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: 3G3ZL

Calculation Name: 3JCU-o-Other547

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | chlorophyll b | pheophytin a | protoporphyrin ix containing fe | digalactosyl diacyl glycerol (dgdg) | 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone | (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol | (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol | (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | ca-mn4-o5 cluster | bicarbonate ion | fe (ii) ion

Ligand 3-letter code: CLA | CHL | PHO | HEM | DGD | PL9 | XAT | NEX | LUT | SQD | BCR | LMG | LHG | OEX | BCT | FE2

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JCU

Chain ID: o

ChEMBL ID:

UniProt ID: P12333

Base Structure: ElectronMicroscopy

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 242
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2729606.64165
FMO2-HF: Nuclear repulsion 2638663.784116
FMO2-HF: Total energy -90942.857535
FMO2-MP2: Total energy -91211.703148


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(o:89:ARG)


Summations of interaction energy for fragment #1(o:89:ARG)
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.
-484.76-482.83634.846-18.73-18.041-0.195
Interaction energy analysis for fragmet #1(o:89:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.622 / q_NPA : 1.772
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].
3o91THR00.1170.0653.838-0.7961.098-0.021-0.852-1.021-0.004
20o108THR0-0.040-0.0434.742-1.675-1.611-0.001-0.005-0.0580.000
23o111GLN0-0.090-0.0363.018-20.311-17.9760.181-0.968-1.549-0.008
24o112CYS00.0270.0323.1359.52010.5950.007-0.563-0.520-0.003
25o113PRO0-0.021-0.0103.385-20.963-19.8610.012-0.424-0.690-0.003
26o114THR0-0.100-0.0742.334-11.146-10.2403.375-1.436-2.845-0.016
27o115VAL00.0060.0114.6216.7406.789-0.001-0.021-0.0270.000
28o116GLU-1-0.870-0.9024.546-85.063-84.967-0.001-0.010-0.0840.000
48o137GLU-1-0.724-0.8431.675-182.305-188.93730.186-14.074-9.480-0.161
49o138PRO0-0.052-0.0235.098-4.140-4.091-0.001-0.001-0.0470.000
50o139THR0-0.051-0.0433.589-1.205-0.9570.005-0.048-0.2050.000
209o298ILE00.0050.0134.578-4.515-4.403-0.001-0.004-0.1060.000
235o324VAL0-0.0460.0012.9401.6172.2431.106-0.324-1.4090.000
4o92TYR00.0480.0056.588-0.330-0.3300.0000.0000.0000.000
5o93ASP-1-0.874-0.9389.093-41.967-41.9670.0000.0000.0000.000
6o94GLU-1-0.875-0.9227.060-66.655-66.6550.0000.0000.0000.000
7o95ILE0-0.051-0.0325.2161.7271.7270.0000.0000.0000.000
8o96GLN0-0.009-0.0039.0124.6154.6150.0000.0000.0000.000
9o97SER0-0.055-0.03311.9733.7413.7410.0000.0000.0000.000
10o98LYS10.8670.9657.08261.50461.5040.0000.0000.0000.000
11o99THR00.001-0.01912.5721.9361.9360.0000.0000.0000.000
12o100TYR00.0570.00314.122-0.740-0.7400.0000.0000.0000.000
13o101LEU0-0.052-0.04915.019-0.820-0.8200.0000.0000.0000.000
14o102GLU-1-0.816-0.88111.870-39.624-39.6240.0000.0000.0000.000
15o103VAL00.0040.0149.786-2.549-2.5490.0000.0000.0000.000
16o104LYS10.9240.97711.30029.52429.5240.0000.0000.0000.000
17o105GLY0-0.0190.00113.260-0.102-0.1020.0000.0000.0000.000
18o106THR0-0.033-0.0208.212-2.969-2.9690.0000.0000.0000.000
19o107GLY00.006-0.0108.362-4.382-4.3820.0000.0000.0000.000
21o109ALA00.0340.0156.920-3.296-3.2960.0000.0000.0000.000
22o110ASN0-0.0080.0247.2696.2256.2250.0000.0000.0000.000
29o117GLY0-0.014-0.0279.0332.8142.8140.0000.0000.0000.000
30o118GLY0-0.086-0.05011.3401.4041.4040.0000.0000.0000.000
31o119VAL0-0.003-0.01013.933-0.702-0.7020.0000.0000.0000.000
32o120ASP-1-0.816-0.89213.257-41.655-41.6550.0000.0000.0000.000
33o121SER00.0050.00414.3632.3172.3170.0000.0000.0000.000
34o122PHE00.003-0.01115.642-1.009-1.0090.0000.0000.0000.000
35o123ALA00.010-0.00217.6241.4511.4510.0000.0000.0000.000
36o124PHE0-0.0300.00216.0211.1721.1720.0000.0000.0000.000
37o125LYS10.9600.98021.35723.38523.3850.0000.0000.0000.000
38o126PRO00.0300.01724.567-0.569-0.5690.0000.0000.0000.000
39o127GLY0-0.014-0.00126.7980.4600.4600.0000.0000.0000.000
40o128LYS10.9240.95825.63019.66619.6660.0000.0000.0000.000
41o129TYR00.022-0.01820.903-0.130-0.1300.0000.0000.0000.000
42o130THR0-0.023-0.00320.908-0.029-0.0290.0000.0000.0000.000
43o131ALA00.001-0.01116.710-0.749-0.7490.0000.0000.0000.000
44o132LYS10.8600.92015.81329.24629.2460.0000.0000.0000.000
45o133LYS10.8960.97111.75442.65942.6590.0000.0000.0000.000
46o134PHE00.0300.00311.847-1.840-1.8400.0000.0000.0000.000
47o136LEU0-0.024-0.0237.365-1.949-1.9490.0000.0000.0000.000
51o140LYS10.8290.9056.40349.19849.1980.0000.0000.0000.000
52o141PHE00.0850.05310.1931.0061.0060.0000.0000.0000.000
53o142ALA0-0.044-0.02413.0320.5900.5900.0000.0000.0000.000
54o143VAL00.0200.02016.0210.4370.4370.0000.0000.0000.000
55o144LYS10.8520.90819.60422.43622.4360.0000.0000.0000.000
56o145ALA0-0.045-0.02122.6730.3060.3060.0000.0000.0000.000
57o146GLU-1-0.791-0.88925.521-19.653-19.6530.0000.0000.0000.000
58o147GLY0-0.0240.00328.6320.7090.7090.0000.0000.0000.000
59o148ILE0-0.003-0.01129.632-0.424-0.4240.0000.0000.0000.000
60o149SER0-0.011-0.00627.823-0.100-0.1000.0000.0000.0000.000
61o150LYS10.9350.95626.40320.54820.5480.0000.0000.0000.000
62o151ASN00.0450.02230.1580.1830.1830.0000.0000.0000.000
63o152SER00.0290.00232.852-0.029-0.0290.0000.0000.0000.000
64o153GLY00.0370.01230.2640.1620.1620.0000.0000.0000.000
65o154PRO0-0.0720.00725.718-0.070-0.0700.0000.0000.0000.000
66o155ASP-1-0.846-0.91222.453-22.914-22.9140.0000.0000.0000.000
67o156PHE0-0.030-0.02716.7960.0500.0500.0000.0000.0000.000
68o157GLN00.0230.01819.434-0.314-0.3140.0000.0000.0000.000
69o158ASN00.019-0.00215.0190.4470.4470.0000.0000.0000.000
70o159THR0-0.064-0.03915.3151.4771.4770.0000.0000.0000.000
71o160LYS10.8610.92115.05925.68425.6840.0000.0000.0000.000
72o161LEU00.0280.02311.4332.0202.0200.0000.0000.0000.000
73o162MET0-0.044-0.02015.1070.9800.9800.0000.0000.0000.000
74o163THR0-0.0020.00215.4870.2930.2930.0000.0000.0000.000
75o164ARG10.9500.98113.93931.85231.8520.0000.0000.0000.000
76o165LEU00.0010.0148.8610.2610.2610.0000.0000.0000.000
77o166THR0-0.020-0.03411.577-0.661-0.6610.0000.0000.0000.000
78o167TYR0-0.024-0.0096.2062.6912.6910.0000.0000.0000.000
79o168THR0-0.022-0.0256.7520.7130.7130.0000.0000.0000.000
80o169LEU0-0.0190.0109.7133.0663.0660.0000.0000.0000.000
81o170ASP-1-0.823-0.9439.668-53.885-53.8850.0000.0000.0000.000
82o171GLU-1-0.987-0.99611.548-33.553-33.5530.0000.0000.0000.000
83o172ILE0-0.0470.00213.6322.2852.2850.0000.0000.0000.000
84o173GLU-1-0.911-0.94815.900-28.993-28.9930.0000.0000.0000.000
85o174GLY0-0.011-0.03218.7540.4260.4260.0000.0000.0000.000
86o175PRO0-0.030-0.00321.117-0.521-0.5210.0000.0000.0000.000
87o176PHE00.036-0.00416.632-0.496-0.4960.0000.0000.0000.000
88o177GLU-1-0.940-0.98821.231-21.496-21.4960.0000.0000.0000.000
89o178VAL00.0040.03021.724-0.093-0.0930.0000.0000.0000.000
90o179SER0-0.001-0.00324.3811.2581.2580.0000.0000.0000.000
91o180SER0-0.021-0.04027.244-0.294-0.2940.0000.0000.0000.000
92o181ASP-1-0.892-0.92028.381-20.970-20.9700.0000.0000.0000.000
93o182GLY00.0020.00825.366-0.127-0.1270.0000.0000.0000.000
94o183THR0-0.119-0.08023.821-1.187-1.1870.0000.0000.0000.000
95o184VAL0-0.001-0.00619.9230.2350.2350.0000.0000.0000.000
96o185LYS10.9090.95023.06621.13821.1380.0000.0000.0000.000
97o186PHE00.0420.04016.4870.3020.3020.0000.0000.0000.000
98o187GLU-1-0.960-0.98120.972-22.330-22.3300.0000.0000.0000.000
99o188GLU-1-0.873-0.93318.229-27.978-27.9780.0000.0000.0000.000
100o189LYS10.8360.93120.20124.68724.6870.0000.0000.0000.000
101o190ASP-1-0.861-0.93420.450-25.180-25.1800.0000.0000.0000.000
102o191GLY00.0480.03918.074-0.265-0.2650.0000.0000.0000.000
103o192ILE0-0.029-0.02814.818-0.940-0.9400.0000.0000.0000.000
104o193ASP-1-0.658-0.80815.054-30.286-30.2860.0000.0000.0000.000
105o194TYR0-0.084-0.02716.9380.5520.5520.0000.0000.0000.000
106o195ALA00.0550.04713.956-0.248-0.2480.0000.0000.0000.000
107o196ALA0-0.027-0.01915.9870.7830.7830.0000.0000.0000.000
108o197VAL00.0000.00514.100-1.606-1.6060.0000.0000.0000.000
109o198THR0-0.033-0.03616.7992.6982.6980.0000.0000.0000.000
110o199VAL00.0250.02815.191-1.254-1.2540.0000.0000.0000.000
111o200GLN0-0.009-0.00718.1461.7831.7830.0000.0000.0000.000
112o201LEU00.0480.03420.151-1.203-1.2030.0000.0000.0000.000
113o202PRO0-0.014-0.01121.0690.4240.4240.0000.0000.0000.000
114o203GLY00.0310.00823.7910.4280.4280.0000.0000.0000.000
115o204GLY0-0.022-0.00425.4400.6710.6710.0000.0000.0000.000
116o205GLU-1-0.846-0.91725.696-21.509-21.5090.0000.0000.0000.000
117o206ARG10.9080.94522.92121.91321.9130.0000.0000.0000.000
118o207VAL00.0670.03220.2870.8210.8210.0000.0000.0000.000
119o208PRO0-0.029-0.01520.517-1.403-1.4030.0000.0000.0000.000
120o209PHE00.025-0.00215.1110.5840.5840.0000.0000.0000.000
121o210LEU00.0170.01918.133-0.843-0.8430.0000.0000.0000.000
122o211PHE0-0.0140.01010.5820.9340.9340.0000.0000.0000.000
123o212THR0-0.057-0.06515.6400.4370.4370.0000.0000.0000.000
124o213ILE00.0320.01513.280-0.284-0.2840.0000.0000.0000.000
125o214LYS10.8720.93017.71926.69026.6900.0000.0000.0000.000
126o215GLN0-0.046-0.04021.2391.0071.0070.0000.0000.0000.000
127o216LEU0-0.0240.00217.3260.4390.4390.0000.0000.0000.000
128o217VAL00.0320.01821.3770.2780.2780.0000.0000.0000.000
129o218ALA0-0.032-0.01719.0010.1950.1950.0000.0000.0000.000
130o219SER0-0.009-0.00220.9640.4340.4340.0000.0000.0000.000
131o220GLY00.0050.00322.795-0.267-0.2670.0000.0000.0000.000
132o221LYS10.9030.93421.78126.46826.4680.0000.0000.0000.000
133o222PRO00.0630.02417.951-0.735-0.7350.0000.0000.0000.000
134o223GLU-1-0.840-0.90117.154-28.984-28.9840.0000.0000.0000.000
135o224SER0-0.093-0.04517.505-1.335-1.3350.0000.0000.0000.000
136o225PHE00.0030.03316.5761.6061.6060.0000.0000.0000.000
137o226SER0-0.021-0.03018.738-1.451-1.4510.0000.0000.0000.000
138o227GLY00.0470.02620.4320.9120.9120.0000.0000.0000.000
139o228ASP-1-0.876-0.93620.871-24.059-24.0590.0000.0000.0000.000
140o229PHE0-0.015-0.01617.9440.0920.0920.0000.0000.0000.000
141o230LEU0-0.063-0.03522.3820.8870.8870.0000.0000.0000.000
142o231VAL00.0400.02220.816-1.248-1.2480.0000.0000.0000.000
143o232PRO0-0.022-0.00622.6741.0851.0850.0000.0000.0000.000
144o233SER00.010-0.00524.190-0.488-0.4880.0000.0000.0000.000
145o234TYR0-0.048-0.03420.111-0.419-0.4190.0000.0000.0000.000
146o235ARG10.7870.90524.37621.97021.9700.0000.0000.0000.000
147o236GLY00.1060.04927.8660.1140.1140.0000.0000.0000.000
148o237SER00.0760.01429.6240.1640.1640.0000.0000.0000.000
149o238SER0-0.055-0.01232.9680.4220.4220.0000.0000.0000.000
150o239PHE0-0.031-0.00930.070-0.104-0.1040.0000.0000.0000.000
151o240LEU0-0.0050.01032.8140.5200.5200.0000.0000.0000.000
152o241ASP-1-0.749-0.83734.043-16.446-16.4460.0000.0000.0000.000
153o242PRO00.003-0.02234.4450.3490.3490.0000.0000.0000.000
154o243LYS10.8450.93537.46314.69714.6970.0000.0000.0000.000
155o244GLY00.0280.01739.1760.4180.4180.0000.0000.0000.000
156o245ARG10.8660.92538.35015.35015.3500.0000.0000.0000.000
157o246GLY00.0490.01136.215-0.555-0.5550.0000.0000.0000.000
158o247GLY00.0010.01435.8560.2820.2820.0000.0000.0000.000
159o248SER0-0.038-0.03936.6440.0550.0550.0000.0000.0000.000
160o249THR0-0.0010.01237.3130.2820.2820.0000.0000.0000.000
161o250GLY0-0.001-0.01038.934-0.289-0.2890.0000.0000.0000.000
162o251TYR0-0.081-0.04541.1090.2370.2370.0000.0000.0000.000
163o252ASP-1-0.804-0.90741.536-13.636-13.6360.0000.0000.0000.000
164o253ASN00.0120.01042.930-0.265-0.2650.0000.0000.0000.000
165o254ALA0-0.011-0.01243.753-0.119-0.1190.0000.0000.0000.000
166o255VAL00.003-0.01744.8820.3240.3240.0000.0000.0000.000
167o256ALA0-0.094-0.04646.3440.2220.2220.0000.0000.0000.000
168o257LEU00.0240.01847.4830.1530.1530.0000.0000.0000.000
169o258PRO0-0.0090.00350.328-0.056-0.0560.0000.0000.0000.000
170o259ALA00.0580.02252.547-0.073-0.0730.0000.0000.0000.000
171o260GLY00.0670.03449.889-0.098-0.0980.0000.0000.0000.000
172o261GLY0-0.029-0.03547.186-0.307-0.3070.0000.0000.0000.000
173o262ARG10.8990.95447.82111.91311.9130.0000.0000.0000.000
174o263GLY0-0.052-0.00950.3430.0830.0830.0000.0000.0000.000
175o264ASP-1-0.879-0.93450.703-11.637-11.6370.0000.0000.0000.000
176o265GLU-1-0.952-0.99245.608-12.770-12.7700.0000.0000.0000.000
177o266GLU-1-0.978-0.99245.584-12.223-12.2230.0000.0000.0000.000
178o267GLU-1-0.989-0.98042.766-14.022-14.0220.0000.0000.0000.000
179o268LEU0-0.031-0.02442.053-0.377-0.3770.0000.0000.0000.000
180o269GLN00.0400.02942.018-0.257-0.2570.0000.0000.0000.000
181o270LYS10.8660.94135.76016.02316.0230.0000.0000.0000.000
182o271GLU-1-0.910-0.97337.519-16.008-16.0080.0000.0000.0000.000
183o272ASN0-0.039-0.01438.722-0.331-0.3310.0000.0000.0000.000
184o273ASN00.0320.02039.916-0.111-0.1110.0000.0000.0000.000
185o274LYS10.8290.91434.86316.41616.4160.0000.0000.0000.000
186o275ASN0-0.026-0.00734.6840.3230.3230.0000.0000.0000.000
187o276VAL0-0.027-0.01930.674-0.436-0.4360.0000.0000.0000.000
188o277ALA0-0.0050.00531.514-0.141-0.1410.0000.0000.0000.000
189o278SER0-0.030-0.03226.278-0.597-0.5970.0000.0000.0000.000
190o279SER00.0110.01226.1040.2920.2920.0000.0000.0000.000
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