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: 9R3G2

Calculation Name: 4ZJU-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nicotinamide-adenine-dinucleotide

Ligand 3-letter code: NAD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4ZJU

Chain ID: A

ChEMBL ID:

UniProt ID:

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 260
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3229805.801465
FMO2-HF: Nuclear repulsion 3132210.008387
FMO2-HF: Total energy -97595.793078
FMO2-MP2: Total energy -97879.840933


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:3:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-52.777-50.0433.471-2.81-3.395-0.011
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.816 / q_NPA : 0.895
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].
3A5LEU0-0.011-0.0102.948-2.3980.5880.144-1.541-1.589-0.011
5A7ALA00.0090.0142.4010.7190.3153.327-1.237-1.6860.000
6A8GLY0-0.0050.0114.1953.2633.4150.000-0.032-0.1200.000
4A6LEU0-0.049-0.0245.3975.2715.2710.0000.0000.0000.000
7A9LYS10.8420.9327.18126.07426.0740.0000.0000.0000.000
8A10ARG10.7910.8899.42616.73816.7380.0000.0000.0000.000
9A11PHE00.0270.00110.6050.6280.6280.0000.0000.0000.000
10A12LEU00.0230.02015.258-0.029-0.0290.0000.0000.0000.000
11A13ILE0-0.045-0.02416.5240.2480.2480.0000.0000.0000.000
12A14ALA00.0560.03220.4270.4010.4010.0000.0000.0000.000
13A15GLY00.0520.01424.2360.0160.0160.0000.0000.0000.000
14A16VAL0-0.050-0.02822.1300.0660.0660.0000.0000.0000.000
15A17ALA0-0.009-0.00225.4050.3300.3300.0000.0000.0000.000
16A18SER0-0.038-0.03227.2090.3090.3090.0000.0000.0000.000
17A19LYS11.0331.01624.15611.62111.6210.0000.0000.0000.000
18A20LEU0-0.007-0.00324.619-0.223-0.2230.0000.0000.0000.000
19A21SER0-0.0170.00025.1280.3020.3020.0000.0000.0000.000
20A22ILE00.0730.02823.119-0.501-0.5010.0000.0000.0000.000
21A23ALA00.0290.01321.582-0.641-0.6410.0000.0000.0000.000
22A24TYR0-0.039-0.01720.229-0.668-0.6680.0000.0000.0000.000
23A25GLY00.0580.03318.874-0.791-0.7910.0000.0000.0000.000
24A26ILE0-0.011-0.01517.079-1.015-1.0150.0000.0000.0000.000
25A27ALA0-0.0060.01315.748-1.195-1.1950.0000.0000.0000.000
26A28GLN00.027-0.00414.446-0.889-0.8890.0000.0000.0000.000
27A29ALA0-0.041-0.01013.025-1.855-1.8550.0000.0000.0000.000
28A30LEU00.007-0.01211.391-2.232-2.2320.0000.0000.0000.000
29A31HIS00.0180.0099.898-2.570-2.5700.0000.0000.0000.000
30A32ARG10.8070.8958.75325.42725.4270.0000.0000.0000.000
31A33GLU-1-0.840-0.9096.576-45.514-45.5140.0000.0000.0000.000
32A34GLY0-0.016-0.0195.357-5.501-5.5010.0000.0000.0000.000
33A35ALA0-0.0210.0016.3361.0241.0240.0000.0000.0000.000
34A36GLU-1-0.895-0.9509.130-21.664-21.6640.0000.0000.0000.000
35A37LEU0-0.056-0.02911.7790.9020.9020.0000.0000.0000.000
36A38ALA00.0220.03915.2540.4640.4640.0000.0000.0000.000
37A39PHE00.008-0.01017.594-0.060-0.0600.0000.0000.0000.000
38A40THR00.0330.01721.9990.2400.2400.0000.0000.0000.000
39A41TYR0-0.017-0.01425.667-0.109-0.1090.0000.0000.0000.000
40A42PRO00.0040.01128.7880.2110.2110.0000.0000.0000.000
41A43ASN00.0750.01731.9270.3390.3390.0000.0000.0000.000
42A44GLU-1-0.824-0.92133.438-9.384-9.3840.0000.0000.0000.000
43A45LYS10.9130.95534.2967.7527.7520.0000.0000.0000.000
44A46LEU0-0.027-0.01430.116-0.062-0.0620.0000.0000.0000.000
45A47LYS10.8630.96228.65810.22710.2270.0000.0000.0000.000
46A48LYS10.9750.98228.5699.1319.1310.0000.0000.0000.000
47A49ARG10.9350.97028.0629.4489.4480.0000.0000.0000.000
48A50VAL0-0.0040.00124.428-0.451-0.4510.0000.0000.0000.000
49A51ASP-1-0.811-0.90423.930-11.641-11.6410.0000.0000.0000.000
50A52GLU-1-0.938-0.97323.472-11.602-11.6020.0000.0000.0000.000
51A53PHE0-0.087-0.06422.075-0.338-0.3380.0000.0000.0000.000
52A54ALA00.0110.01819.656-0.746-0.7460.0000.0000.0000.000
53A55GLU-1-0.843-0.90418.458-15.628-15.6280.0000.0000.0000.000
54A56GLN0-0.057-0.02718.276-0.887-0.8870.0000.0000.0000.000
55A57PHE0-0.046-0.02314.775-0.678-0.6780.0000.0000.0000.000
56A58GLY00.0040.01414.429-1.055-1.0550.0000.0000.0000.000
57A59SER0-0.022-0.02215.6820.4710.4710.0000.0000.0000.000
58A60LYS10.8900.91217.64414.43314.4330.0000.0000.0000.000
59A61LEU0-0.0270.00817.2160.7370.7370.0000.0000.0000.000
60A62VAL0-0.009-0.00620.988-0.191-0.1910.0000.0000.0000.000
61A63PHE00.0100.00121.8960.3580.3580.0000.0000.0000.000
62A64PRO0-0.0150.00126.927-0.134-0.1340.0000.0000.0000.000
63A65CYS0-0.026-0.03728.661-0.129-0.1290.0000.0000.0000.000
64A66ASP-1-0.868-0.92530.659-8.706-8.7060.0000.0000.0000.000
65A67VAL0-0.052-0.04030.2320.0500.0500.0000.0000.0000.000
66A68ALA0-0.021-0.00633.1790.1020.1020.0000.0000.0000.000
67A69VAL0-0.034-0.01335.6680.2760.2760.0000.0000.0000.000
68A70ASP-1-0.850-0.93034.913-8.313-8.3130.0000.0000.0000.000
69A71ALA00.0250.00034.091-0.242-0.2420.0000.0000.0000.000
70A72GLU-1-0.866-0.93232.704-9.040-9.0400.0000.0000.0000.000
71A73ILE0-0.039-0.01429.249-0.429-0.4290.0000.0000.0000.000
72A74ASP-1-0.895-0.95529.292-9.365-9.3650.0000.0000.0000.000
73A75ASN0-0.077-0.03829.940-0.296-0.2960.0000.0000.0000.000
74A76ALA00.0470.02326.752-0.270-0.2700.0000.0000.0000.000
75A77PHE0-0.015-0.01822.600-0.582-0.5820.0000.0000.0000.000
76A78ALA0-0.0030.00525.414-0.286-0.2860.0000.0000.0000.000
77A79GLU-1-0.841-0.91426.700-10.270-10.2700.0000.0000.0000.000
78A80LEU0-0.020-0.00119.400-0.323-0.3230.0000.0000.0000.000
79A81ALA00.0160.00021.747-0.536-0.5360.0000.0000.0000.000
80A82LYS10.7550.87623.57210.23510.2350.0000.0000.0000.000
81A83HIS0-0.046-0.01719.483-0.412-0.4120.0000.0000.0000.000
82A84TRP0-0.051-0.04015.072-0.791-0.7910.0000.0000.0000.000
83A85ASP-1-0.801-0.88016.972-15.035-15.0350.0000.0000.0000.000
84A86GLY00.0260.00517.5230.2480.2480.0000.0000.0000.000
85A87VAL0-0.077-0.03315.862-0.853-0.8530.0000.0000.0000.000
86A88ASP-1-0.697-0.84811.497-20.090-20.0900.0000.0000.0000.000
87A89GLY00.0500.01214.4110.2010.2010.0000.0000.0000.000
88A90VAL0-0.035-0.00716.910-0.136-0.1360.0000.0000.0000.000
89A91VAL00.0150.00718.0830.3100.3100.0000.0000.0000.000
90A92HIS10.8490.91120.91910.84010.8400.0000.0000.0000.000
91A93SER0-0.046-0.03723.6000.2100.2100.0000.0000.0000.000
92A94ILE00.001-0.00325.5620.1450.1450.0000.0000.0000.000
93A95GLY0-0.019-0.02129.1330.0330.0330.0000.0000.0000.000
94A96PHE0-0.051-0.02132.669-0.072-0.0720.0000.0000.0000.000
95A97ALA00.0970.04236.1350.0690.0690.0000.0000.0000.000
96A98PRO0-0.0060.01339.832-0.064-0.0640.0000.0000.0000.000
97A99ALA00.0210.01442.6390.0510.0510.0000.0000.0000.000
98A100HIS00.003-0.01343.536-0.070-0.0700.0000.0000.0000.000
99A101THR0-0.012-0.00843.3650.0210.0210.0000.0000.0000.000
100A102LEU0-0.076-0.04039.653-0.040-0.0400.0000.0000.0000.000
101A103ASP-1-0.967-0.98343.888-6.733-6.7330.0000.0000.0000.000
102A104GLY00.0440.02646.9320.1150.1150.0000.0000.0000.000
103A105ASP-1-0.829-0.92348.853-6.238-6.2380.0000.0000.0000.000
104A106PHE00.002-0.00145.348-0.023-0.0230.0000.0000.0000.000
105A107THR0-0.042-0.01849.005-0.055-0.0550.0000.0000.0000.000
106A108ASP-1-0.931-0.95152.217-5.702-5.7020.0000.0000.0000.000
107A109VAL0-0.083-0.03347.8160.0230.0230.0000.0000.0000.000
108A110THR0-0.081-0.05046.384-0.208-0.2080.0000.0000.0000.000
109A111ASP-1-0.773-0.87148.529-6.422-6.4220.0000.0000.0000.000
110A112ARG10.9460.95648.0345.9205.9200.0000.0000.0000.000
111A113ASP-1-0.896-0.95746.169-6.908-6.9080.0000.0000.0000.000
112A114GLY00.0310.00144.748-0.196-0.1960.0000.0000.0000.000
113A115PHE00.003-0.00843.328-0.212-0.2120.0000.0000.0000.000
114A116LYS10.8610.93741.3167.1667.1660.0000.0000.0000.000
115A117ILE0-0.007-0.01639.914-0.231-0.2310.0000.0000.0000.000
116A118ALA00.0310.02638.815-0.238-0.2380.0000.0000.0000.000
117A119HIS0-0.026-0.03637.387-0.331-0.3310.0000.0000.0000.000
118A120ASP-1-0.864-0.90736.828-8.124-8.1240.0000.0000.0000.000
119A121ILE00.0480.01634.281-0.268-0.2680.0000.0000.0000.000
120A122SER0-0.0110.00632.944-0.437-0.4370.0000.0000.0000.000
121A123ALA0-0.025-0.00432.258-0.303-0.3030.0000.0000.0000.000
122A124TYR00.0050.01532.762-0.260-0.2600.0000.0000.0000.000
123A125SER00.0590.00631.404-0.272-0.2720.0000.0000.0000.000
124A126PHE0-0.021-0.01624.625-0.285-0.2850.0000.0000.0000.000
125A127VAL00.0140.00428.650-0.233-0.2330.0000.0000.0000.000
126A128ALA0-0.026-0.00130.853-0.053-0.0530.0000.0000.0000.000
127A129MET00.018-0.00424.810-0.092-0.0920.0000.0000.0000.000
128A130ALA00.0080.00825.899-0.273-0.2730.0000.0000.0000.000
129A131ARG10.9030.95026.8398.6618.6610.0000.0000.0000.000
130A132ALA00.0170.01028.297-0.042-0.0420.0000.0000.0000.000
131A133ALA00.0030.00422.885-0.208-0.2080.0000.0000.0000.000
132A134LYS10.8590.93923.2969.6869.6860.0000.0000.0000.000
133A135PRO00.0330.01323.652-0.287-0.2870.0000.0000.0000.000
134A136LEU00.0020.00620.210-0.319-0.3190.0000.0000.0000.000
135A137LEU0-0.0210.00318.907-0.695-0.6950.0000.0000.0000.000
136A138GLN0-0.014-0.04019.111-0.367-0.3670.0000.0000.0000.000
137A139ALA0-0.0300.00119.104-0.162-0.1620.0000.0000.0000.000
138A140ARG10.7850.87510.73919.06619.0660.0000.0000.0000.000
139A141GLN0-0.0320.00315.032-0.905-0.9050.0000.0000.0000.000
140A142GLY00.0000.01915.965-0.503-0.5030.0000.0000.0000.000
141A143CYS0-0.116-0.05615.9780.4570.4570.0000.0000.0000.000
142A144LEU00.0160.01118.743-0.121-0.1210.0000.0000.0000.000
143A145LEU0-0.0070.00518.9150.0370.0370.0000.0000.0000.000
144A146THR00.0080.01221.7710.1530.1530.0000.0000.0000.000
145A147LEU00.0020.00422.909-0.203-0.2030.0000.0000.0000.000
146A148THR0-0.021-0.04326.4850.4930.4930.0000.0000.0000.000
147A149TYR0-0.004-0.01129.437-0.169-0.1690.0000.0000.0000.000
148A150GLN00.0420.01432.1860.4390.4390.0000.0000.0000.000
149A151GLY0-0.032-0.01434.6200.2060.2060.0000.0000.0000.000
150A152SER0-0.074-0.04634.0500.2510.2510.0000.0000.0000.000
151A153GLU-1-0.913-0.95235.308-8.184-8.1840.0000.0000.0000.000
152A154ARG10.8630.93837.4408.3768.3760.0000.0000.0000.000
153A155VAL00.0250.01840.042-0.110-0.1100.0000.0000.0000.000
154A156MET0-0.0060.01337.1020.0300.0300.0000.0000.0000.000
155A157PRO0-0.015-0.02840.9370.0950.0950.0000.0000.0000.000
156A158ASN0-0.049-0.02941.281-0.046-0.0460.0000.0000.0000.000
157A159TYR00.0430.03134.281-0.180-0.1800.0000.0000.0000.000
158A160ASN00.0200.00240.795-0.083-0.0830.0000.0000.0000.000
159A161VAL00.0630.03242.018-0.102-0.1020.0000.0000.0000.000
160A162MET0-0.012-0.00434.844-0.092-0.0920.0000.0000.0000.000
161A163GLY00.0220.01537.409-0.246-0.2460.0000.0000.0000.000
162A164MET0-0.030-0.00338.249-0.089-0.0890.0000.0000.0000.000
163A165ALA00.0340.02036.949-0.101-0.1010.0000.0000.0000.000
164A166LYS10.8430.92330.4939.5859.5850.0000.0000.0000.000
165A167ALA00.0850.03634.050-0.207-0.2070.0000.0000.0000.000
166A168SER0-0.065-0.01935.859-0.114-0.1140.0000.0000.0000.000
167A169LEU0-0.027-0.01229.315-0.141-0.1410.0000.0000.0000.000
168A170GLU-1-0.795-0.86930.694-9.717-9.7170.0000.0000.0000.000
169A171ALA0-0.033-0.01131.931-0.097-0.0970.0000.0000.0000.000
170A172GLY00.0190.00632.276-0.038-0.0380.0000.0000.0000.000
171A173VAL0-0.026-0.01026.621-0.144-0.1440.0000.0000.0000.000
172A174ARG10.9921.00628.5638.9268.9260.0000.0000.0000.000
173A175TYR0-0.009-0.00730.8280.0240.0240.0000.0000.0000.000
174A176LEU0-0.014-0.01127.7790.0280.0280.0000.0000.0000.000
175A177ALA00.0060.00726.382-0.157-0.1570.0000.0000.0000.000
176A178SER0-0.037-0.02027.397-0.056-0.0560.0000.0000.0000.000
177A179SER0-0.082-0.02830.1820.0890.0890.0000.0000.0000.000
178A180LEU00.010-0.00725.1940.0550.0550.0000.0000.0000.000
179A181GLY00.0510.03924.371-0.319-0.3190.0000.0000.0000.000
180A182VAL0-0.046-0.02524.648-0.185-0.1850.0000.0000.0000.000
181A183ASP-1-0.848-0.90323.534-10.498-10.4980.0000.0000.0000.000
182A184GLY00.0030.00020.632-0.434-0.4340.0000.0000.0000.000
183A185ILE0-0.056-0.01819.938-0.533-0.5330.0000.0000.0000.000
184A186ARG10.8240.92315.66716.17816.1780.0000.0000.0000.000
185A187VAL0-0.013-0.01021.327-0.289-0.2890.0000.0000.0000.000
186A188ASN00.003-0.00820.6250.6500.6500.0000.0000.0000.000
187A189ALA00.002-0.01023.8170.0070.0070.0000.0000.0000.000
188A190ILE00.0010.01020.554-0.250-0.2500.0000.0000.0000.000
189A191SER0-0.0150.00125.0070.2960.2960.0000.0000.0000.000
190A192ALA00.0050.00026.668-0.174-0.1740.0000.0000.0000.000
191A193GLY00.0270.00728.1220.4540.4540.0000.0000.0000.000
192A194PRO0-0.056-0.01730.146-0.159-0.1590.0000.0000.0000.000
193A195ILE00.0490.02126.165-0.105-0.1050.0000.0000.0000.000
194A196ARG10.8880.94130.4509.2529.2520.0000.0000.0000.000
195A197THR00.0530.03028.540-0.150-0.1500.0000.0000.0000.000
196A198LEU00.007-0.00930.7560.3190.3190.0000.0000.0000.000
197A199ALA00.0320.01532.7530.3110.3110.0000.0000.0000.000
198A200ALA00.0140.02434.4860.2600.2600.0000.0000.0000.000
199A201SER0-0.038-0.02136.2100.2280.2280.0000.0000.0000.000
200A202GLY00.0220.00937.7210.1510.1510.0000.0000.0000.000
201A203ILE00.0500.03139.6230.2700.2700.0000.0000.0000.000
202A204LYS10.9220.95041.2357.0657.0650.0000.0000.0000.000
203A205SER0-0.007-0.00243.3320.0080.0080.0000.0000.0000.000
204A206PHE00.0720.02733.8290.0140.0140.0000.0000.0000.000
205A207ARG10.9230.96038.5217.4147.4140.0000.0000.0000.000
206A208LYS10.9320.96639.5057.0377.0370.0000.0000.0000.000
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