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: GVNN1

Calculation Name: 1PG6-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PG6

Chain ID: A

ChEMBL ID:

UniProt ID:

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 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2545919.13614
FMO2-HF: Nuclear repulsion 2458776.198103
FMO2-HF: Total energy -87142.938037
FMO2-MP2: Total energy -87393.636502


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:5:ARG)


Summations of interaction energy for fragment #1(A:5:ARG)
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.
-404.513-392.83617.419-12.856-16.235-0.124
Interaction energy analysis for fragmet #1(A:5:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.719 / q_NPA : 1.850
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].
3A7ARG10.8790.9373.35248.12849.8770.078-0.762-1.064-0.003
20A24GLU-1-0.855-0.9233.337-96.080-94.9700.016-0.575-0.550-0.005
96A100GLU-1-0.871-0.9294.889-89.932-89.827-0.001-0.001-0.1020.000
113A117ASP-1-0.717-0.8622.701-144.284-136.7381.761-4.847-4.460-0.056
115A119SER0-0.074-0.0321.859-16.101-17.78210.406-4.446-4.279-0.046
116A120ALA0-0.058-0.0143.957-0.576-0.372-0.001-0.055-0.1470.000
144A148LEU00.014-0.0022.489-1.675-1.0853.379-1.078-2.891-0.005
145A149GLY0-0.0030.0062.355-21.757-19.2101.716-1.943-2.319-0.007
146A150THR0-0.009-0.0112.98114.01913.5260.0650.851-0.423-0.002
4A8PHE00.0200.0105.5788.1128.1120.0000.0000.0000.000
5A9THR0-0.035-0.0308.4201.2881.2880.0000.0000.0000.000
6A10ILE0-0.0050.00611.9640.8280.8280.0000.0000.0000.000
7A11ASP-1-0.829-0.91414.379-27.372-27.3720.0000.0000.0000.000
8A12GLN0-0.025-0.02517.3120.4790.4790.0000.0000.0000.000
9A13ASN0-0.050-0.02220.1121.5781.5780.0000.0000.0000.000
10A14MET0-0.077-0.03121.6380.8810.8810.0000.0000.0000.000
11A15GLN0-0.027-0.01322.740-0.340-0.3400.0000.0000.0000.000
12A16PHE0-0.009-0.00323.115-0.006-0.0060.0000.0000.0000.000
13A17PRO0-0.0190.00718.0490.1440.1440.0000.0000.0000.000
14A18LEU00.0410.01517.889-0.144-0.1440.0000.0000.0000.000
15A19VAL0-0.049-0.02511.450-0.756-0.7560.0000.0000.0000.000
16A20GLU-1-0.878-0.93213.439-34.367-34.3670.0000.0000.0000.000
17A21ILE0-0.014-0.0297.717-3.516-3.5160.0000.0000.0000.000
18A22ASP-1-0.791-0.8758.259-44.217-44.2170.0000.0000.0000.000
19A23LEU0-0.062-0.0386.172-9.966-9.9660.0000.0000.0000.000
21A25HIS00.0150.0166.4640.1960.1960.0000.0000.0000.000
22A26GLY0-0.0120.0017.384-3.780-3.7800.0000.0000.0000.000
23A27GLY0-0.032-0.0025.361-3.306-3.3060.0000.0000.0000.000
24A28SER0-0.041-0.0405.9236.4876.4870.0000.0000.0000.000
25A29VAL00.0270.0095.893-9.553-9.5530.0000.0000.0000.000
26A30TYR0-0.0120.0008.2179.5769.5760.0000.0000.0000.000
27A31LEU0-0.001-0.00711.308-1.789-1.7890.0000.0000.0000.000
28A32GLN00.0410.01413.9632.4282.4280.0000.0000.0000.000
29A33GLN0-0.008-0.00317.4970.2520.2520.0000.0000.0000.000
30A34GLY0-0.024-0.02020.1660.8680.8680.0000.0000.0000.000
31A35SER00.0110.00217.016-0.048-0.0480.0000.0000.0000.000
32A36MET0-0.051-0.01414.991-0.772-0.7720.0000.0000.0000.000
33A37VAL0-0.0030.00918.3131.5931.5930.0000.0000.0000.000
34A38TYR0-0.036-0.02517.6431.8101.8100.0000.0000.0000.000
35A39HIS10.9010.92515.79529.89029.8900.0000.0000.0000.000
36A40THR00.0180.01014.9361.3871.3870.0000.0000.0000.000
37A41GLU-1-0.921-0.95816.923-27.603-27.6030.0000.0000.0000.000
38A42ASN0-0.067-0.03613.6410.8880.8880.0000.0000.0000.000
39A43VAL0-0.0180.01012.003-2.287-2.2870.0000.0000.0000.000
40A44THR0-0.003-0.00314.3812.7082.7080.0000.0000.0000.000
41A45LEU00.0140.00114.836-2.385-2.3850.0000.0000.0000.000
42A46ASN0-0.011-0.01415.8403.6793.6790.0000.0000.0000.000
43A47THR00.0590.00417.171-0.581-0.5810.0000.0000.0000.000
44A48LYS10.8530.92017.23133.88233.8820.0000.0000.0000.000
45A49LEU0-0.013-0.01721.5161.1271.1270.0000.0000.0000.000
46A50ASN00.0390.04820.5031.4171.4170.0000.0000.0000.000
47A51GLY00.0660.05223.3180.4250.4250.0000.0000.0000.000
48A52LYS10.7720.85625.25022.79922.7990.0000.0000.0000.000
49A53GLY00.0430.04227.4440.4740.4740.0000.0000.0000.000
50A54SER0-0.054-0.03129.1120.4090.4090.0000.0000.0000.000
51A55GLY00.0910.05532.9050.0530.0530.0000.0000.0000.000
52A56LEU00.0200.00434.890-0.548-0.5480.0000.0000.0000.000
53A57GLY00.0410.00135.4200.4010.4010.0000.0000.0000.000
54A58LYS10.9130.95131.81618.16118.1610.0000.0000.0000.000
55A59LEU00.0940.07329.615-0.667-0.6670.0000.0000.0000.000
56A60VAL00.0490.01229.306-0.661-0.6610.0000.0000.0000.000
57A61GLY0-0.051-0.02129.571-0.122-0.1220.0000.0000.0000.000
58A62ALA0-0.032-0.02025.226-0.539-0.5390.0000.0000.0000.000
59A63ILE00.0690.02624.941-0.757-0.7570.0000.0000.0000.000
60A64GLY00.0100.01226.100-0.509-0.5090.0000.0000.0000.000
61A65ARG10.9460.97423.58824.10224.1020.0000.0000.0000.000
62A66SER0-0.006-0.00121.805-0.414-0.4140.0000.0000.0000.000
63A67MET0-0.020-0.01822.484-0.311-0.3110.0000.0000.0000.000
64A68VAL0-0.035-0.01024.4370.3820.3820.0000.0000.0000.000
65A69SER0-0.060-0.05619.1490.2430.2430.0000.0000.0000.000
66A70GLY00.0260.02719.080-1.144-1.1440.0000.0000.0000.000
67A71GLU-1-0.860-0.90516.820-34.013-34.0130.0000.0000.0000.000
68A72SER00.0530.01318.7151.9041.9040.0000.0000.0000.000
69A73MET0-0.046-0.02420.031-0.774-0.7740.0000.0000.0000.000
70A74PHE0-0.0050.00921.725-0.034-0.0340.0000.0000.0000.000
71A75ILE00.0050.01815.280-0.444-0.4440.0000.0000.0000.000
72A76THR0-0.049-0.02016.6930.3800.3800.0000.0000.0000.000
73A77GLN00.0360.01510.349-5.080-5.0800.0000.0000.0000.000
74A78ALA00.0300.02711.6083.0063.0060.0000.0000.0000.000
75A79MET0-0.030-0.02910.367-3.987-3.9870.0000.0000.0000.000
76A80SER00.0160.0139.1055.4675.4670.0000.0000.0000.000
77A81ASN0-0.050-0.01610.625-2.430-2.4300.0000.0000.0000.000
78A82GLY00.0630.01111.8192.6872.6870.0000.0000.0000.000
79A83ASP-1-0.881-0.9419.521-52.629-52.6290.0000.0000.0000.000
80A84GLY0-0.0130.01410.1614.5764.5760.0000.0000.0000.000
81A85LYS10.8590.91010.78336.52736.5270.0000.0000.0000.000
82A86LEU0-0.018-0.01810.3042.5972.5970.0000.0000.0000.000
83A87ALA00.0270.03013.515-1.827-1.8270.0000.0000.0000.000
84A88LEU0-0.039-0.01812.4691.0141.0140.0000.0000.0000.000
85A89ALA00.0370.00916.1350.1280.1280.0000.0000.0000.000
86A90PRO00.003-0.00218.190-0.417-0.4170.0000.0000.0000.000
87A91ASN0-0.034-0.00619.9561.2171.2170.0000.0000.0000.000
88A92THR0-0.019-0.00322.9521.3791.3790.0000.0000.0000.000
89A93PRO00.008-0.00223.722-0.744-0.7440.0000.0000.0000.000
90A94GLY00.0540.03023.8900.7370.7370.0000.0000.0000.000
91A95GLN00.0290.02620.220-0.462-0.4620.0000.0000.0000.000
92A96ILE00.0320.01113.990-0.337-0.3370.0000.0000.0000.000
93A97VAL0-0.041-0.01715.0750.7020.7020.0000.0000.0000.000
94A98ALA00.0130.0089.849-1.326-1.3260.0000.0000.0000.000
95A99LEU0-0.046-0.02310.5712.3442.3440.0000.0000.0000.000
97A101LEU0-0.069-0.0286.7426.8006.8000.0000.0000.0000.000
98A102GLY00.039-0.0186.431-10.126-10.1260.0000.0000.0000.000
99A103GLU-1-0.979-0.9678.083-39.647-39.6470.0000.0000.0000.000
100A104LYS10.8400.92711.25237.71637.7160.0000.0000.0000.000
101A105GLN0-0.017-0.0108.706-3.443-3.4430.0000.0000.0000.000
102A106TYR00.0290.00811.7803.9513.9510.0000.0000.0000.000
103A107ARG10.8980.95015.17228.14928.1490.0000.0000.0000.000
104A108LEU00.001-0.00314.598-0.243-0.2430.0000.0000.0000.000
105A109ASN00.0550.02618.9720.5170.5170.0000.0000.0000.000
106A110ASP-1-0.805-0.90920.951-26.383-26.3830.0000.0000.0000.000
107A111GLY0-0.050-0.02221.8730.6720.6720.0000.0000.0000.000
108A112ALA00.0480.04019.760-0.564-0.5640.0000.0000.0000.000
109A113PHE0-0.003-0.00512.404-1.121-1.1210.0000.0000.0000.000
110A114LEU0-0.0070.01013.9841.6281.6280.0000.0000.0000.000
111A115ALA00.018-0.01210.5130.3460.3460.0000.0000.0000.000
112A116LEU0-0.028-0.0027.5880.9140.9140.0000.0000.0000.000
114A118GLY00.0070.0125.2194.2464.2460.0000.0000.0000.000
117A121GLN00.0160.0086.0421.3381.3380.0000.0000.0000.000
118A122TYR00.021-0.0139.7611.7061.7060.0000.0000.0000.000
119A123LYS10.9140.95613.05629.07029.0700.0000.0000.0000.000
120A124MET0-0.023-0.00216.692-0.461-0.4610.0000.0000.0000.000
121A125GLU-1-0.892-0.94419.931-24.825-24.8250.0000.0000.0000.000
122A126ARG10.8740.95623.08020.52620.5260.0000.0000.0000.000
123A127GLN00.0120.01424.8620.5360.5360.0000.0000.0000.000
124A128ASN00.0360.01528.2560.7150.7150.0000.0000.0000.000
125A129ILE00.021-0.00831.830-0.125-0.1250.0000.0000.0000.000
126A130GLY0-0.017-0.00134.3840.2200.2200.0000.0000.0000.000
127A131LYS00.0690.03125.8480.0850.0850.0000.0000.0000.000
128A132ALA0-0.023-0.02332.2100.0670.0670.0000.0000.0000.000
129A133LEU0-0.046-0.02533.7170.3380.3380.0000.0000.0000.000
130A134PHE00.0240.04631.7290.3800.3800.0000.0000.0000.000
131A135GLY00.0180.02131.835-0.619-0.6190.0000.0000.0000.000
132A136GLY00.0440.02931.5020.4700.4700.0000.0000.0000.000
133A137GLN0-0.014-0.02432.8590.0810.0810.0000.0000.0000.000
134A138GLY0-0.0100.00530.2710.1250.1250.0000.0000.0000.000
135A139GLY0-0.021-0.01330.370-0.329-0.3290.0000.0000.0000.000
136A140LEU00.005-0.00527.2830.0260.0260.0000.0000.0000.000
137A141PHE0-0.056-0.03523.3580.3450.3450.0000.0000.0000.000
138A142VAL00.0160.02420.893-0.093-0.0930.0000.0000.0000.000
139A143MET0-0.057-0.01415.452-0.983-0.9830.0000.0000.0000.000
140A144THR00.005-0.00915.8570.7480.7480.0000.0000.0000.000
141A145THR00.002-0.00810.9650.4270.4270.0000.0000.0000.000
142A146GLU-1-0.935-0.9769.818-38.949-38.9490.0000.0000.0000.000
143A147GLY00.0330.0326.471-3.112-3.1120.0000.0000.0000.000
147A151LEU0-0.017-0.0015.815-0.376-0.3760.0000.0000.0000.000
148A152LEU0-0.021-0.0109.1681.6151.6150.0000.0000.0000.000
149A153ALA00.0140.00611.5991.2901.2900.0000.0000.0000.000
150A154ASN0-0.071-0.05915.3360.7100.7100.0000.0000.0000.000
151A155SER00.020-0.00918.402-0.009-0.0090.0000.0000.0000.000
152A156PHE00.0190.02522.1120.2640.2640.0000.0000.0000.000
153A157GLY00.028-0.00525.6090.5130.5130.0000.0000.0000.000
154A158SER0-0.035-0.02124.618-1.103-1.1030.0000.0000.0000.000
155A159ILE00.0120.00119.2220.4460.4460.0000.0000.0000.000
156A160LYS10.8780.94623.31122.25722.2570.0000.0000.0000.000
157A161LYS10.9650.99518.44230.32530.3250.0000.0000.0000.000
158A162ILE0-0.034-0.02423.1621.3171.3170.0000.0000.0000.000
159A163THR00.0230.00422.565-1.200-1.2000.0000.0000.0000.000
160A164LEU0-0.040-0.00224.7481.0761.0760.0000.0000.0000.000
161A165ASP-1-0.877-0.94425.360-22.898-22.8980.0000.0000.0000.000
162A166GLY00.0310.01427.3460.7000.7000.0000.0000.0000.000
163A167GLY0-0.038-0.01428.9690.5440.5440.0000.0000.0000.000
164A168THR0-0.052-0.05530.181-0.319-0.3190.0000.0000.0000.000
165A169MET0-0.001-0.00129.4410.1580.1580.0000.0000.0000.000
166A170THR0-0.0030.01530.803-0.366-0.3660.0000.0000.0000.000
167A171ILE0-0.0120.00027.6510.3010.3010.0000.0000.0000.000
168A172ASP-1-0.707-0.83730.986-19.334-19.3340.0000.0000.0000.000
169A173ASN00.0510.00726.282-1.057-1.0570.0000.0000.0000.000
170A174ALA0-0.0140.00227.308-0.880-0.8800.0000.0000.0000.000
171A175HIS0-0.069-0.04028.2480.2000.2000.0000.0000.0000.000
172A176VAL0-0.062-0.01723.378-0.586-0.5860.0000.0000.0000.000
173A177VAL0-0.0290.00519.096-0.198-0.1980.0000.0000.0000.000
174A178ALA00.009-0.02117.207-0.804-0.8040.0000.0000.0000.000
175A179TRP0-0.032-0.00518.8870.7810.7810.0000.0000.0000.000
176A180SER00.000-0.01517.466-1.447-1.4470.0000.0000.0000.000
177A181ARG10.8470.93413.35839.40439.4040.0000.0000.0000.000
178A182GLU-1-0.788-0.88917.194-32.893-32.8930.0000.0000.0000.000
179A183LEU0-0.062-0.00619.8851.0591.0590.0000.0000.0000.000
180A184ASP-1-0.926-0.95023.201-22.805-22.8050.0000.0000.0000.000
181A185TYR0-0.068-0.07623.150-0.413-0.4130.0000.0000.0000.000
182A186ASP-1-0.886-0.94327.008-18.969-18.9690.0000.0000.0000.000
183A187ILE0-0.051-0.01525.9560.0600.0600.0000.0000.0000.000
184A188HIS10.8360.91130.47318.12218.1220.0000.0000.0000.000
185A189LEU00.0240.02534.258-0.099-0.0990.0000.0000.0000.000
186A190GLU-1-0.889-0.94937.158-16.342-16.3420.0000.0000.0000.000
187A191ASN0-0.032-0.01339.5150.4610.4610.0000.0000.0000.000
188A192GLY00.0480.02042.086-0.185-0.1850.0000.0000.0000.000
189A193PHE00.0700.02640.8490.1520.1520.0000.0000.0000.000
190A194MET00.014-0.00843.886-0.050-0.0500.0000.0000.0000.000
191A195GLN0-0.0270.00045.0920.3280.3280.0000.0000.0000.000
192A196SER00.0350.00740.634-0.043-0.0430.0000.0000.0000.000
193A197ILE0-0.064-0.02442.538-0.115-0.1150.0000.0000.0000.000
194A198GLY0-0.027-0.00244.7400.0890.0890.0000.0000.0000.000
195A199THR0-0.039-0.03241.5480.1140.1140.0000.0000.0000.000
196A200GLY0-0.0110.00341.196-0.083-0.0830.0000.0000.0000.000
197A201GLU-1-0.956-0.97336.692-17.153-17.1530.0000.0000.0000.000
198A202GLY00.032-0.00734.8650.2230.2230.0000.0000.0000.000
199A203VAL0-0.124-0.05331.2480.2000.2000.0000.0000.0000.000
200A204VAL0-0.004-0.00332.212-0.567-0.5670.0000.0000.0000.000
201A205ASN0-0.019-0.02825.1850.1490.1490.0000.0000.0000.000
202A206THR0-0.013-0.02029.5850.3850.3850.0000.0000.0000.000
203A207PHE00.0720.02124.243-0.243-0.2430.0000.0000.0000.000
204A208ARG10.9110.95027.54219.63019.6300.0000.0000.0000.000
205A209GLY00.1100.07526.281-0.747-0.7470.0000.0000.0000.000
206A210HIS0-0.064-0.03823.4420.7050.7050.0000.0000.0000.000
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208A212GLU-1-0.929-0.97718.179-30.418-30.4180.0000.0000.0000.000
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