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: RL4G8

Calculation Name: 2ZNR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol | praseodymium ion | zinc ion

Ligand 3-letter code: EDO | PR | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ZNR

Chain ID: A

ChEMBL ID:

UniProt ID: Q96FJ0

Base Structure: X-ray

Registration Date: 2025-10-05

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 178
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1887570.641271
FMO2-HF: Nuclear repulsion 1815818.784681
FMO2-HF: Total energy -71751.85659
FMO2-MP2: Total energy -71954.440264


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:259:GLY)


Summations of interaction energy for fragment #1(A:259:GLY)
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.
-33.186-30.8560.844-1.449-1.725-0.012
Interaction energy analysis for fragmet #1(A:259:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.925
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].
3A261GLY00.0220.0023.775-6.502-5.6520.010-0.472-0.388-0.002
4A262HIS0-0.095-0.0482.331-14.682-13.3250.835-0.940-1.253-0.010
5A263MET00.0000.0034.2397.1947.317-0.001-0.037-0.0840.000
6A264GLU-1-0.887-0.9297.542-36.381-36.3810.0000.0000.0000.000
7A265GLY0-0.023-0.0218.7243.4443.4440.0000.0000.0000.000
8A266LEU0-0.068-0.01411.523-0.870-0.8700.0000.0000.0000.000
9A267ARG10.8450.88813.12220.77720.7770.0000.0000.0000.000
10A268CYS0-0.005-0.00215.1971.1151.1150.0000.0000.0000.000
11A269VAL00.0130.00618.5540.0540.0540.0000.0000.0000.000
12A270VAL00.001-0.00321.7990.4350.4350.0000.0000.0000.000
13A271LEU00.012-0.00224.7550.1270.1270.0000.0000.0000.000
14A272PRO0-0.018-0.01727.9570.1110.1110.0000.0000.0000.000
15A273GLU-1-0.913-0.95931.506-9.145-9.1450.0000.0000.0000.000
16A274ASP-1-0.798-0.90433.595-8.035-8.0350.0000.0000.0000.000
17A275LEU0-0.054-0.01631.5020.2000.2000.0000.0000.0000.000
18A276CYS00.0350.00634.2370.0570.0570.0000.0000.0000.000
19A277HIS0-0.056-0.01736.5550.3430.3430.0000.0000.0000.000
20A278LYS10.9000.94738.7018.3758.3750.0000.0000.0000.000
21A279PHE00.0090.00437.1540.1150.1150.0000.0000.0000.000
22A280LEU00.014-0.00939.2920.1530.1530.0000.0000.0000.000
23A281GLN0-0.026-0.00641.8740.0470.0470.0000.0000.0000.000
24A282LEU0-0.0170.00239.7140.1580.1580.0000.0000.0000.000
25A283ALA00.0570.03741.8740.0930.0930.0000.0000.0000.000
26A284GLU-1-0.934-0.94143.995-6.465-6.4650.0000.0000.0000.000
27A285SER0-0.001-0.00947.1310.0480.0480.0000.0000.0000.000
28A286ASN0-0.026-0.01245.2530.2940.2940.0000.0000.0000.000
29A287THR00.013-0.00844.7420.0000.0000.0000.0000.0000.000
30A288VAL0-0.039-0.03046.8740.0480.0480.0000.0000.0000.000
31A289ARG10.8850.95150.0846.3986.3980.0000.0000.0000.000
32A290GLY0-0.041-0.01048.4340.0540.0540.0000.0000.0000.000
33A291ILE0-0.056-0.03046.106-0.035-0.0350.0000.0000.0000.000
34A292GLU-1-0.855-0.93640.123-8.206-8.2060.0000.0000.0000.000
35A293THR0-0.025-0.03140.8630.2160.2160.0000.0000.0000.000
36A294CYS0-0.024-0.02436.410-0.220-0.2200.0000.0000.0000.000
37A295GLY00.0580.02335.7750.2280.2280.0000.0000.0000.000
38A296ILE0-0.010-0.00830.513-0.315-0.3150.0000.0000.0000.000
39A297LEU0-0.021-0.00628.4690.1550.1550.0000.0000.0000.000
40A298CYS00.0230.01028.495-0.396-0.3960.0000.0000.0000.000
41A299GLY00.008-0.01127.7640.2540.2540.0000.0000.0000.000
42A300LYS11.0091.02624.96511.94411.9440.0000.0000.0000.000
43A301LEU00.0220.00817.518-0.370-0.3700.0000.0000.0000.000
44A302THR0-0.030-0.02221.1030.5850.5850.0000.0000.0000.000
45A303HIS00.0320.00518.578-0.638-0.6380.0000.0000.0000.000
46A304ASN0-0.024-0.01412.071-0.469-0.4690.0000.0000.0000.000
47A305GLU-1-0.918-0.94416.114-16.416-16.4160.0000.0000.0000.000
48A306PHE00.0200.00017.2250.4630.4630.0000.0000.0000.000
49A307THR0-0.081-0.04321.4140.2670.2670.0000.0000.0000.000
50A308ILE00.0250.02225.1100.2030.2030.0000.0000.0000.000
51A309THR0-0.010-0.01227.9580.2550.2550.0000.0000.0000.000
52A310HIS10.8500.91831.0839.9169.9160.0000.0000.0000.000
53A311VAL00.0210.02332.188-0.309-0.3090.0000.0000.0000.000
54A312ILE00.0050.00433.4990.2750.2750.0000.0000.0000.000
55A313VAL00.0090.00436.190-0.191-0.1910.0000.0000.0000.000
56A314PRO00.0120.01337.1380.1570.1570.0000.0000.0000.000
57A315LYS10.8770.92239.7977.3107.3100.0000.0000.0000.000
58A316GLN0-0.008-0.02339.931-0.231-0.2310.0000.0000.0000.000
59A317SER00.0230.01343.1480.2530.2530.0000.0000.0000.000
60A318ALA0-0.032-0.02543.290-0.220-0.2200.0000.0000.0000.000
61A319GLY00.0130.01944.3850.2210.2210.0000.0000.0000.000
62A320PRO0-0.042-0.02545.269-0.074-0.0740.0000.0000.0000.000
63A321ASP-1-0.959-0.99042.387-7.424-7.4240.0000.0000.0000.000
64A322TYR0-0.023-0.00240.232-0.151-0.1510.0000.0000.0000.000
65A323CYS0-0.040-0.01838.7230.2010.2010.0000.0000.0000.000
66A324ASP-1-0.903-0.94839.105-7.999-7.9990.0000.0000.0000.000
67A325MET0-0.067-0.03934.624-0.003-0.0030.0000.0000.0000.000
68A326GLU-1-0.878-0.91939.545-7.147-7.1470.0000.0000.0000.000
69A327ASN0-0.006-0.00240.948-0.060-0.0600.0000.0000.0000.000
70A328VAL00.0240.01236.090-0.129-0.1290.0000.0000.0000.000
71A329GLU-1-0.862-0.94936.859-8.112-8.1120.0000.0000.0000.000
72A330GLU-1-0.862-0.90738.563-7.511-7.5110.0000.0000.0000.000
73A331LEU00.0030.00833.543-0.067-0.0670.0000.0000.0000.000
74A332PHE0-0.011-0.01832.073-0.233-0.2330.0000.0000.0000.000
75A333ASN00.0130.01834.680-0.170-0.1700.0000.0000.0000.000
76A334VAL0-0.051-0.03036.5720.0090.0090.0000.0000.0000.000
77A335GLN0-0.039-0.04129.8090.0470.0470.0000.0000.0000.000
78A336ASP-1-0.937-0.95132.724-9.485-9.4850.0000.0000.0000.000
79A337GLN00.009-0.01233.9080.1120.1120.0000.0000.0000.000
80A338HIS0-0.055-0.03634.3420.0350.0350.0000.0000.0000.000
81A339ASP-1-0.962-0.96229.087-11.192-11.1920.0000.0000.0000.000
82A340LEU0-0.081-0.02829.157-0.286-0.2860.0000.0000.0000.000
83A341LEU00.001-0.00122.484-0.068-0.0680.0000.0000.0000.000
84A342THR00.020-0.00826.3610.1950.1950.0000.0000.0000.000
85A343LEU0-0.043-0.02822.624-0.601-0.6010.0000.0000.0000.000
86A344GLY00.009-0.00824.705-0.409-0.4090.0000.0000.0000.000
87A345TRP0-0.043-0.01027.0390.3910.3910.0000.0000.0000.000
88A346ILE0-0.019-0.01030.645-0.241-0.2410.0000.0000.0000.000
89A347HIS00.0270.02033.4200.2650.2650.0000.0000.0000.000
90A348THR00.0040.00736.697-0.132-0.1320.0000.0000.0000.000
91A349HIS10.8490.94036.7708.6438.6430.0000.0000.0000.000
92A350PRO00.0140.01540.7640.0350.0350.0000.0000.0000.000
93A351THR0-0.001-0.02144.3910.0330.0330.0000.0000.0000.000
94A352GLN00.0140.00841.5900.0560.0560.0000.0000.0000.000
95A353THR00.0550.01638.857-0.016-0.0160.0000.0000.0000.000
96A354ALA00.0550.04334.628-0.051-0.0510.0000.0000.0000.000
97A355PHE0-0.076-0.04733.537-0.190-0.1900.0000.0000.0000.000
98A356LEU0-0.0020.00328.7120.0020.0020.0000.0000.0000.000
99A357SER00.0390.00133.1820.0080.0080.0000.0000.0000.000
100A358SER00.001-0.02734.101-0.230-0.2300.0000.0000.0000.000
101A359VAL00.0390.03234.166-0.241-0.2410.0000.0000.0000.000
102A360ASP-1-0.729-0.83933.069-9.339-9.3390.0000.0000.0000.000
103A361LEU0-0.037-0.01929.143-0.425-0.4250.0000.0000.0000.000
104A362HIS10.8230.89029.1449.6169.6160.0000.0000.0000.000
105A363THR00.0090.01530.068-0.177-0.1770.0000.0000.0000.000
106A364HIS00.0030.01324.0400.1500.1500.0000.0000.0000.000
107A365CYS0-0.055-0.01724.892-0.555-0.5550.0000.0000.0000.000
108A366SER0-0.038-0.03024.802-0.443-0.4430.0000.0000.0000.000
109A367TYR00.0460.01825.347-0.307-0.3070.0000.0000.0000.000
110A368GLN00.022-0.00219.8950.1540.1540.0000.0000.0000.000
111A369LEU0-0.033-0.02820.236-0.870-0.8700.0000.0000.0000.000
112A370MET0-0.0370.00320.347-0.584-0.5840.0000.0000.0000.000
113A371LEU0-0.0090.00118.148-0.548-0.5480.0000.0000.0000.000
114A372PRO00.0230.01515.1960.5130.5130.0000.0000.0000.000
115A373GLU-1-0.774-0.86314.935-20.170-20.1700.0000.0000.0000.000
116A374ALA00.0200.03418.8810.6950.6950.0000.0000.0000.000
117A375ILE0-0.058-0.04122.551-0.080-0.0800.0000.0000.0000.000
118A376ALA00.0270.01625.3310.2990.2990.0000.0000.0000.000
119A377ILE0-0.031-0.02428.893-0.029-0.0290.0000.0000.0000.000
120A378VAL0-0.009-0.00331.4030.2040.2040.0000.0000.0000.000
121A379CYS00.0200.01934.6110.0040.0040.0000.0000.0000.000
122A380SER00.0350.01137.5630.1690.1690.0000.0000.0000.000
123A381PRO00.0320.02240.1730.0770.0770.0000.0000.0000.000
124A382LYS10.9140.97143.1426.8396.8390.0000.0000.0000.000
125A383HIS0-0.073-0.05041.6000.1170.1170.0000.0000.0000.000
126A384LYS10.8910.94742.2926.8646.8640.0000.0000.0000.000
127A385ASP-1-0.838-0.90036.596-9.003-9.0030.0000.0000.0000.000
128A386THR0-0.060-0.05733.2860.1070.1070.0000.0000.0000.000
129A387GLY00.0160.02532.207-0.195-0.1950.0000.0000.0000.000
130A388ILE00.0440.00826.6930.0040.0040.0000.0000.0000.000
131A389PHE0-0.0070.00026.877-0.411-0.4110.0000.0000.0000.000
132A390ARG10.9400.98220.01315.08115.0810.0000.0000.0000.000
133A391LEU00.0170.00123.4230.3300.3300.0000.0000.0000.000
134A392THR0-0.058-0.04221.391-0.893-0.8930.0000.0000.0000.000
135A393ASN00.0500.00716.0010.2750.2750.0000.0000.0000.000
136A394ALA00.0220.02420.2060.1290.1290.0000.0000.0000.000
137A395GLY00.0370.01623.6190.4190.4190.0000.0000.0000.000
138A396MET0-0.0050.00220.2220.5650.5650.0000.0000.0000.000
139A397LEU00.0130.03622.3210.1660.1660.0000.0000.0000.000
140A398GLU-1-0.735-0.82823.821-10.090-10.0900.0000.0000.0000.000
141A399VAL0-0.029-0.03027.0060.4840.4840.0000.0000.0000.000
142A400SER0-0.006-0.02124.2670.3550.3550.0000.0000.0000.000
143A401ALA0-0.0130.00426.9470.3040.3040.0000.0000.0000.000
144A402CYS0-0.098-0.02628.5030.6360.6360.0000.0000.0000.000
145A403LYS11.0100.99831.7139.2779.2770.0000.0000.0000.000
146A404LYS10.9320.97833.6588.5838.5830.0000.0000.0000.000
147A405LYS10.9130.94533.9879.0269.0260.0000.0000.0000.000
148A406GLY00.0940.05937.9940.1810.1810.0000.0000.0000.000
149A407PHE00.0310.01838.363-0.281-0.2810.0000.0000.0000.000
150A408HIS0-0.054-0.04035.318-0.082-0.0820.0000.0000.0000.000
151A409PRO0-0.003-0.00437.873-0.158-0.1580.0000.0000.0000.000
152A410HIS0-0.012-0.02331.056-0.018-0.0180.0000.0000.0000.000
153A411THR0-0.077-0.06930.3500.2350.2350.0000.0000.0000.000
154A412LYS10.9370.94632.0408.6368.6360.0000.0000.0000.000
155A413GLU-1-0.905-0.93429.584-10.847-10.8470.0000.0000.0000.000
156A414PRO00.0330.01725.5510.1070.1070.0000.0000.0000.000
157A415ARG10.9550.97927.70610.94010.9400.0000.0000.0000.000
158A416LEU00.0180.03126.017-0.597-0.5970.0000.0000.0000.000
159A417PHE00.0020.00625.912-0.372-0.3720.0000.0000.0000.000
160A418SER0-0.052-0.03823.444-0.017-0.0170.0000.0000.0000.000
161A419ILE00.0460.03225.2210.0020.0020.0000.0000.0000.000
162A420CYS0-0.051-0.01222.659-0.705-0.7050.0000.0000.0000.000
163A421LYS10.9240.95516.54718.47918.4790.0000.0000.0000.000
164A422HIS00.009-0.00517.943-0.538-0.5380.0000.0000.0000.000
165A423VAL00.0230.02019.628-0.082-0.0820.0000.0000.0000.000
166A424LEU0-0.009-0.00522.8430.1730.1730.0000.0000.0000.000
167A425VAL00.0340.01224.5980.1580.1580.0000.0000.0000.000
168A426LYS10.9250.95926.33011.62711.6270.0000.0000.0000.000
169A427ASP-1-0.849-0.90130.271-8.766-8.7660.0000.0000.0000.000
170A428ILE0-0.044-0.02729.137-0.073-0.0730.0000.0000.0000.000
171A429LYS10.9400.96533.4678.3848.3840.0000.0000.0000.000
172A430ILE00.0320.03132.885-0.260-0.2600.0000.0000.0000.000
173A431ILE0-0.072-0.03735.1430.3630.3630.0000.0000.0000.000
174A432VAL00.0430.01736.286-0.235-0.2350.0000.0000.0000.000
175A433LEU0-0.042-0.01936.2200.1280.1280.0000.0000.0000.000
176A434ASP-1-0.767-0.87039.385-7.583-7.5830.0000.0000.0000.000
177A435LEU0-0.037-0.01138.8150.0850.0850.0000.0000.0000.000
178A436ARG0-0.112-0.06842.9750.5510.5510.0000.0000.0000.000