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: JV869

Calculation Name: 6CZP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | triethylene glycol | glycerol | di(hydroxyethyl)ether | chloride ion

Ligand 3-letter code: FMN | PGE | GOL | PEG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6CZP

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MCD2

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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2437019.363287
FMO2-HF: Nuclear repulsion 2351522.546677
FMO2-HF: Total energy -85496.816609
FMO2-MP2: Total energy -85746.336072


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:ASN)


Summations of interaction energy for fragment #1(A:-1:ASN)
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.
-47.724-42.1751.747-2.786-4.511-0.026
Interaction energy analysis for fragmet #1(A:-1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.882 / q_NPA : 0.934
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].
3A1MET00.0640.0272.9053.1245.2390.085-0.691-1.508-0.002
4A2THR00.0360.0132.321-9.842-7.0241.663-1.942-2.540-0.024
5A3ILE00.0280.0213.8967.6728.1870.000-0.147-0.3680.000
6A4VAL00.0230.0175.3706.6626.763-0.001-0.006-0.0950.000
7A5GLN00.0620.0327.1324.0044.0040.0000.0000.0000.000
8A6ALA00.0200.0397.5053.8893.8890.0000.0000.0000.000
9A7ALA00.0190.0049.1423.5503.5500.0000.0000.0000.000
10A8GLN0-0.063-0.03711.3842.2412.2410.0000.0000.0000.000
11A9SER0-0.033-0.04011.4132.0702.0700.0000.0000.0000.000
12A10ARG10.9240.99713.28919.93019.9300.0000.0000.0000.000
13A11TYR0-0.061-0.06014.9870.5080.5080.0000.0000.0000.000
14A12SER0-0.037-0.01718.743-0.484-0.4840.0000.0000.0000.000
15A13THR00.0250.01821.3720.4020.4020.0000.0000.0000.000
16A14LYS10.8370.90523.13212.22112.2210.0000.0000.0000.000
17A15ALA00.0010.00626.2920.4650.4650.0000.0000.0000.000
18A16PHE00.0060.00221.969-0.459-0.4590.0000.0000.0000.000
19A17ASP-1-0.818-0.89525.406-10.978-10.9780.0000.0000.0000.000
20A18ALA00.0310.01726.874-0.188-0.1880.0000.0000.0000.000
21A19SER0-0.106-0.06928.8050.1750.1750.0000.0000.0000.000
22A20ARG10.8880.95820.10113.92813.9280.0000.0000.0000.000
23A21LYS10.9220.95624.97810.44210.4420.0000.0000.0000.000
24A22LEU0-0.028-0.01718.742-0.420-0.4200.0000.0000.0000.000
25A23PRO0-0.0010.00519.1730.5670.5670.0000.0000.0000.000
26A24GLU-1-0.773-0.90520.440-13.553-13.5530.0000.0000.0000.000
27A25GLU-1-0.942-0.95516.022-17.993-17.9930.0000.0000.0000.000
28A26LYS10.8880.94014.74418.87418.8740.0000.0000.0000.000
29A27VAL0-0.0020.00617.164-0.309-0.3090.0000.0000.0000.000
30A28ALA0-0.019-0.01619.4330.1610.1610.0000.0000.0000.000
31A29ALA00.0210.01414.045-0.031-0.0310.0000.0000.0000.000
32A30VAL00.001-0.00915.861-0.403-0.4030.0000.0000.0000.000
33A31LYS10.8400.90617.30413.21913.2190.0000.0000.0000.000
34A32GLU-1-0.810-0.87317.089-14.638-14.6380.0000.0000.0000.000
35A33LEU0-0.060-0.02512.684-0.147-0.1470.0000.0000.0000.000
36A34ILE0-0.013-0.00515.9950.1240.1240.0000.0000.0000.000
37A35ARG10.8210.89419.12814.32014.3200.0000.0000.0000.000
38A36MET0-0.017-0.00316.8790.4660.4660.0000.0000.0000.000
39A37SER0-0.0260.00917.427-0.786-0.7860.0000.0000.0000.000
40A38ALA00.0140.00817.9590.7710.7710.0000.0000.0000.000
41A39SER00.0380.00819.8150.3800.3800.0000.0000.0000.000
42A40SER0-0.011-0.00423.3240.2440.2440.0000.0000.0000.000
43A41VAL0-0.015-0.00826.0520.2620.2620.0000.0000.0000.000
44A42ASN0-0.012-0.01424.612-0.083-0.0830.0000.0000.0000.000
45A43SER00.011-0.01126.2300.1380.1380.0000.0000.0000.000
46A44GLN0-0.0040.00424.3270.1690.1690.0000.0000.0000.000
47A45PRO0-0.0060.01926.2530.2300.2300.0000.0000.0000.000
48A46TRP0-0.009-0.02621.9620.0920.0920.0000.0000.0000.000
49A47HIS00.0050.00627.8810.0240.0240.0000.0000.0000.000
50A48PHE00.008-0.00423.117-0.122-0.1220.0000.0000.0000.000
51A49ILE0-0.0180.01227.2890.2270.2270.0000.0000.0000.000
52A50VAL00.006-0.00724.396-0.334-0.3340.0000.0000.0000.000
53A51ALA0-0.0060.01327.1150.2280.2280.0000.0000.0000.000
54A52SER00.007-0.01527.223-0.349-0.3490.0000.0000.0000.000
55A53SER0-0.009-0.00428.883-0.067-0.0670.0000.0000.0000.000
56A54GLU-1-0.796-0.89831.689-9.954-9.9540.0000.0000.0000.000
57A55GLU-1-0.814-0.90234.181-8.652-8.6520.0000.0000.0000.000
58A56GLY0-0.012-0.00233.4370.0950.0950.0000.0000.0000.000
59A57LYS10.7580.85928.64210.26910.2690.0000.0000.0000.000
60A58ALA00.001-0.00532.4330.0310.0310.0000.0000.0000.000
61A59ARG10.8220.90035.9518.4078.4070.0000.0000.0000.000
62A60ILE00.0220.00730.0860.0980.0980.0000.0000.0000.000
63A61ALA00.0070.00733.9860.0450.0450.0000.0000.0000.000
64A62LYS10.8590.91334.9587.7287.7280.0000.0000.0000.000
65A63ALA00.0080.01734.9530.1850.1850.0000.0000.0000.000
66A64THR0-0.036-0.01632.185-0.112-0.1120.0000.0000.0000.000
67A65GLN00.008-0.00635.6170.1830.1830.0000.0000.0000.000
68A66GLY00.0270.01639.1890.0040.0040.0000.0000.0000.000
69A67GLY0-0.008-0.00539.870-0.100-0.1000.0000.0000.0000.000
70A68PHE00.006-0.00235.209-0.228-0.2280.0000.0000.0000.000
71A69ALA00.0390.02835.134-0.266-0.2660.0000.0000.0000.000
72A70PHE0-0.030-0.01031.233-0.213-0.2130.0000.0000.0000.000
73A71ASN0-0.041-0.03230.432-0.655-0.6550.0000.0000.0000.000
74A72GLU-1-0.836-0.89831.258-8.687-8.6870.0000.0000.0000.000
75A73ARG10.8500.88332.1268.9648.9640.0000.0000.0000.000
76A74LYS10.8060.90726.81210.48910.4890.0000.0000.0000.000
77A75ILE00.0030.00427.614-0.427-0.4270.0000.0000.0000.000
78A76LEU0-0.015-0.00929.752-0.073-0.0730.0000.0000.0000.000
79A77ASP-1-0.796-0.86229.588-9.708-9.7080.0000.0000.0000.000
80A78ALA0-0.0220.00825.239-0.297-0.2970.0000.0000.0000.000
81A79SER0-0.028-0.02623.5120.4360.4360.0000.0000.0000.000
82A80HIS00.0270.02523.0380.2090.2090.0000.0000.0000.000
83A81VAL0-0.014-0.01224.493-0.315-0.3150.0000.0000.0000.000
84A82VAL00.0050.01321.6970.3310.3310.0000.0000.0000.000
85A83VAL00.003-0.00224.930-0.084-0.0840.0000.0000.0000.000
86A84PHE00.0230.00120.2740.0380.0380.0000.0000.0000.000
87A85CYS0-0.027-0.01026.4530.4150.4150.0000.0000.0000.000
88A86ALA00.0380.02328.745-0.326-0.3260.0000.0000.0000.000
89A87LYS10.8910.96630.4439.3589.3580.0000.0000.0000.000
90A88THR0-0.023-0.02033.287-0.030-0.0300.0000.0000.0000.000
91A89ALA0-0.010-0.00536.4790.1470.1470.0000.0000.0000.000
92A90ILE0-0.028-0.03033.184-0.185-0.1850.0000.0000.0000.000
93A91ASP-1-0.913-0.96437.086-7.718-7.7180.0000.0000.0000.000
94A92GLU-1-0.809-0.90938.308-7.970-7.9700.0000.0000.0000.000
95A93ALA00.0030.01139.509-0.079-0.0790.0000.0000.0000.000
96A94TYR00.037-0.00230.088-0.068-0.0680.0000.0000.0000.000
97A95LEU0-0.047-0.03134.295-0.315-0.3150.0000.0000.0000.000
98A96LEU00.0060.00735.258-0.171-0.1710.0000.0000.0000.000
99A97ASP-1-0.904-0.94735.254-8.411-8.4110.0000.0000.0000.000
100A98LEU0-0.061-0.01628.832-0.166-0.1660.0000.0000.0000.000
101A99LEU0-0.030-0.00831.919-0.249-0.2490.0000.0000.0000.000
102A100GLU-1-0.824-0.91233.935-8.383-8.3830.0000.0000.0000.000
103A101SER0-0.099-0.05630.543-0.161-0.1610.0000.0000.0000.000
104A102GLU-1-0.735-0.85228.366-10.843-10.8430.0000.0000.0000.000
105A103ASP-1-0.814-0.90830.386-8.923-8.9230.0000.0000.0000.000
106A104LYS10.8630.94232.7128.6268.6260.0000.0000.0000.000
107A105ASP-1-0.948-0.95927.087-11.310-11.3100.0000.0000.0000.000
108A106GLY0-0.039-0.01527.863-0.354-0.3540.0000.0000.0000.000
109A107ARG10.8590.92623.72611.98811.9880.0000.0000.0000.000
110A108PHE0-0.055-0.02728.830-0.100-0.1000.0000.0000.0000.000
111A109ALA00.0060.01932.0350.0140.0140.0000.0000.0000.000
112A110ASP-1-0.895-0.94733.927-8.360-8.3600.0000.0000.0000.000
113A111VAL00.025-0.00136.473-0.154-0.1540.0000.0000.0000.000
114A112GLU-1-0.846-0.93038.654-7.558-7.5580.0000.0000.0000.000
115A113ALA0-0.033-0.01232.995-0.088-0.0880.0000.0000.0000.000
116A114LYS10.8000.89634.1278.2198.2190.0000.0000.0000.000
117A115ASN0-0.026-0.02835.606-0.073-0.0730.0000.0000.0000.000
118A116GLY00.000-0.00235.7080.0330.0330.0000.0000.0000.000
119A117MET0-0.029-0.00628.321-0.141-0.1410.0000.0000.0000.000
120A118HIS00.001-0.00933.247-0.311-0.3110.0000.0000.0000.000
121A119ALA00.0090.01835.9610.0360.0360.0000.0000.0000.000
122A120GLY00.0060.00233.4530.0300.0300.0000.0000.0000.000
123A121ARG10.7940.86329.9089.8989.8980.0000.0000.0000.000
124A122SER00.033-0.01233.2220.0080.0080.0000.0000.0000.000
125A123PHE0-0.039-0.00434.7660.1570.1570.0000.0000.0000.000
126A124PHE00.003-0.00330.4860.0400.0400.0000.0000.0000.000
127A125VAL00.0020.00533.4790.0190.0190.0000.0000.0000.000
128A126ASN00.036-0.00235.4130.1100.1100.0000.0000.0000.000
129A127MET00.0310.03935.0010.0530.0530.0000.0000.0000.000
130A128HIS10.8280.87931.6579.6039.6030.0000.0000.0000.000
131A129ARG10.8810.95836.5157.8607.8600.0000.0000.0000.000
132A130PHE0-0.046-0.02539.4650.1510.1510.0000.0000.0000.000
133A131ASP-1-0.890-0.94239.999-7.442-7.4420.0000.0000.0000.000
134A132LEU0-0.038-0.04035.1760.0680.0680.0000.0000.0000.000
135A133LYS10.8690.95739.0317.1137.1130.0000.0000.0000.000
136A134ASP-1-0.779-0.87033.911-9.204-9.2040.0000.0000.0000.000
137A135ALA00.0090.00134.553-0.294-0.2940.0000.0000.0000.000
138A136HIS00.0510.03733.444-0.288-0.2880.0000.0000.0000.000
139A137HIS00.0310.00032.118-0.087-0.0870.0000.0000.0000.000
140A138TRP0-0.089-0.04329.010-0.321-0.3210.0000.0000.0000.000
141A139MET00.0200.01628.820-0.456-0.4560.0000.0000.0000.000
142A140GLU-1-0.826-0.91427.827-10.152-10.1520.0000.0000.0000.000
143A141LYS10.8910.95126.1219.7199.7190.0000.0000.0000.000
144A142GLN0-0.0080.00123.869-1.027-1.0270.0000.0000.0000.000
145A143VAL00.0250.01222.831-0.646-0.6460.0000.0000.0000.000
146A144TYR0-0.058-0.06022.737-0.532-0.5320.0000.0000.0000.000
147A145LEU0-0.046-0.00818.326-0.681-0.6810.0000.0000.0000.000
148A146ASN0-0.008-0.01018.331-1.443-1.4430.0000.0000.0000.000
149A147VAL00.0370.02318.265-0.850-0.8500.0000.0000.0000.000
150A148GLY0-0.008-0.00417.202-0.631-0.6310.0000.0000.0000.000
151A149THR0-0.067-0.04813.925-1.455-1.4550.0000.0000.0000.000
152A150LEU00.0480.02913.560-1.470-1.4700.0000.0000.0000.000
153A151LEU0-0.033-0.02314.847-0.745-0.7450.0000.0000.0000.000
154A152LEU0-0.036-0.0149.110-0.553-0.5530.0000.0000.0000.000
155A153GLY00.0260.00610.168-2.262-2.2620.0000.0000.0000.000
156A154ALA00.0350.00311.189-0.737-0.7370.0000.0000.0000.000
157A155SER0-0.052-0.03011.144-0.317-0.3170.0000.0000.0000.000
158A156ALA0-0.014-0.0136.909-1.035-1.0350.0000.0000.0000.000
159A157MET0-0.052-0.0038.571-0.887-0.8870.0000.0000.0000.000
160A158GLU-1-0.932-0.96310.630-24.028-24.0280.0000.0000.0000.000
161A159ILE0-0.087-0.04413.1891.8711.8710.0000.0000.0000.000
162A160ASP-1-0.825-0.89015.767-16.893-16.8930.0000.0000.0000.000
163A161ALA00.047-0.00117.7270.5570.5570.0000.0000.0000.000
164A162VAL0-0.044-0.02719.546-0.035-0.0350.0000.0000.0000.000
165A163PRO00.0050.01720.7380.2270.2270.0000.0000.0000.000
166A164ILE0-0.054-0.03123.3100.2840.2840.0000.0000.0000.000
167A165GLU-1-0.766-0.86227.149-11.002-11.0020.0000.0000.0000.000
168A166GLY0-0.057-0.01629.6430.3480.3480.0000.0000.0000.000
169A167PHE00.003-0.01330.0020.0280.0280.0000.0000.0000.000
170A168ASP-1-0.831-0.90934.195-7.843-7.8430.0000.0000.0000.000
171A169ALA00.0790.03034.5630.0290.0290.0000.0000.0000.000
172A170LYS10.8960.94936.1477.1867.1860.0000.0000.0000.000
173A171VAL0-0.036-0.01739.0980.1200.1200.0000.0000.0000.000
174A172LEU00.002-0.00331.9750.0360.0360.0000.0000.0000.000
175A173ASP-1-0.714-0.79935.590-8.814-8.8140.0000.0000.0000.000
176A174GLU-1-0.990-0.97237.646-7.121-7.1210.0000.0000.0000.000
177A175GLU-1-0.771-0.85537.879-7.766-7.7660.0000.0000.0000.000
178A176PHE0-0.053-0.04634.372-0.102-0.1020.0000.0000.0000.000
179A177GLY00.0250.03637.829-0.077-0.0770.0000.0000.0000.000
180A178LEU0-0.029-0.02733.742-0.037-0.0370.0000.0000.0000.000
181A179ARG10.8600.91337.5667.9917.9910.0000.0000.0000.000
182A180GLU-1-0.888-0.95139.813-7.461-7.4610.0000.0000.0000.000
183A181LYS10.8890.95037.1857.8967.8960.0000.0000.0000.000
184A182GLY00.0000.01537.553-0.131-0.1310.0000.0000.0000.000
185A183PHE0-0.040-0.02830.977-0.248-0.2480.0000.0000.0000.000
186A184THR0-0.058-0.05333.6360.2720.2720.0000.0000.0000.000
187A185SER0-0.007-0.04031.282-0.342-0.3420.0000.0000.0000.000
188A186VAL0-0.038-0.02427.7780.1450.1450.0000.0000.0000.000
189A187VAL0-0.0070.00124.120-0.122-0.1220.0000.0000.0000.000
190A188ILE0-0.0170.00226.825-0.078-0.0780.0000.0000.0000.000
191A189VAL00.015-0.01220.125-0.257-0.2570.0000.0000.0000.000
192A190PRO0-0.039-0.00323.398-0.095-0.0950.0000.0000.0000.000
193A191LEU00.0090.00218.393-0.687-0.6870.0000.0000.0000.000
194A192GLY00.037-0.00320.4280.7490.7490.0000.0000.0000.000
195A193TYR0-0.0010.00217.897-1.149-1.1490.0000.0000.0000.000
196A194HIS10.8340.90919.85515.16115.1610.0000.0000.0000.000
197A195SER00.0410.02423.178-0.100-0.1000.0000.0000.0000.000
198A196GLU-1-0.860-0.93623.597-13.589-13.5890.0000.0000.0000.000
199A197ASP-1-0.929-0.96826.514-10.101-10.1010.0000.0000.0000.000
200A198ASP-1-0.757-0.85424.751-12.368-12.3680.0000.0000.0000.000
201A199PHE00.0560.00525.962-0.395-0.3950.0000.0000.0000.000
202A200ASN0-0.065-0.04023.7010.0160.0160.0000.0000.0000.000
203A201ALA0-0.0050.00921.666-0.503-0.5030.0000.0000.0000.000
204A202LYS10.8910.94821.82011.08611.0860.0000.0000.0000.000
205A203LEU0-0.0310.00423.9950.3460.3460.0000.0000.0000.000
206A204PRO00.0070.01322.133-0.691-0.6910.0000.0000.0000.000
207A205LYS10.8450.91516.25418.20218.2020.0000.0000.0000.000
208A206SER00.0210.02121.328-0.240-0.2400.0000.0000.0000.000
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