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: ZLY4N

Calculation Name: 3B57-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3B57

Chain ID: A

ChEMBL ID:

UniProt ID: Q92AN1

Base Structure: X-ray

Registration Date: 2025-10-04

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2397551.420312
FMO2-HF: Nuclear repulsion 2316130.099368
FMO2-HF: Total energy -81421.320943
FMO2-MP2: Total energy -81662.306567


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-169.673-155.47319.384-13.506-20.082-0.141
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.919
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].
3A3LYS10.9270.9582.54535.41337.0692.749-1.187-3.2180.001
4A4GLU-1-0.897-0.9353.734-22.194-21.9450.013-0.011-0.2510.000
6A6ILE0-0.059-0.0132.2920.7131.1752.044-0.705-1.802-0.005
49A49PHE00.004-0.0102.967-2.864-1.3500.861-0.780-1.595-0.012
83A83LYS10.8300.9344.22330.88831.065-0.001-0.049-0.1280.000
84A84GLU-1-0.890-0.9471.967-141.330-133.7238.786-8.583-7.810-0.107
85A85ILE0-0.022-0.0092.841-10.297-7.4943.043-2.446-3.401-0.014
86A86PRO00.0270.0092.9294.7244.1881.8890.296-1.649-0.004
87A87SER00.0940.0296.0232.2172.254-0.001-0.005-0.0310.000
89A89LEU0-0.021-0.0144.1981.0131.2440.001-0.036-0.1970.000
5A5GLU-1-0.862-0.9496.581-26.189-26.1890.0000.0000.0000.000
7A7ILE00.0060.0066.5003.1263.1260.0000.0000.0000.000
8A8LEU0-0.008-0.0048.7962.6762.6760.0000.0000.0000.000
9A9SER00.0040.0029.2251.8311.8310.0000.0000.0000.000
10A10ALA00.0230.00610.0791.6261.6260.0000.0000.0000.000
11A11LYS10.9260.97111.76119.42619.4260.0000.0000.0000.000
12A12ASN0-0.058-0.04814.3212.2252.2250.0000.0000.0000.000
13A13TRP0-0.0170.01312.9810.5600.5600.0000.0000.0000.000
14A14MET00.0010.01215.3580.4820.4820.0000.0000.0000.000
15A15HIS0-0.044-0.01817.9320.8790.8790.0000.0000.0000.000
16A16SER0-0.049-0.04118.8520.5760.5760.0000.0000.0000.000
17A17HIS0-0.031-0.02921.310-0.238-0.2380.0000.0000.0000.000
18A18PHE00.0480.01417.4610.4590.4590.0000.0000.0000.000
19A19GLU-1-0.851-0.91122.344-11.172-11.1720.0000.0000.0000.000
20A20ASN0-0.078-0.04225.0570.4220.4220.0000.0000.0000.000
21A21GLU-1-0.890-0.93224.384-11.086-11.0860.0000.0000.0000.000
22A22THR0-0.031-0.02623.9660.3580.3580.0000.0000.0000.000
23A23THR0-0.079-0.04126.3630.5380.5380.0000.0000.0000.000
24A24GLY00.0070.00927.9390.2820.2820.0000.0000.0000.000
25A25HIS-1-0.832-0.92026.629-9.725-9.7250.0000.0000.0000.000
26A26ASP-1-0.729-0.82327.147-10.917-10.9170.0000.0000.0000.000
27A27TRP00.0410.00117.053-0.566-0.5660.0000.0000.0000.000
28A28SER0-0.146-0.10922.399-0.548-0.5480.0000.0000.0000.000
29A29HIS0-0.070-0.04023.812-0.133-0.1330.0000.0000.0000.000
30A30ILE00.0610.05317.974-0.184-0.1840.0000.0000.0000.000
31A31LYS10.8990.95218.96012.75312.7530.0000.0000.0000.000
32A32ARG10.7540.85919.99710.30010.3000.0000.0000.0000.000
33A33VAL00.0660.04218.128-0.059-0.0590.0000.0000.0000.000
34A34TRP0-0.043-0.02412.8430.3340.3340.0000.0000.0000.000
35A35LYS10.8960.94116.50412.13212.1320.0000.0000.0000.000
36A36LEU00.0260.01518.928-0.037-0.0370.0000.0000.0000.000
37A37SER00.008-0.01215.680-0.215-0.2150.0000.0000.0000.000
38A38LYS10.8740.94913.68316.62716.6270.0000.0000.0000.000
39A39GLU-1-0.937-0.97215.952-11.316-11.3160.0000.0000.0000.000
40A40ILE00.0000.02019.0870.2900.2900.0000.0000.0000.000
41A41GLN00.0490.01613.461-0.093-0.0930.0000.0000.0000.000
42A42SER0-0.121-0.07516.7940.0900.0900.0000.0000.0000.000
43A43LYS10.8890.93818.23811.74611.7460.0000.0000.0000.000
44A44GLU-1-0.809-0.87219.009-10.775-10.7750.0000.0000.0000.000
45A45GLY0-0.026-0.00115.5550.0260.0260.0000.0000.0000.000
46A46GLY00.0480.01113.3630.1860.1860.0000.0000.0000.000
47A47ASP-1-0.875-0.9486.472-26.340-26.3400.0000.0000.0000.000
48A48LEU00.0300.0169.235-0.349-0.3490.0000.0000.0000.000
50A50THR0-0.019-0.0226.656-0.318-0.3180.0000.0000.0000.000
51A51ILE0-0.012-0.0107.9740.7740.7740.0000.0000.0000.000
52A52GLU-1-0.855-0.9349.390-19.553-19.5530.0000.0000.0000.000
53A53LEU00.006-0.0086.1130.3280.3280.0000.0000.0000.000
54A54ALA0-0.0060.0029.9050.8400.8400.0000.0000.0000.000
55A55ALA0-0.024-0.02012.5410.9380.9380.0000.0000.0000.000
56A56LEU0-0.058-0.02711.7650.7220.7220.0000.0000.0000.000
57A57PHE00.014-0.02610.3930.1640.1640.0000.0000.0000.000
58A58HIS0-0.025-0.00715.2800.1740.1740.0000.0000.0000.000
59A59ASP-1-0.802-0.89018.119-11.269-11.2690.0000.0000.0000.000
60A60TYR00.0140.01817.773-0.478-0.4780.0000.0000.0000.000
61A61SER0-0.076-0.06719.809-0.698-0.6980.0000.0000.0000.000
62A62ASP-1-0.779-0.85422.129-11.028-11.0280.0000.0000.0000.000
63A63ILE0-0.100-0.05522.330-0.400-0.4000.0000.0000.0000.000
64A64LYS10.9110.95126.57311.37711.3770.0000.0000.0000.000
65A65LEU00.0090.00428.8200.4390.4390.0000.0000.0000.000
66A66THR00.009-0.01428.244-0.230-0.2300.0000.0000.0000.000
67A67THR0-0.072-0.05727.644-0.132-0.1320.0000.0000.0000.000
68A68ASP-1-0.817-0.89325.000-11.430-11.4300.0000.0000.0000.000
69A69GLU-1-0.767-0.85323.663-11.165-11.1650.0000.0000.0000.000
70A70GLN0-0.0160.00922.679-0.843-0.8430.0000.0000.0000.000
71A71GLU-1-0.770-0.88621.162-13.988-13.9880.0000.0000.0000.000
72A72ALA00.0120.03919.729-0.861-0.8610.0000.0000.0000.000
73A73THR00.013-0.00617.883-1.047-1.0470.0000.0000.0000.000
74A74LYS10.7820.85416.48112.43012.4300.0000.0000.0000.000
75A75THR0-0.033-0.02715.753-1.015-1.0150.0000.0000.0000.000
76A76LEU0-0.0110.00113.702-1.551-1.5510.0000.0000.0000.000
77A77ILE0-0.046-0.01711.791-1.869-1.8690.0000.0000.0000.000
78A78ASN00.0340.02410.715-2.314-2.3140.0000.0000.0000.000
79A79TRP00.0140.0228.137-3.707-3.7070.0000.0000.0000.000
80A80MET0-0.020-0.0117.526-3.173-3.1730.0000.0000.0000.000
81A81GLU-1-0.914-0.9675.991-29.170-29.1700.0000.0000.0000.000
82A82THR0-0.046-0.0356.715-3.973-3.9730.0000.0000.0000.000
88A88GLU-1-0.878-0.9318.992-17.509-17.5090.0000.0000.0000.000
90A90ILE00.0330.0247.5231.4431.4430.0000.0000.0000.000
91A91LYS10.8940.9349.60520.70320.7030.0000.0000.0000.000
92A92LYS10.8880.9579.51620.87520.8750.0000.0000.0000.000
93A93ILE00.0270.0136.6130.9920.9920.0000.0000.0000.000
94A94ILE00.0430.01911.1301.0171.0170.0000.0000.0000.000
95A95ARG10.8490.92014.45015.11615.1160.0000.0000.0000.000
96A96ILE0-0.0050.00611.8590.8320.8320.0000.0000.0000.000
97A97ILE00.0570.05013.8570.7390.7390.0000.0000.0000.000
98A98GLN00.0140.00917.1100.8200.8200.0000.0000.0000.000
99A99SER0-0.061-0.03918.1940.6630.6630.0000.0000.0000.000
100A100VAL00.0140.00318.1470.5770.5770.0000.0000.0000.000
101A101SER0-0.015-0.00820.9170.6060.6060.0000.0000.0000.000
102A102PHE00.0190.00323.1940.4410.4410.0000.0000.0000.000
103A103LYS10.7980.90924.33910.58810.5880.0000.0000.0000.000
104A104LYS10.8140.89722.78412.10112.1010.0000.0000.0000.000
105A105GLY00.0050.00626.0840.2880.2880.0000.0000.0000.000
106A106LYS0-0.071-0.03928.7240.3320.3320.0000.0000.0000.000
107A107ASN00.0260.02228.6020.0690.0690.0000.0000.0000.000
108A108THR0-0.008-0.03427.026-0.107-0.1070.0000.0000.0000.000
109A109PHE00.0040.02720.1040.3110.3110.0000.0000.0000.000
110A110LYS10.8830.92024.3849.8359.8350.0000.0000.0000.000
111A111ALA0-0.003-0.00723.301-0.291-0.2910.0000.0000.0000.000
112A112LEU0-0.0400.00420.301-0.294-0.2940.0000.0000.0000.000
113A113THR0-0.018-0.02315.5100.0730.0730.0000.0000.0000.000
114A114ILE00.0450.01315.5190.4000.4000.0000.0000.0000.000
115A115GLU-1-0.800-0.91211.371-16.400-16.4000.0000.0000.0000.000
116A116GLU-1-0.773-0.87014.597-13.859-13.8590.0000.0000.0000.000
117A117LYS10.8320.93317.21611.51711.5170.0000.0000.0000.000
118A118ILE0-0.0100.01016.0490.2830.2830.0000.0000.0000.000
119A119VAL00.0320.01514.3600.3090.3090.0000.0000.0000.000
120A120GLN00.0020.00517.5570.7580.7580.0000.0000.0000.000
121A121ASP-1-0.764-0.90020.912-10.321-10.3210.0000.0000.0000.000
122A122ALA0-0.010-0.00319.3320.3640.3640.0000.0000.0000.000
123A123ASP-1-0.821-0.91821.260-10.991-10.9910.0000.0000.0000.000
124A124ARG10.8280.92422.83210.46210.4620.0000.0000.0000.000
125A125LEU00.0360.01123.5350.3850.3850.0000.0000.0000.000
126A126ASP-1-0.803-0.88224.449-10.375-10.3750.0000.0000.0000.000
127A127ALA00.0030.01626.4750.1520.1520.0000.0000.0000.000
128A128ILE0-0.0010.00029.2070.3420.3420.0000.0000.0000.000
129A129GLY00.028-0.01631.111-0.193-0.1930.0000.0000.0000.000
130A130ALA00.004-0.00333.5920.0530.0530.0000.0000.0000.000
131A131ILE0-0.016-0.00428.2000.0850.0850.0000.0000.0000.000
132A132GLY00.0460.03231.853-0.014-0.0140.0000.0000.0000.000
133A133ILE0-0.013-0.00932.7030.0920.0920.0000.0000.0000.000
134A134ALA00.0140.00634.0210.1120.1120.0000.0000.0000.000
135A135ARG10.8440.92926.85110.15910.1590.0000.0000.0000.000
136A136THR00.0060.01233.4570.0880.0880.0000.0000.0000.000
137A137PHE0-0.007-0.01835.9750.1630.1630.0000.0000.0000.000
138A138THR0-0.028-0.01535.1740.1630.1630.0000.0000.0000.000
139A139TYR0-0.0010.00333.8270.1370.1370.0000.0000.0000.000
140A140GLY00.010-0.00136.3530.0880.0880.0000.0000.0000.000
141A141GLY0-0.004-0.00840.0020.1580.1580.0000.0000.0000.000
142A142ALA0-0.025-0.00437.3940.0790.0790.0000.0000.0000.000
143A143HIS0-0.062-0.03635.528-0.105-0.1050.0000.0000.0000.000
144A144ASN0-0.047-0.02040.8270.0400.0400.0000.0000.0000.000
145A145ARG10.8740.94437.2437.6657.6650.0000.0000.0000.000
146A146GLU-1-0.881-0.94443.501-6.269-6.2690.0000.0000.0000.000
147A147ILE00.0240.01144.522-0.079-0.0790.0000.0000.0000.000
148A148ALA00.0400.00045.005-0.098-0.0980.0000.0000.0000.000
149A149ASN00.0390.01747.6610.1660.1660.0000.0000.0000.000
150A150GLN00.0410.02050.504-0.011-0.0110.0000.0000.0000.000
151A151ASN0-0.0430.00053.1970.0170.0170.0000.0000.0000.000
152A152ASN0-0.033-0.04549.6970.0720.0720.0000.0000.0000.000
153A153PRO00.0740.04048.273-0.091-0.0910.0000.0000.0000.000
154A154LYS10.9210.95446.5545.6065.6060.0000.0000.0000.000
155A155ASN00.0150.02244.5940.0410.0410.0000.0000.0000.000
156A156THR0-0.046-0.01344.172-0.090-0.0900.0000.0000.0000.000
157A157THR0-0.018-0.00639.754-0.169-0.1690.0000.0000.0000.000
158A158LEU0-0.0070.00241.137-0.128-0.1280.0000.0000.0000.000
159A159GLN0-0.044-0.02842.5820.0440.0440.0000.0000.0000.000
160A160HIS00.0610.03434.542-0.023-0.0230.0000.0000.0000.000
161A161PHE00.000-0.01937.953-0.237-0.2370.0000.0000.0000.000
162A162TYR0-0.070-0.05638.893-0.136-0.1360.0000.0000.0000.000
163A163ASP-1-0.862-0.91739.651-6.933-6.9330.0000.0000.0000.000
164A164LYS0-0.029-0.01834.053-0.210-0.2100.0000.0000.0000.000
165A165LEU0-0.027-0.00533.149-0.132-0.1320.0000.0000.0000.000
166A166LEU00.008-0.00634.288-0.159-0.1590.0000.0000.0000.000
167A167LEU00.0180.01635.5090.0130.0130.0000.0000.0000.000
168A168ILE0-0.0200.00329.198-0.187-0.1870.0000.0000.0000.000
169A169LYS10.8790.94430.4248.0168.0160.0000.0000.0000.000
170A170ASP-1-0.927-0.97531.509-8.072-8.0720.0000.0000.0000.000
171A171GLN0-0.014-0.00729.828-0.314-0.3140.0000.0000.0000.000
172A172LEU0-0.0550.00325.532-0.325-0.3250.0000.0000.0000.000
173A173ASN0-0.061-0.04823.3990.0290.0290.0000.0000.0000.000
174A174THR00.0340.01921.747-0.358-0.3580.0000.0000.0000.000
175A175GLU-1-0.828-0.92824.481-9.009-9.0090.0000.0000.0000.000
176A176THR0-0.035-0.04622.7840.2570.2570.0000.0000.0000.000
177A177ALA00.0140.01523.5860.1550.1550.0000.0000.0000.000
178A178LYS10.8960.95525.3719.2499.2490.0000.0000.0000.000
179A179THR0-0.128-0.06627.5900.3090.3090.0000.0000.0000.000
180A180ILE00.0210.01023.8110.2970.2970.0000.0000.0000.000
181A181ALA00.0210.01428.3780.0650.0650.0000.0000.0000.000
182A182LYS10.9120.96730.2138.3218.3210.0000.0000.0000.000
183A183GLU-1-0.911-0.96332.905-8.139-8.1390.0000.0000.0000.000
184A184LYS10.8530.93927.40710.02110.0210.0000.0000.0000.000
185A185GLN00.0540.00233.2830.0090.0090.0000.0000.0000.000
186A186LYS10.8550.91735.6077.1317.1310.0000.0000.0000.000
187A187ILE0-0.012-0.00335.7280.1500.1500.0000.0000.0000.000
188A188MET00.0070.02634.2970.0560.0560.0000.0000.0000.000
189A189GLN0-0.012-0.00138.5010.0640.0640.0000.0000.0000.000
190A190ASP-1-0.843-0.90541.417-6.702-6.7020.0000.0000.0000.000
191A191PHE00.000-0.00140.8190.1250.1250.0000.0000.0000.000
192A192ILE00.0140.01041.3670.1220.1220.0000.0000.0000.000
193A193GLN0-0.026-0.01844.0520.0590.0590.0000.0000.0000.000
194A194ALA0-0.0110.00446.2280.1420.1420.0000.0000.0000.000
195A195LEU00.0380.02344.1080.1260.1260.0000.0000.0000.000
196A196GLU-1-0.858-0.92947.479-6.040-6.0400.0000.0000.0000.000
197A197LYS10.8660.94349.8315.6315.6310.0000.0000.0000.000
198A198GLU-1-0.942-0.98149.262-5.974-5.9740.0000.0000.0000.000
199A199LEU0-0.026-0.01848.9800.0640.0640.0000.0000.0000.000
200A200LYS10.8630.92652.2555.5905.5900.0000.0000.0000.000
201A201VAL0-0.0170.00355.3720.0950.0950.0000.0000.0000.000
202A202LEU0-0.064-0.02455.1850.0800.0800.0000.0000.0000.000
203A203GLU-2-1.894-1.93657.564-10.191-10.1910.0000.0000.0000.000