FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: GXY2P

Calculation Name: 1YIM-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: (2r,3r,4s)-3-(4-hydroxyphenyl)-4-methyl-2-[4-(2-pyrrolidin-1-ylethoxy)phenyl]chroman-6-ol

ligand 3-letter code: CM4

PDB ID: 1YIM

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 (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
LigandResidueName CM4
LigandFragmentNumber 237
LigandCharge CM4=+1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3171552.231496
FMO2-HF: Nuclear repulsion 3072750.254519
FMO2-HF: Total energy -98801.976977
FMO2-MP2: Total energy -99080.859804


3D Structure
Snapshot
 
Ligand structure

CM4

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.
-334.075-310.984137.806-58.813-102.0890.270


Interactive mode: IFIE and PIEDA for fragment #237(A:600:CM4)


Summations of interaction energy for fragment #237(A:600:CM4)
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.
-334.075-310.984137.806-58.813-102.089-0.27
Interaction energy analysis for fragmet #237(A:600:CM4)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.730 / 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].
1A309SER10.85330.5439.4809.4800.0000.0000.0000.000
2A310LEU00.11825.1520.2520.2520.0000.0000.0000.000
3A311THR0-0.00529.2640.0010.0010.0000.0000.0000.000
4A312ALA00.10126.784-0.313-0.3130.0000.0000.0000.000
5A313ASP-1-0.89125.641-9.246-9.2460.0000.0000.0000.000
6A314GLN0-0.02125.929-0.245-0.2450.0000.0000.0000.000
7A315MET0-0.00321.942-0.448-0.4480.0000.0000.0000.000
8A316VAL00.03521.301-0.437-0.4370.0000.0000.0000.000
9A317SER00.02420.713-0.253-0.2530.0000.0000.0000.000
10A318ALA0-0.00921.183-0.270-0.2700.0000.0000.0000.000
11A319LEU0-0.01917.025-0.494-0.4940.0000.0000.0000.000
12A320LEU0-0.04416.289-0.587-0.5870.0000.0000.0000.000
13A321ASP-1-0.94017.017-11.919-11.9190.0000.0000.0000.000
14A322ALA0-0.10915.881-0.334-0.3340.0000.0000.0000.000
15A323GLU-1-0.78511.355-18.022-18.0220.0000.0000.0000.000
16A324PRO0-0.0488.4780.0340.0340.0000.0000.0000.000
17A325PRO0-0.01410.1730.8350.8350.0000.0000.0000.000
18A326ILE00.0157.745-1.622-1.6220.0000.0000.0000.000
19A327LEU0-0.0386.3461.0001.0000.0000.0000.0000.000
20A328TYR00.0437.5230.5380.5380.0000.0000.0000.000
21A329SER0-0.0127.170-1.588-1.5880.0000.0000.0000.000
22A330GLU-1-0.9088.260-22.075-22.0750.0000.0000.0000.000
23A331TYR0-0.05310.388-0.581-0.5810.0000.0000.0000.000
24A332ASP-1-0.77112.921-13.089-13.0890.0000.0000.0000.000
25A333PRO00.01216.1570.0970.0970.0000.0000.0000.000
26A334THR0-0.06217.2030.6480.6480.0000.0000.0000.000
27A335ARG10.81818.04813.84913.8490.0000.0000.0000.000
28A336PRO00.00518.386-0.132-0.1320.0000.0000.0000.000
29A337PHE00.05211.216-0.536-0.5360.0000.0000.0000.000
30A338SER0-0.05015.169-0.669-0.6690.0000.0000.0000.000
31A339GLU-1-0.92316.358-14.151-14.1510.0000.0000.0000.000
32A340ALA0-0.01812.087-0.687-0.6870.0000.0000.0000.000
33A341SER00.0219.054-0.355-0.3550.0000.0000.0000.000
34A342MET00.0406.173-1.033-1.0330.0000.0000.0000.000
35A343MET00.0443.426-3.740-2.2740.342-0.368-1.4400.000
36A344GLY00.0124.288-5.778-5.5410.000-0.030-0.2060.000
37A345LEU00.0076.793-2.386-2.3860.0000.0000.0000.000
38A346LEU0-0.0402.199-6.955-4.2545.338-2.079-5.9600.013
39A347THR00.0091.971-12.583-8.0165.777-3.614-6.730-0.017
40A348ASN0-0.0233.358-6.504-6.4640.0480.658-0.746-0.002
41A349LEU0-0.0492.387-1.5310.1271.349-0.554-2.4530.001
42A350ALA00.0422.864-4.411-0.9002.766-1.525-4.7520.008
43A351ASP-1-0.8561.574-128.226-132.82625.748-13.011-8.138-0.127
44A352ARG10.8793.96633.46133.8910.001-0.113-0.318-0.001
45A353GLU-1-0.7281.645-63.655-67.94419.990-9.583-6.117-0.117
46A354LEU0-0.0042.3402.3012.3402.194-0.373-1.860-0.003
47A355VAL00.0295.3143.4993.564-0.001-0.001-0.0630.000
48A356HIS00.0048.0103.3973.3970.0000.0000.0000.000
49A357MET0-0.0826.5192.1602.1600.0000.0000.0000.000
50A358ILE00.0498.2162.2522.2520.0000.0000.0000.000
51A359ASN0-0.04210.7261.5651.5650.0000.0000.0000.000
52A360TRP00.01911.5530.8260.8260.0000.0000.0000.000
53A361ALA00.05112.2411.2681.2680.0000.0000.0000.000
54A362LYS10.92814.22618.58018.5800.0000.0000.0000.000
55A363ARG10.89116.75515.04015.0400.0000.0000.0000.000
56A364VAL0-0.01515.6990.8010.8010.0000.0000.0000.000
57A365PRO0-0.02618.5110.1780.1780.0000.0000.0000.000
58A366GLY0-0.00121.923-0.091-0.0910.0000.0000.0000.000
59A367PHE00.05213.3660.0470.0470.0000.0000.0000.000
60A368VAL0-0.00318.291-0.225-0.2250.0000.0000.0000.000
61A369ASP-1-0.97020.054-11.473-11.4730.0000.0000.0000.000
62A370LEU0-0.06018.0530.3420.3420.0000.0000.0000.000
63A371THR0-0.09120.281-0.218-0.2180.0000.0000.0000.000
64A372LEU00.05916.088-0.310-0.3100.0000.0000.0000.000
65A373HIS0-0.08415.680-0.789-0.7890.0000.0000.0000.000
66A374ASP-1-0.79015.317-15.552-15.5520.0000.0000.0000.000
67A375GLN0-0.06014.391-1.387-1.3870.0000.0000.0000.000
68A376VAL00.02410.178-1.414-1.4140.0000.0000.0000.000
69A377HIS0-0.01210.845-2.343-2.3430.0000.0000.0000.000
70A378LEU0-0.05011.868-1.019-1.0190.0000.0000.0000.000
71A379LEU00.0138.260-1.033-1.0330.0000.0000.0000.000
72A380GLU-1-0.9457.199-30.918-30.9180.0000.0000.0000.000
73A381CYS0-0.0838.000-1.294-1.2940.0000.0000.0000.000
74A382ALA00.0219.697-0.177-0.1770.0000.0000.0000.000
75A383TRP00.0222.151-12.325-9.1155.041-1.826-6.424-0.019
76A384LEU00.0112.221-3.158-0.9811.278-0.540-2.915-0.003
77A385GLU-1-0.8265.355-17.900-17.9000.0000.0000.0000.000
78A386ILE00.0037.0401.9981.9980.0000.0000.0000.000
79A387LEU0-0.0322.527-2.8141.0471.987-1.434-4.4150.010
80A388MET0-0.0372.4712.3465.3331.108-0.925-3.170-0.001
81A389ILE00.0054.0522.1792.3500.001-0.014-0.1580.000
82A390GLY00.0555.5431.1891.1890.0000.0000.0000.000
83A391LEU0-0.0222.447-2.0200.0131.592-0.805-2.8200.007
84A392VAL0-0.0364.9510.3730.481-0.001-0.008-0.1000.000
85A393TRP00.0308.0020.9300.9300.0000.0000.0000.000
86A394ARG10.7592.23822.06023.9160.857-1.030-1.6830.011
87A395SER0-0.0117.8970.2480.2480.0000.0000.0000.000
88A396MET0-0.01310.5440.6760.6760.0000.0000.0000.000
89A397GLU-1-0.95613.504-11.011-11.0110.0000.0000.0000.000
90A398HIS0-0.03112.6140.4600.4600.0000.0000.0000.000
91A399PRO00.00913.212-0.338-0.3380.0000.0000.0000.000
92A400GLY0-0.06713.5430.1210.1210.0000.0000.0000.000
93A401LYS10.90510.98312.10112.1010.0000.0000.0000.000
94A402LEU00.0384.527-0.0790.063-0.001-0.004-0.1370.000
95A403LEU0-0.0187.839-0.211-0.2110.0000.0000.0000.000
96A404PHE00.0282.289-5.766-1.9243.752-1.463-6.1320.013
97A405ALA00.0554.389-3.334-3.0960.000-0.021-0.2170.000
98A406PRO00.0397.1091.0281.0280.0000.0000.0000.000
99A407ASN00.01610.0530.1720.1720.0000.0000.0000.000
100A408LEU0-0.0435.752-0.153-0.1530.0000.0000.0000.000
101A409LEU00.0378.615-0.238-0.2380.0000.0000.0000.000
102A410LEU0-0.0236.8280.2500.2500.0000.0000.0000.000
103A411ASP-1-0.8179.604-13.211-13.2110.0000.0000.0000.000
104A412ARG10.84410.00412.54712.5470.0000.0000.0000.000
105A413ASN0-0.03510.757-0.364-0.3640.0000.0000.0000.000
106A414GLN00.07210.212-0.023-0.0230.0000.0000.0000.000
107A415GLY00.0697.011-0.971-0.9710.0000.0000.0000.000
108A416LYS10.8437.49411.88711.8870.0000.0000.0000.000
109A417CYS0-0.0779.5160.3480.3480.0000.0000.0000.000
110A418VAL0-0.0024.649-0.510-0.395-0.001-0.003-0.1120.000
111A419GLU-1-0.8517.137-18.415-18.4150.0000.0000.0000.000
112A420GLY00.0476.363-2.298-2.2980.0000.0000.0000.000
113A421MET0-0.0302.609-4.428-3.3261.830-0.567-2.365-0.002
114A422VAL0-0.0384.5751.1121.222-0.001-0.002-0.1080.000
115A423GLU-1-0.8307.236-16.066-16.0660.0000.0000.0000.000
116A424ILE0-0.0012.788-2.3490.5540.796-1.048-2.6510.012
117A425PHE00.0373.5610.1520.7230.004-0.054-0.5200.000
118A426ASP-1-0.7606.999-13.261-13.2610.0000.0000.0000.000
119A427MET0-0.0437.1850.6510.6510.0000.0000.0000.000
120A428LEU00.0542.499-0.3370.2890.775-0.191-1.2100.000
121A429LEU0-0.0307.0790.5970.5970.0000.0000.0000.000
122A430ALA0-0.0259.6640.5690.5690.0000.0000.0000.000
123A431THR00.0039.2960.3750.3750.0000.0000.0000.000
124A432SER0-0.0119.6210.4970.4970.0000.0000.0000.000
125A433SER0-0.04711.4900.5500.5500.0000.0000.0000.000
126A434ARG10.97714.35711.19211.1920.0000.0000.0000.000
127A435PHE00.02010.8940.3940.3940.0000.0000.0000.000
128A436ARG10.95113.74711.98311.9830.0000.0000.0000.000
129A437MET0-0.06217.3660.3920.3920.0000.0000.0000.000
130A438MET0-0.08018.6490.2060.2060.0000.0000.0000.000
131A439ASN00.01619.6170.0580.0580.0000.0000.0000.000
132A440LEU0-0.05814.3240.1260.1260.0000.0000.0000.000
133A441GLN00.00717.762-0.091-0.0910.0000.0000.0000.000
134A442GLY00.05015.844-0.372-0.3720.0000.0000.0000.000
135A443GLU-1-0.87416.406-11.335-11.3350.0000.0000.0000.000
136A444GLU-1-0.75018.400-10.794-10.7940.0000.0000.0000.000
137A445PHE0-0.0029.023-0.451-0.4510.0000.0000.0000.000
138A446VAL00.02913.821-0.652-0.6520.0000.0000.0000.000
139A447CYS0-0.03814.985-0.219-0.2190.0000.0000.0000.000
140A448LEU0-0.01814.337-0.317-0.3170.0000.0000.0000.000
141A449LYS10.8318.88518.30918.3090.0000.0000.0000.000
142A450SER00.02112.705-0.967-0.9670.0000.0000.0000.000
143A451ILE0-0.01015.605-0.114-0.1140.0000.0000.0000.000
144A452ILE0-0.02410.723-0.025-0.0250.0000.0000.0000.000
145A453LEU0-0.01912.181-0.500-0.5000.0000.0000.0000.000
146A454LEU0-0.00714.170-0.124-0.1240.0000.0000.0000.000
147A455ASN0-0.00717.2950.7750.7750.0000.0000.0000.000
148A456SER0-0.07113.3950.7710.7710.0000.0000.0000.000
149A457GLY00.05314.854-0.063-0.0630.0000.0000.0000.000
150A458VAL00.00615.5650.4930.4930.0000.0000.0000.000
151A459TYR0-0.07519.0790.7610.7610.0000.0000.0000.000
152A460THR0-0.02916.1430.4830.4830.0000.0000.0000.000
153A461PHE00.02517.151-0.308-0.3080.0000.0000.0000.000
154A462LEU00.01017.8670.7180.7180.0000.0000.0000.000
155A463SER00.00921.5430.6530.6530.0000.0000.0000.000
156A464SER0-0.04024.318-0.153-0.1530.0000.0000.0000.000
157A465THR00.02525.6360.3810.3810.0000.0000.0000.000
158A466LEU00.05628.251-0.054-0.0540.0000.0000.0000.000
159A467LYS10.98523.97911.83111.8310.0000.0000.0000.000
160A468SER00.02523.856-0.073-0.0730.0000.0000.0000.000
161A469LEU0-0.03525.063-0.165-0.1650.0000.0000.0000.000
162A470GLU-1-0.90027.552-9.857-9.8570.0000.0000.0000.000
163A471GLU-1-0.77321.362-13.153-13.1530.0000.0000.0000.000
164A472LYS10.93422.93011.44411.4440.0000.0000.0000.000
165A473ASP-1-0.88524.402-9.856-9.8560.0000.0000.0000.000
166A474HIS0-0.00923.0390.5850.5850.0000.0000.0000.000
167A475ILE00.03519.3800.0500.0500.0000.0000.0000.000
168A476HIS0-0.01022.974-0.299-0.2990.0000.0000.0000.000
169A477ARG10.90025.38810.33710.3370.0000.0000.0000.000
170A478VAL0-0.04722.3680.2510.2510.0000.0000.0000.000
171A479LEU0-0.01120.1140.0230.0230.0000.0000.0000.000
172A480ASP-1-0.85523.545-10.016-10.0160.0000.0000.0000.000
173A481LYS10.89225.4229.9809.9800.0000.0000.0000.000
174A482ILE0-0.01619.3830.1850.1850.0000.0000.0000.000
175A483THR0-0.02523.0710.0270.0270.0000.0000.0000.000
176A484ASP-1-0.91524.879-9.166-9.1660.0000.0000.0000.000
177A485THR0-0.06223.1020.2760.2760.0000.0000.0000.000
178A486LEU00.00119.7670.1470.1470.0000.0000.0000.000
179A487ILE0-0.00423.7860.2210.2210.0000.0000.0000.000
180A488HIS0-0.00827.2500.3320.3320.0000.0000.0000.000
181A489LEU0-0.03821.9640.2360.2360.0000.0000.0000.000
182A490MET0-0.00822.9710.2970.2970.0000.0000.0000.000
183A491ALA00.01327.1440.2300.2300.0000.0000.0000.000
184A492LYS10.92826.2159.3809.3800.0000.0000.0000.000
185A493ALA0-0.06126.9480.1610.1610.0000.0000.0000.000
186A494GLY0-0.00229.0790.1060.1060.0000.0000.0000.000
187A495LEU0-0.04426.7690.1420.1420.0000.0000.0000.000
188A496THR00.03031.3230.0470.0470.0000.0000.0000.000
189A497LEU00.07332.195-0.182-0.1820.0000.0000.0000.000
190A498GLN0-0.00132.228-0.131-0.1310.0000.0000.0000.000
191A499GLN00.05529.369-0.203-0.2030.0000.0000.0000.000
192A500GLN0-0.01228.044-0.352-0.3520.0000.0000.0000.000
193A501HIS00.03727.165-0.147-0.1470.0000.0000.0000.000
194A502GLN0-0.05226.676-0.334-0.3340.0000.0000.0000.000
195A503ARG10.77721.1099.8899.8890.0000.0000.0000.000
196A504LEU00.02922.447-0.389-0.3890.0000.0000.0000.000
197A505ALA00.01821.967-0.413-0.4130.0000.0000.0000.000
198A506GLN0-0.04720.746-0.443-0.4430.0000.0000.0000.000
199A507LEU00.00817.607-0.397-0.3970.0000.0000.0000.000
200A508LEU00.04117.044-0.598-0.5980.0000.0000.0000.000
201A509LEU0-0.01517.741-0.424-0.4240.0000.0000.0000.000
202A510ILE0-0.07412.930-0.315-0.3150.0000.0000.0000.000
203A511LEU00.05813.209-0.693-0.6930.0000.0000.0000.000
204A512SER0-0.03713.431-0.686-0.6860.0000.0000.0000.000
205A513HIS0-0.00912.242-0.597-0.5970.0000.0000.0000.000
206A514ILE00.0077.923-0.535-0.5350.0000.0000.0000.000
207A515ARG10.9549.00216.61016.6100.0000.0000.0000.000
208A516HIS0-0.0419.626-1.146-1.1460.0000.0000.0000.000
209A517MET00.0026.002-0.479-0.4790.0000.0000.0000.000
210A518SER00.0605.272-1.768-1.7680.0000.0000.0000.000
211A519ASN00.0185.487-2.511-2.5110.0000.0000.0000.000
212A520LYS10.9246.41116.36616.3660.0000.0000.0000.000
213A521GLY00.0212.418-1.288-0.5082.647-1.630-1.7970.011
214A522MET00.0242.991-3.292-3.7320.3481.415-1.323-0.005
215A523GLU-1-0.9305.064-19.743-19.645-0.001-0.005-0.0920.000
216A524HIS0-0.0471.608-25.650-42.83636.040-12.070-6.785-0.056
217A525LEU0-0.0352.396-8.535-3.0053.795-1.810-7.5150.014
218A526TYR0-0.0234.565-2.576-2.2750.000-0.025-0.2760.000
219A527SER0-0.0676.1483.1553.1550.0000.0000.0000.000
220A528MET0-0.0517.140-0.942-0.9420.0000.0000.0000.000
221A529LYS10.8766.19325.32825.3280.0000.0000.0000.000
222A530CYS0-0.0182.370-3.535-2.2422.119-0.801-2.611-0.003
223A531LYS10.9501.76568.27366.0657.971-1.684-4.080-0.006
224A532ASN00.0063.401-10.116-8.9290.073-0.465-0.796-0.003
225A533VAL0-0.0385.6883.6483.6480.0000.0000.0000.000
226A534VAL0-0.0026.205-3.054-3.0540.0000.0000.0000.000
227A535PRO00.0186.612-4.114-4.1140.0000.0000.0000.000
228A536LEU00.0082.324-2.778-2.3921.424-0.315-1.495-0.007
229A537TYR00.0355.3730.8510.888-0.0010.000-0.0360.000
230A538ASP-1-0.8008.727-22.548-22.5480.0000.0000.0000.000
231A539LEU0-0.0243.195-1.333-0.9220.046-0.094-0.363-0.001
232A540LEU0-0.0265.6260.4230.4230.0000.0000.0000.000
233A541LEU0-0.0448.0881.8921.8920.0000.0000.0000.000
234A542GLU-1-0.97310.221-18.854-18.8540.0000.0000.0000.000
235A543MET0-0.1285.4850.1510.1510.0000.0000.0000.000
236A544LEU-1-0.96410.952-17.151-17.1510.0000.0000.0000.000
238A1009HOH0-0.0262.489-0.4570.5680.776-0.801-1.0000.003