FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: Y9K92

Calculation Name: 2F8Y-B-Xray547

Preferred Name: Neurogenic locus notch homolog protein 1

Target Type: SINGLE PROTEIN

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F8Y

Chain ID: B

ChEMBL ID: CHEMBL2146346

UniProt ID: P46531

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 209
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2270727.095415
FMO2-HF: Nuclear repulsion 2189622.731012
FMO2-HF: Total energy -81104.364403
FMO2-MP2: Total energy -81341.039284


3D Structure Molmil
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:1909:ALA)


Summations of interaction energy for fragment #1(A:1909:ALA)
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.
-78.071-76.584-0.01-0.693-0.784-0.002
Interaction energy analysis for fragmet #1(A:1909:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.919
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].
3A1911ILE00.0200.0253.8720.7102.197-0.010-0.693-0.784-0.002
4A1912SER00.0040.0086.1242.4192.4190.0000.0000.0000.000
5A1913ASP-1-0.729-0.8428.560-22.032-22.0320.0000.0000.0000.000
6A1914PHE00.0600.03012.1770.4480.4480.0000.0000.0000.000
7A1915ILE0-0.014-0.0148.8171.0151.0150.0000.0000.0000.000
8A1916TYR0-0.039-0.01410.062-0.002-0.0020.0000.0000.0000.000
9A1917GLN00.0220.02011.7590.6810.6810.0000.0000.0000.000
10A1918GLY00.0160.00414.1581.3171.3170.0000.0000.0000.000
11A1919ALA0-0.046-0.01813.5450.7170.7170.0000.0000.0000.000
12A1920SER0-0.0030.00815.1220.9510.9510.0000.0000.0000.000
13A1921LEU0-0.020-0.01618.653-0.289-0.2890.0000.0000.0000.000
14A1922HIS00.029-0.01020.2990.1560.1560.0000.0000.0000.000
15A1923ASN0-0.083-0.02918.6930.9880.9880.0000.0000.0000.000
16A1924GLN0-0.011-0.01415.653-1.040-1.0400.0000.0000.0000.000
17A1925THR0-0.008-0.00420.0720.1020.1020.0000.0000.0000.000
18A1926ASP-1-0.873-0.93619.493-14.204-14.2040.0000.0000.0000.000
19A1927ARG10.7930.84912.32322.44422.4440.0000.0000.0000.000
20A1928THR0-0.036-0.02816.5070.0990.0990.0000.0000.0000.000
21A1929GLY00.0860.05619.6710.4440.4440.0000.0000.0000.000
22A1930GLU-1-0.855-0.89317.760-16.309-16.3090.0000.0000.0000.000
23A1931THR00.0670.00721.680-0.006-0.0060.0000.0000.0000.000
24A1932ALA00.019-0.00722.075-0.447-0.4470.0000.0000.0000.000
25A1933LEU00.0280.01522.681-0.300-0.3000.0000.0000.0000.000
26A1934HIS00.0460.04821.291-0.243-0.2430.0000.0000.0000.000
27A1935LEU0-0.0180.00016.566-0.659-0.6590.0000.0000.0000.000
28A1936ALA0-0.030-0.02818.600-0.539-0.5390.0000.0000.0000.000
29A1937ALA00.0110.01420.795-0.138-0.1380.0000.0000.0000.000
30A1938ARG10.8550.91014.00017.58317.5830.0000.0000.0000.000
31A1939TYR0-0.038-0.03111.546-0.572-0.5720.0000.0000.0000.000
32A1940SER00.0490.02416.8220.3160.3160.0000.0000.0000.000
33A1941ARG10.8530.93217.86314.75014.7500.0000.0000.0000.000
34A1942SER00.0880.02521.6550.3070.3070.0000.0000.0000.000
35A1943ASP-1-0.843-0.93225.260-10.445-10.4450.0000.0000.0000.000
36A1944ALA0-0.080-0.03023.4560.2560.2560.0000.0000.0000.000
37A1945ALA00.0560.02125.3110.2180.2180.0000.0000.0000.000
38A1946LYS10.8700.94126.81110.23910.2390.0000.0000.0000.000
39A1947ARG10.9921.00424.86411.28811.2880.0000.0000.0000.000
40A1948LEU0-0.069-0.03125.0060.1680.1680.0000.0000.0000.000
41A1949LEU00.0210.01729.5960.1930.1930.0000.0000.0000.000
42A1950GLU-1-0.935-0.97232.313-8.784-8.7840.0000.0000.0000.000
43A1951ALA0-0.095-0.04331.9900.2550.2550.0000.0000.0000.000
44A1952SER0-0.046-0.02434.0790.1220.1220.0000.0000.0000.000
45A1953ALA0-0.045-0.02030.0220.0210.0210.0000.0000.0000.000
46A1954ASP-1-0.849-0.93432.146-9.141-9.1410.0000.0000.0000.000
47A1955ALA0-0.008-0.01030.194-0.375-0.3750.0000.0000.0000.000
48A1956ASN0-0.013-0.01730.008-0.414-0.4140.0000.0000.0000.000
49A1957ILE0-0.0270.00027.824-0.042-0.0420.0000.0000.0000.000
50A1958GLN00.002-0.00127.918-0.208-0.2080.0000.0000.0000.000
51A1959ASP-1-0.785-0.85722.042-13.638-13.6380.0000.0000.0000.000
52A1960ASN0-0.031-0.03621.8150.8120.8120.0000.0000.0000.000
53A1961MET0-0.090-0.04520.867-0.242-0.2420.0000.0000.0000.000
54A1962GLY00.0520.03124.6030.2820.2820.0000.0000.0000.000
55A1963ARG10.8140.88118.84414.99714.9970.0000.0000.0000.000
56A1964THR00.0840.03325.762-0.068-0.0680.0000.0000.0000.000
57A1965PRO0-0.028-0.03424.238-0.483-0.4830.0000.0000.0000.000
58A1966LEU00.0380.03224.677-0.377-0.3770.0000.0000.0000.000
59A1967HIS00.0490.03825.006-0.383-0.3830.0000.0000.0000.000
60A1968ALA0-0.030-0.00520.719-0.467-0.4670.0000.0000.0000.000
61A1969ALA0-0.016-0.01520.843-0.572-0.5720.0000.0000.0000.000
62A1970VAL00.009-0.00122.430-0.299-0.2990.0000.0000.0000.000
63A1971SER0-0.068-0.05019.652-0.215-0.2150.0000.0000.0000.000
64A1972ALA0-0.083-0.03917.812-0.868-0.8680.0000.0000.0000.000
65A1973ASP-1-0.848-0.91918.863-13.290-13.2900.0000.0000.0000.000
66A1974ALA00.0050.03020.4090.2330.2330.0000.0000.0000.000
67A1975GLN00.0640.00221.9930.6340.6340.0000.0000.0000.000
68A1976GLY0-0.027-0.00524.7220.4070.4070.0000.0000.0000.000
69A1977VAL0-0.031-0.01822.8110.4080.4080.0000.0000.0000.000
70A1978PHE00.0350.02625.6970.2620.2620.0000.0000.0000.000
71A1979GLN0-0.030-0.02627.3500.6710.6710.0000.0000.0000.000
72A1980ILE0-0.090-0.04527.5230.3540.3540.0000.0000.0000.000
73A1981LEU0-0.013-0.00626.2580.2870.2870.0000.0000.0000.000
74A1982ILE00.0460.03830.5290.2420.2420.0000.0000.0000.000
75A1983ARG10.8670.95033.1869.1329.1320.0000.0000.0000.000
76A1984ASN0-0.060-0.03133.3420.4560.4560.0000.0000.0000.000
77A1985ARG10.9580.96935.2857.2237.2230.0000.0000.0000.000
78A1986ALA0-0.013-0.00136.3130.1140.1140.0000.0000.0000.000
79A1987THR0-0.043-0.02831.443-0.104-0.1040.0000.0000.0000.000
80A1988ASP-1-0.859-0.93034.162-8.562-8.5620.0000.0000.0000.000
81A1989LEU0-0.023-0.02533.050-0.368-0.3680.0000.0000.0000.000
82A1990ASP-1-0.847-0.91833.533-8.587-8.5870.0000.0000.0000.000
83A1991ALA0-0.0220.00731.457-0.038-0.0380.0000.0000.0000.000
84A1992ARG10.7900.86831.8008.6508.6500.0000.0000.0000.000
85A1993MET0-0.040-0.00624.153-0.250-0.2500.0000.0000.0000.000
86A1994HIS0-0.030-0.02127.4510.5020.5020.0000.0000.0000.000
87A1995ASP-1-0.827-0.89127.599-11.066-11.0660.0000.0000.0000.000
88A1996GLY00.0450.01930.1330.2190.2190.0000.0000.0000.000
89A1997THR0-0.077-0.05726.9480.2600.2600.0000.0000.0000.000
90A1998THR00.0630.03829.909-0.200-0.2000.0000.0000.0000.000
91A1999PRO0-0.011-0.01428.521-0.301-0.3010.0000.0000.0000.000
92A2000LEU00.0510.03329.324-0.248-0.2480.0000.0000.0000.000
93A2001ILE0-0.0030.00329.348-0.101-0.1010.0000.0000.0000.000
94A2002LEU0-0.045-0.02223.428-0.192-0.1920.0000.0000.0000.000
95A2003ALA00.0250.00026.275-0.354-0.3540.0000.0000.0000.000
96A2004ALA0-0.006-0.00128.084-0.072-0.0720.0000.0000.0000.000
97A2005ARG10.8670.93123.74811.88811.8880.0000.0000.0000.000
98A2006LEU0-0.055-0.03121.182-0.356-0.3560.0000.0000.0000.000
99A2007ALA0-0.0380.00323.770-0.365-0.3650.0000.0000.0000.000
100A2008VAL00.0470.03723.708-0.233-0.2330.0000.0000.0000.000
101A2009GLU-1-0.815-0.91926.708-10.550-10.5500.0000.0000.0000.000
102A2010GLY00.0490.02330.0450.2400.2400.0000.0000.0000.000
103A2011MET0-0.081-0.02924.2230.1500.1500.0000.0000.0000.000
104A2012LEU00.0120.01129.9180.2060.2060.0000.0000.0000.000
105A2013GLU-1-0.909-0.96432.253-8.584-8.5840.0000.0000.0000.000
106A2014ASP-1-0.839-0.92032.462-8.941-8.9410.0000.0000.0000.000
107A2015LEU0-0.041-0.01130.2800.2000.2000.0000.0000.0000.000
108A2016ILE00.0260.02634.4810.2300.2300.0000.0000.0000.000
109A2017ASN0-0.042-0.02137.4060.4200.4200.0000.0000.0000.000
110A2018SER0-0.104-0.06936.0800.2290.2290.0000.0000.0000.000
111A2019HIS10.7910.88738.3737.5257.5250.0000.0000.0000.000
112A2020ALA00.0580.04135.7330.0890.0890.0000.0000.0000.000
113A2021ASP-1-0.883-0.95537.745-7.515-7.5150.0000.0000.0000.000
114A2022VAL0-0.026-0.01738.191-0.217-0.2170.0000.0000.0000.000
115A2023ASN0-0.087-0.05239.006-0.104-0.1040.0000.0000.0000.000
116A2024ALA00.0270.03637.0600.0400.0400.0000.0000.0000.000
117A2025VAL0-0.023-0.01936.418-0.168-0.1680.0000.0000.0000.000
118A2026ASP-1-0.751-0.85632.137-9.495-9.4950.0000.0000.0000.000
119A2027ASP-1-0.825-0.92133.365-8.879-8.8790.0000.0000.0000.000
120A2028LEU0-0.121-0.06431.2610.1370.1370.0000.0000.0000.000
121A2029GLY00.0540.02635.4990.1970.1970.0000.0000.0000.000
122A2030LYS10.8480.93431.6799.8639.8630.0000.0000.0000.000
123A2031SER00.0720.02535.187-0.189-0.1890.0000.0000.0000.000
124A2032ALA00.0330.00033.427-0.228-0.2280.0000.0000.0000.000
125A2033LEU00.0280.02333.983-0.198-0.1980.0000.0000.0000.000
126A2034HIS00.0250.01635.661-0.182-0.1820.0000.0000.0000.000
127A2035TRP0-0.037-0.04628.477-0.386-0.3860.0000.0000.0000.000
128A2036ALA00.0170.01331.221-0.253-0.2530.0000.0000.0000.000
129A2037ALA00.0030.00532.658-0.095-0.0950.0000.0000.0000.000
130A2038ALA0-0.045-0.01531.154-0.055-0.0550.0000.0000.0000.000
131A2039VAL0-0.053-0.03427.018-0.200-0.2000.0000.0000.0000.000
132A2040ASN00.0000.00529.0990.0660.0660.0000.0000.0000.000
133A2041ASN0-0.0260.01229.0960.2380.2380.0000.0000.0000.000
134A2042VAL00.0490.01231.5300.2590.2590.0000.0000.0000.000
135A2043ASP-1-0.884-0.93833.078-8.951-8.9510.0000.0000.0000.000
136A2044ALA00.0170.00032.1420.2420.2420.0000.0000.0000.000
137A2045ALA00.0190.00434.2490.2290.2290.0000.0000.0000.000
138A2046VAL0-0.020-0.00636.8980.2910.2910.0000.0000.0000.000
139A2047VAL00.0050.00236.3200.2540.2540.0000.0000.0000.000
140A2048LEU00.0090.00434.7800.1930.1930.0000.0000.0000.000
141A2049LEU0-0.022-0.00739.0130.2100.2100.0000.0000.0000.000
142A2050LYS10.8660.93241.9587.1727.1720.0000.0000.0000.000
143A2051ASN0-0.073-0.04040.7580.2320.2320.0000.0000.0000.000
144A2052GLY00.0060.01343.1260.0020.0020.0000.0000.0000.000
145A2053ALA00.0160.01240.3220.0280.0280.0000.0000.0000.000
146A2054ASN0-0.019-0.02242.3110.1590.1590.0000.0000.0000.000
147A2055LYS10.8470.90642.7726.3806.3800.0000.0000.0000.000
148A2056ASP-1-0.843-0.91543.526-6.760-6.7600.0000.0000.0000.000
149A2057MET0-0.079-0.01841.0760.0190.0190.0000.0000.0000.000
150A2058GLN0-0.027-0.02242.397-0.043-0.0430.0000.0000.0000.000
151A2059ASN0-0.034-0.01536.7540.1490.1490.0000.0000.0000.000
152A2060ASN0-0.010-0.01938.1270.2940.2940.0000.0000.0000.000
153A2061ARG10.7290.85135.3108.6688.6680.0000.0000.0000.000
154A2062GLU-1-0.880-0.94741.000-6.773-6.7730.0000.0000.0000.000
155A2063GLU-1-0.755-0.83337.403-8.504-8.5040.0000.0000.0000.000
156A2064THR00.0730.03940.736-0.128-0.1280.0000.0000.0000.000
157A2065PRO0-0.015-0.01538.196-0.188-0.1880.0000.0000.0000.000
158A2066LEU00.0340.02138.519-0.190-0.1900.0000.0000.0000.000
159A2067PHE00.0420.01539.041-0.127-0.1270.0000.0000.0000.000
160A2068LEU0-0.011-0.01734.597-0.170-0.1700.0000.0000.0000.000
161A2069ALA0-0.005-0.00435.432-0.225-0.2250.0000.0000.0000.000
162A2070ALA00.003-0.00236.491-0.122-0.1220.0000.0000.0000.000
163A2071ARG10.8360.91132.1089.2949.2940.0000.0000.0000.000
164A2072GLU-1-0.828-0.89731.090-9.910-9.9100.0000.0000.0000.000
165A2073GLY0-0.0010.01932.488-0.205-0.2050.0000.0000.0000.000
166A2074SER0-0.056-0.03333.387-0.112-0.1120.0000.0000.0000.000
167A2075TYR00.0310.00734.7120.2100.2100.0000.0000.0000.000
168A2076GLU-1-0.847-0.91934.944-8.790-8.7900.0000.0000.0000.000
169A2077THR0-0.001-0.01634.6400.1910.1910.0000.0000.0000.000
170A2078ALA00.0210.00037.2800.1840.1840.0000.0000.0000.000
171A2079LYS10.8730.93439.9267.3737.3730.0000.0000.0000.000
172A2080VAL0-0.0080.00139.0000.2010.2010.0000.0000.0000.000
173A2081LEU0-0.012-0.01038.9970.1690.1690.0000.0000.0000.000
174A2082LEU00.0080.01242.7280.1740.1740.0000.0000.0000.000
175A2083ASP-1-0.803-0.86044.844-6.812-6.8120.0000.0000.0000.000
176A2084HIS0-0.099-0.05243.3730.1680.1680.0000.0000.0000.000
177A2085PHE0-0.044-0.03346.7820.1050.1050.0000.0000.0000.000
178A2086ALA00.0030.01444.6890.0780.0780.0000.0000.0000.000
179A2087ASN0-0.011-0.01446.6700.0550.0550.0000.0000.0000.000
180A2088ARG10.7880.86846.9326.1836.1830.0000.0000.0000.000
181A2089ASP-1-0.913-0.96448.020-6.215-6.2150.0000.0000.0000.000
182A2090ILE0-0.076-0.02546.4250.0720.0720.0000.0000.0000.000
183A2091THR00.0050.00646.571-0.084-0.0840.0000.0000.0000.000
184A2092ASP-1-0.770-0.88042.212-7.488-7.4880.0000.0000.0000.000
185A2093HIS0-0.042-0.03340.516-0.013-0.0130.0000.0000.0000.000
186A2094MET0-0.132-0.06143.0450.0750.0750.0000.0000.0000.000
187A2095ASP-1-0.908-0.94545.929-6.311-6.3110.0000.0000.0000.000
188A2096ARG10.7200.84940.4337.6477.6470.0000.0000.0000.000
189A2097LEU00.0440.02445.520-0.081-0.0810.0000.0000.0000.000
190A2098PRO0-0.022-0.02642.538-0.164-0.1640.0000.0000.0000.000
191A2099ARG10.7880.84642.7346.4176.4170.0000.0000.0000.000
192A2100ASP-1-0.832-0.91744.667-6.751-6.7510.0000.0000.0000.000
193A2101ILE0-0.0130.00238.452-0.131-0.1310.0000.0000.0000.000
194A2102ALA00.0240.01339.767-0.212-0.2120.0000.0000.0000.000
195A2103GLN0-0.0030.00040.7070.0100.0100.0000.0000.0000.000
196A2104GLU-1-0.907-0.94640.587-7.629-7.6290.0000.0000.0000.000
197A2105ARG10.7780.88432.0839.0989.0980.0000.0000.0000.000
198A2106MET0-0.050-0.02036.953-0.157-0.1570.0000.0000.0000.000
199A2107HIS00.0300.03533.6630.0090.0090.0000.0000.0000.000
200A2108HIS00.001-0.02238.7420.2610.2610.0000.0000.0000.000
201A2109ASP-1-0.864-0.92139.333-7.673-7.6730.0000.0000.0000.000
202A2110ILE0-0.0100.01637.6450.1040.1040.0000.0000.0000.000
203A2111VAL0-0.022-0.01141.3120.1570.1570.0000.0000.0000.000
204A2112ARG10.8480.92042.8697.3787.3780.0000.0000.0000.000
205A2113LEU00.0230.01541.5090.1270.1270.0000.0000.0000.000
206A2114LEU0-0.028-0.02043.2900.1130.1130.0000.0000.0000.000
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