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: P58ZX

Calculation Name: 1QKM-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: genistein

ligand 3-letter code: GEN

PDB ID: 1QKM

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 -3023494.866444
FMO2-HF: Nuclear repulsion 2926998.190598
FMO2-HF: Total energy -96496.675846
FMO2-MP2: Total energy -96767.216286


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.
-118.021-95.22669.547-31.439-60.8990.101


Interactive mode: IFIE and PIEDA for fragment #235(A:600:GEN)


Summations of interaction energy for fragment #235(A:600: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.
-118.021-95.22669.547-31.439-60.899-0.101
Interaction energy analysis for fragmet #235(A:600:GEN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.099 / q_NPA : -0.120
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].
1A264SER10.8590.92327.874-0.040-0.0400.0000.0000.0000.000
2A265PRO00.1880.07926.047-0.014-0.0140.0000.0000.0000.000
3A266GLU-1-0.825-0.91125.2540.0940.0940.0000.0000.0000.000
4A267GLN00.002-0.00525.4170.0080.0080.0000.0000.0000.000
5A268LEU0-0.035-0.00421.518-0.017-0.0170.0000.0000.0000.000
6A269VAL00.025-0.00320.616-0.008-0.0080.0000.0000.0000.000
7A270LEU00.0310.02320.404-0.006-0.0060.0000.0000.0000.000
8A271THR0-0.033-0.02320.649-0.027-0.0270.0000.0000.0000.000
9A272LEU0-0.019-0.01116.675-0.035-0.0350.0000.0000.0000.000
10A273LEU0-0.010-0.01216.316-0.017-0.0170.0000.0000.0000.000
11A274GLU-1-0.941-0.97516.598-0.165-0.1650.0000.0000.0000.000
12A275ALA0-0.114-0.03715.742-0.062-0.0620.0000.0000.0000.000
13A276GLU-1-0.850-0.90311.640-0.060-0.0600.0000.0000.0000.000
14A277PRO0-0.025-0.0188.217-0.051-0.0510.0000.0000.0000.000
15A278PRO0-0.0150.01110.4090.1560.1560.0000.0000.0000.000
16A279HIS00.012-0.0098.949-0.311-0.3110.0000.0000.0000.000
17A280VAL0-0.0030.0035.9560.0760.0760.0000.0000.0000.000
18A281LEU00.0110.0107.585-0.006-0.0060.0000.0000.0000.000
19A282ILE0-0.0090.0046.404-0.311-0.3110.0000.0000.0000.000
20A283SER0-0.007-0.0178.7570.0570.0570.0000.0000.0000.000
21A284ARG10.8120.91512.5360.2500.2500.0000.0000.0000.000
22A285PRO00.0130.01414.0150.0630.0630.0000.0000.0000.000
23A286SER0-0.004-0.00316.9400.0490.0490.0000.0000.0000.000
24A287ALA0-0.024-0.00317.8870.0510.0510.0000.0000.0000.000
25A288PRO0-0.017-0.01318.403-0.021-0.0210.0000.0000.0000.000
26A289PHE00.0650.02115.866-0.054-0.0540.0000.0000.0000.000
27A290THR0-0.025-0.02715.4420.0330.0330.0000.0000.0000.000
28A291GLU-1-0.834-0.90916.793-0.081-0.0810.0000.0000.0000.000
29A292ALA00.0020.00814.132-0.036-0.0360.0000.0000.0000.000
30A293SER00.029-0.00111.4530.0800.0800.0000.0000.0000.000
31A294MET00.0160.0347.419-0.100-0.1000.0000.0000.0000.000
32A295MET00.0650.0372.562-1.709-0.8963.075-0.942-2.9460.010
33A296MET0-0.0150.0155.521-0.292-0.2920.0000.0000.0000.000
34A297SER0-0.036-0.0277.217-0.547-0.5470.0000.0000.0000.000
35A298LEU00.0310.0102.971-5.219-1.2901.129-0.980-4.0780.010
36A299THR0-0.0060.0052.546-11.028-6.6381.479-2.005-3.864-0.019
37A300LYS10.9060.9624.3620.8421.0660.000-0.020-0.2040.000
38A301LEU0-0.025-0.0132.364-0.5740.8421.276-0.599-2.0920.003
39A302ALA00.0340.0182.185-2.527-0.8721.555-1.031-2.180-0.001
40A303ASP-1-0.893-0.9493.967-0.911-0.6500.022-0.103-0.1800.000
41A304LYS10.9200.9566.8472.6162.6160.0000.0000.0000.000
42A305GLU-1-0.859-0.9211.619-39.475-45.33122.156-10.226-6.075-0.110
43A306LEU00.0180.0035.9951.1061.1060.0000.0000.0000.000
44A307VAL00.0580.0458.3530.5320.5320.0000.0000.0000.000
45A308HIS0-0.036-0.0318.5900.5460.5460.0000.0000.0000.000
46A309MET0-0.0200.0047.7910.3930.3930.0000.0000.0000.000
47A310ILE00.0730.0409.7400.3210.3210.0000.0000.0000.000
48A311SER0-0.060-0.03313.0230.2100.2100.0000.0000.0000.000
49A312TRP0-0.062-0.03911.6250.1420.1420.0000.0000.0000.000
50A313ALA00.0580.02313.4840.1140.1140.0000.0000.0000.000
51A314LYS10.9460.97615.2580.5120.5120.0000.0000.0000.000
52A315LYS10.9240.97015.9740.5120.5120.0000.0000.0000.000
53A316ILE0-0.0130.01715.1240.0560.0560.0000.0000.0000.000
54A317PRO0-0.033-0.04019.191-0.005-0.0050.0000.0000.0000.000
55A318GLY00.0480.02122.8690.0200.0200.0000.0000.0000.000
56A319PHE00.0340.01717.8080.0040.0040.0000.0000.0000.000
57A320VAL00.010-0.00521.398-0.009-0.0090.0000.0000.0000.000
58A321GLU-1-0.974-0.97923.244-0.107-0.1070.0000.0000.0000.000
59A322LEU0-0.050-0.00521.6520.0210.0210.0000.0000.0000.000
60A323SER00.0230.01225.516-0.028-0.0280.0000.0000.0000.000
61A324LEU00.0750.01323.0750.0000.0000.0000.0000.0000.000
62A325PHE0-0.0190.01023.095-0.020-0.0200.0000.0000.0000.000
63A326ASP-1-0.733-0.87222.607-0.047-0.0470.0000.0000.0000.000
64A327GLN0-0.076-0.04319.986-0.030-0.0300.0000.0000.0000.000
65A328VAL00.0550.01818.366-0.022-0.0220.0000.0000.0000.000
66A329ARG10.8930.95917.2570.0330.0330.0000.0000.0000.000
67A330LEU0-0.0150.00316.7560.0330.0330.0000.0000.0000.000
68A331LEU00.025-0.00713.3410.0320.0320.0000.0000.0000.000
69A332GLU-1-0.843-0.88612.949-0.166-0.1660.0000.0000.0000.000
70A333SER0-0.081-0.05812.7770.0580.0580.0000.0000.0000.000
71A334CYS0-0.0130.03811.5770.0810.0810.0000.0000.0000.000
72A335TRP00.043-0.0014.073-0.2070.1940.000-0.023-0.3770.000
73A336MET00.0390.0273.017-2.9490.2020.899-0.749-3.3020.005
74A337GLU-1-0.837-0.9154.9641.4011.551-0.001-0.002-0.1470.000
75A338VAL0-0.018-0.0066.6160.2860.2860.0000.0000.0000.000
76A339LEU0-0.0010.0082.725-2.4900.0622.274-1.213-3.6120.007
77A340MET0-0.054-0.0162.561-2.4841.3011.672-1.549-3.909-0.007
78A341MET00.0110.0123.3710.6260.5480.0070.211-0.1390.000
79A342GLY0-0.005-0.0015.398-0.182-0.1820.0000.0000.0000.000
80A343LEU00.0180.0152.760-2.341-0.4640.315-0.601-1.5900.004
81A344MET0-0.039-0.0094.668-1.246-1.1230.000-0.011-0.1120.000
82A345TRP0-0.011-0.0107.581-0.361-0.3610.0000.0000.0000.000
83A346ARG10.8610.9242.185-7.747-6.7262.238-1.307-1.9510.017
84A347SER0-0.014-0.0087.730-0.201-0.2010.0000.0000.0000.000
85A348ILE0-0.030-0.00410.433-0.106-0.1060.0000.0000.0000.000
86A349ASP-1-0.905-0.95412.9410.6860.6860.0000.0000.0000.000
87A350HIS0-0.062-0.03413.721-0.125-0.1250.0000.0000.0000.000
88A351PRO0-0.004-0.00914.2210.2080.2080.0000.0000.0000.000
89A352GLY0-0.007-0.00214.278-0.093-0.0930.0000.0000.0000.000
90A353LYS10.8880.94212.772-1.018-1.0180.0000.0000.0000.000
91A354LEU0-0.016-0.0056.2610.1110.1110.0000.0000.0000.000
92A355ILE0-0.012-0.0158.430-0.209-0.2090.0000.0000.0000.000
93A356PHE00.0280.0062.909-5.558-1.4032.053-1.348-4.8590.020
94A357ALA00.0180.0074.332-1.784-1.5860.000-0.023-0.1750.000
95A358PRO00.0050.0087.0180.4320.4320.0000.0000.0000.000
96A359ASP-1-0.877-0.9669.693-1.001-1.0010.0000.0000.0000.000
97A360LEU0-0.030-0.0135.306-0.176-0.1760.0000.0000.0000.000
98A361VAL0-0.021-0.0077.9870.4150.4150.0000.0000.0000.000
99A362LEU00.0010.0097.262-0.139-0.1390.0000.0000.0000.000
100A363ASP-1-0.844-0.90211.1291.2541.2540.0000.0000.0000.000
101A364ARG10.8390.89410.863-1.095-1.0950.0000.0000.0000.000
102A365ASP-1-0.894-0.97011.3260.8930.8930.0000.0000.0000.000
103A366GLU-1-0.872-0.93811.5410.8090.8090.0000.0000.0000.000
104A367GLY0-0.007-0.0178.800-0.010-0.0100.0000.0000.0000.000
105A368LYS10.8960.9379.463-0.932-0.9320.0000.0000.0000.000
106A369CYS0-0.054-0.01411.738-0.154-0.1540.0000.0000.0000.000
107A370VAL0-0.013-0.0035.864-0.163-0.1630.0000.0000.0000.000
108A371GLU-1-0.855-0.9288.306-0.217-0.2170.0000.0000.0000.000
109A372GLY00.0240.0216.485-1.052-1.0520.0000.0000.0000.000
110A373ILE0-0.016-0.0012.681-1.0530.0720.802-0.421-1.5060.003
111A374LEU0-0.015-0.0065.5411.4121.4120.0000.0000.0000.000
112A375GLU-1-0.914-0.9507.9740.7380.7380.0000.0000.0000.000
113A376ILE00.0310.0142.569-2.046-0.5751.323-0.689-2.1060.007
114A377PHE00.027-0.0054.0590.0570.4760.000-0.035-0.3830.000
115A378ASP-1-0.784-0.8646.8351.2431.2430.0000.0000.0000.000
116A379MET0-0.059-0.0097.986-0.107-0.1070.0000.0000.0000.000
117A380LEU00.0230.0113.505-0.942-0.4540.006-0.067-0.4270.000
118A381LEU00.0310.0188.176-0.530-0.5300.0000.0000.0000.000
119A382ALA0-0.0120.01011.076-0.358-0.3580.0000.0000.0000.000
120A383THR0-0.010-0.02910.491-0.333-0.3330.0000.0000.0000.000
121A384THR00.004-0.0039.469-0.195-0.1950.0000.0000.0000.000
122A385SER0-0.036-0.03011.715-0.298-0.2980.0000.0000.0000.000
123A386ARG10.8900.95715.156-0.945-0.9450.0000.0000.0000.000
124A387PHE00.0310.01211.130-0.154-0.1540.0000.0000.0000.000
125A388ARG10.8990.94714.761-1.276-1.2760.0000.0000.0000.000
126A389GLU-1-0.967-0.97616.9590.5050.5050.0000.0000.0000.000
127A390LEU00.0050.00418.054-0.079-0.0790.0000.0000.0000.000
128A391LYS10.9480.98019.514-0.547-0.5470.0000.0000.0000.000
129A392LEU0-0.0240.00413.767-0.065-0.0650.0000.0000.0000.000
130A393GLN0-0.039-0.03117.724-0.047-0.0470.0000.0000.0000.000
131A394HIS00.0900.03616.5570.0220.0220.0000.0000.0000.000
132A395LYS10.9290.96216.999-0.248-0.2480.0000.0000.0000.000
133A396GLU-1-0.739-0.83418.2660.4400.4400.0000.0000.0000.000
134A397TYR00.0510.0249.2930.0870.0870.0000.0000.0000.000
135A398LEU0-0.0160.00013.9060.0100.0100.0000.0000.0000.000
136A399CYS0-0.048-0.02015.621-0.052-0.0520.0000.0000.0000.000
137A400VAL00.0500.00912.719-0.024-0.0240.0000.0000.0000.000
138A401LYS10.8590.9259.057-0.076-0.0760.0000.0000.0000.000
139A402ALA00.0150.00312.251-0.056-0.0560.0000.0000.0000.000
140A403MET0-0.044-0.02415.135-0.027-0.0270.0000.0000.0000.000
141A404ILE0-0.023-0.0069.937-0.010-0.0100.0000.0000.0000.000
142A405LEU00.0070.01513.185-0.019-0.0190.0000.0000.0000.000
143A406LEU0-0.028-0.03313.962-0.033-0.0330.0000.0000.0000.000
144A407ASN0-0.027-0.01016.540-0.073-0.0730.0000.0000.0000.000
145A408SER0-0.009-0.01313.9970.0640.0640.0000.0000.0000.000
146A409SER0-0.0070.00815.8370.0160.0160.0000.0000.0000.000
147A410MET00.0400.00718.760-0.004-0.0040.0000.0000.0000.000
148A411TYR0-0.034-0.01621.061-0.012-0.0120.0000.0000.0000.000
149A412PRO00.0490.02021.317-0.005-0.0050.0000.0000.0000.000
150A413LEU0-0.030-0.01422.750-0.006-0.0060.0000.0000.0000.000
151A414VAL0-0.033-0.01026.1360.0040.0040.0000.0000.0000.000
152A415THR0-0.009-0.02529.242-0.006-0.0060.0000.0000.0000.000
153A416ALA0-0.046-0.01831.612-0.007-0.0070.0000.0000.0000.000
154A417THR0-0.078-0.04527.001-0.006-0.0060.0000.0000.0000.000
155A418GLN0-0.037-0.00827.079-0.001-0.0010.0000.0000.0000.000
156A419ASP-1-0.782-0.88229.891-0.068-0.0680.0000.0000.0000.000
157A420ALA0-0.013-0.00932.0350.0120.0120.0000.0000.0000.000
158A421ASP-1-0.873-0.93331.654-0.042-0.0420.0000.0000.0000.000
159A422SER00.002-0.01926.3860.0030.0030.0000.0000.0000.000
160A423SER00.0500.04327.3110.0110.0110.0000.0000.0000.000
161A424ARG10.9080.94627.9980.0040.0040.0000.0000.0000.000
162A425LYS10.8030.89627.4090.0770.0770.0000.0000.0000.000
163A426LEU00.0520.04320.8850.0060.0060.0000.0000.0000.000
164A427ALA00.0240.01824.1660.0210.0210.0000.0000.0000.000
165A428HIS0-0.019-0.01026.1950.0210.0210.0000.0000.0000.000
166A429LEU00.0040.00122.0930.0090.0090.0000.0000.0000.000
167A430LEU00.0010.00519.5700.0160.0160.0000.0000.0000.000
168A431ASN00.0220.00622.6110.0440.0440.0000.0000.0000.000
169A432ALA00.0010.01524.9480.0110.0110.0000.0000.0000.000
170A433VAL0-0.019-0.01618.6850.0080.0080.0000.0000.0000.000
171A434THR0-0.015-0.00622.1110.0420.0420.0000.0000.0000.000
172A435ASP-1-0.910-0.96123.1350.1470.1470.0000.0000.0000.000
173A436ALA0-0.088-0.04622.7750.0010.0010.0000.0000.0000.000
174A437LEU00.0370.01319.3560.0100.0100.0000.0000.0000.000
175A438VAL00.0050.00222.5940.0120.0120.0000.0000.0000.000
176A439TRP0-0.029-0.01225.1690.0010.0010.0000.0000.0000.000
177A440VAL0-0.032-0.03021.988-0.005-0.0050.0000.0000.0000.000
178A441ILE0-0.013-0.00322.4790.0050.0050.0000.0000.0000.000
179A442ALA00.0160.03525.805-0.001-0.0010.0000.0000.0000.000
180A443LYS10.8740.94127.942-0.145-0.1450.0000.0000.0000.000
181A444SER0-0.102-0.05926.697-0.004-0.0040.0000.0000.0000.000
182A445GLY00.0180.01128.7150.0020.0020.0000.0000.0000.000
183A446ILE0-0.0370.00127.657-0.008-0.0080.0000.0000.0000.000
184A447SER00.0460.01931.850-0.006-0.0060.0000.0000.0000.000
185A448SER00.1040.03932.1880.0130.0130.0000.0000.0000.000
186A449GLN00.001-0.01032.0520.0250.0250.0000.0000.0000.000
187A450GLN00.0360.02029.7660.0130.0130.0000.0000.0000.000
188A451GLN0-0.029-0.02228.0500.0230.0230.0000.0000.0000.000
189A452SER00.0010.00627.0590.0160.0160.0000.0000.0000.000
190A453MET0-0.032-0.01826.5410.0260.0260.0000.0000.0000.000
191A454ARG10.7820.86920.687-0.442-0.4420.0000.0000.0000.000
192A455LEU00.0280.00722.2920.0470.0470.0000.0000.0000.000
193A456ALA00.0270.01322.0070.0330.0330.0000.0000.0000.000
194A457ASN0-0.047-0.03621.3600.0290.0290.0000.0000.0000.000
195A458LEU00.0020.00517.3670.0770.0770.0000.0000.0000.000
196A459LEU00.0210.00317.1360.0710.0710.0000.0000.0000.000
197A460MET0-0.028-0.02018.1470.0340.0340.0000.0000.0000.000
198A461LEU0-0.0100.00114.5310.0530.0530.0000.0000.0000.000
199A462LEU00.0200.01713.5660.1700.1700.0000.0000.0000.000
200A463SER0-0.0080.00213.7010.0350.0350.0000.0000.0000.000
201A464HIS0-0.020-0.00813.4010.0930.0930.0000.0000.0000.000
202A465VAL00.002-0.0018.1140.2820.2820.0000.0000.0000.000
203A466ARG10.8850.9429.245-0.383-0.3830.0000.0000.0000.000
204A467HIS0-0.026-0.01810.8800.1740.1740.0000.0000.0000.000
205A468ALA00.0660.0186.676-0.014-0.0140.0000.0000.0000.000
206A469SER00.0400.0106.2450.7370.7370.0000.0000.0000.000
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