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: 3ZLGL

Calculation Name: 5J6C-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | imidazole

Ligand 3-letter code: FMN | IMD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5J6C

Chain ID: A

ChEMBL ID:

UniProt ID: C9YJL7

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1830050.982295
FMO2-HF: Nuclear repulsion 1760382.78156
FMO2-HF: Total energy -69668.200734
FMO2-MP2: Total energy -69872.655506


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:7:MET)


Summations of interaction energy for fragment #1(A:7:MET)
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.
81.69787.4232.173-2.259-5.638-0.005
Interaction energy analysis for fragmet #1(A:7:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.929 / q_NPA : 0.961
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].
3A9GLY00.0510.0233.8165.9677.520-0.003-0.597-0.9530.000
4A10PHE0-0.032-0.0152.5750.2852.7830.979-1.085-2.391-0.005
5A11LEU00.0640.0202.2777.4708.9381.194-0.543-2.1190.000
101A107LEU0-0.073-0.0393.586-1.798-1.5910.003-0.034-0.1750.000
6A12LYS10.8510.9175.90135.68535.6850.0000.0000.0000.000
7A13LYS10.9570.9766.68439.18239.1820.0000.0000.0000.000
8A14ARG10.9561.0097.83727.07627.0760.0000.0000.0000.000
9A15ARG10.8600.9189.94020.88220.8820.0000.0000.0000.000
10A16SER0-0.013-0.01513.731-0.493-0.4930.0000.0000.0000.000
11A17ILE0-0.052-0.00915.6650.5810.5810.0000.0000.0000.000
12A18ARG10.9120.96318.43914.32014.3200.0000.0000.0000.000
13A19LYS10.8800.95921.77912.25412.2540.0000.0000.0000.000
14A20TYR00.012-0.00819.460-0.494-0.4940.0000.0000.0000.000
15A21LYS10.8490.90822.57113.41713.4170.0000.0000.0000.000
16A22ASP-1-0.935-0.95125.633-10.447-10.4470.0000.0000.0000.000
17A23VAL0-0.046-0.02824.4710.1900.1900.0000.0000.0000.000
18A24GLU-1-0.910-0.95424.927-11.498-11.4980.0000.0000.0000.000
19A25VAL0-0.030-0.02219.148-0.506-0.5060.0000.0000.0000.000
20A26GLU-1-0.713-0.82520.712-14.689-14.6890.0000.0000.0000.000
21A27LYS10.9330.92721.37511.54411.5440.0000.0000.0000.000
22A28GLU-1-0.866-0.92518.334-17.106-17.1060.0000.0000.0000.000
23A29LYS10.8400.92916.93216.36616.3660.0000.0000.0000.000
24A30LEU00.0480.03016.825-0.782-0.7820.0000.0000.0000.000
25A31ASP-1-0.833-0.90618.246-13.284-13.2840.0000.0000.0000.000
26A32LYS10.8280.90714.30718.59518.5950.0000.0000.0000.000
27A33ILE00.0150.00913.525-0.771-0.7710.0000.0000.0000.000
28A34LEU00.0210.01114.444-0.213-0.2130.0000.0000.0000.000
29A35LYS10.9420.96915.45015.41315.4130.0000.0000.0000.000
30A36ALA00.001-0.00210.422-0.139-0.1390.0000.0000.0000.000
31A37ALA0-0.013-0.00712.079-0.366-0.3660.0000.0000.0000.000
32A38LEU0-0.023-0.01714.1580.3280.3280.0000.0000.0000.000
33A39LEU0-0.062-0.03112.4370.5450.5450.0000.0000.0000.000
34A40ALA0-0.0020.01711.653-0.941-0.9410.0000.0000.0000.000
35A41PRO0-0.028-0.00811.0731.1671.1670.0000.0000.0000.000
36A42SER00.009-0.00313.9610.2430.2430.0000.0000.0000.000
37A43SER00.0210.00816.9890.2470.2470.0000.0000.0000.000
38A44LYS10.9080.94119.56911.06611.0660.0000.0000.0000.000
39A45GLY00.0060.01419.5550.3140.3140.0000.0000.0000.000
40A46LEU0-0.040-0.02520.6110.1000.1000.0000.0000.0000.000
41A47ARG10.8920.96017.85513.88013.8800.0000.0000.0000.000
42A48THR0-0.013-0.03620.5040.3260.3260.0000.0000.0000.000
43A49TRP0-0.041-0.01415.9370.6070.6070.0000.0000.0000.000
44A50GLU-1-0.844-0.90020.488-10.188-10.1880.0000.0000.0000.000
45A51PHE0-0.024-0.02716.683-0.326-0.3260.0000.0000.0000.000
46A52ILE00.0210.01921.4760.3180.3180.0000.0000.0000.000
47A53VAL0-0.009-0.00721.227-0.356-0.3560.0000.0000.0000.000
48A54VAL0-0.040-0.02823.4300.5030.5030.0000.0000.0000.000
49A55ASP-1-0.827-0.92224.674-11.064-11.0640.0000.0000.0000.000
50A56ASP-1-0.820-0.90926.887-8.881-8.8810.0000.0000.0000.000
51A57LYS10.9520.97629.9519.4259.4250.0000.0000.0000.000
52A58GLU-1-0.881-0.93831.390-8.443-8.4430.0000.0000.0000.000
53A59LYS10.8790.93829.7498.8828.8820.0000.0000.0000.000
54A60LEU0-0.024-0.00625.130-0.148-0.1480.0000.0000.0000.000
55A61ILE0-0.025-0.01428.718-0.213-0.2130.0000.0000.0000.000
56A62ASN0-0.0080.00631.692-0.007-0.0070.0000.0000.0000.000
57A63LEU00.0130.00326.171-0.006-0.0060.0000.0000.0000.000
58A64SER0-0.110-0.06027.758-0.154-0.1540.0000.0000.0000.000
59A65GLN0-0.015-0.01528.800-0.196-0.1960.0000.0000.0000.000
60A66CYS0-0.028-0.00626.3830.1280.1280.0000.0000.0000.000
61A67ARG10.8130.90223.67711.01311.0130.0000.0000.0000.000
62A68THR0-0.033-0.02930.241-0.096-0.0960.0000.0000.0000.000
63A69LYS10.8880.94232.5438.1978.1970.0000.0000.0000.000
64A70GLY00.0140.01729.533-0.087-0.0870.0000.0000.0000.000
65A71GLY0-0.055-0.05425.330-0.073-0.0730.0000.0000.0000.000
66A72GLY00.0760.03424.157-0.506-0.5060.0000.0000.0000.000
67A73PHE00.0090.01525.815-0.166-0.1660.0000.0000.0000.000
68A74PHE00.000-0.01921.3060.2530.2530.0000.0000.0000.000
69A75LEU00.0120.00322.985-0.171-0.1710.0000.0000.0000.000
70A76LYS10.9781.00925.5809.4409.4400.0000.0000.0000.000
71A77ASN0-0.053-0.03727.4870.5150.5150.0000.0000.0000.000
72A78ALA0-0.024-0.00922.712-0.305-0.3050.0000.0000.0000.000
73A79PRO0-0.0100.01922.6060.2940.2940.0000.0000.0000.000
74A80LEU00.0180.01119.5270.1030.1030.0000.0000.0000.000
75A81ALA0-0.021-0.01020.618-0.387-0.3870.0000.0000.0000.000
76A82ILE0-0.011-0.00216.8810.1840.1840.0000.0000.0000.000
77A83VAL0-0.0010.00519.581-0.360-0.3600.0000.0000.0000.000
78A84ILE0-0.038-0.01316.397-0.025-0.0250.0000.0000.0000.000
79A85ILE0-0.012-0.00919.9430.2980.2980.0000.0000.0000.000
80A86ALA00.0350.00521.401-0.457-0.4570.0000.0000.0000.000
81A87ASP-1-0.772-0.87023.297-9.201-9.2010.0000.0000.0000.000
82A88LYS10.7830.88926.2839.0669.0660.0000.0000.0000.000
83A89GLU-1-0.893-0.94927.270-8.363-8.3630.0000.0000.0000.000
84A90LYS10.8150.90325.19910.40910.4090.0000.0000.0000.000
85A91ASN0-0.014-0.03122.3570.2330.2330.0000.0000.0000.000
86A92ASP-1-0.847-0.90825.424-10.556-10.5560.0000.0000.0000.000
87A93VAL0-0.047-0.01520.450-0.138-0.1380.0000.0000.0000.000
88A94TRP00.0260.00120.232-0.599-0.5990.0000.0000.0000.000
89A95ILE0-0.014-0.00318.920-0.360-0.3600.0000.0000.0000.000
90A96GLU-1-0.848-0.92416.211-13.715-13.7150.0000.0000.0000.000
91A97ASP-1-0.744-0.84215.071-14.448-14.4480.0000.0000.0000.000
92A98ALA0-0.005-0.00515.390-0.703-0.7030.0000.0000.0000.000
93A99SER0-0.031-0.03513.952-0.553-0.5530.0000.0000.0000.000
94A100ILE0-0.034-0.00210.128-1.320-1.3200.0000.0000.0000.000
95A101ALA00.0480.03410.652-1.376-1.3760.0000.0000.0000.000
96A102ALA00.0320.01812.460-0.582-0.5820.0000.0000.0000.000
97A103SER0-0.061-0.0468.382-1.304-1.3040.0000.0000.0000.000
98A104TYR0-0.022-0.0217.261-2.011-2.0110.0000.0000.0000.000
99A105ILE00.0300.0228.962-0.897-0.8970.0000.0000.0000.000
100A106GLN0-0.032-0.02810.159-0.261-0.2610.0000.0000.0000.000
102A108GLN0-0.023-0.0207.554-1.145-1.1450.0000.0000.0000.000
103A109ALA00.0510.0199.8490.4150.4150.0000.0000.0000.000
104A110HIS0-0.087-0.0427.1931.9421.9420.0000.0000.0000.000
105A111GLU-1-0.981-0.9838.326-31.318-31.3180.0000.0000.0000.000
106A112LEU0-0.0210.0009.5680.6870.6870.0000.0000.0000.000
107A113GLY0-0.014-0.00212.5071.6721.6720.0000.0000.0000.000
108A114LEU0-0.047-0.00914.0661.3621.3620.0000.0000.0000.000
109A115GLY0-0.002-0.00714.193-1.335-1.3350.0000.0000.0000.000
110A116SER00.0430.01613.1940.4660.4660.0000.0000.0000.000
111A117CYS0-0.116-0.05615.600-0.531-0.5310.0000.0000.0000.000
112A118TRP00.0330.02012.8360.0920.0920.0000.0000.0000.000
113A119ILE0-0.031-0.00617.1920.3400.3400.0000.0000.0000.000
114A120GLN0-0.065-0.03019.669-0.404-0.4040.0000.0000.0000.000
115A121VAL00.0190.01621.5150.4730.4730.0000.0000.0000.000
116A122ARG10.9901.00621.09712.27912.2790.0000.0000.0000.000
117A123ASN0-0.024-0.02124.286-0.231-0.2310.0000.0000.0000.000
118A124ARG10.8390.92223.82411.04311.0430.0000.0000.0000.000
119A125MET00.0500.04427.776-0.063-0.0630.0000.0000.0000.000
120A126TYR00.0130.01730.992-0.216-0.2160.0000.0000.0000.000
121A127ASP-1-0.811-0.91032.774-7.763-7.7630.0000.0000.0000.000
122A128ASP-1-0.876-0.94335.474-7.915-7.9150.0000.0000.0000.000
123A129ASN0-0.066-0.02037.6670.2000.2000.0000.0000.0000.000
124A130ILE0-0.0150.00534.3990.0140.0140.0000.0000.0000.000
125A131GLU-1-0.893-0.95730.815-9.017-9.0170.0000.0000.0000.000
126A132ALA0-0.005-0.01627.8500.0650.0650.0000.0000.0000.000
127A133ASP-1-0.761-0.86627.425-9.679-9.6790.0000.0000.0000.000
128A134LYS10.8980.94528.7407.9167.9160.0000.0000.0000.000
129A135TYR0-0.025-0.02430.7890.1820.1820.0000.0000.0000.000
130A136ILE00.007-0.00925.8730.0410.0410.0000.0000.0000.000
131A137ARG10.8360.88829.2669.0199.0190.0000.0000.0000.000
132A138GLU-1-0.861-0.90031.237-7.703-7.7030.0000.0000.0000.000
133A139GLU-1-0.860-0.92631.352-8.527-8.5270.0000.0000.0000.000
134A140LEU0-0.050-0.03527.064-0.021-0.0210.0000.0000.0000.000
135A141LYS10.8980.96131.1617.7077.7070.0000.0000.0000.000
136A142VAL00.0250.02228.3010.0130.0130.0000.0000.0000.000
137A143PRO00.0160.00331.1690.1470.1470.0000.0000.0000.000
138A144SER00.007-0.00331.780-0.255-0.2550.0000.0000.0000.000
139A145LYS10.9370.97530.1469.0369.0360.0000.0000.0000.000
140A146TYR0-0.077-0.06026.230-0.038-0.0380.0000.0000.0000.000
141A147SER0-0.046-0.01925.5600.3680.3680.0000.0000.0000.000
142A148VAL00.013-0.00323.690-0.386-0.3860.0000.0000.0000.000
143A149GLU-1-0.782-0.88118.436-12.723-12.7230.0000.0000.0000.000
144A150CYS0-0.064-0.03516.6800.0200.0200.0000.0000.0000.000
145A151ILE00.0520.03220.3570.1130.1130.0000.0000.0000.000
146A152ILE0-0.024-0.00514.700-0.465-0.4650.0000.0000.0000.000
147A153SER00.016-0.00717.7910.2910.2910.0000.0000.0000.000
148A154ILE0-0.016-0.03516.134-1.118-1.1180.0000.0000.0000.000
149A155GLY00.0840.03318.3300.8370.8370.0000.0000.0000.000
150A156TYR0-0.021-0.03218.131-1.274-1.2740.0000.0000.0000.000
151A157SER00.004-0.00718.1820.8180.8180.0000.0000.0000.000
152A158ASP-1-0.817-0.91020.216-11.806-11.8060.0000.0000.0000.000
153A159GLU-1-0.824-0.89920.741-13.484-13.4840.0000.0000.0000.000
154A160GLU-1-0.907-0.93919.359-14.982-14.9820.0000.0000.0000.000
155A161LYS10.8280.89416.33915.18415.1840.0000.0000.0000.000
156A162LYS10.9851.00716.01216.16016.1600.0000.0000.0000.000
157A163ALA00.0220.01111.095-0.301-0.3010.0000.0000.0000.000
158A164TYR0-0.061-0.02711.1521.6251.6250.0000.0000.0000.000
159A165ASN0-0.027-0.03611.826-2.807-2.8070.0000.0000.0000.000
160A166ASP-1-0.799-0.90611.529-27.378-27.3780.0000.0000.0000.000
161A167SER0-0.0060.00713.7180.4170.4170.0000.0000.0000.000
162A168ASP-1-0.860-0.92314.254-18.156-18.1560.0000.0000.0000.000
163A169LEU0-0.064-0.0149.970-0.371-0.3710.0000.0000.0000.000
164A170ASP-1-0.764-0.88113.792-14.384-14.3840.0000.0000.0000.000
165A171TYR00.034-0.00712.8390.0880.0880.0000.0000.0000.000
166A172LYS10.8740.94316.71914.31414.3140.0000.0000.0000.000
167A173LYS10.8650.92815.93615.79615.7960.0000.0000.0000.000
168A174VAL0-0.0240.00314.381-0.306-0.3060.0000.0000.0000.000
169A175HIS10.7890.87917.00213.92713.9270.0000.0000.0000.000
170A176PHE00.0490.01817.050-0.648-0.6480.0000.0000.0000.000
171A177ASN0-0.013-0.00421.1540.2770.2770.0000.0000.0000.000
172A178ASN0-0.020-0.00623.2870.4730.4730.0000.0000.0000.000
173A179PHE-1-0.823-0.88322.658-12.154-12.1540.0000.0000.0000.000