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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: X6KZP

Calculation Name: 2NV7-B-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 4-(4-hydroxyphenyl)-1-naphthaldehyde oxime

ligand 3-letter code: 555

PDB ID: 2NV7

Chain ID: B

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 -3069725.56819
FMO2-HF: Nuclear repulsion 2973319.743386
FMO2-HF: Total energy -96405.824804
FMO2-MP2: Total energy -96676.375457


3D Structure
Snapshot
 
Ligand structure

555

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.
-81.196-54.10263.382-27.335-63.140-0.018


Interactive mode: IFIE and PIEDA for fragment #235(D:501:555)


Summations of interaction energy for fragment #235(D:501:555)
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.
-81.196-54.10263.382-27.335-63.140.018
Interaction energy analysis for fragmet #235(D:501:555)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.045
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].
1D264SER10.7660.86828.0460.1610.1610.0000.0000.0000.000
2D265PRO00.0770.03625.908-0.016-0.0160.0000.0000.0000.000
3D266GLU-1-0.743-0.87723.870-0.225-0.2250.0000.0000.0000.000
4D267GLN00.0490.03724.269-0.015-0.0150.0000.0000.0000.000
5D268LEU00.0270.03720.835-0.027-0.0270.0000.0000.0000.000
6D269VAL00.0150.00419.751-0.033-0.0330.0000.0000.0000.000
7D270LEU0-0.022-0.02819.267-0.034-0.0340.0000.0000.0000.000
8D271THR0-0.012-0.01219.916-0.032-0.0320.0000.0000.0000.000
9D272LEU0-0.001-0.00215.509-0.045-0.0450.0000.0000.0000.000
10D273LEU0-0.026-0.01415.179-0.065-0.0650.0000.0000.0000.000
11D274GLU-1-0.887-0.92515.760-0.546-0.5460.0000.0000.0000.000
12D275ALA0-0.0130.01114.775-0.041-0.0410.0000.0000.0000.000
13D276GLU-1-0.783-0.85410.315-0.961-0.9610.0000.0000.0000.000
14D277PRO00.0290.0236.6720.0060.0060.0000.0000.0000.000
15D278PRO00.0070.0179.039-0.009-0.0090.0000.0000.0000.000
16D279HIS0-0.050-0.0487.640-0.147-0.1470.0000.0000.0000.000
17D280VAL00.0400.0216.2330.4090.4090.0000.0000.0000.000
18D281LEU00.0130.0088.2030.1800.1800.0000.0000.0000.000
19D282ILE0-0.032-0.0216.176-0.114-0.1140.0000.0000.0000.000
20D283SER0-0.009-0.0259.549-0.011-0.0110.0000.0000.0000.000
21D284ARG10.7630.84611.454-0.083-0.0830.0000.0000.0000.000
22D285PRO0-0.0040.01512.563-0.015-0.0150.0000.0000.0000.000
23D286SER0-0.011-0.01915.5760.0350.0350.0000.0000.0000.000
24D287ALA0-0.027-0.01517.8250.0230.0230.0000.0000.0000.000
25D288PRO00.000-0.00516.456-0.004-0.0040.0000.0000.0000.000
26D289PHE00.0100.01310.562-0.003-0.0030.0000.0000.0000.000
27D290THR00.0150.00112.4940.0600.0600.0000.0000.0000.000
28D291GLU-1-0.717-0.8457.8761.9231.9230.0000.0000.0000.000
29D292ALA00.0750.0257.9290.1030.1030.0000.0000.0000.000
30D293SER0-0.062-0.0298.883-0.276-0.2760.0000.0000.0000.000
31D294MET00.0460.0266.278-0.134-0.1340.0000.0000.0000.000
32D295MET00.0270.0263.036-3.266-0.6942.098-1.245-3.4240.005
33D296MET00.0040.0215.086-1.210-1.032-0.001-0.003-0.1750.000
34D297SER0-0.046-0.0387.438-0.536-0.5360.0000.0000.0000.000
35D298LEU00.0140.0052.831-5.037-1.0240.844-1.047-3.8110.011
36D299THR00.002-0.0182.844-6.434-3.2210.481-1.333-2.360-0.013
37D300LYS10.7760.8744.2931.0231.2170.000-0.011-0.1830.000
38D301LEU0-0.0200.0052.166-0.4600.5021.877-0.568-2.2710.003
39D302ALA00.0490.0132.262-2.114-0.6552.112-1.062-2.5090.005
40D303ASP-1-0.784-0.8964.250-1.428-1.0890.014-0.136-0.2170.000
41D304LYS10.8520.9276.9782.9232.9230.0000.0000.0000.000
42D305GLU-1-0.777-0.8431.546-33.089-44.53324.761-9.171-4.146-0.076
43D306LEU00.0290.0305.8290.8170.8170.0000.0000.0000.000
44D307VAL00.0130.0158.5910.4160.4160.0000.0000.0000.000
45D308HIS0-0.029-0.0147.1800.4310.4310.0000.0000.0000.000
46D309MET0-0.0040.0178.2270.3410.3410.0000.0000.0000.000
47D310ILE00.0130.0059.9560.2630.2630.0000.0000.0000.000
48D311SER0-0.040-0.03712.7940.1920.1920.0000.0000.0000.000
49D312TRP0-0.043-0.02511.2590.1350.1350.0000.0000.0000.000
50D313ALA00.0350.00713.2550.1320.1320.0000.0000.0000.000
51D314LYS10.8330.91515.2470.5620.5620.0000.0000.0000.000
52D315LYS10.8390.89117.1090.6770.6770.0000.0000.0000.000
53D316ILE0-0.0300.00315.0570.0570.0570.0000.0000.0000.000
54D317PRO00.020-0.00119.3880.0200.0200.0000.0000.0000.000
55D318GLY00.0350.01222.7700.0060.0060.0000.0000.0000.000
56D319PHE00.034-0.01117.4630.0140.0140.0000.0000.0000.000
57D320VAL0-0.032-0.01320.2250.0020.0020.0000.0000.0000.000
58D321GLU-1-0.879-0.91922.430-0.220-0.2200.0000.0000.0000.000
59D322LEU0-0.0120.01321.5000.0310.0310.0000.0000.0000.000
60D323SER0-0.012-0.03025.246-0.017-0.0170.0000.0000.0000.000
61D324LEU00.022-0.00623.297-0.017-0.0170.0000.0000.0000.000
62D325PHE00.0560.02723.100-0.021-0.0210.0000.0000.0000.000
63D326ASP-1-0.713-0.80721.922-0.176-0.1760.0000.0000.0000.000
64D327GLN0-0.079-0.04419.500-0.057-0.0570.0000.0000.0000.000
65D328VAL00.0130.02317.141-0.066-0.0660.0000.0000.0000.000
66D329ARG10.8540.92617.1660.1050.1050.0000.0000.0000.000
67D330LEU0-0.026-0.01617.2210.0310.0310.0000.0000.0000.000
68D331LEU00.0110.00713.484-0.020-0.0200.0000.0000.0000.000
69D332GLU-1-0.821-0.93712.695-0.208-0.2080.0000.0000.0000.000
70D333SER0-0.048-0.02112.9720.0590.0590.0000.0000.0000.000
71D334CYS0-0.077-0.04211.4750.0100.0100.0000.0000.0000.000
72D335TRP00.0550.0214.762-0.247-0.027-0.001-0.002-0.2170.000
73D336MET00.0090.0183.867-1.0540.3920.092-0.351-1.1870.002
74D337GLU-1-0.785-0.9004.904-0.0960.040-0.001-0.003-0.1320.000
75D338VAL0-0.024-0.0186.5690.0050.0050.0000.0000.0000.000
76D339LEU00.0050.0042.925-1.949-0.0670.492-0.583-1.7910.004
77D340MET0-0.0300.0012.544-3.3370.6021.862-1.551-4.250-0.002
78D341MET0-0.0040.0033.3050.7900.7180.0110.259-0.1970.000
79D342GLY00.0000.0015.229-0.049-0.0490.0000.0000.0000.000
80D343LEU0-0.0080.0062.543-4.512-1.5253.142-1.371-4.7570.013
81D344MET0-0.0180.0024.353-0.948-0.7260.003-0.062-0.1620.000
82D345TRP0-0.042-0.0277.382-0.092-0.0920.0000.0000.0000.000
83D346ARG10.7510.8362.2026.5157.7180.580-0.708-1.0750.002
84D347SER0-0.007-0.0147.510-0.075-0.0750.0000.0000.0000.000
85D348ILE00.0020.01810.0610.0110.0110.0000.0000.0000.000
86D349ASP-1-0.865-0.94013.036-0.061-0.0610.0000.0000.0000.000
87D350HIS0-0.043-0.00512.6620.0350.0350.0000.0000.0000.000
88D351PRO00.0010.00113.8950.0510.0510.0000.0000.0000.000
89D352GLY00.006-0.00611.8700.0000.0000.0000.0000.0000.000
90D353LYS10.8150.90010.390-0.183-0.1830.0000.0000.0000.000
91D354LEU00.0230.0114.196-0.232-0.0670.000-0.012-0.1520.000
92D355ILE00.0040.0028.315-0.041-0.0410.0000.0000.0000.000
93D356PHE00.0330.0092.303-5.377-1.5093.931-1.542-6.2570.020
94D357ALA00.0020.0044.668-2.506-2.391-0.001-0.011-0.1030.000
95D358PRO0-0.023-0.0237.3430.4540.4540.0000.0000.0000.000
96D359ASP-1-0.808-0.86210.643-0.416-0.4160.0000.0000.0000.000
97D360LEU0-0.0070.0036.1170.1750.1750.0000.0000.0000.000
98D361VAL00.0030.0118.125-0.002-0.0020.0000.0000.0000.000
99D362LEU0-0.0120.0026.4640.0430.0430.0000.0000.0000.000
100D363ASP-1-0.828-0.9149.4360.3680.3680.0000.0000.0000.000
101D364ARG10.8330.8628.124-0.338-0.3380.0000.0000.0000.000
102D365ASP-1-0.824-0.9088.8090.5650.5650.0000.0000.0000.000
103D366GLU-1-0.738-0.8349.9010.3640.3640.0000.0000.0000.000
104D367GLY00.0300.0126.7910.1200.1200.0000.0000.0000.000
105D368LYS10.8230.8927.438-0.481-0.4810.0000.0000.0000.000
106D369CYS0-0.130-0.0459.5870.0500.0500.0000.0000.0000.000
107D370VAL00.023-0.0115.2410.0180.0180.0000.0000.0000.000
108D371GLU-1-0.892-0.9268.3661.4451.4450.0000.0000.0000.000
109D372GLY00.0650.0167.0600.5680.5680.0000.0000.0000.000
110D373ILE0-0.0270.0022.499-1.981-1.4823.872-0.897-3.4740.004
111D374LEU0-0.029-0.0064.034-1.024-0.7400.000-0.094-0.1910.000
112D375GLU-1-0.850-0.9176.5471.1801.1800.0000.0000.0000.000
113D376ILE00.024-0.0012.211-1.964-0.9773.388-0.906-3.4690.003
114D377PHE0-0.013-0.0132.565-2.192-0.4931.361-0.642-2.4180.006
115D378ASP-1-0.757-0.8394.9110.5360.600-0.001-0.004-0.0590.000
116D379MET0-0.050-0.0036.7370.0340.0340.0000.0000.0000.000
117D380LEU00.0380.0242.664-1.069-0.2200.597-0.295-1.151-0.001
118D381LEU00.0170.0266.712-0.016-0.0160.0000.0000.0000.000
119D382ALA0-0.0020.0189.309-0.052-0.0520.0000.0000.0000.000
120D383THR0-0.021-0.02510.108-0.051-0.0510.0000.0000.0000.000
121D384THR0-0.019-0.0329.430-0.032-0.0320.0000.0000.0000.000
122D385SER0-0.051-0.04511.912-0.066-0.0660.0000.0000.0000.000
123D386ARG10.7900.86214.584-0.159-0.1590.0000.0000.0000.000
124D387PHE00.0440.00610.873-0.041-0.0410.0000.0000.0000.000
125D388ARG10.8640.93313.604-0.202-0.2020.0000.0000.0000.000
126D389GLU-1-0.857-0.88517.1580.0830.0830.0000.0000.0000.000
127D390LEU0-0.003-0.00117.656-0.022-0.0220.0000.0000.0000.000
128D391LYS10.7930.90519.645-0.044-0.0440.0000.0000.0000.000
129D392LEU00.0180.02713.259-0.016-0.0160.0000.0000.0000.000
130D393GLN0-0.024-0.02117.545-0.026-0.0260.0000.0000.0000.000
131D394HIS00.0890.04912.7610.0480.0480.0000.0000.0000.000
132D395LYS10.8690.91015.8980.2240.2240.0000.0000.0000.000
133D396GLU-1-0.741-0.86017.628-0.069-0.0690.0000.0000.0000.000
134D397TYR00.004-0.0158.9550.0160.0160.0000.0000.0000.000
135D398LEU0-0.0390.00113.263-0.009-0.0090.0000.0000.0000.000
136D399CYS0-0.024-0.00714.788-0.021-0.0210.0000.0000.0000.000
137D400VAL00.0370.00513.0920.0020.0020.0000.0000.0000.000
138D401LYS10.8030.8918.4590.8400.8400.0000.0000.0000.000
139D402ALA00.0330.01612.101-0.033-0.0330.0000.0000.0000.000
140D403MET0-0.048-0.03415.1270.0170.0170.0000.0000.0000.000
141D404ILE0-0.040-0.0069.6420.0120.0120.0000.0000.0000.000
142D405LEU0-0.0080.00113.2820.0090.0090.0000.0000.0000.000
143D406LEU0-0.035-0.00714.2600.0140.0140.0000.0000.0000.000
144D407ASN0-0.028-0.01516.6320.0190.0190.0000.0000.0000.000
145D408SER0-0.001-0.00115.0410.0440.0440.0000.0000.0000.000
146D409SER00.0100.01516.812-0.003-0.0030.0000.0000.0000.000
147D410MET0-0.039-0.02518.1290.0250.0250.0000.0000.0000.000
148D411TYR0-0.017-0.01218.0650.0080.0080.0000.0000.0000.000
149D412PRO00.0810.04818.5340.0190.0190.0000.0000.0000.000
150D413LEU00.0200.01421.4920.0070.0070.0000.0000.0000.000
151D414VAL00.022-0.01123.296-0.018-0.0180.0000.0000.0000.000
152D415THR0-0.013-0.01426.7380.0050.0050.0000.0000.0000.000
153D416ALA0-0.0030.00424.639-0.009-0.0090.0000.0000.0000.000
154D417THR0-0.0020.00325.593-0.002-0.0020.0000.0000.0000.000
155D418GLN0-0.063-0.02328.4020.0080.0080.0000.0000.0000.000
156D419ASP-1-0.914-0.95131.784-0.062-0.0620.0000.0000.0000.000
157D420ALA00.0170.03330.030-0.008-0.0080.0000.0000.0000.000
158D421ASP-1-0.772-0.86030.161-0.091-0.0910.0000.0000.0000.000
159D422SER0-0.022-0.03825.965-0.010-0.0100.0000.0000.0000.000
160D423SER00.0360.00226.218-0.006-0.0060.0000.0000.0000.000
161D424ARG10.7820.85527.0700.0870.0870.0000.0000.0000.000
162D425LYS10.8170.90426.0910.1930.1930.0000.0000.0000.000
163D426LEU00.0340.01720.312-0.010-0.0100.0000.0000.0000.000
164D427ALA00.0470.02423.447-0.003-0.0030.0000.0000.0000.000
165D428HIS0-0.0160.00225.6610.0110.0110.0000.0000.0000.000
166D429LEU0-0.0140.00622.017-0.003-0.0030.0000.0000.0000.000
167D430LEU00.0330.02519.678-0.010-0.0100.0000.0000.0000.000
168D431ASN0-0.043-0.02122.3440.0130.0130.0000.0000.0000.000
169D432ALA00.0180.01024.3130.0030.0030.0000.0000.0000.000
170D433VAL00.001-0.00618.243-0.008-0.0080.0000.0000.0000.000
171D434THR0-0.006-0.00621.5270.0110.0110.0000.0000.0000.000
172D435ASP-1-0.847-0.92623.596-0.140-0.1400.0000.0000.0000.000
173D436ALA0-0.040-0.01721.8070.0030.0030.0000.0000.0000.000
174D437LEU00.0150.00418.7480.0040.0040.0000.0000.0000.000
175D438VAL00.0280.00721.9120.0100.0100.0000.0000.0000.000
176D439TRP00.0430.02325.1900.0020.0020.0000.0000.0000.000
177D440VAL0-0.025-0.01821.0690.0020.0020.0000.0000.0000.000
178D441ILE0-0.0010.01121.1710.0070.0070.0000.0000.0000.000
179D442ALA0-0.0210.00524.5630.0090.0090.0000.0000.0000.000
180D443LYS10.7930.90926.1040.1570.1570.0000.0000.0000.000
181D444SER0-0.048-0.03824.8840.0010.0010.0000.0000.0000.000
182D445GLY0-0.004-0.00426.9260.0060.0060.0000.0000.0000.000
183D446ILE0-0.0280.00226.4890.0070.0070.0000.0000.0000.000
184D447SER00.0500.01830.631-0.003-0.0030.0000.0000.0000.000
185D448SER00.0570.01931.1730.0030.0030.0000.0000.0000.000
186D449GLN00.0630.04230.727-0.003-0.0030.0000.0000.0000.000
187D450GLN00.0420.00428.8930.0080.0080.0000.0000.0000.000
188D451GLN0-0.033-0.01926.7750.0000.0000.0000.0000.0000.000
189D452SER00.0150.00425.774-0.002-0.0020.0000.0000.0000.000
190D453MET0-0.028-0.01125.7730.0070.0070.0000.0000.0000.000
191D454ARG10.8190.90620.7070.0440.0440.0000.0000.0000.000
192D455LEU00.0240.00621.3440.0050.0050.0000.0000.0000.000
193D456ALA00.0230.00721.0640.0050.0050.0000.0000.0000.000
194D457ASN0-0.021-0.02020.1840.0300.0300.0000.0000.0000.000
195D458LEU00.006-0.00316.1650.0190.0190.0000.0000.0000.000
196D459LEU00.0070.00316.1730.0050.0050.0000.0000.0000.000
197D460MET0-0.0050.00117.6270.0170.0170.0000.0000.0000.000
198D461LEU0-0.0080.00414.5850.0340.0340.0000.0000.0000.000
199D462LEU00.0220.02412.3460.0390.0390.0000.0000.0000.000
200D463SER0-0.028-0.01713.6790.0240.0240.0000.0000.0000.000
201D464HIS0-0.035-0.02113.0760.0770.0770.0000.0000.0000.000
202D465VAL0-0.0060.0028.0750.0840.0840.0000.0000.0000.000
203D466ARG10.8160.9089.009-0.036-0.0360.0000.0000.0000.000
204D467HIS00.0250.02110.5300.1240.1240.0000.0000.0000.000
205D468ALA00.0450.0106.7830.1520.1520.0000.0000.0000.000
206D469SER0-0.011-0.0296.0800.4180.4180.0000.0000.0000.000
207D470ASN0-0.004-0.0107.1270.0700.0700.0000.0000.0000.000
208D471LYS10.8070.8986.797-1.455-1.4550.0000.0000.0000.000
209D472GLY00.0340.0054.2120.5170.8290.005-0.117-0.2010.001
210D473MET0-0.021-0.0044.241-1.063-0.7330.001-0.050-0.2810.000
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