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: LRNQ9

Calculation Name: 4V8P-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion | zinc ion

Ligand 3-letter code: MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4V8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q245F2

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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1753417.95128
FMO2-HF: Nuclear repulsion 1679503.122551
FMO2-HF: Total energy -73914.828728
FMO2-MP2: Total energy -74135.941638


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
215.296216.81-0.012-0.743-0.76-0.002
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.899 / q_NPA : 0.944
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].
3A4GLY00.0930.0533.8862.8414.355-0.012-0.743-0.760-0.002
4A5PRO00.0310.0276.0172.6362.6360.0000.0000.0000.000
5A6ALA00.006-0.0069.141-1.191-1.1910.0000.0000.0000.000
6A7GLY00.0650.04311.2481.6151.6150.0000.0000.0000.000
7A8LYS11.0170.98613.98813.50313.5030.0000.0000.0000.000
8A9ASN00.0250.01714.8141.1641.1640.0000.0000.0000.000
9A10ARG10.8220.9204.94136.28236.2820.0000.0000.0000.000
10A11GLY00.004-0.00812.9810.4340.4340.0000.0000.0000.000
11A12VAL0-0.009-0.01314.2400.8060.8060.0000.0000.0000.000
12A13SER00.0670.03115.0290.4620.4620.0000.0000.0000.000
13A14LYS10.9310.97511.67021.51921.5190.0000.0000.0000.000
14A15ILE00.1110.04716.9010.5260.5260.0000.0000.0000.000
15A16SER0-0.022-0.01518.4190.2480.2480.0000.0000.0000.000
16A17LYS10.8680.94418.31715.55015.5500.0000.0000.0000.000
17A18TRP00.0100.00519.5180.5690.5690.0000.0000.0000.000
18A19TYR00.0180.01723.4910.2570.2570.0000.0000.0000.000
19A20LYS10.9140.95424.4859.6559.6550.0000.0000.0000.000
20A21ALA00.0220.03027.0470.1520.1520.0000.0000.0000.000
21A22ASP-1-0.999-1.02228.871-9.501-9.5010.0000.0000.0000.000
22A23ASP-1-0.866-0.92031.951-9.455-9.4550.0000.0000.0000.000
23A24GLU-1-0.966-0.97031.045-9.618-9.6180.0000.0000.0000.000
24A25ALA0-0.011-0.01034.2730.0400.0400.0000.0000.0000.000
25A26THR0-0.010-0.00333.423-0.164-0.1640.0000.0000.0000.000
26A27PRO0-0.029-0.01735.5310.2240.2240.0000.0000.0000.000
27A28PHE00.0450.02836.908-0.124-0.1240.0000.0000.0000.000
28A29HIS00.0540.02437.1230.0540.0540.0000.0000.0000.000
29A30ARG10.9640.97239.1756.8396.8390.0000.0000.0000.000
30A31ARG10.9840.98042.7506.6756.6750.0000.0000.0000.000
31A32GLN00.007-0.00543.647-0.013-0.0130.0000.0000.0000.000
32A33LEU00.0370.03044.6860.0970.0970.0000.0000.0000.000
33A34LYS10.8890.92937.8958.0138.0130.0000.0000.0000.000
34A35LYS10.9610.99742.4906.1866.1860.0000.0000.0000.000
35A36ALA00.0110.02144.8450.0640.0640.0000.0000.0000.000
36A37THR0-0.028-0.03143.899-0.127-0.1270.0000.0000.0000.000
37A38ALA00.0020.01146.7160.0280.0280.0000.0000.0000.000
38A39THR00.0270.01848.800-0.026-0.0260.0000.0000.0000.000
39A40LYS10.9600.96750.4125.5365.5360.0000.0000.0000.000
40A41LEU0-0.0210.00153.991-0.051-0.0510.0000.0000.0000.000
41A42ARG10.8840.95756.6655.3855.3850.0000.0000.0000.000
42A43ASN00.024-0.01360.039-0.073-0.0730.0000.0000.0000.000
43A44ASP-1-0.767-0.84662.641-5.021-5.0210.0000.0000.0000.000
44A45ILE0-0.073-0.02356.494-0.014-0.0140.0000.0000.0000.000
45A46ALA00.0690.02960.643-0.002-0.0020.0000.0000.0000.000
46A47PRO0-0.0220.00157.766-0.025-0.0250.0000.0000.0000.000
47A48GLY00.0620.02158.8140.0930.0930.0000.0000.0000.000
48A49THR0-0.016-0.01860.6730.0970.0970.0000.0000.0000.000
49A50VAL0-0.011-0.00260.620-0.104-0.1040.0000.0000.0000.000
50A51LEU0-0.0110.01156.7630.0310.0310.0000.0000.0000.000
51A52ILE00.0360.02460.719-0.017-0.0170.0000.0000.0000.000
52A53LEU0-0.034-0.02054.174-0.090-0.0900.0000.0000.0000.000
53A54LEU00.0590.03457.5360.0210.0210.0000.0000.0000.000
54A55ALA00.0800.02954.0250.0140.0140.0000.0000.0000.000
55A56GLY0-0.029-0.00752.238-0.078-0.0780.0000.0000.0000.000
56A57ARG10.9780.97950.7476.1286.1280.0000.0000.0000.000
57A58PHE0-0.042-0.03851.0690.0310.0310.0000.0000.0000.000
58A59ARG10.9300.98054.0085.7405.7400.0000.0000.0000.000
59A60GLY00.0880.03957.8570.0360.0360.0000.0000.0000.000
60A61LYS10.8300.92056.9365.5405.5400.0000.0000.0000.000
61A62ARG10.9340.97060.5074.6644.6640.0000.0000.0000.000
62A63VAL0-0.041-0.01856.042-0.014-0.0140.0000.0000.0000.000
63A64VAL00.0390.03058.4050.0400.0400.0000.0000.0000.000
64A65PHE0-0.0010.00053.634-0.157-0.1570.0000.0000.0000.000
65A66LEU0-0.039-0.01551.6980.0620.0620.0000.0000.0000.000
66A67LYS10.9730.97151.7815.9755.9750.0000.0000.0000.000
67A68GLN00.0400.02151.233-0.051-0.0510.0000.0000.0000.000
68A69LEU0-0.0100.00643.854-0.031-0.0310.0000.0000.0000.000
69A70LYS10.9250.94042.8817.1007.1000.0000.0000.0000.000
70A71SER0-0.042-0.03442.6750.0730.0730.0000.0000.0000.000
71A72GLY0-0.005-0.00344.5680.0150.0150.0000.0000.0000.000
72A73LEU0-0.093-0.03544.3190.1410.1410.0000.0000.0000.000
73A74LEU00.0070.00248.4440.0280.0280.0000.0000.0000.000
74A75LEU0-0.002-0.00147.354-0.086-0.0860.0000.0000.0000.000
75A76VAL0-0.039-0.01950.8310.1370.1370.0000.0000.0000.000
76A77THR00.0600.01352.230-0.150-0.1500.0000.0000.0000.000
77A78GLY00.0290.01654.6660.1120.1120.0000.0000.0000.000
78A79PRO00.0660.03156.222-0.078-0.0780.0000.0000.0000.000
79A80TYR0-0.024-0.01052.6400.0630.0630.0000.0000.0000.000
80A81LYS10.9260.94456.5675.4965.4960.0000.0000.0000.000
81A82VAL0-0.0200.00559.5990.0730.0730.0000.0000.0000.000
82A83ASN00.0170.02058.425-0.012-0.0120.0000.0000.0000.000
83A84GLY00.0520.04156.420-0.003-0.0030.0000.0000.0000.000
84A85VAL0-0.106-0.06053.607-0.087-0.0870.0000.0000.0000.000
85A86PRO0-0.048-0.02050.0860.0460.0460.0000.0000.0000.000
86A87LEU00.0590.05248.4500.0920.0920.0000.0000.0000.000
87A88LYS10.8670.93048.4716.2176.2170.0000.0000.0000.000
88A89ARG10.9570.97940.1827.4917.4910.0000.0000.0000.000
89A90VAL0-0.044-0.03348.075-0.005-0.0050.0000.0000.0000.000
90A91ASN00.0540.03449.4780.0090.0090.0000.0000.0000.000
91A92GLN00.0710.02251.1080.1660.1660.0000.0000.0000.000
92A93ALA00.0260.01653.5770.0940.0940.0000.0000.0000.000
93A94TYR0-0.032-0.01851.5430.0400.0400.0000.0000.0000.000
94A95THR0-0.038-0.03155.590-0.003-0.0030.0000.0000.0000.000
95A96LEU00.0390.04258.202-0.006-0.0060.0000.0000.0000.000
96A97SER0-0.040-0.06561.417-0.103-0.1030.0000.0000.0000.000
97A98THR0-0.068-0.03062.8480.0670.0670.0000.0000.0000.000
98A99SER00.0420.01265.692-0.039-0.0390.0000.0000.0000.000
99A100THR0-0.060-0.02067.1240.0390.0390.0000.0000.0000.000
100A101LYS10.9100.95262.7914.8884.8880.0000.0000.0000.000
101A102VAL0-0.030-0.00963.0530.0720.0720.0000.0000.0000.000
102A103ASP-1-0.835-0.91263.464-5.031-5.0310.0000.0000.0000.000
103A104LEU0-0.072-0.03756.066-0.014-0.0140.0000.0000.0000.000
104A105THR00.044-0.00559.995-0.040-0.0400.0000.0000.0000.000
105A106GLY0-0.0040.01158.665-0.026-0.0260.0000.0000.0000.000
106A107VAL0-0.022-0.02154.671-0.125-0.1250.0000.0000.0000.000
107A108ASN00.003-0.00652.008-0.078-0.0780.0000.0000.0000.000
108A109THR0-0.042-0.04249.813-0.078-0.0780.0000.0000.0000.000
109A110ALA00.0140.01748.442-0.102-0.1020.0000.0000.0000.000
110A111LYS10.9050.96545.8426.3516.3510.0000.0000.0000.000
111A112PHE0-0.093-0.03744.403-0.132-0.1320.0000.0000.0000.000
112A113GLU-1-0.722-0.86041.984-6.788-6.7880.0000.0000.0000.000
113A114ASP-1-0.859-0.90440.326-7.547-7.5470.0000.0000.0000.000
114A115ASP-1-0.846-0.92936.686-8.114-8.1140.0000.0000.0000.000
115A116TYR0-0.055-0.03637.864-0.135-0.1350.0000.0000.0000.000
116A117PHE0-0.092-0.05640.4240.0110.0110.0000.0000.0000.000
117A118GLY00.0380.03036.545-0.088-0.0880.0000.0000.0000.000
118A119ARG10.9170.94236.2188.3818.3810.0000.0000.0000.000
119A120GLU-1-0.821-0.89530.907-9.969-9.9690.0000.0000.0000.000
120A121LYS10.9170.93931.7359.5569.5560.0000.0000.0000.000
121A122ALA00.0920.06530.520-0.291-0.2910.0000.0000.0000.000
122A123ARG10.9630.97421.03413.19313.1930.0000.0000.0000.000
123A124LYS10.8980.97728.6698.6228.6220.0000.0000.0000.000
124A125ASN00.006-0.00625.4680.0140.0140.0000.0000.0000.000
125A126HIS00.0830.02324.694-0.080-0.0800.0000.0000.0000.000
126A127LYS10.9490.98321.44113.72613.7260.0000.0000.0000.000
127A128ASN00.0410.02327.9220.2040.2040.0000.0000.0000.000
128A129LEU00.0370.01830.3820.3440.3440.0000.0000.0000.000
129A130PHE00.004-0.00431.4780.2740.2740.0000.0000.0000.000
130A131LYS10.9600.99433.3998.7638.7630.0000.0000.0000.000
131A132ALA0-0.040-0.04031.920-0.317-0.3170.0000.0000.0000.000
132A133GLU-1-0.911-0.94732.762-8.128-8.1280.0000.0000.0000.000
133A134LEU0-0.065-0.03632.283-0.289-0.2890.0000.0000.0000.000
134A135THR00.0600.03228.3160.2750.2750.0000.0000.0000.000
135A136GLU-1-0.773-0.87831.497-8.679-8.6790.0000.0000.0000.000
136A137GLU-1-0.834-0.92127.019-10.940-10.9400.0000.0000.0000.000
137A138GLN0-0.053-0.04328.6370.4020.4020.0000.0000.0000.000
138A139LYS10.8300.90932.8568.8458.8450.0000.0000.0000.000
139A140LYS10.9481.00434.0178.6318.6310.0000.0000.0000.000
140A141LYS10.9790.98430.19210.10410.1040.0000.0000.0000.000
141A142GLU-1-0.871-0.94734.995-7.999-7.9990.0000.0000.0000.000
142A143THR0-0.064-0.04337.7090.3420.3420.0000.0000.0000.000
143A144GLU-1-0.878-0.94235.656-8.508-8.5080.0000.0000.0000.000
144A145ARG10.8600.93734.8268.7538.7530.0000.0000.0000.000
145A146LYS10.9280.95840.0717.1697.1690.0000.0000.0000.000
146A147ASN0-0.021-0.01142.5150.0820.0820.0000.0000.0000.000
147A148ALA00.0570.02941.6730.1680.1680.0000.0000.0000.000
148A149ARG10.8750.93140.1337.6967.6960.0000.0000.0000.000
149A150LYS10.8740.95045.5056.2546.2540.0000.0000.0000.000
150A151GLN00.0280.01447.0220.2560.2560.0000.0000.0000.000
151A152ASP-1-0.793-0.87545.107-6.737-6.7370.0000.0000.0000.000
152A153GLN0-0.077-0.05948.5770.0310.0310.0000.0000.0000.000
153A154GLN00.0200.02751.2030.1580.1580.0000.0000.0000.000
154A155ALA00.0430.03551.7730.1270.1270.0000.0000.0000.000
155A156VAL0-0.0100.00251.8490.0780.0780.0000.0000.0000.000
156A157ASP-1-0.783-0.91254.519-5.652-5.6520.0000.0000.0000.000
157A158THR0-0.042-0.02456.9250.1320.1320.0000.0000.0000.000
158A159PRO00.0090.00757.4930.1150.1150.0000.0000.0000.000
159A160LEU00.0280.01957.2540.0910.0910.0000.0000.0000.000
160A161LEU0-0.063-0.03659.7470.0950.0950.0000.0000.0000.000
161A162ALA0-0.016-0.01062.7670.0950.0950.0000.0000.0000.000
162A163ALA00.0100.01463.8610.0880.0880.0000.0000.0000.000
163A164VAL0-0.004-0.02363.2640.0700.0700.0000.0000.0000.000
164A165LYS10.9070.94966.1764.7724.7720.0000.0000.0000.000
165A166LYS10.9570.98868.1054.6924.6920.0000.0000.0000.000
166A167VAL00.0110.01969.6900.0560.0560.0000.0000.0000.000
167A168GLU-1-0.877-0.93471.291-4.160-4.1600.0000.0000.0000.000
168A169PHE00.0690.04172.619-0.058-0.0580.0000.0000.0000.000
169A170LEU0-0.030-0.00666.381-0.067-0.0670.0000.0000.0000.000
170A171LYS10.9820.97365.4524.6934.6930.0000.0000.0000.000
171A172ASN00.020-0.00566.480-0.059-0.0590.0000.0000.0000.000
172A173TYR00.0580.03066.160-0.023-0.0230.0000.0000.0000.000
173A174LEU0-0.019-0.00662.309-0.053-0.0530.0000.0000.0000.000
174A175ALA0-0.034-0.02463.489-0.070-0.0700.0000.0000.0000.000
175A176SER0-0.063-0.01964.502-0.016-0.0160.0000.0000.0000.000
176A177LYS10.9030.93159.8735.1395.1390.0000.0000.0000.000
177A178PHE0-0.0020.01364.5790.0610.0610.0000.0000.0000.000
178A179THR0-0.074-0.05465.509-0.086-0.0860.0000.0000.0000.000
179A180LEU00.0020.02367.5470.0230.0230.0000.0000.0000.000
180A181ASN0-0.014-0.01770.413-0.002-0.0020.0000.0000.0000.000
181A182ASN0-0.010-0.02473.879-0.061-0.0610.0000.0000.0000.000
182A183ASN0-0.003-0.00175.2830.0010.0010.0000.0000.0000.000
183A184ASP-1-0.818-0.87772.958-4.314-4.3140.0000.0000.0000.000
184A185ARG10.9770.98273.8044.0584.0580.0000.0000.0000.000
185A186PRO0-0.019-0.03268.437-0.002-0.0020.0000.0000.0000.000
186A187HIS0-0.039-0.00569.738-0.053-0.0530.0000.0000.0000.000
187A188GLU-1-0.910-0.96571.455-4.121-4.1210.0000.0000.0000.000
188A189MET0-0.060-0.01271.2170.0310.0310.0000.0000.0000.000
189A190LYS10.9340.96672.1174.1004.1000.0000.0000.0000.000
190A191PHE-1-0.809-0.89768.236-4.566-4.5660.0000.0000.0000.000