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: LZ7K9

Calculation Name: 4LDS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LDS

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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 OptH
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 421
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7170879.025756
FMO2-HF: Nuclear repulsion 7013506.948317
FMO2-HF: Total energy -157372.077439
FMO2-MP2: Total energy -157835.245461


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:LEU)


Summations of interaction energy for fragment #1(A:7:LEU)
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.
-4.178-0.000999999999999592.843-1.854-5.1660
Interaction energy analysis for fragmet #1(A:7:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.010
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].
3A9PHE00.0380.0013.848-2.469-1.163-0.009-0.548-0.7490.001
4A10ILE00.0100.0152.365-1.853-0.5032.159-0.824-2.6850.000
5A11LEU00.0390.0052.392-1.2530.1730.694-0.474-1.646-0.001
6A12GLY00.0260.0154.7810.2850.380-0.001-0.008-0.0860.000
7A13ALA00.0010.0107.4860.0620.0620.0000.0000.0000.000
8A14LEU0-0.033-0.0105.8160.0270.0270.0000.0000.0000.000
9A15GLY00.0270.0108.7020.0410.0410.0000.0000.0000.000
10A16GLY00.0120.00611.1910.0460.0460.0000.0000.0000.000
11A17LEU0-0.074-0.02910.4190.0200.0200.0000.0000.0000.000
12A18LEU00.0310.01812.5980.0180.0180.0000.0000.0000.000
13A19TYR0-0.023-0.00314.4630.0300.0300.0000.0000.0000.000
14A20GLY00.028-0.00816.7070.0110.0110.0000.0000.0000.000
15A21TYR0-0.041-0.02116.4510.0100.0100.0000.0000.0000.000
16A22ASP-1-0.804-0.91918.317-0.127-0.1270.0000.0000.0000.000
17A23ASN0-0.036-0.03020.9710.0070.0070.0000.0000.0000.000
18A24GLY00.020-0.00221.6590.0060.0060.0000.0000.0000.000
19A25VAL00.0330.02720.9140.0040.0040.0000.0000.0000.000
20A26ILE0-0.050-0.04023.2500.0040.0040.0000.0000.0000.000
21A27SER00.0100.00424.9000.0080.0080.0000.0000.0000.000
22A28GLY00.036-0.00825.3880.0050.0050.0000.0000.0000.000
23A29ALA00.0080.01126.7970.0030.0030.0000.0000.0000.000
24A30LEU0-0.069-0.03929.0030.0040.0040.0000.0000.0000.000
25A31LEU0-0.074-0.01128.5470.0070.0070.0000.0000.0000.000
26A32PHE00.000-0.00729.7770.0030.0030.0000.0000.0000.000
27A33ILE00.0160.03132.6730.0000.0000.0000.0000.0000.000
28A34HIS00.002-0.02434.731-0.003-0.0030.0000.0000.0000.000
29A35LYS10.8990.96535.8440.0730.0730.0000.0000.0000.000
30A36ASP-1-0.852-0.93832.613-0.081-0.0810.0000.0000.0000.000
31A37ILE0-0.089-0.04336.0280.0000.0000.0000.0000.0000.000
32A38PRO0-0.0150.00037.4110.0010.0010.0000.0000.0000.000
33A39LEU0-0.070-0.01939.1550.0020.0020.0000.0000.0000.000
34A40ASN00.0950.02141.5830.0000.0000.0000.0000.0000.000
35A41SER00.0940.05938.818-0.001-0.0010.0000.0000.0000.000
36A42THR0-0.008-0.00138.635-0.001-0.0010.0000.0000.0000.000
37A43THR0-0.021-0.02038.7120.0010.0010.0000.0000.0000.000
38A44GLU-1-0.809-0.92635.032-0.049-0.0490.0000.0000.0000.000
39A45GLY00.0570.04434.546-0.002-0.0020.0000.0000.0000.000
40A46ILE00.0020.06235.2090.0000.0000.0000.0000.0000.000
41A47VAL00.1110.05631.869-0.001-0.0010.0000.0000.0000.000
42A48VAL0-0.0030.05628.851-0.004-0.0040.0000.0000.0000.000
43A49SER0-0.039-0.09830.5300.0030.0030.0000.0000.0000.000
44A50SER0-0.129-0.11431.9910.0000.0000.0000.0000.0000.000
45A51MET0-0.003-0.02225.198-0.001-0.0010.0000.0000.0000.000
46A52LEU00.046-0.00126.5820.0000.0000.0000.0000.0000.000
47A53ILE00.0150.01928.9810.0060.0060.0000.0000.0000.000
48A54GLY0-0.027-0.01128.1990.0040.0040.0000.0000.0000.000
49A55ALA0-0.018-0.00725.5900.0020.0020.0000.0000.0000.000
50A56ILE00.0080.00826.5800.0070.0070.0000.0000.0000.000
51A57VAL0-0.037-0.02029.1960.0060.0060.0000.0000.0000.000
52A58GLY0-0.011-0.00925.8430.0040.0040.0000.0000.0000.000
53A59ALA00.0400.03824.7530.0020.0020.0000.0000.0000.000
54A60GLY0-0.0050.01225.7930.0100.0100.0000.0000.0000.000
55A61SER0-0.079-0.04828.1820.0080.0080.0000.0000.0000.000
56A62SER00.0450.01222.842-0.002-0.0020.0000.0000.0000.000
57A63GLY00.0180.00624.7670.0030.0030.0000.0000.0000.000
58A64PRO00.0370.01125.9920.0030.0030.0000.0000.0000.000
59A65LEU0-0.018-0.00126.4860.0010.0010.0000.0000.0000.000
60A66ALA0-0.029-0.01523.034-0.002-0.0020.0000.0000.0000.000
61A67ASP-1-0.890-0.94024.8610.0750.0750.0000.0000.0000.000
62A68LYS10.8640.96027.541-0.003-0.0030.0000.0000.0000.000
63A69LEU0-0.076-0.06425.9470.0000.0000.0000.0000.0000.000
64A70GLY00.0210.03123.329-0.005-0.0050.0000.0000.0000.000
65A71ARG10.9810.97618.944-0.124-0.1240.0000.0000.0000.000
66A72ARG10.9180.96513.9710.0400.0400.0000.0000.0000.000
67A73ARG10.9450.95417.167-0.007-0.0070.0000.0000.0000.000
68A74LEU00.0070.03619.678-0.018-0.0180.0000.0000.0000.000
69A75VAL00.0580.01313.622-0.015-0.0150.0000.0000.0000.000
70A76MET0-0.0100.00914.019-0.046-0.0460.0000.0000.0000.000
71A77LEU0-0.020-0.00216.264-0.022-0.0220.0000.0000.0000.000
72A78ILE0-0.0110.00017.737-0.007-0.0070.0000.0000.0000.000
73A79ALA00.0130.01014.190-0.007-0.0070.0000.0000.0000.000
74A80ILE00.023-0.00916.056-0.016-0.0160.0000.0000.0000.000
75A81VAL0-0.039-0.01018.7740.0050.0050.0000.0000.0000.000
76A82PHE0-0.0030.00516.7630.0050.0050.0000.0000.0000.000
77A83ILE00.0050.00917.8710.0020.0020.0000.0000.0000.000
78A84ILE0-0.010-0.01419.4940.0090.0090.0000.0000.0000.000
79A85GLY00.0390.00722.7130.0060.0060.0000.0000.0000.000
80A86ALA00.0480.00520.2520.0080.0080.0000.0000.0000.000
81A87LEU00.010-0.00420.7900.0020.0020.0000.0000.0000.000
82A88ILE0-0.066-0.01423.3730.0110.0110.0000.0000.0000.000
83A89LEU0-0.075-0.02125.1810.0100.0100.0000.0000.0000.000
84A90ALA0-0.0170.00324.0370.0000.0000.0000.0000.0000.000
85A91ALA0-0.041-0.01726.1130.0000.0000.0000.0000.0000.000
86A92SER00.007-0.03529.8200.0010.0010.0000.0000.0000.000
87A93THR00.0140.01833.195-0.001-0.0010.0000.0000.0000.000
88A94ASN00.0290.01436.8970.0000.0000.0000.0000.0000.000
89A95LEU00.0480.01236.089-0.003-0.0030.0000.0000.0000.000
90A96ALA00.0060.01235.9090.0000.0000.0000.0000.0000.000
91A97LEU00.0270.01531.3890.0020.0020.0000.0000.0000.000
92A98LEU00.0480.03530.617-0.005-0.0050.0000.0000.0000.000
93A99ILE00.0370.01631.5540.0000.0000.0000.0000.0000.000
94A100ILE00.021-0.02330.9380.0000.0000.0000.0000.0000.000
95A101GLY00.0430.01928.561-0.003-0.0030.0000.0000.0000.000
96A102ARG10.9000.95525.3480.0780.0780.0000.0000.0000.000
97A103LEU0-0.0420.01527.3670.0020.0020.0000.0000.0000.000
98A104ILE0-0.011-0.00424.5490.0020.0020.0000.0000.0000.000
99A105ILE00.0190.01021.684-0.002-0.0020.0000.0000.0000.000
100A106GLY00.0100.01322.663-0.003-0.0030.0000.0000.0000.000
101A107LEU0-0.091-0.04023.9320.0050.0050.0000.0000.0000.000
102A108ALA0-0.0050.00119.6060.0090.0090.0000.0000.0000.000
103A109VAL00.0840.03919.6690.0040.0040.0000.0000.0000.000
104A110GLY0-0.022-0.01720.4830.0120.0120.0000.0000.0000.000
105A111GLY00.0400.00020.6290.0150.0150.0000.0000.0000.000
106A112SER0-0.050-0.02415.8280.0210.0210.0000.0000.0000.000
107A113MET0-0.058-0.01917.9040.0240.0240.0000.0000.0000.000
108A114SER0-0.060-0.02819.9970.0230.0230.0000.0000.0000.000
109A115THR00.004-0.00817.4260.0220.0220.0000.0000.0000.000
110A116VAL00.0160.01012.8440.0300.0300.0000.0000.0000.000
111A117PRO00.0400.00814.5980.0480.0480.0000.0000.0000.000
112A118VAL0-0.006-0.01615.9290.0530.0530.0000.0000.0000.000
113A119TYR00.0030.01412.7460.0200.0200.0000.0000.0000.000
114A120LEU0-0.044-0.02610.4190.0520.0520.0000.0000.0000.000
115A121SER0-0.035-0.01213.3180.0770.0770.0000.0000.0000.000
116A122GLU-1-0.865-0.93116.4870.1640.1640.0000.0000.0000.000
117A123MET0-0.016-0.02010.633-0.010-0.0100.0000.0000.0000.000
118A124ALA0-0.0150.01511.5120.1520.1520.0000.0000.0000.000
119A125PRO00.0310.02613.248-0.097-0.0970.0000.0000.0000.000
120A126THR0-0.054-0.04316.1000.0220.0220.0000.0000.0000.000
121A127GLU-1-0.786-0.90516.7230.3560.3560.0000.0000.0000.000
122A128TYR00.0010.00811.4440.1000.1000.0000.0000.0000.000
123A129ARG10.9030.95414.223-0.323-0.3230.0000.0000.0000.000
124A130GLY00.0370.02715.205-0.058-0.0580.0000.0000.0000.000
125A131SER00.1140.02916.0950.0090.0090.0000.0000.0000.000
126A132LEU00.0710.12610.837-0.014-0.0140.0000.0000.0000.000
127A133GLY00.0340.00912.1570.0090.0090.0000.0000.0000.000
128A134SER0-0.190-0.16314.300-0.045-0.0450.0000.0000.0000.000
129A135LEU00.0960.0439.171-0.036-0.0360.0000.0000.0000.000
130A136ASN0-0.023-0.01911.296-0.097-0.0970.0000.0000.0000.000
131A137GLN0-0.005-0.00712.206-0.064-0.0640.0000.0000.0000.000
132A138LEU0-0.0010.00513.277-0.038-0.0380.0000.0000.0000.000
133A139MET00.0160.0056.924-0.046-0.0460.0000.0000.0000.000
134A140ILE00.0210.01912.070-0.059-0.0590.0000.0000.0000.000
135A141THR0-0.048-0.03414.889-0.028-0.0280.0000.0000.0000.000
136A142ILE00.0400.00911.655-0.010-0.0100.0000.0000.0000.000
137A143GLY00.022-0.01114.300-0.029-0.0290.0000.0000.0000.000
138A144ILE0-0.022-0.00214.906-0.008-0.0080.0000.0000.0000.000
139A145LEU0-0.085-0.00517.832-0.007-0.0070.0000.0000.0000.000
140A146ALA00.058-0.01815.186-0.001-0.0010.0000.0000.0000.000
141A147ALA0-0.0070.02917.182-0.011-0.0110.0000.0000.0000.000
142A148TYR0-0.122-0.11818.798-0.001-0.0010.0000.0000.0000.000
143A149LEU0-0.0320.00717.7980.0050.0050.0000.0000.0000.000
144A150VAL00.008-0.01317.2050.0020.0020.0000.0000.0000.000
145A151ASN0-0.074-0.03720.5780.0030.0030.0000.0000.0000.000
146A152TYR00.0530.00723.3320.0040.0040.0000.0000.0000.000
147A153ALA0-0.0200.00122.2730.0040.0040.0000.0000.0000.000
148A154PHE0-0.065-0.04220.333-0.001-0.0010.0000.0000.0000.000
149A155ALA00.007-0.00225.4180.0070.0070.0000.0000.0000.000
150A156ASP-1-0.899-0.95128.552-0.082-0.0820.0000.0000.0000.000
151A157ILE00.0140.02328.585-0.010-0.0100.0000.0000.0000.000
152A158GLU-1-0.944-0.99428.657-0.102-0.1020.0000.0000.0000.000
153A159GLY00.011-0.00326.249-0.009-0.0090.0000.0000.0000.000
154A160TRP00.0540.00323.336-0.017-0.0170.0000.0000.0000.000
155A161ARG10.9290.98224.2520.0950.0950.0000.0000.0000.000
156A162TRP0-0.020-0.01021.736-0.006-0.0060.0000.0000.0000.000
157A163MET0-0.0840.00820.080-0.019-0.0190.0000.0000.0000.000
158A164LEU00.0430.04920.376-0.009-0.0090.0000.0000.0000.000
159A165GLY00.0170.00520.745-0.008-0.0080.0000.0000.0000.000
160A166LEU0-0.072-0.03616.927-0.027-0.0270.0000.0000.0000.000
161A167ALA00.0410.04416.529-0.026-0.0260.0000.0000.0000.000
162A168VAL0-0.013-0.00916.735-0.019-0.0190.0000.0000.0000.000
163A169VAL0-0.0040.00112.327-0.031-0.0310.0000.0000.0000.000
164A170PRO00.0080.00411.206-0.070-0.0700.0000.0000.0000.000
165A171SER0-0.025-0.02211.850-0.018-0.0180.0000.0000.0000.000
166A172VAL00.028-0.00512.5700.0170.0170.0000.0000.0000.000
167A173ILE0-0.0050.0167.533-0.040-0.0400.0000.0000.0000.000
168A174LEU00.0520.0538.104-0.132-0.1320.0000.0000.0000.000
169A175LEU00.011-0.0049.4700.0320.0320.0000.0000.0000.000
170A176VAL00.017-0.0147.1290.0280.0280.0000.0000.0000.000
171A177GLY0-0.056-0.0246.341-0.083-0.0830.0000.0000.0000.000
172A178ILE0-0.109-0.0677.3300.1550.1550.0000.0000.0000.000
173A179TYR00.0060.00310.0760.0780.0780.0000.0000.0000.000
174A180PHE0-0.036-0.0174.9530.1050.1050.0000.0000.0000.000
175A181MET0-0.102-0.0188.1320.1050.1050.0000.0000.0000.000
176A182PRO00.0740.03111.555-0.037-0.0370.0000.0000.0000.000
177A183GLU-1-0.924-0.96914.8600.0400.0400.0000.0000.0000.000
178A184SER0-0.096-0.02816.7960.0260.0260.0000.0000.0000.000
179A185PRO00.1470.04015.389-0.018-0.0180.0000.0000.0000.000
180A186ARG10.9410.92718.096-0.319-0.3190.0000.0000.0000.000
181A187TRP0-0.0160.01020.603-0.018-0.0180.0000.0000.0000.000
182A188LEU0-0.045-0.01319.649-0.013-0.0130.0000.0000.0000.000
183A189LEU0-0.049-0.05521.657-0.007-0.0070.0000.0000.0000.000
184A190GLU-1-0.945-0.96224.3950.0970.0970.0000.0000.0000.000
185A191ASN0-0.0080.00526.263-0.010-0.0100.0000.0000.0000.000
186A192ARG10.9020.95027.985-0.076-0.0760.0000.0000.0000.000
187A193ASN00.0070.01125.314-0.005-0.0050.0000.0000.0000.000
188A194GLU-1-0.856-0.95824.1630.1730.1730.0000.0000.0000.000
189A195GLU-1-0.879-0.90623.6490.1130.1130.0000.0000.0000.000
190A196ALA0-0.027-0.02219.6910.0200.0200.0000.0000.0000.000
191A197ALA0-0.001-0.00419.2710.0310.0310.0000.0000.0000.000
192A198ARG11.0231.01919.672-0.132-0.1320.0000.0000.0000.000
193A199GLN0-0.020-0.03620.0750.0220.0220.0000.0000.0000.000
194A200VAL00.0190.02614.4680.0260.0260.0000.0000.0000.000
195A201MET0-0.044-0.00915.3560.0910.0910.0000.0000.0000.000
196A202LYS10.8500.93917.107-0.191-0.1910.0000.0000.0000.000
197A203ILE0-0.015-0.00211.8680.0290.0290.0000.0000.0000.000
198A204THR0-0.087-0.03611.1100.0890.0890.0000.0000.0000.000
199A205TYR0-0.022-0.0508.7210.0860.0860.0000.0000.0000.000
200A206ASP-1-0.914-0.93314.2880.3970.3970.0000.0000.0000.000
201A207ASP-1-0.848-0.94217.1500.2370.2370.0000.0000.0000.000
202A208SER0-0.066-0.02420.247-0.038-0.0380.0000.0000.0000.000
203A209GLU-1-0.876-0.95020.4670.2580.2580.0000.0000.0000.000
204A210ILE0-0.040-0.00118.369-0.016-0.0160.0000.0000.0000.000
205A211ASP-1-0.829-0.90421.3960.1760.1760.0000.0000.0000.000
206A212LYS10.8430.89124.769-0.269-0.2690.0000.0000.0000.000
207A213GLU-1-0.817-0.90920.1820.2850.2850.0000.0000.0000.000
208A214LEU0-0.076-0.01922.296-0.010-0.0100.0000.0000.0000.000
209A215LYS10.8850.94423.809-0.211-0.2110.0000.0000.0000.000
210A216GLU-1-0.870-0.92524.2410.2060.2060.0000.0000.0000.000
211A217MET0-0.078-0.03221.803-0.003-0.0030.0000.0000.0000.000
212A218LYS10.9730.99624.915-0.132-0.1320.0000.0000.0000.000
213A219GLU-1-0.949-0.96727.7850.1270.1270.0000.0000.0000.000
214A220ILE0-0.027-0.03724.563-0.014-0.0140.0000.0000.0000.000
215A221ASN00.0020.00525.213-0.008-0.0080.0000.0000.0000.000
216A222ALA00.0330.04328.923-0.012-0.0120.0000.0000.0000.000
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