FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: 7K3JK

Calculation Name: 1FM9-A-Xray547

Preferred Name: Nuclear receptor coactivator 1

Target Type: SINGLE PROTEIN

Ligand Name: 2-(2-benzoyl-phenylamino)-3-{4-[2-(5-methyl-2-phenyl-oxazol-4-yl)-ethoxy]-phenyl}-propionic acid | (9cis)-retinoic acid

Ligand 3-letter code: 570 | 9CR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1FM9

Chain ID: A

ChEMBL ID: CHEMBL1615387

UniProt ID: Q15788

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2915438.6103
FMO2-HF: Nuclear repulsion 2823666.671101
FMO2-HF: Total energy -91771.939199
FMO2-MP2: Total energy -92037.013256


3D Structure Molmil
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:227:ASN)


Summations of interaction energy for fragment #1(A:227:ASN)
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.
-102.374-96.6176.435-5.39-6.801-0.056
Interaction energy analysis for fragmet #1(A:227:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.796 / q_NPA : 0.883
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].
3A229ASP-1-0.799-0.8713.900-34.234-31.751-0.006-1.153-1.324-0.004
5A231PRO0-0.032-0.0082.158-1.268-0.4222.821-1.263-2.404-0.005
6A232VAL00.1070.0414.1373.9454.1930.001-0.082-0.1660.000
7A233GLU-1-0.858-0.9502.057-70.913-68.7333.619-2.892-2.907-0.047
4A230MET0-0.0020.0065.497-1.556-1.5560.0000.0000.0000.000
8A234ARG10.9190.9455.11845.17445.1740.0000.0000.0000.000
9A235ILE0-0.0240.0127.5053.3153.3150.0000.0000.0000.000
10A236LEU0-0.006-0.0079.4622.8432.8430.0000.0000.0000.000
11A237GLU-1-0.944-0.9868.511-30.242-30.2420.0000.0000.0000.000
12A238ALA0-0.030-0.00411.5251.7011.7010.0000.0000.0000.000
13A239GLU-1-0.817-0.89913.476-16.544-16.5440.0000.0000.0000.000
14A240LEU0-0.074-0.04913.5341.4171.4170.0000.0000.0000.000
15A241ALA0-0.0110.00815.4920.9330.9330.0000.0000.0000.000
16A242VAL0-0.0120.00817.2420.6860.6860.0000.0000.0000.000
17A243GLU-1-0.836-0.89719.284-14.495-14.4950.0000.0000.0000.000
18A244PRO0-0.003-0.03422.0250.2280.2280.0000.0000.0000.000
19A245LYS10.8890.96717.26916.17016.1700.0000.0000.0000.000
20A246THR0-0.034-0.02423.8520.1630.1630.0000.0000.0000.000
21A247GLU-1-0.895-0.94327.197-11.236-11.2360.0000.0000.0000.000
22A248THR00.0400.00826.4920.4020.4020.0000.0000.0000.000
23A249TYR0-0.078-0.02529.5810.2280.2280.0000.0000.0000.000
24A250VAL00.006-0.01131.4220.2280.2280.0000.0000.0000.000
25A251GLU-1-0.811-0.90332.579-9.664-9.6640.0000.0000.0000.000
26A252ALA00.0370.01535.4390.2590.2590.0000.0000.0000.000
27A253ASN0-0.073-0.04236.1430.0010.0010.0000.0000.0000.000
28A254MET0-0.044-0.01438.0250.0680.0680.0000.0000.0000.000
29A255GLY00.0270.00939.3730.2120.2120.0000.0000.0000.000
30A256LEU0-0.041-0.01239.870-0.181-0.1810.0000.0000.0000.000
31A257ASN00.0330.02439.489-0.004-0.0040.0000.0000.0000.000
32A258PRO00.0090.00238.1540.2000.2000.0000.0000.0000.000
33A259SER0-0.028-0.01040.7420.0280.0280.0000.0000.0000.000
34A260SER0-0.031-0.01942.6280.2010.2010.0000.0000.0000.000
35A261PRO00.0140.01441.0590.1810.1810.0000.0000.0000.000
36A262ASN0-0.055-0.03444.329-0.097-0.0970.0000.0000.0000.000
37A263ASP-1-0.710-0.84743.105-7.450-7.4500.0000.0000.0000.000
38A264PRO0-0.020-0.00640.623-0.191-0.1910.0000.0000.0000.000
39A265VAL0-0.0010.00439.134-0.311-0.3110.0000.0000.0000.000
40A266THR00.0530.01138.429-0.272-0.2720.0000.0000.0000.000
41A267ASN0-0.071-0.03938.159-0.100-0.1000.0000.0000.0000.000
42A268ILE0-0.020-0.01733.767-0.314-0.3140.0000.0000.0000.000
43A269CYS0-0.059-0.02033.852-0.355-0.3550.0000.0000.0000.000
44A270GLN00.1110.06134.021-0.090-0.0900.0000.0000.0000.000
45A271ALA0-0.061-0.02931.548-0.297-0.2970.0000.0000.0000.000
46A272ALA0-0.028-0.01829.737-0.475-0.4750.0000.0000.0000.000
47A273ASP-1-0.800-0.91629.216-10.488-10.4880.0000.0000.0000.000
48A274LYS10.8500.91728.73710.26210.2620.0000.0000.0000.000
49A275GLN0-0.027-0.04024.276-0.091-0.0910.0000.0000.0000.000
50A276LEU00.0330.05224.815-0.781-0.7810.0000.0000.0000.000
51A277PHE00.0010.00424.856-0.622-0.6220.0000.0000.0000.000
52A278THR0-0.076-0.04622.305-0.648-0.6480.0000.0000.0000.000
53A279LEU00.0100.01020.500-0.995-0.9950.0000.0000.0000.000
54A280VAL00.0310.01619.669-0.977-0.9770.0000.0000.0000.000
55A281GLU-1-0.874-0.91617.711-17.712-17.7120.0000.0000.0000.000
56A282TRP0-0.031-0.04815.694-1.273-1.2730.0000.0000.0000.000
57A283ALA00.0370.01714.966-1.573-1.5730.0000.0000.0000.000
58A284LYS10.9380.97114.05615.12815.1280.0000.0000.0000.000
59A285ARG10.8160.90411.90318.59018.5900.0000.0000.0000.000
60A286ILE00.0270.03310.267-3.814-3.8140.0000.0000.0000.000
61A287PRO0-0.072-0.0425.9080.0720.0720.0000.0000.0000.000
62A288HIS10.8310.8695.88243.01443.0140.0000.0000.0000.000
63A289PHE00.0470.0459.7561.8961.8960.0000.0000.0000.000
64A290SER0-0.022-0.02812.0361.8541.8540.0000.0000.0000.000
65A291GLU-1-0.936-0.9518.693-34.809-34.8090.0000.0000.0000.000
66A292LEU00.0090.03012.9600.7980.7980.0000.0000.0000.000
67A293PRO00.0300.01815.7880.2330.2330.0000.0000.0000.000
68A294LEU00.0140.00819.334-0.050-0.0500.0000.0000.0000.000
69A295ASP-1-0.867-0.94421.039-12.420-12.4200.0000.0000.0000.000
70A296ASP-1-0.732-0.83619.790-14.344-14.3440.0000.0000.0000.000
71A297GLN0-0.090-0.04616.5490.1640.1640.0000.0000.0000.000
72A298VAL00.005-0.00319.8000.1610.1610.0000.0000.0000.000
73A299ILE0-0.012-0.00323.4950.2960.2960.0000.0000.0000.000
74A300LEU0-0.030-0.01618.1230.2270.2270.0000.0000.0000.000
75A301LEU0-0.038-0.02020.0840.1630.1630.0000.0000.0000.000
76A302ARG10.8660.90622.84810.86010.8600.0000.0000.0000.000
77A303ALA0-0.041-0.00724.5580.4780.4780.0000.0000.0000.000
78A304GLY00.0240.02223.6480.1920.1920.0000.0000.0000.000
79A305TRP00.015-0.00824.312-0.106-0.1060.0000.0000.0000.000
80A306ASN00.0140.01825.306-0.307-0.3070.0000.0000.0000.000
81A307GLU-1-0.807-0.90224.835-12.194-12.1940.0000.0000.0000.000
82A308LEU0-0.0180.00519.588-0.181-0.1810.0000.0000.0000.000
83A309LEU00.0280.03122.802-0.381-0.3810.0000.0000.0000.000
84A310ILE00.0000.00025.4940.1320.1320.0000.0000.0000.000
85A311ALA00.0040.00822.6020.1740.1740.0000.0000.0000.000
86A312SER0-0.018-0.02122.389-0.244-0.2440.0000.0000.0000.000
87A313PHE00.006-0.00823.5870.0580.0580.0000.0000.0000.000
88A314SER0-0.024-0.00926.3570.4840.4840.0000.0000.0000.000
89A315HIS0-0.011-0.03120.7660.3280.3280.0000.0000.0000.000
90A316ARG10.8870.94324.41512.11212.1120.0000.0000.0000.000
91A317SER00.006-0.01525.7400.4260.4260.0000.0000.0000.000
92A318ILE00.0230.01324.0320.4460.4460.0000.0000.0000.000
93A319ALA0-0.026-0.00627.8090.3210.3210.0000.0000.0000.000
94A320VAL0-0.0310.00329.4560.3110.3110.0000.0000.0000.000
95A321LYS10.9030.94432.8737.7947.7940.0000.0000.0000.000
96A322ASP-1-0.860-0.93535.792-7.871-7.8710.0000.0000.0000.000
97A323GLY00.0530.01435.6450.2670.2670.0000.0000.0000.000
98A324ILE0-0.0040.00431.127-0.238-0.2380.0000.0000.0000.000
99A325LEU00.0040.02229.4700.2150.2150.0000.0000.0000.000
100A326LEU00.0130.01729.867-0.508-0.5080.0000.0000.0000.000
101A327ALA0-0.008-0.00727.333-0.041-0.0410.0000.0000.0000.000
102A328THR00.0370.01929.007-0.181-0.1810.0000.0000.0000.000
103A329GLY00.006-0.00231.2290.2460.2460.0000.0000.0000.000
104A330LEU0-0.0190.00532.4830.1810.1810.0000.0000.0000.000
105A331HIS00.001-0.00434.467-0.293-0.2930.0000.0000.0000.000
106A332VAL00.0210.01935.6730.3080.3080.0000.0000.0000.000
107A333HIS00.0430.01037.168-0.100-0.1000.0000.0000.0000.000
108A334ARG10.8340.89739.4387.8397.8390.0000.0000.0000.000
109A335ASN00.005-0.00940.677-0.004-0.0040.0000.0000.0000.000
110A336SER00.0140.02541.9410.1290.1290.0000.0000.0000.000
111A337ALA00.0360.02239.8250.0720.0720.0000.0000.0000.000
112A338HIS0-0.037-0.02841.9270.0590.0590.0000.0000.0000.000
113A339SER0-0.063-0.03944.8280.1600.1600.0000.0000.0000.000
114A340ALA0-0.014-0.00143.5790.1200.1200.0000.0000.0000.000
115A341GLY0-0.0010.01145.249-0.035-0.0350.0000.0000.0000.000
116A342VAL00.0080.01340.181-0.052-0.0520.0000.0000.0000.000
117A343GLY00.0550.01440.669-0.208-0.2080.0000.0000.0000.000
118A344ALA0-0.0030.01141.630-0.030-0.0300.0000.0000.0000.000
119A345ILE0-0.001-0.00935.361-0.203-0.2030.0000.0000.0000.000
120A346PHE00.0400.01536.488-0.277-0.2770.0000.0000.0000.000
121A347ASP-1-0.794-0.90636.375-7.907-7.9070.0000.0000.0000.000
122A348ARG10.7870.85834.3398.8728.8720.0000.0000.0000.000
123A349VAL00.0310.02531.203-0.286-0.2860.0000.0000.0000.000
124A350LEU0-0.0040.00031.905-0.277-0.2770.0000.0000.0000.000
125A351THR0-0.058-0.03133.206-0.146-0.1460.0000.0000.0000.000
126A352GLU-1-0.827-0.89031.966-9.349-9.3490.0000.0000.0000.000
127A353LEU0-0.031-0.01227.137-0.412-0.4120.0000.0000.0000.000
128A354VAL00.0120.01028.189-0.217-0.2170.0000.0000.0000.000
129A355SER0-0.061-0.04528.891-0.169-0.1690.0000.0000.0000.000
130A356LYS10.9110.97228.1569.3579.3570.0000.0000.0000.000
131A357MET0-0.004-0.01023.305-0.286-0.2860.0000.0000.0000.000
132A358ARG10.8910.95424.8609.5429.5420.0000.0000.0000.000
133A359ASP-1-0.945-0.97827.337-9.809-9.8090.0000.0000.0000.000
134A360MET0-0.087-0.03721.9170.1420.1420.0000.0000.0000.000
135A361GLN0-0.015-0.00423.672-0.345-0.3450.0000.0000.0000.000
136A362MET0-0.0040.02619.933-0.484-0.4840.0000.0000.0000.000
137A363ASP-1-0.715-0.80415.182-18.117-18.1170.0000.0000.0000.000
138A364LYS10.8610.89815.87215.20915.2090.0000.0000.0000.000
139A365THR00.0110.01210.465-0.901-0.9010.0000.0000.0000.000
140A366GLU-1-0.765-0.84613.163-16.509-16.5090.0000.0000.0000.000
141A367LEU0-0.023-0.00415.7640.1180.1180.0000.0000.0000.000
142A368GLY00.0650.03214.4090.3110.3110.0000.0000.0000.000
143A369CYS0-0.047-0.01812.068-1.196-1.1960.0000.0000.0000.000
144A370LEU0-0.016-0.01014.2250.3930.3930.0000.0000.0000.000
145A371ARG10.8180.90317.27717.02217.0220.0000.0000.0000.000
146A372ALA00.0300.00613.2640.3680.3680.0000.0000.0000.000
147A373ILE0-0.014-0.00515.2810.1910.1910.0000.0000.0000.000
148A374VAL0-0.028-0.01417.3800.6520.6520.0000.0000.0000.000
149A375LEU0-0.030-0.00715.3180.4840.4840.0000.0000.0000.000
150A376PHE0-0.009-0.00611.9290.1870.1870.0000.0000.0000.000
151A377ASN00.0610.01717.6200.1430.1430.0000.0000.0000.000
152A378PRO00.0290.02120.4910.3110.3110.0000.0000.0000.000
153A379ASP-1-0.951-0.96922.431-12.062-12.0620.0000.0000.0000.000
154A380SER0-0.088-0.04923.2420.6540.6540.0000.0000.0000.000
155A381LYS10.8810.91125.7879.7879.7870.0000.0000.0000.000
156A382GLY00.0060.00027.903-0.033-0.0330.0000.0000.0000.000
157A383LEU0-0.0170.00921.175-0.133-0.1330.0000.0000.0000.000
158A384SER0-0.100-0.07721.7440.2530.2530.0000.0000.0000.000
159A385ASN0-0.007-0.01418.7780.7200.7200.0000.0000.0000.000
160A386PRO00.0360.01019.977-0.828-0.8280.0000.0000.0000.000
161A387ALA0-0.0010.00520.482-0.409-0.4090.0000.0000.0000.000
162A388GLU-1-0.919-0.95614.847-20.264-20.2640.0000.0000.0000.000
163A389VAL00.0140.00615.495-1.430-1.4300.0000.0000.0000.000
164A390GLU-1-0.839-0.92516.738-16.518-16.5180.0000.0000.0000.000
165A391ALA00.0110.00514.784-0.721-0.7210.0000.0000.0000.000
166A392LEU0-0.058-0.02710.576-2.386-2.3860.0000.0000.0000.000
167A393ARG10.8170.92112.99714.30314.3030.0000.0000.0000.000
168A394GLU-1-0.935-0.97915.037-17.801-17.8010.0000.0000.0000.000
169A395LYS10.8450.9118.60131.09431.0940.0000.0000.0000.000
170A396VAL0-0.020-0.00610.796-1.562-1.5620.0000.0000.0000.000
171A397TYR0-0.013-0.00712.1670.3690.3690.0000.0000.0000.000
172A398ALA00.0070.01511.5940.5760.5760.0000.0000.0000.000
173A399SER00.027-0.0027.4881.2851.2850.0000.0000.0000.000
174A400LEU0-0.020-0.01510.0430.6140.6140.0000.0000.0000.000
175A401GLU-1-0.830-0.91212.823-15.566-15.5660.0000.0000.0000.000
176A402ALA00.0020.00210.2631.0431.0430.0000.0000.0000.000
177A403TYR0-0.016-0.03310.0790.4830.4830.0000.0000.0000.000
178A404CYS0-0.069-0.04111.8511.4431.4430.0000.0000.0000.000
179A405LYS10.8090.89614.98217.13217.1320.0000.0000.0000.000
180A406HIS0-0.0140.00611.0031.0091.0090.0000.0000.0000.000
181A407LYS10.8280.91612.95719.61819.6180.0000.0000.0000.000
182A408TYR0-0.047-0.05015.3060.9940.9940.0000.0000.0000.000
183A409PRO00.0230.02117.6420.4730.4730.0000.0000.0000.000
184A410GLU-1-0.847-0.92319.965-12.421-12.4210.0000.0000.0000.000
185A411GLN0-0.084-0.03421.9940.5370.5370.0000.0000.0000.000
186A412PRO00.0500.01021.938-0.364-0.3640.0000.0000.0000.000
187A413GLY0-0.0080.00222.410-0.313-0.3130.0000.0000.0000.000
188A414ARG10.7130.81019.01714.30114.3010.0000.0000.0000.000
189A415PHE00.0730.02816.4430.1740.1740.0000.0000.0000.000
190A416ALA00.0580.02920.134-0.047-0.0470.0000.0000.0000.000
191A417LYS10.9110.95323.54111.18211.1820.0000.0000.0000.000
192A418LEU00.0520.01617.3960.4190.4190.0000.0000.0000.000
193A419LEU00.0700.04218.9840.2310.2310.0000.0000.0000.000
194A420LEU0-0.043-0.02422.4510.3930.3930.0000.0000.0000.000
195A421ARG10.8390.92123.72812.11912.1190.0000.0000.0000.000
196A422LEU00.0370.02420.9070.3390.3390.0000.0000.0000.000
197A423PRO0-0.0020.00225.3040.2570.2570.0000.0000.0000.000
198A424ALA00.0320.03128.9930.3210.3210.0000.0000.0000.000
199A425LEU0-0.0060.00123.8090.2340.2340.0000.0000.0000.000
200A426ARG10.9300.95725.37512.23512.2350.0000.0000.0000.000
201A427SER0-0.034-0.02429.0660.3580.3580.0000.0000.0000.000
202A428ILE0-0.011-0.00131.0690.3360.3360.0000.0000.0000.000
203A429GLY00.0570.02429.8450.1830.1830.0000.0000.0000.000
204A430LEU0-0.005-0.01330.8110.1380.1380.0000.0000.0000.000
205A431LYS00.0640.05633.4900.1370.1370.0000.0000.0000.000
206A432CYS0-0.051-0.02832.8210.2240.2240.0000.0000.0000.000
207A433LEU00.0050.00531.0700.1490.1490.0000.0000.0000.000
208A434GLU-1-0.958-0.97135.002-7.807-7.8070.0000.0000.0000.000
209A435HIS0-0.018-0.02137.9810.3300.3300.0000.0000.0000.000
210A436LEU0-0.002-0.00334.7830.1580.1580.0000.0000.0000.000
211A437PHE0-0.051-0.02335.4410.1060.1060.0000.0000.0000.000
212A438PHE00.0010.00140.1610.2430.2430.0000.0000.0000.000
213A439PHE0-0.038-0.02739.8030.1390.1390.0000.0000.0000.000
214A440LYS10.9380.98138.3128.1518.1510.0000.0000.0000.000
215A441LEU0-0.093-0.04542.5640.1150.1150.0000.0000.0000.000
216A442ILE0-0.023-0.01145.4240.1420.1420.0000.0000.0000.000
217A443GLY0-0.0210.00045.7980.1270.1270.0000.0000.0000.000
218A444ASP-1-0.925-0.95646.179-6.553-6.5530.0000.0000.0000.000
219A445THR0-0.075-0.04346.191-0.067-0.0670.0000.0000.0000.000
220A446PRO0-0.0120.00042.402-0.077-0.0770.0000.0000.0000.000
221A447ILE00.0340.00736.547-0.020-0.0200.0000.0000.0000.000
222A448ASP-1-0.881-0.93835.377-8.724-8.7240.0000.0000.0000.000
223A449THR0-0.030-0.03834.4810.0250.0250.0000.0000.0000.000
224A450PHE00.0520.04125.886-0.283-0.2830.0000.0000.0000.000
225A451LEU00.026-0.00231.767-0.131-0.1310.0000.0000.0000.000
226A452MET0-0.019-0.02232.9670.0450.0450.0000.0000.0000.000
227A453GLU-1-0.959-0.96530.225-10.353-10.3530.0000.0000.0000.000
228A454MET0-0.006-0.01325.831-0.114-0.1140.0000.0000.0000.000
229A455LEU0-0.049-0.01931.4450.0610.0610.0000.0000.0000.000
230A456GLU-1-0.982-0.98733.915-9.078-9.0780.0000.0000.0000.000
231A457ALA0-0.029-0.01234.1050.1320.1320.0000.0000.0000.000
232A458PRO-1-0.834-0.89430.265-9.905-9.9050.0000.0000.0000.000