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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: 6X1ZP

Calculation Name: 1XP9-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: (2s,3r)-3-(4-hydroxyphenyl)-2-(4-{[(2s)-2-pyrrolidin-1-ylpropyl]oxy}phenyl)-2,3-dihydro-1,4-benzoxathiin-6-ol

ligand 3-letter code: AIJ

PDB ID: 1XP9

Chain ID: A

ChEMBL ID: CHEMBL206

UniProt ID: P03372

Base Structure: X-ray

Registration Date: 2017-02-24

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement BioStationViewer:StructureComplemation (antagonist templeate: 1YIM)
Water A bridging water among Glu353, Arg394 and ligand.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 238
LigandCharge AIJ=+1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3176234.06788
FMO2-HF: Nuclear repulsion 3077073.584509
FMO2-HF: Total energy -99160.483371
FMO2-MP2: Total energy -99439.341662


3D Structure
Snapshot
 
Ligand structure

AIJ

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.
-335.645-292.852110.685-52.077-101.4010.263


Interactive mode: IFIE and PIEDA for fragment #237(A:600:AIJ)


Summations of interaction energy for fragment #237(A:600:AIJ)
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.
-335.645-292.852110.685-52.077-101.401-0.263
Interaction energy analysis for fragmet #237(A:600:AIJ)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.738 / 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].
1A309SER10.85230.1079.5169.5160.0000.0000.0000.000
2A310LEU00.12324.8050.2830.2830.0000.0000.0000.000
3A311THR0-0.01429.0330.0060.0060.0000.0000.0000.000
4A312ALA00.10826.908-0.313-0.3130.0000.0000.0000.000
5A313ASP-1-0.89625.773-9.134-9.1340.0000.0000.0000.000
6A314GLN00.01226.022-0.221-0.2210.0000.0000.0000.000
7A315MET0-0.00121.871-0.426-0.4260.0000.0000.0000.000
8A316VAL00.01521.316-0.456-0.4560.0000.0000.0000.000
9A317SER00.02820.782-0.189-0.1890.0000.0000.0000.000
10A318ALA0-0.01321.108-0.274-0.2740.0000.0000.0000.000
11A319LEU0-0.02717.067-0.511-0.5110.0000.0000.0000.000
12A320LEU0-0.03816.357-0.581-0.5810.0000.0000.0000.000
13A321ASP-1-0.94116.922-11.884-11.8840.0000.0000.0000.000
14A322ALA0-0.09015.762-0.341-0.3410.0000.0000.0000.000
15A323GLU-1-0.78511.337-17.819-17.8190.0000.0000.0000.000
16A324PRO0-0.0338.3140.0340.0340.0000.0000.0000.000
17A325PRO00.00110.0810.8200.8200.0000.0000.0000.000
18A326ILE00.0087.666-1.656-1.6560.0000.0000.0000.000
19A327LEU0-0.0296.2761.0121.0120.0000.0000.0000.000
20A328TYR00.0327.4880.5790.5790.0000.0000.0000.000
21A329SER00.0017.134-2.487-2.4870.0000.0000.0000.000
22A330GLU-1-0.9138.194-22.049-22.0490.0000.0000.0000.000
23A331TYR0-0.06710.366-0.537-0.5370.0000.0000.0000.000
24A332ASP-1-0.80112.931-13.224-13.2240.0000.0000.0000.000
25A333PRO0-0.00615.9140.0400.0400.0000.0000.0000.000
26A334THR0-0.09417.0860.6990.6990.0000.0000.0000.000
27A335ARG10.83818.39914.28914.2890.0000.0000.0000.000
28A336PRO0-0.01618.249-0.201-0.2010.0000.0000.0000.000
29A337PHE00.05511.227-0.562-0.5620.0000.0000.0000.000
30A338SER0-0.02015.159-0.742-0.7420.0000.0000.0000.000
31A339GLU-1-0.87316.235-14.172-14.1720.0000.0000.0000.000
32A340ALA00.00612.086-0.686-0.6860.0000.0000.0000.000
33A341SER00.0139.127-0.601-0.6010.0000.0000.0000.000
34A342MET00.0466.330-1.092-1.0920.0000.0000.0000.000
35A343MET00.0303.592-3.876-2.4710.256-0.324-1.3390.000
36A344GLY00.0454.358-5.982-5.7410.000-0.024-0.2160.000
37A345LEU00.0016.686-2.440-2.4400.0000.0000.0000.000
38A346LEU0-0.0252.410-7.129-3.3623.754-1.780-5.7410.012
39A347THR0-0.0012.081-13.377-9.9037.423-3.973-6.924-0.016
40A348ASN0-0.0353.155-6.712-6.9390.0600.941-0.774-0.003
41A349LEU0-0.0572.514-1.1800.4321.288-0.543-2.3580.003
42A350ALA00.0412.994-4.502-0.7191.956-1.390-4.3490.008
43A351ASP-1-0.8491.594-125.076-129.43824.877-12.154-8.361-0.128
44A352ARG10.8873.52534.54034.8320.0050.041-0.338-0.001
45A353GLU-1-0.7591.686-65.117-67.19217.545-9.261-6.210-0.115
46A354LEU00.0042.1792.5591.9393.464-0.526-2.318-0.005
47A355VAL00.0395.3893.4673.526-0.001-0.001-0.0560.000
48A356HIS0-0.0298.0883.6913.6910.0000.0000.0000.000
49A357MET0-0.0486.1182.1112.1110.0000.0000.0000.000
50A358ILE00.0418.3122.0882.0880.0000.0000.0000.000
51A359ASN0-0.01810.6501.8981.8980.0000.0000.0000.000
52A360TRP0-0.01111.4640.8510.8510.0000.0000.0000.000
53A361ALA00.04912.1951.2351.2350.0000.0000.0000.000
54A362LYS10.93414.07818.47618.4760.0000.0000.0000.000
55A363ARG10.89116.63414.99914.9990.0000.0000.0000.000
56A364VAL0-0.01015.6670.8210.8210.0000.0000.0000.000
57A365PRO0-0.03918.5100.1860.1860.0000.0000.0000.000
58A366GLY00.01621.987-0.032-0.0320.0000.0000.0000.000
59A367PHE00.03313.4930.0200.0200.0000.0000.0000.000
60A368VAL00.00118.251-0.235-0.2350.0000.0000.0000.000
61A369ASP-1-0.97520.004-11.417-11.4170.0000.0000.0000.000
62A370LEU0-0.05718.1300.3620.3620.0000.0000.0000.000
63A371THR0-0.06420.165-0.226-0.2260.0000.0000.0000.000
64A372LEU00.05115.600-0.287-0.2870.0000.0000.0000.000
65A373HIS0-0.07115.608-0.528-0.5280.0000.0000.0000.000
66A374ASP-1-0.80915.224-15.409-15.4090.0000.0000.0000.000
67A375GLN0-0.04114.556-1.331-1.3310.0000.0000.0000.000
68A376VAL00.01210.109-1.407-1.4070.0000.0000.0000.000
69A377HIS0-0.00310.551-2.539-2.5390.0000.0000.0000.000
70A378LEU0-0.05011.853-0.889-0.8890.0000.0000.0000.000
71A379LEU00.0108.424-0.894-0.8940.0000.0000.0000.000
72A380GLU-1-0.9336.998-31.215-31.2150.0000.0000.0000.000
73A381CYS0-0.1008.000-1.060-1.0600.0000.0000.0000.000
74A382ALA00.02310.143-0.189-0.1890.0000.0000.0000.000
75A383TRP00.0292.316-13.013-8.2273.788-2.104-6.470-0.023
76A384LEU00.0112.190-2.971-0.8151.625-0.575-3.206-0.004
77A385GLU-1-0.8065.488-16.693-16.6930.0000.0000.0000.000
78A386ILE0-0.0067.0092.0582.0580.0000.0000.0000.000
79A387LEU0-0.0202.592-2.4091.5111.544-1.364-4.1000.010
80A388MET0-0.0462.7301.7865.2830.797-1.199-3.095-0.005
81A389ILE00.0173.9451.8772.0170.001-0.009-0.1320.000
82A390GLY00.0485.4861.0551.0550.0000.0000.0000.000
83A391LEU0-0.0072.910-2.5650.2601.015-0.835-3.0040.006
84A392VAL0-0.0424.9540.1780.280-0.001-0.011-0.0910.000
85A393TRP00.0247.8590.7670.7670.0000.0000.0000.000
86A394ARG10.7752.25717.04419.3201.733-1.658-2.3510.022
87A395SER0-0.0197.8060.2040.2040.0000.0000.0000.000
88A396MET0-0.01510.5350.6030.6030.0000.0000.0000.000
89A397GLU-1-0.96013.443-10.820-10.8200.0000.0000.0000.000
90A398HIS0-0.03812.6170.3890.3890.0000.0000.0000.000
91A399PRO00.00714.180-0.320-0.3200.0000.0000.0000.000
92A400GLY0-0.05114.3880.1160.1160.0000.0000.0000.000
93A401LYS10.90511.46612.02012.0200.0000.0000.0000.000
94A402LEU00.0395.3420.1580.1580.0000.0000.0000.000
95A403LEU00.0078.749-0.364-0.3640.0000.0000.0000.000
96A404PHE00.0222.303-5.981-2.0704.455-1.525-6.8410.011
97A405ALA00.0544.366-3.390-3.1110.000-0.022-0.2570.000
98A406PRO00.0177.0561.1141.1140.0000.0000.0000.000
99A407ASN0-0.0019.9050.1860.1860.0000.0000.0000.000
100A408LEU0-0.0345.515-0.310-0.3100.0000.0000.0000.000
101A409LEU00.0038.280-0.223-0.2230.0000.0000.0000.000
102A410LEU0-0.0316.6980.2310.2310.0000.0000.0000.000
103A411ASP-1-0.8179.679-13.228-13.2280.0000.0000.0000.000
104A412ARG10.8529.85312.55312.5530.0000.0000.0000.000
105A413ASN0-0.01410.435-0.399-0.3990.0000.0000.0000.000
106A414GLN00.07310.130-0.101-0.1010.0000.0000.0000.000
107A415GLY00.0866.846-1.063-1.0630.0000.0000.0000.000
108A416LYS10.8247.44312.01312.0130.0000.0000.0000.000
109A417CYS0-0.0839.2190.4520.4520.0000.0000.0000.000
110A418VAL0-0.0265.285-0.407-0.4070.0000.0000.0000.000
111A419GLU-1-0.8987.090-19.068-19.0680.0000.0000.0000.000
112A420GLY00.0476.357-2.293-2.2930.0000.0000.0000.000
113A421MET0-0.0362.238-4.347-3.0651.515-0.523-2.2740.000
114A422VAL0-0.0524.4111.4231.537-0.001-0.003-0.1100.000
115A423GLU-1-0.8247.169-16.025-16.0250.0000.0000.0000.000
116A424ILE00.0052.664-2.4800.5901.665-1.232-3.5030.015
117A425PHE00.0323.1370.4071.1860.023-0.098-0.7050.000
118A426ASP-1-0.7636.802-13.069-13.0690.0000.0000.0000.000
119A427MET0-0.0527.2040.7430.7430.0000.0000.0000.000
120A428LEU00.0624.085-0.3390.4050.042-0.127-0.6580.000
121A429LEU0-0.0368.5180.4670.4670.0000.0000.0000.000
122A430ALA0-0.02110.9910.5120.5120.0000.0000.0000.000
123A431THR0-0.00410.1580.3700.3700.0000.0000.0000.000
124A432SER00.00010.4170.4000.4000.0000.0000.0000.000
125A433SER0-0.05012.0670.4790.4790.0000.0000.0000.000
126A434ARG10.97415.24410.96610.9660.0000.0000.0000.000
127A435PHE00.02410.7770.3350.3350.0000.0000.0000.000
128A436ARG10.96114.58411.68211.6820.0000.0000.0000.000
129A437MET0-0.08017.4970.3590.3590.0000.0000.0000.000
130A438MET0-0.05818.6400.2090.2090.0000.0000.0000.000
131A439ASN00.00119.8970.0190.0190.0000.0000.0000.000
132A440LEU0-0.05514.1230.1060.1060.0000.0000.0000.000
133A441GLN00.00917.904-0.009-0.0090.0000.0000.0000.000
134A442GLY00.05215.783-0.360-0.3600.0000.0000.0000.000
135A443GLU-1-0.88216.319-11.225-11.2250.0000.0000.0000.000
136A444GLU-1-0.75918.446-10.576-10.5760.0000.0000.0000.000
137A445PHE00.0109.013-0.413-0.4130.0000.0000.0000.000
138A446VAL00.01413.731-0.635-0.6350.0000.0000.0000.000
139A447CYS0-0.03614.893-0.291-0.2910.0000.0000.0000.000
140A448LEU0-0.02014.259-0.285-0.2850.0000.0000.0000.000
141A449LYS10.8059.04517.86717.8670.0000.0000.0000.000
142A450SER00.04112.667-0.940-0.9400.0000.0000.0000.000
143A451ILE0-0.01715.507-0.131-0.1310.0000.0000.0000.000
144A452ILE0-0.01310.499-0.050-0.0500.0000.0000.0000.000
145A453LEU0-0.00811.983-0.454-0.4540.0000.0000.0000.000
146A454LEU0-0.00714.118-0.114-0.1140.0000.0000.0000.000
147A455ASN0-0.03917.4270.0730.0730.0000.0000.0000.000
148A456SER0-0.04713.5060.8280.8280.0000.0000.0000.000
149A457GLY00.05414.930-0.045-0.0450.0000.0000.0000.000
150A458VAL00.00215.6800.5360.5360.0000.0000.0000.000
151A459TYR0-0.07019.2250.7550.7550.0000.0000.0000.000
152A460THR0-0.02315.7610.5260.5260.0000.0000.0000.000
153A461PHE00.00517.370-0.286-0.2860.0000.0000.0000.000
154A462LEU00.02818.1660.6920.6920.0000.0000.0000.000
155A463SER0-0.00720.9100.6090.6090.0000.0000.0000.000
156A464SER0-0.02924.084-0.078-0.0780.0000.0000.0000.000
157A465THR00.02725.7060.4080.4080.0000.0000.0000.000
158A466LEU00.06928.167-0.068-0.0680.0000.0000.0000.000
159A467LYS10.97324.22611.68411.6840.0000.0000.0000.000
160A468SER00.00823.632-0.083-0.0830.0000.0000.0000.000
161A469LEU0-0.02325.010-0.189-0.1890.0000.0000.0000.000
162A470GLU-1-0.89927.628-9.778-9.7780.0000.0000.0000.000
163A471GLU-1-0.78821.443-13.034-13.0340.0000.0000.0000.000
164A472LYS10.91822.89711.47711.4770.0000.0000.0000.000
165A473ASP-1-0.87124.504-9.744-9.7440.0000.0000.0000.000
166A474HIS0-0.02023.1320.5950.5950.0000.0000.0000.000
167A475ILE00.03319.5760.0280.0280.0000.0000.0000.000
168A476HIS0-0.03223.176-0.271-0.2710.0000.0000.0000.000
169A477ARG10.89025.58510.20410.2040.0000.0000.0000.000
170A478VAL0-0.04122.3000.2210.2210.0000.0000.0000.000
171A479LEU0-0.01919.8430.0420.0420.0000.0000.0000.000
172A480ASP-1-0.85223.414-9.905-9.9050.0000.0000.0000.000
173A481LYS10.86325.3209.8879.8870.0000.0000.0000.000
174A482ILE0-0.00719.3710.1660.1660.0000.0000.0000.000
175A483THR0-0.01723.1450.0350.0350.0000.0000.0000.000
176A484ASP-1-0.90124.773-9.057-9.0570.0000.0000.0000.000
177A485THR0-0.07323.0310.2840.2840.0000.0000.0000.000
178A486LEU00.01419.7420.1670.1670.0000.0000.0000.000
179A487ILE0-0.02523.7670.2490.2490.0000.0000.0000.000
180A488HIS0-0.01026.9610.3230.3230.0000.0000.0000.000
181A489LEU0-0.04321.7690.2140.2140.0000.0000.0000.000
182A490MET0-0.02622.9350.2800.2800.0000.0000.0000.000
183A491ALA00.00827.1470.2180.2180.0000.0000.0000.000
184A492LYS10.91825.7559.3469.3460.0000.0000.0000.000
185A493ALA0-0.03626.9970.1420.1420.0000.0000.0000.000
186A494GLY0-0.00629.1270.1210.1210.0000.0000.0000.000
187A495LEU0-0.03326.5230.1380.1380.0000.0000.0000.000
188A496THR00.03731.2270.0390.0390.0000.0000.0000.000
189A497LEU00.06532.131-0.177-0.1770.0000.0000.0000.000
190A498GLN0-0.00132.196-0.132-0.1320.0000.0000.0000.000
191A499GLN00.04029.442-0.192-0.1920.0000.0000.0000.000
192A500GLN0-0.00628.008-0.329-0.3290.0000.0000.0000.000
193A501HIS00.06126.980-0.122-0.1220.0000.0000.0000.000
194A502GLN0-0.06326.967-0.319-0.3190.0000.0000.0000.000
195A503ARG10.77420.9979.7239.7230.0000.0000.0000.000
196A504LEU00.02922.590-0.369-0.3690.0000.0000.0000.000
197A505ALA00.00522.200-0.393-0.3930.0000.0000.0000.000
198A506GLN0-0.05221.361-0.434-0.4340.0000.0000.0000.000
199A507LEU00.00417.761-0.379-0.3790.0000.0000.0000.000
200A508LEU00.03917.322-0.548-0.5480.0000.0000.0000.000
201A509LEU0-0.00318.287-0.407-0.4070.0000.0000.0000.000
202A510ILE0-0.07313.541-0.292-0.2920.0000.0000.0000.000
203A511LEU00.06413.368-0.610-0.6100.0000.0000.0000.000
204A512SER0-0.01314.220-0.695-0.6950.0000.0000.0000.000
205A513HIS0-0.02713.420-0.584-0.5840.0000.0000.0000.000
206A514ILE00.0078.539-0.465-0.4650.0000.0000.0000.000
207A515ARG10.9669.25416.24416.2440.0000.0000.0000.000
208A516HIS0-0.0399.598-1.104-1.1040.0000.0000.0000.000
209A517MET0-0.0016.785-0.446-0.4460.0000.0000.0000.000
210A518SER00.0485.246-1.849-1.8490.0000.0000.0000.000
211A519ASN00.0185.451-2.702-2.7020.0000.0000.0000.000
212A520LYS10.9256.42116.20416.2040.0000.0000.0000.000
213A521GLY00.0162.403-1.470-0.6792.429-1.525-1.6950.009
214A522MET00.0012.998-3.874-4.1610.2821.278-1.273-0.005
215A523GLU-1-0.9515.158-19.885-19.799-0.001-0.006-0.0790.000
216A524HIS0-0.0401.814-25.091-30.21318.015-6.650-6.243-0.056
217A525LEU00.0112.625-8.627-2.8223.073-1.697-7.1810.013
218A526TYR0-0.0544.616-3.132-2.8160.000-0.018-0.2970.000
219A527SER0-0.0485.7913.5323.5320.0000.0000.0000.000
220A528MET0-0.0817.962-0.098-0.0980.0000.0000.0000.000
221A529LYS10.9706.99026.54026.5400.0000.0000.0000.000
222A530CYS0-0.0012.979-7.593-6.5391.395-0.573-1.876-0.003
223A531LYS10.9562.01272.59472.8814.140-1.058-3.369-0.001
224A532ASN0-0.0073.131-9.647-8.3840.091-0.502-0.852-0.004
225A533VAL0-0.0105.5864.0564.0560.0000.0000.0000.000
226A534VAL0-0.0046.178-2.897-2.8970.0000.0000.0000.000
227A535PRO00.0146.426-4.341-4.3410.0000.0000.0000.000
228A536LEU00.0102.359-2.509-2.4761.799-0.271-1.560-0.005
229A537TYR00.0605.6690.9660.9660.0000.0000.0000.000
230A538ASP-1-0.8238.929-22.311-22.3110.0000.0000.0000.000
231A539LEU0-0.0503.217-1.003-0.6210.026-0.095-0.313-0.001
232A540LEU0-0.0125.6950.3340.3340.0000.0000.0000.000
233A541LEU0-0.0407.8332.0782.0780.0000.0000.0000.000
234A542GLU-1-0.9969.948-18.838-18.8380.0000.0000.0000.000
235A543MET0-0.1225.0880.0780.0780.0000.0000.0000.000
236A544LEU-1-0.94510.724-17.210-17.2100.0000.0000.0000.000
238A1006HOH0-0.0172.6040.1691.1240.608-0.681-0.8820.003