FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: G5261

Calculation Name: 1Z3X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z3X

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DIJ1

Base Structure: X-ray

Registration Date: 2023-09-23

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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3065459.621411
FMO2-HF: Nuclear repulsion 2971060.480605
FMO2-HF: Total energy -94399.140806
FMO2-MP2: Total energy -94680.056317


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:-2:PRO)


Summations of interaction energy for fragment #1(A:-2:PRO)
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.
-3.755-0.7970.015-1.241-1.732-0.003
Interaction energy analysis for fragmet #1(A:-2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.038
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].
3A0PHE00.0490.0313.334-1.5220.622-0.007-0.887-1.2490.000
4A1MET0-0.038-0.0263.449-1.242-0.4280.022-0.354-0.483-0.003
5A2VAL0-0.040-0.0205.6540.4080.4080.0000.0000.0000.000
6A3THR00.0420.0007.8700.0240.0240.0000.0000.0000.000
7A4THR0-0.068-0.06011.6150.0320.0320.0000.0000.0000.000
8A5GLU-1-0.878-0.94514.842-0.125-0.1250.0000.0000.0000.000
9A6PRO0-0.0120.00314.469-0.014-0.0140.0000.0000.0000.000
10A7ALA0-0.0050.00615.5180.0280.0280.0000.0000.0000.000
11A8LEU0-0.056-0.04815.2360.0190.0190.0000.0000.0000.000
12A9ALA00.0170.01111.793-0.047-0.0470.0000.0000.0000.000
13A10ASP-1-0.900-0.95012.130-0.027-0.0270.0000.0000.0000.000
14A11LEU0-0.040-0.02214.5020.0090.0090.0000.0000.0000.000
15A12GLN00.008-0.0038.7520.0530.0530.0000.0000.0000.000
16A13GLU-1-0.869-0.9239.1760.1650.1650.0000.0000.0000.000
17A14GLN00.0070.00311.0500.0310.0310.0000.0000.0000.000
18A15LEU0-0.055-0.02513.5310.0300.0300.0000.0000.0000.000
19A16TYR0-0.092-0.0818.5300.0850.0850.0000.0000.0000.000
20A17ASN0-0.023-0.0097.902-0.016-0.0160.0000.0000.0000.000
21A18GLY0-0.0020.02012.2370.0630.0630.0000.0000.0000.000
22A19ASN0-0.019-0.01815.831-0.022-0.0220.0000.0000.0000.000
23A20GLU-1-0.788-0.91619.007-0.044-0.0440.0000.0000.0000.000
24A21LYS10.9160.95621.071-0.018-0.0180.0000.0000.0000.000
25A22SER00.016-0.00318.391-0.002-0.0020.0000.0000.0000.000
26A23GLN0-0.0090.00614.9120.0030.0030.0000.0000.0000.000
27A24LEU0-0.013-0.02018.488-0.026-0.0260.0000.0000.0000.000
28A25ALA0-0.021-0.00921.911-0.009-0.0090.0000.0000.0000.000
29A26ALA00.0400.03217.129-0.007-0.0070.0000.0000.0000.000
30A27MET0-0.0060.00918.643-0.018-0.0180.0000.0000.0000.000
31A28SER00.0020.00219.496-0.006-0.0060.0000.0000.0000.000
32A29THR0-0.018-0.00120.7700.0040.0040.0000.0000.0000.000
33A30LEU00.0370.02715.3460.0000.0000.0000.0000.0000.000
34A31SER0-0.062-0.02819.564-0.007-0.0070.0000.0000.0000.000
35A32THR0-0.077-0.04622.3340.0110.0110.0000.0000.0000.000
36A33ALA0-0.011-0.00119.8650.0100.0100.0000.0000.0000.000
37A34GLY00.0100.00520.849-0.016-0.0160.0000.0000.0000.000
38A35THR0-0.010-0.03719.938-0.014-0.0140.0000.0000.0000.000
39A36GLU-1-0.773-0.82913.818-0.522-0.5220.0000.0000.0000.000
40A37GLY00.0360.02216.021-0.048-0.0480.0000.0000.0000.000
41A38TYR0-0.020-0.04117.124-0.023-0.0230.0000.0000.0000.000
42A39HIS00.0150.01311.9400.0470.0470.0000.0000.0000.000
43A40LEU00.0380.01611.727-0.081-0.0810.0000.0000.0000.000
44A41LEU0-0.041-0.00813.238-0.045-0.0450.0000.0000.0000.000
45A42GLN0-0.024-0.01815.4530.0420.0420.0000.0000.0000.000
46A43GLU-1-0.802-0.89010.087-1.097-1.0970.0000.0000.0000.000
47A44PHE00.0500.04111.597-0.057-0.0570.0000.0000.0000.000
48A45LEU0-0.0470.00112.8050.0380.0380.0000.0000.0000.000
49A46LYS10.7760.89110.9711.0791.0790.0000.0000.0000.000
50A47ASP-1-0.781-0.8658.308-1.620-1.6200.0000.0000.0000.000
51A48SER0-0.036-0.04211.0340.1170.1170.0000.0000.0000.000
52A49ALA0-0.083-0.03913.3390.1090.1090.0000.0000.0000.000
53A50THR0-0.047-0.02610.2670.0970.0970.0000.0000.0000.000
54A51PHE0-0.028-0.00610.1000.1120.1120.0000.0000.0000.000
55A52SER0-0.0150.01114.057-0.009-0.0090.0000.0000.0000.000
56A53PRO0-0.015-0.02416.1780.0480.0480.0000.0000.0000.000
57A54PRO0-0.005-0.02018.632-0.010-0.0100.0000.0000.0000.000
58A55PRO00.0410.03317.2270.0180.0180.0000.0000.0000.000
59A56ALA00.0290.02620.104-0.010-0.0100.0000.0000.0000.000
60A57PRO00.0280.00722.153-0.019-0.0190.0000.0000.0000.000
61A58TRP0-0.048-0.01723.807-0.020-0.0200.0000.0000.0000.000
62A59ILE0-0.0170.01518.038-0.009-0.0090.0000.0000.0000.000
63A60ARG10.9370.93916.3060.3210.3210.0000.0000.0000.000
64A61GLY0-0.0070.00620.359-0.013-0.0130.0000.0000.0000.000
65A62GLN00.0470.01823.2120.0030.0030.0000.0000.0000.000
66A63ALA00.0520.02118.625-0.004-0.0040.0000.0000.0000.000
67A64TYR00.013-0.00120.729-0.002-0.0020.0000.0000.0000.000
68A65ARG10.7560.86422.4990.1140.1140.0000.0000.0000.000
69A66LEU0-0.047-0.02321.8830.0070.0070.0000.0000.0000.000
70A67LEU0-0.021-0.01218.4120.0020.0020.0000.0000.0000.000
71A68PHE0-0.018-0.01622.8660.0090.0090.0000.0000.0000.000
72A69HIS0-0.047-0.02726.2450.0040.0040.0000.0000.0000.000
73A70SER0-0.0040.02023.6950.0100.0100.0000.0000.0000.000
74A71PRO0-0.014-0.01026.1520.0020.0020.0000.0000.0000.000
75A72GLU-1-0.858-0.90423.149-0.231-0.2310.0000.0000.0000.000
76A73ALA00.030-0.00325.646-0.006-0.0060.0000.0000.0000.000
77A74SER00.000-0.00421.3330.0010.0010.0000.0000.0000.000
78A75VAL00.0580.03920.555-0.020-0.0200.0000.0000.0000.000
79A76GLN0-0.043-0.03322.462-0.008-0.0080.0000.0000.0000.000
80A77ALA0-0.024-0.00124.0490.0050.0050.0000.0000.0000.000
81A78PHE00.0300.01416.907-0.003-0.0030.0000.0000.0000.000
82A79LEU00.006-0.00721.423-0.005-0.0050.0000.0000.0000.000
83A80GLN0-0.036-0.01323.5050.0130.0130.0000.0000.0000.000
84A81GLN0-0.067-0.04022.3670.0130.0130.0000.0000.0000.000
85A82HIS0-0.037-0.01318.871-0.002-0.0020.0000.0000.0000.000
86A83TYR0-0.031-0.01317.4510.0120.0120.0000.0000.0000.000
87A84PRO00.0450.03424.1160.0160.0160.0000.0000.0000.000
88A85GLN0-0.098-0.05727.5660.0130.0130.0000.0000.0000.000
89A86GLY0-0.0130.00726.3460.0110.0110.0000.0000.0000.000
90A87VAL00.003-0.01221.569-0.010-0.0100.0000.0000.0000.000
91A88ILE0-0.064-0.02123.605-0.001-0.0010.0000.0000.0000.000
92A89PRO0-0.008-0.01224.4460.0050.0050.0000.0000.0000.000
93A90LEU00.0060.00927.2020.0130.0130.0000.0000.0000.000
94A91ARG10.9570.97325.8360.0870.0870.0000.0000.0000.000
95A92SER0-0.034-0.04832.6500.0040.0040.0000.0000.0000.000
96A93ASP-1-0.851-0.93636.412-0.044-0.0440.0000.0000.0000.000
97A94ARG10.7750.86638.8630.0400.0400.0000.0000.0000.000
98A95GLY00.0050.01739.3030.0010.0010.0000.0000.0000.000
99A96VAL0-0.039-0.01039.206-0.001-0.0010.0000.0000.0000.000
100A97ASP-1-0.832-0.89936.723-0.094-0.0940.0000.0000.0000.000
101A98TYR0-0.011-0.06434.3800.0050.0050.0000.0000.0000.000
102A99GLN00.0300.00133.053-0.011-0.0110.0000.0000.0000.000
103A100GLU-1-0.855-0.91634.194-0.099-0.0990.0000.0000.0000.000
104A101LEU0-0.011-0.00235.5100.0000.0000.0000.0000.0000.000
105A102ALA00.0330.00930.6510.0000.0000.0000.0000.0000.000
106A103LYS10.8860.94031.7970.1050.1050.0000.0000.0000.000
107A104LEU0-0.035-0.02833.2780.0000.0000.0000.0000.0000.000
108A105LEU0-0.017-0.00332.4470.0020.0020.0000.0000.0000.000
109A106VAL00.0250.03827.6200.0020.0020.0000.0000.0000.000
110A107ALA00.0400.02930.498-0.001-0.0010.0000.0000.0000.000
111A108GLU-1-0.890-0.94531.564-0.096-0.0960.0000.0000.0000.000
112A109LYS10.8420.92634.5750.0930.0930.0000.0000.0000.000
113A110PHE00.0490.01233.1820.0030.0030.0000.0000.0000.000
114A111GLU-1-0.838-0.91438.666-0.044-0.0440.0000.0000.0000.000
115A112ALA0-0.027-0.02340.6330.0020.0020.0000.0000.0000.000
116A113ALA00.0430.02637.4900.0010.0010.0000.0000.0000.000
117A114ASP-1-0.794-0.89639.416-0.041-0.0410.0000.0000.0000.000
118A115ARG10.8520.92041.7310.0530.0530.0000.0000.0000.000
119A116LEU00.0120.01039.2330.0020.0020.0000.0000.0000.000
120A117THR00.0210.00139.5380.0000.0000.0000.0000.0000.000
121A118THR0-0.0010.00441.4910.0030.0030.0000.0000.0000.000
122A119GLN0-0.039-0.02844.9310.0000.0000.0000.0000.0000.000
123A120LYS10.8430.91340.1910.0650.0650.0000.0000.0000.000
124A121LEU00.0170.01841.2090.0010.0010.0000.0000.0000.000
125A122CYS0-0.078-0.03744.3240.0030.0030.0000.0000.0000.000
126A123GLU-1-0.839-0.91943.106-0.055-0.0550.0000.0000.0000.000
127A124LEU0-0.0150.01040.4810.0020.0020.0000.0000.0000.000
128A125ALA00.0170.01544.7050.0020.0020.0000.0000.0000.000
129A126GLY0-0.0040.01647.9570.0020.0020.0000.0000.0000.000
130A127PRO00.0500.00449.7560.0000.0000.0000.0000.0000.000
131A128LEU0-0.019-0.00552.3620.0000.0000.0000.0000.0000.000
132A129ALA00.0680.02950.6600.0010.0010.0000.0000.0000.000
133A130GLN00.0150.01447.5120.0010.0010.0000.0000.0000.000
134A131LYS10.9230.96451.0810.0280.0280.0000.0000.0000.000
135A132ARG10.7250.81853.2020.0250.0250.0000.0000.0000.000
136A133ARG10.9010.95751.7550.0350.0350.0000.0000.0000.000
137A134TRP0-0.010-0.01351.3810.0000.0000.0000.0000.0000.000
138A135LEU00.0350.02647.0220.0000.0000.0000.0000.0000.000
139A136TYR0-0.009-0.00451.4120.0010.0010.0000.0000.0000.000
140A137PHE00.014-0.01050.400-0.001-0.0010.0000.0000.0000.000
141A138THR00.0450.03049.807-0.001-0.0010.0000.0000.0000.000
142A139GLU-1-0.746-0.83249.528-0.025-0.0250.0000.0000.0000.000
143A140VAL0-0.021-0.01245.135-0.002-0.0020.0000.0000.0000.000
144A141GLU-1-0.884-0.96845.121-0.012-0.0120.0000.0000.0000.000
145A142GLN0-0.085-0.04345.3440.0000.0000.0000.0000.0000.000
146A143LEU0-0.0430.00542.144-0.002-0.0020.0000.0000.0000.000
147A144PRO00.0290.01039.2560.0020.0020.0000.0000.0000.000
148A145ILE00.0200.01034.876-0.002-0.0020.0000.0000.0000.000
149A146PRO00.0200.01433.883-0.002-0.0020.0000.0000.0000.000
150A147ASP-1-0.688-0.79134.235-0.059-0.0590.0000.0000.0000.000
151A148LEU00.0290.01536.189-0.004-0.0040.0000.0000.0000.000
152A149GLN0-0.035-0.02931.717-0.005-0.0050.0000.0000.0000.000
153A150THR0-0.0130.01631.591-0.007-0.0070.0000.0000.0000.000
154A151ILE00.0010.00032.484-0.005-0.0050.0000.0000.0000.000
155A152ASP-1-0.792-0.87133.163-0.041-0.0410.0000.0000.0000.000
156A153GLN00.0130.00127.157-0.008-0.0080.0000.0000.0000.000
157A154LEU0-0.0030.01229.315-0.008-0.0080.0000.0000.0000.000
158A155TRP0-0.009-0.02131.030-0.004-0.0040.0000.0000.0000.000
159A156LEU0-0.0280.02129.006-0.001-0.0010.0000.0000.0000.000
160A157ALA0-0.006-0.00626.455-0.001-0.0010.0000.0000.0000.000
161A158PHE00.0150.00726.540-0.009-0.0090.0000.0000.0000.000
162A159SER00.009-0.02029.6290.0050.0050.0000.0000.0000.000
163A160LEU00.000-0.00226.4230.0090.0090.0000.0000.0000.000
164A161GLY00.0620.02828.5500.0090.0090.0000.0000.0000.000
165A162ARG10.7660.87729.6960.0480.0480.0000.0000.0000.000
166A163PHE0-0.020-0.02333.2030.0060.0060.0000.0000.0000.000
167A164GLY00.0700.02933.648-0.004-0.0040.0000.0000.0000.000
168A165TYR00.0230.00435.8520.0030.0030.0000.0000.0000.000
169A166SER0-0.025-0.04633.2860.0060.0060.0000.0000.0000.000
170A167VAL00.0050.00433.1750.0070.0070.0000.0000.0000.000
171A168GLN0-0.043-0.04535.6760.0050.0050.0000.0000.0000.000
172A169ARG10.9010.96137.4720.0040.0040.0000.0000.0000.000
173A170GLN00.0090.00134.1680.0030.0030.0000.0000.0000.000
174A171LEU0-0.023-0.01037.5750.0040.0040.0000.0000.0000.000
175A172TRP00.0330.02439.7310.0030.0030.0000.0000.0000.000
176A173LEU0-0.009-0.01138.9750.0020.0020.0000.0000.0000.000
177A174GLY00.0030.01140.4440.0030.0030.0000.0000.0000.000
178A175CYS0-0.120-0.06141.2730.0010.0010.0000.0000.0000.000
179A176GLY0-0.007-0.01844.512-0.001-0.0010.0000.0000.0000.000
180A177GLN0-0.027-0.00545.2250.0020.0020.0000.0000.0000.000
181A178ASN0-0.048-0.01746.932-0.001-0.0010.0000.0000.0000.000
182A179TRP00.0510.00246.149-0.001-0.0010.0000.0000.0000.000
183A180ASP-1-0.867-0.92349.425-0.005-0.0050.0000.0000.0000.000
184A181ARG10.9410.96147.218-0.008-0.0080.0000.0000.0000.000
185A182LEU00.0030.01842.777-0.001-0.0010.0000.0000.0000.000
186A183TRP00.007-0.01245.550-0.002-0.0020.0000.0000.0000.000
187A184GLU-1-0.896-0.94947.471-0.011-0.0110.0000.0000.0000.000
188A185LYS10.9040.96740.0050.0000.0000.0000.0000.0000.000
189A186ILE0-0.027-0.01341.268-0.001-0.0010.0000.0000.0000.000
190A187GLY00.0340.03143.110-0.003-0.0030.0000.0000.0000.000
191A188TRP0-0.068-0.05543.6570.0000.0000.0000.0000.0000.000
192A189ARG10.8810.94348.1310.0120.0120.0000.0000.0000.000
193A190GLN00.0010.00350.7930.0000.0000.0000.0000.0000.000
194A191GLY00.0330.01153.3830.0000.0000.0000.0000.0000.000
195A192LYS10.9420.96055.7690.0080.0080.0000.0000.0000.000
196A193ARG10.7530.84954.9330.0200.0200.0000.0000.0000.000
197A194TRP00.0590.02651.2100.0000.0000.0000.0000.0000.000
198A195PRO00.0280.02049.3480.0000.0000.0000.0000.0000.000
199A196ARG10.9190.97252.3460.0260.0260.0000.0000.0000.000
200A197TYR0-0.0030.03746.437-0.001-0.0010.0000.0000.0000.000
201A198PRO00.010-0.01747.7780.0010.0010.0000.0000.0000.000
202A199ASN00.012-0.02648.2790.0000.0000.0000.0000.0000.000
203A200GLU-1-0.761-0.83349.402-0.022-0.0220.0000.0000.0000.000
204A201PHE0-0.0090.00145.2830.0020.0020.0000.0000.0000.000
205A202ILE00.0090.00641.114-0.001-0.0010.0000.0000.0000.000
206A203TRP0-0.034-0.03040.953-0.002-0.0020.0000.0000.0000.000
207A204ASP-1-0.766-0.85937.380-0.053-0.0530.0000.0000.0000.000
208A205LEU0-0.004-0.00731.4850.0040.0040.0000.0000.0000.000
209A206SER0-0.086-0.06135.4750.0050.0050.0000.0000.0000.000
210A207ALA0-0.0170.00937.8900.0050.0050.0000.0000.0000.000
211A208PRO00.0190.01237.9680.0000.0000.0000.0000.0000.000
212A209ARG10.9550.96930.1120.0220.0220.0000.0000.0000.000
213A210GLY00.027-0.00336.9400.0040.0040.0000.0000.0000.000
214A211HIS0-0.066-0.00538.782-0.001-0.0010.0000.0000.0000.000
215A212LEU00.0180.03638.6150.0000.0000.0000.0000.0000.000
216A213PRO00.0610.01237.8030.0000.0000.0000.0000.0000.000
217A214LEU0-0.023-0.00240.7560.0040.0040.0000.0000.0000.000
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