Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: N99YQ

Calculation Name: 5FMS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FMS

Chain ID: A

ChEMBL ID:

UniProt ID: Q62559

Base Structure: X-ray

Registration Date: 2023-06-21

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2927256.639167
FMO2-HF: Nuclear repulsion 2837916.397535
FMO2-HF: Total energy -89340.241632
FMO2-MP2: Total energy -89602.356007


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(A:7:SER)


Summations of interaction energy for fragment #1(A:7: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.
-5.38-3.03810.897-6.89-6.35-0.045
Interaction energy analysis for fragmet #1(A:7:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.028
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].
3A9ILE00.0220.0203.877-0.4811.996-0.021-1.380-1.0770.006
4A10LEU0-0.024-0.0106.9570.0250.0250.0000.0000.0000.000
5A11PHE00.0240.0059.8950.2680.2680.0000.0000.0000.000
6A12ASN0-0.016-0.02113.630-0.057-0.0570.0000.0000.0000.000
7A13ALA0-0.046-0.04415.8220.0200.0200.0000.0000.0000.000
8A14TYR0-0.020-0.00416.7510.0090.0090.0000.0000.0000.000
9A15LYS10.7930.92420.6550.3210.3210.0000.0000.0000.000
10A16LYS10.8540.88522.6450.3100.3100.0000.0000.0000.000
11A17GLU-1-0.748-0.86819.380-0.427-0.4270.0000.0000.0000.000
12A18VAL0-0.059-0.00722.6670.0080.0080.0000.0000.0000.000
13A19PHE0-0.047-0.02820.6470.0050.0050.0000.0000.0000.000
14A20THR00.0750.03718.071-0.035-0.0350.0000.0000.0000.000
15A21THR00.0300.01214.0160.0580.0580.0000.0000.0000.000
16A22ASN00.0040.01417.1550.0220.0220.0000.0000.0000.000
17A23THR0-0.007-0.00820.4530.0610.0610.0000.0000.0000.000
18A24GLY00.0110.01221.438-0.028-0.0280.0000.0000.0000.000
19A25THR00.0610.03517.7380.0400.0400.0000.0000.0000.000
20A26LYS10.8700.93417.6520.3990.3990.0000.0000.0000.000
21A27SER0-0.033-0.04117.891-0.056-0.0560.0000.0000.0000.000
22A28LEU00.0300.02915.0290.0010.0010.0000.0000.0000.000
23A29GLN0-0.073-0.06113.508-0.140-0.1400.0000.0000.0000.000
24A30LYS10.9060.96413.1130.2680.2680.0000.0000.0000.000
25A31ARG10.8390.89514.0440.3850.3850.0000.0000.0000.000
26A32LEU00.0330.0419.772-0.014-0.0140.0000.0000.0000.000
27A33ARG10.9420.9498.7550.7610.7610.0000.0000.0000.000
28A34SER0-0.055-0.0199.834-0.003-0.0030.0000.0000.0000.000
29A35ASN0-0.026-0.0206.8120.3270.3270.0000.0000.0000.000
30A36TRP00.0430.0322.088-2.116-1.1172.807-1.852-1.954-0.008
31A37LYS10.8690.9383.9153.6383.908-0.001-0.066-0.2030.000
32A38ILE00.0320.0175.572-0.221-0.2210.0000.0000.0000.000
33A39GLN00.0000.0058.9400.0860.0860.0000.0000.0000.000
34A40SER0-0.024-0.02710.9300.1150.1150.0000.0000.0000.000
35A41LEU00.0150.01112.989-0.031-0.0310.0000.0000.0000.000
36A42LYS10.8900.93014.5810.7360.7360.0000.0000.0000.000
37A43ASP-1-0.845-0.91917.209-0.427-0.4270.0000.0000.0000.000
38A44GLU-1-0.802-0.91817.151-0.368-0.3680.0000.0000.0000.000
39A45ILE0-0.0080.02013.471-0.019-0.0190.0000.0000.0000.000
40A46THR00.0350.00014.4760.0560.0560.0000.0000.0000.000
41A47SER00.0100.00812.508-0.054-0.0540.0000.0000.0000.000
42A48GLU-1-0.852-0.93911.158-0.141-0.1410.0000.0000.0000.000
43A49LYS10.8140.90110.4730.4020.4020.0000.0000.0000.000
44A50LEU0-0.011-0.0138.142-0.315-0.3150.0000.0000.0000.000
45A51ILE0-0.0090.0186.767-0.164-0.1640.0000.0000.0000.000
46A52GLY00.0420.0303.3100.5500.9870.024-0.161-0.3000.000
47A53VAL0-0.077-0.0381.912-8.846-11.1438.073-3.323-2.454-0.043
48A54LYS10.8170.9213.3500.3740.7890.016-0.106-0.3240.000
49A55LEU00.0080.0125.1000.2430.284-0.001-0.002-0.0380.000
50A56TRP00.002-0.0098.144-0.408-0.4080.0000.0000.0000.000
51A57ILE00.008-0.00211.0680.1540.1540.0000.0000.0000.000
52A58THR00.0110.00213.946-0.018-0.0180.0000.0000.0000.000
53A59ALA00.0020.00817.6760.0550.0550.0000.0000.0000.000
54A60GLY00.0530.01619.5380.0110.0110.0000.0000.0000.000
55A61PRO0-0.025-0.01121.1320.0000.0000.0000.0000.0000.000
56A62ARG10.8270.89723.2920.3140.3140.0000.0000.0000.000
57A63GLU-1-0.788-0.86925.255-0.253-0.2530.0000.0000.0000.000
58A64LYS10.7900.89425.5230.1450.1450.0000.0000.0000.000
59A65PHE0-0.005-0.01019.102-0.021-0.0210.0000.0000.0000.000
60A66THR0-0.017-0.01923.8750.0280.0280.0000.0000.0000.000
61A67ALA00.0590.01823.491-0.010-0.0100.0000.0000.0000.000
62A68ALA00.0290.01122.7410.0040.0040.0000.0000.0000.000
63A69GLU-1-0.726-0.82819.411-0.281-0.2810.0000.0000.0000.000
64A70PHE00.0140.00918.728-0.021-0.0210.0000.0000.0000.000
65A71GLU-1-0.808-0.90619.649-0.065-0.0650.0000.0000.0000.000
66A72VAL0-0.061-0.01814.9750.0220.0220.0000.0000.0000.000
67A73LEU0-0.013-0.01114.334-0.001-0.0010.0000.0000.0000.000
68A74LYS10.8120.89715.4650.0880.0880.0000.0000.0000.000
69A75LYS10.9030.96014.6050.0280.0280.0000.0000.0000.000
70A76TYR0-0.061-0.0377.2030.0540.0540.0000.0000.0000.000
71A77LEU00.0020.01012.1530.0810.0810.0000.0000.0000.000
72A78ASP-1-0.801-0.91414.1960.1510.1510.0000.0000.0000.000
73A79SER0-0.037-0.02311.9830.0390.0390.0000.0000.0000.000
74A80GLY00.0010.01511.3800.1480.1480.0000.0000.0000.000
75A81GLY0-0.021-0.0078.9340.1380.1380.0000.0000.0000.000
76A82ASP-1-0.809-0.9098.7910.0300.0300.0000.0000.0000.000
77A83ILE0-0.005-0.01510.978-0.181-0.1810.0000.0000.0000.000
78A84LEU0-0.004-0.00113.6830.0580.0580.0000.0000.0000.000
79A85VAL00.0240.02215.476-0.055-0.0550.0000.0000.0000.000
80A86MET0-0.036-0.02318.5770.0100.0100.0000.0000.0000.000
81A87LEU0-0.009-0.00121.139-0.023-0.0230.0000.0000.0000.000
82A88GLY00.0170.01024.6490.0100.0100.0000.0000.0000.000
83A89GLU-1-0.824-0.89427.870-0.137-0.1370.0000.0000.0000.000
84A90GLY00.0040.00131.680-0.006-0.0060.0000.0000.0000.000
85A91GLY00.0570.03529.5720.0070.0070.0000.0000.0000.000
86A92GLU-1-0.762-0.88928.069-0.158-0.1580.0000.0000.0000.000
87A93SER0-0.059-0.03130.7620.0030.0030.0000.0000.0000.000
88A94ARG10.8210.89632.1520.1530.1530.0000.0000.0000.000
89A95PHE0-0.038-0.01726.017-0.015-0.0150.0000.0000.0000.000
90A96ASP-1-0.838-0.89529.266-0.166-0.1660.0000.0000.0000.000
91A97THR0-0.042-0.02125.1910.0030.0030.0000.0000.0000.000
92A98ASN00.0160.00426.276-0.003-0.0030.0000.0000.0000.000
93A99ILE00.0300.01120.3590.0060.0060.0000.0000.0000.000
94A100ASN00.010-0.01924.3050.0000.0000.0000.0000.0000.000
95A101PHE0-0.020-0.00326.8710.0100.0100.0000.0000.0000.000
96A102LEU0-0.0220.01318.9530.0050.0050.0000.0000.0000.000
97A103LEU0-0.048-0.03321.0980.0080.0080.0000.0000.0000.000
98A104GLU-1-0.884-0.94524.097-0.062-0.0620.0000.0000.0000.000
99A105GLU-1-0.852-0.91124.125-0.055-0.0550.0000.0000.0000.000
100A106TYR0-0.064-0.04019.4470.0100.0100.0000.0000.0000.000
101A107GLY0-0.021-0.00424.2480.0060.0060.0000.0000.0000.000
102A108ILE0-0.061-0.04822.399-0.001-0.0010.0000.0000.0000.000
103A109MET00.0270.01526.501-0.003-0.0030.0000.0000.0000.000
104A110VAL0-0.042-0.02325.2820.0030.0030.0000.0000.0000.000
105A111ASN00.0010.01528.1580.0060.0060.0000.0000.0000.000
106A112ASN0-0.018-0.02431.301-0.007-0.0070.0000.0000.0000.000
107A113ASP-1-0.772-0.85333.431-0.108-0.1080.0000.0000.0000.000
108A114ALA0-0.036-0.04533.698-0.011-0.0110.0000.0000.0000.000
109A115VAL0-0.0170.01131.8350.0080.0080.0000.0000.0000.000
110A116VAL0-0.043-0.02734.624-0.007-0.0070.0000.0000.0000.000
111A117ARG10.8170.89836.8520.1170.1170.0000.0000.0000.000
112A118ASN00.0250.02338.5170.0040.0040.0000.0000.0000.000
113A119VAL00.0090.00141.2460.0030.0030.0000.0000.0000.000
114A120TYR0-0.023-0.01141.066-0.005-0.0050.0000.0000.0000.000
115A121TYR00.0520.00937.5300.0020.0020.0000.0000.0000.000
116A122LYS10.8180.92335.1370.1060.1060.0000.0000.0000.000
117A123TYR0-0.048-0.04732.079-0.009-0.0090.0000.0000.0000.000
118A124PHE00.0120.02437.0230.0070.0070.0000.0000.0000.000
119A125HIS00.0430.01236.3970.0060.0060.0000.0000.0000.000
120A126PRO00.020-0.01237.497-0.002-0.0020.0000.0000.0000.000
121A127LYS10.9020.94034.4210.1270.1270.0000.0000.0000.000
122A128GLU-1-0.822-0.87632.922-0.167-0.1670.0000.0000.0000.000
123A129ALA00.0160.01932.9010.0090.0090.0000.0000.0000.000
124A130LEU0-0.009-0.01332.102-0.010-0.0100.0000.0000.0000.000
125A131VAL00.0020.01131.0280.0100.0100.0000.0000.0000.000
126A132SER0-0.007-0.02031.886-0.002-0.0020.0000.0000.0000.000
127A133ASP-1-0.757-0.85733.374-0.064-0.0640.0000.0000.0000.000
128A134GLY00.0300.03031.0060.0060.0060.0000.0000.0000.000
129A135VAL0-0.016-0.01626.776-0.009-0.0090.0000.0000.0000.000
130A136LEU0-0.0210.00127.9960.0090.0090.0000.0000.0000.000
131A137ASN0-0.009-0.01425.3960.0150.0150.0000.0000.0000.000
132A138ARG10.9350.95426.838-0.026-0.0260.0000.0000.0000.000
133A139GLU-1-0.807-0.88823.3290.0300.0300.0000.0000.0000.000
134A140ILE0-0.0010.00622.006-0.003-0.0030.0000.0000.0000.000
135A141SER0-0.059-0.01823.839-0.018-0.0180.0000.0000.0000.000
136A142ARG10.7990.87919.924-0.034-0.0340.0000.0000.0000.000
137A143ALA0-0.0030.00223.381-0.003-0.0030.0000.0000.0000.000
138A144ALA0-0.026-0.02124.7200.0110.0110.0000.0000.0000.000
139A145GLY00.0540.02328.240-0.008-0.0080.0000.0000.0000.000
140A146LYS10.8990.94230.7030.0100.0100.0000.0000.0000.000
141A147ALA00.0430.03433.008-0.004-0.0040.0000.0000.0000.000
142A162GLN0-0.021-0.00532.7800.0020.0020.0000.0000.0000.000
143A163ALA0-0.007-0.00332.8730.0010.0010.0000.0000.0000.000
144A164LEU0-0.016-0.00925.680-0.001-0.0010.0000.0000.0000.000
145A165THR0-0.031-0.00730.3710.0020.0020.0000.0000.0000.000
146A166PHE0-0.0010.00226.960-0.012-0.0120.0000.0000.0000.000
147A167VAL00.0050.00228.5570.0100.0100.0000.0000.0000.000
148A168TYR0-0.022-0.03326.305-0.021-0.0210.0000.0000.0000.000
149A169PRO00.0050.00727.3470.0100.0100.0000.0000.0000.000
150A170PHE0-0.003-0.00328.830-0.011-0.0110.0000.0000.0000.000
151A171GLY00.0430.02529.054-0.015-0.0150.0000.0000.0000.000
152A172ALA00.0040.02929.2050.0140.0140.0000.0000.0000.000
153A173THR0-0.037-0.04529.824-0.002-0.0020.0000.0000.0000.000
154A174LEU0-0.041-0.01524.932-0.006-0.0060.0000.0000.0000.000
155A175SER0-0.005-0.00929.2660.0130.0130.0000.0000.0000.000
156A176VAL0-0.052-0.03926.600-0.006-0.0060.0000.0000.0000.000
157A177MET0-0.0190.00428.7150.0090.0090.0000.0000.0000.000
158A178LYS10.9270.97227.165-0.015-0.0150.0000.0000.0000.000
159A179PRO00.0230.00424.626-0.002-0.0020.0000.0000.0000.000
160A180ALA0-0.0020.01623.7300.0100.0100.0000.0000.0000.000
161A181VAL0-0.049-0.03724.0470.0120.0120.0000.0000.0000.000
162A182ALA00.0310.02624.446-0.014-0.0140.0000.0000.0000.000
163A183VAL0-0.020-0.02322.1170.0130.0130.0000.0000.0000.000
164A184LEU00.0010.01223.7170.0000.0000.0000.0000.0000.000
165A185SER00.014-0.00527.131-0.001-0.0010.0000.0000.0000.000
166A186THR00.009-0.03230.490-0.006-0.0060.0000.0000.0000.000
167A187GLY00.0290.02232.848-0.001-0.0010.0000.0000.0000.000
168A188SER0-0.096-0.08334.7470.0010.0010.0000.0000.0000.000
169A189VAL00.001-0.00737.3980.0020.0020.0000.0000.0000.000
170A190CYS0-0.056-0.01135.224-0.007-0.0070.0000.0000.0000.000
171A191PHE0-0.0130.01037.3420.0050.0050.0000.0000.0000.000
172A192PRO00.0530.01635.697-0.006-0.0060.0000.0000.0000.000
173A193LEU00.0500.03936.382-0.003-0.0030.0000.0000.0000.000
174A194ASN0-0.021-0.01634.8160.0010.0010.0000.0000.0000.000
175A195ARG10.8950.96233.1200.0710.0710.0000.0000.0000.000
176A196PRO00.0220.00528.860-0.005-0.0050.0000.0000.0000.000
177A197ILE0-0.006-0.00326.804-0.004-0.0040.0000.0000.0000.000
178A198LEU0-0.004-0.00420.044-0.022-0.0220.0000.0000.0000.000
179A199ALA0-0.0020.00422.8380.0220.0220.0000.0000.0000.000
180A200PHE00.021-0.00618.636-0.026-0.0260.0000.0000.0000.000
181A201TYR00.029-0.01218.2350.0060.0060.0000.0000.0000.000
182A202HIS00.0280.01116.153-0.035-0.0350.0000.0000.0000.000
183A203SER0-0.0120.01118.3920.0390.0390.0000.0000.0000.000
184A204LYS10.8850.94420.144-0.063-0.0630.0000.0000.0000.000
185A205ASN0-0.020-0.02319.1500.0300.0300.0000.0000.0000.000
186A206GLN0-0.063-0.01216.3180.0210.0210.0000.0000.0000.000
187A207GLY00.0600.03515.6280.0020.0020.0000.0000.0000.000
188A208PHE0-0.074-0.06214.0550.0410.0410.0000.0000.0000.000
189A209GLY00.1120.08712.6460.0440.0440.0000.0000.0000.000
190A210LYS10.7680.88512.959-0.167-0.1670.0000.0000.0000.000
191A211LEU00.0000.00414.090-0.063-0.0630.0000.0000.0000.000
192A212ALA0-0.031-0.01816.4930.0330.0330.0000.0000.0000.000
193A213VAL00.0260.01918.012-0.040-0.0400.0000.0000.0000.000
194A214LEU00.020-0.00220.6350.0250.0250.0000.0000.0000.000
195A215GLY00.0290.02722.604-0.017-0.0170.0000.0000.0000.000
196A216SER00.051-0.01824.3850.0000.0000.0000.0000.0000.000
197A217CYS0-0.027-0.00322.059-0.009-0.0090.0000.0000.0000.000
198A218HIS00.0090.00022.427-0.043-0.0430.0000.0000.0000.000
199A219MET00.0010.04022.865-0.005-0.0050.0000.0000.0000.000
200A220PHE00.0620.01518.1060.0010.0010.0000.0000.0000.000
201A221SER0-0.012-0.01220.274-0.041-0.0410.0000.0000.0000.000
202A222ASP-1-0.793-0.91121.495-0.423-0.4230.0000.0000.0000.000
203A223GLN0-0.018-0.00223.8020.0230.0230.0000.0000.0000.000
204A224TYR0-0.061-0.07725.6350.0240.0240.0000.0000.0000.000
205A225LEU0-0.0340.00618.8030.0140.0140.0000.0000.0000.000
206A226ASP-1-0.790-0.88422.774-0.310-0.3100.0000.0000.0000.000
207A227LYS10.8460.95224.8320.2090.2090.0000.0000.0000.000
208A228GLU-1-0.743-0.86227.985-0.115-0.1150.0000.0000.0000.000
209A229GLU-1-0.794-0.88125.819-0.108-0.1080.0000.0000.0000.000
210A230ASN0-0.030-0.02023.7900.0140.0140.0000.0000.0000.000
211A231SER00.0050.00720.891-0.011-0.0110.0000.0000.0000.000
212A232LYS10.9450.96220.1550.1090.1090.0000.0000.0000.000
213A233ILE00.0010.00920.9920.0060.0060.0000.0000.0000.000
214A234MET0-0.040-0.00815.695-0.031-0.0310.0000.0000.0000.000
215A235ASP-1-0.912-0.96716.230-0.316-0.3160.0000.0000.0000.000
216A236VAL00.0390.01915.9350.0000.0000.0000.0000.0000.000
217A237VAL0-0.021-0.01315.8240.0240.0240.0000.0000.0000.000
218A238PHE0-0.015-0.02710.831-0.015-0.0150.0000.0000.0000.000
219A239GLN0-0.031-0.02611.837-0.019-0.0190.0000.0000.0000.000
220A240TRP00.0150.00613.6350.1030.1030.0000.0000.0000.000
221A241LEU0-0.024-0.01011.4400.0630.0630.0000.0000.0000.000
222A242THR0-0.0220.0066.504-0.004-0.0040.0000.0000.0000.000
223A243THR0-0.067-0.0209.2090.0040.0040.0000.0000.0000.000
224A244GLY00.0150.00910.2000.1420.1420.0000.0000.0000.000
225A245ASP-1-0.815-0.90312.8510.0780.0780.0000.0000.0000.000
226A246ILE0-0.0320.00616.325-0.005-0.0050.0000.0000.0000.000
227A247HIS00.0640.02217.7690.0310.0310.0000.0000.0000.000
228A248LEU0-0.071-0.02120.503-0.011-0.0110.0000.0000.0000.000