0.030-0.01426.8010.0160.0160.0000.0000.0000.000
94A726ILE00.0500.03927.844-0.019-0.0190.0000.0000.0000.000
95A727LEU00.002-0.00428.3740.0090.0090.0000.0000.0000.000
96A728GLY00.0510.03031.317-0.003-0.0030.0000.0000.0000.000
97A729PRO0-0.034-0.03733.6190.0090.0090.0000.0000.0000.000
98A730MET0-0.016-0.00535.3660.0000.0000.0000.0000.0000.000
99A731LYS10.8490.91033.9010.1790.1790.0000.0000.0000.000
100A732ASP-1-0.842-0.90935.174-0.154-0.1540.0000.0000.0000.000
101A733ARG10.9160.95138.1780.1120.1120.0000.0000.0000.000
102A734VAL00.0470.02532.1250.0030.0030.0000.0000.0000.000
103A735ASN0-0.024-0.02333.583-0.007-0.0070.0000.0000.0000.000
104A736ASP-1-0.916-0.95535.623-0.118-0.1180.0000.0000.0000.000
105A737ASP-1-0.937-0.95836.586-0.105-0.1050.0000.0000.0000.000
106A738LEU0-0.0170.00330.9540.0040.0040.0000.0000.0000.000
107A739ILE0-0.029-0.01634.8910.0040.0040.0000.0000.0000.000
108A740SER0-0.062-0.04237.1330.0080.0080.0000.0000.0000.000
109A741GLU-1-0.818-0.88636.085-0.092-0.0920.0000.0000.0000.000
110A742PHE0-0.063-0.02733.8880.0060.0060.0000.0000.0000.000
111A743PRO00.0640.03135.311-0.009-0.0090.0000.0000.0000.000
112A744ASP-1-0.918-0.95235.449-0.089-0.0890.0000.0000.0000.000
113A745LYS10.8370.92025.9160.1620.1620.0000.0000.0000.000
114A746PHE00.0220.00729.468-0.021-0.0210.0000.0000.0000.000
115A747GLY00.0310.01733.4950.0120.0120.0000.0000.0000.000
116A748SER00.0070.01234.622-0.009-0.0090.0000.0000.0000.000
117A749CYS0-0.013-0.00534.4130.0030.0030.0000.0000.0000.000
118A750VAL00.0180.03036.4740.0030.0030.0000.0000.0000.000
119A751PRO0-0.0010.03338.954-0.008-0.0080.0000.0000.0000.000
120A752HIS00.030-0.00239.0100.0030.0030.0000.0000.0000.000
121A753THR00.005-0.00142.062-0.001-0.0010.0000.0000.0000.000
122A754THR00.0250.02245.3440.0010.0010.0000.0000.0000.000
123A755ARG10.7360.86348.1390.1030.1030.0000.0000.0000.000
124A756PRO00.008-0.00550.5010.0000.0000.0000.0000.0000.000
125A757LYS10.8100.90651.0970.0790.0790.0000.0000.0000.000
126A758ARG10.8930.93251.2280.0900.0900.0000.0000.0000.000
127A759ASP-1-0.872-0.92854.787-0.068-0.0680.0000.0000.0000.000
128A760TYR00.003-0.00853.685-0.001-0.0010.0000.0000.0000.000
129A761GLU-1-0.764-0.82850.650-0.093-0.0930.0000.0000.0000.000
130A762VAL0-0.021-0.00948.5950.0030.0030.0000.0000.0000.000
131A763ASP-1-0.833-0.92846.710-0.108-0.1080.0000.0000.0000.000
132A764GLY00.0050.01043.7060.0030.0030.0000.0000.0000.000
133A765ARG10.8010.89143.2780.0820.0820.0000.0000.0000.000
134A766ASP-1-0.823-0.89944.046-0.094-0.0940.0000.0000.0000.000
135A767TYR00.032-0.00943.715-0.003-0.0030.0000.0000.0000.000
136A768HIS00.0000.01639.1370.0090.0090.0000.0000.0000.000
137A769PHE0-0.029-0.04144.041-0.004-0.0040.0000.0000.0000.000
138A770VAL0-0.024-0.01643.7510.0020.0020.0000.0000.0000.000
139A771THR00.015-0.00346.9740.0010.0010.0000.0000.0000.000
140A772SER00.0220.00948.5020.0030.0030.0000.0000.0000.000
141A773ARG10.8920.93747.5030.1100.1100.0000.0000.0000.000
142A774GLU-1-0.817-0.88646.790-0.116-0.1160.0000.0000.0000.000
143A775GLN0-0.005-0.01142.2690.0010.0010.0000.0000.0000.000
144A776MET00.0000.00141.502-0.006-0.0060.0000.0000.0000.000
145A777GLU-1-0.866-0.95741.986-0.132-0.1320.0000.0000.0000.000
146A778LYS10.8590.92341.4950.1170.1170.0000.0000.0000.000
147A779ASP-1-0.766-0.86739.022-0.161-0.1610.0000.0000.0000.000
148A780ILE0-0.054-0.03037.395-0.013-0.0130.0000.0000.0000.000
149A781GLN0-0.056-0.02336.694-0.011-0.0110.0000.0000.0000.000
150A782GLU-1-0.966-0.97235.834-0.177-0.1770.0000.0000.0000.000
151A783HIS0-0.075-0.03231.624-0.019-0.0190.0000.0000.0000.000
152A784LYS10.8540.93032.3890.1500.1500.0000.0000.0000.000
153A785PHE0-0.067-0.04934.053-0.001-0.0010.0000.0000.0000.000
154A786ILE00.0240.02129.668-0.009-0.0090.0000.0000.0000.000
155A787GLU-1-0.800-0.88132.172-0.240-0.2400.0000.0000.0000.000
156A788ALA00.0240.01635.2340.0090.0090.0000.0000.0000.000
157A789GLY00.0090.01338.945-0.004-0.0040.0000.0000.0000.000
158A790GLN0-0.031-0.02642.0670.0090.0090.0000.0000.0000.000
159A791TYR00.0250.01645.8580.0010.0010.0000.0000.0000.000
160A792ASN00.0030.00248.3610.0010.0010.0000.0000.0000.000
161A793ASN0-0.001-0.00450.7070.0030.0030.0000.0000.0000.000
162A794HIS00.0200.02249.118-0.001-0.0010.0000.0000.0000.000
163A795LEU00.0080.00444.453-0.004-0.0040.0000.0000.0000.000
164A796TYR00.002-0.00542.5720.0060.0060.0000.0000.0000.000
165A797GLY00.0390.01839.141-0.006-0.0060.0000.0000.0000.000
166A798THR00.0050.00734.0570.0120.0120.0000.0000.0000.000
167A799SER00.0160.00934.690-0.016-0.0160.0000.0000.0000.000
168A800VAL00.0900.03828.913-0.002-0.0020.0000.0000.0000.000
169A801GLN00.0280.01931.213-0.014-0.0140.0000.0000.0000.000
170A802SER0-0.031-0.05933.0940.0050.0050.0000.0000.0000.000
171A803VAL00.0210.00129.1880.0060.0060.0000.0000.0000.000
172A804ARG10.9240.96226.4040.2690.2690.0000.0000.0000.000
173A805ALA0-0.0100.00430.0020.0070.0070.0000.0000.0000.000
174A806VAL0-0.025-0.01931.7010.0100.0100.0000.0000.0000.000
175A807ALA00.0360.02927.0520.0050.0050.0000.0000.0000.000
176A808GLU-1-0.917-0.96828.172-0.203-0.2030.0000.0000.0000.000
177A809LYS10.8330.92229.6500.1500.1500.0000.0000.0000.000
178A810GLY00.0030.01229.2680.0130.0130.0000.0000.0000.000
179A811LYS10.8210.91830.3130.1190.1190.0000.0000.0000.000
180A812HIS0-0.002-0.01424.783-0.003-0.0030.0000.0000.0000.000
181A813CYS0-0.033-0.01729.4170.0170.0170.0000.0000.0000.000
182A814ILE00.0130.01830.429-0.020-0.0200.0000.0000.0000.000
183A815LEU0-0.078-0.04629.4140.0100.0100.0000.0000.0000.000
184A816ASP-1-0.842-0.89932.888-0.183-0.1830.0000.0000.0000.000
185A817VAL0-0.054-0.03331.3310.0040.0040.0000.0000.0000.000
186A818SER0-0.047-0.05433.187-0.007-0.0070.0000.0000.0000.000
187A819GLY00.0500.00629.207-0.011-0.0110.0000.0000.0000.000
188A820ASN0-0.036-0.03028.215-0.035-0.0350.0000.0000.0000.000
189A821ALA0-0.009-0.00128.981-0.016-0.0160.0000.0000.0000.000
190A822ILE0-0.0170.01123.588-0.012-0.0120.0000.0000.0000.000
191A823LYS10.9310.96421.4270.5070.5070.0000.0000.0000.000
192A824ARG10.9170.95624.3170.2550.2550.0000.0000.0000.000
193A825LEU00.0310.02025.3320.0020.0020.0000.0000.0000.000
194A826GLN00.0310.01519.889-0.050-0.0500.0000.0000.0000.000
195A827ILE0-0.065-0.03321.387-0.030-0.0300.0000.0000.0000.000
196A828ALA0-0.043-0.00923.3410.0060.0060.0000.0000.0000.000
197A829GLN0-0.064-0.04318.439-0.008-0.0080.0000.0000.0000.000
198A830LEU0-0.0240.00821.7980.0200.0200.0000.0000.0000.000
199A831TYR00.0570.00816.559-0.011-0.0110.0000.0000.0000.000
200A832PRO0-0.0120.00921.2430.0170.0170.0000.0000.0000.000
201A833ILE00.0080.00621.634-0.051-0.0510.0000.0000.0000.000
202A834SER0-0.006-0.00822.6900.0400.0400.0000.0000.0000.000
203A835ILE00.0340.02023.629-0.029-0.0290.0000.0000.0000.000
204A836PHE0-0.009-0.00525.9490.0250.0250.0000.0000.0000.000
205A837ILE00.0130.01027.9630.0000.0000.0000.0000.0000.000
206A838LYS10.8460.89428.4980.2460.2460.0000.0000.0000.000
207A839PRO0-0.053-0.01731.2110.0100.0100.0000.0000.0000.000
208A840LYS10.8790.91532.5940.1210.1210.0000.0000.0000.000
209A841SER0-0.020-0.01835.0380.0030.0030.0000.0000.0000.000
210A842MET00.031-0.00138.462-0.002-0.0020.0000.0000.0000.000
211A843GLU-1-0.870-0.93241.541-0.086-0.0860.0000.0000.0000.000
212A844ASN00.0220.02036.195-0.007-0.0070.0000.0000.0000.000
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