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: 43VLN

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2428099.792142
FMO2-HF: Nuclear repulsion 2343190.995568
FMO2-HF: Total energy -84908.796574
FMO2-MP2: Total energy -85154.51257


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.
-14.134-8.5074.811-4.185-6.253-0.037
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 : 0.010 / q_NPA : 0.001
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].
3A861LEU0-0.0040.0153.2540.5352.443-0.006-0.809-1.0930.001
4A862THR00.0280.0105.734-0.129-0.1290.0000.0000.0000.000
5A863PRO00.0690.0269.508-0.162-0.1620.0000.0000.0000.000
6A864GLU-1-0.967-0.98211.757-0.256-0.2560.0000.0000.0000.000
7A865LEU0-0.073-0.0418.3580.0290.0290.0000.0000.0000.000
8A866THR0-0.038-0.0088.036-0.327-0.3270.0000.0000.0000.000
9A867PRO0-0.027-0.0048.0660.1870.1870.0000.0000.0000.000
10A868PHE00.0350.02610.413-0.134-0.1340.0000.0000.0000.000
11A869VAL00.0290.00811.9440.1080.1080.0000.0000.0000.000
12A870LEU0-0.0220.00014.4580.0430.0430.0000.0000.0000.000
13A871PHE00.0550.03113.3270.0160.0160.0000.0000.0000.000
14A872THR0-0.029-0.03819.1160.0430.0430.0000.0000.0000.000
15A873GLY0-0.019-0.00222.838-0.002-0.0020.0000.0000.0000.000
16A874PHE0-0.0070.00820.324-0.001-0.0010.0000.0000.0000.000
17A875GLU-1-0.862-0.93023.399-0.145-0.1450.0000.0000.0000.000
18A876PRO00.030-0.00122.251-0.024-0.0240.0000.0000.0000.000
19A877VAL00.0270.00620.718-0.021-0.0210.0000.0000.0000.000
20A878GLN00.0610.03419.113-0.007-0.0070.0000.0000.0000.000
21A879VAL00.0120.01417.497-0.045-0.0450.0000.0000.0000.000
22A880GLN0-0.021-0.01216.155-0.045-0.0450.0000.0000.0000.000
23A881GLN0-0.048-0.02814.588-0.051-0.0510.0000.0000.0000.000
24A882TYR00.0110.00512.879-0.057-0.0570.0000.0000.0000.000
25A883ILE00.0400.02011.827-0.157-0.1570.0000.0000.0000.000
26A884LYS10.9230.95910.3110.0130.0130.0000.0000.0000.000
27A885LYS10.9040.9648.2870.3000.3000.0000.0000.0000.000
28A886LEU00.0080.0167.122-0.485-0.4850.0000.0000.0000.000
29A887TYR00.0380.0156.211-0.553-0.5530.0000.0000.0000.000
30A888ILE0-0.051-0.0053.719-1.502-0.7920.021-0.169-0.5630.000
31A889LEU0-0.031-0.0122.168-7.911-6.4794.075-2.349-3.158-0.030
32A890GLY0-0.018-0.0022.912-2.919-1.6030.667-0.956-1.028-0.008
33A891GLY0-0.006-0.0063.3911.3101.2560.0550.109-0.1090.000
34A892GLU-1-0.949-0.9807.035-0.908-0.9080.0000.0000.0000.000
35A893VAL0-0.028-0.01910.0170.0930.0930.0000.0000.0000.000
36A894ALA0-0.013-0.00713.5620.0270.0270.0000.0000.0000.000
37A895GLU-1-0.901-0.95616.043-0.276-0.2760.0000.0000.0000.000
38A896SER0-0.053-0.03818.6680.0490.0490.0000.0000.0000.000
39A897ALA00.0590.01820.257-0.027-0.0270.0000.0000.0000.000
40A898GLN0-0.006-0.00921.727-0.003-0.0030.0000.0000.0000.000
41A899LYS10.8820.95018.0700.2680.2680.0000.0000.0000.000
42A900CYS0-0.085-0.01616.922-0.043-0.0430.0000.0000.0000.000
43A901THR00.022-0.00914.4080.0220.0220.0000.0000.0000.000
44A902HIS00.0240.01413.5570.0300.0300.0000.0000.0000.000
45A903LEU00.007-0.00616.656-0.015-0.0150.0000.0000.0000.000
46A904ILE0-0.028-0.00815.1070.0040.0040.0000.0000.0000.000
47A905ALA00.009-0.02518.7540.0270.0270.0000.0000.0000.000
48A906SER00.0130.00122.251-0.005-0.0050.0000.0000.0000.000
49A907LYS10.9750.99224.1910.1870.1870.0000.0000.0000.000
50A908VAL00.0050.00026.801-0.015-0.0150.0000.0000.0000.000
51A909THR0-0.052-0.02026.4330.0170.0170.0000.0000.0000.000
52A910ARG10.8800.93328.8510.1120.1120.0000.0000.0000.000
53A911THR0-0.023-0.01626.3460.0080.0080.0000.0000.0000.000
54A912VAL00.0700.01228.149-0.003-0.0030.0000.0000.0000.000
55A913LYS10.9090.95920.8200.2970.2970.0000.0000.0000.000
56A914PHE00.0460.03124.844-0.014-0.0140.0000.0000.0000.000
57A915LEU00.0170.00226.165-0.001-0.0010.0000.0000.0000.000
58A916THR0-0.050-0.02926.0360.0010.0010.0000.0000.0000.000
59A917ALA00.019-0.00322.3860.0000.0000.0000.0000.0000.000
60A918ILE0-0.0440.00124.160-0.008-0.0080.0000.0000.0000.000
61A919SER00.0020.00226.1870.0100.0100.0000.0000.0000.000
62A920VAL0-0.053-0.03622.6680.0090.0090.0000.0000.0000.000
63A921VAL0-0.058-0.00520.019-0.014-0.0140.0000.0000.0000.000
64A922LYS10.9410.97115.9950.3940.3940.0000.0000.0000.000
65A923HIS00.0350.01916.3630.0360.0360.0000.0000.0000.000
66A924ILE00.0030.00419.560-0.022-0.0220.0000.0000.0000.000
67A925VAL00.0020.00716.4510.0190.0190.0000.0000.0000.000
68A926THR00.0430.02419.778-0.014-0.0140.0000.0000.0000.000
69A927PRO0-0.009-0.02017.195-0.048-0.0480.0000.0000.0000.000
70A928GLU-1-0.871-0.95216.512-0.354-0.3540.0000.0000.0000.000
71A929TRP00.0040.00611.472-0.058-0.0580.0000.0000.0000.000
72A930LEU0-0.016-0.00310.200-0.075-0.0750.0000.0000.0000.000
73A931GLU-1-0.887-0.96011.773-0.535-0.5350.0000.0000.0000.000
74A932GLU-1-0.794-0.88813.000-0.400-0.4000.0000.0000.0000.000
75A933CYS0-0.0440.0119.414-0.027-0.0270.0000.0000.0000.000
76A934PHE00.004-0.0097.016-0.136-0.1360.0000.0000.0000.000
77A935ARG10.8180.9178.8260.3880.3880.0000.0000.0000.000
78A936CYS0-0.091-0.04210.6640.1500.1500.0000.0000.0000.000
79A937GLN0-0.080-0.0424.734-0.1870.128-0.001-0.011-0.3020.000
80A938LYS10.9370.9685.521-0.116-0.1160.0000.0000.0000.000
81A939PHE00.024-0.0065.5570.2800.2800.0000.0000.0000.000
82A940ILE0-0.043-0.0308.5820.1860.1860.0000.0000.0000.000
83A941ASP-1-0.833-0.93512.033-0.383-0.3830.0000.0000.0000.000
84A942GLU-1-0.821-0.89713.861-0.612-0.6120.0000.0000.0000.000
85A943GLN00.0030.00817.0240.0430.0430.0000.0000.0000.000
86A944ASN0-0.070-0.03519.6890.0320.0320.0000.0000.0000.000
87A945TYR0-0.021-0.02017.2240.0130.0130.0000.0000.0000.000
88A946ILE00.0180.02220.451-0.012-0.0120.0000.0000.0000.000
89A947LEU0-0.059-0.01522.4110.0190.0190.0000.0000.0000.000
90A948ARG10.9630.97324.5760.2010.2010.0000.0000.0000.000
91A949ASP-1-0.782-0.88928.140-0.158-0.1580.0000.0000.0000.000
92A950ALA00.0500.01430.5780.0060.0060.0000.0000.0000.000
93A951GLU-1-0.914-0.95133.959-0.109-0.1090.0000.0000.0000.000
94A952ALA0-0.006-0.00632.4930.0060.0060.0000.0000.0000.000
95A953GLU-1-0.883-0.94431.244-0.152-0.1520.0000.0000.0000.000
96A954VAL00.0120.01235.1120.0060.0060.0000.0000.0000.000
97A955LEU0-0.079-0.02937.1400.0050.0050.0000.0000.0000.000
98A956PHE0-0.051-0.04935.1860.0030.0030.0000.0000.0000.000
99A957SER0-0.033-0.00338.2830.0020.0020.0000.0000.0000.000
100A958PHE0-0.040-0.02631.3200.0000.0000.0000.0000.0000.000
101A959SER00.0410.03531.910-0.003-0.0030.0000.0000.0000.000
102A960LEU00.027-0.01026.151-0.001-0.0010.0000.0000.0000.000
103A961GLU-1-0.937-0.97627.497-0.176-0.1760.0000.0000.0000.000
104A962GLU-1-0.865-0.93528.549-0.127-0.1270.0000.0000.0000.000
105A963SER0-0.026-0.03229.9380.0060.0060.0000.0000.0000.000
106A964LEU0-0.0030.00123.741-0.001-0.0010.0000.0000.0000.000
107A965LYS10.9500.98227.3290.1520.1520.0000.0000.0000.000
108A966ARG10.7850.88828.8820.1240.1240.0000.0000.0000.000
109A967ALA00.0220.01527.5880.0050.0050.0000.0000.0000.000
110A968HIS0-0.098-0.05023.4580.0110.0110.0000.0000.0000.000
111A969VAL0-0.0490.00027.5190.0070.0070.0000.0000.0000.000
112A970SER0-0.047-0.04330.8740.0110.0110.0000.0000.0000.000
113A971PRO0-0.0020.01730.712-0.002-0.0020.0000.0000.0000.000
114A972LEU00.0260.03732.4060.0090.0090.0000.0000.0000.000
115A973PHE0-0.034-0.02434.7760.0090.0090.0000.0000.0000.000
116A974LYS10.9830.98935.3450.0970.0970.0000.0000.0000.000
117A975ALA0-0.058-0.02736.7180.0050.0050.0000.0000.0000.000
118A976LYS10.9240.98939.1530.0880.0880.0000.0000.0000.000
119A977TYR0-0.057-0.03739.683-0.002-0.0020.0000.0000.0000.000
120A978PHE00.0630.03138.7120.0030.0030.0000.0000.0000.000
121A979TYR0-0.019-0.00942.3280.0010.0010.0000.0000.0000.000
122A980ILE00.0140.00339.6110.0000.0000.0000.0000.0000.000
123A981THR0-0.035-0.00643.7480.0000.0000.0000.0000.0000.000
124A982PRO0-0.005-0.02644.250-0.003-0.0030.0000.0000.0000.000
125A983GLY0-0.0010.01243.989-0.002-0.0020.0000.0000.0000.000
126A984ILE0-0.087-0.01940.499-0.001-0.0010.0000.0000.0000.000
127A985CYS0-0.014-0.00640.385-0.003-0.0030.0000.0000.0000.000
128A986PRO00.0630.01535.7440.0000.0000.0000.0000.0000.000
129A987SER00.0490.02435.5700.0010.0010.0000.0000.0000.000
130A988LEU00.1090.04837.149-0.005-0.0050.0000.0000.0000.000
131A989SER0-0.029-0.02833.845-0.001-0.0010.0000.0000.0000.000
132A990THR0-0.0080.00432.214-0.010-0.0100.0000.0000.0000.000
133A991MET00.0040.00933.198-0.008-0.0080.0000.0000.0000.000
134A992LYS10.9590.98134.3540.1000.1000.0000.0000.0000.000
135A993ALA00.0250.01629.486-0.002-0.0020.0000.0000.0000.000
136A994ILE0-0.015-0.00930.463-0.008-0.0080.0000.0000.0000.000
137A995VAL0-0.014-0.00731.866-0.002-0.0020.0000.0000.0000.000
138A996GLU-1-0.977-0.99231.665-0.120-0.1200.0000.0000.0000.000
139A997CYS0-0.0430.00527.461-0.007-0.0070.0000.0000.0000.000
140A998ALA00.0460.03429.193-0.006-0.0060.0000.0000.0000.000
141A999GLY0-0.030-0.02831.7290.0070.0070.0000.0000.0000.000
142A1000GLY00.0040.02133.2240.0080.0080.0000.0000.0000.000
143A1001LYS10.9110.94434.4830.1000.1000.0000.0000.0000.000
144A1002VAL00.0520.02437.0740.0030.0030.0000.0000.0000.000
145A1003LEU0-0.064-0.04039.5920.0020.0020.0000.0000.0000.000
146A1004SER0-0.006-0.01242.1850.0010.0010.0000.0000.0000.000
147A1005LYS10.9470.96843.6220.0570.0570.0000.0000.0000.000
148A1006GLN00.0370.02847.381-0.003-0.0030.0000.0000.0000.000
149A1007PRO0-0.0010.01148.1110.0020.0020.0000.0000.0000.000
150A1008SER00.0660.05650.8130.0010.0010.0000.0000.0000.000
151A1009PHE00.1020.01454.061-0.001-0.0010.0000.0000.0000.000
152A1010ARG10.8950.95756.2740.0370.0370.0000.0000.0000.000
153A1011LYS10.9230.97047.6370.0570.0570.0000.0000.0000.000
154A1012LEU00.0160.00350.401-0.001-0.0010.0000.0000.0000.000
155A1013MET0-0.036-0.01152.728-0.001-0.0010.0000.0000.0000.000
156A1014GLU-1-0.833-0.93253.963-0.042-0.0420.0000.0000.0000.000
157A1015HIS0-0.028-0.03346.5160.0010.0010.0000.0000.0000.000
158A1016LYS10.9370.97750.7900.0500.0500.0000.0000.0000.000
159A1017GLN0-0.022-0.01052.5170.0000.0000.0000.0000.0000.000
160A1018ASN0-0.056-0.02051.6820.0030.0030.0000.0000.0000.000
161A1019SER00.0420.03049.342-0.002-0.0020.0000.0000.0000.000
162A1020SER0-0.021-0.01147.353-0.003-0.0030.0000.0000.0000.000
163A1021LEU0-0.048-0.02246.518-0.002-0.0020.0000.0000.0000.000
164A1022SER0-0.0120.00042.1210.0000.0000.0000.0000.0000.000
165A1023GLU-1-0.742-0.83844.314-0.071-0.0710.0000.0000.0000.000
166A1024ILE0-0.070-0.04044.340-0.003-0.0030.0000.0000.0000.000
167A1025ILE00.0180.01842.1130.0020.0020.0000.0000.0000.000
168A1026LEU0-0.039-0.01944.836-0.001-0.0010.0000.0000.0000.000
169A1027ILE0-0.0010.00941.750-0.001-0.0010.0000.0000.0000.000
170A1028SER00.012-0.02445.0400.0020.0020.0000.0000.0000.000
171A1029CYS0-0.010-0.01345.494-0.003-0.0030.0000.0000.0000.000
172A1030GLU-1-0.856-0.93047.486-0.057-0.0570.0000.0000.0000.000
173A1031ASN0-0.006-0.01348.2070.0040.0040.0000.0000.0000.000
174A1032ASP-1-0.803-0.89947.707-0.062-0.0620.0000.0000.0000.000
175A1033LEU00.0350.02150.9600.0020.0020.0000.0000.0000.000
176A1034HIS0-0.075-0.04353.0340.0030.0030.0000.0000.0000.000
177A1035LEU0-0.011-0.01450.4900.0020.0020.0000.0000.0000.000
178A1036CYS0-0.029-0.00551.7580.0000.0000.0000.0000.0000.000
179A1037ARG10.9490.99754.5040.0430.0430.0000.0000.0000.000
180A1038GLU-1-0.918-0.96758.141-0.039-0.0390.0000.0000.0000.000
181A1039TYR0-0.059-0.06353.4960.0010.0010.0000.0000.0000.000
182A1040PHE00.0650.02552.8720.0000.0000.0000.0000.0000.000
183A1041ALA0-0.0100.01057.5510.0010.0010.0000.0000.0000.000
184A1042ARG10.8670.93758.4290.0400.0400.0000.0000.0000.000
185A1043GLY00.0060.01558.4510.0000.0000.0000.0000.0000.000
186A1044ILE0-0.120-0.05552.398-0.001-0.0010.0000.0000.0000.000
187A1045ASP-1-0.800-0.90650.557-0.057-0.0570.0000.0000.0000.000
188A1046VAL0-0.053-0.03748.763-0.001-0.0010.0000.0000.0000.000
189A1047HIS00.0080.01445.2250.0000.0000.0000.0000.0000.000
190A1048ASN00.0890.05344.153-0.004-0.0040.0000.0000.0000.000
191A1049ALA00.055-0.00640.004-0.002-0.0020.0000.0000.0000.000
192A1050GLU-1-0.807-0.87739.317-0.111-0.1110.0000.0000.0000.000
193A1051PHE00.0250.01839.820-0.005-0.0050.0000.0000.0000.000
194A1052VAL0-0.042-0.02235.899-0.003-0.0030.0000.0000.0000.000
195A1053LEU0-0.059-0.02534.930-0.008-0.0080.0000.0000.0000.000
196A1054THR00.046-0.00134.991-0.009-0.0090.0000.0000.0000.000
197A1055GLY00.0300.04536.416-0.003-0.0030.0000.0000.0000.000
198A1056VAL00.006-0.01231.162-0.004-0.0040.0000.0000.0000.000
199A1057LEU0-0.047-0.00630.833-0.010-0.0100.0000.0000.0000.000
200A1058THR00.0070.01532.177-0.006-0.0060.0000.0000.0000.000
201A1059GLN0-0.017-0.02431.1950.0070.0070.0000.0000.0000.000
202A1060THR0-0.057-0.03434.5430.0070.0070.0000.0000.0000.000
203A1061LEU0-0.017-0.01338.337-0.001-0.0010.0000.0000.0000.000
204A1062ASP-1-0.760-0.81941.116-0.076-0.0760.0000.0000.0000.000
205A1063TYR0-0.111-0.11043.894-0.001-0.0010.0000.0000.0000.000
206A1064GLU-1-0.904-0.96646.898-0.057-0.0570.0000.0000.0000.000
207A1065SER0-0.054-0.07145.2740.0030.0030.0000.0000.0000.000
208A1066TYR0-0.030-0.02741.9390.0000.0000.0000.0000.0000.000
209A1067LYS10.9010.97646.6510.0570.0570.0000.0000.0000.000
210A1068PHE0-0.028-0.02247.8810.0010.0010.0000.0000.0000.000
211A1069ASN0-0.051-0.01151.9540.0030.0030.0000.0000.0000.000