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: 7NZ7K

Calculation Name: 4XBA-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-monophosphate | guanosine | glycerol | zinc ion

Ligand 3-letter code: 5GP | GMP | GOL | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4XBA

Chain ID: A

ChEMBL ID:

UniProt ID: O74859

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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2398073.118181
FMO2-HF: Nuclear repulsion 2316087.033922
FMO2-HF: Total energy -81986.084259
FMO2-MP2: Total energy -82221.653871


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:33:SER)


Summations of interaction energy for fragment #1(A:33:SER)
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.
-80.863-72.97514.381-11.992-10.279-0.118
Interaction energy analysis for fragmet #1(A:33:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.791 / q_NPA : 0.878
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].
3A35ARG10.9130.9552.55136.72140.5331.062-1.943-2.9320.011
4A36ASP-1-0.746-0.8691.778-119.571-115.82813.319-9.960-7.102-0.129
5A37ASN0-0.010-0.0154.3670.6590.765-0.001-0.039-0.0660.000
112A144ASN0-0.006-0.0373.7826.5596.7860.001-0.050-0.1790.000
6A38LEU00.0160.0006.8043.0203.0200.0000.0000.0000.000
7A39LYS10.8330.9145.80241.69741.6970.0000.0000.0000.000
8A40VAL00.0120.0168.9392.2252.2250.0000.0000.0000.000
9A41TYR0-0.0070.00411.2882.0292.0290.0000.0000.0000.000
10A42ILE00.0350.02011.8621.3451.3450.0000.0000.0000.000
11A43GLU-1-0.845-0.9109.792-31.263-31.2630.0000.0000.0000.000
12A44SER00.0100.00214.0720.8610.8610.0000.0000.0000.000
13A45PRO00.0130.01616.551-0.089-0.0890.0000.0000.0000.000
14A46GLU-1-0.875-0.94618.131-16.071-16.0710.0000.0000.0000.000
15A47SER0-0.051-0.02017.0610.5540.5540.0000.0000.0000.000
16A48TYR0-0.050-0.02312.828-0.585-0.5850.0000.0000.0000.000
17A49LYS10.9830.99018.35514.21414.2140.0000.0000.0000.000
18A50ASN0-0.046-0.03816.2150.6620.6620.0000.0000.0000.000
19A51VAL0-0.017-0.00518.037-0.156-0.1560.0000.0000.0000.000
20A52ILE0-0.049-0.02720.5280.5100.5100.0000.0000.0000.000
21A53TYR0-0.011-0.03422.9440.7070.7070.0000.0000.0000.000
22A54TYR0-0.010-0.01521.074-0.879-0.8790.0000.0000.0000.000
23A55ASP-1-0.708-0.79122.708-12.331-12.3310.0000.0000.0000.000
24A56ASP-1-0.883-0.93922.144-13.502-13.5020.0000.0000.0000.000
25A57ASP-1-0.855-0.89821.634-13.329-13.3290.0000.0000.0000.000
26A58VAL0-0.083-0.05020.110-0.922-0.9220.0000.0000.0000.000
27A59VAL0-0.012-0.01117.5280.2450.2450.0000.0000.0000.000
28A60LEU0-0.0240.00519.335-0.461-0.4610.0000.0000.0000.000
29A61VAL0-0.005-0.01115.9940.2250.2250.0000.0000.0000.000
30A62ARG10.8320.88219.36813.01013.0100.0000.0000.0000.000
31A63ASP-1-0.840-0.92816.225-20.277-20.2770.0000.0000.0000.000
32A64MET0-0.025-0.02215.5181.0301.0300.0000.0000.0000.000
33A65PHE0-0.097-0.03812.8210.3130.3130.0000.0000.0000.000
34A66PRO00.0690.06217.581-0.136-0.1360.0000.0000.0000.000
35A67LYS10.8430.89815.16818.55718.5570.0000.0000.0000.000
36A68SER0-0.029-0.01621.0770.3020.3020.0000.0000.0000.000
37A69LYS10.8940.96024.4649.8969.8960.0000.0000.0000.000
38A70MET00.0520.05325.440-0.124-0.1240.0000.0000.0000.000
39A71HIS0-0.075-0.05217.6890.2250.2250.0000.0000.0000.000
40A72LEU00.0190.01620.807-0.543-0.5430.0000.0000.0000.000
41A73LEU0-0.023-0.01414.464-0.258-0.2580.0000.0000.0000.000
42A74LEU00.0170.01818.5230.1040.1040.0000.0000.0000.000
43A75MET0-0.048-0.02311.835-0.629-0.6290.0000.0000.0000.000
44A76THR00.0210.01516.3041.0221.0220.0000.0000.0000.000
45A77ARG10.8360.89715.95315.36015.3600.0000.0000.0000.000
46A78ASP-1-0.822-0.90116.824-16.600-16.6000.0000.0000.0000.000
47A79PRO0-0.015-0.01614.536-1.067-1.0670.0000.0000.0000.000
48A80HIS0-0.035-0.02414.820-1.456-1.4560.0000.0000.0000.000
49A81LEU0-0.024-0.01417.0730.1460.1460.0000.0000.0000.000
50A82THR0-0.0020.00111.790-0.088-0.0880.0000.0000.0000.000
51A83HIS00.0130.0078.404-1.539-1.5390.0000.0000.0000.000
52A84VAL0-0.0150.01211.9200.2050.2050.0000.0000.0000.000
53A85HIS00.0170.00813.2760.3190.3190.0000.0000.0000.000
54A86PRO00.0870.03214.6341.0541.0540.0000.0000.0000.000
55A87LEU0-0.020-0.00417.5020.7420.7420.0000.0000.0000.000
56A88GLU-1-0.945-0.97418.364-15.290-15.2900.0000.0000.0000.000
57A89ILE0-0.013-0.00317.9500.7400.7400.0000.0000.0000.000
58A90MET0-0.0200.00620.7150.6360.6360.0000.0000.0000.000
59A91MET0-0.022-0.00523.1270.7290.7290.0000.0000.0000.000
60A92LYS10.8850.93622.90712.80212.8020.0000.0000.0000.000
61A93HIS00.0470.03420.6690.4840.4840.0000.0000.0000.000
62A94ARG10.9590.96923.92611.10211.1020.0000.0000.0000.000
63A95SER00.0820.03726.6930.0380.0380.0000.0000.0000.000
64A96LEU0-0.0030.00919.4340.0450.0450.0000.0000.0000.000
65A97VAL0-0.020-0.01223.416-0.114-0.1140.0000.0000.0000.000
66A98GLU-1-0.925-0.96524.959-10.119-10.1190.0000.0000.0000.000
67A99LYS10.8740.93824.67012.23712.2370.0000.0000.0000.000
68A100LEU0-0.0040.00120.4790.0650.0650.0000.0000.0000.000
69A101VAL00.004-0.00624.7840.0920.0920.0000.0000.0000.000
70A102SER0-0.051-0.03727.8730.3040.3040.0000.0000.0000.000
71A103TYR00.000-0.03225.4850.1760.1760.0000.0000.0000.000
72A104VAL0-0.044-0.02825.5010.1270.1270.0000.0000.0000.000
73A105GLN0-0.039-0.02928.1770.3640.3640.0000.0000.0000.000
74A106GLY00.0300.02931.5310.3560.3560.0000.0000.0000.000
75A107ASP-1-0.903-0.94330.354-9.985-9.9850.0000.0000.0000.000
76A108LEU0-0.040-0.02425.423-0.070-0.0700.0000.0000.0000.000
77A109SER0-0.033-0.01129.521-0.036-0.0360.0000.0000.0000.000
78A110GLY00.0160.00331.6990.0130.0130.0000.0000.0000.000
79A111LEU00.0260.01626.7120.0260.0260.0000.0000.0000.000
80A112ILE0-0.007-0.00826.611-0.272-0.2720.0000.0000.0000.000
81A113PHE0-0.003-0.01929.218-0.028-0.0280.0000.0000.0000.000
82A114ASP-1-0.805-0.88532.551-9.080-9.0800.0000.0000.0000.000
83A115GLU-1-0.811-0.86725.637-12.428-12.4280.0000.0000.0000.000
84A116ALA00.025-0.00629.676-0.043-0.0430.0000.0000.0000.000
85A117ARG10.7580.86430.9558.9688.9680.0000.0000.0000.000
86A118ASN0-0.065-0.03230.6300.4380.4380.0000.0000.0000.000
87A119CYS0-0.106-0.05128.088-0.136-0.1360.0000.0000.0000.000
88A120LEU0-0.077-0.02529.824-0.086-0.0860.0000.0000.0000.000
89A121SER00.017-0.00433.0650.2430.2430.0000.0000.0000.000
90A122GLN00.0570.01435.3350.0650.0650.0000.0000.0000.000
91A123GLN0-0.089-0.03338.498-0.010-0.0100.0000.0000.0000.000
92A124LEU00.0150.02435.4770.0880.0880.0000.0000.0000.000
93A125THR00.0470.00438.290-0.178-0.1780.0000.0000.0000.000
94A126ASN00.0770.02636.832-0.299-0.2990.0000.0000.0000.000
95A127GLU-1-0.833-0.89637.069-8.004-8.0040.0000.0000.0000.000
96A128ALA00.0090.01438.762-0.054-0.0540.0000.0000.0000.000
97A129LEU0-0.014-0.01033.076-0.226-0.2260.0000.0000.0000.000
98A130CYS0-0.067-0.03933.444-0.310-0.3100.0000.0000.0000.000
99A131ASN0-0.057-0.01634.005-0.186-0.1860.0000.0000.0000.000
100A132TYR00.0260.00031.836-0.166-0.1660.0000.0000.0000.000
101A133ILE00.0280.01027.722-0.389-0.3890.0000.0000.0000.000
102A134LYS10.7460.86724.33912.20312.2030.0000.0000.0000.000
103A135VAL00.0450.01123.989-0.420-0.4200.0000.0000.0000.000
104A136GLY00.017-0.00122.5280.5130.5130.0000.0000.0000.000
105A137PHE00.0360.02217.410-0.644-0.6440.0000.0000.0000.000
106A138HIS0-0.0100.00115.013-0.466-0.4660.0000.0000.0000.000
107A139ALA00.0400.01416.532-0.465-0.4650.0000.0000.0000.000
108A140GLY0-0.003-0.00713.782-0.139-0.1390.0000.0000.0000.000
109A141PRO0-0.0060.01411.406-0.100-0.1000.0000.0000.0000.000
110A142SER0-0.028-0.0228.679-1.485-1.4850.0000.0000.0000.000
111A143MET0-0.060-0.0096.810-5.556-5.5560.0000.0000.0000.000
113A145ASN00.0120.0267.3213.5123.5120.0000.0000.0000.000
114A146LEU00.0110.01510.0480.6260.6260.0000.0000.0000.000
115A147HIS0-0.067-0.05011.2980.8810.8810.0000.0000.0000.000
116A148LEU0-0.0250.00215.3160.1820.1820.0000.0000.0000.000
117A149HIS00.0130.00915.5840.2700.2700.0000.0000.0000.000
118A150ILE00.0510.01619.8900.6850.6850.0000.0000.0000.000
119A151MET0-0.034-0.00421.271-0.382-0.3820.0000.0000.0000.000
120A152THR00.0540.01124.7440.2150.2150.0000.0000.0000.000
121A153LEU0-0.071-0.02926.652-0.446-0.4460.0000.0000.0000.000
122A154ASP-1-0.724-0.81627.891-11.326-11.3260.0000.0000.0000.000
123A155HIS00.0010.00022.8070.2080.2080.0000.0000.0000.000
124A156VAL0-0.0110.00226.336-0.146-0.1460.0000.0000.0000.000
125A157SER00.019-0.01122.438-0.005-0.0050.0000.0000.0000.000
126A158PRO00.009-0.01124.129-0.072-0.0720.0000.0000.0000.000
127A159SER0-0.015-0.00518.951-0.535-0.5350.0000.0000.0000.000
128A160LEU0-0.0240.01019.227-0.892-0.8920.0000.0000.0000.000
129A161LYS10.9700.97917.74216.50616.5060.0000.0000.0000.000
130A162ASN0-0.020-0.01116.4850.3120.3120.0000.0000.0000.000
131A163SER00.1020.04320.845-0.060-0.0600.0000.0000.0000.000
132A164ALA00.0030.02217.2710.2020.2020.0000.0000.0000.000
133A165HIS00.0290.00413.794-0.027-0.0270.0000.0000.0000.000
134A166TYR00.0240.02118.367-0.075-0.0750.0000.0000.0000.000
135A167ILE00.0550.04121.0690.1590.1590.0000.0000.0000.000
136A168SER0-0.082-0.04217.341-0.001-0.0010.0000.0000.0000.000
137A169PHE00.029-0.00817.292-0.286-0.2860.0000.0000.0000.000
138A170THR0-0.032-0.02421.9870.5560.5560.0000.0000.0000.000
139A171SER00.0000.00822.3530.4000.4000.0000.0000.0000.000
140A172PRO00.026-0.01223.939-0.293-0.2930.0000.0000.0000.000
141A173PHE0-0.0380.00014.762-0.291-0.2910.0000.0000.0000.000
142A174PHE00.0120.01119.636-0.787-0.7870.0000.0000.0000.000
143A175VAL00.000-0.00220.4450.6790.6790.0000.0000.0000.000
144A176LYS10.9921.00122.69810.13510.1350.0000.0000.0000.000
145A177ILE00.0350.01822.9790.0350.0350.0000.0000.0000.000
146A178ASP-1-0.893-0.94625.581-10.360-10.3600.0000.0000.0000.000
147A179THR0-0.084-0.05326.2460.3780.3780.0000.0000.0000.000
148A180PRO00.009-0.00228.348-0.173-0.1730.0000.0000.0000.000
149A181THR00.018-0.01027.452-0.096-0.0960.0000.0000.0000.000
150A182SER0-0.032-0.02928.490-0.173-0.1730.0000.0000.0000.000
151A183ASN0-0.032-0.00329.4620.2140.2140.0000.0000.0000.000
152A184LEU0-0.0150.01023.904-0.250-0.2500.0000.0000.0000.000
153A185PRO0-0.0010.01321.7370.1580.1580.0000.0000.0000.000
154A186THR00.018-0.00321.156-0.299-0.2990.0000.0000.0000.000
155A187ARG10.9150.94915.20816.97916.9790.0000.0000.0000.000
156A188GLY00.0080.01316.7420.3610.3610.0000.0000.0000.000
157A189THR00.002-0.00912.722-1.489-1.4890.0000.0000.0000.000
158A190LEU00.0280.00911.5160.6130.6130.0000.0000.0000.000
159A191THR0-0.025-0.02711.7260.5030.5030.0000.0000.0000.000
160A192SER0-0.010-0.00114.3960.3930.3930.0000.0000.0000.000
161A193LEU0-0.052-0.00217.3190.7890.7890.0000.0000.0000.000
162A194PHE0-0.002-0.01219.334-0.059-0.0590.0000.0000.0000.000
163A195GLN00.003-0.00222.439-0.026-0.0260.0000.0000.0000.000
164A196GLU-1-0.934-0.96426.080-9.443-9.4430.0000.0000.0000.000
165A197ASP-1-0.805-0.89028.967-8.799-8.7990.0000.0000.0000.000
166A198LEU0-0.083-0.03625.293-0.295-0.2950.0000.0000.0000.000
167A199LYS10.9420.96129.0229.0249.0240.0000.0000.0000.000
168A200CYS0-0.0110.03629.686-0.388-0.3880.0000.0000.0000.000
169A201TRP0-0.053-0.03428.9880.2440.2440.0000.0000.0000.000
170A202ARG10.8020.88131.1818.3348.3340.0000.0000.0000.000
171A203CYS00.0340.05634.6170.0900.0900.0000.0000.0000.000
172A204GLY0-0.0100.00334.6410.1700.1700.0000.0000.0000.000
173A205GLU-1-0.897-0.96635.670-7.987-7.9870.0000.0000.0000.000
174A206THR0-0.103-0.07633.297-0.262-0.2620.0000.0000.0000.000
175A207PHE00.0480.02631.5580.1030.1030.0000.0000.0000.000
176A208GLY00.0280.02532.211-0.046-0.0460.0000.0000.0000.000
177A209ARG10.8700.91323.47911.09811.0980.0000.0000.0000.000
178A210HIS0-0.017-0.00328.166-0.417-0.4170.0000.0000.0000.000
179A211PHE00.0560.00823.3350.0970.0970.0000.0000.0000.000
180A212THR0-0.012-0.01027.826-0.131-0.1310.0000.0000.0000.000
181A213LYS10.9850.99929.6218.4748.4740.0000.0000.0000.000
182A214LEU00.0270.03927.4550.0850.0850.0000.0000.0000.000
183A215LYS10.8020.88224.42511.90711.9070.0000.0000.0000.000
184A216ALA00.0010.00529.4010.0230.0230.0000.0000.0000.000
185A217HIS00.014-0.01233.0710.0950.0950.0000.0000.0000.000
186A218LEU0-0.038-0.03127.7550.0610.0610.0000.0000.0000.000
187A219GLN0-0.100-0.05531.859-0.362-0.3620.0000.0000.0000.000
188A220GLU-1-0.861-0.93133.377-7.890-7.8900.0000.0000.0000.000
189A221GLU-1-0.791-0.90833.910-8.339-8.3390.0000.0000.0000.000
190A222TYR0-0.064-0.03432.506-0.093-0.0930.0000.0000.0000.000
191A223ASP-1-0.810-0.90434.643-8.501-8.5010.0000.0000.0000.000
192A224ASP-1-0.786-0.86937.878-7.437-7.4370.0000.0000.0000.000
193A225TRP0-0.021-0.01835.2660.0550.0550.0000.0000.0000.000
194A226LEU0-0.0090.00236.4350.0820.0820.0000.0000.0000.000
195A227ASP-1-0.939-0.97338.682-7.002-7.0020.0000.0000.0000.000
196A228LYS10.8030.89641.6847.4227.4220.0000.0000.0000.000
197A229SER0-0.058-0.03639.1670.0610.0610.0000.0000.0000.000
198A230VAL0-0.087-0.03640.257-0.115-0.1150.0000.0000.0000.000
199A231SER-1-0.916-0.93842.232-6.895-6.8950.0000.0000.0000.000