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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: P7VKX

Calculation Name: 1X7J-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: genistein

ligand 3-letter code: GEN

PDB ID: 1X7J

Chain ID: A

ChEMBL ID: CHEMBL242

UniProt ID: Q92731

Base Structure: X-ray

Registration Date: 2017-06-23

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Homology modeling
Water No
Procedure Auto-FMO protocol ver. 1.2017021
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3035933.81354
FMO2-HF: Nuclear repulsion 2939437.130273
FMO2-HF: Total energy -96496.683267
FMO2-MP2: Total energy -96767.253519


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.
-111.825-80.49559.969-30.254-61.0430.072


Interactive mode: IFIE and PIEDA for fragment #235(A:201:GEN)


Summations of interaction energy for fragment #235(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.
-111.825-80.49559.969-30.254-61.043-0.072
Interaction energy analysis for fragmet #235(A:201:GEN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.072 / q_NPA : -0.090
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].
1A264SER10.8670.91929.494-0.062-0.0620.0000.0000.0000.000
2A265PRO00.1760.08026.409-0.012-0.0120.0000.0000.0000.000
3A266GLU-1-0.929-0.96625.0960.1030.1030.0000.0000.0000.000
4A267GLN00.004-0.01225.076-0.004-0.0040.0000.0000.0000.000
5A268LEU0-0.0150.01122.273-0.018-0.0180.0000.0000.0000.000
6A269VAL00.039-0.01220.087-0.005-0.0050.0000.0000.0000.000
7A270LEU0-0.010-0.00320.0760.0000.0000.0000.0000.0000.000
8A271THR00.0190.02320.505-0.020-0.0200.0000.0000.0000.000
9A272LEU0-0.046-0.02016.725-0.033-0.0330.0000.0000.0000.000
10A273LEU0-0.033-0.01115.971-0.003-0.0030.0000.0000.0000.000
11A274GLU-1-0.943-0.97916.559-0.123-0.1230.0000.0000.0000.000
12A275ALA0-0.078-0.03015.676-0.061-0.0610.0000.0000.0000.000
13A276GLU-1-0.856-0.92311.307-0.023-0.0230.0000.0000.0000.000
14A277PRO0-0.046-0.0048.361-0.050-0.0500.0000.0000.0000.000
15A278PRO0-0.010-0.00210.7740.1060.1060.0000.0000.0000.000
16A279HIS00.0180.0018.924-0.373-0.3730.0000.0000.0000.000
17A280VAL00.0000.0016.3360.1550.1550.0000.0000.0000.000
18A281LEU00.001-0.0027.880-0.009-0.0090.0000.0000.0000.000
19A282ILE0-0.006-0.0016.710-0.199-0.1990.0000.0000.0000.000
20A283SER0-0.059-0.0289.2840.1400.1400.0000.0000.0000.000
21A284ARG10.8970.94811.1190.1460.1460.0000.0000.0000.000
22A285PRO0-0.016-0.01313.4990.0720.0720.0000.0000.0000.000
23A286SER0-0.012-0.00215.8040.0400.0400.0000.0000.0000.000
24A287ALA00.0600.01716.221-0.031-0.0310.0000.0000.0000.000
25A288PRO00.0020.02415.5710.0480.0480.0000.0000.0000.000
26A289PHE00.0120.00910.377-0.077-0.0770.0000.0000.0000.000
27A290THR00.0040.00713.8900.0170.0170.0000.0000.0000.000
28A291GLU-1-0.840-0.9388.832-0.422-0.4220.0000.0000.0000.000
29A292ALA00.0230.0069.1040.0420.0420.0000.0000.0000.000
30A293SER0-0.038-0.0189.826-0.010-0.0100.0000.0000.0000.000
31A294MET00.0540.0317.393-0.094-0.0940.0000.0000.0000.000
32A295MET00.0560.0422.561-1.002-1.0034.030-0.930-3.0980.013
33A296MET0-0.0130.0075.201-0.327-0.3270.0000.0000.0000.000
34A297SER0-0.017-0.0187.172-0.527-0.5270.0000.0000.0000.000
35A298LEU0-0.0070.0012.834-5.733-1.3881.454-1.149-4.6500.012
36A299THR0-0.003-0.0092.646-11.236-7.3081.329-1.995-3.262-0.025
37A300LYS10.9180.9604.3880.6050.8420.000-0.014-0.2230.000
38A301LEU0-0.072-0.0342.160-0.2220.7642.347-0.792-2.5410.004
39A302ALA00.0380.0172.021-1.949-0.8192.341-1.191-2.2800.000
40A303ASP-1-0.851-0.9344.026-0.738-0.3520.024-0.137-0.2730.000
41A304LYS10.8800.9356.8752.6272.6270.0000.0000.0000.000
42A305GLU-1-0.867-0.9401.770-35.103-34.64612.439-7.283-5.613-0.096
43A306LEU00.0380.0326.1660.9670.9670.0000.0000.0000.000
44A307VAL00.0150.0198.4930.5030.5030.0000.0000.0000.000
45A308HIS0-0.046-0.0388.5030.4920.4920.0000.0000.0000.000
46A309MET0-0.0270.0106.9820.3520.3520.0000.0000.0000.000
47A310ILE00.0640.0369.8950.2840.2840.0000.0000.0000.000
48A311SER0-0.071-0.05213.3300.1780.1780.0000.0000.0000.000
49A312TRP0-0.025-0.00911.5460.1080.1080.0000.0000.0000.000
50A313ALA00.0750.02913.6040.0990.0990.0000.0000.0000.000
51A314LYS10.9230.95615.3140.4540.4540.0000.0000.0000.000
52A315LYS10.8740.96516.0730.4340.4340.0000.0000.0000.000
53A316ILE00.0030.02315.1810.0460.0460.0000.0000.0000.000
54A317PRO0-0.014-0.01619.254-0.006-0.0060.0000.0000.0000.000
55A318GLY00.0520.01423.0750.0210.0210.0000.0000.0000.000
56A319PHE00.0340.01817.7610.0030.0030.0000.0000.0000.000
57A320VAL0-0.021-0.01921.610-0.010-0.0100.0000.0000.0000.000
58A321GLU-1-0.956-0.98123.352-0.090-0.0900.0000.0000.0000.000
59A322LEU0-0.092-0.02221.5410.0140.0140.0000.0000.0000.000
60A323SER00.0100.00925.402-0.024-0.0240.0000.0000.0000.000
61A324LEU00.0460.00722.8080.0040.0040.0000.0000.0000.000
62A325PHE00.0310.01223.019-0.013-0.0130.0000.0000.0000.000
63A326ASP-1-0.784-0.89022.585-0.028-0.0280.0000.0000.0000.000
64A327GLN0-0.078-0.04819.791-0.017-0.0170.0000.0000.0000.000
65A328VAL00.0190.01118.236-0.009-0.0090.0000.0000.0000.000
66A329ARG10.9201.00717.718-0.006-0.0060.0000.0000.0000.000
67A330LEU0-0.066-0.02816.8150.0360.0360.0000.0000.0000.000
68A331LEU0-0.001-0.01012.8520.0550.0550.0000.0000.0000.000
69A332GLU-1-0.873-0.94612.720-0.230-0.2300.0000.0000.0000.000
70A333SER0-0.043-0.01913.1880.0560.0560.0000.0000.0000.000
71A334CYS0-0.065-0.01311.3180.0820.0820.0000.0000.0000.000
72A335TRP00.0670.0154.9530.1890.1890.0000.0000.0000.000
73A336MET00.0360.0213.658-1.8120.2480.280-0.478-1.8630.002
74A337GLU-1-0.820-0.9034.8741.1921.342-0.001-0.003-0.1470.000
75A338VAL0-0.026-0.0156.3710.3120.3120.0000.0000.0000.000
76A339LEU00.0070.0142.515-2.710-0.5203.330-1.480-4.0390.007
77A340MET0-0.0330.0312.5030.2953.0842.028-1.329-3.488-0.006
78A341MET0-0.0250.0003.2340.7730.5700.0190.337-0.1530.000
79A342GLY0-0.010-0.0065.268-0.308-0.3080.0000.0000.0000.000
80A343LEU0-0.004-0.0042.770-3.435-0.9840.522-0.849-2.1240.008
81A344MET0-0.036-0.0014.667-1.449-1.2920.000-0.027-0.1300.000
82A345TRP0-0.019-0.0037.649-0.417-0.4170.0000.0000.0000.000
83A346ARG10.8490.9402.131-7.872-6.9692.824-1.562-2.1660.020
84A347SER0-0.007-0.0227.908-0.219-0.2190.0000.0000.0000.000
85A348ILE0-0.0070.01410.416-0.150-0.1500.0000.0000.0000.000
86A349ASP-1-0.914-0.95713.2480.6270.6270.0000.0000.0000.000
87A350HIS0-0.086-0.03913.111-0.127-0.1270.0000.0000.0000.000
88A351PRO0-0.012-0.03014.2390.2110.2110.0000.0000.0000.000
89A352GLY0-0.015-0.00814.919-0.102-0.1020.0000.0000.0000.000
90A353LYS10.9480.99012.713-0.919-0.9190.0000.0000.0000.000
91A354LEU00.0110.0176.3330.0940.0940.0000.0000.0000.000
92A355ILE0-0.014-0.0138.198-0.176-0.1760.0000.0000.0000.000
93A356PHE00.0270.0072.758-6.726-2.1142.745-1.744-5.6120.027
94A357ALA00.0390.0034.338-2.630-2.4190.000-0.024-0.1860.000
95A358PRO0-0.013-0.0016.9280.4670.4670.0000.0000.0000.000
96A359ASP-1-0.810-0.9119.393-0.842-0.8420.0000.0000.0000.000
97A360LEU0-0.046-0.0264.803-0.194-0.1940.0000.0000.0000.000
98A361VAL0-0.021-0.0097.8280.5580.5580.0000.0000.0000.000
99A362LEU00.0040.0066.984-0.187-0.1870.0000.0000.0000.000
100A363ASP-1-0.796-0.91110.8271.3371.3370.0000.0000.0000.000
101A364ARG10.8720.93210.694-0.849-0.8490.0000.0000.0000.000
102A365ASP-1-0.948-0.98211.5160.6880.6880.0000.0000.0000.000
103A366GLU-1-0.921-0.97711.9200.7800.7800.0000.0000.0000.000
104A367GLY00.0200.0128.706-0.022-0.0220.0000.0000.0000.000
105A368LYS10.8820.9408.790-0.750-0.7500.0000.0000.0000.000
106A369CYS0-0.128-0.04711.420-0.192-0.1920.0000.0000.0000.000
107A370VAL00.0810.0315.164-0.155-0.1550.0000.0000.0000.000
108A371GLU-1-0.913-0.9567.948-0.632-0.6320.0000.0000.0000.000
109A372GLY00.0320.0086.544-0.912-0.9120.0000.0000.0000.000
110A373ILE0-0.0030.0112.440-1.502-1.1714.459-0.943-3.8480.005
111A374LEU0-0.0060.0005.0611.5841.626-0.001-0.001-0.0390.000
112A375GLU-1-0.924-0.9647.7450.6330.6330.0000.0000.0000.000
113A376ILE00.024-0.0162.725-1.2850.0180.622-0.480-1.4450.005
114A377PHE00.0380.0273.715-0.2490.4080.004-0.127-0.5340.001
115A378ASP-1-0.796-0.9036.7671.2581.2580.0000.0000.0000.000
116A379MET0-0.082-0.0217.266-0.157-0.1570.0000.0000.0000.000
117A380LEU00.0080.0083.424-0.896-0.3590.009-0.079-0.4660.000
118A381LEU00.0200.0308.039-0.367-0.3670.0000.0000.0000.000
119A382ALA0-0.0010.01311.029-0.308-0.3080.0000.0000.0000.000
120A383THR00.0170.00110.535-0.313-0.3130.0000.0000.0000.000
121A384THR0-0.013-0.0269.424-0.152-0.1520.0000.0000.0000.000
122A385SER0-0.037-0.03511.664-0.256-0.2560.0000.0000.0000.000
123A386ARG10.9310.98714.988-0.904-0.9040.0000.0000.0000.000
124A387PHE00.031-0.01611.033-0.169-0.1690.0000.0000.0000.000
125A388ARG10.9130.97913.918-1.372-1.3720.0000.0000.0000.000
126A389GLU-1-0.979-0.97716.8010.6320.6320.0000.0000.0000.000
127A390LEU0-0.075-0.03117.791-0.087-0.0870.0000.0000.0000.000
128A391LYS10.9620.98219.135-0.563-0.5630.0000.0000.0000.000
129A392LEU0-0.0080.02113.160-0.070-0.0700.0000.0000.0000.000
130A393GLN0-0.037-0.03317.246-0.040-0.0400.0000.0000.0000.000
131A394HIS00.0930.03913.6740.1070.1070.0000.0000.0000.000
132A395LYS10.9930.98215.936-0.185-0.1850.0000.0000.0000.000
133A396GLU-1-0.736-0.82917.5300.4700.4700.0000.0000.0000.000
134A397TYR00.0030.0008.9530.1030.1030.0000.0000.0000.000
135A398LEU0-0.031-0.00913.3730.0230.0230.0000.0000.0000.000
136A399CYS0-0.030-0.00415.039-0.048-0.0480.0000.0000.0000.000
137A400VAL00.0420.02012.510-0.026-0.0260.0000.0000.0000.000
138A401LYS10.8790.9408.813-0.147-0.1470.0000.0000.0000.000
139A402ALA00.0060.00712.037-0.062-0.0620.0000.0000.0000.000
140A403MET0-0.040-0.03315.090-0.033-0.0330.0000.0000.0000.000
141A404ILE0-0.0170.0019.888-0.024-0.0240.0000.0000.0000.000
142A405LEU00.0140.01113.187-0.029-0.0290.0000.0000.0000.000
143A406LEU0-0.034-0.03014.253-0.044-0.0440.0000.0000.0000.000
144A407ASN0-0.012-0.00516.826-0.067-0.0670.0000.0000.0000.000
145A408SER00.0010.00414.4540.0470.0470.0000.0000.0000.000
146A409SER00.0200.01416.904-0.031-0.0310.0000.0000.0000.000
147A410MET00.013-0.00618.712-0.003-0.0030.0000.0000.0000.000
148A411TYR0-0.075-0.06921.520-0.019-0.0190.0000.0000.0000.000
149A412PRO00.021-0.00124.586-0.007-0.0070.0000.0000.0000.000
150A413LEU0-0.0330.00622.4440.0040.0040.0000.0000.0000.000
151A414VAL0-0.0040.00125.997-0.006-0.0060.0000.0000.0000.000
152A415THR0-0.054-0.03128.672-0.010-0.0100.0000.0000.0000.000
153A416ALA00.0000.02429.024-0.001-0.0010.0000.0000.0000.000
154A417THR0-0.001-0.02629.6190.0090.0090.0000.0000.0000.000
155A418GLN0-0.047-0.02632.058-0.001-0.0010.0000.0000.0000.000
156A419ASP-1-0.775-0.83530.2700.0180.0180.0000.0000.0000.000
157A420ALA00.0230.00231.628-0.001-0.0010.0000.0000.0000.000
158A421ASP-1-0.848-0.94231.414-0.005-0.0050.0000.0000.0000.000
159A422SER0-0.015-0.03626.3310.0020.0020.0000.0000.0000.000
160A423SER00.0190.00527.0900.0090.0090.0000.0000.0000.000
161A424ARG10.8720.92627.5750.0070.0070.0000.0000.0000.000
162A425LYS10.8800.95027.2230.0430.0430.0000.0000.0000.000
163A426LEU00.0640.04020.8940.0030.0030.0000.0000.0000.000
164A427ALA00.0220.01824.1700.0180.0180.0000.0000.0000.000
165A428HIS0-0.008-0.00426.1520.0200.0200.0000.0000.0000.000
166A429LEU00.0140.00521.6900.0110.0110.0000.0000.0000.000
167A430LEU0-0.0050.00019.7010.0160.0160.0000.0000.0000.000
168A431ASN0-0.038-0.01622.4090.0220.0220.0000.0000.0000.000
169A432ALA00.0550.03124.6140.0130.0130.0000.0000.0000.000
170A433VAL00.001-0.00518.4210.0100.0100.0000.0000.0000.000
171A434THR0-0.043-0.02621.7870.0380.0380.0000.0000.0000.000
172A435ASP-1-0.943-0.98022.7930.1560.1560.0000.0000.0000.000
173A436ALA0-0.001-0.00322.248-0.001-0.0010.0000.0000.0000.000
174A437LEU00.000-0.00918.9210.0100.0100.0000.0000.0000.000
175A438VAL00.0070.00221.9760.0150.0150.0000.0000.0000.000
176A439TRP00.0190.01224.457-0.001-0.0010.0000.0000.0000.000
177A440VAL0-0.025-0.02121.194-0.005-0.0050.0000.0000.0000.000
178A441ILE0-0.0050.00422.1520.0010.0010.0000.0000.0000.000
179A442ALA00.0160.03625.076-0.003-0.0030.0000.0000.0000.000
180A443LYS10.8340.92026.953-0.182-0.1820.0000.0000.0000.000
181A444SER0-0.075-0.05325.782-0.007-0.0070.0000.0000.0000.000
182A445GLY00.0260.02227.642-0.001-0.0010.0000.0000.0000.000
183A446ILE0-0.0360.00426.909-0.006-0.0060.0000.0000.0000.000
184A447SER00.0380.00831.039-0.009-0.0090.0000.0000.0000.000
185A448SER00.0910.03631.3570.0160.0160.0000.0000.0000.000
186A449GLN00.0210.00031.3790.0250.0250.0000.0000.0000.000
187A450GLN00.031-0.01029.0040.0300.0300.0000.0000.0000.000
188A451GLN0-0.022-0.00227.3280.0240.0240.0000.0000.0000.000
189A452SER00.0190.01426.4040.0160.0160.0000.0000.0000.000
190A453MET00.0000.00126.3360.0170.0170.0000.0000.0000.000
191A454ARG10.7320.84020.329-0.453-0.4530.0000.0000.0000.000
192A455LEU00.0330.01421.8620.0460.0460.0000.0000.0000.000
193A456ALA00.0240.00621.5820.0300.0300.0000.0000.0000.000
194A457ASN0-0.026-0.03320.9450.0490.0490.0000.0000.0000.000
195A458LEU0-0.020-0.00116.8990.0740.0740.0000.0000.0000.000
196A459LEU00.015-0.00316.6690.0720.0720.0000.0000.0000.000
197A460MET0-0.030-0.01117.6220.0230.0230.0000.0000.0000.000
198A461LEU0-0.025-0.01514.2790.0340.0340.0000.0000.0000.000
199A462LEU00.0290.02612.6020.1630.1630.0000.0000.0000.000
200A463SER0-0.0040.00212.9630.0850.0850.0000.0000.0000.000
201A464HIS0-0.013-0.01013.2650.0610.0610.0000.0000.0000.000
202A465VAL00.0200.0157.6450.2410.2410.0000.0000.0000.000
203A466ARG10.8960.9248.768-0.373-0.3730.0000.0000.0000.000
204A467HIS0-0.045-0.02510.672-0.195-0.1950.0000.0000.0000.000
205A468ALA00.0350.0036.634-0.089-0.0890.0000.0000.0000.000
206A469SER00.014-0.0355.9530.7510.7510.0000.0000.0000.000
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