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: 153YZ

Calculation Name: 1HK0-X-Xray547

Preferred Name: Gamma-crystallin D

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HK0

Chain ID: X

ChEMBL ID: CHEMBL4296286

UniProt ID: P07320

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1996567.675431
FMO2-HF: Nuclear repulsion 1922802.742005
FMO2-HF: Total energy -73764.933425
FMO2-MP2: Total energy -73975.946286


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-133.531-129.76712.214-8.553-7.423-0.093
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.813 / q_NPA : 0.899
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].
3A3ILE0-0.0140.0063.819-1.618-1.008-0.005-0.265-0.3400.000
37A37VAL0-0.0180.0044.358-2.222-2.178-0.001-0.016-0.0260.000
38A38ASP-1-0.830-0.9183.529-40.855-40.6760.007-0.061-0.1250.000
39A39SER0-0.019-0.0242.299-12.030-9.9403.644-3.020-2.714-0.027
40A40GLY0-0.021-0.0051.904-40.054-40.2338.212-4.684-3.348-0.061
41A41CYS0-0.043-0.0243.53212.43312.4700.0010.037-0.0750.000
42A42TRP00.0140.0043.2652.5302.8560.001-0.164-0.1630.000
80A80LEU00.0030.0132.535-4.268-3.6110.355-0.380-0.632-0.005
4A4THR00.0160.0036.7873.2893.2890.0000.0000.0000.000
5A5LEU0-0.018-0.01910.0740.5340.5340.0000.0000.0000.000
6A6TYR00.0610.01712.7570.0610.0610.0000.0000.0000.000
7A7GLU-1-0.751-0.85516.739-14.115-14.1150.0000.0000.0000.000
8A8ASP-1-0.833-0.89620.316-12.855-12.8550.0000.0000.0000.000
9A9ARG10.8700.91819.86512.65412.6540.0000.0000.0000.000
10A10GLY0-0.019-0.00519.7170.3950.3950.0000.0000.0000.000
11A11PHE0-0.062-0.03714.5860.1270.1270.0000.0000.0000.000
12A12GLN0-0.043-0.01317.5500.4820.4820.0000.0000.0000.000
13A13GLY00.0540.02420.097-0.312-0.3120.0000.0000.0000.000
14A14ARG10.8300.90819.99714.38414.3840.0000.0000.0000.000
15A15HIS0-0.012-0.00914.916-0.552-0.5520.0000.0000.0000.000
16A16TYR0-0.015-0.00213.6610.9340.9340.0000.0000.0000.000
17A17GLU-1-0.835-0.9139.188-29.566-29.5660.0000.0000.0000.000
18A18CYS0-0.056-0.0018.5982.6582.6580.0000.0000.0000.000
19A19SER00.042-0.0025.149-7.900-7.9000.0000.0000.0000.000
20A20SER0-0.008-0.0015.374-3.451-3.4510.0000.0000.0000.000
21A21ASP-1-0.819-0.9097.389-29.233-29.2330.0000.0000.0000.000
22A22HIS0-0.014-0.01410.0490.4350.4350.0000.0000.0000.000
23A23PRO00.0220.01912.7400.3460.3460.0000.0000.0000.000
24A24ASN00.0710.01616.2101.0761.0760.0000.0000.0000.000
25A25LEU00.0280.01213.2510.0210.0210.0000.0000.0000.000
26A26GLN00.0140.00917.3720.6710.6710.0000.0000.0000.000
27A27PRO0-0.030-0.00920.0720.4160.4160.0000.0000.0000.000
28A28TYR0-0.028-0.01017.2710.4760.4760.0000.0000.0000.000
29A29LEU0-0.037-0.01915.702-0.223-0.2230.0000.0000.0000.000
30A30SER0-0.074-0.05619.3060.2640.2640.0000.0000.0000.000
31A31ARG10.8130.90921.15214.00214.0020.0000.0000.0000.000
32A32CYS0-0.035-0.01614.967-0.863-0.8630.0000.0000.0000.000
33A33ASN0-0.032-0.04618.4390.5100.5100.0000.0000.0000.000
34A34SER0-0.044-0.01316.6570.0950.0950.0000.0000.0000.000
35A35ALA00.006-0.00111.364-0.421-0.4210.0000.0000.0000.000
36A36ARG10.9010.9419.63223.52723.5270.0000.0000.0000.000
43A43MET0-0.0320.0167.4182.9272.9270.0000.0000.0000.000
44A44LEU0-0.0040.00211.088-0.768-0.7680.0000.0000.0000.000
45A45TYR00.0750.02913.2610.3910.3910.0000.0000.0000.000
46A46GLU-1-0.810-0.89716.886-13.624-13.6240.0000.0000.0000.000
47A47GLN0-0.0300.00920.0600.7710.7710.0000.0000.0000.000
48A48PRO00.0250.00819.001-0.930-0.9300.0000.0000.0000.000
49A49ASN0-0.055-0.04018.441-0.104-0.1040.0000.0000.0000.000
50A50TYR0-0.018-0.01113.1820.7200.7200.0000.0000.0000.000
51A51SER00.0080.00817.4550.0720.0720.0000.0000.0000.000
52A52GLY0-0.016-0.02020.594-0.238-0.2380.0000.0000.0000.000
53A53LEU0-0.069-0.04421.163-0.343-0.3430.0000.0000.0000.000
54A54GLN00.0470.02416.523-1.557-1.5570.0000.0000.0000.000
55A55TYR0-0.022-0.00915.2910.9670.9670.0000.0000.0000.000
56A56PHE00.020-0.0019.529-1.241-1.2410.0000.0000.0000.000
57A57LEU0-0.036-0.0109.3851.3161.3160.0000.0000.0000.000
58A58ARG10.9200.9437.34622.51922.5190.0000.0000.0000.000
59A59ARG10.8120.8856.31539.00139.0010.0000.0000.0000.000
60A60GLY00.0000.0087.4004.8714.8710.0000.0000.0000.000
61A61ASP-1-0.876-0.9249.994-26.328-26.3280.0000.0000.0000.000
62A62TYR0-0.004-0.00110.3820.8500.8500.0000.0000.0000.000
63A63ALA00.0260.00014.915-0.033-0.0330.0000.0000.0000.000
64A64ASP-1-0.807-0.90418.127-13.587-13.5870.0000.0000.0000.000
65A65HIS00.0300.00518.237-0.181-0.1810.0000.0000.0000.000
66A66GLN00.0100.01519.093-0.631-0.6310.0000.0000.0000.000
67A67GLN0-0.0080.00017.336-0.820-0.8200.0000.0000.0000.000
68A68TRP0-0.0080.00914.564-1.084-1.0840.0000.0000.0000.000
69A69MET0-0.042-0.03616.4230.2870.2870.0000.0000.0000.000
70A70GLY00.0240.02519.2830.4150.4150.0000.0000.0000.000
71A71LEU0-0.021-0.01920.2040.5630.5630.0000.0000.0000.000
72A72SER0-0.032-0.01822.4750.5080.5080.0000.0000.0000.000
73A73ASP-1-0.808-0.88820.631-14.207-14.2070.0000.0000.0000.000
74A74SER00.0060.00420.688-0.370-0.3700.0000.0000.0000.000
75A75VAL0-0.016-0.01014.781-0.300-0.3000.0000.0000.0000.000
76A76ARG10.8620.91218.11813.91913.9190.0000.0000.0000.000
77A77SER0-0.033-0.00715.3130.1000.1000.0000.0000.0000.000
78A78CYS0-0.0270.00010.3140.0480.0480.0000.0000.0000.000
79A79ARG10.9250.9659.78323.92623.9260.0000.0000.0000.000
81A81ILE0-0.039-0.0266.3524.1594.1590.0000.0000.0000.000
82A82PRO0-0.019-0.0086.764-4.821-4.8210.0000.0000.0000.000
83A83HIS00.0140.0026.6821.2291.2290.0000.0000.0000.000
84A84SER0-0.009-0.0268.5482.2712.2710.0000.0000.0000.000
85A85GLY0-0.023-0.00412.012-0.672-0.6720.0000.0000.0000.000
86A87SER0-0.060-0.03913.9660.6220.6220.0000.0000.0000.000
87A88HIS00.0130.00612.9600.2350.2350.0000.0000.0000.000
88A89ARG10.8010.87117.94214.04114.0410.0000.0000.0000.000
89A90ILE0-0.0160.00920.432-0.258-0.2580.0000.0000.0000.000
90A91ARG10.8970.94422.67811.80711.8070.0000.0000.0000.000
91A92LEU00.0160.00023.992-0.245-0.2450.0000.0000.0000.000
92A93TYR00.0120.00127.7770.2370.2370.0000.0000.0000.000
93A94GLU-1-0.773-0.86831.257-8.451-8.4510.0000.0000.0000.000
94A95ARG10.8080.88234.2578.3048.3040.0000.0000.0000.000
95A96GLU-1-0.835-0.90932.868-9.613-9.6130.0000.0000.0000.000
96A97ASP-1-0.872-0.91232.629-9.130-9.1300.0000.0000.0000.000
97A98TYR0-0.112-0.09127.0110.1730.1730.0000.0000.0000.000
98A99ARG10.8830.94332.8268.8258.8250.0000.0000.0000.000
99A100GLY0-0.024-0.01535.604-0.101-0.1010.0000.0000.0000.000
100A101GLN0-0.009-0.01936.169-0.191-0.1910.0000.0000.0000.000
101A102MET0-0.032-0.00630.302-0.311-0.3110.0000.0000.0000.000
102A103ILE0-0.0090.00628.6320.2230.2230.0000.0000.0000.000
103A104GLU-1-0.784-0.89026.341-12.011-12.0110.0000.0000.0000.000
104A105PHE0-0.016-0.01323.3760.2950.2950.0000.0000.0000.000
105A106THR00.0560.01221.564-0.132-0.1320.0000.0000.0000.000
106A107GLU-1-0.993-0.98420.658-13.668-13.6680.0000.0000.0000.000
107A108ASP-1-0.818-0.87718.033-17.761-17.7610.0000.0000.0000.000
108A109CYS0-0.058-0.01520.8900.8800.8800.0000.0000.0000.000
109A110SER00.0440.02323.931-0.131-0.1310.0000.0000.0000.000
110A111CYS0-0.027-0.03124.8910.1290.1290.0000.0000.0000.000
111A112LEU00.0210.01927.3700.0870.0870.0000.0000.0000.000
112A113GLN0-0.014-0.04028.8630.0970.0970.0000.0000.0000.000
113A114ASP-1-0.882-0.93531.278-9.659-9.6590.0000.0000.0000.000
114A115ARG10.8800.94127.59511.23111.2310.0000.0000.0000.000
115A116PHE00.0290.00731.4180.2060.2060.0000.0000.0000.000
116A117ARG10.9250.97233.2618.4868.4860.0000.0000.0000.000
117A118PHE00.0280.01533.6740.2810.2810.0000.0000.0000.000
118A119ASN0-0.017-0.00432.953-0.343-0.3430.0000.0000.0000.000
119A120GLU-1-0.896-0.95031.032-9.615-9.6150.0000.0000.0000.000
120A121ILE0-0.033-0.00527.1170.1090.1090.0000.0000.0000.000
121A122HIS0-0.017-0.02429.235-0.331-0.3310.0000.0000.0000.000
122A123SER0-0.046-0.02628.591-0.035-0.0350.0000.0000.0000.000
123A124LEU0-0.029-0.01222.4680.0470.0470.0000.0000.0000.000
124A125ASN0-0.0030.00424.515-0.446-0.4460.0000.0000.0000.000
125A126VAL0-0.0060.01217.9770.0640.0640.0000.0000.0000.000
126A127LEU00.0040.00120.653-0.200-0.2000.0000.0000.0000.000
127A128GLU-1-0.792-0.86218.231-15.195-15.1950.0000.0000.0000.000
128A129GLY00.0670.02914.2540.0210.0210.0000.0000.0000.000
129A130SER00.0010.00411.5841.5711.5710.0000.0000.0000.000
130A131TRP0-0.022-0.02713.900-0.231-0.2310.0000.0000.0000.000
131A132VAL0-0.026-0.01014.159-0.541-0.5410.0000.0000.0000.000
132A133LEU00.0090.01516.8700.6100.6100.0000.0000.0000.000
133A134TYR00.022-0.00616.771-0.636-0.6360.0000.0000.0000.000
134A135GLU-1-0.823-0.90422.461-11.240-11.2400.0000.0000.0000.000
135A136LEU0-0.021-0.01225.3600.6650.6650.0000.0000.0000.000
136A137SER00.0430.03625.361-0.506-0.5060.0000.0000.0000.000
137A138ASN0-0.063-0.04924.277-0.115-0.1150.0000.0000.0000.000
138A139TYR0-0.023-0.00619.607-0.234-0.2340.0000.0000.0000.000
139A140ARG10.8870.94521.15711.23711.2370.0000.0000.0000.000
140A141GLY00.0240.01023.6820.2130.2130.0000.0000.0000.000
141A142ARG10.9200.95122.62211.32711.3270.0000.0000.0000.000
142A143GLN00.0500.02416.621-0.774-0.7740.0000.0000.0000.000
143A144TYR0-0.015-0.00919.2570.1790.1790.0000.0000.0000.000
144A145LEU0-0.004-0.01212.514-0.278-0.2780.0000.0000.0000.000
145A146LEU0-0.0330.00216.1190.9190.9190.0000.0000.0000.000
146A147MET0-0.015-0.01312.924-2.258-2.2580.0000.0000.0000.000
147A148PRO00.0150.00114.9541.0931.0930.0000.0000.0000.000
148A149GLY00.0400.02717.924-0.100-0.1000.0000.0000.0000.000
149A150ASP-1-0.863-0.90221.331-12.082-12.0820.0000.0000.0000.000
150A151TYR0-0.027-0.02218.747-0.246-0.2460.0000.0000.0000.000
151A152ARG10.9030.91725.49010.21610.2160.0000.0000.0000.000
152A153ARG10.9580.97628.54210.66810.6680.0000.0000.0000.000
153A154TYR00.0320.01327.467-0.235-0.2350.0000.0000.0000.000
154A155GLN0-0.025-0.01626.618-0.503-0.5030.0000.0000.0000.000
155A156ASP-1-0.857-0.92124.863-11.943-11.9430.0000.0000.0000.000
156A157TRP0-0.0160.00221.491-0.641-0.6410.0000.0000.0000.000
157A158GLY0-0.013-0.01222.074-0.496-0.4960.0000.0000.0000.000
158A159ALA0-0.0240.00524.1550.0610.0610.0000.0000.0000.000
159A160THR0-0.007-0.02626.3170.2520.2520.0000.0000.0000.000
160A161ASN0-0.041-0.02829.4540.4120.4120.0000.0000.0000.000
161A162ALA00.0960.04729.119-0.412-0.4120.0000.0000.0000.000
162A163ARG10.9080.97729.3979.7829.7820.0000.0000.0000.000
163A164VAL00.0020.00425.002-0.461-0.4610.0000.0000.0000.000
164A165GLY00.0240.02326.5430.4590.4590.0000.0000.0000.000
165A166SER0-0.076-0.04823.315-0.080-0.0800.0000.0000.0000.000
166A167LEU0-0.0100.00620.894-0.162-0.1620.0000.0000.0000.000
167A168ARG10.9180.97415.75119.03119.0310.0000.0000.0000.000
168A169ARG10.9010.93315.16117.51317.5130.0000.0000.0000.000
169A170VAL0-0.045-0.0239.253-0.590-0.5900.0000.0000.0000.000
170A171ILE0-0.001-0.00710.386-0.652-0.6520.0000.0000.0000.000
171A172ASP-1-0.774-0.8746.142-45.466-45.4660.0000.0000.0000.000
172A173PHE0-0.034-0.0248.6682.0192.0190.0000.0000.0000.000
173A174SER-1-0.888-0.9148.922-31.222-31.2220.0000.0000.0000.000