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: X6Y5Z

Calculation Name: 1D1Z-A-Xray18

Preferred Name: SH2 domain-containing protein 1A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1D1Z

Chain ID: A

ChEMBL ID: CHEMBL2321636

UniProt ID: O60880

Base Structure: X-ray

Registration Date: 2018-06-04

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1027316.252564
FMO2-HF: Nuclear repulsion 979209.570034
FMO2-HF: Total energy -48106.68253
FMO2-MP2: Total energy -48244.777999


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:1003:ACE)


Summations of interaction energy for fragment #1(A:1003:ACE)
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.
4.7214.8640.5320.495-1.171-0.005
Interaction energy analysis for fragmet #1(A:1003:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.034
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].
3A1005ALA00.0700.0433.9010.6711.245-0.007-0.200-0.3660.000
4A1006VAL00.0080.0116.3920.2080.2080.0000.0000.0000.000
5A1007TYR0-0.114-0.0794.2560.0840.171-0.001-0.013-0.0730.000
6A1008HIS0-0.0080.0036.6400.2140.2140.0000.0000.0000.000
7A1009GLY00.0440.0328.203-0.021-0.0210.0000.0000.0000.000
8A1010LYS10.8730.9309.486-0.065-0.0650.0000.0000.0000.000
9A1011ILE00.0070.03112.6590.0090.0090.0000.0000.0000.000
10A1012SER00.0400.00914.821-0.028-0.0280.0000.0000.0000.000
11A1013ARG10.9610.96317.3370.0580.0580.0000.0000.0000.000
12A1014GLU-1-0.914-0.95718.907-0.037-0.0370.0000.0000.0000.000
13A1015THR00.0400.02917.2090.0030.0030.0000.0000.0000.000
14A1016GLY00.0560.02816.371-0.005-0.0050.0000.0000.0000.000
15A1017GLU-1-0.860-0.92917.006-0.115-0.1150.0000.0000.0000.000
16A1018LYS10.8960.96720.1960.0310.0310.0000.0000.0000.000
17A1019LEU00.0180.02115.0320.0030.0030.0000.0000.0000.000
18A1020LEU00.009-0.00416.341-0.003-0.0030.0000.0000.0000.000
19A1021LEU00.0060.01119.5200.0010.0010.0000.0000.0000.000
20A1022ALA0-0.0300.00221.9390.0060.0060.0000.0000.0000.000
21A1023THR0-0.066-0.02919.0380.0000.0000.0000.0000.0000.000
22A1024GLY00.0240.02222.3970.0030.0030.0000.0000.0000.000
23A1025LEU0-0.027-0.01421.3300.0060.0060.0000.0000.0000.000
24A1026ASP-1-0.762-0.86422.523-0.118-0.1180.0000.0000.0000.000
25A1027GLY00.034-0.00220.924-0.001-0.0010.0000.0000.0000.000
26A1028SER00.0270.02018.315-0.035-0.0350.0000.0000.0000.000
27A1029TYR0-0.0060.02112.0480.0140.0140.0000.0000.0000.000
28A1030LEU00.0270.01911.951-0.023-0.0230.0000.0000.0000.000
29A1031LEU0-0.063-0.0257.617-0.016-0.0160.0000.0000.0000.000
30A1032ARG10.8120.8689.8870.1320.1320.0000.0000.0000.000
31A1033ASP-1-0.719-0.81710.299-0.092-0.0920.0000.0000.0000.000
32A1034SER0-0.065-0.02712.5160.0180.0180.0000.0000.0000.000
33A1035GLU-1-0.705-0.84015.938-0.021-0.0210.0000.0000.0000.000
34A1036SER0-0.0300.00118.6730.0150.0150.0000.0000.0000.000
35A1037VAL0-0.019-0.00418.6030.0090.0090.0000.0000.0000.000
36A1038PRO00.0530.02816.385-0.017-0.0170.0000.0000.0000.000
37A1039GLY00.0520.04613.3550.0020.0020.0000.0000.0000.000
38A1040VAL0-0.0080.03613.328-0.041-0.0410.0000.0000.0000.000
39A1041TYR0-0.0070.0248.305-0.024-0.0240.0000.0000.0000.000
40A1042CYS0-0.018-0.00312.7430.0240.0240.0000.0000.0000.000
41A1043LEU0-0.0100.00213.019-0.042-0.0420.0000.0000.0000.000
42A1044CYS0-0.0270.00414.5760.0560.0560.0000.0000.0000.000
43A1045VAL00.0410.00316.435-0.027-0.0270.0000.0000.0000.000
44A1046LEU0-0.0070.02119.0620.0210.0210.0000.0000.0000.000
45A1047TYR0-0.054-0.08621.933-0.004-0.0040.0000.0000.0000.000
46A1048HIS10.8830.92625.2430.0970.0970.0000.0000.0000.000
47A1049GLY00.0680.04327.1710.0060.0060.0000.0000.0000.000
48A1050TYR0-0.047-0.00826.2900.0060.0060.0000.0000.0000.000
49A1051ILE00.0400.01120.121-0.012-0.0120.0000.0000.0000.000
50A1052TYR0-0.048-0.02521.7680.0130.0130.0000.0000.0000.000
51A1053THR00.016-0.01417.924-0.027-0.0270.0000.0000.0000.000
52A1054TYR00.0090.01317.7890.0170.0170.0000.0000.0000.000
53A1055ARG10.9100.94316.6830.0910.0910.0000.0000.0000.000
54A1056VAL0-0.023-0.01711.996-0.011-0.0110.0000.0000.0000.000
55A1057SER0-0.0030.00113.7490.0150.0150.0000.0000.0000.000
56A1058GLN0-0.004-0.0269.953-0.063-0.0630.0000.0000.0000.000
57A1059THR0-0.036-0.02413.6030.0430.0430.0000.0000.0000.000
58A1060GLU-1-0.809-0.91215.527-0.081-0.0810.0000.0000.0000.000
59A1061THR0-0.039-0.02716.8460.0180.0180.0000.0000.0000.000
60A1062GLY0-0.0350.00313.1100.0070.0070.0000.0000.0000.000
61A1063SER0-0.091-0.03912.380-0.061-0.0610.0000.0000.0000.000
62A1064TRP00.0290.0188.032-0.086-0.0860.0000.0000.0000.000
63A1065SER00.008-0.02313.6800.0180.0180.0000.0000.0000.000
64A1066ALA00.010-0.00815.918-0.019-0.0190.0000.0000.0000.000
65A1067GLU-1-0.885-0.93317.594-0.118-0.1180.0000.0000.0000.000
66A1068THR0-0.0310.03320.645-0.011-0.0110.0000.0000.0000.000
67A1069ALA0-0.0030.00522.8290.0110.0110.0000.0000.0000.000
68A1070PRO00.0610.01626.527-0.003-0.0030.0000.0000.0000.000
69A1071GLY0-0.015-0.00528.9370.0010.0010.0000.0000.0000.000
70A1072VAL0-0.058-0.01224.3800.0020.0020.0000.0000.0000.000
71A1073HIS0-0.038-0.02124.2320.0040.0040.0000.0000.0000.000
72A1074LYS10.8670.94020.3140.1430.1430.0000.0000.0000.000
73A1075ARG10.8220.89719.6370.2260.2260.0000.0000.0000.000
74A1076TYR00.0530.02417.449-0.021-0.0210.0000.0000.0000.000
75A1077PHE0-0.033-0.01913.570-0.003-0.0030.0000.0000.0000.000
76A1078ARG10.9940.98513.1970.2140.2140.0000.0000.0000.000
77A1079LYS10.9180.9577.0090.4020.4020.0000.0000.0000.000
78A1080ILE00.1440.0886.0190.0180.0180.0000.0000.0000.000
79A1081LYS10.9850.9916.9500.6490.6490.0000.0000.0000.000
80A1082ASN0-0.021-0.0148.5960.1470.1470.0000.0000.0000.000
81A1083LEU00.0440.05611.6890.0760.0760.0000.0000.0000.000
82A1084ILE00.0300.0129.3340.0740.0740.0000.0000.0000.000
83A1085SER00.0260.02512.2550.1090.1090.0000.0000.0000.000
84A1086ALA0-0.050-0.01114.2510.0660.0660.0000.0000.0000.000
85A1087PHE00.0410.01615.7150.0470.0470.0000.0000.0000.000
86A1088GLN00.0510.05714.026-0.048-0.0480.0000.0000.0000.000
87A1089LYS10.9070.97018.2500.2540.2540.0000.0000.0000.000
88A1090PRO00.0640.02421.405-0.006-0.0060.0000.0000.0000.000
89A1091ASP-1-0.851-0.92424.428-0.128-0.1280.0000.0000.0000.000
90A1092GLN0-0.0140.02820.458-0.014-0.0140.0000.0000.0000.000
91A1093GLY00.1100.05422.541-0.008-0.0080.0000.0000.0000.000
92A1094ILE0-0.028-0.01018.7760.0010.0010.0000.0000.0000.000
93A1095VAL00.0070.00622.8820.0080.0080.0000.0000.0000.000
94A1096ILE0-0.025-0.00722.2190.0140.0140.0000.0000.0000.000
95A1097PRO0-0.044-0.00920.819-0.018-0.0180.0000.0000.0000.000
96A1098LEU0-0.014-0.00814.3140.0060.0060.0000.0000.0000.000
97A1099GLN0-0.035-0.02117.9580.0040.0040.0000.0000.0000.000
98A1100TYR0-0.0130.01117.682-0.001-0.0010.0000.0000.0000.000
99A1101PRO00.0070.01612.2150.0010.0010.0000.0000.0000.000
100A1102VAL00.0530.01813.6130.0470.0470.0000.0000.0000.000
101A1103GLU-1-0.874-0.91410.277-0.421-0.4210.0000.0000.0000.000
102A1104LYS00.0590.04610.5120.0380.0380.0000.0000.0000.000
103A5001SO4-2-1.604-1.70518.671-0.210-0.2100.0000.0000.0000.000
104A6002HOH00.001-0.01619.252-0.004-0.0040.0000.0000.0000.000
105A6003HOH0-0.015-0.01811.6840.0030.0030.0000.0000.0000.000
106A6007HOH0-0.008-0.01820.1180.0050.0050.0000.0000.0000.000
107A6010HOH0-0.012-0.01718.219-0.013-0.0130.0000.0000.0000.000
108A6012HOH00.0160.01628.874-0.002-0.0020.0000.0000.0000.000
109A6013HOH0-0.041-0.03822.7670.0000.0000.0000.0000.0000.000
110A6015HOH00.0220.00522.3560.0030.0030.0000.0000.0000.000
111A6027HOH0-0.023-0.02117.9450.0030.0030.0000.0000.0000.000
112A6028HOH0-0.015-0.0139.879-0.020-0.0200.0000.0000.0000.000
113A6032HOH00.0110.00220.890-0.008-0.0080.0000.0000.0000.000
114A6035HOH00.0020.01022.853-0.004-0.0040.0000.0000.0000.000
115A6044HOH0-0.030-0.02119.6940.0040.0040.0000.0000.0000.000
116A6047HOH0-0.038-0.02520.7010.0050.0050.0000.0000.0000.000
117A6049HOH0-0.0010.00010.491-0.044-0.0440.0000.0000.0000.000
118A6051HOH0-0.039-0.02723.8220.0020.0020.0000.0000.0000.000
119A6059HOH00.0220.02025.747-0.004-0.0040.0000.0000.0000.000
120A6062HOH00.0300.03519.940-0.002-0.0020.0000.0000.0000.000
121A6063HOH00.0180.01734.343-0.001-0.0010.0000.0000.0000.000
122A6070HOH00.0070.00721.220-0.002-0.0020.0000.0000.0000.000
123A6073HOH0-0.038-0.02216.4320.0020.0020.0000.0000.0000.000
124A6080HOH00.0050.00621.063-0.003-0.0030.0000.0000.0000.000
125A6087HOH00.0570.03314.9610.0040.0040.0000.0000.0000.000
126A6093HOH0-0.036-0.02615.268-0.006-0.0060.0000.0000.0000.000
127A6095HOH00.0400.03519.541-0.008-0.0080.0000.0000.0000.000
128A6101HOH00.0060.01730.440-0.002-0.0020.0000.0000.0000.000
129A6105HOH0-0.061-0.04727.9540.0010.0010.0000.0000.0000.000
130A6109HOH0-0.010-0.01521.174-0.002-0.0020.0000.0000.0000.000
131A6114HOH0-0.037-0.02720.9370.0020.0020.0000.0000.0000.000
132A6118HOH0-0.006-0.01426.595-0.001-0.0010.0000.0000.0000.000
133A6125HOH00.0240.01721.8540.0010.0010.0000.0000.0000.000
134A6126HOH0-0.004-0.01119.701-0.007-0.0070.0000.0000.0000.000
135A6128HOH0-0.059-0.04619.5850.0080.0080.0000.0000.0000.000
136A6146HOH0-0.019-0.0138.0590.0620.0620.0000.0000.0000.000
137A6152HOH0-0.008-0.01125.4720.0040.0040.0000.0000.0000.000
138A6153HOH0-0.038-0.02815.1670.0000.0000.0000.0000.0000.000
139A6164HOH00.0140.01716.0620.0020.0020.0000.0000.0000.000
140A6171HOH0-0.035-0.03811.0010.0300.0300.0000.0000.0000.000
141A6173HOH0-0.0050.00727.488-0.002-0.0020.0000.0000.0000.000
142A6174HOH0-0.028-0.01724.667-0.004-0.0040.0000.0000.0000.000
143A6177HOH0-0.004-0.01027.3530.0010.0010.0000.0000.0000.000
144A6191HOH00.0560.05315.789-0.009-0.0090.0000.0000.0000.000
145A6196HOH00.0120.01120.1820.0000.0000.0000.0000.0000.000
146A6197HOH0-0.055-0.04822.9300.0020.0020.0000.0000.0000.000
147A6199HOH00.0080.01111.4050.0220.0220.0000.0000.0000.000
148A6200HOH00.0080.01523.6840.0030.0030.0000.0000.0000.000
149A6204HOH0-0.030-0.02618.3470.0070.0070.0000.0000.0000.000
150A6205HOH0-0.039-0.03022.0380.0040.0040.0000.0000.0000.000
151A6207HOH0-0.024-0.02131.1150.0020.0020.0000.0000.0000.000
152A6213HOH0-0.006-0.01416.2340.0080.0080.0000.0000.0000.000
153A6226HOH0-0.007-0.02813.667-0.018-0.0180.0000.0000.0000.000
154A6228HOH0-0.043-0.04113.7570.0140.0140.0000.0000.0000.000
155A6230HOH0-0.056-0.04011.388-0.012-0.0120.0000.0000.0000.000
156A6236HOH0-0.012-0.03014.4370.0220.0220.0000.0000.0000.000
157A6240HOH00.0120.00524.752-0.003-0.0030.0000.0000.0000.000
158A6241HOH0-0.034-0.02818.6550.0020.0020.0000.0000.0000.000
159A6243HOH00.0240.00915.784-0.002-0.0020.0000.0000.0000.000
160A6248HOH0-0.042-0.04212.472-0.003-0.0030.0000.0000.0000.000
161A6250HOH0-0.047-0.0334.7340.2340.258-0.001-0.003-0.0210.000
162A6252HOH00.0200.00929.6520.0020.0020.0000.0000.0000.000
163A6257HOH00.0260.0176.284-0.188-0.1880.0000.0000.0000.000
164A6258HOH0-0.003-0.04521.3050.0000.0000.0000.0000.0000.000
165A6259HOH0-0.047-0.0307.7090.0720.0720.0000.0000.0000.000
166A6265HOH0-0.045-0.03328.5090.0010.0010.0000.0000.0000.000
167A6267HOH00.0180.01618.7920.0110.0110.0000.0000.0000.000
168A6270HOH0-0.0030.0007.574-0.043-0.0430.0000.0000.0000.000
169A6276HOH0-0.027-0.03010.781-0.060-0.0600.0000.0000.0000.000
170A6278HOH0-0.025-0.02313.2560.0130.0130.0000.0000.0000.000
171A6300HOH0-0.008-0.01220.358-0.005-0.0050.0000.0000.0000.000
172A6306HOH0-0.014-0.01625.1790.0010.0010.0000.0000.0000.000
173A6318HOH0-0.030-0.01923.9210.0030.0030.0000.0000.0000.000
174A6326HOH0-0.042-0.03326.120-0.001-0.0010.0000.0000.0000.000
175A6336HOH00.0250.01318.078-0.002-0.0020.0000.0000.0000.000
176A6353HOH0-0.018-0.02025.404-0.001-0.0010.0000.0000.0000.000
177A6356HOH00.000-0.00914.0660.0210.0210.0000.0000.0000.000
178A6360HOH00.0250.02525.932-0.002-0.0020.0000.0000.0000.000
179A6369HOH00.006-0.00717.503-0.007-0.0070.0000.0000.0000.000
180A6384HOH00.0340.02326.079-0.005-0.0050.0000.0000.0000.000
181A6403HOH0-0.049-0.02712.4440.0040.0040.0000.0000.0000.000
182A6406HOH0-0.048-0.03123.5100.0010.0010.0000.0000.0000.000
183A6413HOH0-0.021-0.00615.4920.0040.0040.0000.0000.0000.000
184A6432HOH0-0.049-0.03611.9650.0220.0220.0000.0000.0000.000
185A6437HOH0-0.010-0.01618.7380.0000.0000.0000.0000.0000.000
186A6441HOH0-0.012-0.0139.7870.0230.0230.0000.0000.0000.000
187A6451HOH0-0.018-0.03519.5510.0010.0010.0000.0000.0000.000
188A6464HOH00.005-0.00322.2540.0070.0070.0000.0000.0000.000
189A6467HOH0-0.040-0.01829.7610.0020.0020.0000.0000.0000.000
190A6468HOH00.0530.03720.2340.0030.0030.0000.0000.0000.000
191A6488HOH00.0420.08130.4790.0000.0000.0000.0000.0000.000
192A6489HOH00.0350.03327.0300.0010.0010.0000.0000.0000.000
193A6498HOH0-0.063-0.04728.743-0.001-0.0010.0000.0000.0000.000
194A6500HOH00.0240.01124.6260.0010.0010.0000.0000.0000.000
195A6506HOH00.0200.00615.904-0.005-0.0050.0000.0000.0000.000
196A6510HOH00.0410.02526.687-0.004-0.0040.0000.0000.0000.000
197A6525HOH00.0040.00212.4820.0020.0020.0000.0000.0000.000
198A6528HOH0-0.025-0.0422.9012.2201.6780.5410.711-0.711-0.005
199A6531HOH0-0.048-0.04713.8150.0170.0170.0000.0000.0000.000
200A6557HOH0-0.084-0.08720.6230.0010.0010.0000.0000.0000.000
201A6559HOH0-0.052-0.03426.9650.0020.0020.0000.0000.0000.000
202A6578HOH0-0.012-0.01229.704-0.003-0.0030.0000.0000.0000.000
203A6600HOH00.002-0.0167.834-0.040-0.0400.0000.0000.0000.000
204A6612HOH00.0220.01426.208-0.002-0.0020.0000.0000.0000.000
205B6029HOH0-0.002-0.00518.242-0.001-0.0010.0000.0000.0000.000
206B6120HOH00.0330.03421.762-0.001-0.0010.0000.0000.0000.000
207B6148HOH0-0.046-0.02616.6050.0050.0050.0000.0000.0000.000