Manual

About

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: P45NX

Calculation Name: 1X7J-B-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: genistein

ligand 3-letter code: GEN

PDB ID: 1X7J

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 -3042865.7578
FMO2-HF: Nuclear repulsion 2946369.210517
FMO2-HF: Total energy -96496.547283
FMO2-MP2: Total energy -96767.146912


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.
-116.761-100.68179.377-37.723-57.7310.098


Interactive mode: IFIE and PIEDA for fragment #235(B:202:GEN)


Summations of interaction energy for fragment #235(B:202: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.
-116.761-100.68179.377-37.723-57.731-0.098
Interaction energy analysis for fragmet #235(B:202:GEN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.096 / q_NPA : -0.133
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].
1B264SER10.8630.92028.998-0.072-0.0720.0000.0000.0000.000
2B265PRO00.1830.07726.085-0.012-0.0120.0000.0000.0000.000
3B266GLU-1-0.895-0.93924.9080.1220.1220.0000.0000.0000.000
4B267GLN00.018-0.00324.8310.0020.0020.0000.0000.0000.000
5B268LEU00.0110.04121.867-0.020-0.0200.0000.0000.0000.000
6B269VAL00.017-0.00520.373-0.002-0.0020.0000.0000.0000.000
7B270LEU0-0.042-0.03619.9720.0040.0040.0000.0000.0000.000
8B271THR00.0150.00620.357-0.025-0.0250.0000.0000.0000.000
9B272LEU0-0.021-0.01916.485-0.037-0.0370.0000.0000.0000.000
10B273LEU0-0.055-0.02915.869-0.002-0.0020.0000.0000.0000.000
11B274GLU-1-0.968-0.97616.332-0.163-0.1630.0000.0000.0000.000
12B275ALA0-0.078-0.05215.696-0.063-0.0630.0000.0000.0000.000
13B276GLU-1-0.809-0.88210.4910.0910.0910.0000.0000.0000.000
14B277PRO0-0.037-0.0028.322-0.053-0.0530.0000.0000.0000.000
15B278PRO0-0.019-0.00210.2100.1250.1250.0000.0000.0000.000
16B279HIS00.036-0.0047.822-0.516-0.5160.0000.0000.0000.000
17B280VAL00.0070.0156.0960.3150.3150.0000.0000.0000.000
18B281LEU0-0.024-0.0167.7890.0460.0460.0000.0000.0000.000
19B282ILE0-0.050-0.0236.015-0.097-0.0970.0000.0000.0000.000
20B283SER0-0.010-0.0139.0330.2300.2300.0000.0000.0000.000
21B284ARG10.8870.95811.483-0.726-0.7260.0000.0000.0000.000
22B285PRO0-0.059-0.01411.450-0.046-0.0460.0000.0000.0000.000
23B286SER00.012-0.00814.3860.0720.0720.0000.0000.0000.000
24B287ALA0-0.029-0.00318.1110.0510.0510.0000.0000.0000.000
25B288PRO00.015-0.00416.7580.0140.0140.0000.0000.0000.000
26B289PHE0-0.007-0.00210.218-0.038-0.0380.0000.0000.0000.000
27B290THR00.0070.00413.183-0.020-0.0200.0000.0000.0000.000
28B291GLU-1-0.813-0.9178.256-0.864-0.8640.0000.0000.0000.000
29B292ALA00.0450.0168.694-0.039-0.0390.0000.0000.0000.000
30B293SER00.0140.0019.667-0.037-0.0370.0000.0000.0000.000
31B294MET00.0350.0257.213-0.014-0.0140.0000.0000.0000.000
32B295MET00.0480.0383.755-1.980-0.1430.202-0.589-1.4490.005
33B296MET0-0.0030.0395.534-0.395-0.3950.0000.0000.0000.000
34B297SER0-0.025-0.0247.290-0.457-0.4570.0000.0000.0000.000
35B298LEU0-0.013-0.0052.981-4.911-1.0920.823-0.967-3.6750.009
36B299THR00.000-0.0362.844-9.167-5.8190.525-1.557-2.316-0.017
37B300LYS10.9160.9604.8110.7450.928-0.001-0.005-0.1770.000
38B301LEU0-0.049-0.0082.227-0.1430.5852.632-0.809-2.5500.004
39B302ALA00.0540.0242.063-1.616-0.5051.418-0.800-1.728-0.003
40B303ASP-1-0.920-0.9534.119-1.051-0.7190.010-0.116-0.2260.000
41B304LYS10.9840.9726.8922.5622.5620.0000.0000.0000.000
42B305GLU-1-0.850-0.9281.800-35.571-35.45313.095-7.288-5.926-0.096
43B306LEU00.0100.0175.9931.1251.1250.0000.0000.0000.000
44B307VAL00.0130.0148.3740.5810.5810.0000.0000.0000.000
45B308HIS0-0.016-0.0178.2540.5260.5260.0000.0000.0000.000
46B309MET0-0.0340.0097.8850.3180.3180.0000.0000.0000.000
47B310ILE00.0330.0219.7510.3210.3210.0000.0000.0000.000
48B311SER0-0.045-0.02913.0310.1900.1900.0000.0000.0000.000
49B312TRP0-0.019-0.01911.4020.1300.1300.0000.0000.0000.000
50B313ALA00.0640.02513.4610.1210.1210.0000.0000.0000.000
51B314LYS10.8800.94215.1360.4510.4510.0000.0000.0000.000
52B315LYS10.9370.98016.4490.3720.3720.0000.0000.0000.000
53B316ILE0-0.0130.01114.8790.0560.0560.0000.0000.0000.000
54B317PRO0-0.020-0.02418.889-0.012-0.0120.0000.0000.0000.000
55B318GLY00.0550.03122.7240.0220.0220.0000.0000.0000.000
56B319PHE00.0270.01217.6710.0010.0010.0000.0000.0000.000
57B320VAL0-0.026-0.02321.209-0.015-0.0150.0000.0000.0000.000
58B321GLU-1-0.964-0.98223.078-0.061-0.0610.0000.0000.0000.000
59B322LEU0-0.061-0.00821.5290.0120.0120.0000.0000.0000.000
60B323SER00.018-0.00325.445-0.026-0.0260.0000.0000.0000.000
61B324LEU00.018-0.00322.4750.0010.0010.0000.0000.0000.000
62B325PHE00.0400.00622.644-0.019-0.0190.0000.0000.0000.000
63B326ASP-1-0.765-0.84822.336-0.065-0.0650.0000.0000.0000.000
64B327GLN0-0.071-0.04119.584-0.023-0.0230.0000.0000.0000.000
65B328VAL0-0.0060.00217.951-0.014-0.0140.0000.0000.0000.000
66B329ARG10.9130.98617.3070.0110.0110.0000.0000.0000.000
67B330LEU0-0.066-0.03316.7080.0320.0320.0000.0000.0000.000
68B331LEU0-0.007-0.01612.7240.0520.0520.0000.0000.0000.000
69B332GLU-1-0.858-0.94412.656-0.314-0.3140.0000.0000.0000.000
70B333SER0-0.041-0.00412.9780.0700.0700.0000.0000.0000.000
71B334CYS0-0.069-0.01911.0620.1140.1140.0000.0000.0000.000
72B335TRP00.0660.0064.623-0.0850.173-0.001-0.004-0.2530.000
73B336MET00.0330.0233.029-2.7840.2030.774-0.744-3.0180.004
74B337GLU-1-0.847-0.9194.7401.4871.654-0.001-0.004-0.1620.000
75B338VAL0-0.033-0.0186.5330.3060.3060.0000.0000.0000.000
76B339LEU00.0090.0112.546-2.326-0.4583.427-1.347-3.9470.006
77B340MET0-0.0300.0102.249-0.2631.9383.295-1.588-3.908-0.009
78B341MET0-0.0040.0043.1691.0650.7340.0190.507-0.1940.000
79B342GLY0-0.003-0.0035.025-0.256-0.2560.0000.0000.0000.000
80B343LEU0-0.0170.0012.613-2.919-0.6380.639-0.755-2.1660.006
81B344MET0-0.0010.0014.435-1.572-1.3960.001-0.032-0.1440.000
82B345TRP0-0.0110.0057.407-0.497-0.4970.0000.0000.0000.000
83B346ARG10.8270.9082.112-8.825-7.5632.756-1.699-2.3200.023
84B347SER0-0.0100.0047.914-0.214-0.2140.0000.0000.0000.000
85B348ILE00.0040.01710.448-0.150-0.1500.0000.0000.0000.000
86B349ASP-1-0.949-0.97212.9590.7960.7960.0000.0000.0000.000
87B350HIS0-0.043-0.02413.258-0.120-0.1200.0000.0000.0000.000
88B351PRO0-0.014-0.01414.2360.2240.2240.0000.0000.0000.000
89B352GLY0-0.010-0.01014.244-0.098-0.0980.0000.0000.0000.000
90B353LYS10.9060.96212.739-1.278-1.2780.0000.0000.0000.000
91B354LEU00.0060.0136.1360.1170.1170.0000.0000.0000.000
92B355ILE0-0.006-0.0138.255-0.215-0.2150.0000.0000.0000.000
93B356PHE00.0360.0132.888-5.547-1.1911.695-1.575-4.4760.024
94B357ALA00.0340.0144.499-2.174-1.996-0.001-0.014-0.1630.000
95B358PRO0-0.024-0.0137.1190.4210.4210.0000.0000.0000.000
96B359ASP-1-0.887-0.94410.5380.0780.0780.0000.0000.0000.000
97B360LEU0-0.013-0.0035.715-0.104-0.1040.0000.0000.0000.000
98B361VAL0-0.008-0.0088.4010.5490.5490.0000.0000.0000.000
99B362LEU0-0.027-0.0117.078-0.310-0.3100.0000.0000.0000.000
100B363ASP-1-0.850-0.93610.8401.5971.5970.0000.0000.0000.000
101B364ARG10.8680.94010.373-1.162-1.1620.0000.0000.0000.000
102B365ASP-1-0.876-0.93811.0661.0761.0760.0000.0000.0000.000
103B366GLU-1-0.790-0.91711.7240.8750.8750.0000.0000.0000.000
104B367GLY00.0240.0198.741-0.069-0.0690.0000.0000.0000.000
105B368LYS10.8550.9128.891-0.928-0.9280.0000.0000.0000.000
106B369CYS0-0.085-0.01510.916-0.233-0.2330.0000.0000.0000.000
107B370VAL00.0350.0044.717-0.294-0.199-0.001-0.003-0.0910.000
108B371GLU-1-0.933-0.9677.803-1.049-1.0490.0000.0000.0000.000
109B372GLY00.0030.0026.650-0.753-0.7530.0000.0000.0000.000
110B373ILE00.0030.0132.563-2.240-0.5320.852-0.565-1.9950.006
111B374LEU0-0.028-0.0234.9861.9592.009-0.001-0.001-0.0480.000
112B375GLU-1-0.916-0.9567.6440.8720.8720.0000.0000.0000.000
113B376ILE00.0400.0052.466-2.099-0.9872.105-0.761-2.4560.007
114B377PHE00.0330.0033.565-0.5960.2730.014-0.207-0.6760.001
115B378ASP-1-0.818-0.9026.4671.3731.3730.0000.0000.0000.000
116B379MET0-0.037-0.0087.345-0.107-0.1070.0000.0000.0000.000
117B380LEU00.0290.0183.173-1.083-0.4320.022-0.116-0.5560.000
118B381LEU00.0290.0417.812-0.471-0.4710.0000.0000.0000.000
119B382ALA0-0.025-0.00410.726-0.372-0.3720.0000.0000.0000.000
120B383THR00.005-0.01310.629-0.372-0.3720.0000.0000.0000.000
121B384THR0-0.017-0.0369.583-0.171-0.1710.0000.0000.0000.000
122B385SER0-0.039-0.03811.702-0.297-0.2970.0000.0000.0000.000
123B386ARG10.9140.98615.073-1.031-1.0310.0000.0000.0000.000
124B387PHE00.0460.00310.869-0.192-0.1920.0000.0000.0000.000
125B388ARG10.8730.94613.864-1.579-1.5790.0000.0000.0000.000
126B389GLU-1-0.962-0.98116.7340.6570.6570.0000.0000.0000.000
127B390LEU0-0.057-0.02917.862-0.103-0.1030.0000.0000.0000.000
128B391LYS10.9020.96818.889-0.616-0.6160.0000.0000.0000.000
129B392LEU0-0.033-0.00313.093-0.075-0.0750.0000.0000.0000.000
130B393GLN0-0.026-0.01917.110-0.039-0.0390.0000.0000.0000.000
131B394HIS00.0880.03113.7540.1020.1020.0000.0000.0000.000
132B395LYS10.9550.96216.032-0.241-0.2410.0000.0000.0000.000
133B396GLU-1-0.783-0.88717.5600.5360.5360.0000.0000.0000.000
134B397TYR00.0500.0268.8930.0620.0620.0000.0000.0000.000
135B398LEU0-0.044-0.00613.3470.0190.0190.0000.0000.0000.000
136B399CYS0-0.020-0.00314.832-0.055-0.0550.0000.0000.0000.000
137B400VAL00.0370.01212.732-0.036-0.0360.0000.0000.0000.000
138B401LYS10.8180.8928.471-0.350-0.3500.0000.0000.0000.000
139B402ALA00.0240.00911.861-0.068-0.0680.0000.0000.0000.000
140B403MET0-0.057-0.03014.746-0.038-0.0380.0000.0000.0000.000
141B404ILE0-0.0110.0049.861-0.036-0.0360.0000.0000.0000.000
142B405LEU00.0140.00213.020-0.034-0.0340.0000.0000.0000.000
143B406LEU0-0.034-0.02914.137-0.045-0.0450.0000.0000.0000.000
144B407ASN00.000-0.00216.801-0.076-0.0760.0000.0000.0000.000
145B408SER0-0.0490.00814.578-0.002-0.0020.0000.0000.0000.000
146B409SER00.019-0.00516.700-0.042-0.0420.0000.0000.0000.000
147B410MET0-0.062-0.03217.6640.0120.0120.0000.0000.0000.000
148B411TYR00.0380.00119.723-0.025-0.0250.0000.0000.0000.000
149B412PRO00.0530.04820.031-0.007-0.0070.0000.0000.0000.000
150B413LEU0-0.020-0.01323.0940.0170.0170.0000.0000.0000.000
151B414VAL00.0140.01724.571-0.008-0.0080.0000.0000.0000.000
152B415THR0-0.039-0.03126.3700.0010.0010.0000.0000.0000.000
153B416ALA0-0.0040.02429.1070.0100.0100.0000.0000.0000.000
154B417THR0-0.041-0.02730.075-0.014-0.0140.0000.0000.0000.000
155B418GLN0-0.018-0.02332.9410.0020.0020.0000.0000.0000.000
156B419ASP-1-0.908-0.94135.993-0.019-0.0190.0000.0000.0000.000
157B420ALA00.0810.01334.6150.0050.0050.0000.0000.0000.000
158B421ASP-1-0.866-0.91032.344-0.008-0.0080.0000.0000.0000.000
159B422SER0-0.020-0.03226.5550.0060.0060.0000.0000.0000.000
160B423SER00.0290.00426.6250.0150.0150.0000.0000.0000.000
161B424ARG10.8570.90227.3220.0170.0170.0000.0000.0000.000
162B425LYS10.9200.97426.5940.0590.0590.0000.0000.0000.000
163B426LEU00.0290.01720.7170.0040.0040.0000.0000.0000.000
164B427ALA00.0270.01223.8690.0210.0210.0000.0000.0000.000
165B428HIS0-0.015-0.00725.7560.0260.0260.0000.0000.0000.000
166B429LEU0-0.005-0.00322.4430.0110.0110.0000.0000.0000.000
167B430LEU00.0170.01419.6770.0170.0170.0000.0000.0000.000
168B431ASN00.0230.00522.3380.0490.0490.0000.0000.0000.000
169B432ALA00.0240.03124.4150.0120.0120.0000.0000.0000.000
170B433VAL00.0130.00418.2340.0090.0090.0000.0000.0000.000
171B434THR0-0.013-0.00821.6770.0440.0440.0000.0000.0000.000
172B435ASP-1-0.962-0.98822.5770.1770.1770.0000.0000.0000.000
173B436ALA0-0.022-0.01722.1250.0000.0000.0000.0000.0000.000
174B437LEU0-0.022-0.01418.8570.0140.0140.0000.0000.0000.000
175B438VAL00.013-0.00121.9620.0170.0170.0000.0000.0000.000
176B439TRP00.0120.00825.1180.0000.0000.0000.0000.0000.000
177B440VAL0-0.051-0.03221.090-0.005-0.0050.0000.0000.0000.000
178B441ILE00.0280.01221.7450.0030.0030.0000.0000.0000.000
179B442ALA00.0220.05124.881-0.001-0.0010.0000.0000.0000.000
180B443LYS10.8560.93825.630-0.243-0.2430.0000.0000.0000.000
181B444SER0-0.095-0.06825.712-0.002-0.0020.0000.0000.0000.000
182B445GLY00.0060.00127.661-0.001-0.0010.0000.0000.0000.000
183B446ILE0-0.0440.00226.885-0.010-0.0100.0000.0000.0000.000
184B447SER00.0570.01231.013-0.007-0.0070.0000.0000.0000.000
185B448SER00.0640.02131.4690.0190.0190.0000.0000.0000.000
186B449GLN00.0450.00631.4600.0200.0200.0000.0000.0000.000
187B450GLN00.0610.02429.0230.0100.0100.0000.0000.0000.000
188B451GLN0-0.035-0.00127.3120.0280.0280.0000.0000.0000.000
189B452SER00.0100.00826.3620.0190.0190.0000.0000.0000.000
190B453MET0-0.004-0.00526.3470.0270.0270.0000.0000.0000.000
191B454ARG10.8220.90120.105-0.517-0.5170.0000.0000.0000.000
192B455LEU00.0190.00821.6920.0520.0520.0000.0000.0000.000
193B456ALA00.0320.01221.4530.0360.0360.0000.0000.0000.000
194B457ASN0-0.029-0.02621.1980.0450.0450.0000.0000.0000.000
195B458LEU0-0.022-0.00416.8680.0820.0820.0000.0000.0000.000
196B459LEU00.0270.00816.6500.0870.0870.0000.0000.0000.000
197B460MET0-0.052-0.01617.5590.0320.0320.0000.0000.0000.000
198B461LEU0-0.011-0.00114.1750.0350.0350.0000.0000.0000.000
199B462LEU00.0150.00612.7560.1830.1830.0000.0000.0000.000
200B463SER00.0020.01313.2470.0460.0460.0000.0000.0000.000
201B464HIS00.0260.01012.9430.0310.0310.0000.0000.0000.000
202B465VAL00.0070.0077.8340.2980.2980.0000.0000.0000.000
203B466ARG10.9120.9318.742-0.368-0.3680.0000.0000.0000.000
204B467HIS0-0.035-0.01510.415-0.013-0.0130.0000.0000.0000.000
205B468ALA00.0540.0076.112-0.098-0.0980.0000.0000.0000.000
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