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

tag_button

FMODB ID: 67G5Z

Calculation Name: 3NRJ-I-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | chloride ion

Ligand 3-letter code: PO4 | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3NRJ

Chain ID: I

ChEMBL ID:

UniProt ID: Q48EB9

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1788621.276302
FMO2-HF: Nuclear repulsion 1721104.784876
FMO2-HF: Total energy -67516.491425
FMO2-MP2: Total energy -67712.878364


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
3.0814.806-0.014-0.664-1.0450.003
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.042
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].
3A6MET00.0940.0413.8481.1982.643-0.014-0.594-0.8360.003
5A8GLN00.0140.0033.984-0.584-0.3040.000-0.070-0.2090.000
4A7SER00.0340.0126.6401.3231.3230.0000.0000.0000.000
6A9ASP-1-0.833-0.8835.198-3.307-3.3070.0000.0000.0000.000
7A10LEU00.0270.0106.4341.4311.4310.0000.0000.0000.000
8A11MET0-0.025-0.0078.8510.7840.7840.0000.0000.0000.000
9A12GLN0-0.014-0.0047.6650.5100.5100.0000.0000.0000.000
10A13ARG10.7950.8718.4153.4483.4480.0000.0000.0000.000
11A14GLY00.0440.01311.9870.3870.3870.0000.0000.0000.000
12A15LYS10.8520.92811.1302.8802.8800.0000.0000.0000.000
13A16ALA0-0.0050.00615.1220.2000.2000.0000.0000.0000.000
14A17ILE0-0.078-0.01816.4900.1640.1640.0000.0000.0000.000
15A18LYS10.9220.95419.1900.8950.8950.0000.0000.0000.000
16A19LEU00.0180.02022.5940.0470.0470.0000.0000.0000.000
17A20ALA00.0040.00622.347-0.084-0.0840.0000.0000.0000.000
18A21VAL0-0.037-0.02523.2670.0910.0910.0000.0000.0000.000
19A22PHE00.0160.00424.060-0.085-0.0850.0000.0000.0000.000
20A23ASP-1-0.734-0.86926.441-0.533-0.5330.0000.0000.0000.000
21A24VAL0-0.049-0.04228.414-0.019-0.0190.0000.0000.0000.000
22A25ASP-1-0.822-0.92331.224-0.506-0.5060.0000.0000.0000.000
23A26GLY00.0920.06629.7060.0040.0040.0000.0000.0000.000
24A27VAL0-0.051-0.00325.468-0.076-0.0760.0000.0000.0000.000
25A28LEU0-0.032-0.02827.740-0.036-0.0360.0000.0000.0000.000
26A29THR0-0.011-0.00830.2630.0090.0090.0000.0000.0000.000
27A30ASP-1-0.794-0.89130.953-0.598-0.5980.0000.0000.0000.000
28A31GLY00.0320.01032.416-0.004-0.0040.0000.0000.0000.000
29A32ARG10.7820.89433.1930.5780.5780.0000.0000.0000.000
30A33LEU0-0.040-0.01636.928-0.002-0.0020.0000.0000.0000.000
31A34TYR0-0.016-0.00438.5170.0080.0080.0000.0000.0000.000
32A35PHE00.011-0.00841.8960.0010.0010.0000.0000.0000.000
33A36MET0-0.024-0.00645.745-0.004-0.0040.0000.0000.0000.000
34A37GLU-1-0.920-0.96649.440-0.223-0.2230.0000.0000.0000.000
35A38ASP-1-0.866-0.90051.332-0.243-0.2430.0000.0000.0000.000
36A39GLY0-0.024-0.00748.8950.0050.0050.0000.0000.0000.000
37A40SER0-0.112-0.07247.590-0.014-0.0140.0000.0000.0000.000
38A41GLU-1-0.778-0.88840.264-0.388-0.3880.0000.0000.0000.000
39A42ILE0-0.034-0.01742.2750.0000.0000.0000.0000.0000.000
40A43LYS10.7800.87836.8410.4440.4440.0000.0000.0000.000
41A44THR00.0040.01436.6010.0090.0090.0000.0000.0000.000
42A45PHE00.017-0.01133.685-0.011-0.0110.0000.0000.0000.000
43A46ASN00.0360.02630.8940.0080.0080.0000.0000.0000.000
44A47THR0-0.010-0.01832.930-0.007-0.0070.0000.0000.0000.000
45A48LEU00.0430.02828.553-0.004-0.0040.0000.0000.0000.000
46A49ASP-1-0.769-0.90127.179-0.979-0.9790.0000.0000.0000.000
47A50GLY0-0.020-0.01628.744-0.007-0.0070.0000.0000.0000.000
48A51GLN0-0.031-0.03229.5040.0490.0490.0000.0000.0000.000
49A52GLY00.016-0.00226.339-0.015-0.0150.0000.0000.0000.000
50A53ILE00.0460.00526.425-0.016-0.0160.0000.0000.0000.000
51A54LYS10.9240.96927.9790.5950.5950.0000.0000.0000.000
52A55MET00.0080.02125.8530.0330.0330.0000.0000.0000.000
53A56LEU00.0030.01222.112-0.014-0.0140.0000.0000.0000.000
54A57ILE00.0070.01225.5170.0080.0080.0000.0000.0000.000
55A58ALA0-0.033-0.01828.5160.0290.0290.0000.0000.0000.000
56A59SER0-0.079-0.04324.307-0.010-0.0100.0000.0000.0000.000
57A60GLY0-0.0010.00525.469-0.010-0.0100.0000.0000.0000.000
58A61VAL0-0.076-0.02722.1060.0030.0030.0000.0000.0000.000
59A62THR0-0.013-0.02925.3350.0120.0120.0000.0000.0000.000
60A63THR00.0480.00426.272-0.041-0.0410.0000.0000.0000.000
61A64ALA0-0.020-0.01827.7550.0660.0660.0000.0000.0000.000
62A65ILE0-0.0160.00128.420-0.046-0.0460.0000.0000.0000.000
63A66ILE0-0.003-0.00227.7330.0520.0520.0000.0000.0000.000
64A67SER00.0350.01930.134-0.017-0.0170.0000.0000.0000.000
65A68GLY00.0750.04932.8330.0280.0280.0000.0000.0000.000
66A69ARG10.8180.89734.8870.4150.4150.0000.0000.0000.000
67A70LYS10.9950.97437.3100.2820.2820.0000.0000.0000.000
68A71THR00.0130.00839.3810.0140.0140.0000.0000.0000.000
69A72ALA00.0560.02040.669-0.014-0.0140.0000.0000.0000.000
70A73ILE0-0.031-0.00739.579-0.007-0.0070.0000.0000.0000.000
71A74VAL00.0690.02835.307-0.017-0.0170.0000.0000.0000.000
72A75GLU-1-0.879-0.92337.314-0.346-0.3460.0000.0000.0000.000
73A76ARG10.9400.96839.4110.3340.3340.0000.0000.0000.000
74A77ARG10.9110.96732.8270.5990.5990.0000.0000.0000.000
75A78ALA00.0480.01334.819-0.021-0.0210.0000.0000.0000.000
76A79LYS10.8760.92635.8390.3400.3400.0000.0000.0000.000
77A80SER0-0.074-0.02638.219-0.008-0.0080.0000.0000.0000.000
78A81LEU0-0.071-0.03331.688-0.011-0.0110.0000.0000.0000.000
79A82GLY00.0160.02533.452-0.026-0.0260.0000.0000.0000.000
80A83ILE0-0.031-0.02030.878-0.007-0.0070.0000.0000.0000.000
81A84GLU-1-0.844-0.89031.745-0.492-0.4920.0000.0000.0000.000
82A85HIS10.8660.94530.9700.5100.5100.0000.0000.0000.000
83A86LEU0-0.013-0.00232.674-0.033-0.0330.0000.0000.0000.000
84A87PHE0-0.0040.00232.1810.0360.0360.0000.0000.0000.000
85A88GLN00.0320.00634.286-0.027-0.0270.0000.0000.0000.000
86A89GLY0-0.023-0.00436.9030.0230.0230.0000.0000.0000.000
87A90ARG10.7270.83333.9570.3060.3060.0000.0000.0000.000
88A91GLU-1-0.793-0.91133.106-0.394-0.3940.0000.0000.0000.000
89A92ASP-1-0.856-0.88631.620-0.304-0.3040.0000.0000.0000.000
90A93LYS10.8230.87727.9080.5850.5850.0000.0000.0000.000
91A94LEU0-0.0170.00024.647-0.023-0.0230.0000.0000.0000.000
92A95VAL00.0250.02127.8260.0090.0090.0000.0000.0000.000
93A96VAL0-0.081-0.03730.8030.0160.0160.0000.0000.0000.000
94A97LEU00.0220.01523.6000.0010.0010.0000.0000.0000.000
95A98ASP-1-0.776-0.88226.658-0.320-0.3200.0000.0000.0000.000
96A99LYS10.8900.94928.7490.2860.2860.0000.0000.0000.000
97A100LEU00.0240.01328.5120.0110.0110.0000.0000.0000.000
98A101LEU0-0.0040.00124.252-0.016-0.0160.0000.0000.0000.000
99A102ALA0-0.007-0.00128.3120.0180.0180.0000.0000.0000.000
100A103GLU-1-1.039-1.01931.259-0.301-0.3010.0000.0000.0000.000
101A104LEU0-0.044-0.03328.6950.0010.0010.0000.0000.0000.000
102A105GLN0-0.060-0.01629.500-0.007-0.0070.0000.0000.0000.000
103A106LEU0-0.034-0.00824.342-0.020-0.0200.0000.0000.0000.000
104A107GLY00.0380.02422.1420.0370.0370.0000.0000.0000.000
105A108TYR0-0.049-0.06719.682-0.063-0.0630.0000.0000.0000.000
106A109GLU-1-0.860-0.95416.347-0.601-0.6010.0000.0000.0000.000
107A110GLN00.0210.01917.213-0.113-0.1130.0000.0000.0000.000
108A111VAL00.0160.01019.570-0.004-0.0040.0000.0000.0000.000
109A112ALA00.0110.01218.560-0.124-0.1240.0000.0000.0000.000
110A113TYR0-0.055-0.07319.2160.1540.1540.0000.0000.0000.000
111A114LEU0-0.0150.00919.840-0.119-0.1190.0000.0000.0000.000
112A115GLY00.036-0.00921.8980.1120.1120.0000.0000.0000.000
113A116ASP-1-0.910-0.97323.093-0.810-0.8100.0000.0000.0000.000
114A117ASP-1-0.772-0.87325.072-0.538-0.5380.0000.0000.0000.000
115A118LEU0-0.036-0.04425.226-0.016-0.0160.0000.0000.0000.000
116A119PRO0-0.010-0.01526.4320.0060.0060.0000.0000.0000.000
117A120ASP-1-0.705-0.81623.884-0.687-0.6870.0000.0000.0000.000
118A121LEU0-0.0020.01819.765-0.023-0.0230.0000.0000.0000.000
119A122PRO0-0.082-0.05121.690-0.003-0.0030.0000.0000.0000.000
120A123VAL00.0340.03122.3350.0400.0400.0000.0000.0000.000
121A124ILE00.0270.02017.740-0.020-0.0200.0000.0000.0000.000
122A125ARG10.9060.94817.0230.3860.3860.0000.0000.0000.000
123A126ARG10.8430.92917.2730.4030.4030.0000.0000.0000.000
124A127VAL0-0.0290.00017.7180.0410.0410.0000.0000.0000.000
125A128GLY00.0170.01615.086-0.077-0.0770.0000.0000.0000.000
126A129LEU0-0.038-0.01913.244-0.322-0.3220.0000.0000.0000.000
127A130GLY00.0430.02015.1220.1550.1550.0000.0000.0000.000
128A131MET0-0.059-0.03215.374-0.244-0.2440.0000.0000.0000.000
129A132ALA00.0250.02017.4950.1930.1930.0000.0000.0000.000
130A133VAL00.0410.00919.552-0.160-0.1600.0000.0000.0000.000
131A134ALA00.0050.00921.6100.0310.0310.0000.0000.0000.000
132A135ASN0-0.023-0.02722.557-0.022-0.0220.0000.0000.0000.000
133A136ALA0-0.0130.01822.4130.0720.0720.0000.0000.0000.000
134A137ALA00.0370.02024.420-0.002-0.0020.0000.0000.0000.000
135A138SER0-0.062-0.03922.495-0.035-0.0350.0000.0000.0000.000
136A139PHE00.0450.02120.957-0.087-0.0870.0000.0000.0000.000
137A140VAL00.0010.00220.666-0.006-0.0060.0000.0000.0000.000
138A141ARG10.8900.94618.4020.9340.9340.0000.0000.0000.000
139A142GLU-1-0.918-0.96416.526-0.924-0.9240.0000.0000.0000.000
140A143HIS0-0.106-0.04916.0680.0990.0990.0000.0000.0000.000
141A144ALA0-0.0010.00515.6010.1000.1000.0000.0000.0000.000
142A145HIS0-0.0040.00111.034-0.233-0.2330.0000.0000.0000.000
143A146GLY0-0.004-0.00511.078-0.667-0.6670.0000.0000.0000.000
144A147ILE0-0.044-0.01613.6070.3450.3450.0000.0000.0000.000
145A148THR0-0.053-0.01816.665-0.206-0.2060.0000.0000.0000.000
146A149ARG10.9140.93215.6402.3682.3680.0000.0000.0000.000
147A150ALA00.0040.01220.5680.1200.1200.0000.0000.0000.000
148A151GLN0-0.023-0.03123.496-0.050-0.0500.0000.0000.0000.000
149A152GLY00.0510.01526.237-0.018-0.0180.0000.0000.0000.000
150A153GLY0-0.036-0.00527.7570.0460.0460.0000.0000.0000.000
151A154GLU-1-0.926-0.95528.399-0.769-0.7690.0000.0000.0000.000
152A155GLY0-0.0060.00426.553-0.033-0.0330.0000.0000.0000.000
153A156ALA0-0.0050.01123.153-0.092-0.0920.0000.0000.0000.000
154A157ALA00.0560.01622.534-0.100-0.1000.0000.0000.0000.000
155A158ARG10.7850.89223.7391.0341.0340.0000.0000.0000.000
156A159GLU-1-0.781-0.88018.692-1.911-1.9110.0000.0000.0000.000
157A160PHE00.009-0.00618.786-0.162-0.1620.0000.0000.0000.000
158A161CYS0-0.057-0.02519.446-0.027-0.0270.0000.0000.0000.000
159A162GLU-1-0.792-0.89420.586-1.306-1.3060.0000.0000.0000.000
160A163LEU0-0.0200.00513.168-0.142-0.1420.0000.0000.0000.000
161A164ILE00.022-0.00316.130-0.156-0.1560.0000.0000.0000.000
162A165LEU0-0.006-0.00617.864-0.006-0.0060.0000.0000.0000.000
163A166SER0-0.0020.00315.4080.0760.0760.0000.0000.0000.000
164A167ALA0-0.065-0.02813.745-0.099-0.0990.0000.0000.0000.000
165A168GLN0-0.095-0.05514.6850.0750.0750.0000.0000.0000.000
166A169GLY0-0.0110.01017.4640.1500.1500.0000.0000.0000.000
167A170ASN00.0330.00819.0080.1150.1150.0000.0000.0000.000
168A171LEU0-0.030-0.00919.9630.0820.0820.0000.0000.0000.000
169A172GLU-1-0.902-0.94920.790-1.268-1.2680.0000.0000.0000.000
170A173ALA0-0.0100.01423.9620.0890.0890.0000.0000.0000.000
171A174ALA0-0.015-0.01025.6720.0680.0680.0000.0000.0000.000
172A175HIS0-0.003-0.02323.5740.1150.1150.0000.0000.0000.000
173A176SER0-0.012-0.02127.6720.0500.0500.0000.0000.0000.000
174A177VAL0-0.0180.00729.8550.0440.0440.0000.0000.0000.000
175A178TYR0-0.092-0.04830.5600.0350.0350.0000.0000.0000.000
176A179LEU0-0.079-0.04628.415-0.018-0.0180.0000.0000.0000.000
177A180GLU-2-1.925-1.93032.962-1.039-1.0390.0000.0000.0000.000