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

tag_button

FMODB ID: 5J7YZ

Calculation Name: 2FY8-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FY8

Chain ID: H

ChEMBL ID:

UniProt ID: O27564

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2439397.247903
FMO2-HF: Nuclear repulsion 2352911.447588
FMO2-HF: Total energy -86485.800315
FMO2-MP2: Total energy -86737.453844


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(H:115:SER)


Summations of interaction energy for fragment #1(H:115:SER)
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.
-15.228-10.5255.793-5.196-5.299-0.039
Interaction energy analysis for fragmet #1(H:115:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : 0.001
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].
3H117HIS00.0210.0292.600-1.7612.1930.572-2.235-2.291-0.005
4H118VAL0-0.0090.0034.957-1.516-1.507-0.001-0.003-0.0050.000
5H119VAL00.0060.0017.2740.2450.2450.0000.0000.0000.000
6H120ILE00.0050.0069.804-0.047-0.0470.0000.0000.0000.000
7H121CYS0-0.032-0.00913.6000.0370.0370.0000.0000.0000.000
8H122GLY00.0860.02715.8040.0020.0020.0000.0000.0000.000
9H123TRP0-0.054-0.05518.6030.0250.0250.0000.0000.0000.000
10H124SER00.0590.02821.2480.0040.0040.0000.0000.0000.000
11H125GLU-1-0.753-0.89122.880-0.024-0.0240.0000.0000.0000.000
12H126SER00.006-0.01522.0630.0240.0240.0000.0000.0000.000
13H127THR0-0.034-0.01417.688-0.007-0.0070.0000.0000.0000.000
14H128LEU0-0.059-0.02619.2760.0240.0240.0000.0000.0000.000
15H129GLU-1-0.861-0.93821.1800.0490.0490.0000.0000.0000.000
16H130CYS0-0.024-0.01415.928-0.002-0.0020.0000.0000.0000.000
17H131LEU0-0.042-0.03415.2310.0320.0320.0000.0000.0000.000
18H132ARG10.6890.83817.592-0.039-0.0390.0000.0000.0000.000
19H133GLU-1-0.756-0.87118.7320.1430.1430.0000.0000.0000.000
20H134LEU0-0.056-0.02612.3350.0410.0410.0000.0000.0000.000
21H135ARG10.9100.95814.317-0.149-0.1490.0000.0000.0000.000
22H136GLY0-0.035-0.02214.7790.0090.0090.0000.0000.0000.000
23H137SER0-0.055-0.03510.2060.0980.0980.0000.0000.0000.000
24H138GLU-1-0.896-0.9317.5921.3621.3620.0000.0000.0000.000
25H139VAL00.0280.0078.647-0.086-0.0860.0000.0000.0000.000
26H140PHE0-0.021-0.0047.554-0.010-0.0100.0000.0000.0000.000
27H141VAL00.0120.00711.433-0.107-0.1070.0000.0000.0000.000
28H142LEU0-0.021-0.00314.2650.0360.0360.0000.0000.0000.000
29H143ALA00.0230.00016.161-0.017-0.0170.0000.0000.0000.000
30H144GLU-1-0.885-0.94019.967-0.148-0.1480.0000.0000.0000.000
31H145ASP-1-0.777-0.86923.128-0.040-0.0400.0000.0000.0000.000
32H146GLU-1-0.726-0.84823.784-0.011-0.0110.0000.0000.0000.000
33H147ASN0-0.159-0.10225.0270.0310.0310.0000.0000.0000.000
34H148VAL00.0520.02920.5290.0170.0170.0000.0000.0000.000
35H149ARG10.8470.90820.682-0.007-0.0070.0000.0000.0000.000
36H150LYS10.8390.91921.8340.0180.0180.0000.0000.0000.000
37H151LYS10.7670.89123.3000.0390.0390.0000.0000.0000.000
38H152VAL00.0470.03717.0400.0130.0130.0000.0000.0000.000
39H153LEU00.0000.00018.8530.0300.0300.0000.0000.0000.000
40H154ARG10.8850.94420.632-0.054-0.0540.0000.0000.0000.000
41H155SER0-0.038-0.02619.542-0.001-0.0010.0000.0000.0000.000
42H156GLY0-0.032-0.00718.3430.0160.0160.0000.0000.0000.000
43H157ALA00.0070.01614.2610.0600.0600.0000.0000.0000.000
44H158ASN0-0.020-0.01810.958-0.064-0.0640.0000.0000.0000.000
45H159PHE00.002-0.01914.648-0.055-0.0550.0000.0000.0000.000
46H160VAL0-0.044-0.02213.3850.0290.0290.0000.0000.0000.000
47H161HIS00.0080.01216.650-0.039-0.0390.0000.0000.0000.000
48H162GLY00.0400.00219.197-0.009-0.0090.0000.0000.0000.000
49H163ASP-1-0.788-0.86019.835-0.287-0.2870.0000.0000.0000.000
50H164PRO0-0.008-0.01717.428-0.031-0.0310.0000.0000.0000.000
51H165THR0-0.023-0.02917.725-0.054-0.0540.0000.0000.0000.000
52H166ARG10.8300.92119.6750.2280.2280.0000.0000.0000.000
53H167VAL00.0500.00615.938-0.007-0.0070.0000.0000.0000.000
54H168SER00.000-0.02815.529-0.044-0.0440.0000.0000.0000.000
55H169ASP-1-0.801-0.86415.992-0.248-0.2480.0000.0000.0000.000
56H170LEU00.0610.03513.1360.0050.0050.0000.0000.0000.000
57H171GLU-1-0.867-0.94311.227-0.922-0.9220.0000.0000.0000.000
58H172LYS10.7250.84511.1520.2080.2080.0000.0000.0000.000
59H173ALA0-0.0250.00311.3420.1010.1010.0000.0000.0000.000
60H174ASN0-0.019-0.0086.299-0.088-0.0880.0000.0000.0000.000
61H175VAL00.0440.0226.108-0.697-0.6970.0000.0000.0000.000
62H176ARG10.8220.9097.0590.7890.7890.0000.0000.0000.000
63H177GLY00.0280.0223.9750.2620.4320.000-0.073-0.0970.000
64H178ALA0-0.040-0.0112.043-9.870-9.6955.223-2.810-2.588-0.034
65H179ARG10.9080.9603.987-0.421-0.1130.000-0.070-0.2380.000
66H180ALA0-0.001-0.0055.1400.5270.614-0.001-0.005-0.0800.000
67H181VAL0-0.008-0.0098.1410.0000.0000.0000.0000.0000.000
68H182ILE00.0110.01310.6160.0750.0750.0000.0000.0000.000
69H183VAL0-0.019-0.01714.0270.0060.0060.0000.0000.0000.000
70H184ASN0-0.016-0.00116.9830.0430.0430.0000.0000.0000.000
71H185LEU00.0050.00419.3890.0150.0150.0000.0000.0000.000
72H186GLU-1-0.915-0.95422.649-0.133-0.1330.0000.0000.0000.000
73H187SER0-0.032-0.03925.8520.0100.0100.0000.0000.0000.000
74H188ASP-1-0.694-0.84925.279-0.240-0.2400.0000.0000.0000.000
75H189SER0-0.055-0.02625.158-0.026-0.0260.0000.0000.0000.000
76H190GLU-1-0.851-0.89123.767-0.215-0.2150.0000.0000.0000.000
77H191THR0-0.005-0.00720.561-0.037-0.0370.0000.0000.0000.000
78H192ILE00.008-0.01220.499-0.046-0.0460.0000.0000.0000.000
79H193HIS0-0.025-0.00521.416-0.051-0.0510.0000.0000.0000.000
80H194CYS0-0.026-0.01417.117-0.047-0.0470.0000.0000.0000.000
81H195ILE0-0.0140.00216.733-0.073-0.0730.0000.0000.0000.000
82H196LEU0-0.0100.00717.038-0.065-0.0650.0000.0000.0000.000
83H197GLY0-0.027-0.01017.752-0.028-0.0280.0000.0000.0000.000
84H198ILE00.005-0.02011.630-0.054-0.0540.0000.0000.0000.000
85H199ARG10.8110.89911.9770.9710.9710.0000.0000.0000.000
86H200LYS10.8950.96315.5480.4440.4440.0000.0000.0000.000
87H201ILE0-0.109-0.03510.7400.0250.0250.0000.0000.0000.000
88H202ASP-1-0.788-0.9018.903-2.242-2.2420.0000.0000.0000.000
89H203GLU-1-0.941-0.95911.889-0.723-0.7230.0000.0000.0000.000
90H204SER0-0.112-0.0729.313-0.022-0.0220.0000.0000.0000.000
91H205VAL0-0.0020.0147.3100.0280.0280.0000.0000.0000.000
92H206ARG10.8580.9338.8000.9780.9780.0000.0000.0000.000
93H207ILE0-0.021-0.01710.859-0.064-0.0640.0000.0000.0000.000
94H208ILE0-0.046-0.02912.7220.0880.0880.0000.0000.0000.000
95H209ALA00.0240.01715.7870.0220.0220.0000.0000.0000.000
96H210GLU-1-0.901-0.93318.707-0.146-0.1460.0000.0000.0000.000
97H211ALA0-0.011-0.00321.6890.0000.0000.0000.0000.0000.000
98H212GLU-1-0.809-0.88924.957-0.139-0.1390.0000.0000.0000.000
99H213ARG10.7440.83927.9670.1640.1640.0000.0000.0000.000
100H214TYR00.017-0.00929.185-0.013-0.0130.0000.0000.0000.000
101H215GLU-1-0.924-0.96231.020-0.147-0.1470.0000.0000.0000.000
102H216ASN0-0.034-0.02827.667-0.004-0.0040.0000.0000.0000.000
103H217ILE00.0160.02125.540-0.021-0.0210.0000.0000.0000.000
104H218GLU-1-0.800-0.89425.138-0.282-0.2820.0000.0000.0000.000
105H219GLN0-0.012-0.01725.747-0.029-0.0290.0000.0000.0000.000
106H220LEU0-0.0010.00121.889-0.026-0.0260.0000.0000.0000.000
107H221ARG10.8930.93721.2920.2590.2590.0000.0000.0000.000
108H222MET0-0.101-0.04721.685-0.027-0.0270.0000.0000.0000.000
109H223ALA0-0.027-0.00821.129-0.012-0.0120.0000.0000.0000.000
110H224GLY00.0310.01618.409-0.042-0.0420.0000.0000.0000.000
111H225ALA0-0.012-0.00916.903-0.092-0.0920.0000.0000.0000.000
112H226ASP-1-0.818-0.90814.410-0.839-0.8390.0000.0000.0000.000
113H227GLN0-0.0060.00216.8410.0260.0260.0000.0000.0000.000
114H228VAL0-0.012-0.00518.663-0.021-0.0210.0000.0000.0000.000
115H229ILE00.0180.01819.0580.0320.0320.0000.0000.0000.000
116H230SER00.030-0.01022.697-0.004-0.0040.0000.0000.0000.000
117H231PRO00.0560.04625.1020.0140.0140.0000.0000.0000.000
118H232PHE00.0380.01127.5590.0170.0170.0000.0000.0000.000
119H233VAL00.0020.00429.5950.0100.0100.0000.0000.0000.000
120H234ILE0-0.014-0.00527.0140.0080.0080.0000.0000.0000.000
121H235SER00.0400.01730.4590.0120.0120.0000.0000.0000.000
122H236GLY00.0160.00732.8510.0080.0080.0000.0000.0000.000
123H237ARG10.9310.96430.3350.1190.1190.0000.0000.0000.000
124H238LEU00.0560.04231.2180.0060.0060.0000.0000.0000.000
125H239MET0-0.030-0.00135.3980.0050.0050.0000.0000.0000.000
126H240SER0-0.096-0.05838.2470.0040.0040.0000.0000.0000.000
127H241ARG10.8600.91336.4700.0510.0510.0000.0000.0000.000
128H242SER0-0.053-0.05138.1230.0070.0070.0000.0000.0000.000
129H243ILE0-0.072-0.02140.7740.0020.0020.0000.0000.0000.000
130H244ASP-1-0.942-0.95844.187-0.021-0.0210.0000.0000.0000.000
131H245ASP-1-0.883-0.95042.520-0.006-0.0060.0000.0000.0000.000
132H246GLY00.007-0.00339.3470.0030.0030.0000.0000.0000.000
133H247TYR0-0.032-0.01937.9170.0020.0020.0000.0000.0000.000
134H248GLU-1-0.824-0.89335.572-0.036-0.0360.0000.0000.0000.000
135H249ALA00.0060.00933.772-0.002-0.0020.0000.0000.0000.000
136H250MET00.0080.00432.9980.0030.0030.0000.0000.0000.000
137H251PHE00.0100.00131.1850.0060.0060.0000.0000.0000.000
138H252VAL0-0.006-0.01428.5730.0030.0030.0000.0000.0000.000
139H253GLN0-0.040-0.02228.394-0.008-0.0080.0000.0000.0000.000
140H254ASP-1-0.849-0.89928.2270.0490.0490.0000.0000.0000.000
141H255VAL0-0.075-0.03527.4100.0130.0130.0000.0000.0000.000
142H256LEU0-0.008-0.00823.7900.0000.0000.0000.0000.0000.000
143H257ALA00.0100.03323.4310.0010.0010.0000.0000.0000.000
144H258GLU-1-0.806-0.90120.2670.2060.2060.0000.0000.0000.000
145H259GLU-1-0.900-0.93123.2410.1390.1390.0000.0000.0000.000
146H260SER0-0.057-0.03326.5340.0030.0030.0000.0000.0000.000
147H261THR0-0.071-0.05227.9560.0090.0090.0000.0000.0000.000
148H262ARG10.7620.83629.550-0.067-0.0670.0000.0000.0000.000
149H263ARG10.8280.91522.340-0.173-0.1730.0000.0000.0000.000
150H264MET0-0.008-0.00923.7580.0010.0010.0000.0000.0000.000
151H265VAL0-0.021-0.01320.4230.0150.0150.0000.0000.0000.000
152H266GLU-1-0.899-0.94317.084-0.155-0.1550.0000.0000.0000.000
153H267VAL0-0.066-0.04817.7480.0540.0540.0000.0000.0000.000
154H268PRO00.004-0.00113.741-0.021-0.0210.0000.0000.0000.000
155H269ILE00.0030.01616.7680.0600.0600.0000.0000.0000.000
156H270PRO0-0.027-0.01915.303-0.026-0.0260.0000.0000.0000.000
157H271GLU-1-0.893-0.94313.2130.1070.1070.0000.0000.0000.000
158H272GLY0-0.058-0.02917.2450.0190.0190.0000.0000.0000.000
159H273SER0-0.046-0.04019.523-0.020-0.0200.0000.0000.0000.000
160H274LYS10.8470.92823.182-0.221-0.2210.0000.0000.0000.000
161H275LEU00.0510.02624.097-0.007-0.0070.0000.0000.0000.000
162H276GLU-1-0.856-0.92522.301-0.031-0.0310.0000.0000.0000.000
163H277GLY0-0.038-0.01025.0680.0040.0040.0000.0000.0000.000
164H278VAL0-0.058-0.01727.975-0.004-0.0040.0000.0000.0000.000
165H279SER0-0.032-0.04728.982-0.006-0.0060.0000.0000.0000.000
166H280VAL00.012-0.00929.2600.0100.0100.0000.0000.0000.000
167H281LEU0-0.055-0.02131.4670.0050.0050.0000.0000.0000.000
168H282ASP-1-0.889-0.91232.7100.0220.0220.0000.0000.0000.000
169H283ALA0-0.014-0.00429.4660.0070.0070.0000.0000.0000.000
170H284ASP-1-0.889-0.92931.5270.0480.0480.0000.0000.0000.000
171H285ILE00.014-0.00226.6310.0080.0080.0000.0000.0000.000
172H286HIS00.0200.01530.5760.0080.0080.0000.0000.0000.000
173H287ASP-1-0.934-0.95832.7850.0640.0640.0000.0000.0000.000
174H288VAL0-0.027-0.00630.7880.0090.0090.0000.0000.0000.000
175H289THR0-0.061-0.04727.3900.0190.0190.0000.0000.0000.000
176H290GLY0-0.059-0.02430.1230.0110.0110.0000.0000.0000.000
177H291VAL0-0.062-0.02626.024-0.003-0.0030.0000.0000.0000.000
178H292ILE00.0310.02029.307-0.005-0.0050.0000.0000.0000.000
179H293ILE0-0.029-0.01826.546-0.001-0.0010.0000.0000.0000.000
180H294ILE00.000-0.00427.804-0.005-0.0050.0000.0000.0000.000
181H295GLY00.0330.00527.099-0.010-0.0100.0000.0000.0000.000
182H296VAL0-0.056-0.01923.3180.0170.0170.0000.0000.0000.000
183H297GLY00.0080.01821.475-0.012-0.0120.0000.0000.0000.000
184H298ARG10.7470.81520.9450.0940.0940.0000.0000.0000.000
185H299GLY0-0.014-0.00619.5420.0000.0000.0000.0000.0000.000
186H300ASP-1-0.879-0.94517.880-0.428-0.4280.0000.0000.0000.000
187H301GLU-1-0.895-0.92420.762-0.143-0.1430.0000.0000.0000.000
188H302LEU0-0.056-0.04223.6320.0040.0040.0000.0000.0000.000
189H303ILE00.0170.01525.6000.0090.0090.0000.0000.0000.000
190H304ILE0-0.014-0.02228.2760.0110.0110.0000.0000.0000.000
191H305ASP-1-0.973-0.98230.098-0.022-0.0220.0000.0000.0000.000
192H306PRO0-0.0080.01629.173-0.003-0.0030.0000.0000.0000.000
193H307PRO00.0100.00831.6880.0080.0080.0000.0000.0000.000
194H308ARG10.9450.95033.5020.0100.0100.0000.0000.0000.000
195H309ASP-1-0.887-0.95434.619-0.028-0.0280.0000.0000.0000.000
196H310TYR0-0.051-0.02924.627-0.010-0.0100.0000.0000.0000.000
197H311SER00.0050.00829.1570.0060.0060.0000.0000.0000.000
198H312PHE00.0260.01124.322-0.014-0.0140.0000.0000.0000.000
199H313ARG10.9170.95822.1630.0960.0960.0000.0000.0000.000
200H314ALA00.0100.00417.9090.0060.0060.0000.0000.0000.000
201H315GLY0-0.052-0.02916.073-0.038-0.0380.0000.0000.0000.000
202H316ASP-1-0.748-0.83117.098-0.110-0.1100.0000.0000.0000.000
203H317ILE0-0.035-0.02015.5160.0360.0360.0000.0000.0000.000
204H318ILE00.0000.01219.339-0.013-0.0130.0000.0000.0000.000
205H319LEU00.0340.01821.3460.0110.0110.0000.0000.0000.000
206H320GLY00.0250.00323.579-0.003-0.0030.0000.0000.0000.000
207H321ILE0-0.0190.00025.3610.0050.0050.0000.0000.0000.000
208H322GLY00.017-0.00327.267-0.001-0.0010.0000.0000.0000.000
209H323LYS10.8700.93627.624-0.109-0.1090.0000.0000.0000.000
210H324PRO00.0360.01725.0290.0050.0050.0000.0000.0000.000
211H325GLU-1-0.810-0.90225.4270.1530.1530.0000.0000.0000.000
212H326GLU-1-0.802-0.84827.8420.0870.0870.0000.0000.0000.000
213H327ILE00.0650.02921.8980.0050.0050.0000.0000.0000.000
214H328GLU-1-0.876-0.93420.7740.3480.3480.0000.0000.0000.000
215H329ARG10.8690.94223.644-0.112-0.1120.0000.0000.0000.000
216H330LEU00.0520.03422.4230.0020.0020.0000.0000.0000.000
217H331LYS10.8820.92317.677-0.322-0.3220.0000.0000.0000.000
218H332ASN0-0.091-0.06121.2850.0190.0190.0000.0000.0000.000
219H333TYR0-0.071-0.03923.4160.0000.0000.0000.0000.0000.000
220H334ILE00.0360.02819.695-0.010-0.0100.0000.0000.0000.000
221H335SER0-0.032-0.00919.482-0.010-0.0100.0000.0000.0000.000
222H336ALA00.002-0.00519.207-0.033-0.0330.0000.0000.0000.000