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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: P23RX

Calculation Name: 2NV7-A-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: 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 -3072780.039642
FMO2-HF: Nuclear repulsion 2976374.302613
FMO2-HF: Total energy -96405.737029
FMO2-MP2: Total energy -96676.266272


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.
-81.842-49.20854.916-24.280-63.2740.005


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


Summations of interaction energy for fragment #235(C: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.
-81.842-49.20854.916-24.28-63.274-0.005
Interaction energy analysis for fragmet #235(C:501:555)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.041
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].
1C264SER10.7970.89930.2650.0920.0920.0000.0000.0000.000
2C265PRO00.1580.07625.997-0.010-0.0100.0000.0000.0000.000
3C266GLU-1-0.799-0.86524.997-0.101-0.1010.0000.0000.0000.000
4C267GLN00.0320.00524.554-0.003-0.0030.0000.0000.0000.000
5C268LEU00.0160.03122.274-0.017-0.0170.0000.0000.0000.000
6C269VAL00.023-0.00719.234-0.021-0.0210.0000.0000.0000.000
7C270LEU0-0.019-0.01019.891-0.016-0.0160.0000.0000.0000.000
8C271THR00.0170.00620.710-0.021-0.0210.0000.0000.0000.000
9C272LEU0-0.0080.00516.721-0.027-0.0270.0000.0000.0000.000
10C273LEU0-0.013-0.00715.992-0.039-0.0390.0000.0000.0000.000
11C274GLU-1-0.910-0.95316.447-0.398-0.3980.0000.0000.0000.000
12C275ALA00.0060.00615.333-0.049-0.0490.0000.0000.0000.000
13C276GLU-1-0.781-0.84610.893-0.757-0.7570.0000.0000.0000.000
14C277PRO0-0.0020.0088.0370.0400.0400.0000.0000.0000.000
15C278PRO0-0.0020.00011.0220.1360.1360.0000.0000.0000.000
16C279HIS0-0.002-0.0189.680-0.364-0.3640.0000.0000.0000.000
17C280VAL0-0.0130.0016.1840.2350.2350.0000.0000.0000.000
18C281LEU00.0200.0187.379-0.319-0.3190.0000.0000.0000.000
19C282ILE00.0270.0236.292-0.215-0.2150.0000.0000.0000.000
20C283SER0-0.076-0.0448.8710.0340.0340.0000.0000.0000.000
21C284ARG10.8090.90111.001-0.358-0.3580.0000.0000.0000.000
22C285PRO00.0310.00613.640-0.021-0.0210.0000.0000.0000.000
23C286SER0-0.0120.00313.9260.1000.1000.0000.0000.0000.000
24C287ALA0-0.017-0.00814.9930.0040.0040.0000.0000.0000.000
25C288PRO00.0060.00514.9330.0330.0330.0000.0000.0000.000
26C289PHE00.0280.00211.028-0.097-0.0970.0000.0000.0000.000
27C290THR00.0300.01911.7950.2080.2080.0000.0000.0000.000
28C291GLU-1-0.848-0.91112.3660.9520.9520.0000.0000.0000.000
29C292ALA00.0490.0128.6950.3540.3540.0000.0000.0000.000
30C293SER0-0.077-0.0349.093-0.019-0.0190.0000.0000.0000.000
31C294MET00.0350.0536.506-0.118-0.1180.0000.0000.0000.000
32C295MET00.0180.0242.777-1.484-1.0262.323-0.650-2.1310.008
33C296MET00.0230.0205.531-1.164-1.1640.0000.0000.0000.000
34C297SER0-0.064-0.0557.367-0.846-0.8460.0000.0000.0000.000
35C298LEU00.0070.0002.852-6.969-1.9542.352-1.344-6.0220.016
36C299THR00.004-0.0162.648-9.192-5.6930.854-1.600-2.753-0.021
37C300LYS10.8570.9324.5080.2540.4240.000-0.009-0.1600.000
38C301LEU0-0.063-0.0222.282-1.0470.2102.439-0.861-2.8360.006
39C302ALA00.0280.0122.175-1.953-0.5141.744-0.973-2.2090.001
40C303ASP-1-0.828-0.9114.040-1.298-0.9920.014-0.106-0.2140.000
41C304LYS10.8430.9087.0652.0712.0710.0000.0000.0000.000
42C305GLU-1-0.786-0.8781.615-31.858-38.84918.178-7.025-4.161-0.072
43C306LEU00.0390.0256.0340.7910.7910.0000.0000.0000.000
44C307VAL00.0140.0128.5520.4440.4440.0000.0000.0000.000
45C308HIS0-0.031-0.0288.5300.4390.4390.0000.0000.0000.000
46C309MET0-0.0150.0196.6720.3270.3270.0000.0000.0000.000
47C310ILE00.0220.00710.0190.2770.2770.0000.0000.0000.000
48C311SER0-0.088-0.05412.9290.1960.1960.0000.0000.0000.000
49C312TRP0-0.026-0.00411.0000.0690.0690.0000.0000.0000.000
50C313ALA00.0630.01813.0660.1220.1220.0000.0000.0000.000
51C314LYS10.8680.92915.0650.5810.5810.0000.0000.0000.000
52C315LYS10.7870.90814.9750.7240.7240.0000.0000.0000.000
53C316ILE0-0.0230.00215.3890.0510.0510.0000.0000.0000.000
54C317PRO0-0.013-0.01119.7630.0100.0100.0000.0000.0000.000
55C318GLY0-0.013-0.02122.8390.0100.0100.0000.0000.0000.000
56C319PHE0-0.006-0.01517.2600.0090.0090.0000.0000.0000.000
57C320VAL00.0010.00121.107-0.013-0.0130.0000.0000.0000.000
58C321GLU-1-0.871-0.92522.952-0.241-0.2410.0000.0000.0000.000
59C322LEU0-0.0290.01221.4680.0280.0280.0000.0000.0000.000
60C323SER0-0.019-0.04025.073-0.019-0.0190.0000.0000.0000.000
61C324LEU00.004-0.01522.554-0.018-0.0180.0000.0000.0000.000
62C325PHE00.0520.03220.388-0.020-0.0200.0000.0000.0000.000
63C326ASP-1-0.753-0.80921.135-0.285-0.2850.0000.0000.0000.000
64C327GLN0-0.024-0.02519.397-0.051-0.0510.0000.0000.0000.000
65C328VAL0-0.0170.01116.453-0.061-0.0610.0000.0000.0000.000
66C329ARG10.9160.94916.5490.2320.2320.0000.0000.0000.000
67C330LEU0-0.033-0.00617.1730.0200.0200.0000.0000.0000.000
68C331LEU00.0230.01211.4120.0220.0220.0000.0000.0000.000
69C332GLU-1-0.874-0.96212.603-0.488-0.4880.0000.0000.0000.000
70C333SER0-0.036-0.02613.4420.0200.0200.0000.0000.0000.000
71C334CYS0-0.091-0.02911.4170.0500.0500.0000.0000.0000.000
72C335TRP00.0770.0234.8570.1030.1030.0000.0000.0000.000
73C336MET00.0090.0273.756-1.1480.8640.284-0.463-1.8330.003
74C337GLU-1-0.811-0.9134.8380.4630.599-0.001-0.002-0.1330.000
75C338VAL0-0.034-0.0186.5450.1930.1930.0000.0000.0000.000
76C339LEU0-0.0190.0022.666-3.977-1.2043.581-1.571-4.7830.011
77C340MET0-0.040-0.0022.518-2.4461.1012.418-1.276-4.6900.005
78C341MET00.0040.0043.3760.1900.1710.0150.175-0.1710.000
79C342GLY00.0050.0035.340-0.210-0.2100.0000.0000.0000.000
80C343LEU0-0.0060.0102.695-4.393-1.5291.234-1.105-2.9930.013
81C344MET0-0.019-0.0034.647-1.019-0.8600.000-0.023-0.1360.000
82C345TRP0-0.005-0.0037.656-0.175-0.1750.0000.0000.0000.000
83C346ARG10.7560.8522.3695.5206.4970.229-0.466-0.7400.001
84C347SER0-0.006-0.0137.747-0.029-0.0290.0000.0000.0000.000
85C348ILE00.0240.02910.332-0.015-0.0150.0000.0000.0000.000
86C349ASP-1-0.861-0.93413.0490.2380.2380.0000.0000.0000.000
87C350HIS0-0.036-0.01113.1000.0040.0040.0000.0000.0000.000
88C351PRO00.0170.02013.7980.0770.0770.0000.0000.0000.000
89C352GLY00.0150.00312.567-0.007-0.0070.0000.0000.0000.000
90C353LYS10.8660.91811.103-0.361-0.3610.0000.0000.0000.000
91C354LEU00.0060.0064.722-0.148-0.035-0.001-0.003-0.1090.000
92C355ILE0-0.033-0.0148.5490.0620.0620.0000.0000.0000.000
93C356PHE00.0380.0122.093-4.926-1.7104.450-1.566-6.1010.018
94C357ALA00.0550.0244.998-1.967-1.881-0.001-0.005-0.0810.000
95C358PRO0-0.001-0.0077.7260.4150.4150.0000.0000.0000.000
96C359ASP-1-0.754-0.88010.080-0.781-0.7810.0000.0000.0000.000
97C360LEU0-0.014-0.0095.3570.0030.0030.0000.0000.0000.000
98C361VAL0-0.0180.0058.4370.2360.2360.0000.0000.0000.000
99C362LEU00.0170.0206.2100.0150.0150.0000.0000.0000.000
100C363ASP-1-0.811-0.9199.8970.8250.8250.0000.0000.0000.000
101C364ARG10.8250.8788.950-0.455-0.4550.0000.0000.0000.000
102C365ASP-1-0.866-0.9239.9550.7910.7910.0000.0000.0000.000
103C366GLU-1-0.719-0.88910.5221.1361.1360.0000.0000.0000.000
104C367GLY00.0440.0177.0840.2690.2690.0000.0000.0000.000
105C368LYS10.7290.8417.560-0.758-0.7580.0000.0000.0000.000
106C369CYS0-0.126-0.04210.011-0.134-0.1340.0000.0000.0000.000
107C370VAL00.0510.0236.320-0.079-0.0790.0000.0000.0000.000
108C371GLU-1-0.799-0.8847.0631.6811.6810.0000.0000.0000.000
109C372GLY00.0390.0328.104-0.057-0.0570.0000.0000.0000.000
110C373ILE00.0290.0252.491-2.721-1.0161.496-0.675-2.5270.003
111C374LEU0-0.025-0.0154.376-0.688-0.520-0.001-0.023-0.1450.000
112C375GLU-1-0.840-0.9146.8060.2300.2300.0000.0000.0000.000
113C376ILE00.0310.0082.509-2.025-0.4631.671-0.584-2.6490.001
114C377PHE00.005-0.0072.630-1.911-0.2100.967-0.558-2.1100.006
115C378ASP-1-0.752-0.8395.2050.7070.762-0.001-0.002-0.0520.000
116C379MET0-0.0240.0006.927-0.016-0.0160.0000.0000.0000.000
117C380LEU00.0210.0252.350-0.968-0.3361.086-0.373-1.3460.000
118C381LEU0-0.0090.0176.665-0.057-0.0570.0000.0000.0000.000
119C382ALA0-0.014-0.0019.593-0.096-0.0960.0000.0000.0000.000
120C383THR0-0.010-0.0319.739-0.104-0.1040.0000.0000.0000.000
121C384THR0-0.031-0.0339.251-0.029-0.0290.0000.0000.0000.000
122C385SER0-0.063-0.05411.344-0.101-0.1010.0000.0000.0000.000
123C386ARG10.8160.90514.408-0.329-0.3290.0000.0000.0000.000
124C387PHE00.0500.00510.533-0.074-0.0740.0000.0000.0000.000
125C388ARG10.8650.93413.789-0.565-0.5650.0000.0000.0000.000
126C389GLU-1-0.837-0.88916.7220.2700.2700.0000.0000.0000.000
127C390LEU0-0.039-0.01317.389-0.038-0.0380.0000.0000.0000.000
128C391LYS10.8780.94718.988-0.190-0.1900.0000.0000.0000.000
129C392LEU00.0050.02613.472-0.034-0.0340.0000.0000.0000.000
130C393GLN0-0.008-0.01817.326-0.018-0.0180.0000.0000.0000.000
131C394HIS00.0260.01813.403-0.023-0.0230.0000.0000.0000.000
132C395LYS10.8620.90416.2870.1080.1080.0000.0000.0000.000
133C396GLU-1-0.724-0.82217.8680.0560.0560.0000.0000.0000.000
134C397TYR0-0.016-0.0329.0910.0030.0030.0000.0000.0000.000
135C398LEU0-0.0200.00413.574-0.001-0.0010.0000.0000.0000.000
136C399CYS0-0.032-0.00915.158-0.030-0.0300.0000.0000.0000.000
137C400VAL00.0210.00312.564-0.009-0.0090.0000.0000.0000.000
138C401LYS10.8450.9108.4300.6920.6920.0000.0000.0000.000
139C402ALA00.0150.01412.366-0.048-0.0480.0000.0000.0000.000
140C403MET0-0.036-0.02815.6940.0020.0020.0000.0000.0000.000
141C404ILE0-0.028-0.0189.6210.0010.0010.0000.0000.0000.000
142C405LEU00.0040.00213.452-0.019-0.0190.0000.0000.0000.000
143C406LEU0-0.025-0.01214.638-0.017-0.0170.0000.0000.0000.000
144C407ASN0-0.068-0.03917.0400.0190.0190.0000.0000.0000.000
145C408SER00.0120.01214.9880.0250.0250.0000.0000.0000.000
146C409SER0-0.017-0.00816.437-0.003-0.0030.0000.0000.0000.000
147C410MET00.0130.00819.4060.0190.0190.0000.0000.0000.000
148C411TYR00.0420.02121.206-0.020-0.0200.0000.0000.0000.000
149C412PRO0-0.022-0.00224.5580.0140.0140.0000.0000.0000.000
150C413LEU0-0.053-0.02227.0250.0030.0030.0000.0000.0000.000
151C414VAL00.0450.01928.9540.0050.0050.0000.0000.0000.000
152C415THR00.022-0.00931.475-0.006-0.0060.0000.0000.0000.000
153C416ALA0-0.031-0.01232.596-0.004-0.0040.0000.0000.0000.000
154C417THR0-0.027-0.01532.1960.0040.0040.0000.0000.0000.000
155C418GLN0-0.025-0.00527.2310.0020.0020.0000.0000.0000.000
156C419ASP-1-0.760-0.88328.400-0.165-0.1650.0000.0000.0000.000
157C420ALA00.0190.00631.3390.0060.0060.0000.0000.0000.000
158C421ASP-1-0.882-0.95131.113-0.150-0.1500.0000.0000.0000.000
159C422SER00.006-0.00925.754-0.003-0.0030.0000.0000.0000.000
160C423SER00.0150.00025.503-0.002-0.0020.0000.0000.0000.000
161C424ARG10.8310.91326.5830.1320.1320.0000.0000.0000.000
162C425LYS10.8460.91926.5430.2000.2000.0000.0000.0000.000
163C426LEU00.0480.03920.177-0.001-0.0010.0000.0000.0000.000
164C427ALA00.0310.01923.2900.0060.0060.0000.0000.0000.000
165C428HIS0-0.028-0.01225.2920.0190.0190.0000.0000.0000.000
166C429LEU00.0100.00920.8280.0110.0110.0000.0000.0000.000
167C430LEU00.0200.01619.3350.0050.0050.0000.0000.0000.000
168C431ASN0-0.0130.01022.1970.0250.0250.0000.0000.0000.000
169C432ALA00.006-0.00325.1780.0110.0110.0000.0000.0000.000
170C433VAL00.006-0.00618.6010.0040.0040.0000.0000.0000.000
171C434THR0-0.022-0.02021.5750.0200.0200.0000.0000.0000.000
172C435ASP-1-0.929-0.97022.960-0.052-0.0520.0000.0000.0000.000
173C436ALA0-0.031-0.03022.3510.0060.0060.0000.0000.0000.000
174C437LEU00.0010.00318.7050.0060.0060.0000.0000.0000.000
175C438VAL00.0250.01022.0270.0140.0140.0000.0000.0000.000
176C439TRP00.0480.01525.5000.0020.0020.0000.0000.0000.000
177C440VAL0-0.028-0.02521.3330.0010.0010.0000.0000.0000.000
178C441ILE00.0000.01221.7700.0110.0110.0000.0000.0000.000
179C442ALA0-0.0100.01124.9780.0070.0070.0000.0000.0000.000
180C443LYS10.8280.90625.9490.0620.0620.0000.0000.0000.000
181C444SER0-0.076-0.04925.1240.0040.0040.0000.0000.0000.000
182C445GLY00.0030.00227.1410.0060.0060.0000.0000.0000.000
183C446ILE0-0.0320.00026.3580.0030.0030.0000.0000.0000.000
184C447SER00.0520.01930.497-0.004-0.0040.0000.0000.0000.000
185C448SER00.0570.01631.2490.0050.0050.0000.0000.0000.000
186C449GLN00.0360.03331.0150.0030.0030.0000.0000.0000.000
187C450GLN00.0230.00228.6140.0030.0030.0000.0000.0000.000
188C451GLN0-0.013-0.01226.8780.0040.0040.0000.0000.0000.000
189C452SER00.0110.00026.1290.0010.0010.0000.0000.0000.000
190C453MET00.0000.00125.4800.0080.0080.0000.0000.0000.000
191C454ARG10.7550.84420.695-0.072-0.0720.0000.0000.0000.000
192C455LEU00.0380.01321.5270.0120.0120.0000.0000.0000.000
193C456ALA00.0150.00621.5850.0060.0060.0000.0000.0000.000
194C457ASN0-0.038-0.03619.8310.0310.0310.0000.0000.0000.000
195C458LEU00.0250.00716.3390.0220.0220.0000.0000.0000.000
196C459LEU00.0070.00516.7170.0080.0080.0000.0000.0000.000
197C460MET0-0.011-0.00117.8870.0070.0070.0000.0000.0000.000
198C461LEU0-0.039-0.01313.8120.0170.0170.0000.0000.0000.000
199C462LEU00.0290.02913.0330.0570.0570.0000.0000.0000.000
200C463SER00.002-0.01812.9450.0120.0120.0000.0000.0000.000
201C464HIS0-0.045-0.01412.5950.0400.0400.0000.0000.0000.000
202C465VAL00.0390.0137.2550.0760.0760.0000.0000.0000.000
203C466ARG10.8350.9158.7290.1280.1280.0000.0000.0000.000
204C467HIS0-0.045-0.01410.406-0.068-0.0680.0000.0000.0000.000
205C468ALA00.0180.0036.189-0.038-0.0380.0000.0000.0000.000
206C469SER00.037-0.0205.6210.2550.2550.0000.0000.0000.000
207C470ASN00.0220.0166.673-0.252-0.2520.0000.0000.0000.000
208C471LYS10.8000.8885.784-0.391-0.3910.0000.0000.0000.000
209C472GLY00.003-0.0023.414-1.184-0.0830.205-0.482-0.8240.004
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