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: MLMYZ

Calculation Name: 1NG0-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NG0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9E958

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 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2025079.950944
FMO2-HF: Nuclear repulsion 1950617.289787
FMO2-HF: Total energy -74462.661157
FMO2-MP2: Total energy -74678.643808


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:62:ASP)


Summations of interaction energy for fragment #1(A:62:ASP)
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.
-100.542-101.95619.398-10.473-7.5080.099
Interaction energy analysis for fragmet #1(A:62:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.004
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].
3A64PHE0-0.014-0.0073.059-21.859-18.7590.080-1.782-1.397-0.007
132A193TRP0-0.035-0.0194.6501.2981.422-0.001-0.006-0.1160.000
183A244LYS10.8970.9041.838-80.466-85.10419.319-8.685-5.9950.106
4A65ASP-1-0.794-0.8755.961-0.026-0.0260.0000.0000.0000.000
5A66THR00.0140.0008.851-0.220-0.2200.0000.0000.0000.000
6A67GLY00.0120.01412.2270.0870.0870.0000.0000.0000.000
7A68MET0-0.049-0.02814.1590.3660.3660.0000.0000.0000.000
8A69ILE0-0.039-0.01516.123-0.115-0.1150.0000.0000.0000.000
9A70THR00.023-0.00219.5390.1660.1660.0000.0000.0000.000
10A71SER0-0.057-0.04322.681-0.040-0.0400.0000.0000.0000.000
11A72TYR0-0.029-0.01224.8870.0430.0430.0000.0000.0000.000
12A73LEU0-0.025-0.00725.6920.0200.0200.0000.0000.0000.000
13A74GLY00.0480.02328.7780.0580.0580.0000.0000.0000.000
14A75GLY00.0020.01632.548-0.035-0.0350.0000.0000.0000.000
15A76PHE0-0.004-0.01235.5430.0330.0330.0000.0000.0000.000
16A77GLN0-0.014-0.02037.039-0.039-0.0390.0000.0000.0000.000
17A78ARG10.7830.86739.665-0.020-0.0200.0000.0000.0000.000
18A79THR00.001-0.01342.617-0.019-0.0190.0000.0000.0000.000
19A80ALA00.0470.03045.049-0.002-0.0020.0000.0000.0000.000
20A81GLY00.0020.01746.0210.0010.0010.0000.0000.0000.000
21A82THR0-0.016-0.02445.103-0.001-0.0010.0000.0000.0000.000
22A83THR0-0.045-0.03040.7370.0060.0060.0000.0000.0000.000
23A84ASP-1-0.841-0.91640.5660.2310.2310.0000.0000.0000.000
24A85SER0-0.042-0.02536.259-0.006-0.0060.0000.0000.0000.000
25A86GLN0-0.025-0.01033.6900.0000.0000.0000.0000.0000.000
26A87VAL00.0360.01129.6340.0040.0040.0000.0000.0000.000
27A88PHE0-0.022-0.01327.022-0.010-0.0100.0000.0000.0000.000
28A89ILE00.0520.02422.5410.0440.0440.0000.0000.0000.000
29A90VAL0-0.047-0.01319.233-0.085-0.0850.0000.0000.0000.000
30A91SER00.0760.01718.7690.2270.2270.0000.0000.0000.000
31A92PRO0-0.026-0.03115.701-0.183-0.1830.0000.0000.0000.000
32A93ALA0-0.0050.01019.038-0.188-0.1880.0000.0000.0000.000
33A94ALA00.0320.01821.222-0.080-0.0800.0000.0000.0000.000
34A95LEU0-0.054-0.01420.347-0.102-0.1020.0000.0000.0000.000
35A96ASP-1-0.859-0.93622.140-0.495-0.4950.0000.0000.0000.000
36A97ARG10.9620.99318.5841.2021.2020.0000.0000.0000.000
37A98VAL00.006-0.00116.632-0.121-0.1210.0000.0000.0000.000
38A99GLY00.0670.03817.2320.0520.0520.0000.0000.0000.000
39A100THR0-0.017-0.02718.5360.1050.1050.0000.0000.0000.000
40A101ILE0-0.060-0.03013.251-0.087-0.0870.0000.0000.0000.000
41A102ALA00.015-0.00913.905-0.055-0.0550.0000.0000.0000.000
42A103LYS10.8720.94414.555-0.312-0.3120.0000.0000.0000.000
43A104ALA0-0.0300.00612.9850.2420.2420.0000.0000.0000.000
44A105TYR0-0.036-0.0237.6430.2020.2020.0000.0000.0000.000
45A106ALA00.0280.02110.409-0.136-0.1360.0000.0000.0000.000
46A107LEU0-0.060-0.0316.6220.2740.2740.0000.0000.0000.000
47A108TRP00.0460.0119.409-0.557-0.5570.0000.0000.0000.000
48A109ARG10.8840.9417.528-5.519-5.5190.0000.0000.0000.000
49A110PRO00.0640.04311.405-0.663-0.6630.0000.0000.0000.000
50A111LYS10.8460.91611.155-0.902-0.9020.0000.0000.0000.000
51A112HIS0-0.007-0.01214.881-0.060-0.0600.0000.0000.0000.000
52A113TRP00.0670.01118.223-0.018-0.0180.0000.0000.0000.000
53A114GLU-1-0.768-0.84820.823-0.201-0.2010.0000.0000.0000.000
54A115ILE00.0170.02224.444-0.076-0.0760.0000.0000.0000.000
55A116VAL0-0.016-0.01727.4390.0110.0110.0000.0000.0000.000
56A117TYR0-0.002-0.01929.9430.0080.0080.0000.0000.0000.000
57A118LEU0-0.041-0.02032.155-0.032-0.0320.0000.0000.0000.000
58A119PRO00.0020.01235.4730.0140.0140.0000.0000.0000.000
59A120ARG10.8380.92638.8970.0690.0690.0000.0000.0000.000
60A121CYS0-0.057-0.01341.3270.0090.0090.0000.0000.0000.000
61A122SER00.0310.01544.785-0.016-0.0160.0000.0000.0000.000
62A123THR00.0360.01146.7780.0110.0110.0000.0000.0000.000
63A124GLN0-0.020-0.00848.4210.0030.0030.0000.0000.0000.000
64A125THR0-0.063-0.03646.2060.0110.0110.0000.0000.0000.000
65A126ASP-1-0.870-0.92947.6220.0040.0040.0000.0000.0000.000
66A127GLY00.0080.01146.1850.0040.0040.0000.0000.0000.000
67A128SER0-0.087-0.07242.005-0.017-0.0170.0000.0000.0000.000
68A129ILE0-0.0080.00535.5190.0130.0130.0000.0000.0000.000
69A130GLU-1-0.762-0.84537.1650.1840.1840.0000.0000.0000.000
70A131MET0-0.038-0.02631.4350.0060.0060.0000.0000.0000.000
71A132GLY00.0550.03730.190-0.019-0.0190.0000.0000.0000.000
72A133PHE0-0.038-0.02624.0640.0200.0200.0000.0000.0000.000
73A134LEU0-0.030-0.01127.560-0.028-0.0280.0000.0000.0000.000
74A135LEU0-0.028-0.02623.054-0.005-0.0050.0000.0000.0000.000
75A136ASP-1-0.772-0.84524.2111.1451.1450.0000.0000.0000.000
76A137TYR0-0.016-0.03224.922-0.127-0.1270.0000.0000.0000.000
77A138ALA0-0.041-0.03227.175-0.072-0.0720.0000.0000.0000.000
78A139ASP-1-0.917-0.93630.0020.7000.7000.0000.0000.0000.000
79A140SER0-0.037-0.02431.966-0.009-0.0090.0000.0000.0000.000
80A141VAL00.0360.01133.2670.0030.0030.0000.0000.0000.000
81A142PRO0-0.006-0.00834.235-0.026-0.0260.0000.0000.0000.000
82A143THR00.0240.01337.331-0.022-0.0220.0000.0000.0000.000
83A144ASN0-0.034-0.01140.510-0.031-0.0310.0000.0000.0000.000
84A145THR00.0600.00740.3410.0190.0190.0000.0000.0000.000
85A146ARG10.9080.96040.214-0.255-0.2550.0000.0000.0000.000
86A147THR0-0.022-0.02838.2820.0140.0140.0000.0000.0000.000
87A148MET00.0270.02633.6530.0400.0400.0000.0000.0000.000
88A149ALA0-0.029-0.00235.2970.0130.0130.0000.0000.0000.000
89A150SER0-0.068-0.02935.400-0.003-0.0030.0000.0000.0000.000
90A151SER0-0.040-0.01731.3930.0370.0370.0000.0000.0000.000
91A152THR00.0260.00125.546-0.053-0.0530.0000.0000.0000.000
92A153SER0-0.047-0.04826.179-0.006-0.0060.0000.0000.0000.000
93A154PHE00.0100.04029.274-0.051-0.0510.0000.0000.0000.000
94A155THR0-0.034-0.01232.460-0.036-0.0360.0000.0000.0000.000
95A156THR0-0.041-0.03334.4820.0160.0160.0000.0000.0000.000
96A157SER00.0200.01537.868-0.024-0.0240.0000.0000.0000.000
97A158ASN00.0060.00640.3140.0120.0120.0000.0000.0000.000
98A159VAL00.0530.02441.577-0.015-0.0150.0000.0000.0000.000
99A160TRP00.0040.01641.490-0.018-0.0180.0000.0000.0000.000
100A161GLY0-0.0100.01040.939-0.023-0.0230.0000.0000.0000.000
101A162GLY00.0640.01236.8560.0140.0140.0000.0000.0000.000
102A163GLY0-0.019-0.00335.639-0.024-0.0240.0000.0000.0000.000
103A164ASP-1-0.814-0.89435.600-0.288-0.2880.0000.0000.0000.000
104A165GLY00.010-0.01231.929-0.041-0.0410.0000.0000.0000.000
105A166SER0-0.038-0.03330.926-0.043-0.0430.0000.0000.0000.000
106A167SER00.0180.00830.787-0.051-0.0510.0000.0000.0000.000
107A168LEU0-0.027-0.01527.169-0.082-0.0820.0000.0000.0000.000
108A169LEU00.0030.00925.727-0.055-0.0550.0000.0000.0000.000
109A170HIS0-0.0030.01125.213-0.009-0.0090.0000.0000.0000.000
110A171THR0-0.0120.01024.900-0.133-0.1330.0000.0000.0000.000
111A172SER00.010-0.00720.352-0.026-0.0260.0000.0000.0000.000
112A173MET0-0.034-0.00922.6290.0090.0090.0000.0000.0000.000
113A174LYS10.9910.98523.8270.3820.3820.0000.0000.0000.000
114A175SER00.0450.03026.857-0.031-0.0310.0000.0000.0000.000
115A176MET00.000-0.00429.852-0.005-0.0050.0000.0000.0000.000
116A177GLY00.0010.01133.273-0.012-0.0120.0000.0000.0000.000
117A178ASN0-0.035-0.04136.9010.0230.0230.0000.0000.0000.000
118A179ALA0-0.0170.00432.3250.0160.0160.0000.0000.0000.000
119A180VAL00.0540.03334.0080.0210.0210.0000.0000.0000.000
120A181THR0-0.087-0.06128.5490.0030.0030.0000.0000.0000.000
121A182SER00.0350.00528.8830.0430.0430.0000.0000.0000.000
122A183ALA0-0.016-0.01623.855-0.024-0.0240.0000.0000.0000.000
123A184LEU00.0350.04019.8280.0260.0260.0000.0000.0000.000
124A185PRO00.0280.01621.172-0.055-0.0550.0000.0000.0000.000
125A186CYS0-0.055-0.02416.1600.1350.1350.0000.0000.0000.000
126A187ASP-1-0.942-0.97015.8761.0671.0670.0000.0000.0000.000
127A188GLU-1-0.848-0.90516.7531.6521.6520.0000.0000.0000.000
128A189PHE00.0440.00214.2130.4050.4050.0000.0000.0000.000
129A190SER0-0.130-0.07612.5910.7430.7430.0000.0000.0000.000
130A191ASN00.002-0.00410.8780.7600.7600.0000.0000.0000.000
131A192LYS10.8910.97310.740-2.353-2.3530.0000.0000.0000.000
133A194PHE00.0530.03810.410-0.230-0.2300.0000.0000.0000.000
134A195LYS10.9540.96512.023-4.025-4.0250.0000.0000.0000.000
135A196LEU0-0.048-0.02012.367-0.382-0.3820.0000.0000.0000.000
136A197SER00.0210.02015.3430.0540.0540.0000.0000.0000.000
137A198TRP0-0.063-0.05316.725-0.321-0.3210.0000.0000.0000.000
138A199SER0-0.0150.01022.056-0.138-0.1380.0000.0000.0000.000
139A200THR0-0.042-0.02224.317-0.003-0.0030.0000.0000.0000.000
140A201PRO0-0.005-0.00525.1720.0110.0110.0000.0000.0000.000
141A202GLU-1-0.922-0.95027.3290.7020.7020.0000.0000.0000.000
142A203GLU-1-0.911-0.96230.4820.5740.5740.0000.0000.0000.000
143A204SER0-0.080-0.03833.6050.0000.0000.0000.0000.0000.000
144A205GLU-1-0.806-0.85625.9791.2901.2900.0000.0000.0000.000
145A206ASN0-0.020-0.01729.577-0.036-0.0360.0000.0000.0000.000
146A207ALA00.0940.04028.2750.0870.0870.0000.0000.0000.000
147A208HIS00.0360.00926.7540.1190.1190.0000.0000.0000.000
148A209LEU0-0.054-0.02123.2680.1420.1420.0000.0000.0000.000
149A210THR00.001-0.02223.1410.1440.1440.0000.0000.0000.000
150A211ASP-1-0.858-0.92622.5451.5661.5660.0000.0000.0000.000
151A212THR0-0.109-0.05819.6000.2440.2440.0000.0000.0000.000
152A213TYR0-0.148-0.10717.6480.4590.4590.0000.0000.0000.000
153A214VAL0-0.018-0.00218.378-0.016-0.0160.0000.0000.0000.000
154A215PRO0-0.091-0.04116.619-0.030-0.0300.0000.0000.0000.000
155A216ALA00.0740.03319.267-0.072-0.0720.0000.0000.0000.000
156A217ARG10.8120.90222.881-0.780-0.7800.0000.0000.0000.000
157A218PHE00.008-0.01226.025-0.033-0.0330.0000.0000.0000.000
158A219VAL00.0180.00427.6420.0020.0020.0000.0000.0000.000
159A220VAL00.0120.00031.495-0.035-0.0350.0000.0000.0000.000
160A221ARG10.8880.93234.283-0.196-0.1960.0000.0000.0000.000
161A222SER0-0.011-0.01638.112-0.029-0.0290.0000.0000.0000.000
162A223ASP-1-0.825-0.88841.5280.1060.1060.0000.0000.0000.000
163A224PHE0-0.020-0.00143.9040.0070.0070.0000.0000.0000.000
164A225PRO0-0.0030.00546.009-0.005-0.0050.0000.0000.0000.000
165A226VAL0-0.0200.00046.200-0.012-0.0120.0000.0000.0000.000
166A227VAL0-0.001-0.00548.9200.0080.0080.0000.0000.0000.000
167A228THR0-0.048-0.03549.9360.0000.0000.0000.0000.0000.000
168A229ALA00.0220.01945.062-0.002-0.0020.0000.0000.0000.000
169A230ASP-1-0.788-0.87144.6060.0140.0140.0000.0000.0000.000
170A231GLN0-0.034-0.03038.711-0.009-0.0090.0000.0000.0000.000
171A232PRO00.0100.01640.936-0.028-0.0280.0000.0000.0000.000
172A233GLY00.0780.02938.315-0.024-0.0240.0000.0000.0000.000
173A234HIS0-0.038-0.00333.6930.0410.0410.0000.0000.0000.000
174A235LEU00.0110.01630.837-0.016-0.0160.0000.0000.0000.000
175A236TRP00.014-0.00428.330-0.024-0.0240.0000.0000.0000.000
176A237LEU00.0140.02221.7210.0170.0170.0000.0000.0000.000
177A238ARG10.7490.85722.4260.4290.4290.0000.0000.0000.000
178A239SER0-0.008-0.00318.7290.0500.0500.0000.0000.0000.000
179A240ARG10.8510.89910.9402.0022.0020.0000.0000.0000.000
180A241ILE00.0230.01112.7230.3980.3980.0000.0000.0000.000
181A242LEU0-0.049-0.0157.137-0.756-0.7560.0000.0000.0000.000
182A243LEU00.0170.0158.2641.4501.4500.0000.0000.0000.000
184A245GLY00.0080.0145.6500.4090.4090.0000.0000.0000.000
185A246SER00.0180.0107.068-1.203-1.2030.0000.0000.0000.000
186A247VAL0-0.0060.00010.1440.6580.6580.0000.0000.0000.000
187A248SER00.0320.02113.721-0.535-0.5350.0000.0000.0000.000
188A249PRO00.0650.01816.7860.2030.2030.0000.0000.0000.000
189A250SER0-0.025-0.01318.9440.0770.0770.0000.0000.0000.000
190A251THR0-0.037-0.01917.937-0.031-0.0310.0000.0000.0000.000
191A252ASN0-0.058-0.02415.0860.3570.3570.0000.0000.0000.000
192A253LEU-1-0.779-0.87618.2911.3011.3010.0000.0000.0000.000