FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 94LY2

Calculation Name: 4YBQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YBQ

Chain ID: A

ChEMBL ID:

UniProt ID: P43427

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptHSide
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 452
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8331024.949364
FMO2-HF: Nuclear repulsion 8158496.358272
FMO2-HF: Total energy -172528.591092
FMO2-MP2: Total energy -173032.656247


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:GLU)


Summations of interaction energy for fragment #1(A:7:GLU)
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.
-152.966-153.16512.87-7.138-5.5340.091
Interaction energy analysis for fragmet #1(A:7:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.857 / q_NPA : -0.930
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].
3A9THR00.0190.0103.789-0.7581.103-0.016-0.836-1.0100.004
4A10GLY0-0.004-0.0035.720-3.009-3.0090.0000.0000.0000.000
5A11LYS10.9350.9728.139-19.240-19.2400.0000.0000.0000.000
6A12LEU00.0330.01011.8600.0200.0200.0000.0000.0000.000
7A13THR0-0.004-0.00614.470-1.049-1.0490.0000.0000.0000.000
8A14LEU00.0540.01517.095-0.121-0.1210.0000.0000.0000.000
9A15VAL00.0340.01318.626-0.356-0.3560.0000.0000.0000.000
10A16LEU00.0400.02213.896-0.252-0.2520.0000.0000.0000.000
11A17ALA00.0200.01418.014-0.141-0.1410.0000.0000.0000.000
12A18LEU00.0150.00420.291-0.437-0.4370.0000.0000.0000.000
13A19ALA00.0080.01420.078-0.425-0.4250.0000.0000.0000.000
14A20THR0-0.002-0.03319.027-0.103-0.1030.0000.0000.0000.000
15A21PHE0-0.032-0.00921.498-0.323-0.3230.0000.0000.0000.000
16A22LEU0-0.014-0.00624.815-0.417-0.4170.0000.0000.0000.000
17A23ALA0-0.0010.00023.547-0.346-0.3460.0000.0000.0000.000
18A24ALA00.0050.00524.148-0.332-0.3320.0000.0000.0000.000
19A25PHE00.0030.02726.085-0.396-0.3960.0000.0000.0000.000
20A26GLY00.0500.01429.280-0.298-0.2980.0000.0000.0000.000
21A27SER00.002-0.00528.162-0.237-0.2370.0000.0000.0000.000
22A28SER0-0.023-0.04027.350-0.036-0.0360.0000.0000.0000.000
23A29PHE00.0110.01629.568-0.177-0.1770.0000.0000.0000.000
24A30GLN0-0.0050.01331.964-0.187-0.1870.0000.0000.0000.000
25A31TYR0-0.0170.00130.153-0.353-0.3530.0000.0000.0000.000
26A32GLY00.003-0.00632.790-0.204-0.2040.0000.0000.0000.000
27A33TYR0-0.025-0.00833.996-0.250-0.2500.0000.0000.0000.000
28A34ASN00.010-0.00536.780-0.411-0.4110.0000.0000.0000.000
29A35VAL0-0.028-0.00835.180-0.236-0.2360.0000.0000.0000.000
30A36ALA0-0.014-0.00638.261-0.164-0.1640.0000.0000.0000.000
31A37ALA0-0.0210.00140.649-0.201-0.2010.0000.0000.0000.000
32A38VAL0-0.064-0.00839.902-0.422-0.4220.0000.0000.0000.000
33A61ILE00.0660.01463.661-0.009-0.0090.0000.0000.0000.000
34A62GLU-1-0.873-0.91362.0925.1585.1580.0000.0000.0000.000
35A63SER00.0600.02159.6770.0880.0880.0000.0000.0000.000
36A64PHE0-0.012-0.00657.9030.1030.1030.0000.0000.0000.000
37A65THR0-0.004-0.02257.6850.0990.0990.0000.0000.0000.000
38A66LEU00.0190.01355.3960.1160.1160.0000.0000.0000.000
39A67THR0-0.015-0.01254.0420.1130.1130.0000.0000.0000.000
40A68LEU0-0.009-0.01052.7580.1510.1510.0000.0000.0000.000
41A69LEU00.0150.02552.4100.1400.1400.0000.0000.0000.000
42A70TRP00.0150.01449.0960.1490.1490.0000.0000.0000.000
43A71SER0-0.020-0.00848.6560.1710.1710.0000.0000.0000.000
44A72LEU00.0540.02847.5760.1740.1740.0000.0000.0000.000
45A73THR0-0.025-0.02947.3030.1660.1660.0000.0000.0000.000
46A74VAL0-0.019-0.00844.5700.1790.1790.0000.0000.0000.000
47A75SER0-0.066-0.03343.3210.2160.2160.0000.0000.0000.000
48A76MET0-0.009-0.01742.9550.1400.1400.0000.0000.0000.000
49A77PHE00.0250.02836.4300.1690.1690.0000.0000.0000.000
50A78PRO00.0060.00737.7510.2360.2360.0000.0000.0000.000
51A79PHE00.0350.01737.7020.2310.2310.0000.0000.0000.000
52A80GLY00.0400.01639.0140.0940.0940.0000.0000.0000.000
53A81GLY00.0340.02235.1370.1820.1820.0000.0000.0000.000
54A82PHE0-0.021-0.00434.0040.3580.3580.0000.0000.0000.000
55A83ILE00.0300.01234.8440.2240.2240.0000.0000.0000.000
56A84GLY00.0320.00134.3470.1320.1320.0000.0000.0000.000
57A85SER0-0.048-0.04730.6570.4310.4310.0000.0000.0000.000
58A86LEU0-0.032-0.00730.6920.3410.3410.0000.0000.0000.000
59A87MET0-0.048-0.00932.4770.0740.0740.0000.0000.0000.000
60A88VAL00.0150.01026.6150.1310.1310.0000.0000.0000.000
61A89GLY00.025-0.00326.9450.2460.2460.0000.0000.0000.000
62A90PHE00.0010.00327.8560.2160.2160.0000.0000.0000.000
63A91LEU00.0480.02729.6840.0930.0930.0000.0000.0000.000
64A92VAL00.0190.00723.4730.1520.1520.0000.0000.0000.000
65A93ASN0-0.045-0.01924.1350.8010.8010.0000.0000.0000.000
66A94ASN0-0.063-0.01926.125-0.113-0.1130.0000.0000.0000.000
67A95LEU0-0.027-0.01028.1840.0720.0720.0000.0000.0000.000
68A96GLY00.0140.02824.3190.1430.1430.0000.0000.0000.000
69A97ARG10.8250.87919.356-15.222-15.2220.0000.0000.0000.000
70A98LYS10.8370.91523.098-12.273-12.2730.0000.0000.0000.000
71A99GLY00.0180.01025.399-0.427-0.4270.0000.0000.0000.000
72A100ALA0-0.005-0.00626.755-0.433-0.4330.0000.0000.0000.000
73A101LEU00.000-0.00624.656-0.298-0.2980.0000.0000.0000.000
74A102LEU0-0.017-0.00528.686-0.330-0.3300.0000.0000.0000.000
75A103PHE00.016-0.00831.487-0.364-0.3640.0000.0000.0000.000
76A104ASN00.0190.01830.969-0.407-0.4070.0000.0000.0000.000
77A105ASN00.0410.01232.292-0.069-0.0690.0000.0000.0000.000
78A106ILE0-0.0120.00934.451-0.251-0.2510.0000.0000.0000.000
79A107PHE0-0.020-0.02535.177-0.262-0.2620.0000.0000.0000.000
80A108SER0-0.025-0.02135.685-0.235-0.2350.0000.0000.0000.000
81A109ILE0-0.013-0.01037.785-0.198-0.1980.0000.0000.0000.000
82A110LEU00.0020.00040.121-0.218-0.2180.0000.0000.0000.000
83A111PRO00.019-0.00540.990-0.226-0.2260.0000.0000.0000.000
84A112ALA00.0420.03042.567-0.170-0.1700.0000.0000.0000.000
85A113ILE00.0100.00343.733-0.181-0.1810.0000.0000.0000.000
86A114LEU00.0010.00345.930-0.187-0.1870.0000.0000.0000.000
87A115MET0-0.009-0.00246.841-0.207-0.2070.0000.0000.0000.000
88A116GLY00.0050.00848.661-0.133-0.1330.0000.0000.0000.000
89A117CYS0-0.038-0.03250.250-0.153-0.1530.0000.0000.0000.000
90A118SER0-0.016-0.00751.580-0.110-0.1100.0000.0000.0000.000
91A119LYS10.7560.86951.983-6.169-6.1690.0000.0000.0000.000
92A120ILE0-0.0300.00254.571-0.111-0.1110.0000.0000.0000.000
93A121ALA0-0.025-0.00456.015-0.111-0.1110.0000.0000.0000.000
94A122LYS10.9700.99053.318-5.848-5.8480.0000.0000.0000.000
95A123SER0-0.015-0.03454.890-0.070-0.0700.0000.0000.0000.000
96A124PHE00.0710.00852.7620.1270.1270.0000.0000.0000.000
97A125GLU-1-0.808-0.88452.4495.8645.8640.0000.0000.0000.000
98A126ILE00.0050.00950.3620.1710.1710.0000.0000.0000.000
99A127ILE0-0.013-0.00349.2220.1690.1690.0000.0000.0000.000
100A128ILE00.0130.01447.7900.1950.1950.0000.0000.0000.000
101A129ALA00.0000.00146.4290.1840.1840.0000.0000.0000.000
102A130SER0-0.045-0.02444.9510.2060.2060.0000.0000.0000.000
103A131ARG10.9650.95443.332-6.736-6.7360.0000.0000.0000.000
104A132LEU0-0.0090.01441.6640.2190.2190.0000.0000.0000.000
105A133LEU0-0.019-0.01540.5140.2560.2560.0000.0000.0000.000
106A134VAL00.0410.01438.9310.2620.2620.0000.0000.0000.000
107A135GLY00.0370.01237.5410.2520.2520.0000.0000.0000.000
108A136ILE0-0.055-0.02236.0240.3140.3140.0000.0000.0000.000
109A137CYS0-0.043-0.01534.2460.3340.3340.0000.0000.0000.000
110A138ALA00.0660.05633.0100.3720.3720.0000.0000.0000.000
111A139GLY00.0170.02931.6380.3800.3800.0000.0000.0000.000
112A140ILE0-0.048-0.01829.9360.4650.4650.0000.0000.0000.000
113A141SER0-0.033-0.03428.5360.5230.5230.0000.0000.0000.000
114A142SER0-0.042-0.04727.1550.5500.5500.0000.0000.0000.000
115A143ASN0-0.035-0.02425.5530.7300.7300.0000.0000.0000.000
116A144VAL00.009-0.00123.9390.6660.6660.0000.0000.0000.000
117A145VAL0-0.0010.00822.9770.6340.6340.0000.0000.0000.000
118A146PRO00.0330.01020.6730.6640.6640.0000.0000.0000.000
119A147MET0-0.0390.00918.9061.0211.0210.0000.0000.0000.000
120A148TYR0-0.053-0.04718.4530.7500.7500.0000.0000.0000.000
121A149LEU0-0.003-0.00318.0850.6690.6690.0000.0000.0000.000
122A150GLY00.0090.00715.4321.0911.0910.0000.0000.0000.000
123A151GLU-1-0.765-0.84613.84118.21018.2100.0000.0000.0000.000
124A152LEU0-0.0430.00114.0190.7480.7480.0000.0000.0000.000
125A153ALA00.0170.01213.0480.8720.8720.0000.0000.0000.000
126A154PRO00.0230.0237.8941.0101.0100.0000.0000.0000.000
127A155LYS10.9170.9281.699-114.831-117.34412.889-6.271-4.1060.087
128A156ASN00.0380.0268.648-1.436-1.4360.0000.0000.0000.000
129A157LEU0-0.026-0.02110.371-2.353-2.3530.0000.0000.0000.000
130A158ARG10.7390.8999.036-30.708-30.7080.0000.0000.0000.000
131A159GLY00.0290.00712.749-1.528-1.5280.0000.0000.0000.000
132A160ALA00.000-0.00714.530-1.484-1.4840.0000.0000.0000.000
133A161LEU0-0.022-0.03016.084-1.190-1.1900.0000.0000.0000.000
134A162GLY00.0460.02817.040-0.717-0.7170.0000.0000.0000.000
135A163VAL0-0.020-0.01718.327-0.852-0.8520.0000.0000.0000.000
136A164VAL0-0.036-0.02020.579-0.844-0.8440.0000.0000.0000.000
137A165PRO00.0470.01821.714-0.713-0.7130.0000.0000.0000.000
138A166GLN00.0450.02324.473-0.481-0.4810.0000.0000.0000.000
139A167LEU0-0.014-0.00524.991-0.432-0.4320.0000.0000.0000.000
140A168PHE0-0.002-0.01725.273-0.487-0.4870.0000.0000.0000.000
141A169ILE00.0110.01528.010-0.452-0.4520.0000.0000.0000.000
142A170THR0-0.013-0.00629.470-0.413-0.4130.0000.0000.0000.000
143A171VAL00.0050.00130.209-0.383-0.3830.0000.0000.0000.000
144A172GLY00.0240.00832.670-0.328-0.3280.0000.0000.0000.000
145A173ILE00.0170.00234.116-0.287-0.2870.0000.0000.0000.000
146A174LEU0-0.0280.00235.453-0.308-0.3080.0000.0000.0000.000
147A175VAL0-0.016-0.02835.924-0.273-0.2730.0000.0000.0000.000
148A176ALA00.0040.01838.495-0.243-0.2430.0000.0000.0000.000
149A177GLN00.0310.02140.417-0.149-0.1490.0000.0000.0000.000
150A178LEU0-0.008-0.00339.390-0.219-0.2190.0000.0000.0000.000
151A179PHE0-0.023-0.01842.094-0.201-0.2010.0000.0000.0000.000
152A180GLY00.0350.02743.922-0.160-0.1600.0000.0000.0000.000
153A181LEU00.000-0.00545.289-0.187-0.1870.0000.0000.0000.000
154A182ARG10.9340.96846.322-6.641-6.6410.0000.0000.0000.000
155A183SER0-0.0040.00047.818-0.115-0.1150.0000.0000.0000.000
156A184VAL00.0190.01949.505-0.129-0.1290.0000.0000.0000.000
157A185LEU0-0.077-0.04250.631-0.118-0.1180.0000.0000.0000.000
158A186ALA0-0.071-0.01951.425-0.109-0.1090.0000.0000.0000.000
159A187SER0-0.083-0.05152.850-0.103-0.1030.0000.0000.0000.000
160A188GLU-1-0.890-0.94553.4565.5595.5590.0000.0000.0000.000
161A189GLU-1-0.839-0.91851.9336.2036.2030.0000.0000.0000.000
162A190GLY00.0390.02249.251-0.058-0.0580.0000.0000.0000.000
163A191TRP00.0650.02148.7280.1570.1570.0000.0000.0000.000
164A192PRO00.0180.01648.2280.1310.1310.0000.0000.0000.000
165A193ILE00.0260.00845.1110.1470.1470.0000.0000.0000.000
166A194LEU00.0290.00844.3290.1950.1950.0000.0000.0000.000
167A195LEU00.0010.00143.3380.1970.1970.0000.0000.0000.000
168A196GLY00.0050.01243.0100.1460.1460.0000.0000.0000.000
169A197LEU0-0.038-0.01338.7560.2250.2250.0000.0000.0000.000
170A198THR0-0.019-0.02038.7390.2360.2360.0000.0000.0000.000
171A199GLY00.0320.02138.4110.2060.2060.0000.0000.0000.000
172A200VAL00.004-0.00135.8970.1920.1920.0000.0000.0000.000
173A201PRO0-0.0140.01233.0490.1960.1960.0000.0000.0000.000
174A202ALA00.0390.01832.9640.2770.2770.0000.0000.0000.000
175A203GLY00.0150.00634.5100.0860.0860.0000.0000.0000.000
176A204LEU00.013-0.00631.9060.0980.0980.0000.0000.0000.000
177A205GLN0-0.0140.00128.5580.3310.3310.0000.0000.0000.000
178A206LEU0-0.024-0.02630.4200.2290.2290.0000.0000.0000.000
179A207LEU0-0.021-0.00232.7000.0290.0290.0000.0000.0000.000
180A208LEU00.0270.00428.8460.1300.1300.0000.0000.0000.000
181A209LEU00.0190.01423.9000.2960.2960.0000.0000.0000.000
182A210PRO0-0.014-0.01126.0420.5200.5200.0000.0000.0000.000
183A211PHE0-0.0210.00327.0970.1530.1530.0000.0000.0000.000
184A212PHE0-0.0140.00821.8090.3550.3550.0000.0000.0000.000
185A213PRO0-0.0040.01418.639-0.253-0.2530.0000.0000.0000.000
186A214GLU-1-0.757-0.88320.69013.47513.4750.0000.0000.0000.000
187A215SER0-0.016-0.04417.4860.9280.9280.0000.0000.0000.000
188A216PRO00.0410.01413.660-0.663-0.6630.0000.0000.0000.000
189A217ARG10.7740.8438.185-28.288-28.2880.0000.0000.0000.000
190A218TYR0-0.005-0.00515.461-0.618-0.6180.0000.0000.0000.000
191A219LEU0-0.044-0.01618.533-0.708-0.7080.0000.0000.0000.000
192A220LEU00.0400.03813.617-0.656-0.6560.0000.0000.0000.000
193A221ILE0-0.033-0.00514.339-0.582-0.5820.0000.0000.0000.000
194A222GLN0-0.032-0.03118.462-0.329-0.3290.0000.0000.0000.000
195A223LYS10.8890.94421.499-12.224-12.2240.0000.0000.0000.000
196A224LYS10.9320.98120.976-12.597-12.5970.0000.0000.0000.000
197A225ASN0-0.005-0.00721.223-0.049-0.0490.0000.0000.0000.000
198A226GLU-1-0.768-0.88017.34516.19616.1960.0000.0000.0000.000
199A227SER00.0550.02218.0100.4290.4290.0000.0000.0000.000
200A228ALA0-0.023-0.01419.4650.2420.2420.0000.0000.0000.000
201A229ALA00.0060.00315.9110.1810.1810.0000.0000.0000.000
202A230GLU-1-0.736-0.86414.84215.76115.7610.0000.0000.0000.000
203A231LYS10.8640.91815.411-13.375-13.3750.0000.0000.0000.000
204A232ALA0-0.020-0.00717.045-0.001-0.0010.0000.0000.0000.000
205A233LEU00.024-0.00110.5350.0740.0740.0000.0000.0000.000
206A234GLN0-0.068-0.02612.9630.0360.0360.0000.0000.0000.000
207A235THR0-0.052-0.03414.8130.0700.0700.0000.0000.0000.000
208A236LEU0-0.032-0.00613.991-0.137-0.1370.0000.0000.0000.000
209A237ARG10.7270.8328.718-25.035-25.0350.0000.0000.0000.000
210A238GLY0-0.009-0.01312.1140.0630.0630.0000.0000.0000.000
211A239TRP0-0.045-0.0266.598-0.761-0.7610.0000.0000.0000.000
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