Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: P2LLR

Calculation Name: 1YPH-E-Xray29

Preferred Name: Alpha-chymotrypsin

Target Type: SINGLE PROTEIN

Ligand Name: sulfate ion

ligand 3-letter code: SO4

PDB ID: 1YPH

Chain ID: E

ChEMBL ID: CHEMBL3314

UniProt ID: P00766

Base Structure: X-ray

Registration Date: 2018-09-06

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -801128.769746
FMO2-HF: Nuclear repulsion 755006.48411
FMO2-HF: Total energy -46122.285636
FMO2-MP2: Total energy -46245.960303


3D Structure
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(E:149:ALA)


Summations of interaction energy for fragment #1(E:149:ALA)
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.
-76.073-78.23716.46-8.232-6.063-0.069
Interaction energy analysis for fragmet #1(E:149:ALA)
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 : 0.891
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].
3E151THR00.0340.0262.6422.3836.5570.792-2.232-2.735-0.015
4E152PRO0-0.0370.0084.336-4.064-4.006-0.001-0.010-0.0470.000
5E153ASP-1-0.759-0.8846.746-34.204-34.2040.0000.0000.0000.000
6E154ARG10.8500.9228.75429.70429.7040.0000.0000.0000.000
7E155LEU00.0460.01311.857-1.056-1.0560.0000.0000.0000.000
8E156GLN0-0.0100.01411.7590.6470.6470.0000.0000.0000.000
9E157GLN0-0.026-0.02214.7801.0591.0590.0000.0000.0000.000
10E158ALA00.0360.00917.845-0.530-0.5300.0000.0000.0000.000
11E159SER0-0.0160.00419.7140.3650.3650.0000.0000.0000.000
12E160LEU0-0.004-0.01820.905-0.221-0.2210.0000.0000.0000.000
13E161PRO0-0.0040.02424.3620.3580.3580.0000.0000.0000.000
14E162LEU00.0570.02026.935-0.204-0.2040.0000.0000.0000.000
15E163LEU00.0320.04327.0440.2820.2820.0000.0000.0000.000
16E164SER0-0.030-0.01430.471-0.007-0.0070.0000.0000.0000.000
17E165ASN00.0740.01331.724-0.374-0.3740.0000.0000.0000.000
18E166THR0-0.025-0.02832.997-0.027-0.0270.0000.0000.0000.000
19E167ASN00.0590.02732.4180.0780.0780.0000.0000.0000.000
20E182CYS0-0.0160.01825.796-0.656-0.6560.0000.0000.0000.000
21E169LYS10.8870.94729.5798.5248.5240.0000.0000.0000.000
22E170LYS10.8870.94531.3439.6349.6340.0000.0000.0000.000
23E171TYR0-0.0270.00026.4170.1630.1630.0000.0000.0000.000
24E172TRP00.0410.02221.9150.2820.2820.0000.0000.0000.000
25E173GLY00.0050.01728.4960.1340.1340.0000.0000.0000.000
26E174THR0-0.058-0.06132.131-0.047-0.0470.0000.0000.0000.000
27E175LYS10.8700.95025.48911.93311.9330.0000.0000.0000.000
28E176ILE00.0160.01727.495-0.100-0.1000.0000.0000.0000.000
29E177LYS10.8820.91730.6479.6749.6740.0000.0000.0000.000
30E178ASP-1-0.869-0.93632.234-8.823-8.8230.0000.0000.0000.000
31E179ALA00.0540.02431.714-0.010-0.0100.0000.0000.0000.000
32E180MET0-0.0160.05427.665-0.360-0.3600.0000.0000.0000.000
33E181ILE0-0.050-0.02627.3240.4940.4940.0000.0000.0000.000
34E183ALA00.010-0.00323.9450.4380.4380.0000.0000.0000.000
35E184GLY00.0290.04222.630-0.551-0.5510.0000.0000.0000.000
36E185ALA0-0.051-0.02022.5490.6470.6470.0000.0000.0000.000
37E186SER0-0.051-0.05323.2460.2840.2840.0000.0000.0000.000
38E187GLY00.0570.03020.8680.1880.1880.0000.0000.0000.000
39E188VAL0-0.044-0.01817.944-0.860-0.8600.0000.0000.0000.000
40E189SER0-0.012-0.02115.8801.2221.2220.0000.0000.0000.000
41E190SER00.0000.01215.136-0.658-0.6580.0000.0000.0000.000
42E220CYS0-0.041-0.00211.037-1.655-1.6550.0000.0000.0000.000
43E192MET00.0610.0099.355-0.297-0.2970.0000.0000.0000.000
44E193GLY00.0110.0119.335-2.668-2.6680.0000.0000.0000.000
45E194ASP-1-0.872-0.91511.192-20.894-20.8940.0000.0000.0000.000
46E195SER0-0.001-0.00614.0521.5751.5750.0000.0000.0000.000
47E196GLY0-0.036-0.02316.666-0.205-0.2050.0000.0000.0000.000
48E197GLY00.0330.02118.1940.6360.6360.0000.0000.0000.000
49E198PRO0-0.0180.00219.3250.5250.5250.0000.0000.0000.000
50E199LEU00.0350.03321.130-0.476-0.4760.0000.0000.0000.000
51E200VAL0-0.024-0.01823.6950.5820.5820.0000.0000.0000.000
52E201CYS0-0.0120.00126.431-0.143-0.1430.0000.0000.0000.000
53E202LYS10.9410.98729.4839.9779.9770.0000.0000.0000.000
54E203LYS10.9360.95731.9518.5188.5180.0000.0000.0000.000
55E204ASN00.010-0.00435.4740.0410.0410.0000.0000.0000.000
56E205GLY00.0480.03936.0890.0850.0850.0000.0000.0000.000
57E206ALA0-0.016-0.00433.313-0.149-0.1490.0000.0000.0000.000
58E207TRP0-0.012-0.01827.4890.0090.0090.0000.0000.0000.000
59E208THR00.0200.01230.6110.1700.1700.0000.0000.0000.000
60E209LEU00.007-0.00324.896-0.236-0.2360.0000.0000.0000.000
61E210VAL0-0.040-0.02227.7970.3650.3650.0000.0000.0000.000
62E211GLY00.0400.01325.7630.3030.3030.0000.0000.0000.000
63E212ILE0-0.0050.01022.358-0.146-0.1460.0000.0000.0000.000
64E213VAL0-0.031-0.01416.9340.3220.3220.0000.0000.0000.000
65E214SER0-0.043-0.01620.206-0.147-0.1470.0000.0000.0000.000
66E215TRP00.018-0.00719.238-0.293-0.2930.0000.0000.0000.000
67E216GLY00.023-0.00319.2860.3970.3970.0000.0000.0000.000
68E217SER0-0.038-0.01817.894-0.547-0.5470.0000.0000.0000.000
69E218SER00.0450.03216.783-1.488-1.4880.0000.0000.0000.000
70E219THR0-0.066-0.04513.900-1.471-1.4710.0000.0000.0000.000
71E221SER00.0690.04915.061-0.415-0.4150.0000.0000.0000.000
72E222THR00.018-0.00516.4560.9780.9780.0000.0000.0000.000
73E223SER0-0.025-0.01319.0810.5400.5400.0000.0000.0000.000
74E224THR00.0010.01821.0400.8490.8490.0000.0000.0000.000
75E225PRO0-0.0130.00421.652-0.597-0.5970.0000.0000.0000.000
76E226GLY00.1060.06920.831-0.210-0.2100.0000.0000.0000.000
77E227VAL0-0.001-0.01321.5250.8100.8100.0000.0000.0000.000
78E228TYR0-0.0150.00419.665-0.473-0.4730.0000.0000.0000.000
79E229ALA00.0300.01224.2440.5350.5350.0000.0000.0000.000
80E230ARG10.7810.87426.6909.4569.4560.0000.0000.0000.000
81E231VAL00.0500.01828.0810.3210.3210.0000.0000.0000.000
82E232THR0-0.012-0.03430.7130.1640.1640.0000.0000.0000.000
83E233ALA0-0.057-0.02233.1770.2860.2860.0000.0000.0000.000
84E234LEU00.0090.00029.6450.1280.1280.0000.0000.0000.000
85E235VAL00.0080.02033.5720.0260.0260.0000.0000.0000.000
86E236ASN00.013-0.00434.7800.0810.0810.0000.0000.0000.000
87E237TRP00.0130.01930.775-0.076-0.0760.0000.0000.0000.000
88E238VAL00.0040.01431.6770.0040.0040.0000.0000.0000.000
89E239GLN00.0100.00534.4890.1430.1430.0000.0000.0000.000
90E240GLN00.0610.05337.7390.0490.0490.0000.0000.0000.000
91E241THR00.0610.03634.1870.1460.1460.0000.0000.0000.000
92E242LEU0-0.040-0.02733.5580.0250.0250.0000.0000.0000.000
93E243ALA0-0.030-0.00837.3180.1110.1110.0000.0000.0000.000
94E244ALA0-0.075-0.03240.2860.1810.1810.0000.0000.0000.000
95E245ASN-1-0.906-0.92737.245-7.911-7.9110.0000.0000.0000.000
96C1303SO4-2-1.817-1.90235.308-16.785-16.7850.0000.0000.0000.000
97E1300SO4-2-1.640-1.78821.033-28.344-28.3440.0000.0000.0000.000
98F1301SO4-2-1.721-1.85122.021-25.954-25.9540.0000.0000.0000.000
99A368HOH00.0230.01329.983-0.004-0.0040.0000.0000.0000.000
100C1306HOH00.0350.01726.125-0.148-0.1480.0000.0000.0000.000
101C1307HOH0-0.046-0.02515.6870.3560.3560.0000.0000.0000.000
102C1310HOH00.0350.02615.9630.2160.2160.0000.0000.0000.000
103C1323HOH0-0.027-0.02213.048-0.524-0.5240.0000.0000.0000.000
104C1328HOH00.0350.01313.908-0.152-0.1520.0000.0000.0000.000
105C1331HOH00.0200.01637.252-0.039-0.0390.0000.0000.0000.000
106C1334HOH0-0.019-0.01627.2730.1050.1050.0000.0000.0000.000
107C1344HOH0-0.050-0.02435.5940.0190.0190.0000.0000.0000.000
108C1384HOH00.0260.02129.3400.0150.0150.0000.0000.0000.000
109C1394HOH00.0190.00639.344-0.050-0.0500.0000.0000.0000.000
110C1434HOH00.0380.03236.3470.0410.0410.0000.0000.0000.000
111C1439HOH00.0380.01711.776-0.409-0.4090.0000.0000.0000.000
112E1301HOH0-0.006-0.00828.160-0.155-0.1550.0000.0000.0000.000
113E1302HOH0-0.033-0.02422.3160.1050.1050.0000.0000.0000.000
114E1303HOH00.0060.00230.6560.1100.1100.0000.0000.0000.000
115E1304HOH00.006-0.00320.1600.3190.3190.0000.0000.0000.000
116E1305HOH00.0070.00013.4840.4890.4890.0000.0000.0000.000
117E1306HOH0-0.006-0.00136.9910.0220.0220.0000.0000.0000.000
118E1307HOH00.0210.01622.458-0.124-0.1240.0000.0000.0000.000
119E1308HOH0-0.011-0.02330.276-0.147-0.1470.0000.0000.0000.000
120E1310HOH0-0.038-0.02639.931-0.055-0.0550.0000.0000.0000.000
121E1311HOH0-0.016-0.01532.6090.0220.0220.0000.0000.0000.000
122E1312HOH0-0.017-0.01036.1330.0060.0060.0000.0000.0000.000
123E1313HOH0-0.016-0.01219.806-0.334-0.3340.0000.0000.0000.000
124E1314HOH00.0390.02636.136-0.085-0.0850.0000.0000.0000.000
125E1315HOH0-0.039-0.02614.810-0.256-0.2560.0000.0000.0000.000
126E1316HOH00.0210.01513.849-0.053-0.0530.0000.0000.0000.000
127E1317HOH00.0190.0146.772-1.804-1.8040.0000.0000.0000.000
128E1318HOH0-0.050-0.03234.9700.0000.0000.0000.0000.0000.000
129E1319HOH00.0090.00636.293-0.113-0.1130.0000.0000.0000.000
130E1320HOH0-0.010-0.03420.030-0.086-0.0860.0000.0000.0000.000
131E1322HOH00.0250.00532.1850.0760.0760.0000.0000.0000.000
132E1323HOH0-0.023-0.01913.845-0.302-0.3020.0000.0000.0000.000
133E1324HOH0-0.038-0.0247.407-0.587-0.5870.0000.0000.0000.000
134E1325HOH00.0100.00534.506-0.056-0.0560.0000.0000.0000.000
135E1326HOH00.0310.03236.366-0.047-0.0470.0000.0000.0000.000
136E1327HOH00.0160.01523.0430.1860.1860.0000.0000.0000.000
137E1328HOH0-0.019-0.01613.9020.0410.0410.0000.0000.0000.000
138E1329HOH0-0.017-0.02220.3940.2160.2160.0000.0000.0000.000
139E1330HOH0-0.005-0.00516.137-0.275-0.2750.0000.0000.0000.000
140E1332HOH00.0430.04318.1060.0870.0870.0000.0000.0000.000
141E1333HOH00.0150.00715.595-0.484-0.4840.0000.0000.0000.000
142E1334HOH00.000-0.00532.268-0.127-0.1270.0000.0000.0000.000
143E1335HOH0-0.031-0.02441.6530.0400.0400.0000.0000.0000.000
144E1336HOH0-0.040-0.05619.5500.1270.1270.0000.0000.0000.000
145E1337HOH00.000-0.00623.8180.1240.1240.0000.0000.0000.000
146E1338HOH00.0180.01718.1670.3040.3040.0000.0000.0000.000
147E1339HOH00.0300.01735.941-0.030-0.0300.0000.0000.0000.000
148E1345HOH00.0150.01034.4710.0200.0200.0000.0000.0000.000
149E1346HOH0-0.032-0.02425.6820.2010.2010.0000.0000.0000.000
150E1347HOH00.0180.01321.491-0.192-0.1920.0000.0000.0000.000
151E1348HOH0-0.022-0.02820.658-0.354-0.3540.0000.0000.0000.000
152E1349HOH00.0280.02137.4110.0580.0580.0000.0000.0000.000
153E1350HOH00.0140.01242.255-0.037-0.0370.0000.0000.0000.000
154E1354HOH00.0150.02434.7750.0480.0480.0000.0000.0000.000
155E1355HOH0-0.028-0.02139.1040.0010.0010.0000.0000.0000.000
156E1356HOH0-0.038-0.02435.614-0.046-0.0460.0000.0000.0000.000
157E1359HOH0-0.036-0.02640.758-0.062-0.0620.0000.0000.0000.000
158E1361HOH0-0.030-0.0195.2943.5823.5820.0000.0000.0000.000
159E1363HOH00.0400.03232.5390.0530.0530.0000.0000.0000.000
160E1367HOH00.0150.01325.487-0.028-0.0280.0000.0000.0000.000
161E1368HOH00.0250.02822.097-0.013-0.0130.0000.0000.0000.000
162E1369HOH00.0040.00227.0710.1940.1940.0000.0000.0000.000
163E1370HOH00.0520.0391.704-24.143-31.87515.581-5.163-2.686-0.049
164E1371HOH0-0.036-0.03633.100-0.115-0.1150.0000.0000.0000.000
165E1373HOH00.0020.01218.906-0.302-0.3020.0000.0000.0000.000
166E1375HOH00.0330.02737.567-0.108-0.1080.0000.0000.0000.000
167E1376HOH0-0.012-0.02134.801-0.105-0.1050.0000.0000.0000.000
168E1377HOH00.0340.02036.576-0.102-0.1020.0000.0000.0000.000
169E1378HOH0-0.053-0.03736.7840.0960.0960.0000.0000.0000.000
170E1380HOH00.0100.01216.0050.4520.4520.0000.0000.0000.000
171E1383HOH00.0070.00038.013-0.057-0.0570.0000.0000.0000.000
172E1384HOH0-0.029-0.02313.089-0.053-0.0530.0000.0000.0000.000
173E1385HOH0-0.029-0.02039.1740.0830.0830.0000.0000.0000.000
174E1386HOH0-0.037-0.02325.3980.1500.1500.0000.0000.0000.000
175E1391HOH0-0.037-0.02928.6110.1570.1570.0000.0000.0000.000
176E1394HOH0-0.019-0.01632.007-0.075-0.0750.0000.0000.0000.000
177E1396HOH0-0.012-0.0103.8444.9515.2100.000-0.137-0.1220.000
178E1397HOH0-0.032-0.02037.164-0.089-0.0890.0000.0000.0000.000
179E1400HOH00.0220.01640.3790.0000.0000.0000.0000.0000.000
180E1402HOH0-0.026-0.02130.1760.1360.1360.0000.0000.0000.000
181E1406HOH0-0.003-0.00226.1010.1840.1840.0000.0000.0000.000
182E1407HOH0-0.080-0.05037.815-0.016-0.0160.0000.0000.0000.000
183E1408HOH0-0.033-0.0309.6020.1580.1580.0000.0000.0000.000
184E1412HOH0-0.030-0.01538.345-0.009-0.0090.0000.0000.0000.000
185E1413HOH0-0.022-0.02524.0590.1920.1920.0000.0000.0000.000
186E1414HOH0-0.021-0.01728.7200.0360.0360.0000.0000.0000.000
187E1415HOH0-0.026-0.01436.890-0.085-0.0850.0000.0000.0000.000
188E1416HOH0-0.016-0.01329.2250.1580.1580.0000.0000.0000.000
189E1417HOH0-0.053-0.03615.7910.4350.4350.0000.0000.0000.000
190E1418HOH0-0.029-0.0184.240-4.502-4.4380.000-0.027-0.0360.000
191E1419HOH00.0230.0258.5800.4180.4180.0000.0000.0000.000
192E1423HOH0-0.045-0.04338.5020.0160.0160.0000.0000.0000.000
193E1425HOH0-0.018-0.01438.964-0.026-0.0260.0000.0000.0000.000
194D2309HOH00.0380.0213.260-7.394-6.3810.088-0.663-0.437-0.005
195D2452HOH0-0.017-0.0097.9650.8250.8250.0000.0000.0000.000
196F1352HOH0-0.061-0.04623.8010.1570.1570.0000.0000.0000.000