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: 1VJ7Z

Calculation Name: 4JYO-X-Xray547

Preferred Name: Angiopoietin-1

Target Type: SINGLE PROTEIN

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4JYO

Chain ID: X

ChEMBL ID: CHEMBL3217395

UniProt ID: Q15389

Base Structure: X-ray

Registration Date: 2025-10-06

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2828833.89794
FMO2-HF: Nuclear repulsion 2738780.921441
FMO2-HF: Total energy -90052.976499
FMO2-MP2: Total energy -90307.376335


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(X:3:PRO)


Summations of interaction energy for fragment #1(X:3:PRO)
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.
-10.215-7.6910.046-0.745-1.826-0.002
Interaction energy analysis for fragmet #1(X:3:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.913
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].
3X5ARG10.9320.9343.86147.79849.225-0.010-0.476-0.9410.000
22X24TYR0-0.018-0.0273.3872.4843.1380.054-0.135-0.573-0.001
23X25ILE00.0020.0153.782-6.707-6.4210.003-0.128-0.162-0.001
24X26ASN00.0480.0074.601-4.395-4.238-0.001-0.006-0.1500.000
4X6ASP-1-0.757-0.8365.545-26.453-26.4530.0000.0000.0000.000
5X7CYS0-0.041-0.0268.677-3.446-3.4460.0000.0000.0000.000
6X8ALA00.0410.04111.0311.1721.1720.0000.0000.0000.000
7X9ASP-1-0.765-0.8425.561-48.726-48.7260.0000.0000.0000.000
8X10VAL0-0.048-0.0147.651-0.562-0.5620.0000.0000.0000.000
9X11TYR00.0480.0039.0661.3231.3230.0000.0000.0000.000
10X12GLN0-0.004-0.0139.3721.1351.1350.0000.0000.0000.000
11X13ALA0-0.069-0.0217.1950.1580.1580.0000.0000.0000.000
12X14GLY00.0230.0169.2730.9280.9280.0000.0000.0000.000
13X15PHE0-0.041-0.0119.2431.7901.7900.0000.0000.0000.000
14X16ASN0-0.006-0.00913.698-0.198-0.1980.0000.0000.0000.000
15X17LYS10.9670.98716.58515.87515.8750.0000.0000.0000.000
16X18SER00.009-0.02016.946-1.328-1.3280.0000.0000.0000.000
17X19GLY00.0030.00317.7030.7070.7070.0000.0000.0000.000
18X20ILE0-0.037-0.00715.029-0.693-0.6930.0000.0000.0000.000
19X21TYR0-0.022-0.02510.554-0.916-0.9160.0000.0000.0000.000
20X22THR0-0.036-0.0348.5682.0022.0020.0000.0000.0000.000
21X23ILE0-0.043-0.0056.613-2.642-2.6420.0000.0000.0000.000
25X27ASN0-0.036-0.0296.6051.7331.7330.0000.0000.0000.000
26X28MET0-0.0240.0068.6373.1483.1480.0000.0000.0000.000
27X29PRO0-0.028-0.0059.206-1.845-1.8450.0000.0000.0000.000
28X30GLU-1-0.926-0.95810.429-19.084-19.0840.0000.0000.0000.000
29X31PRO0-0.049-0.0317.761-1.087-1.0870.0000.0000.0000.000
30X32LYS10.8740.9699.23720.72220.7220.0000.0000.0000.000
31X33LYS10.9160.96111.01517.53617.5360.0000.0000.0000.000
32X34VAL00.0150.00211.8480.8730.8730.0000.0000.0000.000
33X35PHE00.0360.01814.640-0.279-0.2790.0000.0000.0000.000
34X37ASN00.0400.01015.5590.7760.7760.0000.0000.0000.000
35X38MET0-0.055-0.02012.839-0.505-0.5050.0000.0000.0000.000
36X39ASP-1-0.826-0.87918.289-14.179-14.1790.0000.0000.0000.000
37X40VAL0-0.053-0.02921.9840.2880.2880.0000.0000.0000.000
38X41ASN0-0.060-0.02221.915-0.095-0.0950.0000.0000.0000.000
39X42GLY00.0600.02020.6670.5040.5040.0000.0000.0000.000
40X43GLY00.0110.02917.715-0.747-0.7470.0000.0000.0000.000
41X44GLY00.0430.01414.0170.2400.2400.0000.0000.0000.000
42X45TRP0-0.025-0.01914.491-0.929-0.9290.0000.0000.0000.000
43X46THR00.021-0.00612.517-0.991-0.9910.0000.0000.0000.000
44X47VAL0-0.0120.00315.1340.7900.7900.0000.0000.0000.000
45X48ILE0-0.021-0.01916.489-0.643-0.6430.0000.0000.0000.000
46X49GLN0-0.025-0.01218.8070.3870.3870.0000.0000.0000.000
47X50HIS0-0.0050.00122.275-0.339-0.3390.0000.0000.0000.000
48X51ARG10.8470.92524.52410.42410.4240.0000.0000.0000.000
49X52GLU-1-0.923-0.95027.735-11.366-11.3660.0000.0000.0000.000
50X53ASP-1-0.836-0.90330.627-9.816-9.8160.0000.0000.0000.000
51X54GLY0-0.019-0.00432.0160.3300.3300.0000.0000.0000.000
52X55SER0-0.095-0.05730.2860.0900.0900.0000.0000.0000.000
53X56LEU0-0.096-0.02625.936-0.035-0.0350.0000.0000.0000.000
54X57ASP-1-0.785-0.89630.262-9.317-9.3170.0000.0000.0000.000
55X58PHE00.0330.01326.089-0.444-0.4440.0000.0000.0000.000
56X59GLN0-0.0300.00230.3610.0530.0530.0000.0000.0000.000
57X60ARG10.8250.90327.51410.92910.9290.0000.0000.0000.000
58X61GLY00.0240.01229.7410.2220.2220.0000.0000.0000.000
59X62TRP0-0.029-0.04625.628-0.433-0.4330.0000.0000.0000.000
60X63LYS10.9720.96724.80610.26510.2650.0000.0000.0000.000
61X64GLU-1-0.844-0.91423.582-11.332-11.3320.0000.0000.0000.000
62X65TYR00.021-0.01623.206-0.604-0.6040.0000.0000.0000.000
63X66LYS10.8170.92319.95213.37313.3730.0000.0000.0000.000
64X67MET0-0.005-0.00717.537-0.821-0.8210.0000.0000.0000.000
65X68GLY0-0.013-0.00518.605-0.930-0.9300.0000.0000.0000.000
66X69PHE0-0.039-0.02420.6410.2320.2320.0000.0000.0000.000
67X70GLY00.0520.01923.204-0.039-0.0390.0000.0000.0000.000
68X71ASN0-0.006-0.01021.646-0.789-0.7890.0000.0000.0000.000
69X72PRO0-0.009-0.01017.1750.2750.2750.0000.0000.0000.000
70X73SER0-0.055-0.04619.707-0.074-0.0740.0000.0000.0000.000
71X74GLY00.0760.04722.1880.4550.4550.0000.0000.0000.000
72X75GLU-1-0.710-0.83923.856-10.888-10.8880.0000.0000.0000.000
73X76TYR0-0.044-0.04217.469-0.351-0.3510.0000.0000.0000.000
74X77TRP00.0150.02822.0960.1200.1200.0000.0000.0000.000
75X78LEU0-0.005-0.00614.234-0.166-0.1660.0000.0000.0000.000
76X79GLY00.0380.01017.574-0.529-0.5290.0000.0000.0000.000
77X80ASN0-0.014-0.02217.654-1.114-1.1140.0000.0000.0000.000
78X81GLU-1-0.808-0.88915.769-16.047-16.0470.0000.0000.0000.000
79X82PHE00.0280.00712.185-0.971-0.9710.0000.0000.0000.000
80X83ILE00.0030.01013.455-1.240-1.2400.0000.0000.0000.000
81X84PHE00.0090.01615.539-0.454-0.4540.0000.0000.0000.000
82X85ALA00.0050.01811.225-0.501-0.5010.0000.0000.0000.000
83X86ILE0-0.011-0.02010.198-1.470-1.4700.0000.0000.0000.000
84X87THR0-0.073-0.06211.521-0.565-0.5650.0000.0000.0000.000
85X88SER0-0.012-0.00312.8411.2041.2040.0000.0000.0000.000
86X89GLN0-0.087-0.0436.822-4.177-4.1770.0000.0000.0000.000
87X90ARG10.8480.9018.73329.26529.2650.0000.0000.0000.000
88X91GLN00.0390.02612.8731.8831.8830.0000.0000.0000.000
89X92TYR0-0.021-0.03010.340-0.383-0.3830.0000.0000.0000.000
90X93MET0-0.0120.01717.0181.3791.3790.0000.0000.0000.000
91X94LEU0-0.043-0.02519.008-0.724-0.7240.0000.0000.0000.000
92X95ARG10.8240.90121.41213.18913.1890.0000.0000.0000.000
93X96ILE0-0.018-0.01123.110-0.384-0.3840.0000.0000.0000.000
94X97GLU-1-0.819-0.89925.470-11.334-11.3340.0000.0000.0000.000
95X98LEU0-0.010-0.01127.6830.0220.0220.0000.0000.0000.000
96X99MET0-0.021-0.00931.0360.1470.1470.0000.0000.0000.000
97X100ASP-1-0.791-0.88333.696-8.182-8.1820.0000.0000.0000.000
98X101TRP00.033-0.00937.078-0.088-0.0880.0000.0000.0000.000
99X102GLU-1-0.868-0.90639.722-7.468-7.4680.0000.0000.0000.000
100X103GLY0-0.0030.01438.0030.0920.0920.0000.0000.0000.000
101X104ASN0-0.086-0.04937.431-0.133-0.1330.0000.0000.0000.000
102X105ARG10.9720.96630.14210.02810.0280.0000.0000.0000.000
103X106ALA0-0.0240.00133.1380.2170.2170.0000.0000.0000.000
104X107TYR00.0420.01728.223-0.295-0.2950.0000.0000.0000.000
105X108SER00.004-0.00528.8400.4470.4470.0000.0000.0000.000
106X109GLN00.0170.00324.342-0.639-0.6390.0000.0000.0000.000
107X110TYR0-0.010-0.03324.1390.5600.5600.0000.0000.0000.000
108X111ASP-1-0.842-0.91923.248-12.735-12.7350.0000.0000.0000.000
109X112ARG10.8010.89221.00013.69213.6920.0000.0000.0000.000
110X113PHE00.0350.00018.4890.6740.6740.0000.0000.0000.000
111X114HIS0-0.022-0.00918.279-0.456-0.4560.0000.0000.0000.000
112X115ILE0-0.0070.01318.9390.8380.8380.0000.0000.0000.000
113X116GLY00.0210.01719.713-0.610-0.6100.0000.0000.0000.000
114X117ASN00.015-0.00319.7670.1080.1080.0000.0000.0000.000
115X118GLU-1-0.748-0.85720.946-12.075-12.0750.0000.0000.0000.000
116X119LYS10.9290.95722.80313.17813.1780.0000.0000.0000.000
117X120GLN0-0.0260.00422.973-0.083-0.0830.0000.0000.0000.000
118X121ASN00.0090.00426.127-0.144-0.1440.0000.0000.0000.000
119X122TYR0-0.066-0.07419.3880.3700.3700.0000.0000.0000.000
120X123ARG10.8480.92023.62310.07610.0760.0000.0000.0000.000
121X124LEU0-0.020-0.00223.810-0.561-0.5610.0000.0000.0000.000
122X125TYR00.0180.00923.6450.7020.7020.0000.0000.0000.000
123X126LEU00.000-0.00123.907-0.555-0.5550.0000.0000.0000.000
124X127LYS10.9190.95125.71411.28911.2890.0000.0000.0000.000
125X128GLY00.0300.02426.421-0.338-0.3380.0000.0000.0000.000
126X129HIS00.0010.02028.023-0.444-0.4440.0000.0000.0000.000
127X130THR00.001-0.00128.5100.3090.3090.0000.0000.0000.000
128X131GLY00.0280.01030.133-0.288-0.2880.0000.0000.0000.000
129X132THR0-0.007-0.01031.8650.3070.3070.0000.0000.0000.000
130X133ALA0-0.0260.00632.2710.3380.3380.0000.0000.0000.000
131X134GLY00.0500.01834.3010.0280.0280.0000.0000.0000.000
132X135LYS10.9410.95835.4257.7877.7870.0000.0000.0000.000
133X136GLN0-0.004-0.00235.777-0.087-0.0870.0000.0000.0000.000
134X137SER00.0130.00731.091-0.183-0.1830.0000.0000.0000.000
135X138SER00.008-0.01132.8820.3180.3180.0000.0000.0000.000
136X139LEU00.0100.04226.6920.0820.0820.0000.0000.0000.000
137X140ILE00.0050.02030.8790.0450.0450.0000.0000.0000.000
138X141LEU0-0.006-0.01529.550-0.289-0.2890.0000.0000.0000.000
139X142HIS0-0.046-0.02830.068-0.384-0.3840.0000.0000.0000.000
140X143GLY00.0170.02929.184-0.003-0.0030.0000.0000.0000.000
141X144ALA0-0.007-0.01229.2650.3560.3560.0000.0000.0000.000
142X145ASP-1-0.745-0.85028.323-10.665-10.6650.0000.0000.0000.000
143X146PHE0-0.037-0.01225.7810.1370.1370.0000.0000.0000.000
144X147SER00.0180.01927.9610.2280.2280.0000.0000.0000.000
145X148THR0-0.023-0.05128.300-0.215-0.2150.0000.0000.0000.000
146X149LYS10.8810.92831.4499.3629.3620.0000.0000.0000.000
147X150ASP-1-0.842-0.88531.229-9.684-9.6840.0000.0000.0000.000
148X151ALA0-0.038-0.01330.5130.0150.0150.0000.0000.0000.000
149X152ASP-1-0.818-0.90032.527-8.318-8.3180.0000.0000.0000.000
150X153ASN0-0.009-0.02130.0940.2490.2490.0000.0000.0000.000
151X154ASP-1-0.806-0.88733.489-8.527-8.5270.0000.0000.0000.000
152X155ASN0-0.047-0.03934.8070.0460.0460.0000.0000.0000.000
153X156CYS0-0.138-0.06737.5880.3860.3860.0000.0000.0000.000
154X157MET00.0120.01340.5140.0540.0540.0000.0000.0000.000
155X159LYS10.9520.95238.6307.6387.6380.0000.0000.0000.000
156X160CYS0-0.070-0.05236.2720.2820.2820.0000.0000.0000.000
157X161ALA00.0050.00933.715-0.008-0.0080.0000.0000.0000.000
158X162LEU0-0.044-0.01835.350-0.018-0.0180.0000.0000.0000.000
159X163MET0-0.038-0.00738.6520.1140.1140.0000.0000.0000.000
160X164LEU0-0.051-0.03136.3400.0900.0900.0000.0000.0000.000
161X165THR0-0.029-0.01435.816-0.174-0.1740.0000.0000.0000.000
162X166GLY00.0360.02231.755-0.148-0.1480.0000.0000.0000.000
163X167GLY00.006-0.01028.9900.1530.1530.0000.0000.0000.000
164X168TRP0-0.005-0.00926.903-0.501-0.5010.0000.0000.0000.000
165X169TRP0-0.0120.00322.6600.0730.0730.0000.0000.0000.000
166X170PHE0-0.057-0.02629.4100.1630.1630.0000.0000.0000.000
167X171ASP-1-0.721-0.86533.236-8.601-8.6010.0000.0000.0000.000
168X172ALA00.0150.01935.6030.0280.0280.0000.0000.0000.000
169X174GLY00.0170.02235.6010.1210.1210.0000.0000.0000.000
170X175PRO0-0.017-0.02134.9580.0770.0770.0000.0000.0000.000
171X176SER0-0.004-0.03232.091-0.129-0.1290.0000.0000.0000.000
172X177ASN00.0100.00431.605-0.268-0.2680.0000.0000.0000.000
173X178LEU00.0010.01127.8130.1830.1830.0000.0000.0000.000
174X179ASN0-0.001-0.01625.925-0.251-0.2510.0000.0000.0000.000
175X180GLY00.0210.03630.0180.0970.0970.0000.0000.0000.000
176X181MET0-0.005-0.00133.484-0.255-0.2550.0000.0000.0000.000
177X182PHE00.0390.01832.7110.1030.1030.0000.0000.0000.000
178X183TYR0-0.081-0.06435.7570.2590.2590.0000.0000.0000.000
179X184THR00.0390.00538.577-0.134-0.1340.0000.0000.0000.000
180X185ALA00.0190.00740.0860.1310.1310.0000.0000.0000.000
181X186GLY00.0030.01642.1280.1360.1360.0000.0000.0000.000
182X187GLN0-0.019-0.01042.8370.0050.0050.0000.0000.0000.000
183X188ASN0-0.0240.00140.5560.0830.0830.0000.0000.0000.000
184X189HIS00.0590.02642.051-0.086-0.0860.0000.0000.0000.000
185X190GLY00.0090.00644.9050.0880.0880.0000.0000.0000.000
186X191LYS10.8640.93841.5927.1497.1490.0000.0000.0000.000
187X192LEU00.0430.01141.626-0.144-0.1440.0000.0000.0000.000
188X193ASN00.0330.03438.823-0.073-0.0730.0000.0000.0000.000
189X194GLY00.0370.02237.530-0.145-0.1450.0000.0000.0000.000
190X195ILE0-0.0310.01131.716-0.136-0.1360.0000.0000.0000.000
191X196LYS10.9040.95834.4418.3298.3290.0000.0000.0000.000
192X197TRP00.057-0.00329.165-0.245-0.2450.0000.0000.0000.000
193X198HIS00.0350.03335.0570.1200.1200.0000.0000.0000.000
194X199TYR0-0.026-0.01236.0370.2160.2160.0000.0000.0000.000
195X200PHE0-0.0410.00534.8900.0290.0290.0000.0000.0000.000
196X201LYS10.8760.93737.5968.0808.0800.0000.0000.0000.000
197X202GLY00.0180.03539.8950.2020.2020.0000.0000.0000.000
198X203PRO0-0.020-0.03439.923-0.183-0.1830.0000.0000.0000.000
199X204SER0-0.023-0.01441.499-0.056-0.0560.0000.0000.0000.000
200X205TYR0-0.011-0.02038.6850.0260.0260.0000.0000.0000.000
201X206SER0-0.034-0.01337.456-0.264-0.2640.0000.0000.0000.000
202X207LEU0-0.031-0.03733.4000.1260.1260.0000.0000.0000.000
203X208ARG10.8680.92633.2549.2619.2610.0000.0000.0000.000
204X209SER0-0.064-0.04629.348-0.156-0.1560.0000.0000.0000.000
205X210THR0-0.033-0.02327.7370.3160.3160.0000.0000.0000.000
206X211THR00.0150.00022.556-0.128-0.1280.0000.0000.0000.000
207X212MET0-0.0520.00322.5940.1680.1680.0000.0000.0000.000
208X213MET0-0.0030.00119.081-0.663-0.6630.0000.0000.0000.000
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