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: YR5L2

Calculation Name: 4XGN-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nicotinamide-adenine-dinucleotide | glycerol | 1,2-ethanediol

Ligand 3-letter code: NAD | GOL | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4XGN

Chain ID: A

ChEMBL ID:

UniProt ID: Q2T0K5

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 255
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2984468.397469
FMO2-HF: Nuclear repulsion 2890488.962268
FMO2-HF: Total energy -93979.435201
FMO2-MP2: Total energy -94248.458005


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:-2:HIS)


Summations of interaction energy for fragment #1(A:-2:HIS)
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.
-43.423-38.3290.533-2.463-3.165-0.016
Interaction energy analysis for fragmet #1(A:-2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.861 / 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].
3A0HIS10.8930.9453.34349.92951.984-0.005-0.956-1.095-0.002
4A1MET00.0530.0503.446-12.485-11.6680.006-0.484-0.339-0.004
136A133PRO0-0.033-0.0442.617-4.130-3.4570.421-0.368-0.726-0.004
137A134THR0-0.102-0.0612.711-12.145-10.6520.112-0.649-0.957-0.006
138A135GLY00.0080.0134.9225.0725.128-0.001-0.006-0.0480.000
5A2GLU-1-0.877-0.9175.805-35.746-35.7460.0000.0000.0000.000
6A3ILE0-0.014-0.0157.3522.7202.7200.0000.0000.0000.000
7A4ARG10.9180.95310.68423.72423.7240.0000.0000.0000.000
8A5ASP-1-0.876-0.94511.416-22.355-22.3550.0000.0000.0000.000
9A6ASN0-0.0190.0049.7771.7531.7530.0000.0000.0000.000
10A7VAL00.0020.01613.6720.8350.8350.0000.0000.0000.000
11A8PHE0-0.004-0.00612.108-0.772-0.7720.0000.0000.0000.000
12A9LEU00.0020.01517.9300.8420.8420.0000.0000.0000.000
13A10ILE0-0.030-0.01020.683-0.234-0.2340.0000.0000.0000.000
14A11THR00.0360.00723.3280.6540.6540.0000.0000.0000.000
15A12GLY00.0280.00526.649-0.075-0.0750.0000.0000.0000.000
16A13GLY0-0.024-0.00926.573-0.076-0.0760.0000.0000.0000.000
17A14ALA00.0160.01127.301-0.116-0.1160.0000.0000.0000.000
18A15SER0-0.016-0.01630.0330.3020.3020.0000.0000.0000.000
19A16GLY00.0440.01229.412-0.322-0.3220.0000.0000.0000.000
20A17LEU00.0100.00926.158-0.257-0.2570.0000.0000.0000.000
21A18GLY00.0670.04824.988-0.636-0.6360.0000.0000.0000.000
22A19ALA00.0320.01424.767-0.514-0.5140.0000.0000.0000.000
23A20GLY0-0.016-0.01725.428-0.215-0.2150.0000.0000.0000.000
24A21THR0-0.011-0.04219.852-0.668-0.6680.0000.0000.0000.000
25A22ALA00.0080.00320.627-0.791-0.7910.0000.0000.0000.000
26A23ARG10.8330.90021.49310.88010.8800.0000.0000.0000.000
27A24LEU00.0030.00817.429-0.452-0.4520.0000.0000.0000.000
28A25LEU0-0.021-0.02115.318-1.024-1.0240.0000.0000.0000.000
29A26THR00.0180.00216.909-0.898-0.8980.0000.0000.0000.000
30A27GLU-1-0.950-0.96418.714-14.972-14.9720.0000.0000.0000.000
31A28ALA0-0.079-0.03913.673-0.681-0.6810.0000.0000.0000.000
32A29GLY0-0.011-0.01313.910-1.644-1.6440.0000.0000.0000.000
33A30GLY0-0.0030.01015.162-0.640-0.6400.0000.0000.0000.000
34A31LYS10.8070.89415.82519.78319.7830.0000.0000.0000.000
35A32VAL00.0210.01018.800-0.237-0.2370.0000.0000.0000.000
36A33VAL00.0090.00621.1760.5280.5280.0000.0000.0000.000
37A34LEU0-0.039-0.01323.671-0.255-0.2550.0000.0000.0000.000
38A35ALA00.0290.01326.4110.4050.4050.0000.0000.0000.000
39A36ASP-1-0.791-0.91128.380-10.154-10.1540.0000.0000.0000.000
40A37LEU00.0060.00531.6270.2050.2050.0000.0000.0000.000
41A38ASN0-0.054-0.03334.5300.3410.3410.0000.0000.0000.000
42A39GLN00.0450.01434.475-0.226-0.2260.0000.0000.0000.000
43A40ASP-1-0.882-0.93135.333-8.317-8.3170.0000.0000.0000.000
44A41ALA0-0.021-0.02334.282-0.127-0.1270.0000.0000.0000.000
45A42GLY00.0310.00331.085-0.304-0.3040.0000.0000.0000.000
46A43GLU-1-0.820-0.89930.598-10.176-10.1760.0000.0000.0000.000
47A44ALA0-0.038-0.01231.978-0.180-0.1800.0000.0000.0000.000
48A45LEU0-0.0010.00227.604-0.173-0.1730.0000.0000.0000.000
49A46ALA00.001-0.00227.173-0.438-0.4380.0000.0000.0000.000
50A47ARG10.8210.88727.4379.0789.0780.0000.0000.0000.000
51A48GLU-1-0.859-0.88828.792-10.922-10.9220.0000.0000.0000.000
52A49LEU0-0.050-0.02923.813-0.232-0.2320.0000.0000.0000.000
53A50GLY0-0.0140.00823.702-0.597-0.5970.0000.0000.0000.000
54A51GLY0-0.0140.00523.785-0.462-0.4620.0000.0000.0000.000
55A52VAL0-0.039-0.02824.6260.5320.5320.0000.0000.0000.000
56A53PHE00.0130.01626.596-0.259-0.2590.0000.0000.0000.000
57A54VAL0-0.026-0.01928.0880.1120.1120.0000.0000.0000.000
58A55ARG10.9280.97130.5778.7008.7000.0000.0000.0000.000
59A56CYS0-0.072-0.05230.533-0.063-0.0630.0000.0000.0000.000
60A57ASP-1-0.941-0.97332.640-8.836-8.8360.0000.0000.0000.000
61A58VAL00.0470.00729.691-0.001-0.0010.0000.0000.0000.000
62A59ALA0-0.0150.00631.985-0.191-0.1910.0000.0000.0000.000
63A60ARG10.8040.90034.6048.8158.8150.0000.0000.0000.000
64A61GLU-1-0.821-0.87532.641-9.898-9.8980.0000.0000.0000.000
65A62GLU-1-0.814-0.92232.227-9.022-9.0220.0000.0000.0000.000
66A63ASP-1-0.779-0.86632.697-9.263-9.2630.0000.0000.0000.000
67A64ALA00.0600.02128.713-0.329-0.3290.0000.0000.0000.000
68A65GLN0-0.022-0.00927.842-0.343-0.3430.0000.0000.0000.000
69A66ALA0-0.0010.00428.313-0.346-0.3460.0000.0000.0000.000
70A67ALA00.001-0.00126.734-0.274-0.2740.0000.0000.0000.000
71A68VAL00.0130.00022.700-0.552-0.5520.0000.0000.0000.000
72A69ALA0-0.0060.01123.791-0.530-0.5300.0000.0000.0000.000
73A70ALA0-0.006-0.00725.518-0.185-0.1850.0000.0000.0000.000
74A71ALA0-0.018-0.01620.766-0.314-0.3140.0000.0000.0000.000
75A72THR0-0.006-0.02620.219-0.360-0.3600.0000.0000.0000.000
76A73LYS10.9100.96821.60910.95810.9580.0000.0000.0000.000
77A74LEU0-0.035-0.00520.6290.0890.0890.0000.0000.0000.000
78A75GLY00.0220.00618.083-0.466-0.4660.0000.0000.0000.000
79A76THR0-0.016-0.01113.3710.2110.2110.0000.0000.0000.000
80A77LEU0-0.0020.01515.067-0.855-0.8550.0000.0000.0000.000
81A78ARG10.8220.89910.72026.80526.8050.0000.0000.0000.000
82A79GLY00.0150.00813.674-0.808-0.8080.0000.0000.0000.000
83A80LEU0-0.030-0.00315.8680.9040.9040.0000.0000.0000.000
84A81VAL00.018-0.00118.890-0.508-0.5080.0000.0000.0000.000
85A82ASN0-0.010-0.00421.2570.7780.7780.0000.0000.0000.000
86A83CYS0-0.0390.00124.846-0.080-0.0800.0000.0000.0000.000
87A84ALA0-0.0110.00826.9750.4520.4520.0000.0000.0000.000
88A85GLY0-0.008-0.01830.096-0.095-0.0950.0000.0000.0000.000
89A86ILE0-0.047-0.01533.1360.1350.1350.0000.0000.0000.000
90A87ALA00.0520.00636.556-0.107-0.1070.0000.0000.0000.000
91A88PRO0-0.0100.01538.3440.1530.1530.0000.0000.0000.000
92A89ALA00.008-0.00241.866-0.090-0.0900.0000.0000.0000.000
93A90ALA00.000-0.00344.3740.1890.1890.0000.0000.0000.000
94A91LYS10.9360.97046.7126.2196.2190.0000.0000.0000.000
95A92THR00.0190.00148.0110.0150.0150.0000.0000.0000.000
96A93VAL00.0160.01549.6190.0610.0610.0000.0000.0000.000
97A94GLY0-0.017-0.00353.159-0.061-0.0610.0000.0000.0000.000
98A95LYS10.8090.88254.0945.5975.5970.0000.0000.0000.000
99A96ASP-1-0.803-0.89956.643-5.513-5.5130.0000.0000.0000.000
100A97GLY00.0350.03756.8050.0640.0640.0000.0000.0000.000
101A98PRO0-0.005-0.00852.620-0.072-0.0720.0000.0000.0000.000
102A99HIS0-0.006-0.01145.072-0.106-0.1060.0000.0000.0000.000
103A100PRO00.0100.00248.8490.0010.0010.0000.0000.0000.000
104A101LEU00.0440.02446.686-0.163-0.1630.0000.0000.0000.000
105A102GLU-1-0.896-0.95645.312-7.321-7.3210.0000.0000.0000.000
106A103LEU00.0830.04644.054-0.192-0.1920.0000.0000.0000.000
107A104PHE00.0020.00841.840-0.246-0.2460.0000.0000.0000.000
108A105ALA00.0390.01741.334-0.239-0.2390.0000.0000.0000.000
109A106LYS10.9711.00840.3737.6107.6100.0000.0000.0000.000
110A107THR0-0.021-0.02837.914-0.253-0.2530.0000.0000.0000.000
111A108ILE0-0.002-0.00636.653-0.329-0.3290.0000.0000.0000.000
112A109THR0-0.028-0.02735.658-0.285-0.2850.0000.0000.0000.000
113A110VAL0-0.010-0.00233.715-0.225-0.2250.0000.0000.0000.000
114A111ASN0-0.034-0.01932.416-0.425-0.4250.0000.0000.0000.000
115A112LEU0-0.0210.00931.113-0.382-0.3820.0000.0000.0000.000
116A113ILE00.0050.00131.237-0.321-0.3210.0000.0000.0000.000
117A114GLY00.0390.01831.857-0.204-0.2040.0000.0000.0000.000
118A115THR0-0.019-0.02126.497-0.411-0.4110.0000.0000.0000.000
119A116PHE00.023-0.00227.079-0.462-0.4620.0000.0000.0000.000
120A117ASN0-0.064-0.03627.930-0.304-0.3040.0000.0000.0000.000
121A118MET00.0090.00925.710-0.023-0.0230.0000.0000.0000.000
122A119ILE0-0.010-0.00422.913-0.528-0.5280.0000.0000.0000.000
123A120ARG10.7740.86223.5119.8469.8460.0000.0000.0000.000
124A121VAL00.0120.00925.143-0.214-0.2140.0000.0000.0000.000
125A122ALA00.0350.01520.847-0.312-0.3120.0000.0000.0000.000
126A123ALA00.002-0.00220.095-0.757-0.7570.0000.0000.0000.000
127A124ALA0-0.026-0.01020.667-0.505-0.5050.0000.0000.0000.000
128A125ALA00.0000.00521.270-0.104-0.1040.0000.0000.0000.000
129A126MET0-0.033-0.01016.432-0.642-0.6420.0000.0000.0000.000
130A127ALA0-0.039-0.02616.742-1.123-1.1230.0000.0000.0000.000
131A128ALA0-0.025-0.00618.785-0.093-0.0930.0000.0000.0000.000
132A129ASN0-0.065-0.03413.9550.7460.7460.0000.0000.0000.000
133A130GLU-1-0.874-0.94012.943-20.682-20.6820.0000.0000.0000.000
134A131PRO0-0.033-0.0199.958-1.090-1.0900.0000.0000.0000.000
135A132ALA00.0190.0186.124-1.131-1.1310.0000.0000.0000.000
139A136GLU-1-0.771-0.8527.273-36.817-36.8170.0000.0000.0000.000
140A137ARG10.8780.9509.73318.75818.7580.0000.0000.0000.000
141A138GLY00.0340.01512.3650.2030.2030.0000.0000.0000.000
142A139VAL0-0.040-0.02011.671-0.321-0.3210.0000.0000.0000.000
143A140ILE00.0160.00414.5120.7590.7590.0000.0000.0000.000
144A141VAL00.0300.01517.2300.0370.0370.0000.0000.0000.000
145A142SER00.0380.02019.8270.7370.7370.0000.0000.0000.000
146A143THR0-0.008-0.00823.653-0.307-0.3070.0000.0000.0000.000
147A144ALA00.0410.01826.4430.4880.4880.0000.0000.0000.000
148A145SER00.011-0.01229.0280.2330.2330.0000.0000.0000.000
149A146VAL00.0390.03031.267-0.048-0.0480.0000.0000.0000.000
150A147ALA00.0120.00932.9090.1660.1660.0000.0000.0000.000
151A148ALA0-0.052-0.02231.9570.2080.2080.0000.0000.0000.000
152A149PHE0-0.055-0.03629.341-0.029-0.0290.0000.0000.0000.000
153A150ASP-1-0.742-0.83535.506-9.023-9.0230.0000.0000.0000.000
154A151GLY0-0.001-0.00537.8700.0790.0790.0000.0000.0000.000
155A152GLN0-0.018-0.00639.6330.0640.0640.0000.0000.0000.000
156A153ILE0-0.019-0.02142.5050.0710.0710.0000.0000.0000.000
157A154GLY0-0.041-0.02045.5730.0110.0110.0000.0000.0000.000
158A155GLN00.0600.02638.659-0.106-0.1060.0000.0000.0000.000
159A156ALA00.0080.01140.740-0.190-0.1900.0000.0000.0000.000
160A157ALA00.0450.02041.170-0.131-0.1310.0000.0000.0000.000
161A158TYR00.0000.00933.829-0.282-0.2820.0000.0000.0000.000
162A159ALA00.0690.04036.281-0.293-0.2930.0000.0000.0000.000
163A160ALA00.0070.01136.059-0.256-0.2560.0000.0000.0000.000
164A161SER0-0.048-0.02735.255-0.287-0.2870.0000.0000.0000.000
165A162LYS10.8840.93630.12610.15110.1510.0000.0000.0000.000
166A163ALA00.0380.01531.194-0.408-0.4080.0000.0000.0000.000
167A164GLY0-0.0030.00732.002-0.211-0.2110.0000.0000.0000.000
168A165VAL0-0.026-0.01827.134-0.282-0.2820.0000.0000.0000.000
169A166ALA00.0130.00927.410-0.453-0.4530.0000.0000.0000.000
170A167GLY00.0020.01427.378-0.418-0.4180.0000.0000.0000.000
171A168MET0-0.029-0.01826.977-0.041-0.0410.0000.0000.0000.000
172A169THR00.0040.00422.162-0.383-0.3830.0000.0000.0000.000
173A170LEU00.0470.03023.178-0.509-0.5090.0000.0000.0000.000
174A171PRO0-0.047-0.02024.144-0.328-0.3280.0000.0000.0000.000
175A172ILE00.0540.02222.448-0.182-0.1820.0000.0000.0000.000
176A173ALA00.0300.02719.906-0.482-0.4820.0000.0000.0000.000
177A174ARG10.9110.95020.16611.90111.9010.0000.0000.0000.000
178A175ASP-1-0.849-0.90022.417-12.680-12.6800.0000.0000.0000.000
179A176LEU0-0.018-0.01119.272-0.046-0.0460.0000.0000.0000.000
180A177SER0-0.018-0.01817.655-1.032-1.0320.0000.0000.0000.000
181A178ARG10.8490.92217.24812.44912.4490.0000.0000.0000.000
182A179ASN0-0.018-0.01618.1620.3300.3300.0000.0000.0000.000
183A180ALA00.0130.02112.812-0.750-0.7500.0000.0000.0000.000
184A181ILE0-0.021-0.00113.321-1.635-1.6350.0000.0000.0000.000
185A182ARG10.7370.8699.54629.09529.0950.0000.0000.0000.000
186A183VAL00.000-0.00715.2580.3000.3000.0000.0000.0000.000
187A184MET0-0.0050.02016.8080.0100.0100.0000.0000.0000.000
188A185THR0-0.021-0.02519.7550.3090.3090.0000.0000.0000.000
189A186ILE00.0160.02120.382-0.115-0.1150.0000.0000.0000.000
190A187ALA00.005-0.01023.9280.4730.4730.0000.0000.0000.000
191A188PRO0-0.013-0.00626.8570.0850.0850.0000.0000.0000.000
192A189GLY00.0140.00428.8360.3300.3300.0000.0000.0000.000
193A190ILE00.0110.00932.0520.1360.1360.0000.0000.0000.000
194A191PHE0-0.032-0.01527.174-0.189-0.1890.0000.0000.0000.000
195A192GLU-1-0.899-0.94332.375-9.089-9.0890.0000.0000.0000.000
196A193THR0-0.045-0.03031.123-0.310-0.3100.0000.0000.0000.000
197A194PRO00.0300.00133.7740.2180.2180.0000.0000.0000.000
198A195MET0-0.0360.00033.8820.1710.1710.0000.0000.0000.000
199A196LEU00.0100.00936.3890.1570.1570.0000.0000.0000.000
200A197LEU0-0.0030.00439.0210.2220.2220.0000.0000.0000.000
201A198GLY00.002-0.00241.4120.0450.0450.0000.0000.0000.000
202A199MET0-0.041-0.00240.8360.1390.1390.0000.0000.0000.000
203A200PRO0-0.0010.00543.775-0.096-0.0960.0000.0000.0000.000
204A201GLN00.004-0.02240.665-0.013-0.0130.0000.0000.0000.000
205A202GLU-1-0.884-0.93344.320-6.749-6.7490.0000.0000.0000.000
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