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: 8QNLY

Calculation Name: 2D4C-B-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D4C

Chain ID: B

ChEMBL ID:

UniProt ID: Q99962

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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2397668.400156
FMO2-HF: Nuclear repulsion 2304162.918366
FMO2-HF: Total energy -93505.48179
FMO2-MP2: Total energy -93776.114468


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:GLN)


Summations of interaction energy for fragment #1(A:9:GLN)
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.
-0.71999999999999-0.850999999999998.531-3.91-4.490.039
Interaction energy analysis for fragmet #1(A:9:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.902 / q_NPA : 0.933
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].
3A11HIS00.0820.0503.843-0.6680.977-0.024-0.795-0.8260.000
4A12LYS10.9570.9701.87424.87023.0948.555-3.115-3.6640.039
5A13ALA00.0320.0315.8500.2590.2590.0000.0000.0000.000
6A14THR00.0690.0289.4760.2240.2240.0000.0000.0000.000
7A15GLN00.0270.0106.1071.4771.4770.0000.0000.0000.000
8A16LYS10.9330.9696.34428.22528.2250.0000.0000.0000.000
9A17VAL00.0520.03210.1890.9700.9700.0000.0000.0000.000
10A18SER00.0020.00511.2970.8310.8310.0000.0000.0000.000
11A19GLU-1-1.002-0.9929.732-23.601-23.6010.0000.0000.0000.000
12A20LYS10.8630.93712.79618.87618.8760.0000.0000.0000.000
13A21VAL00.0320.01615.5790.6250.6250.0000.0000.0000.000
14A22GLY0-0.013-0.00716.4070.7640.7640.0000.0000.0000.000
15A23GLY0-0.016-0.00315.785-0.130-0.1300.0000.0000.0000.000
16A24ALA0-0.020-0.01016.3050.8940.8940.0000.0000.0000.000
17A25GLU-1-0.824-0.92017.446-14.661-14.6610.0000.0000.0000.000
18A26GLY00.0230.01819.1540.6620.6620.0000.0000.0000.000
19A27THR0-0.059-0.03020.9040.4640.4640.0000.0000.0000.000
20A28LYS10.8460.92522.32911.81011.8100.0000.0000.0000.000
21A29LEU00.0200.02123.7480.4400.4400.0000.0000.0000.000
22A30ASP-1-0.831-0.90925.333-10.990-10.9900.0000.0000.0000.000
23A31ASP-1-0.877-0.94426.092-11.339-11.3390.0000.0000.0000.000
24A32ASP-1-0.823-0.91027.371-10.542-10.5420.0000.0000.0000.000
25A33PHE0-0.022-0.02828.7090.4200.4200.0000.0000.0000.000
26A34LYS10.8660.92228.63911.24211.2420.0000.0000.0000.000
27A35GLU-1-0.993-0.98732.629-8.911-8.9110.0000.0000.0000.000
28A36MET0-0.0410.00332.5670.4040.4040.0000.0000.0000.000
29A37GLU-1-0.865-0.94235.247-8.663-8.6630.0000.0000.0000.000
30A38ARG10.9580.98837.1658.4278.4270.0000.0000.0000.000
31A39LYS10.8310.91038.7097.7607.7600.0000.0000.0000.000
32A40VAL00.0350.03840.3850.2550.2550.0000.0000.0000.000
33A41ASP-1-0.823-0.89041.793-7.102-7.1020.0000.0000.0000.000
34A42VAL0-0.060-0.03142.9060.1990.1990.0000.0000.0000.000
35A43THR0-0.012-0.01944.1480.1940.1940.0000.0000.0000.000
36A44SER00.0110.01146.1960.2360.2360.0000.0000.0000.000
37A45ARG10.8320.87344.6187.1697.1690.0000.0000.0000.000
38A46ALA00.0000.00649.0390.1490.1490.0000.0000.0000.000
39A47VAL00.0280.01450.2830.1520.1520.0000.0000.0000.000
40A48MET00.0300.02552.2500.1360.1360.0000.0000.0000.000
41A49GLU-1-0.967-0.97253.784-5.713-5.7130.0000.0000.0000.000
42A50ILE00.0210.00152.9430.1410.1410.0000.0000.0000.000
43A51MET00.0020.03556.3500.1290.1290.0000.0000.0000.000
44A52THR0-0.033-0.02458.0540.1400.1400.0000.0000.0000.000
45A53LYS10.8430.90358.9155.4515.4510.0000.0000.0000.000
46A54THR00.000-0.01059.7800.1000.1000.0000.0000.0000.000
47A55ILE00.0310.01462.2190.1130.1130.0000.0000.0000.000
48A56GLU-1-0.938-0.98163.330-5.005-5.0050.0000.0000.0000.000
49A57TYR0-0.032-0.00764.6600.0700.0700.0000.0000.0000.000
50A58LEU00.0050.01465.3440.0780.0780.0000.0000.0000.000
51A59GLN0-0.076-0.04068.4070.1200.1200.0000.0000.0000.000
52A60PRO00.0650.04569.955-0.023-0.0230.0000.0000.0000.000
53A61ASN00.0210.02271.073-0.011-0.0110.0000.0000.0000.000
54A62PRO00.0450.01371.001-0.016-0.0160.0000.0000.0000.000
55A63ALA0-0.0050.00071.857-0.032-0.0320.0000.0000.0000.000
56A64SER00.021-0.00573.9130.0060.0060.0000.0000.0000.000
57A65ARG10.8710.93766.6424.7514.7510.0000.0000.0000.000
58A66ALA0-0.0150.00269.020-0.062-0.0620.0000.0000.0000.000
59A67LYS10.8500.90770.0244.2214.2210.0000.0000.0000.000
60A68LEU0-0.0010.00667.6060.0140.0140.0000.0000.0000.000
61A69SER0-0.027-0.03165.757-0.073-0.0730.0000.0000.0000.000
62A70MET0-0.120-0.05166.570-0.045-0.0450.0000.0000.0000.000
63A71ILE-1-0.899-0.91566.719-4.787-4.7870.0000.0000.0000.000
64A84PRO10.9010.94973.6634.2684.2680.0000.0000.0000.000
65A85GLY00.0400.03474.5390.0560.0560.0000.0000.0000.000
66A86TYR0-0.074-0.06972.3260.0060.0060.0000.0000.0000.000
67A87PRO00.0370.03577.728-0.011-0.0110.0000.0000.0000.000
68A88GLN00.0410.00074.040-0.063-0.0630.0000.0000.0000.000
69A89ALA0-0.016-0.01577.9600.0560.0560.0000.0000.0000.000
70A90GLU-1-0.843-0.93676.728-4.134-4.1340.0000.0000.0000.000
71A91ALA00.0140.01781.1160.0560.0560.0000.0000.0000.000
72A92LEU00.0150.00281.7850.0540.0540.0000.0000.0000.000
73A93LEU0-0.036-0.01283.5860.0550.0550.0000.0000.0000.000
74A94ALA00.0390.01985.2930.0560.0560.0000.0000.0000.000
75A95GLU-1-0.946-0.97585.964-3.690-3.6900.0000.0000.0000.000
76A96ALA0-0.043-0.01988.7060.0580.0580.0000.0000.0000.000
77A97MET0-0.040-0.01787.7520.0430.0430.0000.0000.0000.000
78A98LEU00.0400.02289.8080.0550.0550.0000.0000.0000.000
79A99LYS10.7960.91693.1073.4123.4120.0000.0000.0000.000
80A100PHE00.019-0.01493.8090.0410.0410.0000.0000.0000.000
81A101GLY00.0480.03495.4510.0340.0340.0000.0000.0000.000
82A102ARG10.9170.95596.9353.2653.2650.0000.0000.0000.000
83A103GLU-1-0.973-0.98599.045-3.229-3.2290.0000.0000.0000.000
84A104LEU0-0.035-0.01198.3990.0340.0340.0000.0000.0000.000
85A105GLY00.0140.016101.4270.0360.0360.0000.0000.0000.000
86A106ASP-1-0.935-0.995101.624-3.187-3.1870.0000.0000.0000.000
87A107ASP-1-0.978-0.969103.767-2.961-2.9610.0000.0000.0000.000
88A108CYS0-0.077-0.007102.359-0.008-0.0080.0000.0000.0000.000
89A109ASN00.0740.00599.753-0.036-0.0360.0000.0000.0000.000
90A110PHE0-0.011-0.01694.352-0.035-0.0350.0000.0000.0000.000
91A111GLY00.0630.01997.034-0.036-0.0360.0000.0000.0000.000
92A112PRO00.0210.01597.076-0.043-0.0430.0000.0000.0000.000
93A113ALA00.0030.00794.521-0.036-0.0360.0000.0000.0000.000
94A114LEU0-0.043-0.01892.443-0.052-0.0520.0000.0000.0000.000
95A115GLY00.0260.01392.106-0.037-0.0370.0000.0000.0000.000
96A116GLU-1-0.787-0.86991.782-3.424-3.4240.0000.0000.0000.000
97A117VAL0-0.005-0.01087.364-0.046-0.0460.0000.0000.0000.000
98A118GLY00.0280.00687.414-0.051-0.0510.0000.0000.0000.000
99A119GLU-1-0.933-0.97187.430-3.616-3.6160.0000.0000.0000.000
100A120ALA00.0430.02384.967-0.046-0.0460.0000.0000.0000.000
101A121MET0-0.051-0.02883.125-0.078-0.0780.0000.0000.0000.000
102A122ARG10.8620.92282.4933.6923.6920.0000.0000.0000.000
103A123GLU-1-0.904-0.95982.401-3.826-3.8260.0000.0000.0000.000
104A124LEU0-0.015-0.01678.294-0.065-0.0650.0000.0000.0000.000
105A125SER00.0210.00477.941-0.066-0.0660.0000.0000.0000.000
106A126GLU-1-0.871-0.91477.839-3.920-3.9200.0000.0000.0000.000
107A127VAL00.0130.01974.745-0.062-0.0620.0000.0000.0000.000
108A128LYS10.7900.87772.0024.3624.3620.0000.0000.0000.000
109A129ASP-1-0.865-0.94973.055-4.253-4.2530.0000.0000.0000.000
110A130SER0-0.065-0.03772.767-0.053-0.0530.0000.0000.0000.000
111A131LEU00.0000.01167.506-0.072-0.0720.0000.0000.0000.000
112A132ASP-1-0.728-0.82368.269-4.583-4.5830.0000.0000.0000.000
113A133ILE0-0.013-0.01268.028-0.062-0.0620.0000.0000.0000.000
114A134GLU-1-0.909-0.94865.492-4.841-4.8410.0000.0000.0000.000
115A135VAL00.000-0.01062.773-0.098-0.0980.0000.0000.0000.000
116A136LYS10.7880.88462.9224.8784.8780.0000.0000.0000.000
117A137GLN00.010-0.00462.758-0.025-0.0250.0000.0000.0000.000
118A138ASN0-0.019-0.01661.210-0.092-0.0920.0000.0000.0000.000
119A139PHE0-0.055-0.02156.122-0.093-0.0930.0000.0000.0000.000
120A140ILE00.0080.00258.126-0.099-0.0990.0000.0000.0000.000
121A141ASP-1-0.770-0.87658.607-5.208-5.2080.0000.0000.0000.000
122A142PRO0-0.055-0.03155.912-0.108-0.1080.0000.0000.0000.000
123A143LEU0-0.0160.00153.282-0.146-0.1460.0000.0000.0000.000
124A144GLN0-0.007-0.02254.017-0.043-0.0430.0000.0000.0000.000
125A145ASN0-0.055-0.02652.189-0.051-0.0510.0000.0000.0000.000
126A146LEU0-0.0070.00748.272-0.117-0.1170.0000.0000.0000.000
127A147HIS0-0.023-0.01449.531-0.228-0.2280.0000.0000.0000.000
128A148ASP-1-0.867-0.93150.177-6.015-6.0150.0000.0000.0000.000
129A149LYS10.8860.95249.2636.2476.2470.0000.0000.0000.000
130A150ASP-1-0.842-0.90947.207-6.557-6.5570.0000.0000.0000.000
131A151LEU00.0290.00644.932-0.216-0.2160.0000.0000.0000.000
132A152ARG10.8410.93144.4366.1356.1350.0000.0000.0000.000
133A153GLU-1-0.908-0.96944.515-6.823-6.8230.0000.0000.0000.000
134A154ILE00.0310.02039.993-0.244-0.2440.0000.0000.0000.000
135A155GLN0-0.010-0.01039.631-0.423-0.4230.0000.0000.0000.000
136A156SER0-0.062-0.03539.461-0.225-0.2250.0000.0000.0000.000
137A157ALA0-0.003-0.00838.361-0.231-0.2310.0000.0000.0000.000
138A158LEU00.0240.01135.251-0.326-0.3260.0000.0000.0000.000
139A159GLN00.0090.00734.483-0.233-0.2330.0000.0000.0000.000
140A160HIS0-0.037-0.00634.413-0.418-0.4180.0000.0000.0000.000
141A161HIS00.025-0.00231.856-0.469-0.4690.0000.0000.0000.000
142A162LEU00.0310.04029.528-0.431-0.4310.0000.0000.0000.000
143A163LYS10.9460.96629.4338.8288.8280.0000.0000.0000.000
144A164LYS10.8460.91129.3199.0869.0860.0000.0000.0000.000
145A165LEU00.0030.02124.067-0.458-0.4580.0000.0000.0000.000
146A166GLU-1-0.804-0.89124.021-13.534-13.5340.0000.0000.0000.000
147A167GLY00.0020.00124.409-0.438-0.4380.0000.0000.0000.000
148A168ARG10.8670.93823.57710.68310.6830.0000.0000.0000.000
149A169ARG10.8810.93119.99713.72513.7250.0000.0000.0000.000
150A170LEU0-0.032-0.01319.581-1.030-1.0300.0000.0000.0000.000
151A171ASP-1-0.916-0.95520.262-13.072-13.0720.0000.0000.0000.000
152A172PHE0-0.041-0.02613.815-0.722-0.7220.0000.0000.0000.000
153A173ASP-1-0.873-0.94514.636-20.870-20.8700.0000.0000.0000.000
154A174TYR00.024-0.00715.856-0.700-0.7000.0000.0000.0000.000
155A175LYS10.8140.91717.55115.00915.0090.0000.0000.0000.000
156A176LYS10.8910.94610.30323.96023.9600.0000.0000.0000.000
157A177LYS10.9170.94913.05115.99315.9930.0000.0000.0000.000
158A178ARG10.8980.97514.53314.78414.7840.0000.0000.0000.000
159A179GLN00.0280.00615.073-0.176-0.1760.0000.0000.0000.000
160A180GLY00.0030.01710.824-0.839-0.8390.0000.0000.0000.000
161A181LYS10.8660.91910.54419.43319.4330.0000.0000.0000.000
162A182ILE00.0170.00611.9601.3181.3180.0000.0000.0000.000
163A183PRO0-0.021-0.03114.040-0.908-0.9080.0000.0000.0000.000
164A184ASP-1-0.868-0.94114.010-18.803-18.8030.0000.0000.0000.000
165A185GLU-1-0.781-0.86516.094-13.072-13.0720.0000.0000.0000.000
166A186GLU-1-0.847-0.92418.521-14.536-14.5360.0000.0000.0000.000
167A187LEU0-0.100-0.04112.810-0.229-0.2290.0000.0000.0000.000
168A188ARG10.8990.92217.08213.34213.3420.0000.0000.0000.000
169A189GLN00.0270.01719.4530.2030.2030.0000.0000.0000.000
170A190ALA0-0.048-0.02018.6220.4250.4250.0000.0000.0000.000
171A191LEU0-0.019-0.02315.7760.0720.0720.0000.0000.0000.000
172A192GLU-1-0.924-0.95020.075-11.141-11.1410.0000.0000.0000.000
173A193LYS10.9510.97923.64712.15912.1590.0000.0000.0000.000
174A194PHE0-0.022-0.01219.7230.1940.1940.0000.0000.0000.000
175A195ASP-1-0.932-0.96722.705-11.697-11.6970.0000.0000.0000.000
176A196GLU-1-0.791-0.89824.287-9.942-9.9420.0000.0000.0000.000
177A197SER0-0.073-0.05826.0170.3790.3790.0000.0000.0000.000
178A198LYS10.8890.93520.93813.22213.2220.0000.0000.0000.000
179A199GLU-1-0.895-0.93826.929-9.743-9.7430.0000.0000.0000.000
180A200ILE0-0.036-0.02229.7710.3570.3570.0000.0000.0000.000
181A201ALA0-0.0090.00929.2630.3070.3070.0000.0000.0000.000
182A202GLU-1-0.905-0.96329.745-9.492-9.4920.0000.0000.0000.000
183A203SER0-0.014-0.00631.9180.3710.3710.0000.0000.0000.000
184A204SER0-0.044-0.03734.6180.3280.3280.0000.0000.0000.000
185A205MET0-0.006-0.00533.0860.3080.3080.0000.0000.0000.000
186A206PHE00.000-0.01933.5550.2230.2230.0000.0000.0000.000
187A207ASN00.0170.01537.8490.3230.3230.0000.0000.0000.000
188A208LEU0-0.015-0.02337.7890.1900.1900.0000.0000.0000.000
189A209LEU0-0.031-0.01037.5840.0960.0960.0000.0000.0000.000
190A210GLU-1-0.953-0.96041.425-6.672-6.6720.0000.0000.0000.000
191A211MET00.0330.00244.1590.0760.0760.0000.0000.0000.000
192A212ASP-1-0.910-0.92943.405-6.986-6.9860.0000.0000.0000.000
193A213ILE00.0260.00645.5520.1540.1540.0000.0000.0000.000
194A214GLU-1-0.909-0.93648.022-6.187-6.1870.0000.0000.0000.000
195A215GLN00.001-0.01847.4820.0270.0270.0000.0000.0000.000
196A216VAL0-0.028-0.01449.1430.1400.1400.0000.0000.0000.000
197A217SER0-0.032-0.02551.7610.1640.1640.0000.0000.0000.000
198A218GLN00.0220.00752.2380.0520.0520.0000.0000.0000.000
199A219LEU0-0.018-0.01652.6450.1190.1190.0000.0000.0000.000
200A220SER0-0.037-0.02255.6380.1140.1140.0000.0000.0000.000
201A221ALA00.0150.01758.0040.1130.1130.0000.0000.0000.000
202A222LEU0-0.0290.00359.3850.1070.1070.0000.0000.0000.000
203A223VAL00.0120.00059.5660.1000.1000.0000.0000.0000.000
204A224GLN0-0.034-0.01562.1390.0360.0360.0000.0000.0000.000
205A225ALA00.0780.04764.0260.0880.0880.0000.0000.0000.000
206A226GLN0-0.028-0.03363.5430.0390.0390.0000.0000.0000.000
207A227LEU0-0.050-0.02065.6100.0870.0870.0000.0000.0000.000
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