FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 8P92X

Calculation Name: 3HM1-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3HM1

Chain ID: A

ChEMBL ID: CHEMBL206

UniProt ID: P03372

Base Structure: X-ray

Registration Date: 2017-02-24

Reference:

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement BioStationViewer:StructureComplemation (agonist templeate: 1A52)
Water A bridging water among Glu353, Arg394 and ligand are complementated by template structure (PDBID: 2YJA).
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 238
LigandResidueName J3Z
LigandFragmentNumber 237
LigandCharge J3Z=0
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3125453.758742
FMO2-HF: Nuclear repulsion 3027470.714238
FMO2-HF: Total energy -97983.044504
FMO2-MP2: Total energy -98259.360844


3D Structure
Snapshot
 
Ligand structure

J3Z

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.
-96.423-77.00871.910-33.503-57.8210.112


Interactive mode: IFIE and PIEDA for fragment #237(A:2:J3Z)


Summations of interaction energy for fragment #237(A:2:J3Z)
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.
-96.423-77.00871.91-33.503-57.821-0.112
Interaction energy analysis for fragmet #237(A:2:J3Z)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.115 / q_NPA : ******
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].
1A309SER10.84830.5980.1480.1480.0000.0000.0000.000
2A310LEU00.14326.1270.0070.0070.0000.0000.0000.000
3A311THR00.00729.7290.0030.0030.0000.0000.0000.000
4A312ALA00.10127.191-0.010-0.0100.0000.0000.0000.000
5A313ASP-1-0.85926.081-0.135-0.1350.0000.0000.0000.000
6A314GLN0-0.04925.819-0.012-0.0120.0000.0000.0000.000
7A315MET0-0.05822.809-0.020-0.0200.0000.0000.0000.000
8A316VAL00.05721.602-0.019-0.0190.0000.0000.0000.000
9A317SER0-0.02020.975-0.020-0.0200.0000.0000.0000.000
10A318ALA00.01121.509-0.018-0.0180.0000.0000.0000.000
11A319LEU0-0.00617.601-0.031-0.0310.0000.0000.0000.000
12A320LEU0-0.02516.683-0.041-0.0410.0000.0000.0000.000
13A321ASP-1-0.90017.268-0.390-0.3900.0000.0000.0000.000
14A322ALA00.00116.359-0.037-0.0370.0000.0000.0000.000
15A323GLU-1-0.92911.364-0.580-0.5800.0000.0000.0000.000
16A324PRO0-0.0238.587-0.021-0.0210.0000.0000.0000.000
17A325PRO0-0.00710.0660.0930.0930.0000.0000.0000.000
18A326ILE00.0257.337-0.367-0.3670.0000.0000.0000.000
19A327LEU0-0.0316.0360.3590.3590.0000.0000.0000.000
20A328TYR00.0327.4410.1610.1610.0000.0000.0000.000
21A329SER00.0177.458-0.383-0.3830.0000.0000.0000.000
22A330GLU-1-0.9318.711-0.534-0.5340.0000.0000.0000.000
23A331TYR0-0.01210.8780.2050.2050.0000.0000.0000.000
24A332ASP-1-0.85512.470-0.155-0.1550.0000.0000.0000.000
25A333PRO0-0.06716.0430.0720.0720.0000.0000.0000.000
26A334THR0-0.03617.7050.0450.0450.0000.0000.0000.000
27A335ARG10.94214.833-0.042-0.0420.0000.0000.0000.000
28A336PRO0-0.00416.9060.0020.0020.0000.0000.0000.000
29A337PHE00.00410.2530.0100.0100.0000.0000.0000.000
30A338SER00.01612.7120.0010.0010.0000.0000.0000.000
31A339GLU-1-0.85810.2981.3441.3440.0000.0000.0000.000
32A340ALA00.0748.8200.2470.2470.0000.0000.0000.000
33A341SER0-0.0499.604-0.071-0.0710.0000.0000.0000.000
34A342MET0-0.0406.799-0.262-0.2620.0000.0000.0000.000
35A343MET00.0402.805-2.576-1.1620.481-0.486-1.4090.005
36A344GLY00.0274.917-0.365-0.218-0.001-0.002-0.1440.000
37A345LEU0-0.0686.952-0.612-0.6120.0000.0000.0000.000
38A346LEU0-0.0272.041-3.665-1.6823.288-1.085-4.1860.003
39A347THR00.0062.254-8.853-6.7135.096-2.079-5.158-0.030
40A348ASN00.0543.821-0.506-0.2720.010-0.014-0.2290.000
41A349LEU0-0.0722.565-0.4400.8100.261-0.356-1.1550.000
42A350ALA00.0472.390-3.452-1.7002.174-1.114-2.8110.004
43A351ASP-1-0.7343.618-0.623-0.3500.040-0.022-0.2900.001
44A352ARG10.8206.4512.9412.9410.0000.0000.0000.000
45A353GLU-1-0.8051.448-39.854-53.61735.448-16.734-4.951-0.110
46A354LEU00.0265.8920.9120.9120.0000.0000.0000.000
47A355VAL00.0328.2820.4210.4210.0000.0000.0000.000
48A356HIS0-0.0608.5810.3960.3960.0000.0000.0000.000
49A357MET0-0.0157.3370.3380.3380.0000.0000.0000.000
50A358ILE00.03210.1090.2320.2320.0000.0000.0000.000
51A359ASN0-0.03613.3200.2210.2210.0000.0000.0000.000
52A360TRP00.01211.9530.0870.0870.0000.0000.0000.000
53A361ALA00.04813.8390.0940.0940.0000.0000.0000.000
54A362LYS10.88715.5160.5830.5830.0000.0000.0000.000
55A363ARG10.79017.3740.5060.5060.0000.0000.0000.000
56A364VAL00.00016.2030.0340.0340.0000.0000.0000.000
57A365PRO0-0.02318.9080.0130.0130.0000.0000.0000.000
58A366GLY00.00222.5650.0050.0050.0000.0000.0000.000
59A367PHE00.04617.9320.0110.0110.0000.0000.0000.000
60A368VAL0-0.02221.7780.0040.0040.0000.0000.0000.000
61A369ASP-1-0.93023.817-0.201-0.2010.0000.0000.0000.000
62A370LEU0-0.06922.4920.0190.0190.0000.0000.0000.000
63A371THR0-0.04025.297-0.010-0.0100.0000.0000.0000.000
64A372LEU00.01621.945-0.013-0.0130.0000.0000.0000.000
65A373HIS0-0.02221.509-0.016-0.0160.0000.0000.0000.000
66A374ASP-1-0.83221.184-0.220-0.2200.0000.0000.0000.000
67A375GLN0-0.10219.911-0.063-0.0630.0000.0000.0000.000
68A376VAL00.03116.455-0.050-0.0500.0000.0000.0000.000
69A377HIS00.04215.873-0.051-0.0510.0000.0000.0000.000
70A378LEU0-0.05315.735-0.024-0.0240.0000.0000.0000.000
71A379LEU0-0.00513.523-0.043-0.0430.0000.0000.0000.000
72A380GLU-1-0.91111.629-0.493-0.4930.0000.0000.0000.000
73A381CYS0-0.10010.871-0.047-0.0470.0000.0000.0000.000
74A382ALA0-0.01210.686-0.091-0.0910.0000.0000.0000.000
75A383TRP00.0393.343-1.141-0.4470.027-0.081-0.6410.000
76A384LEU00.0242.424-2.481-0.6991.825-0.480-3.127-0.005
77A385GLU-1-0.8424.629-0.321-0.174-0.001-0.006-0.1410.000
78A386ILE0-0.0416.8180.3400.3400.0000.0000.0000.000
79A387LEU00.0132.762-3.472-0.1631.650-1.061-3.8980.008
80A388MET0-0.0492.355-1.4031.4541.731-1.029-3.559-0.007
81A389ILE00.0023.8950.2640.4240.004-0.005-0.1590.000
82A390GLY00.0505.843-0.067-0.0670.0000.0000.0000.000
83A391LEU0-0.0202.307-2.406-0.9562.416-0.909-2.9570.007
84A392VAL00.0094.520-0.705-0.6040.000-0.022-0.0790.000
85A393TRP00.0067.612-0.162-0.1620.0000.0000.0000.000
86A394ARG10.8492.870-4.793-2.8290.101-0.975-1.0900.011
87A395SER0-0.0667.293-0.028-0.0280.0000.0000.0000.000
88A396MET00.02110.059-0.075-0.0750.0000.0000.0000.000
89A397GLU-1-0.97312.8560.0390.0390.0000.0000.0000.000
90A398HIS0-0.03612.889-0.028-0.0280.0000.0000.0000.000
91A399PRO0-0.02513.7250.0750.0750.0000.0000.0000.000
92A400GLY0-0.01614.045-0.015-0.0150.0000.0000.0000.000
93A401LYS10.90511.413-0.273-0.2730.0000.0000.0000.000
94A402LEU00.0334.995-0.019-0.0190.0000.0000.0000.000
95A403LEU0-0.0197.747-0.052-0.0520.0000.0000.0000.000
96A404PHE00.0432.609-4.654-0.9281.126-1.067-3.7850.012
97A405ALA00.0464.384-2.140-1.997-0.001-0.013-0.1300.000
98A406PRO0-0.0137.1000.4260.4260.0000.0000.0000.000
99A407ASN0-0.01210.578-0.036-0.0360.0000.0000.0000.000
100A408LEU0-0.0456.5990.0080.0080.0000.0000.0000.000
101A409LEU00.0148.8950.2510.2510.0000.0000.0000.000
102A410LEU00.0167.059-0.115-0.1150.0000.0000.0000.000
103A411ASP-1-0.85910.3250.4570.4570.0000.0000.0000.000
104A412ARG10.93311.271-0.322-0.3220.0000.0000.0000.000
105A413ASN0-0.08512.1430.0010.0010.0000.0000.0000.000
106A414GLN0-0.00911.3160.0090.0090.0000.0000.0000.000
107A415GLY00.0659.0430.0750.0750.0000.0000.0000.000
108A416LYS10.8949.342-0.424-0.4240.0000.0000.0000.000
109A417CYS0-0.07310.925-0.013-0.0130.0000.0000.0000.000
110A418VAL00.0236.1490.0650.0650.0000.0000.0000.000
111A419GLU-1-0.9058.6250.7140.7140.0000.0000.0000.000
112A420GLY00.0477.7010.3310.3310.0000.0000.0000.000
113A421MET0-0.0252.108-1.279-0.3981.579-0.399-2.0610.001
114A422VAL0-0.0276.070-0.189-0.1890.0000.0000.0000.000
115A423GLU-1-0.9078.7540.2320.2320.0000.0000.0000.000
116A424ILE00.0322.831-1.142-0.1100.147-0.182-0.9970.000
117A425PHE00.0064.8360.1730.1730.0000.0000.0000.000
118A426ASP-1-0.8007.1840.4350.4350.0000.0000.0000.000
119A427MET0-0.0097.967-0.017-0.0170.0000.0000.0000.000
120A428LEU00.0663.433-0.6670.0120.043-0.122-0.5990.000
121A429LEU00.0077.3570.0220.0220.0000.0000.0000.000
122A430ALA0-0.01710.088-0.060-0.0600.0000.0000.0000.000
123A431THR00.0129.589-0.070-0.0700.0000.0000.0000.000
124A432SER0-0.0379.688-0.057-0.0570.0000.0000.0000.000
125A433SER0-0.05211.557-0.064-0.0640.0000.0000.0000.000
126A434ARG10.88614.181-0.114-0.1140.0000.0000.0000.000
127A435PHE00.02010.815-0.033-0.0330.0000.0000.0000.000
128A436ARG10.96514.505-0.275-0.2750.0000.0000.0000.000
129A437MET0-0.07517.269-0.029-0.0290.0000.0000.0000.000
130A438MET0-0.07117.385-0.022-0.0220.0000.0000.0000.000
131A439ASN00.01919.413-0.012-0.0120.0000.0000.0000.000
132A440LEU0-0.05514.024-0.018-0.0180.0000.0000.0000.000
133A441GLN00.05717.9430.0140.0140.0000.0000.0000.000
134A442GLY00.05115.9640.0010.0010.0000.0000.0000.000
135A443GLU-1-0.87616.759-0.145-0.1450.0000.0000.0000.000
136A444GLU-1-0.73818.352-0.044-0.0440.0000.0000.0000.000
137A445PHE0-0.0319.4860.0030.0030.0000.0000.0000.000
138A446VAL00.01714.136-0.006-0.0060.0000.0000.0000.000
139A447CYS0-0.04415.504-0.035-0.0350.0000.0000.0000.000
140A448LEU0-0.00614.016-0.016-0.0160.0000.0000.0000.000
141A449LYS10.9309.0210.5010.5010.0000.0000.0000.000
142A450SER00.00812.818-0.065-0.0650.0000.0000.0000.000
143A451ILE0-0.01215.935-0.011-0.0110.0000.0000.0000.000
144A452ILE0-0.04110.4600.0000.0000.0000.0000.0000.000
145A453LEU0-0.01914.036-0.029-0.0290.0000.0000.0000.000
146A454LEU00.00514.835-0.004-0.0040.0000.0000.0000.000
147A455ASN0-0.01816.9660.0280.0280.0000.0000.0000.000
148A456SER0-0.06112.7610.0450.0450.0000.0000.0000.000
149A457GLY00.10115.8050.0000.0000.0000.0000.0000.000
150A458VAL00.03117.5250.0220.0220.0000.0000.0000.000
151A459TYR0-0.07517.6770.0130.0130.0000.0000.0000.000
152A460THR0-0.06117.7650.0210.0210.0000.0000.0000.000
153A461PHE00.06221.066-0.003-0.0030.0000.0000.0000.000
154A462LEU00.05923.1760.0200.0200.0000.0000.0000.000
155A463SER0-0.07425.7100.0020.0020.0000.0000.0000.000
156A464SER0-0.01428.4230.0060.0060.0000.0000.0000.000
157A465THR0-0.00731.3640.0060.0060.0000.0000.0000.000
158A466LEU00.05032.324-0.006-0.0060.0000.0000.0000.000
159A467LYS10.90729.4150.1590.1590.0000.0000.0000.000
160A468SER0-0.00527.850-0.013-0.0130.0000.0000.0000.000
161A469LEU0-0.05528.475-0.003-0.0030.0000.0000.0000.000
162A470GLU-1-0.91030.426-0.115-0.1150.0000.0000.0000.000
163A471GLU-1-0.66626.561-0.190-0.1900.0000.0000.0000.000
164A472LYS10.88925.3850.1160.1160.0000.0000.0000.000
165A473ASP-1-0.89926.792-0.120-0.1200.0000.0000.0000.000
166A474HIS0-0.02626.9980.0120.0120.0000.0000.0000.000
167A475ILE00.04122.151-0.004-0.0040.0000.0000.0000.000
168A476HIS00.03924.168-0.008-0.0080.0000.0000.0000.000
169A477ARG10.93426.0490.1420.1420.0000.0000.0000.000
170A478VAL0-0.06423.1890.0050.0050.0000.0000.0000.000
171A479LEU0-0.00719.842-0.005-0.0050.0000.0000.0000.000
172A480ASP-1-0.86023.646-0.110-0.1100.0000.0000.0000.000
173A481LYS10.85626.0620.1600.1600.0000.0000.0000.000
174A482ILE00.00019.7160.0060.0060.0000.0000.0000.000
175A483THR0-0.01023.1450.0100.0100.0000.0000.0000.000
176A484ASP-1-0.91024.597-0.099-0.0990.0000.0000.0000.000
177A485THR0-0.12123.2870.0020.0020.0000.0000.0000.000
178A486LEU00.02319.7650.0070.0070.0000.0000.0000.000
179A487ILE00.04523.6220.0100.0100.0000.0000.0000.000
180A488HIS0-0.03827.0290.0110.0110.0000.0000.0000.000
181A489LEU0-0.01422.0360.0050.0050.0000.0000.0000.000
182A490MET0-0.03622.8330.0090.0090.0000.0000.0000.000
183A491ALA0-0.00527.0790.0060.0060.0000.0000.0000.000
184A492LYS10.90127.2740.0970.0970.0000.0000.0000.000
185A493ALA0-0.04226.9970.0010.0010.0000.0000.0000.000
186A494GLY0-0.01129.1180.0060.0060.0000.0000.0000.000
187A495LEU0-0.04426.9650.0050.0050.0000.0000.0000.000
188A496THR00.01531.346-0.004-0.0040.0000.0000.0000.000
189A497LEU00.06932.290-0.001-0.0010.0000.0000.0000.000
190A498GLN00.02731.9580.0000.0000.0000.0000.0000.000
191A499GLN00.02129.801-0.002-0.0020.0000.0000.0000.000
192A500GLN00.01128.035-0.003-0.0030.0000.0000.0000.000
193A501HIS00.03527.076-0.001-0.0010.0000.0000.0000.000
194A502GLN0-0.05427.0820.0010.0010.0000.0000.0000.000
195A503ARG10.80420.7720.0130.0130.0000.0000.0000.000
196A504LEU00.02822.5130.0030.0030.0000.0000.0000.000
197A505ALA00.01221.967-0.005-0.0050.0000.0000.0000.000
198A506GLN0-0.03321.258-0.001-0.0010.0000.0000.0000.000
199A507LEU0-0.01617.4730.0110.0110.0000.0000.0000.000
200A508LEU00.03917.010-0.002-0.0020.0000.0000.0000.000
201A509LEU0-0.03617.812-0.013-0.0130.0000.0000.0000.000
202A510ILE0-0.03212.9760.0010.0010.0000.0000.0000.000
203A511LEU00.03412.869-0.002-0.0020.0000.0000.0000.000
204A512SER0-0.01213.161-0.056-0.0560.0000.0000.0000.000
205A513HIS00.00410.765-0.050-0.0500.0000.0000.0000.000
206A514ILE0-0.0087.829-0.025-0.0250.0000.0000.0000.000
207A515ARG10.9458.7430.1820.1820.0000.0000.0000.000
208A516HIS0-0.05510.032-0.111-0.1110.0000.0000.0000.000
209A517MET0-0.0255.997-0.001-0.0010.0000.0000.0000.000
210A518SER00.0585.563-0.595-0.5950.0000.0000.0000.000
211A519ASN0-0.0116.075-0.271-0.2710.0000.0000.0000.000
212A520LYS10.9486.8600.1340.1340.0000.0000.0000.000
213A521GLY00.0012.848-0.0180.4820.457-0.339-0.6170.001
214A522MET00.0512.216-5.417-4.5863.269-1.444-2.656-0.032
215A523GLU-1-0.9144.8971.3481.430-0.001-0.003-0.0790.000
216A524HIS0-0.0352.464-3.996-1.6871.408-1.334-2.3830.003
217A525LEU00.0192.0211.3151.1239.002-2.137-6.6720.009
218A526TYR00.0673.400-0.713-0.8960.1140.518-0.4490.003
219A527SER0-0.0656.558-0.460-0.4600.0000.0000.0000.000
220A528MET00.0173.153-2.201-1.0400.212-0.402-0.9710.004
221A529LYS10.9776.682-1.783-1.7830.0000.0000.0000.000
222A530CYS0-0.0968.333-0.588-0.5880.0000.0000.0000.000
223A531LYS10.83910.290-1.411-1.4110.0000.0000.0000.000
224A532ASN0-0.02810.822-0.205-0.2050.0000.0000.0000.000
225A533VAL00.0258.268-0.156-0.1560.0000.0000.0000.000
226A534VAL0-0.0286.483-0.214-0.2140.0000.0000.0000.000
227A535PRO0-0.0319.0850.2800.2800.0000.0000.0000.000
228A536LEU00.0045.3160.0880.0880.0000.0000.0000.000
229A537SER0-0.0618.3720.0030.0030.0000.0000.0000.000
230A538ASP-1-0.89410.100-0.072-0.0720.0000.0000.0000.000
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