Manual

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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: 8XR8X

Calculation Name: 1X7R-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: genistein

ligand 3-letter code: GEN

PDB ID: 1X7R

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 (agonist templeate: 1A52)
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 GEN=0
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3155575.520233
FMO2-HF: Nuclear repulsion 3057140.588668
FMO2-HF: Total energy -98434.931565
FMO2-MP2: Total energy -98712.540025


3D Structure
Snapshot
 
Ligand structure

GEN

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.
-135.776-134.875108.833-49.083-60.6550.126


Interactive mode: IFIE and PIEDA for fragment #237(A:201:GEN)


Summations of interaction energy for fragment #237(A:201:GEN)
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.
-135.776-134.875108.833-49.083-60.655-0.126
Interaction energy analysis for fragmet #237(A:201:GEN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.126 / 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].
1A309SER10.86029.882-0.039-0.0390.0000.0000.0000.000
2A310LEU00.10524.8770.0040.0040.0000.0000.0000.000
3A311THR00.01328.8190.0130.0130.0000.0000.0000.000
4A312ALA00.08726.506-0.002-0.0020.0000.0000.0000.000
5A313ASP-1-0.85425.3020.1630.1630.0000.0000.0000.000
6A314GLN0-0.02325.348-0.005-0.0050.0000.0000.0000.000
7A315MET0-0.00821.990-0.026-0.0260.0000.0000.0000.000
8A316VAL00.03720.287-0.005-0.0050.0000.0000.0000.000
9A317SER0-0.06020.249-0.009-0.0090.0000.0000.0000.000
10A318ALA00.03620.881-0.017-0.0170.0000.0000.0000.000
11A319LEU0-0.02016.624-0.033-0.0330.0000.0000.0000.000
12A320LEU0-0.04516.203-0.018-0.0180.0000.0000.0000.000
13A321ASP-1-0.97316.550-0.144-0.1440.0000.0000.0000.000
14A322ALA0-0.04816.056-0.064-0.0640.0000.0000.0000.000
15A323GLU-1-0.81111.1800.2170.2170.0000.0000.0000.000
16A324PRO0-0.0268.443-0.100-0.1000.0000.0000.0000.000
17A325PRO0-0.00810.6110.1310.1310.0000.0000.0000.000
18A326ILE00.0058.646-0.302-0.3020.0000.0000.0000.000
19A327LEU0-0.0286.5600.1060.1060.0000.0000.0000.000
20A328TYR00.0037.6950.0840.0840.0000.0000.0000.000
21A329SER00.0087.179-0.341-0.3410.0000.0000.0000.000
22A330GLU-1-0.8268.276-1.515-1.5150.0000.0000.0000.000
23A331TYR0-0.05810.9660.1490.1490.0000.0000.0000.000
24A332ASP-1-0.80112.440-0.298-0.2980.0000.0000.0000.000
25A333PRO0-0.03516.0950.0510.0510.0000.0000.0000.000
26A334THR0-0.07017.9250.0650.0650.0000.0000.0000.000
27A335ARG10.91414.1980.4670.4670.0000.0000.0000.000
28A336PRO0-0.01717.1290.0420.0420.0000.0000.0000.000
29A337PHE00.00612.065-0.025-0.0250.0000.0000.0000.000
30A338SER00.01713.388-0.022-0.0220.0000.0000.0000.000
31A339GLU-1-0.8018.236-0.696-0.6960.0000.0000.0000.000
32A340ALA00.0578.5080.0140.0140.0000.0000.0000.000
33A341SER0-0.0699.392-0.065-0.0650.0000.0000.0000.000
34A342MET0-0.0427.109-0.114-0.1140.0000.0000.0000.000
35A343MET00.0532.241-2.372-2.1254.095-1.099-3.2440.012
36A344GLY00.0085.386-0.468-0.4680.0000.0000.0000.000
37A345LEU0-0.0157.061-0.570-0.5700.0000.0000.0000.000
38A346LEU0-0.0182.915-5.343-1.3011.916-1.193-4.7650.012
39A347THR00.0032.583-11.263-7.2451.073-1.848-3.242-0.023
40A348ASN0-0.0084.195-0.864-0.6350.000-0.015-0.2140.000
41A349LEU0-0.0202.231-0.5371.0081.177-0.626-2.0960.001
42A350ALA00.0122.078-2.533-1.1512.322-1.223-2.481-0.001
43A351ASP-1-0.8544.019-0.913-0.5590.030-0.128-0.2570.000
44A352ARG10.9036.9283.3133.3130.0000.0000.0000.000
45A353GLU-1-0.7711.522-43.690-52.91430.646-15.174-6.247-0.132
46A354LEU00.0135.9851.2531.2530.0000.0000.0000.000
47A355VAL00.0058.3990.6200.6200.0000.0000.0000.000
48A356HIS0-0.0258.6040.5820.5820.0000.0000.0000.000
49A357MET0-0.0186.9780.4480.4480.0000.0000.0000.000
50A358ILE00.0509.7950.3480.3480.0000.0000.0000.000
51A359ASN0-0.05313.1540.2370.2370.0000.0000.0000.000
52A360TRP00.03311.5890.1290.1290.0000.0000.0000.000
53A361ALA00.06413.4690.1160.1160.0000.0000.0000.000
54A362LYS10.88415.1120.5960.5960.0000.0000.0000.000
55A363ARG10.86616.8370.4000.4000.0000.0000.0000.000
56A364VAL00.03715.5470.0530.0530.0000.0000.0000.000
57A365PRO0-0.09318.474-0.011-0.0110.0000.0000.0000.000
58A366GLY00.04422.1930.0290.0290.0000.0000.0000.000
59A367PHE00.02417.554-0.010-0.0100.0000.0000.0000.000
60A368VAL0-0.04221.179-0.020-0.0200.0000.0000.0000.000
61A369ASP-1-0.90723.258-0.057-0.0570.0000.0000.0000.000
62A370LEU0-0.02921.6220.0080.0080.0000.0000.0000.000
63A371THR0-0.08525.491-0.034-0.0340.0000.0000.0000.000
64A372LEU00.01922.066-0.001-0.0010.0000.0000.0000.000
65A373HIS0-0.03222.615-0.035-0.0350.0000.0000.0000.000
66A374ASP-1-0.77422.396-0.098-0.0980.0000.0000.0000.000
67A375GLN0-0.10619.662-0.028-0.0280.0000.0000.0000.000
68A376VAL00.01217.957-0.013-0.0130.0000.0000.0000.000
69A377HIS00.05217.3030.0220.0220.0000.0000.0000.000
70A378LEU0-0.02916.8600.0290.0290.0000.0000.0000.000
71A379LEU0-0.02212.5990.0560.0560.0000.0000.0000.000
72A380GLU-1-0.90412.918-0.358-0.3580.0000.0000.0000.000
73A381CYS0-0.05213.1810.0560.0560.0000.0000.0000.000
74A382ALA0-0.04111.5540.1480.1480.0000.0000.0000.000
75A383TRP00.0634.641-0.0660.185-0.001-0.004-0.2470.000
76A384LEU00.0193.674-0.7990.1870.038-0.192-0.8320.001
77A385GLU-1-0.8315.1001.6441.771-0.001-0.001-0.1260.000
78A386ILE0-0.0116.7550.3670.3670.0000.0000.0000.000
79A387LEU0-0.0062.537-2.273-0.2413.509-1.380-4.1610.007
80A388MET0-0.0352.550-1.5861.1631.718-1.349-3.118-0.017
81A389ILE00.0023.5630.6290.6890.0030.095-0.1590.000
82A390GLY00.0325.222-0.266-0.2660.0000.0000.0000.000
83A391LEU0-0.0132.481-2.844-0.5461.029-0.845-2.4820.008
84A392VAL0-0.0274.450-1.123-0.9910.000-0.020-0.1130.000
85A393TRP00.0257.533-0.441-0.4410.0000.0000.0000.000
86A394ARG10.8242.047-12.173-11.9183.923-1.733-2.4440.023
87A395SER0-0.0527.502-0.284-0.2840.0000.0000.0000.000
88A396MET0-0.02510.181-0.199-0.1990.0000.0000.0000.000
89A397GLU-1-0.92613.0280.7570.7570.0000.0000.0000.000
90A398HIS0-0.04312.778-0.163-0.1630.0000.0000.0000.000
91A399PRO00.00014.1610.2210.2210.0000.0000.0000.000
92A400VAL0-0.05514.329-0.080-0.0800.0000.0000.0000.000
93A401LYS10.87212.423-1.136-1.1360.0000.0000.0000.000
94A402LEU00.0296.0050.0910.0910.0000.0000.0000.000
95A403LEU0-0.0208.443-0.317-0.3170.0000.0000.0000.000
96A404PHE00.0222.925-5.762-1.3401.363-1.553-4.2320.024
97A405ALA00.0574.594-1.823-1.688-0.001-0.009-0.1250.000
98A406PRO0-0.0067.2930.4760.4760.0000.0000.0000.000
99A407ASN0-0.02210.1590.0420.0420.0000.0000.0000.000
100A408LEU0-0.0266.122-0.095-0.0950.0000.0000.0000.000
101A409LEU00.0308.8480.4940.4940.0000.0000.0000.000
102A410LEU0-0.0277.550-0.281-0.2810.0000.0000.0000.000
103A411ASP-1-0.80511.0361.5191.5190.0000.0000.0000.000
104A412ARG11.00510.428-1.056-1.0560.0000.0000.0000.000
105A413ASN0-0.06810.7100.0040.0040.0000.0000.0000.000
106A414GLN00.02110.125-0.199-0.1990.0000.0000.0000.000
107A415GLY00.0887.820-0.045-0.0450.0000.0000.0000.000
108A416LYS10.8648.261-1.106-1.1060.0000.0000.0000.000
109A417CYS0-0.10910.044-0.253-0.2530.0000.0000.0000.000
110A418VAL0-0.0124.868-0.142-0.1420.0000.0000.0000.000
111A419GLU-1-0.9117.784-0.620-0.6200.0000.0000.0000.000
112A420GLY00.0286.386-0.938-0.9380.0000.0000.0000.000
113A421MET0-0.0402.860-1.888-0.1781.058-0.687-2.0800.010
114A422VAL0-0.0395.2451.7251.765-0.0010.000-0.0390.000
115A423GLU-1-0.8267.6860.9320.9320.0000.0000.0000.000
116A424ILE00.0422.361-0.888-0.9113.826-0.913-2.8910.012
117A425PHE0-0.0013.467-0.4280.4100.010-0.197-0.6510.001
118A426ASP-1-0.8456.4101.4201.4200.0000.0000.0000.000
119A427MET0-0.0607.367-0.293-0.2930.0000.0000.0000.000
120A428LEU00.0563.365-1.011-0.4050.014-0.107-0.5130.000
121A429LEU0-0.0107.972-0.523-0.5230.0000.0000.0000.000
122A430ALA0-0.04710.777-0.376-0.3760.0000.0000.0000.000
123A431THR00.01210.282-0.353-0.3530.0000.0000.0000.000
124A432SER00.00710.251-0.306-0.3060.0000.0000.0000.000
125A433SER0-0.04511.859-0.307-0.3070.0000.0000.0000.000
126A434ARG10.92614.925-1.059-1.0590.0000.0000.0000.000
127A435PHE00.05610.433-0.169-0.1690.0000.0000.0000.000
128A436ARG10.92614.651-1.452-1.4520.0000.0000.0000.000
129A437MET0-0.08817.005-0.144-0.1440.0000.0000.0000.000
130A438MET0-0.05818.229-0.058-0.0580.0000.0000.0000.000
131A439ASN00.00619.250-0.116-0.1160.0000.0000.0000.000
132A440LEU0-0.03813.522-0.061-0.0610.0000.0000.0000.000
133A441GLN00.01917.1550.0000.0000.0000.0000.0000.000
134A442GLY00.06615.4180.0560.0560.0000.0000.0000.000
135A443GLU-1-0.89216.2340.3730.3730.0000.0000.0000.000
136A444GLU-1-0.76517.6610.5510.5510.0000.0000.0000.000
137A445PHE0-0.0088.7380.0400.0400.0000.0000.0000.000
138A446VAL00.04113.2820.0400.0400.0000.0000.0000.000
139A447CYS0-0.04314.750-0.081-0.0810.0000.0000.0000.000
140A448LEU00.00513.438-0.028-0.0280.0000.0000.0000.000
141A449LYS10.8289.017-0.378-0.3780.0000.0000.0000.000
142A450SER00.02012.065-0.105-0.1050.0000.0000.0000.000
143A451ILE0-0.01015.198-0.052-0.0520.0000.0000.0000.000
144A452ILE0-0.0319.894-0.045-0.0450.0000.0000.0000.000
145A453LEU0-0.02113.408-0.050-0.0500.0000.0000.0000.000
146A454LEU0-0.00614.293-0.055-0.0550.0000.0000.0000.000
147A455ASN0-0.00717.094-0.060-0.0600.0000.0000.0000.000
148A456SER0-0.07313.9370.0230.0230.0000.0000.0000.000
149A457GLY00.08516.367-0.013-0.0130.0000.0000.0000.000
150A458VAL00.05018.473-0.037-0.0370.0000.0000.0000.000
151A459TYR0-0.10718.634-0.034-0.0340.0000.0000.0000.000
152A460THR0-0.05020.614-0.002-0.0020.0000.0000.0000.000
153A461PHE00.05621.298-0.025-0.0250.0000.0000.0000.000
154A462LEU00.01824.7510.0120.0120.0000.0000.0000.000
155A463SER00.01928.0740.0140.0140.0000.0000.0000.000
156A464SER0-0.04230.8090.0040.0040.0000.0000.0000.000
157A465THR0-0.04232.142-0.014-0.0140.0000.0000.0000.000
158A466LEU00.02033.1900.0050.0050.0000.0000.0000.000
159A467LYS11.04830.9120.0990.0990.0000.0000.0000.000
160A468SER00.01028.538-0.002-0.0020.0000.0000.0000.000
161A469LEU0-0.02228.9340.0100.0100.0000.0000.0000.000
162A470GLU-1-0.89330.633-0.012-0.0120.0000.0000.0000.000
163A471GLU-1-0.80026.456-0.065-0.0650.0000.0000.0000.000
164A472LYS10.88325.843-0.047-0.0470.0000.0000.0000.000
165A473ASP-1-0.92626.6770.0720.0720.0000.0000.0000.000
166A474HIS0-0.10326.1770.0260.0260.0000.0000.0000.000
167A475ILE00.02021.6230.0130.0130.0000.0000.0000.000
168A476HIS00.01523.9000.0380.0380.0000.0000.0000.000
169A477ARG10.97725.787-0.049-0.0490.0000.0000.0000.000
170A478VAL0-0.04422.5240.0120.0120.0000.0000.0000.000
171A479LEU00.00619.4030.0250.0250.0000.0000.0000.000
172A480ASP-1-0.88323.0010.1970.1970.0000.0000.0000.000
173A481LYS10.86725.481-0.097-0.0970.0000.0000.0000.000
174A482ILE0-0.01819.0930.0120.0120.0000.0000.0000.000
175A483THR00.01822.6010.0460.0460.0000.0000.0000.000
176A484ASP-1-0.91724.0080.1910.1910.0000.0000.0000.000
177A485THR0-0.08522.696-0.009-0.0090.0000.0000.0000.000
178A486LEU00.01618.8760.0120.0120.0000.0000.0000.000
179A487ILE0-0.01323.0010.0130.0130.0000.0000.0000.000
180A488HIS0-0.02326.4360.0090.0090.0000.0000.0000.000
181A489LEU00.01121.393-0.010-0.0100.0000.0000.0000.000
182A490MET0-0.01923.3080.0120.0120.0000.0000.0000.000
183A491ALA0-0.01426.196-0.006-0.0060.0000.0000.0000.000
184A492LYS10.90826.077-0.225-0.2250.0000.0000.0000.000
185A493ALA0-0.04626.203-0.006-0.0060.0000.0000.0000.000
186A494GLY0-0.01628.3050.0080.0080.0000.0000.0000.000
187A495LEU0-0.03325.8270.0010.0010.0000.0000.0000.000
188A496THR00.03230.365-0.017-0.0170.0000.0000.0000.000
189A497LEU00.05631.2920.0130.0130.0000.0000.0000.000
190A498GLN0-0.01331.3400.0100.0100.0000.0000.0000.000
191A499GLN00.04828.7390.0070.0070.0000.0000.0000.000
192A500GLN0-0.00627.0660.0270.0270.0000.0000.0000.000
193A501HIS00.03026.2120.0340.0340.0000.0000.0000.000
194A502GLN0-0.03526.2750.0380.0380.0000.0000.0000.000
195A503ARG10.77820.242-0.546-0.5460.0000.0000.0000.000
196A504LEU00.04321.6490.0560.0560.0000.0000.0000.000
197A505ALA00.01521.4650.0320.0320.0000.0000.0000.000
198A506GLN0-0.03820.7140.0560.0560.0000.0000.0000.000
199A507LEU00.00716.6730.0880.0880.0000.0000.0000.000
200A508LEU00.03816.6540.0850.0850.0000.0000.0000.000
201A509LEU0-0.03117.8620.0220.0220.0000.0000.0000.000
202A510ILE0-0.02913.1190.0490.0490.0000.0000.0000.000
203A511LEU00.01412.8640.1730.1730.0000.0000.0000.000
204A512SER00.01413.6830.0330.0330.0000.0000.0000.000
205A513HIS0-0.03413.3900.0740.0740.0000.0000.0000.000
206A514ILE0-0.0048.2560.2070.2070.0000.0000.0000.000
207A515ARG10.9149.520-0.443-0.4430.0000.0000.0000.000
208A516HIS0-0.03311.544-0.093-0.0930.0000.0000.0000.000
209A517MET0-0.0027.0590.0630.0630.0000.0000.0000.000
210A518SER00.0746.7630.4530.4530.0000.0000.0000.000
211A519ASN0-0.0148.025-0.266-0.2660.0000.0000.0000.000
212A520LYS10.8207.578-0.680-0.6800.0000.0000.0000.000
213A521GLY00.0243.811-1.071-0.7360.009-0.101-0.2430.000
214A522MET00.0224.199-2.132-1.6190.010-0.081-0.4420.000
215A523GLU-1-0.8946.307-0.491-0.4910.0000.0000.0000.000
216A524HIS00.0031.544-30.051-51.52744.104-16.472-6.156-0.078
217A525LEU00.0711.982-2.773-0.6903.734-1.431-4.3850.002
218A526TYR0-0.0553.380-0.194-0.4460.1300.600-0.4790.003
219A527SER0-0.0685.1100.1800.1800.0000.0000.0000.000
220A528MET00.0223.3890.0930.5810.016-0.121-0.3830.000
221A529LYS10.9676.1590.8490.8490.0000.0000.0000.000
222A530CYS0-0.0838.0780.0660.0660.0000.0000.0000.000
223A531LYS10.8698.6080.8800.8800.0000.0000.0000.000
224A532ASN0-0.07010.8120.0400.0400.0000.0000.0000.000
225A533VAL0-0.0147.9640.0300.0300.0000.0000.0000.000
226A534VAL0-0.0225.1090.0630.0630.0000.0000.0000.000
227A535PRO0-0.0377.5510.0460.0460.0000.0000.0000.000
228A536LEU0-0.0039.530-0.078-0.0780.0000.0000.0000.000
229A537TYR0-0.0307.7110.0240.0240.0000.0000.0000.000
230A538ASP-1-0.84810.645-0.990-0.9900.0000.0000.0000.000
231A539LEU00.03210.6450.0930.0930.0000.0000.0000.000
232A540LEU0-0.0174.719-0.190-0.017-0.001-0.006-0.1660.000
233A541LEU0-0.1098.3850.2850.2850.0000.0000.0000.000
234A542GLU-1-0.97610.418-0.651-0.6510.0000.0000.0000.000
235A543MET0-0.0629.0560.1320.1320.0000.0000.0000.000
236A544LEU-1-0.8596.603-0.291-0.2910.0000.0000.0000.000
238A7HOH0-0.0192.241-1.237-1.4113.085-1.270-1.6420.009