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: PLN59

Calculation Name: 2VIF-A-Xray26

Preferred Name: Stem cell growth factor receptor

Target Type: SINGLE PROTEIN

Ligand Name: o-phosphotyrosine

ligand 3-letter code: PTR

PDB ID: 2VIF

Chain ID: A

ChEMBL ID: CHEMBL1936

UniProt ID: P10721

Base Structure: X-ray

Registration Date: 2018-07-26

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 225
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1404640.037264
FMO2-HF: Nuclear repulsion 1345299.845239
FMO2-HF: Total energy -59340.192025
FMO2-MP2: Total energy -59511.828318


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:-1:SER)


Summations of interaction energy for fragment #1(A:-1: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.
-1.421-0.023-0.025-0.649-0.7230.001
Interaction energy analysis for fragmet #1(A:-1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.022
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].
3A361VAL00.0180.0183.781-2.756-1.358-0.025-0.649-0.7230.001
4A362GLN0-0.007-0.0076.8170.6680.6680.0000.0000.0000.000
5A363SER0-0.003-0.00110.203-0.014-0.0140.0000.0000.0000.000
6A364NME00.0050.00313.176-0.086-0.0860.0000.0000.0000.000
7A370ACE00.0510.01626.8900.0030.0030.0000.0000.0000.000
8A371SER00.014-0.00627.681-0.014-0.0140.0000.0000.0000.000
9A372LEU00.1110.07226.0260.0120.0120.0000.0000.0000.000
10A373THR00.0110.00228.7670.0060.0060.0000.0000.0000.000
11A374GLU-1-0.841-0.91831.895-0.047-0.0470.0000.0000.0000.000
12A375GLU-1-0.753-0.85329.436-0.018-0.0180.0000.0000.0000.000
13A376LEU00.0400.01030.5120.0070.0070.0000.0000.0000.000
14A377LYS10.9000.97233.9930.0650.0650.0000.0000.0000.000
15A378LYS10.9721.00434.3240.0130.0130.0000.0000.0000.000
16A379LEU00.0480.00233.2440.0040.0040.0000.0000.0000.000
17A380ALA0-0.0030.01137.3940.0020.0020.0000.0000.0000.000
18A381LYS10.9270.96339.4420.0230.0230.0000.0000.0000.000
19A382GLN0-0.025-0.02740.3650.0040.0040.0000.0000.0000.000
20A383GLY00.0100.02041.1500.0020.0020.0000.0000.0000.000
21A384TRP00.0380.02433.935-0.002-0.0020.0000.0000.0000.000
22A385TYR0-0.064-0.05533.8120.0010.0010.0000.0000.0000.000
23A386TRP0-0.001-0.02937.176-0.002-0.0020.0000.0000.0000.000
24A387GLY00.0080.02736.322-0.001-0.0010.0000.0000.0000.000
25A388PRO00.0500.03636.7450.0010.0010.0000.0000.0000.000
26A389ILE0-0.026-0.00237.7930.0030.0030.0000.0000.0000.000
27A390THR00.0260.03037.242-0.001-0.0010.0000.0000.0000.000
28A391ARG10.8660.91435.8090.0420.0420.0000.0000.0000.000
29A392TRP00.0790.03437.7280.0040.0040.0000.0000.0000.000
30A393GLU-1-0.802-0.85841.320-0.041-0.0410.0000.0000.0000.000
31A394ALA00.0070.00238.7490.0040.0040.0000.0000.0000.000
32A395GLU-1-0.829-0.90939.542-0.022-0.0220.0000.0000.0000.000
33A396GLY00.0340.03442.2640.0040.0040.0000.0000.0000.000
34A397LYS10.8960.94742.8880.0290.0290.0000.0000.0000.000
35A398LEU00.0100.01539.3610.0030.0030.0000.0000.0000.000
36A399ALA0-0.033-0.00243.9320.0030.0030.0000.0000.0000.000
37A400ASN0-0.061-0.02946.7650.0030.0030.0000.0000.0000.000
38A401VAL0-0.0080.01143.9130.0000.0000.0000.0000.0000.000
39A402PRO00.0020.00345.8770.0000.0000.0000.0000.0000.000
40A403ASP-1-0.740-0.82742.7040.0130.0130.0000.0000.0000.000
41A404GLY00.0530.03039.6410.0030.0030.0000.0000.0000.000
42A405SER0-0.010-0.00139.4360.0010.0010.0000.0000.0000.000
43A406PHE0-0.010-0.00735.908-0.003-0.0030.0000.0000.0000.000
44A407LEU0-0.0080.00136.6630.0000.0000.0000.0000.0000.000
45A408VAL00.0400.02231.8750.0000.0000.0000.0000.0000.000
46A409ARG10.8360.92033.4420.0460.0460.0000.0000.0000.000
47A410ASP-1-0.718-0.82132.164-0.075-0.0750.0000.0000.0000.000
48A411SER0-0.054-0.01728.9390.0100.0100.0000.0000.0000.000
49A412SER00.0260.01231.324-0.003-0.0030.0000.0000.0000.000
50A413ASP-1-0.852-0.88927.045-0.124-0.1240.0000.0000.0000.000
51A414ASP-1-0.800-0.91327.439-0.141-0.1410.0000.0000.0000.000
52A415ARG10.8310.92722.9270.1270.1270.0000.0000.0000.000
53A416TYR0-0.043-0.00921.373-0.007-0.0070.0000.0000.0000.000
54A417LEU00.0600.03925.0310.0030.0030.0000.0000.0000.000
55A418LEU00.0160.01427.2690.0110.0110.0000.0000.0000.000
56A419SER0-0.056-0.04828.117-0.003-0.0030.0000.0000.0000.000
57A420LEU00.0180.02630.5780.0010.0010.0000.0000.0000.000
58A421SER0-0.023-0.03732.321-0.003-0.0030.0000.0000.0000.000
59A422PHE00.0350.00432.5930.0030.0030.0000.0000.0000.000
60A423ARG10.9371.00437.3890.0000.0000.0000.0000.0000.000
61A424SER00.0460.01938.8160.0050.0050.0000.0000.0000.000
62A425HIS0-0.017-0.01340.772-0.001-0.0010.0000.0000.0000.000
63A426GLY0-0.014-0.01243.401-0.001-0.0010.0000.0000.0000.000
64A427LYS10.8740.95339.813-0.012-0.0120.0000.0000.0000.000
65A428THR0-0.031-0.05038.6020.0030.0030.0000.0000.0000.000
66A429LEU0-0.060-0.01634.891-0.003-0.0030.0000.0000.0000.000
67A430HIS00.007-0.00533.303-0.002-0.0020.0000.0000.0000.000
68A431THR0-0.0330.00027.611-0.002-0.0020.0000.0000.0000.000
69A432ARG10.9350.98926.0690.0740.0740.0000.0000.0000.000
70A433ILE00.0120.01224.8870.0110.0110.0000.0000.0000.000
71A434GLU-1-0.782-0.86619.673-0.156-0.1560.0000.0000.0000.000
72A435HIS0-0.051-0.03221.1720.0150.0150.0000.0000.0000.000
73A436SER00.0090.00216.186-0.045-0.0450.0000.0000.0000.000
74A437ASN00.023-0.00312.875-0.005-0.0050.0000.0000.0000.000
75A438GLY00.0060.00916.7440.0360.0360.0000.0000.0000.000
76A439ARG10.8530.92117.554-0.045-0.0450.0000.0000.0000.000
77A440PHE0-0.031-0.01620.445-0.034-0.0340.0000.0000.0000.000
78A441SER00.0690.03920.2070.0200.0200.0000.0000.0000.000
79A442PHE0-0.037-0.01122.201-0.024-0.0240.0000.0000.0000.000
80A443TYR0-0.018-0.01721.7230.0030.0030.0000.0000.0000.000
81A444GLU-1-0.922-0.96920.231-0.059-0.0590.0000.0000.0000.000
82A445GLN00.0010.02619.7860.0250.0250.0000.0000.0000.000
83A446PRO00.0200.00514.940-0.008-0.0080.0000.0000.0000.000
84A447ASP-1-0.859-0.90911.6840.3840.3840.0000.0000.0000.000
85A448VAL0-0.0440.00414.1970.0450.0450.0000.0000.0000.000
86A449GLU-1-0.940-0.97815.8960.3410.3410.0000.0000.0000.000
87A450GLY00.0000.00917.355-0.047-0.0470.0000.0000.0000.000
88A451HIS00.0420.04920.0690.0210.0210.0000.0000.0000.000
89A452THR00.0500.00522.252-0.017-0.0170.0000.0000.0000.000
90A453SER0-0.127-0.07423.971-0.019-0.0190.0000.0000.0000.000
91A454ILE00.0360.01926.8650.0080.0080.0000.0000.0000.000
92A455VAL0-0.028-0.03028.6170.0070.0070.0000.0000.0000.000
93A456ASP-1-0.816-0.85927.2200.0440.0440.0000.0000.0000.000
94A457LEU0-0.0090.01824.5970.0110.0110.0000.0000.0000.000
95A458ILE0-0.020-0.02827.3800.0070.0070.0000.0000.0000.000
96A459GLU-1-0.822-0.87430.9490.0510.0510.0000.0000.0000.000
97A460HIS00.0160.01826.4380.0020.0020.0000.0000.0000.000
98A461SER0-0.020-0.01929.1460.0070.0070.0000.0000.0000.000
99A462ILE0-0.039-0.01330.7170.0000.0000.0000.0000.0000.000
100A463GLY00.0800.05433.0170.0010.0010.0000.0000.0000.000
101A464ASP-1-0.757-0.85728.6070.1130.1130.0000.0000.0000.000
102A465SER0-0.100-0.05032.124-0.001-0.0010.0000.0000.0000.000
103A466GLU-1-0.903-0.93435.2300.0490.0490.0000.0000.0000.000
104A467ASN0-0.023-0.00233.013-0.001-0.0010.0000.0000.0000.000
105A468GLY0-0.051-0.00335.7360.0030.0030.0000.0000.0000.000
106A469ALA0-0.013-0.00230.1620.0030.0030.0000.0000.0000.000
107A470PHE0-0.0020.02329.9640.0010.0010.0000.0000.0000.000
108A471CYS0-0.031-0.03430.621-0.005-0.0050.0000.0000.0000.000
109A472TYR0-0.033-0.01929.974-0.002-0.0020.0000.0000.0000.000
110A473SER00.0210.00727.9010.0040.0040.0000.0000.0000.000
111A474ARG10.9050.94130.452-0.018-0.0180.0000.0000.0000.000
112A475SER00.0010.00328.552-0.011-0.0110.0000.0000.0000.000
113A476ARG10.9590.98422.688-0.022-0.0220.0000.0000.0000.000
114A477LEU00.0220.04124.1910.0100.0100.0000.0000.0000.000
115A478PRO00.0580.03823.2960.0070.0070.0000.0000.0000.000
116A479GLY00.0380.01225.805-0.006-0.0060.0000.0000.0000.000
117A480SER0-0.069-0.03328.311-0.009-0.0090.0000.0000.0000.000
118A481ALA00.0080.01330.2690.0100.0100.0000.0000.0000.000
119A482THR00.0190.01429.441-0.007-0.0070.0000.0000.0000.000
120A483TYR0-0.013-0.01732.537-0.001-0.0010.0000.0000.0000.000
121A484PRO00.0690.04934.519-0.001-0.0010.0000.0000.0000.000
122A485VAL0-0.057-0.03235.194-0.008-0.0080.0000.0000.0000.000
123A486ARG11.0061.00836.263-0.030-0.0300.0000.0000.0000.000
124A487LEU0-0.032-0.00533.377-0.006-0.0060.0000.0000.0000.000
125A488THR0-0.149-0.10237.8660.0020.0020.0000.0000.0000.000
126A489ASN00.0650.04139.7880.0040.0040.0000.0000.0000.000
127A490PRO00.0160.02538.478-0.002-0.0020.0000.0000.0000.000
128A491VAL00.000-0.00540.1590.0000.0000.0000.0000.0000.000
129A492SER0-0.009-0.02441.717-0.005-0.0050.0000.0000.0000.000
130A493ARG10.9040.95941.6940.0320.0320.0000.0000.0000.000
131A494PHE0-0.084-0.03644.495-0.002-0.0020.0000.0000.0000.000
132A495MET00.0270.01047.9490.0010.0010.0000.0000.0000.000
133A496GLN00.001-0.00751.1720.0030.0030.0000.0000.0000.000
134A497NME00.0080.02250.275-0.001-0.0010.0000.0000.0000.000
135A1497EDO0-0.022-0.02532.2930.0000.0000.0000.0000.0000.000
136A2005HOH0-0.023-0.01530.8180.0020.0020.0000.0000.0000.000
137A2006HOH0-0.013-0.00834.3200.0000.0000.0000.0000.0000.000
138A2007HOH0-0.071-0.05436.2920.0020.0020.0000.0000.0000.000
139A2008HOH0-0.034-0.03427.425-0.005-0.0050.0000.0000.0000.000
140A2010HOH0-0.036-0.02640.1090.0010.0010.0000.0000.0000.000
141A2011HOH0-0.010-0.00540.4180.0010.0010.0000.0000.0000.000
142A2012HOH0-0.033-0.02239.3010.0000.0000.0000.0000.0000.000
143A2013HOH0-0.035-0.02541.3670.0010.0010.0000.0000.0000.000
144A2014HOH0-0.009-0.01735.316-0.001-0.0010.0000.0000.0000.000
145A2015HOH0-0.011-0.02041.7800.0000.0000.0000.0000.0000.000
146A2016HOH0-0.040-0.03944.3720.0000.0000.0000.0000.0000.000
147A2017HOH0-0.058-0.05940.878-0.001-0.0010.0000.0000.0000.000
148A2019HOH0-0.010-0.01447.0200.0000.0000.0000.0000.0000.000
149A2020HOH0-0.060-0.06343.5420.0010.0010.0000.0000.0000.000
150A2021HOH0-0.049-0.04445.7930.0010.0010.0000.0000.0000.000
151A2022HOH00.0270.01947.3250.0000.0000.0000.0000.0000.000
152A2023HOH00.028-0.02044.2470.0000.0000.0000.0000.0000.000
153A2024HOH0-0.042-0.03135.3570.0010.0010.0000.0000.0000.000
154A2025HOH0-0.029-0.01730.649-0.001-0.0010.0000.0000.0000.000
155A2026HOH0-0.017-0.01233.0000.0020.0020.0000.0000.0000.000
156A2027HOH0-0.022-0.02636.2350.0020.0020.0000.0000.0000.000
157A2028HOH0-0.030-0.02533.1840.0030.0030.0000.0000.0000.000
158A2029HOH0-0.044-0.02829.9860.0040.0040.0000.0000.0000.000
159A2030HOH0-0.048-0.02328.268-0.001-0.0010.0000.0000.0000.000
160A2031HOH00.0380.02129.6020.0030.0030.0000.0000.0000.000
161A2032HOH0-0.040-0.03520.207-0.007-0.0070.0000.0000.0000.000
162A2033HOH0-0.040-0.02721.023-0.002-0.0020.0000.0000.0000.000
163A2034HOH0-0.004-0.02224.5850.0000.0000.0000.0000.0000.000
164A2035HOH0-0.025-0.02130.557-0.001-0.0010.0000.0000.0000.000
165A2038HOH00.0310.02643.8790.0010.0010.0000.0000.0000.000
166A2039HOH00.0130.01340.7030.0010.0010.0000.0000.0000.000
167A2040HOH0-0.013-0.01124.8720.0050.0050.0000.0000.0000.000
168A2043HOH0-0.029-0.02418.2620.0110.0110.0000.0000.0000.000
169A2044HOH0-0.009-0.01523.4180.0090.0090.0000.0000.0000.000
170A2045HOH00.0070.00623.711-0.008-0.0080.0000.0000.0000.000
171A2046HOH00.0090.01021.1840.0050.0050.0000.0000.0000.000
172A2047HOH00.0350.03016.6810.0170.0170.0000.0000.0000.000
173A2048HOH0-0.011-0.00917.669-0.017-0.0170.0000.0000.0000.000
174A2049HOH0-0.022-0.02427.794-0.004-0.0040.0000.0000.0000.000
175A2050HOH0-0.025-0.04322.806-0.005-0.0050.0000.0000.0000.000
176A2051HOH00.0250.01525.343-0.003-0.0030.0000.0000.0000.000
177A2052HOH0-0.061-0.05012.5430.0480.0480.0000.0000.0000.000
178A2053HOH0-0.035-0.04916.976-0.008-0.0080.0000.0000.0000.000
179A2054HOH00.0350.02712.5860.0110.0110.0000.0000.0000.000
180A2055HOH00.0060.00514.1250.0300.0300.0000.0000.0000.000
181A2056HOH00.0390.02618.612-0.020-0.0200.0000.0000.0000.000
182A2058HOH00.0280.02220.571-0.011-0.0110.0000.0000.0000.000
183A2059HOH0-0.020-0.01421.187-0.002-0.0020.0000.0000.0000.000
184A2061HOH0-0.005-0.00525.6600.0000.0000.0000.0000.0000.000
185A2062HOH0-0.010-0.02625.081-0.001-0.0010.0000.0000.0000.000
186A2063HOH0-0.009-0.01030.2280.0040.0040.0000.0000.0000.000
187A2064HOH0-0.024-0.02828.7990.0060.0060.0000.0000.0000.000
188A2065HOH0-0.057-0.03833.7100.0020.0020.0000.0000.0000.000
189A2066HOH0-0.059-0.05134.4200.0000.0000.0000.0000.0000.000
190A2067HOH0-0.023-0.01229.4910.0000.0000.0000.0000.0000.000
191A2068HOH0-0.026-0.02726.9200.0040.0040.0000.0000.0000.000
192A2070HOH0-0.019-0.01334.6470.0030.0030.0000.0000.0000.000
193A2071HOH0-0.039-0.03227.2640.0060.0060.0000.0000.0000.000
194A2072HOH0-0.039-0.03628.328-0.005-0.0050.0000.0000.0000.000
195A2073HOH0-0.025-0.03130.114-0.003-0.0030.0000.0000.0000.000
196A2074HOH0-0.0040.00237.3850.0000.0000.0000.0000.0000.000
197A2075HOH0-0.035-0.02729.071-0.001-0.0010.0000.0000.0000.000
198A2076HOH0-0.066-0.05935.1350.0030.0030.0000.0000.0000.000
199A2077HOH00.0140.00437.3090.0000.0000.0000.0000.0000.000
200A2078HOH00.0160.01538.839-0.002-0.0020.0000.0000.0000.000
201A2079HOH0-0.022-0.03325.953-0.005-0.0050.0000.0000.0000.000
202A2080HOH0-0.018-0.02027.1660.0030.0030.0000.0000.0000.000
203A2081HOH0-0.039-0.02331.506-0.001-0.0010.0000.0000.0000.000
204A2082HOH0-0.023-0.01821.335-0.005-0.0050.0000.0000.0000.000
205A2083HOH0-0.052-0.04923.2040.0070.0070.0000.0000.0000.000
206A2084HOH00.0380.02925.2670.0060.0060.0000.0000.0000.000
207A2085HOH00.0040.03125.708-0.001-0.0010.0000.0000.0000.000
208A2086HOH00.0140.01025.442-0.004-0.0040.0000.0000.0000.000
209A2087HOH0-0.0050.00132.948-0.003-0.0030.0000.0000.0000.000
210A2088HOH00.0290.01427.6810.0010.0010.0000.0000.0000.000
211A2089HOH0-0.032-0.02530.7750.0030.0030.0000.0000.0000.000
212A2090HOH0-0.048-0.04236.057-0.002-0.0020.0000.0000.0000.000
213A2093HOH00.0390.03637.791-0.002-0.0020.0000.0000.0000.000
214A2094HOH00.004-0.00238.186-0.002-0.0020.0000.0000.0000.000
215A2097HOH0-0.018-0.01744.3210.0010.0010.0000.0000.0000.000
216A2098HOH0-0.056-0.04538.5630.0010.0010.0000.0000.0000.000
217A2101HOH00.000-0.00539.643-0.001-0.0010.0000.0000.0000.000
218A2102HOH0-0.024-0.01539.761-0.001-0.0010.0000.0000.0000.000
219A2103HOH00.0800.08543.9450.0000.0000.0000.0000.0000.000
220A2107HOH0-0.049-0.03442.4650.0000.0000.0000.0000.0000.000
221A2110HOH0-0.061-0.04846.9620.0000.0000.0000.0000.0000.000
222A2111HOH00.0290.03247.2660.0000.0000.0000.0000.0000.000
223A2118HOH00.0110.01134.495-0.002-0.0020.0000.0000.0000.000
224P2009HOH00.0120.00435.5980.0020.0020.0000.0000.0000.000
225P2010HOH00.0250.01328.354-0.003-0.0030.0000.0000.0000.000