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: 3J79L

Calculation Name: 1C4X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1C4X

Chain ID: A

ChEMBL ID:

UniProt ID: Q75WN8

Base Structure: X-ray

Registration Date: 2023-09-22

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 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 281
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4070236.233786
FMO2-HF: Nuclear repulsion 3959762.044126
FMO2-HF: Total energy -110474.18966
FMO2-MP2: Total energy -110793.293866


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:3:THR)


Summations of interaction energy for fragment #1(A:3:THR)
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.
0.0251.505-0.013-0.606-0.860.001
Interaction energy analysis for fragmet #1(A:3:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.033
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].
3A5GLU-1-0.966-0.9693.873-1.1310.349-0.013-0.606-0.8600.001
4A6ILE0-0.019-0.0275.4850.2260.2260.0000.0000.0000.000
5A7ILE0-0.0130.0059.1030.1290.1290.0000.0000.0000.000
6A8GLU-1-0.755-0.84812.0080.0850.0850.0000.0000.0000.000
7A9LYS10.8990.95714.8800.2510.2510.0000.0000.0000.000
8A10ARG10.8160.88418.3890.0450.0450.0000.0000.0000.000
9A11PHE00.0100.00516.573-0.026-0.0260.0000.0000.0000.000
10A12PRO00.0160.01122.7950.0180.0180.0000.0000.0000.000
11A13SER0-0.027-0.00825.505-0.005-0.0050.0000.0000.0000.000
12A14GLY00.0250.00727.1200.0090.0090.0000.0000.0000.000
13A15THR0-0.036-0.03130.837-0.002-0.0020.0000.0000.0000.000
14A16LEU00.0110.02030.5840.0040.0040.0000.0000.0000.000
15A17ALA00.0170.03526.374-0.005-0.0050.0000.0000.0000.000
16A18SER00.014-0.02924.2830.0120.0120.0000.0000.0000.000
17A19HIS0-0.051-0.03218.299-0.032-0.0320.0000.0000.0000.000
18A20ALA0-0.006-0.00718.7650.0180.0180.0000.0000.0000.000
19A21LEU0-0.0050.00813.471-0.016-0.0160.0000.0000.0000.000
20A22VAL0-0.035-0.01413.6110.0260.0260.0000.0000.0000.000
21A23ALA0-0.004-0.0059.213-0.075-0.0750.0000.0000.0000.000
22A24GLY00.1040.0619.7020.1450.1450.0000.0000.0000.000
23A25ASP-1-0.850-0.91110.644-0.737-0.7370.0000.0000.0000.000
24A26PRO0-0.016-0.02212.7050.1030.1030.0000.0000.0000.000
25A27GLN0-0.086-0.04515.9900.1170.1170.0000.0000.0000.000
26A28SER0-0.068-0.01513.6810.0340.0340.0000.0000.0000.000
27A29PRO0-0.007-0.01116.1410.0210.0210.0000.0000.0000.000
28A30ALA00.0460.03217.283-0.008-0.0080.0000.0000.0000.000
29A31VAL0-0.020-0.00716.7570.0350.0350.0000.0000.0000.000
30A32VAL00.0010.00817.894-0.008-0.0080.0000.0000.0000.000
31A33LEU00.006-0.00715.5450.0240.0240.0000.0000.0000.000
32A34LEU0-0.004-0.00319.726-0.003-0.0030.0000.0000.0000.000
33A35HIS0-0.019-0.00421.4500.0040.0040.0000.0000.0000.000
34A36GLY00.0620.03423.017-0.012-0.0120.0000.0000.0000.000
35A37ALA0-0.057-0.01926.071-0.002-0.0020.0000.0000.0000.000
36A38GLY00.0380.00428.8100.0070.0070.0000.0000.0000.000
37A39PRO00.0060.02329.232-0.003-0.0030.0000.0000.0000.000
38A40GLY00.0870.05927.6380.0100.0100.0000.0000.0000.000
39A41ALA0-0.057-0.00824.7840.0110.0110.0000.0000.0000.000
40A42HIS0-0.030-0.04619.6530.0080.0080.0000.0000.0000.000
41A43ALA00.0470.04018.7410.0250.0250.0000.0000.0000.000
42A44ALA0-0.018-0.00616.2350.0270.0270.0000.0000.0000.000
43A45SER0-0.035-0.03816.5560.0410.0410.0000.0000.0000.000
44A46ASN0-0.014-0.00918.9760.0070.0070.0000.0000.0000.000
45A47TRP00.0580.01515.4270.0130.0130.0000.0000.0000.000
46A48ARG10.8610.90311.512-0.087-0.0870.0000.0000.0000.000
47A49PRO0-0.044-0.03410.8810.0540.0540.0000.0000.0000.000
48A50ILE00.0320.03310.7240.1170.1170.0000.0000.0000.000
49A51ILE0-0.0150.0009.632-0.022-0.0220.0000.0000.0000.000
50A52PRO00.009-0.0085.088-0.201-0.2010.0000.0000.0000.000
51A53ASP-1-0.795-0.8847.1640.9770.9770.0000.0000.0000.000
52A54LEU0-0.026-0.0139.269-0.164-0.1640.0000.0000.0000.000
53A55ALA00.000-0.0078.146-0.112-0.1120.0000.0000.0000.000
54A56GLU-1-0.971-0.9776.1510.3810.3810.0000.0000.0000.000
55A57ASN0-0.053-0.0217.993-0.239-0.2390.0000.0000.0000.000
56A58PHE0-0.016-0.01611.7330.0150.0150.0000.0000.0000.000
57A59PHE0-0.0050.01412.816-0.045-0.0450.0000.0000.0000.000
58A60VAL00.0090.00312.1550.0790.0790.0000.0000.0000.000
59A61VAL00.0280.00414.817-0.044-0.0440.0000.0000.0000.000
60A62ALA00.0090.00116.2130.0370.0370.0000.0000.0000.000
61A63PRO00.006-0.00118.0220.0010.0010.0000.0000.0000.000
62A64ASP-1-0.748-0.88820.9760.0550.0550.0000.0000.0000.000
63A65LEU0-0.0140.00823.015-0.015-0.0150.0000.0000.0000.000
64A66ILE00.0220.00326.2780.0070.0070.0000.0000.0000.000
65A67GLY00.0310.00829.6430.0040.0040.0000.0000.0000.000
66A68PHE0-0.054-0.03226.3810.0080.0080.0000.0000.0000.000
67A69GLY00.0330.01924.203-0.008-0.0080.0000.0000.0000.000
68A70GLN0-0.0180.00321.0340.0120.0120.0000.0000.0000.000
69A71SER0-0.019-0.03124.774-0.018-0.0180.0000.0000.0000.000
70A72GLU-1-0.854-0.88526.032-0.032-0.0320.0000.0000.0000.000
71A73TYR0-0.029-0.02628.3420.0050.0050.0000.0000.0000.000
72A74PRO0-0.029-0.01032.493-0.004-0.0040.0000.0000.0000.000
73A75GLU-1-0.902-0.96135.868-0.016-0.0160.0000.0000.0000.000
74A76THR0-0.050-0.02038.8730.0020.0020.0000.0000.0000.000
75A77TYR00.0170.00335.9470.0010.0010.0000.0000.0000.000
76A78PRO00.0010.00838.1410.0010.0010.0000.0000.0000.000
77A79GLY00.0370.01040.3280.0030.0030.0000.0000.0000.000
78A80HIS00.0190.00841.4940.0020.0020.0000.0000.0000.000
79A81ILE00.0350.03534.764-0.003-0.0030.0000.0000.0000.000
80A82MET00.0320.00736.952-0.001-0.0010.0000.0000.0000.000
81A83SER0-0.012-0.02437.868-0.003-0.0030.0000.0000.0000.000
82A84TRP00.034-0.00233.901-0.004-0.0040.0000.0000.0000.000
83A85VAL0-0.057-0.02833.231-0.001-0.0010.0000.0000.0000.000
84A86GLY00.0750.04133.275-0.003-0.0030.0000.0000.0000.000
85A87MET0-0.027-0.01233.726-0.004-0.0040.0000.0000.0000.000
86A88ARG10.8560.92729.248-0.018-0.0180.0000.0000.0000.000
87A89VAL0-0.0130.00029.360-0.005-0.0050.0000.0000.0000.000
88A90GLU-1-0.892-0.95430.564-0.051-0.0510.0000.0000.0000.000
89A91GLN0-0.019-0.00125.1050.0010.0010.0000.0000.0000.000
90A92ILE0-0.014-0.01224.142-0.012-0.0120.0000.0000.0000.000
91A93LEU00.0460.02326.489-0.014-0.0140.0000.0000.0000.000
92A94GLY00.0260.01728.615-0.011-0.0110.0000.0000.0000.000
93A95LEU0-0.032-0.03321.155-0.013-0.0130.0000.0000.0000.000
94A96MET0-0.061-0.01723.809-0.016-0.0160.0000.0000.0000.000
95A97ASN00.0220.01325.067-0.017-0.0170.0000.0000.0000.000
96A98HIS0-0.058-0.01420.786-0.010-0.0100.0000.0000.0000.000
97A99PHE0-0.023-0.02418.021-0.015-0.0150.0000.0000.0000.000
98A100GLY00.0200.01922.703-0.018-0.0180.0000.0000.0000.000
99A101ILE0-0.009-0.00120.569-0.001-0.0010.0000.0000.0000.000
100A102GLU-1-0.941-0.95924.529-0.123-0.1230.0000.0000.0000.000
101A103LYS10.8080.89125.6100.0950.0950.0000.0000.0000.000
102A104SER0-0.020-0.02722.130-0.026-0.0260.0000.0000.0000.000
103A105HIS00.0220.01419.7500.0200.0200.0000.0000.0000.000
104A106ILE0-0.021-0.00322.183-0.009-0.0090.0000.0000.0000.000
105A107VAL00.0190.01019.2070.0140.0140.0000.0000.0000.000
106A108GLY00.0220.01922.336-0.006-0.0060.0000.0000.0000.000
107A109ASN0-0.037-0.04123.002-0.002-0.0020.0000.0000.0000.000
108A110SER0-0.007-0.00124.991-0.013-0.0130.0000.0000.0000.000
109A111MET0-0.003-0.03128.579-0.010-0.0100.0000.0000.0000.000
110A112GLY00.0820.05825.946-0.009-0.0090.0000.0000.0000.000
111A113GLY0-0.0090.00026.994-0.009-0.0090.0000.0000.0000.000
112A114ALA0-0.024-0.01428.309-0.007-0.0070.0000.0000.0000.000
113A115VAL00.001-0.00728.553-0.005-0.0050.0000.0000.0000.000
114A116THR00.011-0.00826.401-0.008-0.0080.0000.0000.0000.000
115A117LEU0-0.051-0.03128.603-0.005-0.0050.0000.0000.0000.000
116A118GLN0-0.053-0.04532.081-0.001-0.0010.0000.0000.0000.000
117A119LEU00.0110.02027.367-0.004-0.0040.0000.0000.0000.000
118A120VAL0-0.027-0.00829.486-0.006-0.0060.0000.0000.0000.000
119A121VAL0-0.055-0.04132.028-0.001-0.0010.0000.0000.0000.000
120A122GLU-1-0.889-0.93934.837-0.021-0.0210.0000.0000.0000.000
121A123ALA00.0050.01732.220-0.003-0.0030.0000.0000.0000.000
122A124PRO0-0.0170.00132.163-0.004-0.0040.0000.0000.0000.000
123A125GLU-1-0.876-0.95231.975-0.058-0.0580.0000.0000.0000.000
124A126ARG10.8060.89027.9280.0890.0890.0000.0000.0000.000
125A127PHE00.0310.00925.537-0.007-0.0070.0000.0000.0000.000
126A128ASP-1-0.876-0.91125.320-0.069-0.0690.0000.0000.0000.000
127A129LYS10.8420.93423.5560.0510.0510.0000.0000.0000.000
128A130VAL00.0240.00324.758-0.002-0.0020.0000.0000.0000.000
129A131ALA00.0140.01722.6360.0080.0080.0000.0000.0000.000
130A132LEU0-0.029-0.01124.787-0.003-0.0030.0000.0000.0000.000
131A133MET0-0.0190.01620.8680.0140.0140.0000.0000.0000.000
132A134GLY00.0500.02126.257-0.001-0.0010.0000.0000.0000.000
133A135SER00.0030.00229.172-0.004-0.0040.0000.0000.0000.000
134A136VAL00.0430.01130.4270.0010.0010.0000.0000.0000.000
135A137GLY00.0210.03333.346-0.003-0.0030.0000.0000.0000.000
136A138ALA0-0.050-0.02635.106-0.004-0.0040.0000.0000.0000.000
137A139PRO0-0.0070.00037.8410.0020.0020.0000.0000.0000.000
138A140MET0-0.023-0.00736.2810.0040.0040.0000.0000.0000.000
139A141ASN0-0.043-0.01940.499-0.004-0.0040.0000.0000.0000.000
140A142ALA00.0280.00341.909-0.002-0.0020.0000.0000.0000.000
141A143ARG10.9360.97839.487-0.041-0.0410.0000.0000.0000.000
142A144PRO00.0480.04336.593-0.002-0.0020.0000.0000.0000.000
143A145PRO00.005-0.01439.343-0.002-0.0020.0000.0000.0000.000
144A146GLU-1-0.762-0.86934.7010.0830.0830.0000.0000.0000.000
145A147LEU00.0330.02434.506-0.001-0.0010.0000.0000.0000.000
146A148ALA0-0.067-0.04736.592-0.004-0.0040.0000.0000.0000.000
147A149ARG10.9340.95537.972-0.071-0.0710.0000.0000.0000.000
148A150LEU00.0100.01231.8670.0000.0000.0000.0000.0000.000
149A151LEU0-0.040-0.01435.462-0.002-0.0020.0000.0000.0000.000
150A152ALA0-0.004-0.00637.618-0.003-0.0030.0000.0000.0000.000
151A153PHE00.0120.02434.287-0.001-0.0010.0000.0000.0000.000
152A154TYR0-0.045-0.05533.4180.0010.0010.0000.0000.0000.000
153A155ALA0-0.0190.00039.231-0.002-0.0020.0000.0000.0000.000
154A156ASP-1-0.822-0.87540.7120.0650.0650.0000.0000.0000.000
155A157PRO00.0080.03337.4550.0050.0050.0000.0000.0000.000
156A158ARG10.8000.84036.815-0.066-0.0660.0000.0000.0000.000
157A159LEU00.0550.02330.5550.0020.0020.0000.0000.0000.000
158A160THR00.000-0.00833.5420.0050.0050.0000.0000.0000.000
159A161PRO00.0050.00135.1030.0050.0050.0000.0000.0000.000
160A162TYR0-0.006-0.01927.9390.0040.0040.0000.0000.0000.000
161A163ARG10.8590.91330.309-0.134-0.1340.0000.0000.0000.000
162A164GLU-1-0.913-0.96231.0050.1220.1220.0000.0000.0000.000
163A165LEU0-0.063-0.00931.5910.0010.0010.0000.0000.0000.000
164A166ILE00.0160.01826.1390.0020.0020.0000.0000.0000.000
165A167HIS00.017-0.02127.9090.0080.0080.0000.0000.0000.000
166A168SER0-0.083-0.05829.4390.0000.0000.0000.0000.0000.000
167A169PHE00.006-0.01326.348-0.008-0.0080.0000.0000.0000.000
168A170VAL0-0.032-0.00523.8590.0060.0060.0000.0000.0000.000
169A171TYR0-0.029-0.02326.481-0.017-0.0170.0000.0000.0000.000
170A172ASP-1-0.871-0.92325.9330.1980.1980.0000.0000.0000.000
171A173PRO0-0.006-0.01325.6890.0190.0190.0000.0000.0000.000
172A174GLU-1-0.919-0.95925.9860.1780.1780.0000.0000.0000.000
173A175ASN0-0.079-0.05824.0110.0200.0200.0000.0000.0000.000
174A176PHE0-0.0180.00519.9110.0350.0350.0000.0000.0000.000
175A177PRO00.0130.00317.235-0.008-0.0080.0000.0000.0000.000
176A178GLY00.0330.00718.9560.0050.0050.0000.0000.0000.000
177A179MET0-0.0210.02220.266-0.028-0.0280.0000.0000.0000.000
178A180GLU-1-0.746-0.85623.5480.1440.1440.0000.0000.0000.000
179A181GLU-1-0.826-0.89920.9730.2020.2020.0000.0000.0000.000
180A182ILE0-0.0060.02419.529-0.017-0.0170.0000.0000.0000.000
181A183VAL0-0.018-0.01022.989-0.021-0.0210.0000.0000.0000.000
182A184LYS10.7950.87625.481-0.200-0.2000.0000.0000.0000.000
183A185SER0-0.036-0.03722.436-0.014-0.0140.0000.0000.0000.000
184A186ARG10.8680.92421.976-0.128-0.1280.0000.0000.0000.000
185A187PHE00.0170.01325.817-0.015-0.0150.0000.0000.0000.000
186A188GLU-1-0.910-0.96727.7370.0950.0950.0000.0000.0000.000
187A189VAL0-0.038-0.01524.928-0.010-0.0100.0000.0000.0000.000
188A190ALA0-0.028-0.00528.331-0.010-0.0100.0000.0000.0000.000
189A191ASN0-0.029-0.02730.904-0.012-0.0120.0000.0000.0000.000
190A192ASP-1-0.808-0.88030.9300.0380.0380.0000.0000.0000.000
191A193PRO0-0.028-0.03032.979-0.002-0.0020.0000.0000.0000.000
192A194GLU-1-0.937-0.95833.5390.0090.0090.0000.0000.0000.000
193A195VAL00.0130.00229.418-0.002-0.0020.0000.0000.0000.000
194A196ARG10.8190.90832.597-0.049-0.0490.0000.0000.0000.000
195A197ARG10.8240.90435.520-0.028-0.0280.0000.0000.0000.000
196A198ILE00.0070.00332.639-0.002-0.0020.0000.0000.0000.000
197A199GLN00.005-0.00130.3540.0070.0070.0000.0000.0000.000
198A200GLU-1-0.751-0.84434.6750.0380.0380.0000.0000.0000.000
199A201VAL0-0.023-0.00438.3290.0000.0000.0000.0000.0000.000
200A202MET00.0130.04031.323-0.003-0.0030.0000.0000.0000.000
201A203PHE00.026-0.00232.6080.0000.0000.0000.0000.0000.000
202A204GLU-1-0.814-0.89237.6130.0290.0290.0000.0000.0000.000
203A205SER0-0.056-0.02238.448-0.002-0.0020.0000.0000.0000.000
204A206MET0-0.013-0.00232.8940.0000.0000.0000.0000.0000.000
205A207LYS10.7910.87438.857-0.028-0.0280.0000.0000.0000.000
206A208ALA0-0.068-0.04841.553-0.002-0.0020.0000.0000.0000.000
207A209GLY00.0770.05242.273-0.002-0.0020.0000.0000.0000.000
208A210MET0-0.038-0.02136.814-0.001-0.0010.0000.0000.0000.000
209A211GLU-1-0.928-0.95139.7780.0180.0180.0000.0000.0000.000
210A212SER0-0.040-0.04240.993-0.002-0.0020.0000.0000.0000.000
211A213LEU0-0.018-0.00634.941-0.003-0.0030.0000.0000.0000.000
212A214VAL0-0.051-0.01137.5250.0010.0010.0000.0000.0000.000
213A215ILE00.0540.03735.855-0.004-0.0040.0000.0000.0000.000
214A216PRO00.0260.01939.2080.0020.0020.0000.0000.0000.000
215A217PRO00.0320.00841.390-0.002-0.0020.0000.0000.0000.000
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