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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: ZV5MN

Calculation Name: 3CJW-A-Xray372

Preferred Name: COUP transcription factor 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3CJW

Chain ID: A

ChEMBL ID: CHEMBL1961790

UniProt ID: P24468

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2446801.871629
FMO2-HF: Nuclear repulsion 2364423.646096
FMO2-HF: Total energy -82378.225533
FMO2-MP2: Total energy -82616.583259


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:171:GLY)


Summations of interaction energy for fragment #1(A:171:GLY)
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.
-1.1551.0049.266-5.653-5.77-0.001
Interaction energy analysis for fragmet #1(A:171:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : -0.004
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].
3A173ASN00.0150.0213.503-0.5111.363-0.006-0.934-0.934-0.001
4A174SER00.0410.0232.2680.6771.6212.517-1.907-1.5540.007
5A175HIS00.0060.0143.2932.9602.525-0.0030.882-0.4440.000
6A176SER0-0.035-0.0145.6520.0540.0540.0000.0000.0000.000
7A177TYR0-0.015-0.0152.039-1.549-2.2246.755-3.578-2.502-0.007
8A178LEU00.0050.0133.962-1.316-0.9630.003-0.095-0.2600.000
9A179SER00.0130.0145.669-1.072-1.0720.0000.0000.0000.000
10A180GLY00.004-0.0027.236-0.387-0.3870.0000.0000.0000.000
11A181TYR0-0.025-0.0496.269-0.453-0.4530.0000.0000.0000.000
12A182ILE00.0720.0448.212-0.329-0.3290.0000.0000.0000.000
13A183SER0-0.025-0.02011.176-0.232-0.2320.0000.0000.0000.000
14A184LEU0-0.060-0.0369.593-0.172-0.1720.0000.0000.0000.000
15A185LEU0-0.0130.00511.582-0.120-0.1200.0000.0000.0000.000
16A186LEU0-0.004-0.00414.075-0.080-0.0800.0000.0000.0000.000
17A187ARG10.9150.95715.720-0.442-0.4420.0000.0000.0000.000
18A188ALA00.0020.01616.588-0.042-0.0420.0000.0000.0000.000
19A189GLU-1-0.842-0.91318.3820.2380.2380.0000.0000.0000.000
20A190PRO00.0110.02521.146-0.005-0.0050.0000.0000.0000.000
21A191TYR0-0.042-0.05524.565-0.014-0.0140.0000.0000.0000.000
22A192PRO0-0.054-0.00225.2420.0080.0080.0000.0000.0000.000
23A193THR00.0190.01921.0470.0210.0210.0000.0000.0000.000
24A207MET0-0.014-0.03042.750-0.001-0.0010.0000.0000.0000.000
25A208GLY0-0.010-0.00842.9710.0020.0020.0000.0000.0000.000
26A209ILE0-0.027-0.00540.8730.0000.0000.0000.0000.0000.000
27A210GLU-1-0.780-0.87535.5410.1030.1030.0000.0000.0000.000
28A211ASN00.0080.00740.0100.0010.0010.0000.0000.0000.000
29A212ILE00.0470.00938.3500.0030.0030.0000.0000.0000.000
30A213CYS0-0.004-0.01537.9100.0020.0020.0000.0000.0000.000
31A214GLU-1-0.896-0.94737.5140.0790.0790.0000.0000.0000.000
32A215LEU0-0.0190.01733.7040.0070.0070.0000.0000.0000.000
33A216ALA0-0.027-0.02933.5300.0070.0070.0000.0000.0000.000
34A217ALA00.0570.01532.7660.0040.0040.0000.0000.0000.000
35A218ARG10.9260.99030.500-0.113-0.1130.0000.0000.0000.000
36A219MET0-0.051-0.02029.0050.0130.0130.0000.0000.0000.000
37A220LEU00.0000.00627.7910.0090.0090.0000.0000.0000.000
38A221PHE00.020-0.01527.6680.0040.0040.0000.0000.0000.000
39A222SER0-0.038-0.01925.5280.0100.0100.0000.0000.0000.000
40A223ALA00.0010.00323.4020.0170.0170.0000.0000.0000.000
41A224VAL00.0100.00322.6190.0100.0100.0000.0000.0000.000
42A225GLU-1-0.808-0.90323.1270.1610.1610.0000.0000.0000.000
43A226TRP0-0.007-0.00516.136-0.003-0.0030.0000.0000.0000.000
44A227ALA0-0.010-0.02118.6590.0290.0290.0000.0000.0000.000
45A228ARG10.7800.88418.480-0.125-0.1250.0000.0000.0000.000
46A229ASN00.0230.05818.4950.0040.0040.0000.0000.0000.000
47A230ILE0-0.081-0.00413.9260.0540.0540.0000.0000.0000.000
48A231PRO0-0.002-0.01010.203-0.032-0.0320.0000.0000.0000.000
49A232PHE00.0180.0056.560-0.011-0.0110.0000.0000.0000.000
50A233PHE00.023-0.00112.538-0.052-0.0520.0000.0000.0000.000
51A234PRO00.0110.01015.537-0.035-0.0350.0000.0000.0000.000
52A235ASP-1-0.989-0.99714.9800.0210.0210.0000.0000.0000.000
53A236LEU0-0.0080.02615.304-0.031-0.0310.0000.0000.0000.000
54A237GLN00.0480.01418.1470.0150.0150.0000.0000.0000.000
55A238ILE00.0480.01921.7500.0060.0060.0000.0000.0000.000
56A239THR00.006-0.01424.0740.0060.0060.0000.0000.0000.000
57A240ASP-1-0.753-0.85220.654-0.001-0.0010.0000.0000.0000.000
58A241GLN0-0.041-0.01419.9290.0170.0170.0000.0000.0000.000
59A242VAL0-0.031-0.02722.0680.0070.0070.0000.0000.0000.000
60A243ALA00.0140.02224.2700.0030.0030.0000.0000.0000.000
61A244LEU00.001-0.00118.6130.0010.0010.0000.0000.0000.000
62A245LEU00.0060.01422.5360.0060.0060.0000.0000.0000.000
63A246ARG10.8320.90924.552-0.044-0.0440.0000.0000.0000.000
64A247LEU0-0.0400.01224.372-0.002-0.0020.0000.0000.0000.000
65A248THR00.019-0.01821.9950.0050.0050.0000.0000.0000.000
66A249TRP00.0000.01325.1070.0130.0130.0000.0000.0000.000
67A250SER0-0.005-0.00926.8600.0090.0090.0000.0000.0000.000
68A251GLU-1-0.821-0.91824.1260.1030.1030.0000.0000.0000.000
69A252LEU00.0240.00620.6980.0120.0120.0000.0000.0000.000
70A253PHE0-0.0280.00024.5090.0080.0080.0000.0000.0000.000
71A254VAL00.002-0.00527.9380.0020.0020.0000.0000.0000.000
72A255LEU00.0040.00721.5340.0030.0030.0000.0000.0000.000
73A256ASN00.0430.01924.2450.0230.0230.0000.0000.0000.000
74A257ALA0-0.004-0.00626.397-0.002-0.0020.0000.0000.0000.000
75A258ALA0-0.063-0.04027.316-0.005-0.0050.0000.0000.0000.000
76A259GLN00.0250.01522.031-0.006-0.0060.0000.0000.0000.000
77A260CYS0-0.034-0.01026.8920.0030.0030.0000.0000.0000.000
78A261SER0-0.078-0.05229.667-0.010-0.0100.0000.0000.0000.000
79A262MET0-0.0290.00732.393-0.007-0.0070.0000.0000.0000.000
80A263PRO00.001-0.01334.299-0.002-0.0020.0000.0000.0000.000
81A264LEU00.0380.01435.992-0.002-0.0020.0000.0000.0000.000
82A265HIS00.016-0.01138.453-0.004-0.0040.0000.0000.0000.000
83A266VAL0-0.078-0.03640.222-0.004-0.0040.0000.0000.0000.000
84A267ALA00.0910.06443.0790.0000.0000.0000.0000.0000.000
85A268PRO0-0.0610.00345.9880.0000.0000.0000.0000.0000.000
86A286VAL00.033-0.01947.4530.0010.0010.0000.0000.0000.000
87A287ALA0-0.068-0.02944.6840.0010.0010.0000.0000.0000.000
88A288PHE00.034-0.01744.276-0.002-0.0020.0000.0000.0000.000
89A289MET0-0.009-0.00443.1510.0000.0000.0000.0000.0000.000
90A290ASP-1-0.780-0.85942.9720.0480.0480.0000.0000.0000.000
91A291HIS00.0260.00140.7650.0030.0030.0000.0000.0000.000
92A292ILE0-0.021-0.00639.4770.0030.0030.0000.0000.0000.000
93A293ARG10.9400.95739.360-0.049-0.0490.0000.0000.0000.000
94A294ILE0-0.081-0.08137.0450.0020.0020.0000.0000.0000.000
95A295PHE00.0290.02632.1010.0040.0040.0000.0000.0000.000
96A296GLN0-0.0290.00833.8750.0050.0050.0000.0000.0000.000
97A297GLU-1-0.759-0.85333.5300.0790.0790.0000.0000.0000.000
98A298GLN0-0.019-0.02830.0170.0110.0110.0000.0000.0000.000
99A299VAL00.0360.02030.1580.0100.0100.0000.0000.0000.000
100A300GLU-1-0.940-0.98531.0010.0890.0890.0000.0000.0000.000
101A301LYS10.8340.90330.251-0.077-0.0770.0000.0000.0000.000
102A302LEU0-0.0070.01324.6850.0060.0060.0000.0000.0000.000
103A303LYS10.8990.96927.707-0.111-0.1110.0000.0000.0000.000
104A304ALA0-0.021-0.00129.9570.0030.0030.0000.0000.0000.000
105A305LEU0-0.049-0.01925.025-0.003-0.0030.0000.0000.0000.000
106A306HIS0-0.010-0.00826.4110.0150.0150.0000.0000.0000.000
107A307VAL0-0.057-0.01421.8080.0120.0120.0000.0000.0000.000
108A308ASP-1-0.710-0.79019.8910.3470.3470.0000.0000.0000.000
109A309SER0-0.003-0.02020.8390.0090.0090.0000.0000.0000.000
110A310ALA00.0640.03715.7010.0140.0140.0000.0000.0000.000
111A311GLU-1-0.751-0.84516.3070.3200.3200.0000.0000.0000.000
112A312TYR00.0410.00018.198-0.019-0.0190.0000.0000.0000.000
113A313SER00.0140.01816.177-0.016-0.0160.0000.0000.0000.000
114A314CYS0-0.042-0.02213.3660.0470.0470.0000.0000.0000.000
115A315LEU0-0.020-0.01414.976-0.033-0.0330.0000.0000.0000.000
116A316LYS10.7820.86418.029-0.283-0.2830.0000.0000.0000.000
117A317ALA00.0200.01913.388-0.029-0.0290.0000.0000.0000.000
118A318ILE0-0.036-0.02214.406-0.040-0.0400.0000.0000.0000.000
119A319VAL0-0.0320.00515.993-0.035-0.0350.0000.0000.0000.000
120A320LEU0-0.024-0.01417.064-0.024-0.0240.0000.0000.0000.000
121A321PHE0-0.042-0.02112.512-0.025-0.0250.0000.0000.0000.000
122A322THR00.0390.02216.601-0.021-0.0210.0000.0000.0000.000
123A323SER00.028-0.02719.2960.0040.0040.0000.0000.0000.000
124A324ASP-1-0.848-0.91320.6000.0230.0230.0000.0000.0000.000
125A325ALA0-0.097-0.02823.075-0.001-0.0010.0000.0000.0000.000
126A326CYS0-0.017-0.01924.858-0.010-0.0100.0000.0000.0000.000
127A327GLY0-0.009-0.01627.0080.0050.0050.0000.0000.0000.000
128A328LEU0-0.0210.00420.3710.0010.0010.0000.0000.0000.000
129A329SER0-0.131-0.08821.697-0.013-0.0130.0000.0000.0000.000
130A330ASP-1-0.882-0.95317.489-0.135-0.1350.0000.0000.0000.000
131A331VAL00.0460.02218.0400.0040.0040.0000.0000.0000.000
132A332ALA00.0250.02616.2900.0040.0040.0000.0000.0000.000
133A333HIS00.0380.02011.243-0.061-0.0610.0000.0000.0000.000
134A334VAL00.005-0.00113.0160.0140.0140.0000.0000.0000.000
135A335GLU-1-0.839-0.91414.227-0.043-0.0430.0000.0000.0000.000
136A336SER0-0.001-0.0039.989-0.016-0.0160.0000.0000.0000.000
137A337LEU0-0.082-0.0309.2930.0080.0080.0000.0000.0000.000
138A338GLN0-0.039-0.01810.7180.0880.0880.0000.0000.0000.000
139A339GLU-1-0.945-0.9629.532-0.144-0.1440.0000.0000.0000.000
140A340LYS10.9040.9383.5500.6240.7220.000-0.021-0.0760.000
141A341SER0-0.035-0.0107.9350.3150.3150.0000.0000.0000.000
142A342GLN00.0300.02210.5850.1100.1100.0000.0000.0000.000
143A343CYS00.0220.0217.9400.1330.1330.0000.0000.0000.000
144A344ALA00.013-0.0128.0120.1330.1330.0000.0000.0000.000
145A345LEU00.0170.0139.352-0.035-0.0350.0000.0000.0000.000
146A346GLU-1-0.789-0.86912.5020.2900.2900.0000.0000.0000.000
147A347GLU-1-0.876-0.9518.3641.0991.0990.0000.0000.0000.000
148A348TYR0-0.067-0.05212.087-0.037-0.0370.0000.0000.0000.000
149A349VAL00.0110.00913.986-0.073-0.0730.0000.0000.0000.000
150A350ARG10.7620.86911.467-0.439-0.4390.0000.0000.0000.000
151A351SER0-0.085-0.06014.375-0.040-0.0400.0000.0000.0000.000
152A352GLN0-0.029-0.01916.811-0.074-0.0740.0000.0000.0000.000
153A353TYR0-0.091-0.07719.184-0.055-0.0550.0000.0000.0000.000
154A354PRO00.0310.03620.936-0.022-0.0220.0000.0000.0000.000
155A355ASN0-0.062-0.04521.915-0.028-0.0280.0000.0000.0000.000
156A356GLN00.003-0.00423.878-0.017-0.0170.0000.0000.0000.000
157A357PRO00.0640.03622.4600.0130.0130.0000.0000.0000.000
158A358THR0-0.031-0.02922.4600.0030.0030.0000.0000.0000.000
159A359ARG10.7520.85021.569-0.234-0.2340.0000.0000.0000.000
160A360PHE00.0740.03715.324-0.001-0.0010.0000.0000.0000.000
161A361GLY00.0620.03519.821-0.005-0.0050.0000.0000.0000.000
162A362LYS10.8700.92422.161-0.127-0.1270.0000.0000.0000.000
163A363LEU0-0.0070.01419.308-0.011-0.0110.0000.0000.0000.000
164A364LEU00.0690.02517.036-0.008-0.0080.0000.0000.0000.000
165A365LEU0-0.035-0.00721.171-0.016-0.0160.0000.0000.0000.000
166A366ARG10.8680.93223.966-0.122-0.1220.0000.0000.0000.000
167A367LEU00.0350.02019.432-0.006-0.0060.0000.0000.0000.000
168A368PRO00.0280.01924.080-0.007-0.0070.0000.0000.0000.000
169A369SER0-0.041-0.01926.997-0.004-0.0040.0000.0000.0000.000
170A370LEU00.0180.01623.843-0.004-0.0040.0000.0000.0000.000
171A371ARG10.8210.91123.265-0.070-0.0700.0000.0000.0000.000
172A372THR0-0.117-0.06028.024-0.008-0.0080.0000.0000.0000.000
173A373VAL0-0.0010.01929.956-0.004-0.0040.0000.0000.0000.000
174A374SER00.004-0.00732.449-0.001-0.0010.0000.0000.0000.000
175A375SER00.0740.01931.9370.0040.0040.0000.0000.0000.000
176A376SER00.0500.02534.1320.0020.0020.0000.0000.0000.000
177A377VAL0-0.028-0.00337.440-0.001-0.0010.0000.0000.0000.000
178A378ILE00.0380.02431.9640.0010.0010.0000.0000.0000.000
179A379GLU-1-0.839-0.93235.7060.0570.0570.0000.0000.0000.000
180A380GLN0-0.014-0.01437.774-0.003-0.0030.0000.0000.0000.000
181A381LEU0-0.067-0.03137.652-0.002-0.0020.0000.0000.0000.000
182A382PHE0-0.037-0.02435.8080.0000.0000.0000.0000.0000.000
183A383PHE00.0340.01233.1420.0000.0000.0000.0000.0000.000
184A384VAL00.0370.02638.899-0.002-0.0020.0000.0000.0000.000
185A385ARG10.8890.94842.438-0.054-0.0540.0000.0000.0000.000
186A386LEU0-0.030-0.01137.554-0.001-0.0010.0000.0000.0000.000
187A387VAL00.0510.04137.177-0.001-0.0010.0000.0000.0000.000
188A388GLY0-0.008-0.00940.624-0.004-0.0040.0000.0000.0000.000
189A389LYS10.9000.95142.149-0.033-0.0330.0000.0000.0000.000
190A390THR0-0.078-0.03038.878-0.001-0.0010.0000.0000.0000.000
191A391PRO00.0790.03136.7060.0030.0030.0000.0000.0000.000
192A392ILE00.0700.03831.619-0.001-0.0010.0000.0000.0000.000
193A393GLU-1-0.900-0.95431.4250.0450.0450.0000.0000.0000.000
194A394THR0-0.073-0.05132.167-0.002-0.0020.0000.0000.0000.000
195A395LEU0-0.003-0.00833.993-0.002-0.0020.0000.0000.0000.000
196A396ILE0-0.0020.01127.3770.0030.0030.0000.0000.0000.000
197A397ARG10.9730.97228.914-0.034-0.0340.0000.0000.0000.000
198A398ASP-1-0.896-0.94329.9150.0520.0520.0000.0000.0000.000
199A399MET0-0.045-0.01929.6920.0050.0050.0000.0000.0000.000
200A400LEU0-0.0110.00223.2000.0070.0070.0000.0000.0000.000
201A401LEU0-0.022-0.00526.7180.0060.0060.0000.0000.0000.000
202A402SER0-0.089-0.05529.029-0.006-0.0060.0000.0000.0000.000
203A403GLY0-0.043-0.03228.8480.0030.0030.0000.0000.0000.000
204A404SER0-0.051-0.02827.9220.0090.0090.0000.0000.0000.000
205A405SER00.0340.00125.139-0.002-0.0020.0000.0000.0000.000
206A406PHE0-0.0110.03124.1440.0000.0000.0000.0000.0000.000
207A407ASN0-0.040-0.05920.9270.0110.0110.0000.0000.0000.000