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: KQQ43

Calculation Name: 4M0C-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | glycerol | zinc ion

Ligand 3-letter code: FMN | GOL | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4M0C

Chain ID: A

ChEMBL ID:

UniProt ID: Q81UB2

Base Structure: X-ray

Registration Date: 2025-10-06

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2556032.367113
FMO2-HF: Nuclear repulsion 2470453.887733
FMO2-HF: Total energy -85578.47938
FMO2-MP2: Total energy -85827.970719


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-148.108-144.1953.336-2.015-5.231-0.015
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.803 / q_NPA : 0.892
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].
3A3LYS10.8460.8992.45133.69037.1591.306-1.504-3.272-0.012
4A4THR00.0200.0184.4753.3653.4740.000-0.032-0.0760.000
38A38ASN0-0.084-0.0583.985-5.129-4.6980.000-0.094-0.3360.000
39A39GLU-1-0.817-0.8764.562-49.777-49.713-0.001-0.013-0.0490.000
40A40THR0-0.057-0.0222.4624.9924.6402.032-0.355-1.324-0.003
42A42GLU-1-0.807-0.8775.141-27.840-27.758-0.0010.000-0.0810.000
92A92ALA0-0.0050.0064.657-5.600-5.4900.000-0.017-0.0930.000
5A5LEU0-0.029-0.0097.7650.6740.6740.0000.0000.0000.000
6A6ILE0-0.021-0.0129.4771.1401.1400.0000.0000.0000.000
7A7ILE0-0.002-0.00512.9700.3530.3530.0000.0000.0000.000
8A8ASN0-0.016-0.03015.5560.9770.9770.0000.0000.0000.000
9A9ALA00.0100.00518.4980.3470.3470.0000.0000.0000.000
10A10HIS00.0510.01321.6470.6660.6660.0000.0000.0000.000
11A11PRO0-0.026-0.01824.032-0.065-0.0650.0000.0000.0000.000
12A12LYS10.8300.90326.6349.4019.4010.0000.0000.0000.000
13A13VAL00.0380.03321.1470.0240.0240.0000.0000.0000.000
14A14ASP-1-0.876-0.92821.785-11.990-11.9900.0000.0000.0000.000
15A15ASP-1-0.756-0.84123.462-9.364-9.3640.0000.0000.0000.000
16A16THR00.0370.00725.739-0.024-0.0240.0000.0000.0000.000
17A17SER0-0.055-0.05027.8760.1550.1550.0000.0000.0000.000
18A18SER0-0.047-0.02626.7810.1910.1910.0000.0000.0000.000
19A19VAL00.0510.02527.793-0.259-0.2590.0000.0000.0000.000
20A20SER00.0420.00224.094-0.135-0.1350.0000.0000.0000.000
21A21ILE0-0.0150.00522.878-0.525-0.5250.0000.0000.0000.000
22A22LYS10.8610.93223.2139.3599.3590.0000.0000.0000.000
23A23VAL00.0030.00523.256-0.260-0.2600.0000.0000.0000.000
24A24PHE00.0250.01115.735-0.299-0.2990.0000.0000.0000.000
25A25LYS10.8800.94019.33511.51411.5140.0000.0000.0000.000
26A26HIS10.7950.87120.45011.98211.9820.0000.0000.0000.000
27A27PHE00.0280.02014.346-0.090-0.0900.0000.0000.0000.000
28A28LEU0-0.030-0.02013.625-0.677-0.6770.0000.0000.0000.000
29A29GLU-1-0.896-0.93916.687-13.220-13.2200.0000.0000.0000.000
30A30SER00.0430.00518.545-0.343-0.3430.0000.0000.0000.000
31A31TYR0-0.033-0.03310.076-0.086-0.0860.0000.0000.0000.000
32A32LYS10.8810.92813.20016.46316.4630.0000.0000.0000.000
33A33GLU-1-0.976-0.97015.313-14.258-14.2580.0000.0000.0000.000
34A34LEU0-0.039-0.01016.3680.1910.1910.0000.0000.0000.000
35A35ILE0-0.0100.01310.331-0.944-0.9440.0000.0000.0000.000
36A36SER00.0190.0138.5200.8940.8940.0000.0000.0000.000
37A37ASN0-0.010-0.0199.668-1.706-1.7060.0000.0000.0000.000
41A41ILE00.0320.0025.417-0.871-0.8710.0000.0000.0000.000
43A43GLN0-0.038-0.0468.620-0.046-0.0460.0000.0000.0000.000
44A44ILE0-0.0150.01212.2150.2200.2200.0000.0000.0000.000
45A45ASN00.0400.02614.692-0.149-0.1490.0000.0000.0000.000
46A46LEU0-0.009-0.01117.3150.4720.4720.0000.0000.0000.000
47A47TYR0-0.061-0.04620.3090.4670.4670.0000.0000.0000.000
48A48ASP-1-0.933-0.96021.081-11.620-11.6200.0000.0000.0000.000
49A49ASP-1-0.812-0.89016.774-14.600-14.6000.0000.0000.0000.000
50A50VAL0-0.032-0.02519.5070.3010.3010.0000.0000.0000.000
51A51VAL00.0560.03218.346-0.665-0.6650.0000.0000.0000.000
52A52PRO0-0.0140.00320.2360.6220.6220.0000.0000.0000.000
53A53MET00.0180.02822.948-0.227-0.2270.0000.0000.0000.000
54A54ILE00.0150.00725.7100.0230.0230.0000.0000.0000.000
55A55ASP-1-0.812-0.91227.476-9.352-9.3520.0000.0000.0000.000
56A56LYS10.9430.94830.4287.7717.7710.0000.0000.0000.000
57A57THR0-0.0170.00428.9180.1800.1800.0000.0000.0000.000
58A58VAL00.0350.01625.261-0.061-0.0610.0000.0000.0000.000
59A59LEU0-0.025-0.00627.568-0.096-0.0960.0000.0000.0000.000
60A60SER0-0.051-0.04430.2710.1140.1140.0000.0000.0000.000
61A61ALA00.007-0.00326.7590.0450.0450.0000.0000.0000.000
62A62TRP00.019-0.00722.6560.0220.0220.0000.0000.0000.000
63A63GLU-1-0.890-0.92227.838-8.910-8.9100.0000.0000.0000.000
64A64LYS10.8010.88530.3258.8598.8590.0000.0000.0000.000
65A65GLN00.007-0.01123.572-0.132-0.1320.0000.0000.0000.000
66A66GLY0-0.045-0.00428.068-0.233-0.2330.0000.0000.0000.000
67A67ASN0-0.086-0.06130.1640.0720.0720.0000.0000.0000.000
68A68GLY0-0.0210.00630.2550.1660.1660.0000.0000.0000.000
69A69GLN0-0.061-0.03831.3320.1450.1450.0000.0000.0000.000
70A70GLU-1-0.858-0.91629.145-10.058-10.0580.0000.0000.0000.000
71A71LEU0-0.055-0.03526.1390.1730.1730.0000.0000.0000.000
72A72THR0-0.058-0.05830.0820.1240.1240.0000.0000.0000.000
73A73ARG10.9850.97027.7919.0299.0290.0000.0000.0000.000
74A74GLU-1-0.833-0.90427.214-9.817-9.8170.0000.0000.0000.000
75A75GLU-1-0.716-0.79026.778-9.394-9.3940.0000.0000.0000.000
76A76GLN0-0.0280.00324.698-0.369-0.3690.0000.0000.0000.000
77A77LYS10.8850.93922.9279.6439.6430.0000.0000.0000.000
78A78VAL0-0.016-0.00521.957-0.441-0.4410.0000.0000.0000.000
79A79THR0-0.003-0.02521.635-0.481-0.4810.0000.0000.0000.000
80A80GLU-1-0.892-0.91716.833-15.046-15.0460.0000.0000.0000.000
81A81ARG10.8110.88814.29514.35914.3590.0000.0000.0000.000
82A82MET0-0.027-0.02617.042-0.375-0.3750.0000.0000.0000.000
83A83SER0-0.009-0.01016.209-0.712-0.7120.0000.0000.0000.000
84A84GLU-1-0.888-0.93212.834-16.473-16.4730.0000.0000.0000.000
85A85ILE0-0.033-0.00812.007-1.317-1.3170.0000.0000.0000.000
86A86LEU0-0.0200.00413.086-1.118-1.1180.0000.0000.0000.000
87A87GLN0-0.020-0.03010.386-2.693-2.6930.0000.0000.0000.000
88A88GLN0-0.050-0.0228.231-1.124-1.1240.0000.0000.0000.000
89A89PHE00.0170.0128.284-2.484-2.4840.0000.0000.0000.000
90A90LYS10.8340.9029.97319.57319.5730.0000.0000.0000.000
91A91SER0-0.081-0.0245.027-3.097-3.0970.0000.0000.0000.000
93A93ASN00.009-0.0045.5611.4921.4920.0000.0000.0000.000
94A94THR00.0390.0297.8273.1163.1160.0000.0000.0000.000
95A95TYR0-0.021-0.0279.671-0.346-0.3460.0000.0000.0000.000
96A96VAL00.0090.00012.3840.8940.8940.0000.0000.0000.000
97A97ILE00.0050.01414.9980.3500.3500.0000.0000.0000.000
98A98VAL0-0.0010.00817.8310.4440.4440.0000.0000.0000.000
99A99LEU00.003-0.00820.4480.1740.1740.0000.0000.0000.000
100A100PRO0-0.0350.00923.9460.1040.1040.0000.0000.0000.000
101A101LEU0-0.002-0.00527.674-0.124-0.1240.0000.0000.0000.000
102A102HIS00.008-0.00129.8330.4220.4220.0000.0000.0000.000
103A103ASN0-0.026-0.02931.8760.0070.0070.0000.0000.0000.000
104A104PHE00.0190.00833.2910.0510.0510.0000.0000.0000.000
105A105ASN00.0320.02729.817-0.383-0.3830.0000.0000.0000.000
106A106ILE00.0110.00224.414-0.107-0.1070.0000.0000.0000.000
107A107PRO0-0.0070.00424.7330.3060.3060.0000.0000.0000.000
108A108SER00.0270.01025.665-0.367-0.3670.0000.0000.0000.000
109A109LYS10.8550.90922.94011.18711.1870.0000.0000.0000.000
110A110LEU00.0340.01419.709-0.513-0.5130.0000.0000.0000.000
111A111LYS10.7940.88122.07410.69210.6920.0000.0000.0000.000
112A112ASP-1-0.792-0.89223.363-11.180-11.1800.0000.0000.0000.000
113A113TYR00.0600.02313.135-0.334-0.3340.0000.0000.0000.000
114A114MET0-0.023-0.01319.011-0.747-0.7470.0000.0000.0000.000
115A115ASP-1-0.824-0.89120.806-11.724-11.7240.0000.0000.0000.000
116A116ASN0-0.044-0.04517.924-0.011-0.0110.0000.0000.0000.000
117A117ILE00.0120.01115.135-0.437-0.4370.0000.0000.0000.000
118A118MET0-0.0190.01617.423-0.646-0.6460.0000.0000.0000.000
119A119ILE00.0300.01719.1290.8000.8000.0000.0000.0000.000
120A120ALA00.0260.01319.964-0.534-0.5340.0000.0000.0000.000
121A121ARG10.8630.91120.47912.85112.8510.0000.0000.0000.000
122A122GLU-1-0.818-0.87215.510-18.931-18.9310.0000.0000.0000.000
123A123THR0-0.003-0.02414.662-1.069-1.0690.0000.0000.0000.000
124A124PHE0-0.0020.00816.866-0.073-0.0730.0000.0000.0000.000
125A125LYS10.9460.98020.18714.43314.4330.0000.0000.0000.000
126A126TYR00.0620.01822.7780.1100.1100.0000.0000.0000.000
127A127THR0-0.064-0.05325.540-0.405-0.4050.0000.0000.0000.000
128A128GLU-1-0.879-0.93628.107-9.394-9.3940.0000.0000.0000.000
129A129THR0-0.036-0.01528.9660.1790.1790.0000.0000.0000.000
130A130GLY00.0290.01830.3240.1840.1840.0000.0000.0000.000
131A131SER0-0.049-0.02125.442-0.168-0.1680.0000.0000.0000.000
132A132VAL0-0.040-0.01521.2610.1450.1450.0000.0000.0000.000
133A133GLY00.0470.03619.415-0.095-0.0950.0000.0000.0000.000
134A134LEU0-0.081-0.05115.9060.3180.3180.0000.0000.0000.000
135A135LEU0-0.0100.00911.822-0.989-0.9890.0000.0000.0000.000
136A136LYS10.8830.95313.92415.86315.8630.0000.0000.0000.000
137A137ASP-1-0.845-0.8859.044-29.677-29.6770.0000.0000.0000.000
138A138GLY0-0.010-0.0059.669-2.736-2.7360.0000.0000.0000.000
139A139ARG10.7300.8348.54930.73430.7340.0000.0000.0000.000
140A140ARG10.8400.91311.22728.34228.3420.0000.0000.0000.000
141A141MET0-0.048-0.01912.967-0.498-0.4980.0000.0000.0000.000
142A142LEU0-0.0070.01115.6520.9960.9960.0000.0000.0000.000
143A143VAL0-0.015-0.00817.686-0.181-0.1810.0000.0000.0000.000
144A144ILE00.0190.01319.3000.5020.5020.0000.0000.0000.000
145A145GLN00.0240.01722.3680.0750.0750.0000.0000.0000.000
146A146ALA0-0.013-0.00325.6820.1670.1670.0000.0000.0000.000
147A147SER00.001-0.01228.650-0.041-0.0410.0000.0000.0000.000
148A148GLY00.0130.03632.1040.0780.0780.0000.0000.0000.000
149A149GLY00.0660.03135.8380.1710.1710.0000.0000.0000.000
150A150ILE00.0150.00135.118-0.304-0.3040.0000.0000.0000.000
151A151TYR00.003-0.00932.7790.1960.1960.0000.0000.0000.000
152A152THR0-0.0430.00132.153-0.189-0.1890.0000.0000.0000.000
153A153ASN00.0010.00435.109-0.063-0.0630.0000.0000.0000.000
154A154ASP-1-0.916-0.94436.933-8.567-8.5670.0000.0000.0000.000
155A155ASP-1-0.829-0.91439.106-7.720-7.7200.0000.0000.0000.000
156A156TRP00.019-0.00639.672-0.183-0.1830.0000.0000.0000.000
157A157TYR00.000-0.01536.979-0.124-0.1240.0000.0000.0000.000
158A158THR0-0.028-0.02734.653-0.186-0.1860.0000.0000.0000.000
159A159ASP-1-0.938-0.97135.273-8.436-8.4360.0000.0000.0000.000
160A160VAL0-0.051-0.01136.119-0.193-0.1930.0000.0000.0000.000
161A161GLU-1-0.733-0.82130.227-10.610-10.6100.0000.0000.0000.000
162A162TYR0-0.028-0.02830.828-0.312-0.3120.0000.0000.0000.000
163A163SER0-0.003-0.00827.003-0.206-0.2060.0000.0000.0000.000
164A164HIS00.0520.02425.950-0.763-0.7630.0000.0000.0000.000
165A165LYS10.8390.92226.3228.9138.9130.0000.0000.0000.000
166A166TYR00.0050.00324.069-0.081-0.0810.0000.0000.0000.000
167A167LEU00.0190.00721.148-0.382-0.3820.0000.0000.0000.000
168A168LYS10.9620.99422.32511.94011.9400.0000.0000.0000.000
169A169ALA0-0.017-0.00123.238-0.423-0.4230.0000.0000.0000.000
170A170MET0-0.014-0.00622.475-0.243-0.2430.0000.0000.0000.000
171A171PHE00.0540.01116.863-0.495-0.4950.0000.0000.0000.000
172A172ASN0-0.030-0.03019.030-0.032-0.0320.0000.0000.0000.000
173A173PHE0-0.053-0.01220.760-0.282-0.2820.0000.0000.0000.000
174A174LEU00.008-0.02117.374-0.163-0.1630.0000.0000.0000.000
175A175GLY0-0.027-0.02416.589-0.701-0.7010.0000.0000.0000.000
176A176ILE00.0100.01914.258-0.680-0.6800.0000.0000.0000.000
177A177GLU-1-0.899-0.95116.357-15.065-15.0650.0000.0000.0000.000
178A178ASP-1-0.881-0.90315.642-18.323-18.3230.0000.0000.0000.000
179A179TYR00.023-0.00717.140-0.725-0.7250.0000.0000.0000.000
180A180GLN00.0350.02319.6050.0450.0450.0000.0000.0000.000
181A181ILE0-0.044-0.02620.981-0.324-0.3240.0000.0000.0000.000
182A182VAL00.0130.01822.6720.3240.3240.0000.0000.0000.000
183A183ARG10.7920.86224.97810.78510.7850.0000.0000.0000.000
184A184ALA00.0440.02427.8270.2840.2840.0000.0000.0000.000
185A185GLN00.016-0.01429.4600.1890.1890.0000.0000.0000.000
186A186GLY00.0540.00932.5560.0720.0720.0000.0000.0000.000
187A187THR0-0.051-0.04132.5530.2370.2370.0000.0000.0000.000
188A188ALA0-0.057-0.02735.8280.1090.1090.0000.0000.0000.000
189A189VAL0-0.068-0.03439.0700.2110.2110.0000.0000.0000.000
190A190LEU0-0.0120.00836.3580.1380.1380.0000.0000.0000.000
191A191ASP-1-0.818-0.89039.318-7.782-7.7820.0000.0000.0000.000
192A192PRO0-0.006-0.02235.861-0.259-0.2590.0000.0000.0000.000
193A193THR0-0.046-0.03134.606-0.343-0.3430.0000.0000.0000.000
194A194GLU-1-0.891-0.94834.795-8.340-8.3400.0000.0000.0000.000
195A195VAL0-0.017-0.00331.554-0.293-0.2930.0000.0000.0000.000
196A196LEU0-0.043-0.02429.543-0.388-0.3880.0000.0000.0000.000
197A197GLN00.0080.00029.775-0.311-0.3110.0000.0000.0000.000
198A198ASN0-0.036-0.01230.462-0.368-0.3680.0000.0000.0000.000
199A199ALA00.0730.03127.103-0.369-0.3690.0000.0000.0000.000
200A200TYR0-0.037-0.04125.771-0.540-0.5400.0000.0000.0000.000
201A201LYS10.9861.00725.4149.8329.8320.0000.0000.0000.000
202A202GLU-1-0.877-0.95125.311-11.800-11.8000.0000.0000.0000.000
203A203VAL0-0.059-0.03621.046-0.683-0.6830.0000.0000.0000.000
204A204GLU-1-0.814-0.86920.911-12.650-12.6500.0000.0000.0000.000
205A205GLU-1-0.929-0.96321.714-12.698-12.6980.0000.0000.0000.000
206A206ALA0-0.044-0.02819.236-0.700-0.7000.0000.0000.0000.000
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