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: 87VJY

Calculation Name: 5NLC-B-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5NLC

Chain ID: B

ChEMBL ID:

UniProt ID: Q31LH9

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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2528162.780045
FMO2-HF: Nuclear repulsion 2446190.874787
FMO2-HF: Total energy -81971.905258
FMO2-MP2: Total energy -82214.739765


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:3:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-30.386-28.6414.878-7.005-9.618-0.086
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.802 / q_NPA : 0.897
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].
3A5ALA00.0200.0012.5796.1577.9350.128-0.618-1.2880.000
4A6GLU-1-0.899-0.9422.814-38.476-37.2570.069-0.376-0.912-0.004
5A7ARG10.9020.9643.71559.79760.3870.001-0.144-0.447-0.001
33A35GLU-1-0.821-0.9171.936-88.824-90.66514.680-5.867-6.971-0.081
6A8LEU0-0.019-0.0155.9556.7546.7540.0000.0000.0000.000
7A9ALA0-0.0100.0027.7844.3274.3270.0000.0000.0000.000
8A10SER00.0030.0058.2194.3514.3510.0000.0000.0000.000
9A11LEU00.0290.0209.8312.7962.7960.0000.0000.0000.000
10A12ARG10.8540.90410.89327.11127.1110.0000.0000.0000.000
11A13SER0-0.068-0.03012.9981.9161.9160.0000.0000.0000.000
12A14GLN0-0.029-0.01814.0410.1480.1480.0000.0000.0000.000
13A15LEU0-0.035-0.00816.3720.8560.8560.0000.0000.0000.000
14A16PRO00.0370.03119.0660.1260.1260.0000.0000.0000.000
15A17PRO00.031-0.00622.254-0.250-0.2500.0000.0000.0000.000
16A18SER0-0.0120.00123.4270.1540.1540.0000.0000.0000.000
17A19VAL0-0.040-0.01120.1960.2110.2110.0000.0000.0000.000
18A20GLN0-0.011-0.00419.760-0.970-0.9700.0000.0000.0000.000
19A21LEU00.0180.01012.8630.1310.1310.0000.0000.0000.000
20A22ILE0-0.037-0.02016.613-0.143-0.1430.0000.0000.0000.000
21A23ALA00.0320.01711.943-0.476-0.4760.0000.0000.0000.000
22A24VAL0-0.067-0.05913.9641.1391.1390.0000.0000.0000.000
23A25SER00.032-0.01013.375-1.003-1.0030.0000.0000.0000.000
24A26LYS10.9060.96814.44717.76317.7630.0000.0000.0000.000
25A27ASN0-0.076-0.04815.643-0.827-0.8270.0000.0000.0000.000
26A28HIS00.0470.0489.740-0.390-0.3900.0000.0000.0000.000
27A29PRO00.0130.0019.9221.5291.5290.0000.0000.0000.000
28A30ALA00.0720.02511.166-1.607-1.6070.0000.0000.0000.000
29A31ALA00.0340.0178.120-0.606-0.6060.0000.0000.0000.000
30A32ALA00.0280.0186.696-2.769-2.7690.0000.0000.0000.000
31A33ILE0-0.004-0.0047.789-1.831-1.8310.0000.0000.0000.000
32A34ARG10.8060.8548.92319.44219.4420.0000.0000.0000.000
34A36ALA00.007-0.0105.795-0.308-0.3080.0000.0000.0000.000
35A37TYR0-0.046-0.0357.6371.0291.0290.0000.0000.0000.000
36A38ALA00.0060.0137.1401.7731.7730.0000.0000.0000.000
37A39ALA0-0.0280.0025.8220.8730.8730.0000.0000.0000.000
38A40GLY00.0540.0287.9480.8180.8180.0000.0000.0000.000
39A41GLN0-0.075-0.03910.6230.9300.9300.0000.0000.0000.000
40A42ARG10.8870.92912.21519.76019.7600.0000.0000.0000.000
41A43HIS00.0720.06715.5980.7390.7390.0000.0000.0000.000
42A44PHE00.0540.03511.201-1.333-1.3330.0000.0000.0000.000
43A45GLY00.0280.00016.4361.3741.3740.0000.0000.0000.000
44A46GLU-1-0.757-0.84816.895-18.700-18.7000.0000.0000.0000.000
45A47ASN00.021-0.01120.2760.3550.3550.0000.0000.0000.000
46A48ARG10.9500.97222.65812.99112.9910.0000.0000.0000.000
47A49VAL00.0540.01923.240-0.364-0.3640.0000.0000.0000.000
48A50GLN0-0.001-0.00824.7140.2190.2190.0000.0000.0000.000
49A51GLU-1-0.866-0.93719.703-15.369-15.3690.0000.0000.0000.000
50A52ALA00.0230.00919.810-0.503-0.5030.0000.0000.0000.000
51A53ILE0-0.025-0.01320.449-0.124-0.1240.0000.0000.0000.000
52A54ALA0-0.0040.00120.5230.0570.0570.0000.0000.0000.000
53A55LYS10.8330.90315.15618.47318.4730.0000.0000.0000.000
54A56GLN0-0.020-0.02117.0870.2080.2080.0000.0000.0000.000
55A57ALA0-0.0110.00319.4920.0960.0960.0000.0000.0000.000
56A58GLU-1-0.938-0.96515.349-16.989-16.9890.0000.0000.0000.000
57A59LEU0-0.054-0.03712.705-1.113-1.1130.0000.0000.0000.000
58A60THR0-0.019-0.00316.5230.1570.1570.0000.0000.0000.000
59A61ASP-1-0.787-0.84115.854-16.327-16.3270.0000.0000.0000.000
60A62LEU0-0.048-0.01712.877-0.278-0.2780.0000.0000.0000.000
61A63PRO00.0540.03917.2970.3580.3580.0000.0000.0000.000
62A64ASP-1-0.892-0.95418.115-15.560-15.5600.0000.0000.0000.000
63A65LEU0-0.046-0.01614.475-0.583-0.5830.0000.0000.0000.000
64A66THR0-0.034-0.00418.4181.1261.1260.0000.0000.0000.000
65A67TRP00.0160.00116.440-0.948-0.9480.0000.0000.0000.000
66A68HIS10.7950.86719.92815.52315.5230.0000.0000.0000.000
67A69LEU0-0.043-0.00721.733-0.542-0.5420.0000.0000.0000.000
68A70LEU00.0170.00120.0540.2890.2890.0000.0000.0000.000
69A71GLY0-0.0230.00224.1950.0300.0300.0000.0000.0000.000
70A72LYS10.8410.91426.0019.6929.6920.0000.0000.0000.000
71A73LEU00.0290.02329.737-0.115-0.1150.0000.0000.0000.000
72A74GLN00.0180.00130.5080.0750.0750.0000.0000.0000.000
73A75SER00.0890.04733.192-0.070-0.0700.0000.0000.0000.000
74A76ASN00.0390.00934.944-0.171-0.1710.0000.0000.0000.000
75A77LYS10.8890.95129.53810.44410.4440.0000.0000.0000.000
76A78ALA00.0440.02331.659-0.230-0.2300.0000.0000.0000.000
77A79ARG10.8840.92733.0858.0668.0660.0000.0000.0000.000
78A80LYS11.0001.00429.2179.8169.8160.0000.0000.0000.000
79A81ALA0-0.002-0.01128.344-0.382-0.3820.0000.0000.0000.000
80A82VAL00.0380.01928.692-0.341-0.3410.0000.0000.0000.000
81A83GLU-1-0.909-0.94829.683-9.832-9.8320.0000.0000.0000.000
82A84HIS10.8220.91524.82911.29611.2960.0000.0000.0000.000
83A85PHE0-0.0070.01122.241-0.593-0.5930.0000.0000.0000.000
84A86ASP-1-0.801-0.89323.617-12.200-12.2000.0000.0000.0000.000
85A87TRP0-0.020-0.01223.8700.4450.4450.0000.0000.0000.000
86A88ILE0-0.008-0.01325.665-0.429-0.4290.0000.0000.0000.000
87A89HIS00.0430.01124.3650.0550.0550.0000.0000.0000.000
88A90SER00.004-0.01827.8510.2750.2750.0000.0000.0000.000
89A91VAL0-0.019-0.01130.0080.2410.2410.0000.0000.0000.000
90A92ASP-1-0.777-0.88433.437-9.232-9.2320.0000.0000.0000.000
91A93SER00.0190.01835.8180.2580.2580.0000.0000.0000.000
92A94TRP00.1420.06439.085-0.270-0.2700.0000.0000.0000.000
93A95ALA00.0490.03241.295-0.073-0.0730.0000.0000.0000.000
94A96LEU0-0.123-0.05134.205-0.066-0.0660.0000.0000.0000.000
95A97ALA00.0330.00737.229-0.133-0.1330.0000.0000.0000.000
96A98GLU-1-0.838-0.91938.253-7.267-7.2670.0000.0000.0000.000
97A99ARG10.8130.89837.3018.3588.3580.0000.0000.0000.000
98A100LEU0-0.048-0.03833.373-0.084-0.0840.0000.0000.0000.000
99A101ASP-1-0.724-0.85236.825-8.139-8.1390.0000.0000.0000.000
100A102ARG10.9580.96838.9397.5107.5100.0000.0000.0000.000
101A103ILE0-0.069-0.03835.4090.0110.0110.0000.0000.0000.000
102A104ALA0-0.018-0.01235.478-0.083-0.0830.0000.0000.0000.000
103A105GLY00.0310.02236.686-0.031-0.0310.0000.0000.0000.000
104A106GLU-1-0.836-0.89639.575-7.623-7.6230.0000.0000.0000.000
105A107LEU0-0.061-0.03334.3980.0280.0280.0000.0000.0000.000
106A108GLY00.0270.03535.303-0.184-0.1840.0000.0000.0000.000
107A109ARG10.7900.89027.18810.53810.5380.0000.0000.0000.000
108A110SER00.0320.00232.3010.1610.1610.0000.0000.0000.000
109A111PRO0-0.046-0.01029.822-0.301-0.3010.0000.0000.0000.000
110A112LYS10.9170.96427.05211.61311.6130.0000.0000.0000.000
111A113LEU00.007-0.00529.200-0.378-0.3780.0000.0000.0000.000
112A114CYS0-0.075-0.02128.421-0.027-0.0270.0000.0000.0000.000
113A115LEU00.0550.02730.954-0.008-0.0080.0000.0000.0000.000
114A116GLN0-0.032-0.02729.815-0.446-0.4460.0000.0000.0000.000
115A117VAL00.0260.01332.6770.2890.2890.0000.0000.0000.000
116A118LYS10.7910.89733.5878.7628.7620.0000.0000.0000.000
117A119LEU00.0140.00433.6340.2420.2420.0000.0000.0000.000
118A120LEU00.0170.01733.0660.1520.1520.0000.0000.0000.000
119A121PRO0-0.003-0.00735.658-0.105-0.1050.0000.0000.0000.000
120A122ASP-1-0.755-0.89530.703-10.806-10.8060.0000.0000.0000.000
121A123PRO0-0.0170.00733.2640.1840.1840.0000.0000.0000.000
122A124ASN0-0.052-0.02930.1020.0770.0770.0000.0000.0000.000
123A125LYS10.8880.95426.15011.68111.6810.0000.0000.0000.000
124A126ALA00.0200.02332.3240.3140.3140.0000.0000.0000.000
125A127GLY0-0.002-0.02733.450-0.382-0.3820.0000.0000.0000.000
126A128TRP00.0060.00335.4500.2590.2590.0000.0000.0000.000
127A129ASP-1-0.771-0.87738.176-7.772-7.7720.0000.0000.0000.000
128A130PRO00.003-0.02139.4480.0140.0140.0000.0000.0000.000
129A131ALA0-0.024-0.00741.5290.0720.0720.0000.0000.0000.000
130A132ASP-1-0.867-0.93343.044-7.283-7.2830.0000.0000.0000.000
131A133LEU0-0.069-0.04137.9990.0070.0070.0000.0000.0000.000
132A134ARG10.8440.89342.1947.4607.4600.0000.0000.0000.000
133A135ALA0-0.0160.00544.9470.1090.1090.0000.0000.0000.000
134A136GLU-1-0.844-0.92443.464-7.011-7.0110.0000.0000.0000.000
135A137LEU0-0.058-0.00840.429-0.064-0.0640.0000.0000.0000.000
136A138PRO00.0120.00143.806-0.065-0.0650.0000.0000.0000.000
137A139GLN0-0.004-0.00645.5430.1050.1050.0000.0000.0000.000
138A140LEU0-0.047-0.03939.193-0.125-0.1250.0000.0000.0000.000
139A141SER0-0.042-0.03141.340-0.194-0.1940.0000.0000.0000.000
140A142GLN0-0.042-0.02043.3950.0730.0730.0000.0000.0000.000
141A143LEU0-0.071-0.01739.4750.0310.0310.0000.0000.0000.000
142A144GLN0-0.021-0.01041.6490.0820.0820.0000.0000.0000.000
143A145GLN0-0.050-0.02038.2680.1090.1090.0000.0000.0000.000
144A146VAL0-0.033-0.01634.865-0.331-0.3310.0000.0000.0000.000
145A147GLN00.0050.00432.0320.0210.0210.0000.0000.0000.000
146A148ILE00.0380.02232.889-0.417-0.4170.0000.0000.0000.000
147A149ARG10.7650.87229.36010.45710.4570.0000.0000.0000.000
148A150GLY00.0830.04731.950-0.047-0.0470.0000.0000.0000.000
149A151LEU00.0090.02831.9250.1040.1040.0000.0000.0000.000
150A152MET0-0.117-0.04025.153-0.426-0.4260.0000.0000.0000.000
151A153VAL00.0280.01728.2980.3580.3580.0000.0000.0000.000
152A154ILE0-0.071-0.06525.695-0.740-0.7400.0000.0000.0000.000
153A155ALA00.0800.05626.3570.4520.4520.0000.0000.0000.000
154A156PRO00.0040.01027.649-0.331-0.3310.0000.0000.0000.000
155A157LEU0-0.046-0.04425.363-0.241-0.2410.0000.0000.0000.000
156A158GLY00.0070.00027.3970.3550.3550.0000.0000.0000.000
157A159LEU0-0.0270.01628.7840.2450.2450.0000.0000.0000.000
158A160THR0-0.013-0.03427.946-0.469-0.4690.0000.0000.0000.000
159A161ALA00.0280.00026.220-0.062-0.0620.0000.0000.0000.000
160A162ALA00.0350.02027.776-0.010-0.0100.0000.0000.0000.000
161A163GLU-1-0.805-0.87531.384-9.574-9.5740.0000.0000.0000.000
162A164THR0-0.020-0.02325.9600.0320.0320.0000.0000.0000.000
163A165GLN0-0.046-0.03528.654-0.256-0.2560.0000.0000.0000.000
164A166ALA00.0240.01829.7330.1110.1110.0000.0000.0000.000
165A167LEU0-0.016-0.00429.5360.1690.1690.0000.0000.0000.000
166A168PHE00.000-0.02525.0580.0560.0560.0000.0000.0000.000
167A169ALA00.0240.01730.4850.0750.0750.0000.0000.0000.000
168A170GLN0-0.025-0.02033.2050.1920.1920.0000.0000.0000.000
169A171ALA00.0060.00231.7280.1950.1950.0000.0000.0000.000
170A172ARG10.8100.88931.63010.01410.0140.0000.0000.0000.000
171A173THR0-0.013-0.00933.8840.1570.1570.0000.0000.0000.000
172A174PHE0-0.0060.00437.0760.1740.1740.0000.0000.0000.000
173A175ALA00.0300.00534.4550.1360.1360.0000.0000.0000.000
174A176ALA0-0.0030.00036.5620.1330.1330.0000.0000.0000.000
175A177GLU-1-0.843-0.88738.772-7.348-7.3480.0000.0000.0000.000
176A178LEU00.016-0.00138.1980.1660.1660.0000.0000.0000.000
177A179GLN0-0.061-0.04537.728-0.120-0.1200.0000.0000.0000.000
178A180GLN0-0.009-0.00540.3660.1370.1370.0000.0000.0000.000
179A181GLN0-0.057-0.03143.8660.0660.0660.0000.0000.0000.000
180A182ALA0-0.001-0.00342.2390.1710.1710.0000.0000.0000.000
181A183PRO00.0100.00642.034-0.205-0.2050.0000.0000.0000.000
182A184GLN0-0.034-0.00642.6290.0770.0770.0000.0000.0000.000
183A185LEU0-0.0210.00238.511-0.181-0.1810.0000.0000.0000.000
184A186ARG10.9120.94832.2029.3989.3980.0000.0000.0000.000
185A187LEU00.0090.00834.199-0.421-0.4210.0000.0000.0000.000
186A188THR00.0320.00731.1500.0560.0560.0000.0000.0000.000
187A189GLU-1-0.870-0.89427.589-11.811-11.8110.0000.0000.0000.000
188A190LEU00.0650.02828.4630.2970.2970.0000.0000.0000.000
189A191SER0-0.0040.00825.553-0.726-0.7260.0000.0000.0000.000
190A192MET0-0.051-0.00825.6010.2100.2100.0000.0000.0000.000
191A193GLY00.1140.04922.152-0.282-0.2820.0000.0000.0000.000
192A194MET0-0.082-0.01019.800-0.788-0.7880.0000.0000.0000.000
193A195SER00.027-0.02115.331-0.402-0.4020.0000.0000.0000.000
194A196SER0-0.052-0.04116.474-0.603-0.6030.0000.0000.0000.000
195A197ASP-1-0.755-0.87519.123-13.791-13.7910.0000.0000.0000.000
196A198TRP00.0190.00314.9060.7220.7220.0000.0000.0000.000
197A199PRO00.0120.00918.5450.4270.4270.0000.0000.0000.000
198A200LEU00.0150.01621.1450.4830.4830.0000.0000.0000.000
199A201ALA0-0.0100.00923.0870.4790.4790.0000.0000.0000.000
200A202VAL0-0.013-0.01420.5510.3150.3150.0000.0000.0000.000
201A203ALA0-0.0200.00023.8890.3730.3730.0000.0000.0000.000
202A204GLU-1-0.797-0.87126.585-9.818-9.8180.0000.0000.0000.000
203A205GLY00.0060.00927.5570.3630.3630.0000.0000.0000.000
204A206ALA0-0.034-0.02124.3830.2120.2120.0000.0000.0000.000
205A207THR00.008-0.01825.326-0.144-0.1440.0000.0000.0000.000
206A208TRP0-0.102-0.05220.387-0.857-0.8570.0000.0000.0000.000
207A209ILE00.0330.03717.2210.2130.2130.0000.0000.0000.000
208A210ARG10.8530.92518.12613.42213.4220.0000.0000.0000.000
209A211VAL00.0240.00012.5680.4060.4060.0000.0000.0000.000
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