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: QKGZY

Calculation Name: 1RYP-H-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RYP

Chain ID: H

ChEMBL ID:

UniProt ID: P21243

Base Structure: X-ray

Registration Date: 2025-10-03

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 205
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2319131.638961
FMO2-HF: Nuclear repulsion 2240268.814995
FMO2-HF: Total energy -78862.823966
FMO2-MP2: Total energy -79092.095875


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:-9:LEU)


Summations of interaction energy for fragment #1(A:-9:LEU)
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.
-174.072-165.93316.056-9.571-14.624-0.094
Interaction energy analysis for fragmet #1(A:-9:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.900
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].
3A-7LYS10.9530.9623.38230.20931.7000.024-0.645-0.8710.000
4A-6GLY00.002-0.0044.7285.4155.543-0.001-0.006-0.1200.000
5A-5GLU-1-0.795-0.8492.338-73.419-69.8154.970-3.651-4.922-0.042
6A-4VAL00.004-0.0034.122-1.275-1.0290.000-0.051-0.1950.000
7A-3SER0-0.0050.0102.361-4.502-3.6600.570-0.324-1.0880.000
8A-2LEU0-0.006-0.0144.0144.4294.5770.004-0.036-0.1170.000
56A47GLY00.0570.0283.656-1.166-1.0370.005-0.036-0.0990.000
57A48SER00.012-0.0282.2323.1384.1751.552-0.878-1.710-0.004
58A49ALA0-0.010-0.0013.3574.4094.1580.0800.332-0.1610.000
60A51ASP-1-0.757-0.8864.926-48.207-48.131-0.001-0.005-0.0700.000
103A94THR0-0.099-0.0571.928-34.496-34.2388.853-4.083-5.028-0.047
104A95ALA00.0370.0214.1971.1001.5310.000-0.188-0.243-0.001
9A-1GLY0-0.007-0.0045.8262.7642.7640.0000.0000.0000.000
10A1ALA0-0.004-0.0017.228-0.576-0.5760.0000.0000.0000.000
11A2SER00.0210.00710.687-0.033-0.0330.0000.0000.0000.000
12A3ILE0-0.046-0.01811.4160.9340.9340.0000.0000.0000.000
13A4MET0-0.0140.00714.666-0.123-0.1230.0000.0000.0000.000
14A5ALA0-0.0010.01117.6910.1220.1220.0000.0000.0000.000
15A6VAL00.0220.00920.449-0.082-0.0820.0000.0000.0000.000
16A7THR0-0.045-0.02424.0690.3250.3250.0000.0000.0000.000
17A8PHE00.006-0.00527.1800.1190.1190.0000.0000.0000.000
18A9LYS10.9040.96830.4968.0008.0000.0000.0000.0000.000
19A10ASP-1-0.890-0.96533.306-8.349-8.3490.0000.0000.0000.000
20A11GLY0-0.020-0.02530.4310.0620.0620.0000.0000.0000.000
21A12VAL0-0.030-0.00423.924-0.061-0.0610.0000.0000.0000.000
22A13ILE0-0.042-0.00723.9280.1720.1720.0000.0000.0000.000
23A14LEU0-0.0040.00318.689-0.376-0.3760.0000.0000.0000.000
24A15GLY00.0510.00719.2670.5780.5780.0000.0000.0000.000
25A16ALA0-0.002-0.01015.033-0.894-0.8940.0000.0000.0000.000
26A17ASP-1-0.635-0.78613.473-18.218-18.2180.0000.0000.0000.000
27A18SER0-0.036-0.01914.764-0.321-0.3210.0000.0000.0000.000
28A19ARG10.8560.94511.00616.94316.9430.0000.0000.0000.000
29A20THR0-0.0050.0048.487-1.100-1.1000.0000.0000.0000.000
30A21THR00.003-0.0116.4730.6690.6690.0000.0000.0000.000
31A22THR00.0060.0025.700-2.732-2.7320.0000.0000.0000.000
32A23GLY0-0.003-0.0025.9001.9211.9210.0000.0000.0000.000
33A24ALA00.0330.0037.769-0.101-0.1010.0000.0000.0000.000
34A25TYR0-0.0190.01010.4371.1401.1400.0000.0000.0000.000
35A26ILE00.013-0.00510.033-1.465-1.4650.0000.0000.0000.000
36A27ALA0-0.0030.00710.0210.9390.9390.0000.0000.0000.000
37A28ASN00.0330.01311.8121.6531.6530.0000.0000.0000.000
38A29ARG11.0141.00413.09912.09112.0910.0000.0000.0000.000
39A30VAL00.0140.01615.7680.4710.4710.0000.0000.0000.000
40A31THR0-0.0020.01311.4110.3060.3060.0000.0000.0000.000
41A32ASP-1-0.788-0.88314.794-14.135-14.1350.0000.0000.0000.000
42A33LYS10.7400.87210.38320.19520.1950.0000.0000.0000.000
43A34LEU0-0.0310.00913.651-0.540-0.5400.0000.0000.0000.000
44A35THR00.008-0.00215.1150.2240.2240.0000.0000.0000.000
45A36ARG10.8770.93117.26911.36611.3660.0000.0000.0000.000
46A37VAL0-0.013-0.01118.207-0.387-0.3870.0000.0000.0000.000
47A38HIS00.030-0.00321.1010.2270.2270.0000.0000.0000.000
48A39ASP-1-0.817-0.88624.783-10.590-10.5900.0000.0000.0000.000
49A40LYS10.8470.91726.9509.3259.3250.0000.0000.0000.000
50A41ILE00.0270.00721.830-0.097-0.0970.0000.0000.0000.000
51A42TRP0-0.0050.00220.215-0.286-0.2860.0000.0000.0000.000
52A43CYS0-0.034-0.01415.049-0.221-0.2210.0000.0000.0000.000
53A44CYS0-0.0180.00414.7730.3190.3190.0000.0000.0000.000
54A45ARG10.8710.9359.86020.70520.7050.0000.0000.0000.000
55A46SER0-0.013-0.0287.9110.1740.1740.0000.0000.0000.000
59A50ALA00.0090.0085.9602.6562.6560.0000.0000.0000.000
61A52THR0-0.024-0.0377.0444.0874.0870.0000.0000.0000.000
62A53GLN0-0.036-0.0109.0841.6401.6400.0000.0000.0000.000
63A54ALA00.0470.02810.8331.3891.3890.0000.0000.0000.000
64A55ILE0-0.009-0.0099.4631.2141.2140.0000.0000.0000.000
65A56ALA00.012-0.00312.9891.4261.4260.0000.0000.0000.000
66A57ASP-1-0.913-0.95415.027-16.327-16.3270.0000.0000.0000.000
67A58ILE0-0.021-0.00915.3541.0941.0940.0000.0000.0000.000
68A59VAL00.007-0.00316.6050.8910.8910.0000.0000.0000.000
69A60GLN0-0.012-0.00719.0031.2131.2130.0000.0000.0000.000
70A61TYR0-0.0140.00420.8600.8230.8230.0000.0000.0000.000
71A62HIS00.0270.00520.2981.0591.0590.0000.0000.0000.000
72A63LEU0-0.021-0.01122.1130.5950.5950.0000.0000.0000.000
73A64GLU-1-0.938-0.94025.033-10.667-10.6670.0000.0000.0000.000
74A65LEU00.0000.00826.5850.5340.5340.0000.0000.0000.000
75A66TYR00.012-0.00427.3900.4150.4150.0000.0000.0000.000
76A67THR0-0.031-0.03828.5940.4080.4080.0000.0000.0000.000
77A68SER0-0.076-0.04730.8110.4240.4240.0000.0000.0000.000
78A69GLN0-0.074-0.02731.5750.0360.0360.0000.0000.0000.000
79A70TYR0-0.047-0.02430.6670.3740.3740.0000.0000.0000.000
80A71GLY00.0100.02833.8070.1790.1790.0000.0000.0000.000
81A72THR0-0.020-0.03330.035-0.253-0.2530.0000.0000.0000.000
82A73PRO00.0240.03326.6710.1240.1240.0000.0000.0000.000
83A74SER00.0800.04728.453-0.129-0.1290.0000.0000.0000.000
84A75THR00.012-0.01123.340-0.378-0.3780.0000.0000.0000.000
85A76GLU-1-0.945-0.95723.506-11.852-11.8520.0000.0000.0000.000
86A77THR00.003-0.00423.987-0.465-0.4650.0000.0000.0000.000
87A78ALA00.0190.00521.591-0.481-0.4810.0000.0000.0000.000
88A79ALA0-0.020-0.01419.464-0.885-0.8850.0000.0000.0000.000
89A80SER0-0.006-0.00119.343-1.083-1.0830.0000.0000.0000.000
90A81VAL00.0250.01619.328-0.558-0.5580.0000.0000.0000.000
91A82PHE00.039-0.00314.096-0.946-0.9460.0000.0000.0000.000
92A83LYS10.9500.99015.38413.92113.9210.0000.0000.0000.000
93A84GLU-1-0.907-0.94815.774-16.263-16.2630.0000.0000.0000.000
94A85LEU0-0.051-0.01814.333-0.829-0.8290.0000.0000.0000.000
95A86CYS0-0.050-0.03911.482-1.975-1.9750.0000.0000.0000.000
96A87TYR0-0.027-0.01011.399-2.208-2.2080.0000.0000.0000.000
97A88GLU-1-0.911-0.96013.661-18.193-18.1930.0000.0000.0000.000
98A89ASN0-0.054-0.02711.3720.3860.3860.0000.0000.0000.000
99A90LYS10.8470.9309.30119.64119.6410.0000.0000.0000.000
100A91ASP-1-0.918-0.9507.509-31.538-31.5380.0000.0000.0000.000
101A92ASN0-0.079-0.0396.521-4.485-4.4850.0000.0000.0000.000
102A93LEU0-0.0160.0095.855-4.024-4.0240.0000.0000.0000.000
105A96GLY00.0150.0187.1560.6530.6530.0000.0000.0000.000
106A97ILE0-0.0200.0029.2570.4380.4380.0000.0000.0000.000
107A98ILE0-0.0040.00712.2640.7400.7400.0000.0000.0000.000
108A99VAL0-0.0010.00515.6290.1860.1860.0000.0000.0000.000
109A100ALA00.020-0.00618.3890.4130.4130.0000.0000.0000.000
110A101GLY00.0350.01221.566-0.087-0.0870.0000.0000.0000.000
111A102TYR0-0.059-0.02024.9190.2030.2030.0000.0000.0000.000
112A103ASP-1-0.855-0.92828.658-9.701-9.7010.0000.0000.0000.000
113A104ASP-1-0.954-0.97631.329-8.112-8.1120.0000.0000.0000.000
114A105LYS10.9450.97335.0898.5088.5080.0000.0000.0000.000
115A106ASN0-0.065-0.04931.1370.2250.2250.0000.0000.0000.000
116A107LYS10.8860.96931.6828.7348.7340.0000.0000.0000.000
117A108GLY00.0210.00828.327-0.195-0.1950.0000.0000.0000.000
118A109GLU-1-0.826-0.89425.855-11.047-11.0470.0000.0000.0000.000
119A110VAL00.020-0.00520.220-0.341-0.3410.0000.0000.0000.000
120A111TYR0-0.022-0.04420.1920.1920.1920.0000.0000.0000.000
121A112THR0-0.020-0.00515.396-0.957-0.9570.0000.0000.0000.000
122A113ILE00.0350.01613.5340.6810.6810.0000.0000.0000.000
123A114PRO0-0.0080.00311.612-1.934-1.9340.0000.0000.0000.000
124A115LEU00.047-0.0085.5800.3870.3870.0000.0000.0000.000
125A116GLY0-0.0120.0238.969-0.975-0.9750.0000.0000.0000.000
126A117GLY00.0520.02011.5960.9690.9690.0000.0000.0000.000
127A118SER0-0.059-0.04213.6011.0601.0600.0000.0000.0000.000
128A119VAL00.026-0.01216.098-0.588-0.5880.0000.0000.0000.000
129A120HIS0-0.0170.01117.412-0.120-0.1200.0000.0000.0000.000
130A121LYS10.9030.96720.64610.84710.8470.0000.0000.0000.000
131A122LEU0-0.040-0.02120.1530.1960.1960.0000.0000.0000.000
132A123PRO00.0400.03424.004-0.033-0.0330.0000.0000.0000.000
133A124TYR00.0100.01021.400-0.055-0.0550.0000.0000.0000.000
134A125ALA00.0020.00717.747-0.249-0.2490.0000.0000.0000.000
135A126ILE00.019-0.00116.6670.2160.2160.0000.0000.0000.000
136A127ALA0-0.009-0.01011.447-0.530-0.5300.0000.0000.0000.000
137A128GLY00.0440.0188.8570.7340.7340.0000.0000.0000.000
138A129SER0-0.065-0.0567.8240.1990.1990.0000.0000.0000.000
139A130GLY00.0440.0169.7520.9310.9310.0000.0000.0000.000
140A131SER0-0.069-0.04212.6361.2631.2630.0000.0000.0000.000
141A132THR00.028-0.00513.2100.6580.6580.0000.0000.0000.000
142A133PHE0-0.042-0.01913.4460.8470.8470.0000.0000.0000.000
143A134ILE0-0.0020.00717.6570.7910.7910.0000.0000.0000.000
144A135TYR00.0110.01615.0250.7590.7590.0000.0000.0000.000
145A136GLY00.0090.00620.8690.4640.4640.0000.0000.0000.000
146A137TYR0-0.0070.00123.2280.4520.4520.0000.0000.0000.000
147A138CYS0-0.006-0.01421.8920.2380.2380.0000.0000.0000.000
148A139ASP-1-0.954-0.97624.256-10.798-10.7980.0000.0000.0000.000
149A140LYS10.9190.96226.23510.20110.2010.0000.0000.0000.000
150A141ASN0-0.061-0.03327.6560.6340.6340.0000.0000.0000.000
151A142PHE00.0040.01226.3970.1720.1720.0000.0000.0000.000
152A143ARG10.8280.88328.5079.1899.1890.0000.0000.0000.000
153A144GLU-1-0.874-0.94330.242-9.894-9.8940.0000.0000.0000.000
154A145ASN0-0.113-0.07231.9970.2550.2550.0000.0000.0000.000
155A146MET00.0430.05329.1790.1930.1930.0000.0000.0000.000
156A147SER00.006-0.03833.350-0.149-0.1490.0000.0000.0000.000
157A148LYS10.8730.91631.1098.8088.8080.0000.0000.0000.000
158A149GLU-1-0.880-0.90530.944-8.336-8.3360.0000.0000.0000.000
159A150GLU-1-0.710-0.83731.460-8.860-8.8600.0000.0000.0000.000
160A151THR0-0.031-0.02726.726-0.318-0.3180.0000.0000.0000.000
161A152VAL00.003-0.00626.844-0.448-0.4480.0000.0000.0000.000
162A153ASP-1-0.854-0.93626.818-9.697-9.6970.0000.0000.0000.000
163A154PHE0-0.0150.00024.311-0.307-0.3070.0000.0000.0000.000
164A155ILE00.013-0.00921.373-0.479-0.4790.0000.0000.0000.000
165A156LYS10.8530.93422.6409.3399.3390.0000.0000.0000.000
166A157HIS00.0570.03023.953-0.461-0.4610.0000.0000.0000.000
167A158SER0-0.004-0.01221.350-0.284-0.2840.0000.0000.0000.000
168A159LEU0-0.026-0.03117.311-0.552-0.5520.0000.0000.0000.000
169A160SER0-0.022-0.00219.271-0.382-0.3820.0000.0000.0000.000
170A161GLN00.0300.01120.867-0.452-0.4520.0000.0000.0000.000
171A162ALA0-0.034-0.01515.993-0.340-0.3400.0000.0000.0000.000
172A163ILE0-0.035-0.02916.000-0.823-0.8230.0000.0000.0000.000
173A164LYS10.9170.98317.18511.03911.0390.0000.0000.0000.000
174A165TRP0-0.040-0.01817.5340.3200.3200.0000.0000.0000.000
175A166ASP-1-0.728-0.79710.893-22.466-22.4660.0000.0000.0000.000
176A167GLY00.0360.02013.1480.2740.2740.0000.0000.0000.000
177A168SER0-0.109-0.0637.932-0.348-0.3480.0000.0000.0000.000
178A169SER0-0.034-0.02510.052-0.885-0.8850.0000.0000.0000.000
179A170GLY00.026-0.01012.8940.6920.6920.0000.0000.0000.000
180A171GLY0-0.049-0.01915.897-0.467-0.4670.0000.0000.0000.000
181A172VAL0-0.009-0.00118.2200.6570.6570.0000.0000.0000.000
182A173ILE00.0240.02418.844-0.725-0.7250.0000.0000.0000.000
183A174ARG10.8240.89317.66314.43814.4380.0000.0000.0000.000
184A175MET0-0.010-0.00920.406-0.262-0.2620.0000.0000.0000.000
185A176VAL0-0.034-0.01521.2000.2260.2260.0000.0000.0000.000
186A177VAL00.0030.01523.722-0.178-0.1780.0000.0000.0000.000
187A178LEU0-0.0040.00424.3370.1680.1680.0000.0000.0000.000
188A179THR00.0370.01527.9700.1470.1470.0000.0000.0000.000
189A180ALA00.0710.03931.635-0.044-0.0440.0000.0000.0000.000
190A181ALA0-0.027-0.01534.8890.0330.0330.0000.0000.0000.000
191A182GLY00.0030.00032.6160.1310.1310.0000.0000.0000.000
192A183VAL0-0.010-0.00426.222-0.206-0.2060.0000.0000.0000.000
193A184GLU-1-0.813-0.87528.298-9.046-9.0460.0000.0000.0000.000
194A185ARG10.8310.89919.67612.58612.5860.0000.0000.0000.000
195A186LEU00.0060.00724.9650.3620.3620.0000.0000.0000.000
196A187ILE0-0.050-0.03422.955-0.622-0.6220.0000.0000.0000.000
197A188PHE00.0400.02623.8510.4020.4020.0000.0000.0000.000
198A189TYR00.023-0.00923.601-0.643-0.6430.0000.0000.0000.000
199A190PRO00.0320.00822.0850.1980.1980.0000.0000.0000.000
200A191ASP-1-0.906-0.94724.526-9.667-9.6670.0000.0000.0000.000
201A192GLU-1-0.936-0.95227.627-9.412-9.4120.0000.0000.0000.000
202A193TYR0-0.040-0.06120.253-0.149-0.1490.0000.0000.0000.000
203A194GLU-1-0.952-0.98622.464-11.839-11.8390.0000.0000.0000.000
204A195GLN0-0.113-0.05825.530-0.068-0.0680.0000.0000.0000.000
205A196LEU-1-0.962-0.95426.402-9.671-9.6710.0000.0000.0000.000