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: 4QV5N

Calculation Name: 1RYP-A-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: A

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 243
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3089083.643896
FMO2-HF: Nuclear repulsion 2993316.617498
FMO2-HF: Total energy -95767.026398
FMO2-MP2: Total energy -96046.24748


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:10:ALA)


Summations of interaction energy for fragment #1(A:10: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.
-3.971-0.35799999999998-0.003-1.707-1.902-0.006
Interaction energy analysis for fragmet #1(A:10:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.871 / q_NPA : 0.911
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].
3A12TYR00.0080.0053.1674.0917.488-0.002-1.682-1.712-0.006
4A13ASP-1-0.865-0.9434.874-41.067-40.851-0.001-0.025-0.1900.000
5A14ARG10.9520.9816.35834.03134.0310.0000.0000.0000.000
6A15HIS0-0.027-0.0118.2731.5051.5050.0000.0000.0000.000
7A16ILE00.0170.0166.7022.5452.5450.0000.0000.0000.000
8A17THR0-0.038-0.02110.058-1.666-1.6660.0000.0000.0000.000
9A18ILE0-0.027-0.0035.0360.0080.0080.0000.0000.0000.000
10A19PHE0-0.013-0.0119.6410.6440.6440.0000.0000.0000.000
11A20SER0-0.015-0.0217.412-4.010-4.0100.0000.0000.0000.000
12A21PRO0-0.009-0.0156.7111.6761.6760.0000.0000.0000.000
13A22GLU-1-0.834-0.8849.176-24.741-24.7410.0000.0000.0000.000
14A23GLY00.0100.01411.4301.7371.7370.0000.0000.0000.000
15A24ARG10.7890.87112.13420.75620.7560.0000.0000.0000.000
16A25LEU00.0680.03411.577-2.287-2.2870.0000.0000.0000.000
17A26TYR0-0.030-0.04210.4231.9471.9470.0000.0000.0000.000
18A27GLN0-0.013-0.01811.9852.6552.6550.0000.0000.0000.000
19A28VAL00.0290.02214.4001.2871.2870.0000.0000.0000.000
20A29GLU-1-0.833-0.87816.349-17.942-17.9420.0000.0000.0000.000
21A30TYR0-0.046-0.03213.3350.3460.3460.0000.0000.0000.000
22A31ALA00.0210.01718.4600.9190.9190.0000.0000.0000.000
23A32PHE00.035-0.00120.3930.8910.8910.0000.0000.0000.000
24A33LYS10.9090.96921.68414.39814.3980.0000.0000.0000.000
25A34ALA0-0.0040.01122.7070.5330.5330.0000.0000.0000.000
26A35THR0-0.027-0.02324.4520.6810.6810.0000.0000.0000.000
27A36ASN00.0390.00727.2350.6680.6680.0000.0000.0000.000
28A37GLN0-0.027-0.00925.8320.5620.5620.0000.0000.0000.000
29A38THR0-0.013-0.00928.9850.1510.1510.0000.0000.0000.000
30A39ASN0-0.011-0.00232.2530.3450.3450.0000.0000.0000.000
31A40ILE00.0050.02434.1070.3420.3420.0000.0000.0000.000
32A41ASN00.008-0.00534.748-0.484-0.4840.0000.0000.0000.000
33A42SER0-0.021-0.02935.8040.2070.2070.0000.0000.0000.000
34A43LEU0-0.011-0.00438.097-0.170-0.1700.0000.0000.0000.000
35A44ALA0-0.0060.00540.0370.0880.0880.0000.0000.0000.000
36A45VAL00.022-0.00241.684-0.078-0.0780.0000.0000.0000.000
37A46ARG10.7950.89743.9407.1917.1910.0000.0000.0000.000
38A47GLY00.0600.01946.9070.0410.0410.0000.0000.0000.000
39A48LYS10.9070.94950.5735.6705.6700.0000.0000.0000.000
40A49ASP-1-0.921-0.95552.253-5.949-5.9490.0000.0000.0000.000
41A50CYS0-0.0100.00350.165-0.037-0.0370.0000.0000.0000.000
42A51THR0-0.056-0.04443.504-0.048-0.0480.0000.0000.0000.000
43A52VAL00.0150.02146.105-0.008-0.0080.0000.0000.0000.000
44A53VAL0-0.051-0.02540.435-0.182-0.1820.0000.0000.0000.000
45A54ILE00.0690.03342.6830.1340.1340.0000.0000.0000.000
46A55SER0-0.017-0.02739.181-0.358-0.3580.0000.0000.0000.000
47A56GLN00.0350.02639.730-0.031-0.0310.0000.0000.0000.000
48A57LYS10.8310.92140.3917.0457.0450.0000.0000.0000.000
49A58LYS10.9240.94538.0378.4718.4710.0000.0000.0000.000
50A59VAL00.0050.00240.712-0.195-0.1950.0000.0000.0000.000
51A60PRO0-0.031-0.00139.1880.1410.1410.0000.0000.0000.000
52A61ASP-1-0.840-0.93141.512-7.408-7.4080.0000.0000.0000.000
53A62LYS10.9600.96243.3366.5726.5720.0000.0000.0000.000
54A63LEU0-0.028-0.00744.4400.1730.1730.0000.0000.0000.000
55A64LEU0-0.054-0.01340.194-0.063-0.0630.0000.0000.0000.000
56A65ASP-1-0.790-0.86144.332-6.621-6.6210.0000.0000.0000.000
57A66PRO00.0370.00344.975-0.178-0.1780.0000.0000.0000.000
58A67THR0-0.069-0.05145.799-0.095-0.0950.0000.0000.0000.000
59A68THR0-0.063-0.03342.455-0.150-0.1500.0000.0000.0000.000
60A69VAL0-0.067-0.02439.595-0.270-0.2700.0000.0000.0000.000
61A70SER0-0.024-0.04539.7500.1310.1310.0000.0000.0000.000
62A71TYR0-0.060-0.04333.294-0.397-0.3970.0000.0000.0000.000
63A72ILE0-0.0150.00037.306-0.191-0.1910.0000.0000.0000.000
64A73PHE0-0.026-0.01735.4800.1230.1230.0000.0000.0000.000
65A74CYS00.0200.01939.9720.0460.0460.0000.0000.0000.000
66A75ILE0-0.076-0.05037.201-0.097-0.0970.0000.0000.0000.000
67A76SER00.0520.02140.5040.0020.0020.0000.0000.0000.000
68A77ARG10.9180.96843.4196.4826.4820.0000.0000.0000.000
69A78THR00.0730.02845.3060.0470.0470.0000.0000.0000.000
70A79ILE0-0.0060.01039.207-0.025-0.0250.0000.0000.0000.000
71A80GLY00.0340.01841.4910.0430.0430.0000.0000.0000.000
72A81MET0-0.057-0.02633.797-0.220-0.2200.0000.0000.0000.000
73A82VAL00.0320.03037.0020.0960.0960.0000.0000.0000.000
74A83VAL0-0.054-0.02831.297-0.258-0.2580.0000.0000.0000.000
75A84ASN00.0210.03231.6010.2620.2620.0000.0000.0000.000
76A85GLY00.1020.03428.651-0.442-0.4420.0000.0000.0000.000
77A86PRO0-0.027-0.00525.9700.4320.4320.0000.0000.0000.000
78A87ILE00.0600.03029.280-0.090-0.0900.0000.0000.0000.000
79A88PRO0-0.017-0.00827.9960.1610.1610.0000.0000.0000.000
80A89ASP-1-0.718-0.82924.582-12.954-12.9540.0000.0000.0000.000
81A90ALA00.0440.02428.0790.0790.0790.0000.0000.0000.000
82A91ARG10.9520.97931.3529.0599.0590.0000.0000.0000.000
83A92ASN0-0.049-0.01327.3210.1260.1260.0000.0000.0000.000
84A93ALA00.0550.02129.3440.1220.1220.0000.0000.0000.000
85A94ALA00.0190.00530.7860.1970.1970.0000.0000.0000.000
86A95LEU0-0.021-0.01033.1480.2590.2590.0000.0000.0000.000
87A96ARG10.8500.90928.04910.80310.8030.0000.0000.0000.000
88A97ALA00.0480.01032.7760.1310.1310.0000.0000.0000.000
89A98LYS10.9230.97334.7498.2598.2590.0000.0000.0000.000
90A99ALA0-0.0240.00034.9140.1980.1980.0000.0000.0000.000
91A100GLU-1-0.738-0.83332.170-9.736-9.7360.0000.0000.0000.000
92A101ALA00.002-0.00136.1720.1710.1710.0000.0000.0000.000
93A102ALA0-0.013-0.00539.4570.2090.2090.0000.0000.0000.000
94A103GLU-1-0.902-0.94936.626-8.576-8.5760.0000.0000.0000.000
95A104PHE00.0100.00138.5130.0830.0830.0000.0000.0000.000
96A105ARG10.9280.97140.5716.8256.8250.0000.0000.0000.000
97A106TYR0-0.073-0.02942.7240.2480.2480.0000.0000.0000.000
98A107LYS10.8460.91737.3738.5738.5730.0000.0000.0000.000
99A108TYR0-0.019-0.01139.037-0.053-0.0530.0000.0000.0000.000
100A109GLY0-0.0180.00544.6960.1020.1020.0000.0000.0000.000
101A110TYR00.0360.02143.4750.0830.0830.0000.0000.0000.000
102A111ASP-1-0.898-0.96845.027-6.980-6.9800.0000.0000.0000.000
103A112MET0-0.069-0.01836.658-0.119-0.1190.0000.0000.0000.000
104A113PRO00.0800.05140.778-0.023-0.0230.0000.0000.0000.000
105A114CYS0-0.056-0.01839.424-0.321-0.3210.0000.0000.0000.000
106A115ASP-1-0.828-0.92736.973-8.482-8.4820.0000.0000.0000.000
107A116VAL0-0.0140.00235.590-0.380-0.3800.0000.0000.0000.000
108A117LEU00.0260.01134.665-0.324-0.3240.0000.0000.0000.000
109A118ALA0-0.024-0.01033.146-0.357-0.3570.0000.0000.0000.000
110A119LYS10.9890.99231.3009.2429.2420.0000.0000.0000.000
111A120ARG10.8240.89629.6439.7609.7600.0000.0000.0000.000
112A121MET0-0.010-0.01129.363-0.374-0.3740.0000.0000.0000.000
113A122ALA00.0100.02027.063-0.506-0.5060.0000.0000.0000.000
114A123ASN00.006-0.01425.489-0.625-0.6250.0000.0000.0000.000
115A124LEU0-0.044-0.01824.646-0.494-0.4940.0000.0000.0000.000
116A125SER00.0060.00522.866-0.602-0.6020.0000.0000.0000.000
117A126GLN00.004-0.00420.572-0.533-0.5330.0000.0000.0000.000
118A127ILE0-0.001-0.00719.933-0.890-0.8900.0000.0000.0000.000
119A128TYR0-0.029-0.02618.659-0.692-0.6920.0000.0000.0000.000
120A129THR0-0.018-0.00116.724-1.416-1.4160.0000.0000.0000.000
121A130GLN0-0.0070.01315.629-0.454-0.4540.0000.0000.0000.000
122A131ARG10.9040.95715.04215.37515.3750.0000.0000.0000.000
123A132ALA00.0520.02010.8470.6420.6420.0000.0000.0000.000
124A133TYR0-0.028-0.01212.849-0.548-0.5480.0000.0000.0000.000
125A134MET0-0.047-0.01115.3530.9950.9950.0000.0000.0000.000
126A135ARG10.8210.88116.59013.87113.8710.0000.0000.0000.000
127A136PRO00.0370.00816.5650.8810.8810.0000.0000.0000.000
128A137LEU0-0.0050.00719.788-0.014-0.0140.0000.0000.0000.000
129A138GLY0-0.023-0.01423.141-0.148-0.1480.0000.0000.0000.000
130A139VAL0-0.042-0.04123.9340.4100.4100.0000.0000.0000.000
131A140ILE00.0020.00426.785-0.267-0.2670.0000.0000.0000.000
132A141LEU0-0.024-0.01329.2150.3150.3150.0000.0000.0000.000
133A142THR00.001-0.00632.009-0.079-0.0790.0000.0000.0000.000
134A143PHE00.0170.00132.3760.1760.1760.0000.0000.0000.000
135A144VAL00.012-0.01137.4360.0320.0320.0000.0000.0000.000
136A145SER00.0350.00341.1780.0010.0010.0000.0000.0000.000
137A146VAL0-0.0120.01944.2080.0050.0050.0000.0000.0000.000
138A147ASP-1-0.862-0.93344.308-7.178-7.1780.0000.0000.0000.000
139A148GLU-1-0.981-0.99746.612-6.369-6.3690.0000.0000.0000.000
140A149GLU-1-0.956-0.96246.632-6.718-6.7180.0000.0000.0000.000
141A150LEU0-0.063-0.04742.1230.0250.0250.0000.0000.0000.000
142A151GLY00.0500.04146.3640.0200.0200.0000.0000.0000.000
143A152PRO0-0.032-0.01446.372-0.181-0.1810.0000.0000.0000.000
144A153SER0-0.0120.00241.852-0.138-0.1380.0000.0000.0000.000
145A154ILE0-0.0040.00238.219-0.045-0.0450.0000.0000.0000.000
146A155TYR00.0130.01335.618-0.157-0.1570.0000.0000.0000.000
147A156LYS10.8270.91931.8189.5979.5970.0000.0000.0000.000
148A157THR00.0260.00728.878-0.050-0.0500.0000.0000.0000.000
149A158ASP-1-0.811-0.91624.971-12.457-12.4570.0000.0000.0000.000
150A159PRO0-0.008-0.01221.758-0.164-0.1640.0000.0000.0000.000
151A160ALA0-0.019-0.00920.675-0.773-0.7730.0000.0000.0000.000
152A161GLY0-0.044-0.01521.729-0.201-0.2010.0000.0000.0000.000
153A162TYR0-0.056-0.01024.4160.3100.3100.0000.0000.0000.000
154A163TYR00.009-0.02826.6400.0750.0750.0000.0000.0000.000
155A164VAL0-0.0270.00930.3870.0290.0290.0000.0000.0000.000
156A165GLY00.0630.01733.7190.0310.0310.0000.0000.0000.000
157A166TYR0-0.057-0.04432.908-0.139-0.1390.0000.0000.0000.000
158A167LYS10.9680.99239.2557.5397.5390.0000.0000.0000.000
159A168ALA00.0650.02641.4210.1760.1760.0000.0000.0000.000
160A169THR0-0.059-0.02536.200-0.289-0.2890.0000.0000.0000.000
161A170ALA00.0600.03536.9660.1950.1950.0000.0000.0000.000
162A171THR0-0.031-0.02031.869-0.388-0.3880.0000.0000.0000.000
163A172GLY00.0770.05032.4350.2590.2590.0000.0000.0000.000
164A173PRO0-0.068-0.04331.967-0.110-0.1100.0000.0000.0000.000
165A174LYS10.9751.00433.0018.1868.1860.0000.0000.0000.000
166A175GLN0-0.023-0.00132.6820.0090.0090.0000.0000.0000.000
167A176GLN00.0170.02333.1730.3530.3530.0000.0000.0000.000
168A177GLU-1-0.812-0.90536.197-8.518-8.5180.0000.0000.0000.000
169A178ILE00.0340.00938.5290.2130.2130.0000.0000.0000.000
170A179THR0-0.044-0.03136.5350.1150.1150.0000.0000.0000.000
171A180THR0-0.009-0.01938.5130.2490.2490.0000.0000.0000.000
172A181ASN00.0140.02940.9990.2480.2480.0000.0000.0000.000
173A182LEU00.0370.01641.3420.1930.1930.0000.0000.0000.000
174A183GLU-1-0.902-0.95938.948-7.991-7.9910.0000.0000.0000.000
175A184ASN0-0.029-0.01943.3320.1540.1540.0000.0000.0000.000
176A185HIS00.0400.03046.3950.2030.2030.0000.0000.0000.000
177A186PHE00.0040.01444.4900.1240.1240.0000.0000.0000.000
178A187LYS10.8600.93041.4697.7167.7160.0000.0000.0000.000
179A188LYS10.9220.97047.8856.4016.4010.0000.0000.0000.000
180A189SER0-0.017-0.03350.5530.1110.1110.0000.0000.0000.000
181A190LYS10.8710.94149.9966.2656.2650.0000.0000.0000.000
182A191ILE00.0170.02650.267-0.033-0.0330.0000.0000.0000.000
183A192ASP-1-0.878-0.93645.904-6.930-6.9300.0000.0000.0000.000
184A193HIS0-0.051-0.02246.381-0.070-0.0700.0000.0000.0000.000
185A194ILE00.006-0.00148.4270.0680.0680.0000.0000.0000.000
186A195ASN0-0.016-0.01251.1790.0290.0290.0000.0000.0000.000
187A196GLU-1-0.828-0.91554.601-5.642-5.6420.0000.0000.0000.000
188A197GLU-1-0.933-0.97855.313-5.591-5.5910.0000.0000.0000.000
189A198SER0-0.033-0.01656.9490.0050.0050.0000.0000.0000.000
190A199TRP00.0800.00351.999-0.152-0.1520.0000.0000.0000.000
191A200GLU-1-0.860-0.91552.701-5.831-5.8310.0000.0000.0000.000
192A201LYS10.9560.98854.2415.4615.4610.0000.0000.0000.000
193A202VAL0-0.015-0.00249.183-0.101-0.1010.0000.0000.0000.000
194A203VAL0-0.031-0.02449.354-0.179-0.1790.0000.0000.0000.000
195A204GLU-1-0.770-0.87150.322-5.838-5.8380.0000.0000.0000.000
196A205PHE00.0130.01947.807-0.094-0.0940.0000.0000.0000.000
197A206ALA0-0.045-0.04046.271-0.112-0.1120.0000.0000.0000.000
198A207ILE0-0.007-0.00946.884-0.176-0.1760.0000.0000.0000.000
199A208THR00.0490.02348.508-0.063-0.0630.0000.0000.0000.000
200A209HIS10.8510.90946.3246.6006.6000.0000.0000.0000.000
201A210MET0-0.069-0.02741.037-0.191-0.1910.0000.0000.0000.000
202A211ILE00.0350.02745.133-0.176-0.1760.0000.0000.0000.000
203A212ASP-1-0.894-0.95147.387-6.560-6.5600.0000.0000.0000.000
204A213ALA0-0.118-0.05142.496-0.080-0.0800.0000.0000.0000.000
205A214LEU0-0.069-0.05140.036-0.208-0.2080.0000.0000.0000.000
206A215GLY0-0.0070.02243.493-0.061-0.0610.0000.0000.0000.000
207A216THR0-0.137-0.07844.802-0.020-0.0200.0000.0000.0000.000
208A217GLU-1-0.843-0.91447.099-6.219-6.2190.0000.0000.0000.000
209A218PHE0-0.043-0.04744.594-0.215-0.2150.0000.0000.0000.000
210A219SER00.024-0.00849.5220.1610.1610.0000.0000.0000.000
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