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: 94M12

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 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 421
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7171383.601029
FMO2-HF: Nuclear repulsion 7014006.514351
FMO2-HF: Total energy -157377.086678
FMO2-MP2: Total energy -157839.743942


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.
-3.9360.1522.884-1.836-5.1350
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 : 0.051 / q_NPA : 0.008
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].
3A9PHE00.0470.0053.848-2.425-1.088-0.009-0.561-0.7670.001
4A10ILE00.0050.0082.391-1.849-0.5322.345-0.854-2.8080.000
5A11LEU00.0530.0192.434-1.1280.2130.549-0.414-1.475-0.001
6A12GLY00.0130.0094.8400.2800.373-0.001-0.007-0.0850.000
7A13ALA0-0.0030.0067.5060.0660.0660.0000.0000.0000.000
8A14LEU0-0.021-0.0086.0760.0310.0310.0000.0000.0000.000
9A15GLY00.0290.0108.7310.0420.0420.0000.0000.0000.000
10A16GLY00.0170.00711.2340.0480.0480.0000.0000.0000.000
11A17LEU0-0.067-0.02610.6120.0210.0210.0000.0000.0000.000
12A18LEU00.0250.01612.6240.0190.0190.0000.0000.0000.000
13A19TYR0-0.025-0.01314.4980.0340.0340.0000.0000.0000.000
14A20GLY00.0290.00216.7390.0110.0110.0000.0000.0000.000
15A21TYR0-0.023-0.02416.4960.0130.0130.0000.0000.0000.000
16A22ASP-1-0.741-0.89418.351-0.109-0.1090.0000.0000.0000.000
17A23ASN00.003-0.01221.0000.0070.0070.0000.0000.0000.000
18A24GLY00.0200.00021.7660.0060.0060.0000.0000.0000.000
19A25VAL0-0.0080.00920.9530.0040.0040.0000.0000.0000.000
20A26ILE0-0.008-0.01823.3890.0040.0040.0000.0000.0000.000
21A27SER0-0.0020.00325.4660.0090.0090.0000.0000.0000.000
22A28GLY00.0330.00025.7610.0050.0050.0000.0000.0000.000
23A29ALA00.0150.01727.0960.0030.0030.0000.0000.0000.000
24A30LEU0-0.044-0.03429.1540.0040.0040.0000.0000.0000.000
25A31LEU0-0.044-0.00229.1690.0060.0060.0000.0000.0000.000
26A32PHE0-0.011-0.01029.0270.0040.0040.0000.0000.0000.000
27A33ILE00.0180.02232.758-0.001-0.0010.0000.0000.0000.000
28A34HIS0-0.014-0.02234.795-0.003-0.0030.0000.0000.0000.000
29A35LYS10.8010.89534.4920.0780.0780.0000.0000.0000.000
30A36ASP-1-0.872-0.94432.526-0.083-0.0830.0000.0000.0000.000
31A37ILE0-0.097-0.04635.9830.0000.0000.0000.0000.0000.000
32A38PRO00.0220.02037.2390.0010.0010.0000.0000.0000.000
33A39LEU0-0.061-0.02239.1020.0020.0020.0000.0000.0000.000
34A40ASN00.050-0.00341.606-0.001-0.0010.0000.0000.0000.000
35A41SER00.0560.00138.840-0.001-0.0010.0000.0000.0000.000
36A42THR0-0.016-0.01338.659-0.001-0.0010.0000.0000.0000.000
37A43THR0-0.044-0.01938.9000.0010.0010.0000.0000.0000.000
38A44GLU-1-0.712-0.85434.906-0.049-0.0490.0000.0000.0000.000
39A45GLY00.0450.03534.577-0.002-0.0020.0000.0000.0000.000
40A46ILE0-0.047-0.00835.2450.0000.0000.0000.0000.0000.000
41A47VAL00.0640.04231.807-0.002-0.0020.0000.0000.0000.000
42A48VAL0-0.0110.00928.914-0.004-0.0040.0000.0000.0000.000
43A49SER0-0.007-0.03430.5710.0030.0030.0000.0000.0000.000
44A50SER0-0.026-0.03332.0410.0020.0020.0000.0000.0000.000
45A51MET0-0.064-0.03524.9780.0010.0010.0000.0000.0000.000
46A52LEU00.020-0.00626.777-0.001-0.0010.0000.0000.0000.000
47A53ILE0-0.0020.01229.0320.0060.0060.0000.0000.0000.000
48A54GLY0-0.022-0.00828.2640.0030.0030.0000.0000.0000.000
49A55ALA0-0.017-0.00825.5310.0010.0010.0000.0000.0000.000
50A56ILE00.0170.01126.6420.0060.0060.0000.0000.0000.000
51A57VAL0-0.036-0.02029.2660.0050.0050.0000.0000.0000.000
52A58GLY0-0.008-0.00225.9180.0030.0030.0000.0000.0000.000
53A59ALA00.0460.04724.8120.0010.0010.0000.0000.0000.000
54A60GLY0-0.0080.00625.8650.0100.0100.0000.0000.0000.000
55A61SER0-0.073-0.04428.2620.0080.0080.0000.0000.0000.000
56A62SER00.0410.00823.103-0.005-0.0050.0000.0000.0000.000
57A63GLY00.0070.00324.8520.0020.0020.0000.0000.0000.000
58A64PRO00.0520.01926.0040.0030.0030.0000.0000.0000.000
59A65LEU0-0.020-0.00426.5740.0010.0010.0000.0000.0000.000
60A66ALA0-0.024-0.01322.965-0.002-0.0020.0000.0000.0000.000
61A67ASP-1-0.876-0.93224.8610.0630.0630.0000.0000.0000.000
62A68LYS10.8820.96527.5410.0060.0060.0000.0000.0000.000
63A69LEU0-0.064-0.04926.0810.0000.0000.0000.0000.0000.000
64A70GLY00.0440.03723.317-0.007-0.0070.0000.0000.0000.000
65A71ARG10.8900.91219.006-0.102-0.1020.0000.0000.0000.000
66A72ARG10.8720.94314.9780.0600.0600.0000.0000.0000.000
67A73ARG10.9030.93017.1470.0030.0030.0000.0000.0000.000
68A74LEU00.0190.03219.658-0.018-0.0180.0000.0000.0000.000
69A75VAL00.0560.01913.896-0.013-0.0130.0000.0000.0000.000
70A76MET0-0.0180.00214.302-0.049-0.0490.0000.0000.0000.000
71A77LEU0-0.017-0.00316.234-0.020-0.0200.0000.0000.0000.000
72A78ILE00.0030.00817.506-0.007-0.0070.0000.0000.0000.000
73A79ALA00.0070.01114.166-0.006-0.0060.0000.0000.0000.000
74A80ILE00.0270.00016.142-0.014-0.0140.0000.0000.0000.000
75A81VAL0-0.036-0.01718.8610.0070.0070.0000.0000.0000.000
76A82PHE0-0.003-0.00716.9560.0050.0050.0000.0000.0000.000
77A83ILE00.0130.02518.1670.0030.0030.0000.0000.0000.000
78A84ILE0-0.035-0.02419.5630.0110.0110.0000.0000.0000.000
79A85GLY00.0360.00522.7880.0070.0070.0000.0000.0000.000
80A86ALA00.0150.00120.3550.0090.0090.0000.0000.0000.000
81A87LEU00.0310.00221.4890.0030.0030.0000.0000.0000.000
82A88ILE0-0.079-0.02323.5160.0110.0110.0000.0000.0000.000
83A89LEU0-0.085-0.02724.9900.0100.0100.0000.0000.0000.000
84A90ALA00.0120.00724.1360.0010.0010.0000.0000.0000.000
85A91ALA0-0.050-0.02126.1850.0000.0000.0000.0000.0000.000
86A92SER00.043-0.00929.9020.0010.0010.0000.0000.0000.000
87A93THR0-0.0090.00333.2560.0010.0010.0000.0000.0000.000
88A94ASN00.0420.01436.9700.0020.0020.0000.0000.0000.000
89A95LEU00.0610.01936.299-0.003-0.0030.0000.0000.0000.000
90A96ALA00.0120.02035.9580.0000.0000.0000.0000.0000.000
91A97LEU00.0040.00331.5500.0010.0010.0000.0000.0000.000
92A98LEU00.0420.03230.723-0.005-0.0050.0000.0000.0000.000
93A99ILE00.0310.01531.6040.0000.0000.0000.0000.0000.000
94A100ILE00.005-0.02231.075-0.001-0.0010.0000.0000.0000.000
95A101GLY00.0480.03028.624-0.003-0.0030.0000.0000.0000.000
96A102ARG10.8390.92124.3440.0880.0880.0000.0000.0000.000
97A103LEU0-0.0080.02127.4230.0010.0010.0000.0000.0000.000
98A104ILE0-0.016-0.00824.6480.0020.0020.0000.0000.0000.000
99A105ILE00.0220.00920.804-0.004-0.0040.0000.0000.0000.000
100A106GLY00.0210.01822.724-0.004-0.0040.0000.0000.0000.000
101A107LEU0-0.083-0.04123.9960.0040.0040.0000.0000.0000.000
102A108ALA0-0.013-0.00119.7590.0080.0080.0000.0000.0000.000
103A109VAL00.0470.02319.7380.0030.0030.0000.0000.0000.000
104A110GLY0-0.018-0.01020.5440.0120.0120.0000.0000.0000.000
105A111GLY00.0480.00820.6980.0150.0150.0000.0000.0000.000
106A112SER0-0.046-0.02915.6420.0180.0180.0000.0000.0000.000
107A113MET0-0.053-0.01417.9690.0250.0250.0000.0000.0000.000
108A114SER0-0.056-0.03020.0540.0230.0230.0000.0000.0000.000
109A115THR0-0.012-0.01018.1380.0210.0210.0000.0000.0000.000
110A116VAL0-0.0010.00112.8840.0290.0290.0000.0000.0000.000
111A117PRO00.0420.01214.5980.0440.0440.0000.0000.0000.000
112A118VAL0-0.002-0.00915.9370.0530.0530.0000.0000.0000.000
113A119TYR00.0070.00512.3390.0290.0290.0000.0000.0000.000
114A120LEU0-0.031-0.02110.4780.0440.0440.0000.0000.0000.000
115A121SER0-0.031-0.00913.3180.0780.0780.0000.0000.0000.000
116A122GLU-1-0.817-0.89016.5400.1460.1460.0000.0000.0000.000
117A123MET0-0.010-0.02310.451-0.004-0.0040.0000.0000.0000.000
118A124ALA0-0.0080.01711.4440.1410.1410.0000.0000.0000.000
119A125PRO00.0300.02413.248-0.089-0.0890.0000.0000.0000.000
120A126THR0-0.088-0.04816.0890.0170.0170.0000.0000.0000.000
121A127GLU-1-0.797-0.90817.1270.3610.3610.0000.0000.0000.000
122A128TYR00.0120.01811.2210.1100.1100.0000.0000.0000.000
123A129ARG10.8880.94414.223-0.319-0.3190.0000.0000.0000.000
124A130GLY00.0450.03415.203-0.058-0.0580.0000.0000.0000.000
125A131SER00.0840.02316.0940.0130.0130.0000.0000.0000.000
126A132LEU00.0300.04210.764-0.016-0.0160.0000.0000.0000.000
127A133GLY00.0490.01712.1580.0100.0100.0000.0000.0000.000
128A134SER0-0.105-0.07314.303-0.069-0.0690.0000.0000.0000.000
129A135LEU00.0580.0339.135-0.031-0.0310.0000.0000.0000.000
130A136ASN0-0.044-0.03211.282-0.103-0.1030.0000.0000.0000.000
131A137GLN00.0050.00012.218-0.057-0.0570.0000.0000.0000.000
132A138LEU00.0110.00813.298-0.039-0.0390.0000.0000.0000.000
133A139MET00.0050.0027.196-0.056-0.0560.0000.0000.0000.000
134A140ILE00.0090.01512.179-0.061-0.0610.0000.0000.0000.000
135A141THR0-0.027-0.00415.002-0.030-0.0300.0000.0000.0000.000
136A142ILE00.0380.00911.880-0.011-0.0110.0000.0000.0000.000
137A143GLY00.022-0.00714.662-0.030-0.0300.0000.0000.0000.000
138A144ILE0-0.0340.00115.246-0.009-0.0090.0000.0000.0000.000
139A145LEU0-0.072-0.01117.911-0.008-0.0080.0000.0000.0000.000
140A146ALA00.047-0.01015.561-0.002-0.0020.0000.0000.0000.000
141A147ALA00.0110.03717.545-0.011-0.0110.0000.0000.0000.000
142A148TYR0-0.065-0.05619.228-0.004-0.0040.0000.0000.0000.000
143A149LEU0-0.0280.00518.5900.0050.0050.0000.0000.0000.000
144A150VAL00.002-0.01317.3690.0010.0010.0000.0000.0000.000
145A151ASN0-0.074-0.02020.7970.0030.0030.0000.0000.0000.000
146A152TYR00.029-0.00123.4610.0050.0050.0000.0000.0000.000
147A153ALA0-0.0110.00822.3520.0050.0050.0000.0000.0000.000
148A154PHE0-0.068-0.03720.1830.0000.0000.0000.0000.0000.000
149A155ALA00.0150.00225.2810.0070.0070.0000.0000.0000.000
150A156ASP-1-0.809-0.88628.440-0.080-0.0800.0000.0000.0000.000
151A157ILE00.0240.00928.501-0.010-0.0100.0000.0000.0000.000
152A158GLU-1-0.832-0.92128.623-0.102-0.1020.0000.0000.0000.000
153A159GLY0-0.014-0.01226.225-0.009-0.0090.0000.0000.0000.000
154A160TRP00.0490.02224.097-0.016-0.0160.0000.0000.0000.000
155A161ARG10.8230.92224.2170.0970.0970.0000.0000.0000.000
156A162TRP0-0.009-0.00421.474-0.006-0.0060.0000.0000.0000.000
157A163MET0-0.063-0.02620.318-0.026-0.0260.0000.0000.0000.000
158A164LEU00.0480.03920.349-0.010-0.0100.0000.0000.0000.000
159A165GLY00.0140.01220.810-0.009-0.0090.0000.0000.0000.000
160A166LEU0-0.052-0.04216.685-0.028-0.0280.0000.0000.0000.000
161A167ALA00.0400.03616.528-0.025-0.0250.0000.0000.0000.000
162A168VAL0-0.026-0.01216.790-0.019-0.0190.0000.0000.0000.000
163A169VAL0-0.0130.02212.389-0.034-0.0340.0000.0000.0000.000
164A170PRO00.0190.00511.275-0.067-0.0670.0000.0000.0000.000
165A171SER0-0.044-0.04511.907-0.023-0.0230.0000.0000.0000.000
166A172VAL00.0430.00012.8120.0120.0120.0000.0000.0000.000
167A173ILE0-0.0070.0127.461-0.046-0.0460.0000.0000.0000.000
168A174LEU00.0500.0538.189-0.147-0.1470.0000.0000.0000.000
169A175LEU00.0080.0079.5540.0190.0190.0000.0000.0000.000
170A176VAL00.007-0.0157.2220.0180.0180.0000.0000.0000.000
171A177GLY0-0.053-0.0246.310-0.105-0.1050.0000.0000.0000.000
172A178ILE0-0.090-0.0747.2970.1330.1330.0000.0000.0000.000
173A179TYR00.0080.00310.0260.0820.0820.0000.0000.0000.000
174A180PHE0-0.048-0.0185.0740.1000.1000.0000.0000.0000.000
175A181MET0-0.070-0.0058.0280.1250.1250.0000.0000.0000.000
176A182PRO00.0450.02411.740-0.023-0.0230.0000.0000.0000.000
177A183GLU-1-0.855-0.93214.803-0.007-0.0070.0000.0000.0000.000
178A184SER0-0.055-0.01116.7270.0230.0230.0000.0000.0000.000
179A185PRO00.1010.03315.308-0.014-0.0140.0000.0000.0000.000
180A186ARG10.9060.92617.260-0.314-0.3140.0000.0000.0000.000
181A187TRP0-0.0040.00420.526-0.017-0.0170.0000.0000.0000.000
182A188LEU0-0.048-0.02219.678-0.012-0.0120.0000.0000.0000.000
183A189LEU0-0.034-0.04022.159-0.006-0.0060.0000.0000.0000.000
184A190GLU-1-0.956-0.96924.3170.0930.0930.0000.0000.0000.000
185A191ASN0-0.048-0.01926.184-0.011-0.0110.0000.0000.0000.000
186A192ARG10.9380.97027.879-0.068-0.0680.0000.0000.0000.000
187A193ASN00.0010.00525.319-0.006-0.0060.0000.0000.0000.000
188A194GLU-1-0.885-0.96024.0940.1510.1510.0000.0000.0000.000
189A195GLU-1-0.865-0.89623.5750.0970.0970.0000.0000.0000.000
190A196ALA0-0.023-0.03219.6920.0200.0200.0000.0000.0000.000
191A197ALA00.0050.00119.1990.0280.0280.0000.0000.0000.000
192A198ARG10.9250.97019.596-0.120-0.1200.0000.0000.0000.000
193A199GLN00.025-0.00820.0070.0270.0270.0000.0000.0000.000
194A200VAL00.0100.01814.1590.0240.0240.0000.0000.0000.000
195A201MET0-0.021-0.02015.2840.0910.0910.0000.0000.0000.000
196A202LYS10.7380.85617.035-0.200-0.2000.0000.0000.0000.000
197A203ILE0-0.049-0.01912.1600.0290.0290.0000.0000.0000.000
198A204THR0-0.078-0.03710.7510.0820.0820.0000.0000.0000.000
199A205TYR0-0.001-0.0339.6590.2610.2610.0000.0000.0000.000
200A206ASP-1-0.899-0.92214.2880.3960.3960.0000.0000.0000.000
201A207ASP-1-0.757-0.87317.0900.2160.2160.0000.0000.0000.000
202A208SER0-0.059-0.02120.229-0.037-0.0370.0000.0000.0000.000
203A209GLU-1-0.837-0.93020.3940.2540.2540.0000.0000.0000.000
204A210ILE0-0.057-0.01418.170-0.019-0.0190.0000.0000.0000.000
205A211ASP-1-0.774-0.86421.3960.1600.1600.0000.0000.0000.000
206A212LYS10.8170.88322.943-0.300-0.3000.0000.0000.0000.000
207A213GLU-1-0.783-0.88919.7930.3190.3190.0000.0000.0000.000
208A214LEU0-0.076-0.03322.326-0.011-0.0110.0000.0000.0000.000
209A215LYS10.8200.89323.767-0.195-0.1950.0000.0000.0000.000
210A216GLU-1-0.852-0.91624.3830.2100.2100.0000.0000.0000.000
211A217MET0-0.040-0.00821.778-0.001-0.0010.0000.0000.0000.000
212A218LYS10.9120.96724.915-0.124-0.1240.0000.0000.0000.000
213A219GLU-1-0.878-0.92627.7400.1170.1170.0000.0000.0000.000
214A220ILE0-0.033-0.03824.568-0.013-0.0130.0000.0000.0000.000
215A221ASN0-0.0010.00225.181-0.005-0.0050.0000.0000.0000.000
216A222ALA00.0380.03028.923-0.012-0.0120.0000.0000.0000.000
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