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: 53VNZ

Calculation Name: 3SQD-A-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 3SQD

Chain ID: A

ChEMBL ID:

UniProt ID: P16104

Base Structure: X-ray

Registration Date: 2023-06-19

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2429571.005655
FMO2-HF: Nuclear repulsion 2344661.333966
FMO2-HF: Total energy -84909.671689
FMO2-MP2: Total energy -85155.395982


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:859:MET)


Summations of interaction energy for fragment #1(A:859:MET)
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.
-13.067-6.3512.395-3.638-5.472-0.03
Interaction energy analysis for fragmet #1(A:859:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.002
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].
3A861LEU00.0030.0193.3680.5592.407-0.009-0.785-1.0540.001
4A862THR00.0360.0095.651-0.074-0.0740.0000.0000.0000.000
5A863PRO00.0660.0289.442-0.163-0.1630.0000.0000.0000.000
6A864GLU-1-0.966-0.97911.689-0.293-0.2930.0000.0000.0000.000
7A865LEU0-0.074-0.0438.4840.0360.0360.0000.0000.0000.000
8A866THR0-0.046-0.0127.995-0.329-0.3290.0000.0000.0000.000
9A867PRO0-0.019-0.0028.1220.1970.1970.0000.0000.0000.000
10A868PHE00.0250.02110.433-0.134-0.1340.0000.0000.0000.000
11A869VAL00.0170.00211.6630.1110.1110.0000.0000.0000.000
12A870LEU0-0.0130.00314.4740.0430.0430.0000.0000.0000.000
13A871PHE00.0560.03113.2980.0160.0160.0000.0000.0000.000
14A872THR0-0.025-0.02819.1270.0420.0420.0000.0000.0000.000
15A873GLY0-0.0080.00322.848-0.002-0.0020.0000.0000.0000.000
16A874PHE0-0.0160.00320.6610.0000.0000.0000.0000.0000.000
17A875GLU-1-0.856-0.93023.403-0.142-0.1420.0000.0000.0000.000
18A876PRO00.0340.00222.299-0.024-0.0240.0000.0000.0000.000
19A877VAL00.003-0.00420.838-0.020-0.0200.0000.0000.0000.000
20A878GLN00.0710.04219.342-0.010-0.0100.0000.0000.0000.000
21A879VAL00.0110.01117.723-0.044-0.0440.0000.0000.0000.000
22A880GLN0-0.011-0.01016.161-0.042-0.0420.0000.0000.0000.000
23A881GLN0-0.060-0.02814.819-0.047-0.0470.0000.0000.0000.000
24A882TYR00.0180.00813.105-0.047-0.0470.0000.0000.0000.000
25A883ILE00.0330.01711.829-0.149-0.1490.0000.0000.0000.000
26A884LYS10.9240.96010.3190.0380.0380.0000.0000.0000.000
27A885LYS10.8020.8858.5030.2810.2810.0000.0000.0000.000
28A886LEU0-0.0030.0077.357-0.445-0.4450.0000.0000.0000.000
29A887TYR0-0.026-0.0346.220-0.551-0.5510.0000.0000.0000.000
30A888ILE0-0.056-0.0073.885-1.328-0.8040.007-0.096-0.4350.000
31A889LEU0-0.035-0.0122.420-7.465-4.5571.712-1.936-2.684-0.024
32A890GLY0-0.029-0.0062.937-2.936-1.6820.635-0.911-0.977-0.007
33A891GLY0-0.017-0.0103.4141.2511.1940.0510.099-0.0930.000
34A892GLU-1-0.862-0.9207.054-0.902-0.9020.0000.0000.0000.000
35A893VAL0-0.029-0.01710.0400.0980.0980.0000.0000.0000.000
36A894ALA0-0.013-0.00613.5830.0240.0240.0000.0000.0000.000
37A895GLU-1-0.838-0.91516.067-0.282-0.2820.0000.0000.0000.000
38A896SER0-0.048-0.03618.6940.0500.0500.0000.0000.0000.000
39A897ALA00.0520.01420.281-0.027-0.0270.0000.0000.0000.000
40A898GLN0-0.007-0.01021.749-0.004-0.0040.0000.0000.0000.000
41A899LYS10.8330.91818.1460.2940.2940.0000.0000.0000.000
42A900CYS0-0.100-0.02416.933-0.046-0.0460.0000.0000.0000.000
43A901THR00.031-0.01214.4080.0220.0220.0000.0000.0000.000
44A902HIS00.0180.02113.2550.0300.0300.0000.0000.0000.000
45A903LEU00.003-0.00516.668-0.014-0.0140.0000.0000.0000.000
46A904ILE0-0.017-0.00614.9240.0040.0040.0000.0000.0000.000
47A905ALA0-0.003-0.02818.7610.0270.0270.0000.0000.0000.000
48A906SER00.0300.00822.256-0.005-0.0050.0000.0000.0000.000
49A907LYS10.9690.99024.1920.1790.1790.0000.0000.0000.000
50A908VAL00.005-0.00426.806-0.015-0.0150.0000.0000.0000.000
51A909THR0-0.031-0.01726.6500.0170.0170.0000.0000.0000.000
52A910ARG10.8190.88628.8610.1110.1110.0000.0000.0000.000
53A911THR0-0.036-0.02226.3010.0070.0070.0000.0000.0000.000
54A912VAL00.0760.01528.291-0.003-0.0030.0000.0000.0000.000
55A913LYS10.9060.96020.8400.2980.2980.0000.0000.0000.000
56A914PHE00.0580.03324.860-0.014-0.0140.0000.0000.0000.000
57A915LEU00.0140.00326.179-0.002-0.0020.0000.0000.0000.000
58A916THR0-0.053-0.03926.2120.0010.0010.0000.0000.0000.000
59A917ALA00.021-0.00222.3740.0000.0000.0000.0000.0000.000
60A918ILE0-0.0420.00424.178-0.009-0.0090.0000.0000.0000.000
61A919SER0-0.0020.00026.2020.0100.0100.0000.0000.0000.000
62A920VAL0-0.055-0.03922.9530.0080.0080.0000.0000.0000.000
63A921VAL0-0.057-0.00320.030-0.015-0.0150.0000.0000.0000.000
64A922LYS10.9480.97915.5130.4450.4450.0000.0000.0000.000
65A923HIS00.0180.01616.0560.0480.0480.0000.0000.0000.000
66A924ILE0-0.008-0.00319.570-0.022-0.0220.0000.0000.0000.000
67A925VAL00.0030.00516.4410.0190.0190.0000.0000.0000.000
68A926THR0-0.009-0.02019.781-0.010-0.0100.0000.0000.0000.000
69A927PRO0-0.006-0.01317.191-0.049-0.0490.0000.0000.0000.000
70A928GLU-1-0.835-0.91416.530-0.347-0.3470.0000.0000.0000.000
71A929TRP00.0090.00911.482-0.059-0.0590.0000.0000.0000.000
72A930LEU00.0010.00510.136-0.070-0.0700.0000.0000.0000.000
73A931GLU-1-0.803-0.89111.942-0.514-0.5140.0000.0000.0000.000
74A932GLU-1-0.794-0.87413.125-0.345-0.3450.0000.0000.0000.000
75A933CYS0-0.047-0.0059.455-0.010-0.0100.0000.0000.0000.000
76A934PHE00.003-0.0077.087-0.116-0.1160.0000.0000.0000.000
77A935ARG10.8380.9188.9010.3560.3560.0000.0000.0000.000
78A936CYS0-0.092-0.04610.6670.1590.1590.0000.0000.0000.000
79A937GLN0-0.085-0.0474.861-0.0180.221-0.001-0.009-0.2290.000
80A938LYS10.9360.9695.461-0.125-0.1250.0000.0000.0000.000
81A939PHE00.0220.0005.5750.2910.2910.0000.0000.0000.000
82A940ILE0-0.029-0.0208.6380.1740.1740.0000.0000.0000.000
83A941ASP-1-0.801-0.90512.089-0.376-0.3760.0000.0000.0000.000
84A942GLU-1-0.805-0.89713.979-0.606-0.6060.0000.0000.0000.000
85A943GLN0-0.041-0.03117.0670.0500.0500.0000.0000.0000.000
86A944ASN0-0.057-0.02519.7430.0350.0350.0000.0000.0000.000
87A945TYR0-0.008-0.02117.5010.0150.0150.0000.0000.0000.000
88A946ILE00.0140.02120.512-0.013-0.0130.0000.0000.0000.000
89A947LEU0-0.059-0.01522.4600.0200.0200.0000.0000.0000.000
90A948ARG10.9190.94324.5770.2000.2000.0000.0000.0000.000
91A949ASP-1-0.791-0.88428.140-0.155-0.1550.0000.0000.0000.000
92A950ALA00.0610.01930.5790.0060.0060.0000.0000.0000.000
93A951GLU-1-0.917-0.95333.958-0.106-0.1060.0000.0000.0000.000
94A952ALA00.000-0.01032.5000.0060.0060.0000.0000.0000.000
95A953GLU-1-0.852-0.92431.598-0.151-0.1510.0000.0000.0000.000
96A954VAL0-0.0010.00335.1160.0060.0060.0000.0000.0000.000
97A955LEU0-0.079-0.02437.0510.0050.0050.0000.0000.0000.000
98A956PHE0-0.048-0.04835.5050.0030.0030.0000.0000.0000.000
99A957SER0-0.040-0.00538.2900.0020.0020.0000.0000.0000.000
100A958PHE0-0.040-0.02531.320-0.001-0.0010.0000.0000.0000.000
101A959SER00.0030.01032.029-0.003-0.0030.0000.0000.0000.000
102A960LEU00.021-0.01026.138-0.001-0.0010.0000.0000.0000.000
103A961GLU-1-0.843-0.91626.837-0.183-0.1830.0000.0000.0000.000
104A962GLU-1-0.866-0.92828.576-0.132-0.1320.0000.0000.0000.000
105A963SER0-0.022-0.03030.0390.0060.0060.0000.0000.0000.000
106A964LEU0-0.0030.00223.780-0.001-0.0010.0000.0000.0000.000
107A965LYS10.8940.94127.3410.1570.1570.0000.0000.0000.000
108A966ARG10.7820.87028.8880.1280.1280.0000.0000.0000.000
109A967ALA00.0140.00927.6400.0050.0050.0000.0000.0000.000
110A968HIS0-0.103-0.05623.2710.0100.0100.0000.0000.0000.000
111A969VAL0-0.0440.00027.5090.0070.0070.0000.0000.0000.000
112A970SER0-0.041-0.03930.8600.0110.0110.0000.0000.0000.000
113A971PRO0-0.0060.01430.634-0.002-0.0020.0000.0000.0000.000
114A972LEU00.0240.03832.3910.0100.0100.0000.0000.0000.000
115A973PHE0-0.046-0.03334.7960.0090.0090.0000.0000.0000.000
116A974LYS10.9930.99435.2220.1050.1050.0000.0000.0000.000
117A975ALA0-0.050-0.02336.6960.0050.0050.0000.0000.0000.000
118A976LYS10.8800.95239.1770.0920.0920.0000.0000.0000.000
119A977TYR0-0.053-0.03439.706-0.002-0.0020.0000.0000.0000.000
120A978PHE00.0650.03038.5800.0030.0030.0000.0000.0000.000
121A979TYR0-0.018-0.01242.3500.0000.0000.0000.0000.0000.000
122A980ILE00.011-0.00139.5020.0000.0000.0000.0000.0000.000
123A981THR0-0.041-0.02143.7700.0000.0000.0000.0000.0000.000
124A982PRO00.000-0.02544.264-0.003-0.0030.0000.0000.0000.000
125A983GLY0-0.0050.01444.010-0.002-0.0020.0000.0000.0000.000
126A984ILE0-0.078-0.01740.601-0.001-0.0010.0000.0000.0000.000
127A985CYS0-0.013-0.00440.408-0.003-0.0030.0000.0000.0000.000
128A986PRO00.0600.01335.6940.0000.0000.0000.0000.0000.000
129A987SER00.0490.03135.6220.0000.0000.0000.0000.0000.000
130A988LEU00.1100.04937.169-0.005-0.0050.0000.0000.0000.000
131A989SER0-0.027-0.02534.003-0.001-0.0010.0000.0000.0000.000
132A990THR0-0.009-0.00532.181-0.011-0.0110.0000.0000.0000.000
133A991MET00.0040.01233.219-0.009-0.0090.0000.0000.0000.000
134A992LYS10.9490.98334.3320.1070.1070.0000.0000.0000.000
135A993ALA00.0070.00929.537-0.003-0.0030.0000.0000.0000.000
136A994ILE00.0060.00030.485-0.009-0.0090.0000.0000.0000.000
137A995VAL0-0.005-0.00531.886-0.002-0.0020.0000.0000.0000.000
138A996GLU-1-0.895-0.94131.834-0.123-0.1230.0000.0000.0000.000
139A997CYS0-0.054-0.00527.646-0.006-0.0060.0000.0000.0000.000
140A998ALA00.0530.03629.214-0.006-0.0060.0000.0000.0000.000
141A999GLY0-0.024-0.02531.7490.0080.0080.0000.0000.0000.000
142A1000GLY00.0120.02933.2460.0080.0080.0000.0000.0000.000
143A1001LYS10.8030.87533.2210.1160.1160.0000.0000.0000.000
144A1002VAL00.0410.01637.2260.0030.0030.0000.0000.0000.000
145A1003LEU0-0.069-0.03939.6160.0020.0020.0000.0000.0000.000
146A1004SER00.001-0.00942.2280.0020.0020.0000.0000.0000.000
147A1005LYS10.9380.96543.6480.0620.0620.0000.0000.0000.000
148A1006GLN00.0550.03747.406-0.003-0.0030.0000.0000.0000.000
149A1007PRO0-0.0110.01048.1980.0020.0020.0000.0000.0000.000
150A1008SER00.0610.03550.8370.0010.0010.0000.0000.0000.000
151A1009PHE00.0960.01354.085-0.001-0.0010.0000.0000.0000.000
152A1010ARG10.8380.91656.2970.0400.0400.0000.0000.0000.000
153A1011LYS10.9190.95647.8100.0600.0600.0000.0000.0000.000
154A1012LEU00.0240.00950.248-0.001-0.0010.0000.0000.0000.000
155A1013MET0-0.025-0.01452.751-0.001-0.0010.0000.0000.0000.000
156A1014GLU-1-0.791-0.89453.951-0.045-0.0450.0000.0000.0000.000
157A1015HIS0-0.010-0.00946.5970.0010.0010.0000.0000.0000.000
158A1016LYS10.9380.97950.7630.0510.0510.0000.0000.0000.000
159A1017GLN0-0.024-0.00752.5130.0000.0000.0000.0000.0000.000
160A1018ASN0-0.056-0.02551.5630.0030.0030.0000.0000.0000.000
161A1019SER00.0440.02849.273-0.002-0.0020.0000.0000.0000.000
162A1020SER0-0.016-0.00847.327-0.003-0.0030.0000.0000.0000.000
163A1021LEU0-0.057-0.02646.480-0.002-0.0020.0000.0000.0000.000
164A1022SER0-0.0020.00342.3270.0000.0000.0000.0000.0000.000
165A1023GLU-1-0.702-0.80544.287-0.075-0.0750.0000.0000.0000.000
166A1024ILE0-0.066-0.03744.362-0.003-0.0030.0000.0000.0000.000
167A1025ILE00.0000.01042.0480.0020.0020.0000.0000.0000.000
168A1026LEU0-0.030-0.01244.857-0.001-0.0010.0000.0000.0000.000
169A1027ILE0-0.008-0.00141.737-0.001-0.0010.0000.0000.0000.000
170A1028SER00.009-0.02345.0590.0020.0020.0000.0000.0000.000
171A1029CYS0-0.018-0.01645.492-0.003-0.0030.0000.0000.0000.000
172A1030GLU-1-0.841-0.92347.504-0.058-0.0580.0000.0000.0000.000
173A1031ASN0-0.003-0.01347.6600.0040.0040.0000.0000.0000.000
174A1032ASP-1-0.807-0.88847.545-0.064-0.0640.0000.0000.0000.000
175A1033LEU00.0240.02250.8210.0020.0020.0000.0000.0000.000
176A1034HIS0-0.048-0.02652.9090.0030.0030.0000.0000.0000.000
177A1035LEU0-0.024-0.02050.4710.0020.0020.0000.0000.0000.000
178A1036CYS0-0.026-0.00751.7660.0000.0000.0000.0000.0000.000
179A1037ARG10.9580.99854.5240.0440.0440.0000.0000.0000.000
180A1038GLU-1-0.926-0.97458.161-0.041-0.0410.0000.0000.0000.000
181A1039TYR0-0.057-0.04753.3400.0010.0010.0000.0000.0000.000
182A1040PHE00.0640.02452.7540.0000.0000.0000.0000.0000.000
183A1041ALA0-0.0100.01257.5700.0010.0010.0000.0000.0000.000
184A1042ARG10.8670.93758.4620.0420.0420.0000.0000.0000.000
185A1043GLY00.0130.01958.4710.0000.0000.0000.0000.0000.000
186A1044ILE0-0.116-0.05752.470-0.001-0.0010.0000.0000.0000.000
187A1045ASP-1-0.788-0.89150.445-0.059-0.0590.0000.0000.0000.000
188A1046VAL0-0.069-0.04148.779-0.001-0.0010.0000.0000.0000.000
189A1047HIS00.0200.01845.2770.0000.0000.0000.0000.0000.000
190A1048ASN00.0750.04844.077-0.004-0.0040.0000.0000.0000.000
191A1049ALA00.0580.00140.066-0.003-0.0030.0000.0000.0000.000
192A1050GLU-1-0.745-0.81839.273-0.114-0.1140.0000.0000.0000.000
193A1051PHE00.0280.01839.835-0.005-0.0050.0000.0000.0000.000
194A1052VAL0-0.054-0.02835.900-0.004-0.0040.0000.0000.0000.000
195A1053LEU0-0.066-0.02834.967-0.008-0.0080.0000.0000.0000.000
196A1054THR00.055-0.00235.006-0.010-0.0100.0000.0000.0000.000
197A1055GLY00.0230.04036.429-0.003-0.0030.0000.0000.0000.000
198A1056VAL0-0.005-0.02031.075-0.004-0.0040.0000.0000.0000.000
199A1057LEU0-0.042-0.00230.827-0.010-0.0100.0000.0000.0000.000
200A1058THR00.0130.02232.189-0.006-0.0060.0000.0000.0000.000
201A1059GLN0-0.010-0.01631.2660.0060.0060.0000.0000.0000.000
202A1060THR0-0.045-0.02534.5520.0070.0070.0000.0000.0000.000
203A1061LEU0-0.032-0.01438.346-0.001-0.0010.0000.0000.0000.000
204A1062ASP-1-0.767-0.85341.131-0.078-0.0780.0000.0000.0000.000
205A1063TYR0-0.106-0.10143.908-0.001-0.0010.0000.0000.0000.000
206A1064GLU-1-0.824-0.92046.914-0.059-0.0590.0000.0000.0000.000
207A1065SER0-0.024-0.02645.2890.0030.0030.0000.0000.0000.000
208A1066TYR0-0.029-0.03142.0980.0000.0000.0000.0000.0000.000
209A1067LYS10.7900.90046.6660.0610.0610.0000.0000.0000.000
210A1068PHE0-0.024-0.01947.8580.0010.0010.0000.0000.0000.000
211A1069ASN0-0.044-0.01251.9700.0030.0030.0000.0000.0000.000