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: RK9N8

Calculation Name: 7PTB-A-Xray549

Preferred Name:

Target Type:

Ligand Name: nitrate ion

Ligand 3-letter code: NO3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7PTB

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 317
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -4311139.072247
FMO2-HF: Nuclear repulsion 4186512.554389
FMO2-HF: Total energy -124626.517859
FMO2-MP2: Total energy -124991.920616


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:1763:PRO)


Summations of interaction energy for fragment #1(A:1763:PRO)
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.
151.716155.5011.272-1.63-3.427-0.007
Interaction energy analysis for fragmet #1(A:1763:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.890 / q_NPA : 0.931
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].
3A1765ILE00.0470.0263.8694.5176.065-0.013-0.673-0.862-0.001
4A1766LEU0-0.029-0.0102.372-7.993-7.2040.988-0.426-1.350-0.003
5A1767SER00.031-0.0085.3173.8883.874-0.001-0.0010.0160.000
30A1792ASN0-0.026-0.0252.5079.88011.3420.298-0.530-1.231-0.003
6A1768ASN00.0250.0198.974-0.786-0.7860.0000.0000.0000.000
7A1769LYS10.8710.94011.69816.92316.9230.0000.0000.0000.000
8A1770GLN00.0440.0238.655-1.568-1.5680.0000.0000.0000.000
9A1771PHE0-0.028-0.01912.4860.0650.0650.0000.0000.0000.000
10A1772LEU0-0.0060.00216.091-0.059-0.0590.0000.0000.0000.000
11A1773ALA0-0.006-0.01019.2690.3110.3110.0000.0000.0000.000
12A1774TRP0-0.039-0.02821.986-0.289-0.2890.0000.0000.0000.000
13A1775GLY00.0210.03025.8430.2320.2320.0000.0000.0000.000
14A1776GLY00.0380.00628.403-0.065-0.0650.0000.0000.0000.000
15A1777VAL0-0.0040.00030.298-0.065-0.0650.0000.0000.0000.000
16A1778PRO00.000-0.00533.0150.1300.1300.0000.0000.0000.000
17A1779LEU00.0560.02136.162-0.117-0.1170.0000.0000.0000.000
18A1780GLY0-0.0070.00737.1820.1880.1880.0000.0000.0000.000
19A1781ARG10.9090.96635.0867.8647.8640.0000.0000.0000.000
20A1782THR00.008-0.00431.235-0.146-0.1460.0000.0000.0000.000
21A1783GLN00.0390.02427.0460.3700.3700.0000.0000.0000.000
22A1784LEU0-0.0160.00124.611-0.360-0.3600.0000.0000.0000.000
23A1785GLN0-0.022-0.02521.157-0.543-0.5430.0000.0000.0000.000
24A1786LYS10.9620.98719.12912.81612.8160.0000.0000.0000.000
25A1787LEU0-0.0190.00413.0530.1130.1130.0000.0000.0000.000
26A1788ALA00.0110.00513.3100.6390.6390.0000.0000.0000.000
27A1789LEU0-0.011-0.0019.800-1.381-1.3810.0000.0000.0000.000
28A1790ARG10.8630.8877.57726.48126.4810.0000.0000.0000.000
29A1791ASN0-0.036-0.0196.806-8.736-8.7360.0000.0000.0000.000
31A1793SER00.0300.0095.853-0.490-0.4900.0000.0000.0000.000
32A1794ALA00.021-0.0027.4582.1852.1850.0000.0000.0000.000
33A1795SER00.0040.01210.2851.5221.5220.0000.0000.0000.000
34A1796THR00.0170.0259.4221.0541.0540.0000.0000.0000.000
35A1797THR00.0310.01711.493-0.932-0.9320.0000.0000.0000.000
36A1798GLN0-0.024-0.0017.9672.7822.7820.0000.0000.0000.000
37A1799HIS00.0290.00312.3621.8561.8560.0000.0000.0000.000
38A1800LEU00.0030.00410.529-0.991-0.9910.0000.0000.0000.000
39A1801ARG10.8500.92014.45415.71915.7190.0000.0000.0000.000
40A1802LEU0-0.0080.00315.141-0.847-0.8470.0000.0000.0000.000
41A1803LEU0-0.026-0.03117.8310.9990.9990.0000.0000.0000.000
42A1804ILE00.0260.02919.349-0.741-0.7410.0000.0000.0000.000
43A1805ARG10.8600.92521.07413.00513.0050.0000.0000.0000.000
44A1806GLY00.000-0.01622.461-0.449-0.4490.0000.0000.0000.000
45A1807GLN00.0330.03024.7470.0000.0000.0000.0000.0000.000
46A1808ASP-1-0.698-0.83927.408-9.920-9.9200.0000.0000.0000.000
47A1809GLN0-0.037-0.03025.712-0.345-0.3450.0000.0000.0000.000
48A1810ASP-1-0.732-0.82827.082-9.769-9.7690.0000.0000.0000.000
49A1811CYS0-0.0220.01729.7570.2270.2270.0000.0000.0000.000
50A1812PHE0-0.024-0.00924.255-0.210-0.2100.0000.0000.0000.000
51A1813GLN0-0.002-0.00825.868-0.213-0.2130.0000.0000.0000.000
52A1814LEU0-0.014-0.01419.608-0.157-0.1570.0000.0000.0000.000
53A1815GLN0-0.029-0.01023.2770.7420.7420.0000.0000.0000.000
54A1816ASN00.013-0.00223.083-0.538-0.5380.0000.0000.0000.000
55A1817THR0-0.0230.00217.890-0.406-0.4060.0000.0000.0000.000
56A1818PHE00.0140.00019.8860.5170.5170.0000.0000.0000.000
57A1819GLY00.017-0.00817.455-0.891-0.8910.0000.0000.0000.000
58A1820SER00.0000.00216.0150.3770.3770.0000.0000.0000.000
59A1821GLU-1-0.924-0.94917.433-16.792-16.7920.0000.0000.0000.000
60A1822GLN0-0.123-0.07317.3150.9900.9900.0000.0000.0000.000
61A1823ARG11.0070.99221.46010.58510.5850.0000.0000.0000.000
62A1824LEU0-0.015-0.01323.248-0.363-0.3630.0000.0000.0000.000
63A1825THR00.0140.01022.2330.5600.5600.0000.0000.0000.000
64A1826SER00.0320.01224.238-0.359-0.3590.0000.0000.0000.000
65A1827ASN00.0090.01623.2720.1240.1240.0000.0000.0000.000
66A1828CYS00.0210.01621.435-0.438-0.4380.0000.0000.0000.000
67A1829GLU-1-0.881-0.93519.076-15.248-15.2480.0000.0000.0000.000
68A1830ILE00.0040.00316.3720.5130.5130.0000.0000.0000.000
69A1831ARG10.9470.97516.34313.70313.7030.0000.0000.0000.000
70A1832ILE00.0020.01510.4260.2590.2590.0000.0000.0000.000
71A1833HIS10.9210.95213.01616.14216.1420.0000.0000.0000.000
72A1834PRO00.006-0.00311.076-1.464-1.4640.0000.0000.0000.000
73A1835LYS10.8590.9256.99336.50536.5050.0000.0000.0000.000
74A1836GLU-1-0.770-0.84911.159-17.036-17.0360.0000.0000.0000.000
75A1837ASP-1-0.790-0.85211.305-24.891-24.8910.0000.0000.0000.000
76A1838ILE00.008-0.01812.9671.4141.4140.0000.0000.0000.000
77A1839PHE0-0.026-0.01714.467-0.845-0.8450.0000.0000.0000.000
78A1840ILE00.0120.01214.5950.9280.9280.0000.0000.0000.000
79A1841SER0-0.001-0.00817.9020.1880.1880.0000.0000.0000.000
80A1842VAL0-0.004-0.00819.9360.0460.0460.0000.0000.0000.000
81A1843LEU00.0010.00022.7460.0800.0800.0000.0000.0000.000
82A1844PHE0-0.0080.00526.400-0.110-0.1100.0000.0000.0000.000
83A1845ALA00.027-0.01227.8790.2530.2530.0000.0000.0000.000
84A1846PRO00.0160.02731.1880.1140.1140.0000.0000.0000.000
85A1847THR00.029-0.00633.2090.2640.2640.0000.0000.0000.000
86A1848ARG10.7670.84031.7349.6059.6050.0000.0000.0000.000
87A1849LEU0-0.030-0.02335.849-0.188-0.1880.0000.0000.0000.000
88A1850SER00.0530.03232.9070.1520.1520.0000.0000.0000.000
89A1851CYS0-0.044-0.01530.062-0.144-0.1440.0000.0000.0000.000
90A1852MET0-0.065-0.00528.681-0.013-0.0130.0000.0000.0000.000
91A1853LEU0-0.003-0.01524.478-0.509-0.5090.0000.0000.0000.000
92A1854ALA0-0.037-0.02123.1820.2470.2470.0000.0000.0000.000
93A1855ARG10.9110.96618.19614.17614.1760.0000.0000.0000.000
94A1856LEU00.0520.03715.8200.5650.5650.0000.0000.0000.000
95A1857GLU-1-0.839-0.91015.525-17.984-17.9840.0000.0000.0000.000
96A1858ILE00.0290.00611.5520.7270.7270.0000.0000.0000.000
97A1859LYS10.9450.96912.06614.94214.9420.0000.0000.0000.000
98A1860GLN00.0840.0607.436-2.243-2.2430.0000.0000.0000.000
99A1861LEU0-0.033-0.02611.4330.1520.1520.0000.0000.0000.000
100A1862GLY00.0220.01913.052-0.993-0.9930.0000.0000.0000.000
101A1863ASN0-0.002-0.00711.4841.6331.6330.0000.0000.0000.000
102A1864ARG10.9710.98615.38414.81814.8180.0000.0000.0000.000
103A1865SER00.0210.02013.489-0.537-0.5370.0000.0000.0000.000
104A1866GLN0-0.029-0.0108.231-4.494-4.4940.0000.0000.0000.000
105A1867PRO00.0510.0229.9821.7871.7870.0000.0000.0000.000
106A1868GLY0-0.006-0.01011.082-1.440-1.4400.0000.0000.0000.000
107A1869ILE0-0.024-0.0056.390-0.465-0.4650.0000.0000.0000.000
108A1870LYS10.8270.90610.16218.52518.5250.0000.0000.0000.000
109A1871PHE00.0260.0134.890-1.386-1.3860.0000.0000.0000.000
110A1872THR0-0.019-0.03310.3761.5371.5370.0000.0000.0000.000
111A1873ILE00.0020.01510.989-0.791-0.7910.0000.0000.0000.000
112A1874PRO0-0.026-0.01914.6051.1421.1420.0000.0000.0000.000
113A1875LEU0-0.029-0.00517.864-0.216-0.2160.0000.0000.0000.000
114A1876SER0-0.001-0.00620.9390.1440.1440.0000.0000.0000.000
115A1877GLY00.0430.01023.907-0.203-0.2030.0000.0000.0000.000
116A1878TYR0-0.052-0.02427.300-0.055-0.0550.0000.0000.0000.000
117A1879GLY00.0520.02031.051-0.007-0.0070.0000.0000.0000.000
118A1880GLY0-0.006-0.01633.9610.1900.1900.0000.0000.0000.000
119A1881THR0-0.007-0.02535.271-0.264-0.2640.0000.0000.0000.000
120A1882SER0-0.067-0.04737.5250.2490.2490.0000.0000.0000.000
121A1883ASN0-0.042-0.04340.013-0.246-0.2460.0000.0000.0000.000
122A1884LEU0-0.0110.01442.0310.1760.1760.0000.0000.0000.000
123A1885ILE0-0.0090.00244.731-0.048-0.0480.0000.0000.0000.000
124A1886LEU0-0.027-0.01247.9400.0390.0390.0000.0000.0000.000
125A1887GLU-1-0.863-0.93551.119-5.857-5.8570.0000.0000.0000.000
126A1888GLY00.0180.00254.5700.0230.0230.0000.0000.0000.000
127A1889VAL0-0.031-0.01053.6380.0660.0660.0000.0000.0000.000
128A1890LYS10.9800.99356.1605.1415.1410.0000.0000.0000.000
129A1891LYS10.8620.93647.8726.3356.3350.0000.0000.0000.000
130A1892LEU00.0020.00352.0770.1140.1140.0000.0000.0000.000
131A1893SER00.012-0.01949.074-0.033-0.0330.0000.0000.0000.000
132A1894ASP-1-0.868-0.91445.589-6.792-6.7920.0000.0000.0000.000
133A1895SER0-0.063-0.03546.512-0.064-0.0640.0000.0000.0000.000
134A1896TYR00.0360.01748.157-0.015-0.0150.0000.0000.0000.000
135A1897MET0-0.017-0.00752.148-0.001-0.0010.0000.0000.0000.000
136A1898VAL0-0.005-0.00455.5040.0490.0490.0000.0000.0000.000
137A1899THR00.0240.02358.457-0.071-0.0710.0000.0000.0000.000
138A1900VAL0-0.034-0.01160.7730.0370.0370.0000.0000.0000.000
139A1901ASN00.021-0.00163.4380.0540.0540.0000.0000.0000.000
140A1902GLY00.0250.02067.0480.0120.0120.0000.0000.0000.000
141A1903LEU0-0.0260.01064.1850.0410.0410.0000.0000.0000.000
142A1904VAL00.023-0.00468.8510.0680.0680.0000.0000.0000.000
143A1905PRO0-0.005-0.00369.497-0.038-0.0380.0000.0000.0000.000
144A1906GLY00.0140.01769.3170.0680.0680.0000.0000.0000.000
145A1907LYS10.8650.92969.5274.3794.3790.0000.0000.0000.000
146A1908GLU-1-0.773-0.88563.926-5.009-5.0090.0000.0000.0000.000
147A1909SER0-0.032-0.01365.5750.0820.0820.0000.0000.0000.000
148A1910LYS10.8730.93062.6844.8594.8590.0000.0000.0000.000
149A1911ILE00.0200.02159.2740.0650.0650.0000.0000.0000.000
150A1912VAL0-0.014-0.00858.540-0.069-0.0690.0000.0000.0000.000
151A1913PHE0-0.0080.01151.8100.0330.0330.0000.0000.0000.000
152A1914SER00.013-0.00454.2830.0280.0280.0000.0000.0000.000
153A1915VAL0-0.0030.01347.492-0.056-0.0560.0000.0000.0000.000
154A1916ARG10.8730.92149.6385.9465.9460.0000.0000.0000.000
155A1917ASN00.000-0.00943.044-0.186-0.1860.0000.0000.0000.000
156A1918THR00.009-0.00445.8700.0460.0460.0000.0000.0000.000
157A1919GLY0-0.0080.01142.370-0.038-0.0380.0000.0000.0000.000
158A1920SER0-0.054-0.04839.8260.1150.1150.0000.0000.0000.000
159A1921ARG10.7410.86235.2258.6088.6080.0000.0000.0000.000
160A1922ALA00.0230.02640.5580.0870.0870.0000.0000.0000.000
161A1923ALA00.0040.00240.128-0.250-0.2500.0000.0000.0000.000
162A1924PHE00.0050.01536.4230.1680.1680.0000.0000.0000.000
163A1925VAL0-0.008-0.01041.690-0.058-0.0580.0000.0000.0000.000
164A1926LYS10.8710.92842.7266.8536.8530.0000.0000.0000.000
165A1927ALA0-0.023-0.00644.692-0.065-0.0650.0000.0000.0000.000
166A1928VAL0-0.011-0.01644.483-0.002-0.0020.0000.0000.0000.000
167A1929GLY00.0240.01547.7370.0010.0010.0000.0000.0000.000
168A1930PHE0-0.040-0.02945.567-0.038-0.0380.0000.0000.0000.000
169A1931LYS10.9880.99151.2235.5345.5340.0000.0000.0000.000
170A1932ASP-1-0.842-0.92551.511-5.983-5.9830.0000.0000.0000.000
171A1933SER0-0.002-0.00648.007-0.092-0.0920.0000.0000.0000.000
172A1934GLN0-0.028-0.00547.019-0.168-0.1680.0000.0000.0000.000
173A1935LYS10.9280.95146.8365.7685.7680.0000.0000.0000.000
174A1936LYS10.8400.93141.5827.3597.3590.0000.0000.0000.000
175A1937VAL00.0060.01447.670-0.018-0.0180.0000.0000.0000.000
176A1938LEU00.0450.00747.4910.0400.0400.0000.0000.0000.000
177A1939LEU0-0.025-0.00551.1980.1050.1050.0000.0000.0000.000
178A1940ASP-1-0.806-0.90054.005-5.444-5.4440.0000.0000.0000.000
179A1941PRO00.004-0.00154.6210.0710.0710.0000.0000.0000.000
180A1942LYS10.9180.94356.8625.3235.3230.0000.0000.0000.000
181A1943VAL0-0.027-0.00159.5990.0970.0970.0000.0000.0000.000
182A1944LEU0-0.009-0.00556.7280.0500.0500.0000.0000.0000.000
183A1945ARG10.8450.94355.3485.1715.1710.0000.0000.0000.000
184A1946ILE00.0070.00351.1150.0700.0700.0000.0000.0000.000
185A1947PHE0-0.0190.00753.849-0.046-0.0460.0000.0000.0000.000
186A1948PRO00.0870.05351.1630.0950.0950.0000.0000.0000.000
187A1949ASP-1-0.866-0.93648.572-6.441-6.4410.0000.0000.0000.000
188A1950LYS10.8520.92445.3876.4686.4680.0000.0000.0000.000
189A1951PHE00.0300.02246.1550.0720.0720.0000.0000.0000.000
190A1952VAL0-0.008-0.00442.879-0.198-0.1980.0000.0000.0000.000
191A1953LEU00.0260.03544.9310.1070.1070.0000.0000.0000.000
192A1954LYS10.8910.92744.0116.7926.7920.0000.0000.0000.000
193A1955GLU-1-0.802-0.88743.434-6.989-6.9890.0000.0000.0000.000
194A1956ARG10.8950.95244.6336.8496.8490.0000.0000.0000.000
195A1957THR0-0.023-0.00948.4640.1670.1670.0000.0000.0000.000
196A1958GLN00.032-0.00649.910-0.124-0.1240.0000.0000.0000.000
197A1959GLU-1-0.842-0.91250.435-6.076-6.0760.0000.0000.0000.000
198A1960ASN0-0.005-0.00553.095-0.067-0.0670.0000.0000.0000.000
199A1961VAL00.0040.00751.448-0.027-0.0270.0000.0000.0000.000
200A1962THR0-0.014-0.00954.8980.1170.1170.0000.0000.0000.000
201A1963LEU0-0.039-0.01654.543-0.101-0.1010.0000.0000.0000.000
202A1964ILE0-0.033-0.02758.0950.1200.1200.0000.0000.0000.000
203A1965TYR00.005-0.04460.126-0.078-0.0780.0000.0000.0000.000
204A1966ASN0-0.067-0.04362.2570.1480.1480.0000.0000.0000.000
205A1967PRO00.0590.04864.455-0.034-0.0340.0000.0000.0000.000
206A1968SER00.004-0.01365.2330.1020.1020.0000.0000.0000.000
207A1969ASP-1-0.855-0.94067.018-4.475-4.4750.0000.0000.0000.000
208A1970ARG10.9420.95867.1704.6994.6990.0000.0000.0000.000
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