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: NLL3Q

Calculation Name: 2NYT-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2NYT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y235

Base Structure: X-ray

Registration Date: 2025-10-05

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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2152423.850361
FMO2-HF: Nuclear repulsion 2076300.966789
FMO2-HF: Total energy -76122.883572
FMO2-MP2: Total energy -76344.755041


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:36:SER)


Summations of interaction energy for fragment #1(A:36: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.
-66.665-64.497-0.029-1.17-0.968-0.003
Interaction energy analysis for fragmet #1(A:36:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.896
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].
3A38GLY00.0170.0123.8252.4524.590-0.028-1.083-1.027-0.003
155A190ASN0-0.111-0.0703.988-10.329-10.299-0.001-0.0870.0590.000
4A39GLY00.0420.0296.5270.5230.5230.0000.0000.0000.000
5A40MET0-0.073-0.02510.180-0.380-0.3800.0000.0000.0000.000
6A41ILE00.0010.01113.1701.5011.5010.0000.0000.0000.000
7A42VAL00.0370.02715.099-0.492-0.4920.0000.0000.0000.000
8A43THR0-0.026-0.01916.7941.0741.0740.0000.0000.0000.000
9A44GLY00.0180.01018.060-0.254-0.2540.0000.0000.0000.000
10A45GLU-1-0.861-0.92819.220-13.756-13.7560.0000.0000.0000.000
11A46ARG10.9220.94515.27216.13616.1360.0000.0000.0000.000
12A47LEU00.0190.02116.559-0.931-0.9310.0000.0000.0000.000
13A48PRO00.0370.01014.2430.4470.4470.0000.0000.0000.000
14A49ALA00.0250.00416.6740.2750.2750.0000.0000.0000.000
15A50ASN0-0.019-0.01120.0680.7570.7570.0000.0000.0000.000
16A51PHE00.0440.02915.8900.2800.2800.0000.0000.0000.000
17A52PHE0-0.026-0.03613.5520.3340.3340.0000.0000.0000.000
18A53LYS10.8790.95519.59314.06814.0680.0000.0000.0000.000
19A54PHE0-0.059-0.01523.0550.6730.6730.0000.0000.0000.000
20A55GLN00.0400.01820.8550.0090.0090.0000.0000.0000.000
21A56PHE00.0280.01716.4800.2510.2510.0000.0000.0000.000
22A57ARG10.9290.97120.87910.95110.9510.0000.0000.0000.000
23A58ASN00.0560.01723.5310.2600.2600.0000.0000.0000.000
24A59VAL0-0.103-0.04925.3360.2410.2410.0000.0000.0000.000
25A60GLU-1-0.709-0.85327.735-10.901-10.9010.0000.0000.0000.000
26A61TYR00.001-0.00830.4780.2150.2150.0000.0000.0000.000
27A62SER00.005-0.00334.177-0.096-0.0960.0000.0000.0000.000
28A63SER0-0.031-0.01036.8470.2280.2280.0000.0000.0000.000
29A64GLY00.0280.02037.343-0.110-0.1100.0000.0000.0000.000
30A65ARG10.8840.92634.9098.8998.8990.0000.0000.0000.000
31A66ASN00.0050.00931.8930.0770.0770.0000.0000.0000.000
32A67LYS10.9360.99724.31812.85212.8520.0000.0000.0000.000
33A68THR0-0.061-0.03825.941-0.099-0.0990.0000.0000.0000.000
34A69PHE00.021-0.00317.697-0.308-0.3080.0000.0000.0000.000
35A70LEU0-0.033-0.01018.8250.0780.0780.0000.0000.0000.000
36A71CYS00.0020.02514.1560.0160.0160.0000.0000.0000.000
37A72TYR0-0.005-0.00715.3280.3210.3210.0000.0000.0000.000
38A73VAL00.0350.01010.767-1.490-1.4900.0000.0000.0000.000
39A74VAL0-0.020-0.01013.7441.6601.6600.0000.0000.0000.000
40A75GLU-1-0.911-0.94411.239-26.685-26.6850.0000.0000.0000.000
41A76ALA0-0.016-0.02215.6531.1041.1040.0000.0000.0000.000
42A77GLN0-0.025-0.00818.5310.1310.1310.0000.0000.0000.000
43A78GLY00.0830.04120.6520.6310.6310.0000.0000.0000.000
44A79LYS10.8920.94823.79510.87110.8710.0000.0000.0000.000
45A80GLY00.027-0.00825.2310.5740.5740.0000.0000.0000.000
46A81GLY0-0.0130.00622.6720.1270.1270.0000.0000.0000.000
47A82GLN0-0.0070.00921.687-0.446-0.4460.0000.0000.0000.000
48A83VAL00.0170.00215.776-0.117-0.1170.0000.0000.0000.000
49A84GLN0-0.011-0.00117.0120.4810.4810.0000.0000.0000.000
50A85ALA00.0270.01311.941-0.004-0.0040.0000.0000.0000.000
51A86SER0-0.025-0.00713.047-0.462-0.4620.0000.0000.0000.000
52A87ARG10.8810.9346.17338.50838.5080.0000.0000.0000.000
53A88GLY00.0590.01512.4850.1440.1440.0000.0000.0000.000
54A89TYR0-0.065-0.07114.887-0.933-0.9330.0000.0000.0000.000
55A90LEU0-0.0010.00817.3600.4910.4910.0000.0000.0000.000
56A91GLU-1-0.849-0.91621.146-14.689-14.6890.0000.0000.0000.000
57A92ASP-1-0.825-0.91023.565-10.548-10.5480.0000.0000.0000.000
58A93GLU-1-0.916-0.95727.332-10.740-10.7400.0000.0000.0000.000
59A94HIS0-0.106-0.07429.7550.3040.3040.0000.0000.0000.000
60A95ALA00.0780.07229.4810.2660.2660.0000.0000.0000.000
61A96ALA0-0.107-0.06531.6280.2730.2730.0000.0000.0000.000
62A97ALA00.0010.01231.2690.2160.2160.0000.0000.0000.000
63A98HIS10.8540.91129.0179.9139.9130.0000.0000.0000.000
64A99ALA00.0840.04123.7400.0210.0210.0000.0000.0000.000
65A100GLU-1-0.833-0.92325.047-12.369-12.3690.0000.0000.0000.000
66A101GLU-1-0.886-0.95326.041-9.816-9.8160.0000.0000.0000.000
67A102ALA00.0320.02626.2190.0930.0930.0000.0000.0000.000
68A103PHE00.0410.02219.291-0.119-0.1190.0000.0000.0000.000
69A104PHE00.012-0.01424.421-0.137-0.1370.0000.0000.0000.000
70A105ASN0-0.062-0.03326.9000.4930.4930.0000.0000.0000.000
71A106THR0-0.086-0.04726.3310.1490.1490.0000.0000.0000.000
72A107ILE0-0.0380.00620.145-0.192-0.1920.0000.0000.0000.000
73A108LEU0-0.047-0.02621.061-0.484-0.4840.0000.0000.0000.000
74A109PRO00.0260.01723.9850.3090.3090.0000.0000.0000.000
75A110ALA0-0.047-0.02426.8600.5080.5080.0000.0000.0000.000
76A111PHE00.0270.01024.016-0.495-0.4950.0000.0000.0000.000
77A112ASP-1-0.815-0.88925.873-11.660-11.6600.0000.0000.0000.000
78A113PRO0-0.019-0.03927.592-0.294-0.2940.0000.0000.0000.000
79A114ALA0-0.037-0.00228.4370.0180.0180.0000.0000.0000.000
80A115LEU0-0.0150.01721.901-0.377-0.3770.0000.0000.0000.000
81A116ARG10.8810.93623.18212.75412.7540.0000.0000.0000.000
82A117TYR00.010-0.02320.656-0.845-0.8450.0000.0000.0000.000
83A118ASN0-0.017-0.02416.1801.5501.5500.0000.0000.0000.000
84A119VAL00.0180.01516.866-1.094-1.0940.0000.0000.0000.000
85A120THR0-0.005-0.00913.8280.5730.5730.0000.0000.0000.000
86A121TRP0-0.010-0.01115.654-0.424-0.4240.0000.0000.0000.000
87A122TYR00.022-0.00211.477-0.571-0.5710.0000.0000.0000.000
88A123VAL00.0210.01616.6650.1270.1270.0000.0000.0000.000
89A124SER00.0940.04119.985-0.016-0.0160.0000.0000.0000.000
90A125SER0-0.090-0.04622.0270.3360.3360.0000.0000.0000.000
91A126SER00.0120.01424.374-0.183-0.1830.0000.0000.0000.000
92A127PRO0-0.014-0.00425.3050.2400.2400.0000.0000.0000.000
93A128CYS0-0.041-0.01527.9160.3770.3770.0000.0000.0000.000
94A129ALA00.0610.01631.675-0.114-0.1140.0000.0000.0000.000
95A130ALA00.0040.00634.100-0.013-0.0130.0000.0000.0000.000
96A131CYS0-0.049-0.02128.9200.1460.1460.0000.0000.0000.000
97A132ALA00.0160.02529.904-0.222-0.2220.0000.0000.0000.000
98A133ASP-1-0.888-0.95630.926-8.842-8.8420.0000.0000.0000.000
99A134ARG10.8820.93231.4249.8039.8030.0000.0000.0000.000
100A135ILE00.0160.02726.191-0.098-0.0980.0000.0000.0000.000
101A136ILE0-0.0020.00929.196-0.063-0.0630.0000.0000.0000.000
102A137LYS10.9290.95231.7288.5078.5070.0000.0000.0000.000
103A138THR00.000-0.00727.8700.1580.1580.0000.0000.0000.000
104A139LEU00.0330.02625.420-0.008-0.0080.0000.0000.0000.000
105A140SER0-0.065-0.02229.4180.1560.1560.0000.0000.0000.000
106A141LYS10.9360.96432.6848.9318.9310.0000.0000.0000.000
107A142THR0-0.0060.00228.211-0.019-0.0190.0000.0000.0000.000
108A143LYS10.9270.95528.4799.1339.1330.0000.0000.0000.000
109A144ASN0-0.059-0.03026.7520.0100.0100.0000.0000.0000.000
110A145LEU00.0020.01422.522-0.635-0.6350.0000.0000.0000.000
111A146ARG10.8860.95820.07315.05115.0510.0000.0000.0000.000
112A147LEU00.0370.01220.348-0.544-0.5440.0000.0000.0000.000
113A148LEU0-0.077-0.03315.6800.6260.6260.0000.0000.0000.000
114A149ILE00.0120.00518.799-0.441-0.4410.0000.0000.0000.000
115A150LEU00.0070.00614.4990.6240.6240.0000.0000.0000.000
116A151VAL0-0.004-0.00618.285-0.144-0.1440.0000.0000.0000.000
117A152GLY00.0150.01720.152-0.172-0.1720.0000.0000.0000.000
118A153ARG10.9060.95721.00111.81911.8190.0000.0000.0000.000
119A154LEU00.0480.02024.582-0.154-0.1540.0000.0000.0000.000
120A155PHE0-0.047-0.03527.5220.0270.0270.0000.0000.0000.000
121A156MET0-0.0040.00730.1200.1310.1310.0000.0000.0000.000
122A157TRP00.0120.00231.1890.0080.0080.0000.0000.0000.000
123A158GLU-1-0.825-0.91633.169-9.174-9.1740.0000.0000.0000.000
124A159GLU-1-0.897-0.94136.455-7.814-7.8140.0000.0000.0000.000
125A160PRO00.0160.00237.204-0.231-0.2310.0000.0000.0000.000
126A161GLU-1-0.890-0.95638.687-7.885-7.8850.0000.0000.0000.000
127A162ILE0-0.029-0.01732.367-0.170-0.1700.0000.0000.0000.000
128A163GLN0-0.017-0.02233.922-0.149-0.1490.0000.0000.0000.000
129A164ALA0-0.045-0.01735.217-0.087-0.0870.0000.0000.0000.000
130A165ALA0-0.028-0.01633.820-0.091-0.0910.0000.0000.0000.000
131A166LEU00.033-0.00428.579-0.286-0.2860.0000.0000.0000.000
132A167LYS10.9320.99530.7838.3618.3610.0000.0000.0000.000
133A168LYS11.0291.01232.6888.1788.1780.0000.0000.0000.000
134A169LEU0-0.026-0.01226.893-0.132-0.1320.0000.0000.0000.000
135A170LYS10.8700.93328.3569.7419.7410.0000.0000.0000.000
136A171GLU-1-0.971-0.99329.395-8.991-8.9910.0000.0000.0000.000
137A172ALA0-0.064-0.02730.5030.0560.0560.0000.0000.0000.000
138A173GLY0-0.0060.00128.094-0.191-0.1910.0000.0000.0000.000
139A174CYS0-0.054-0.00824.580-0.786-0.7860.0000.0000.0000.000
140A175LYS10.8910.94918.87415.92615.9260.0000.0000.0000.000
141A176LEU00.0710.04221.557-0.705-0.7050.0000.0000.0000.000
142A177ARG10.8430.90619.63313.59213.5920.0000.0000.0000.000
143A178ILE00.0350.03120.710-0.203-0.2030.0000.0000.0000.000
144A179MET0-0.073-0.01615.815-1.042-1.0420.0000.0000.0000.000
145A180LYS10.9340.98315.34717.57517.5750.0000.0000.0000.000
146A181PRO00.027-0.00515.347-1.074-1.0740.0000.0000.0000.000
147A182GLN00.0800.02611.109-0.026-0.0260.0000.0000.0000.000
148A183ASP-1-0.857-0.92210.453-24.561-24.5610.0000.0000.0000.000
149A184PHE00.003-0.00411.676-1.173-1.1730.0000.0000.0000.000
150A185GLU-1-0.902-0.9348.269-29.880-29.8800.0000.0000.0000.000
151A186TYR0-0.028-0.0165.263-4.445-4.4450.0000.0000.0000.000
152A187VAL00.002-0.0197.826-3.151-3.1510.0000.0000.0000.000
153A188TRP00.0330.0069.957-0.089-0.0890.0000.0000.0000.000
154A189GLN0-0.0040.0035.130-0.179-0.1790.0000.0000.0000.000
156A191PHE0-0.025-0.0087.1460.7840.7840.0000.0000.0000.000
157A192VAL00.0230.02910.8521.7481.7480.0000.0000.0000.000
158A193GLU-1-0.978-0.99910.081-23.074-23.0740.0000.0000.0000.000
159A194GLN00.0080.0259.1071.9091.9090.0000.0000.0000.000
160A195GLU-1-0.897-0.9429.600-20.654-20.6540.0000.0000.0000.000
161A196GLU-1-0.891-0.94710.602-20.694-20.6940.0000.0000.0000.000
162A197GLY0-0.025-0.0218.455-1.394-1.3940.0000.0000.0000.000
163A198GLU-1-0.904-0.9569.285-21.506-21.5060.0000.0000.0000.000
164A199SER0-0.049-0.04112.0470.6650.6650.0000.0000.0000.000
165A200LYS10.8140.9275.21135.20135.2010.0000.0000.0000.000
166A201ALA00.0300.0377.872-3.346-3.3460.0000.0000.0000.000
167A202PHE0-0.021-0.0249.8521.2411.2410.0000.0000.0000.000
168A203GLN0-0.027-0.02011.5281.4591.4590.0000.0000.0000.000
169A204PRO0-0.041-0.02015.0920.3480.3480.0000.0000.0000.000
170A205TRP00.001-0.01016.6320.2570.2570.0000.0000.0000.000
171A206GLU-1-0.907-0.97020.943-12.565-12.5650.0000.0000.0000.000
172A207ASP-1-0.839-0.90124.317-12.056-12.0560.0000.0000.0000.000
173A208ILE0-0.084-0.03016.671-0.200-0.2000.0000.0000.0000.000
174A209GLN00.013-0.00119.410-0.399-0.3990.0000.0000.0000.000
175A210GLU-1-0.834-0.92922.011-12.583-12.5830.0000.0000.0000.000
176A211ASN0-0.068-0.04023.5680.6980.6980.0000.0000.0000.000
177A212PHE0-0.018-0.01220.565-0.004-0.0040.0000.0000.0000.000
178A213LEU00.0070.00022.6770.2860.2860.0000.0000.0000.000
179A214TYR00.0210.02225.1460.4730.4730.0000.0000.0000.000
180A215TYR00.037-0.00624.9990.2620.2620.0000.0000.0000.000
181A216GLU-1-0.943-0.98322.174-13.862-13.8620.0000.0000.0000.000
182A217GLU-1-0.843-0.90525.528-9.556-9.5560.0000.0000.0000.000
183A218LYS10.8580.91429.2539.6229.6220.0000.0000.0000.000
184A219LEU0-0.067-0.03224.3970.1240.1240.0000.0000.0000.000
185A220ALA0-0.058-0.02928.4160.0280.0280.0000.0000.0000.000
186A221ASP-1-0.889-0.94329.739-9.196-9.1960.0000.0000.0000.000
187A222ILE0-0.055-0.00330.8470.2660.2660.0000.0000.0000.000
188A223LEU0-0.043-0.03827.7020.1070.1070.0000.0000.0000.000
189A224LYS00.0120.03429.8851.0571.0570.0000.0000.0000.000