Manual

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: R8G38

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2446158.829899
FMO2-HF: Nuclear repulsion 2363777.652833
FMO2-HF: Total energy -82381.177066
FMO2-MP2: Total energy -82619.310403


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.
0.2411.09514.066-7.812-7.1080.002
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 : 0.077 / q_NPA : 0.020
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].
3A173ASN0-0.0120.0033.541-0.9061.894-0.008-1.563-1.2290.004
4A174SER00.0190.0121.8061.2700.6706.011-3.446-1.9660.015
5A175HIS00.0060.0032.8651.9341.2260.0171.408-0.717-0.005
6A176SER00.0260.0005.7090.4780.4780.0000.0000.0000.000
7A177TYR0-0.068-0.0352.1350.591-0.6428.036-4.018-2.786-0.011
8A178LEU00.0120.0153.3991.2321.7760.012-0.184-0.372-0.001
9A179SER00.0610.0345.016-0.027-0.019-0.001-0.001-0.0050.000
10A180GLY0-0.037-0.0146.990-0.008-0.0080.0000.0000.0000.000
11A181TYR0-0.019-0.0416.6980.0020.0020.0000.0000.0000.000
12A182ILE00.0740.0438.390-0.240-0.2400.0000.0000.0000.000
13A183SER0-0.043-0.03210.839-0.170-0.1700.0000.0000.0000.000
14A184LEU0-0.053-0.0269.378-0.133-0.1330.0000.0000.0000.000
15A185LEU0-0.0150.00112.014-0.110-0.1100.0000.0000.0000.000
16A186LEU00.007-0.00114.462-0.102-0.1020.0000.0000.0000.000
17A187ARG10.9030.95015.690-0.573-0.5730.0000.0000.0000.000
18A188ALA00.0060.02117.013-0.044-0.0440.0000.0000.0000.000
19A189GLU-1-0.836-0.89518.7130.3530.3530.0000.0000.0000.000
20A190PRO00.0190.03121.523-0.017-0.0170.0000.0000.0000.000
21A191TYR0-0.053-0.06524.906-0.024-0.0240.0000.0000.0000.000
22A192PRO0-0.0280.02225.2620.0030.0030.0000.0000.0000.000
23A193THR00.0040.00320.9750.0100.0100.0000.0000.0000.000
24A207MET0-0.018-0.03042.611-0.003-0.0030.0000.0000.0000.000
25A208GLY0-0.011-0.01143.2850.0040.0040.0000.0000.0000.000
26A209ILE0-0.032-0.00840.6810.0010.0010.0000.0000.0000.000
27A210GLU-1-0.776-0.85535.8280.1380.1380.0000.0000.0000.000
28A211ASN0-0.025-0.02340.369-0.003-0.0030.0000.0000.0000.000
29A212ILE00.0390.01338.6110.0060.0060.0000.0000.0000.000
30A213CYS00.002-0.00538.3840.0050.0050.0000.0000.0000.000
31A214GLU-1-0.854-0.92638.1300.1160.1160.0000.0000.0000.000
32A215LEU0-0.0270.00634.0150.0110.0110.0000.0000.0000.000
33A216ALA0-0.012-0.01934.0250.0110.0110.0000.0000.0000.000
34A217ALA00.0520.01533.4030.0110.0110.0000.0000.0000.000
35A218ARG10.8870.94930.977-0.143-0.1430.0000.0000.0000.000
36A219MET0-0.0270.00729.5110.0200.0200.0000.0000.0000.000
37A220LEU0-0.0020.00928.4230.0180.0180.0000.0000.0000.000
38A221PHE00.013-0.02028.4900.0160.0160.0000.0000.0000.000
39A222SER0-0.051-0.04226.1750.0200.0200.0000.0000.0000.000
40A223ALA00.0020.00624.1200.0280.0280.0000.0000.0000.000
41A224VAL00.0040.00823.4650.0330.0330.0000.0000.0000.000
42A225GLU-1-0.801-0.89824.0010.3330.3330.0000.0000.0000.000
43A226TRP0-0.0020.00916.6810.0290.0290.0000.0000.0000.000
44A227ALA0-0.012-0.02319.5450.0650.0650.0000.0000.0000.000
45A228ARG10.8010.87919.384-0.250-0.2500.0000.0000.0000.000
46A229ASN0-0.0180.02018.9450.0160.0160.0000.0000.0000.000
47A230ILE0-0.066-0.00214.7090.0690.0690.0000.0000.0000.000
48A231PRO0-0.011-0.01410.7190.0000.0000.0000.0000.0000.000
49A232PHE00.0190.0097.2610.1460.1460.0000.0000.0000.000
50A233PHE00.0370.00313.343-0.116-0.1160.0000.0000.0000.000
51A234PRO00.0210.01116.268-0.063-0.0630.0000.0000.0000.000
52A235ASP-1-0.992-0.99215.0630.6120.6120.0000.0000.0000.000
53A236LEU0-0.0210.01916.254-0.028-0.0280.0000.0000.0000.000
54A237GLN00.0430.01718.785-0.052-0.0520.0000.0000.0000.000
55A238ILE00.0510.01522.2740.0020.0020.0000.0000.0000.000
56A239THR00.007-0.00424.754-0.005-0.0050.0000.0000.0000.000
57A240ASP-1-0.777-0.87121.6880.3120.3120.0000.0000.0000.000
58A241GLN0-0.048-0.01920.896-0.012-0.0120.0000.0000.0000.000
59A242VAL0-0.013-0.02823.071-0.012-0.0120.0000.0000.0000.000
60A243ALA00.0060.02425.253-0.013-0.0130.0000.0000.0000.000
61A244LEU00.000-0.00419.553-0.017-0.0170.0000.0000.0000.000
62A245LEU00.0060.01823.304-0.016-0.0160.0000.0000.0000.000
63A246ARG10.7850.87225.508-0.204-0.2040.0000.0000.0000.000
64A247LEU0-0.0460.00525.279-0.018-0.0180.0000.0000.0000.000
65A248THR00.008-0.02522.817-0.010-0.0100.0000.0000.0000.000
66A249TRP00.0060.01925.9970.0000.0000.0000.0000.0000.000
67A250SER0-0.007-0.01627.7430.0040.0040.0000.0000.0000.000
68A251GLU-1-0.801-0.89525.1290.2320.2320.0000.0000.0000.000
69A252LEU00.0300.01321.492-0.002-0.0020.0000.0000.0000.000
70A253PHE0-0.032-0.00425.177-0.007-0.0070.0000.0000.0000.000
71A254VAL00.0070.00328.393-0.009-0.0090.0000.0000.0000.000
72A255LEU00.0010.00621.785-0.012-0.0120.0000.0000.0000.000
73A256ASN00.0290.00424.6010.0070.0070.0000.0000.0000.000
74A257ALA00.009-0.00426.745-0.014-0.0140.0000.0000.0000.000
75A258ALA0-0.058-0.03327.499-0.014-0.0140.0000.0000.0000.000
76A259GLN00.0070.01222.000-0.001-0.0010.0000.0000.0000.000
77A260CYS0-0.047-0.01926.923-0.004-0.0040.0000.0000.0000.000
78A261SER0-0.050-0.03029.739-0.015-0.0150.0000.0000.0000.000
79A262MET0-0.0240.00932.526-0.006-0.0060.0000.0000.0000.000
80A263PRO0-0.006-0.01934.476-0.004-0.0040.0000.0000.0000.000
81A264LEU0-0.001-0.00735.2790.0020.0020.0000.0000.0000.000
82A265HIS00.0000.00838.633-0.001-0.0010.0000.0000.0000.000
83A266VAL0-0.055-0.02940.598-0.004-0.0040.0000.0000.0000.000
84A267ALA00.0960.04443.3080.0020.0020.0000.0000.0000.000
85A268PRO0-0.0600.00946.1260.0000.0000.0000.0000.0000.000
86A286VAL00.012-0.01147.759-0.001-0.0010.0000.0000.0000.000
87A287ALA0-0.047-0.03945.0080.0040.0040.0000.0000.0000.000
88A288PHE00.032-0.00745.205-0.003-0.0030.0000.0000.0000.000
89A289MET0-0.0030.00544.008-0.002-0.0020.0000.0000.0000.000
90A290ASP-1-0.791-0.86443.6280.0750.0750.0000.0000.0000.000
91A291HIS00.013-0.01641.2840.0020.0020.0000.0000.0000.000
92A292ILE0-0.029-0.01039.9360.0050.0050.0000.0000.0000.000
93A293ARG10.9190.94639.683-0.071-0.0710.0000.0000.0000.000
94A294ILE0-0.051-0.03137.6300.0020.0020.0000.0000.0000.000
95A295PHE00.0340.01132.5970.0050.0050.0000.0000.0000.000
96A296GLN00.016-0.00434.1650.0050.0050.0000.0000.0000.000
97A297GLU-1-0.807-0.86434.3700.0920.0920.0000.0000.0000.000
98A298GLN00.032-0.00230.2550.0050.0050.0000.0000.0000.000
99A299VAL00.0430.02330.2650.0060.0060.0000.0000.0000.000
100A300GLU-1-0.957-0.99330.9950.0850.0850.0000.0000.0000.000
101A301LYS10.8470.90330.163-0.090-0.0900.0000.0000.0000.000
102A302LEU0-0.0090.01024.835-0.002-0.0020.0000.0000.0000.000
103A303LYS10.9120.96627.478-0.120-0.1200.0000.0000.0000.000
104A304ALA0-0.031-0.00729.738-0.005-0.0050.0000.0000.0000.000
105A305LEU0-0.046-0.01824.161-0.011-0.0110.0000.0000.0000.000
106A306HIS0-0.016-0.01225.9060.0020.0020.0000.0000.0000.000
107A307VAL0-0.044-0.00521.597-0.001-0.0010.0000.0000.0000.000
108A308ASP-1-0.699-0.80219.2160.2020.2020.0000.0000.0000.000
109A309SER00.011-0.01219.6000.0090.0090.0000.0000.0000.000
110A310ALA00.0430.02415.2940.0450.0450.0000.0000.0000.000
111A311GLU-1-0.759-0.84516.1480.2230.2230.0000.0000.0000.000
112A312TYR00.029-0.00617.9540.0170.0170.0000.0000.0000.000
113A313SER00.001-0.00716.3760.0040.0040.0000.0000.0000.000
114A314CYS0-0.058-0.03113.4790.0920.0920.0000.0000.0000.000
115A315LEU0-0.013-0.01215.1670.0180.0180.0000.0000.0000.000
116A316LYS10.8060.89018.319-0.355-0.3550.0000.0000.0000.000
117A317ALA00.0020.00414.162-0.006-0.0060.0000.0000.0000.000
118A318ILE0-0.033-0.01914.7120.0030.0030.0000.0000.0000.000
119A319VAL0-0.035-0.00316.672-0.030-0.0300.0000.0000.0000.000
120A320LEU0-0.024-0.01518.311-0.025-0.0250.0000.0000.0000.000
121A321PHE0-0.040-0.01613.6960.0020.0020.0000.0000.0000.000
122A322THR00.0180.00617.523-0.010-0.0100.0000.0000.0000.000
123A323SER00.023-0.03619.7670.0030.0030.0000.0000.0000.000
124A324ASP-1-0.861-0.90821.2650.1910.1910.0000.0000.0000.000
125A325ALA0-0.094-0.03023.879-0.020-0.0200.0000.0000.0000.000
126A326CYS0-0.012-0.01825.712-0.005-0.0050.0000.0000.0000.000
127A327GLY00.000-0.01027.9240.0080.0080.0000.0000.0000.000
128A328LEU0-0.031-0.00321.2350.0070.0070.0000.0000.0000.000
129A329SER0-0.100-0.07222.727-0.020-0.0200.0000.0000.0000.000
130A330ASP-1-0.891-0.95217.8800.3770.3770.0000.0000.0000.000
131A331VAL00.0430.01918.7710.0500.0500.0000.0000.0000.000
132A332ALA00.0430.02816.5260.0270.0270.0000.0000.0000.000
133A333HIS00.0290.02412.0100.0860.0860.0000.0000.0000.000
134A334VAL00.0140.00113.7630.1380.1380.0000.0000.0000.000
135A335GLU-1-0.822-0.89814.9860.3310.3310.0000.0000.0000.000
136A336SER0-0.041-0.02510.465-0.007-0.0070.0000.0000.0000.000
137A337LEU0-0.073-0.02810.2330.2980.2980.0000.0000.0000.000
138A338GLN0-0.016-0.00111.5870.0850.0850.0000.0000.0000.000
139A339GLU-1-0.877-0.9249.5430.2330.2330.0000.0000.0000.000
140A340LYS10.8860.9394.837-4.691-4.648-0.001-0.008-0.0330.000
141A341SER0-0.031-0.0208.5300.0520.0520.0000.0000.0000.000
142A342GLN0-0.006-0.00911.120-0.131-0.1310.0000.0000.0000.000
143A343CYS00.0020.0198.125-0.205-0.2050.0000.0000.0000.000
144A344ALA0-0.002-0.0267.981-0.153-0.1530.0000.0000.0000.000
145A345LEU00.0150.0119.051-0.166-0.1660.0000.0000.0000.000
146A346GLU-1-0.807-0.86712.211-0.223-0.2230.0000.0000.0000.000
147A347GLU-1-0.760-0.8527.539-0.831-0.8310.0000.0000.0000.000
148A348TYR0-0.064-0.03911.346-0.061-0.0610.0000.0000.0000.000
149A349VAL00.000-0.00113.127-0.042-0.0420.0000.0000.0000.000
150A350ARG10.6990.80510.8760.2760.2760.0000.0000.0000.000
151A351SER0-0.074-0.05213.382-0.017-0.0170.0000.0000.0000.000
152A352GLN0-0.053-0.02815.8460.0000.0000.0000.0000.0000.000
153A353TYR0-0.083-0.06718.241-0.010-0.0100.0000.0000.0000.000
154A354PRO00.0380.03619.8920.0000.0000.0000.0000.0000.000
155A355ASN0-0.058-0.03921.087-0.015-0.0150.0000.0000.0000.000
156A356GLN0-0.006-0.00523.1000.0160.0160.0000.0000.0000.000
157A357PRO00.0760.03821.8890.0110.0110.0000.0000.0000.000
158A358THR0-0.029-0.02022.0130.0050.0050.0000.0000.0000.000
159A359ARG10.7390.84120.917-0.097-0.0970.0000.0000.0000.000
160A360PHE00.0910.04315.1730.0050.0050.0000.0000.0000.000
161A361GLY00.0670.03819.3490.0210.0210.0000.0000.0000.000
162A362LYS10.8620.91721.863-0.029-0.0290.0000.0000.0000.000
163A363LEU00.0030.01318.9350.0070.0070.0000.0000.0000.000
164A364LEU00.0700.03417.1970.0140.0140.0000.0000.0000.000
165A365LEU0-0.037-0.01621.2250.0030.0030.0000.0000.0000.000
166A366ARG10.8250.89724.126-0.135-0.1350.0000.0000.0000.000
167A367LEU00.0360.02419.7550.0010.0010.0000.0000.0000.000
168A368PRO00.0290.02024.4590.0000.0000.0000.0000.0000.000
169A369SER0-0.019-0.00127.453-0.005-0.0050.0000.0000.0000.000
170A370LEU00.0030.00724.138-0.006-0.0060.0000.0000.0000.000
171A371ARG10.8110.89023.990-0.225-0.2250.0000.0000.0000.000
172A372THR0-0.100-0.05428.708-0.011-0.0110.0000.0000.0000.000
173A373VAL0-0.0030.01630.949-0.011-0.0110.0000.0000.0000.000
174A374SER00.000-0.00333.1820.0070.0070.0000.0000.0000.000
175A375SER00.0550.00432.7700.0000.0000.0000.0000.0000.000
176A376SER00.0840.04734.981-0.001-0.0010.0000.0000.0000.000
177A377VAL0-0.041-0.00738.021-0.004-0.0040.0000.0000.0000.000
178A378ILE00.0340.02332.493-0.003-0.0030.0000.0000.0000.000
179A379GLU-1-0.834-0.92936.4090.1360.1360.0000.0000.0000.000
180A380GLN0-0.016-0.01738.596-0.009-0.0090.0000.0000.0000.000
181A381LEU0-0.081-0.02938.460-0.005-0.0050.0000.0000.0000.000
182A382PHE0-0.009-0.02035.980-0.003-0.0030.0000.0000.0000.000
183A383PHE00.0440.02033.7620.0000.0000.0000.0000.0000.000
184A384VAL00.0290.02339.697-0.002-0.0020.0000.0000.0000.000
185A385ARG10.8960.95443.282-0.088-0.0880.0000.0000.0000.000
186A386LEU0-0.025-0.00638.332-0.002-0.0020.0000.0000.0000.000
187A387VAL00.0430.02838.0290.0020.0020.0000.0000.0000.000
188A388GLY0-0.027-0.00341.521-0.003-0.0030.0000.0000.0000.000
189A389LYS10.9130.95043.037-0.085-0.0850.0000.0000.0000.000
190A390THR0-0.050-0.02539.5180.0000.0000.0000.0000.0000.000
191A391PRO00.0860.03737.5350.0020.0020.0000.0000.0000.000
192A392ILE00.0650.04432.4440.0030.0030.0000.0000.0000.000
193A393GLU-1-0.851-0.91632.3810.1710.1710.0000.0000.0000.000
194A394THR0-0.065-0.04833.1410.0040.0040.0000.0000.0000.000
195A395LEU0-0.035-0.02034.936-0.001-0.0010.0000.0000.0000.000
196A396ILE00.0080.00728.4200.0070.0070.0000.0000.0000.000
197A397ARG10.8950.94129.892-0.162-0.1620.0000.0000.0000.000
198A398ASP-1-0.833-0.91030.8830.1740.1740.0000.0000.0000.000
199A399MET0-0.034-0.00530.5370.0060.0060.0000.0000.0000.000
200A400LEU0-0.0050.00824.1180.0050.0050.0000.0000.0000.000
201A401LEU0-0.024-0.00627.5810.0150.0150.0000.0000.0000.000
202A402SER0-0.087-0.05729.803-0.018-0.0180.0000.0000.0000.000
203A403GLY0-0.018-0.01829.4320.0090.0090.0000.0000.0000.000
204A404SER0-0.077-0.04428.3590.0080.0080.0000.0000.0000.000
205A405SER00.0370.01225.0630.0010.0010.0000.0000.0000.000
206A406PHE0-0.0200.02023.4580.0100.0100.0000.0000.0000.000
207A407ASN0-0.019-0.03520.8810.0370.0370.0000.0000.0000.000