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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: V2LV1

Calculation Name: 1QKM-A-Xray165

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: 2020-10-14

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Water(s) essential for molecular recognition.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 232
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2962377.478855
FMO2-HF: Nuclear repulsion 2867108.190997
FMO2-HF: Total energy -95269.287857
FMO2-MP2: Total energy -95536.25392


3D Structure
Snapshot
 
Ligand structure

GEN

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy (frag 1-230,232 : frag 231)
"
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.
-121.0811-101.968280.3182-37.3059-62.12520.1157


Interactive mode: IFIE and PIEDA for fragment #231(A:600:GEN )


Summations of interaction energy for fragment #231(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.
-121.081-101.9780.318-37.305-62.128-0.106
Interaction energy analysis for fragmet #231(A:600:GEN )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.106 / q_NPA : ******
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].
1A266GLU 0-0.00226.235-0.015-0.0150.0000.0000.0000.000
2A267GLN 00.10525.3250.0170.0170.0000.0000.0000.000
3A268LEU 00.03421.430-0.009-0.0090.0000.0000.0000.000
4A269VAL 00.01720.491-0.001-0.0010.0000.0000.0000.000
5A270LEU 00.04720.3390.0070.0070.0000.0000.0000.000
6A271THR 0-0.02020.603-0.024-0.0240.0000.0000.0000.000
7A272LEU 0-0.01216.627-0.027-0.0270.0000.0000.0000.000
8A273LEU 0-0.00816.2490.0040.0040.0000.0000.0000.000
9A274GLU -1-0.93816.510-0.022-0.0220.0000.0000.0000.000
10A275ALA 0-0.11415.693-0.061-0.0610.0000.0000.0000.000
11A276GLU -1-0.85011.5500.3290.3290.0000.0000.0000.000
12A277PRO 0-0.0228.136-0.069-0.0690.0000.0000.0000.000
13A278PRO 0-0.01610.3160.1350.1350.0000.0000.0000.000
14A279HIS 00.0198.835-0.275-0.2750.0000.0000.0000.000
15A280VAL 00.0075.8540.0660.0660.0000.0000.0000.000
16A281LEU 00.0247.471-0.033-0.0330.0000.0000.0000.000
17A282ILE 00.0206.455-0.180-0.1800.0000.0000.0000.000
18A283SER 0-0.0258.8170.0600.0600.0000.0000.0000.000
19A284ARG 10.89211.3090.1400.1400.0000.0000.0000.000
20A285PRO 00.12013.5970.0890.0890.0000.0000.0000.000
21A286SER 00.01317.2260.0510.0510.0000.0000.0000.000
22A287ALA 0-0.06218.6750.0090.0090.0000.0000.0000.000
23A288PRO 0-0.05514.674-0.021-0.0210.0000.0000.0000.000
24A289PHE 00.05814.9870.0530.0530.0000.0000.0000.000
25A290THR 00.01914.755-0.011-0.0110.0000.0000.0000.000
26A291GLU -1-0.79712.722-0.326-0.3260.0000.0000.0000.000
27A292ALA 0-0.0789.9510.0560.0560.0000.0000.0000.000
28A293SER 0-0.01710.539-0.054-0.0540.0000.0000.0000.000
29A294MET 00.0127.337-0.025-0.0250.0000.0000.0000.000
30A295MET 00.0412.546-1.295-0.7313.707-1.067-3.2040.012
31A296MET 00.0045.560-0.363-0.3630.0000.0000.0000.000
32A297SER 0-0.0617.292-0.489-0.4890.0000.0000.0000.000
33A298LEU 00.0252.919-5.497-1.3241.293-1.039-4.4270.010
34A299THR 00.0032.618-11.578-6.8661.531-2.147-4.096-0.020
35A300LYS 10.9334.1520.8841.1250.000-0.017-0.2240.000
36A301LEU 0-0.0392.341-0.5430.9021.722-0.707-2.4600.005
37A302ALA 00.0202.112-2.367-0.9072.168-1.235-2.3930.000
38A303ASP -1-0.8783.921-0.822-0.5260.027-0.118-0.2050.000
39A304LYS 10.9146.7832.4452.4450.0000.0000.0000.000
40A305GLU -1-0.7851.504-36.945-49.36732.063-13.930-5.712-0.117
41A306LEU 00.0305.9881.0481.0480.0000.0000.0000.000
42A307VAL 00.0598.3970.4560.4560.0000.0000.0000.000
43A308HIS 0-0.0438.5450.4890.4890.0000.0000.0000.000
44A309MET 0-0.0147.8130.4020.4020.0000.0000.0000.000
45A310ILE 00.0789.7460.2670.2670.0000.0000.0000.000
46A311SER 0-0.06813.0200.1630.1630.0000.0000.0000.000
47A312TRP 0-0.06111.6340.1280.1280.0000.0000.0000.000
48A313ALA 00.06213.4860.0850.0850.0000.0000.0000.000
49A314LYS 10.93615.2640.3530.3530.0000.0000.0000.000
50A315LYS 10.92515.9150.3050.3050.0000.0000.0000.000
51A316ILE 0-0.01315.1240.0450.0450.0000.0000.0000.000
52A317PRO 0-0.02619.176-0.017-0.0170.0000.0000.0000.000
53A318GLY 00.05322.8680.0210.0210.0000.0000.0000.000
54A319PHE 00.03217.853-0.002-0.0020.0000.0000.0000.000
55A320VAL 00.00021.413-0.014-0.0140.0000.0000.0000.000
56A321GLU -1-0.95123.263-0.052-0.0520.0000.0000.0000.000
57A322LEU 0-0.05121.6960.0120.0120.0000.0000.0000.000
58A323SER 00.01025.557-0.024-0.0240.0000.0000.0000.000
59A324LEU 00.08723.1260.0060.0060.0000.0000.0000.000
60A325PHE 0-0.05623.150-0.019-0.0190.0000.0000.0000.000
61A326ASP 0-0.05422.6670.0060.0060.0000.0000.0000.000
62A327GLN 0-0.04920.036-0.009-0.0090.0000.0000.0000.000
63A328VAL 00.06418.3890.0030.0030.0000.0000.0000.000
64A329ARG 10.93117.6210.0810.0810.0000.0000.0000.000
65A330LEU 0-0.01916.8030.0290.0290.0000.0000.0000.000
66A331LEU 00.02213.3960.0660.0660.0000.0000.0000.000
67A332GLU -1-0.88213.023-0.172-0.1720.0000.0000.0000.000
68A333SER 0-0.05112.8550.0500.0500.0000.0000.0000.000
69A334CYS 00.01210.5650.0610.0610.0000.0000.0000.000
70A335TRP 00.0134.140-0.0610.3230.000-0.023-0.3610.000
71A336MET 00.0503.030-2.3980.7170.886-0.714-3.2870.005
72A337GLU -1-0.8355.0471.7971.940-0.001-0.001-0.1410.000
73A338VAL 0-0.0296.6360.3300.3300.0000.0000.0000.000
74A339LEU 0-0.0112.716-2.708-0.1692.490-1.278-3.7510.009
75A340MET 0-0.0322.548-2.2081.5681.524-1.537-3.762-0.008
76A341MET 00.0073.3670.4000.3130.0060.222-0.1430.000
77A342GLY 00.0045.383-0.339-0.3390.0000.0000.0000.000
78A343LEU 00.0122.687-2.951-0.8080.577-0.725-1.9950.006
79A344MET 0-0.0284.601-1.396-1.2610.000-0.015-0.1190.000
80A345TRP 0-0.0157.520-0.449-0.4490.0000.0000.0000.000
81A346ARG 10.7762.192-5.584-4.7922.337-1.217-1.9110.012
82A347SER 0-0.0137.656-0.246-0.2460.0000.0000.0000.000
83A348ILE 0-0.03110.361-0.134-0.1340.0000.0000.0000.000
84A349ASP -1-0.90412.8720.8030.8030.0000.0000.0000.000
85A350HIS 0-0.06913.654-0.152-0.1520.0000.0000.0000.000
86A351PRO 0-0.00414.1500.2180.2180.0000.0000.0000.000
87A352GLY 0-0.00814.116-0.104-0.1040.0000.0000.0000.000
88A353LYS 10.94912.623-1.005-1.0050.0000.0000.0000.000
89A354LEU 0-0.0026.1240.1350.1350.0000.0000.0000.000
90A355ILE 0-0.0208.494-0.226-0.2260.0000.0000.0000.000
91A356PHE 00.0512.639-6.460-2.1452.522-1.494-5.3430.022
92A357ALA 0-0.0074.221-2.239-2.0390.000-0.029-0.1710.000
93A358PRO 0-0.0276.8390.3850.3850.0000.0000.0000.000
94A359ASP -1-0.89210.522-0.098-0.0980.0000.0000.0000.000
95A360LEU 0-0.0835.701-0.190-0.1900.0000.0000.0000.000
96A361VAL 0-0.0278.3530.5020.5020.0000.0000.0000.000
97A362LEU 00.0127.072-0.143-0.1430.0000.0000.0000.000
98A363ASP -1-0.88410.9381.3911.3910.0000.0000.0000.000
99A364ARG 10.82210.710-1.084-1.0840.0000.0000.0000.000
100A365ASP -1-0.89711.2040.8840.8840.0000.0000.0000.000
101A366GLU -1-0.86911.3620.8660.8660.0000.0000.0000.000
102A367GLY 0-0.0098.699-0.024-0.0240.0000.0000.0000.000
103A368LYS 10.8929.430-0.962-0.9620.0000.0000.0000.000
104A369CYS 0-0.05511.733-0.162-0.1620.0000.0000.0000.000
105A370VAL 0-0.0025.920-0.186-0.1860.0000.0000.0000.000
106A371GLU -1-0.8568.391-0.470-0.4700.0000.0000.0000.000
107A372GLY 00.0186.588-1.148-1.1480.0000.0000.0000.000
108A373ILE 0-0.0152.727-1.1400.0150.809-0.420-1.5450.002
109A374LEU 0-0.0105.5561.5671.5670.0000.0000.0000.000
110A375GLU -1-0.8828.0140.5260.5260.0000.0000.0000.000
111A376ILE 00.0282.602-1.743-0.3461.224-0.624-1.9970.007
112A377PHE 00.0343.8900.1540.6460.001-0.058-0.4340.000
113A378ASP -1-0.7836.7691.2631.2630.0000.0000.0000.000
114A379MET 0-0.0628.047-0.146-0.1460.0000.0000.0000.000
115A380LEU 00.0233.441-0.942-0.4420.006-0.069-0.4370.000
116A381LEU 00.0358.117-0.517-0.5170.0000.0000.0000.000
117A382ALA 0-0.01310.968-0.365-0.3650.0000.0000.0000.000
118A383THR 0-0.01310.455-0.344-0.3440.0000.0000.0000.000
119A384THR 00.0049.413-0.182-0.1820.0000.0000.0000.000
120A385SER 0-0.03511.659-0.312-0.3120.0000.0000.0000.000
121A386ARG 10.89015.107-1.030-1.0300.0000.0000.0000.000
122A387PHE 00.02911.097-0.164-0.1640.0000.0000.0000.000
123A388ARG 10.90014.694-1.403-1.4030.0000.0000.0000.000
124A389GLU -1-0.96516.8980.5660.5660.0000.0000.0000.000
125A390LEU 00.00518.014-0.086-0.0860.0000.0000.0000.000
126A391LYS 10.94919.458-0.627-0.6270.0000.0000.0000.000
127A392LEU 0-0.02313.720-0.069-0.0690.0000.0000.0000.000
128A393GLN 0-0.03917.672-0.048-0.0480.0000.0000.0000.000
129A394HIS 00.09216.4600.0420.0420.0000.0000.0000.000
130A395LYS 10.91916.889-0.345-0.3450.0000.0000.0000.000
131A396GLU -1-0.73818.2290.5560.5560.0000.0000.0000.000
132A397TYR 00.0569.1740.1170.1170.0000.0000.0000.000
133A398LEU 0-0.01913.8850.0290.0290.0000.0000.0000.000
134A399CYS 0-0.05415.495-0.050-0.0500.0000.0000.0000.000
135A400VAL 00.05512.707-0.028-0.0280.0000.0000.0000.000
136A401LYS 10.8628.919-0.558-0.5580.0000.0000.0000.000
137A402ALA 00.01212.249-0.044-0.0440.0000.0000.0000.000
138A403MET 0-0.04315.145-0.043-0.0430.0000.0000.0000.000
139A404ILE 0-0.0219.958-0.030-0.0300.0000.0000.0000.000
140A405LEU 00.01113.218-0.036-0.0360.0000.0000.0000.000
141A406LEU 0-0.03413.995-0.066-0.0660.0000.0000.0000.000
142A407ASN 0-0.02816.568-0.106-0.1060.0000.0000.0000.000
143A408SER 0-0.00914.0390.0500.0500.0000.0000.0000.000
144A409SER 00.01215.880-0.019-0.0190.0000.0000.0000.000
145A410MET 00.04718.8540.0000.0000.0000.0000.0000.000
146A411TYR 0-0.01021.173-0.017-0.0170.0000.0000.0000.000
147A412PRO 00.01421.368-0.010-0.0100.0000.0000.0000.000
148A413LEU 0-0.00923.685-0.004-0.0040.0000.0000.0000.000
149A414VAL 0-0.02626.190-0.004-0.0040.0000.0000.0000.000
150A415THR 0-0.05426.714-0.009-0.0090.0000.0000.0000.000
151A416ALA 00.01326.270-0.017-0.0170.0000.0000.0000.000
152A417THR 0-0.01628.245-0.002-0.0020.0000.0000.0000.000
153A418GLN 00.00328.7080.0040.0040.0000.0000.0000.000
154A419ASP -1-0.74726.726-0.015-0.0150.0000.0000.0000.000
155A420ALA 00.03730.2470.0110.0110.0000.0000.0000.000
156A421ASP -1-0.90631.8490.0070.0070.0000.0000.0000.000
157A422SER 00.05026.4220.0050.0050.0000.0000.0000.000
158A423SER 00.03227.3530.0150.0150.0000.0000.0000.000
159A424ARG 10.90628.037-0.030-0.0300.0000.0000.0000.000
160A425LYS 10.83927.4440.0250.0250.0000.0000.0000.000
161A426LEU 00.04820.9210.0090.0090.0000.0000.0000.000
162A427ALA 00.02824.1960.0270.0270.0000.0000.0000.000
163A428HIS 0-0.01526.2180.0230.0230.0000.0000.0000.000
164A429LEU 00.00722.1130.0110.0110.0000.0000.0000.000
165A430LEU 0-0.00119.5920.0240.0240.0000.0000.0000.000
166A431ASN 00.02022.6300.0490.0490.0000.0000.0000.000
167A432ALA 00.02224.9590.0110.0110.0000.0000.0000.000
168A433VAL 0-0.02618.6890.0110.0110.0000.0000.0000.000
169A434THR 0-0.01622.1150.0460.0460.0000.0000.0000.000
170A435ASP -1-0.90123.1350.2140.2140.0000.0000.0000.000
171A436ALA 0-0.08722.781-0.001-0.0010.0000.0000.0000.000
172A437LEU 00.02819.3420.0100.0100.0000.0000.0000.000
173A438VAL 00.01222.5790.0080.0080.0000.0000.0000.000
174A439TRP 0-0.03325.041-0.002-0.0020.0000.0000.0000.000
175A440VAL 0-0.04521.956-0.009-0.0090.0000.0000.0000.000
176A441ILE 0-0.00722.4550.0010.0010.0000.0000.0000.000
177A442ALA 00.01825.774-0.005-0.0050.0000.0000.0000.000
178A443LYS 10.88027.910-0.224-0.2240.0000.0000.0000.000
179A444SER 0-0.10126.658-0.008-0.0080.0000.0000.0000.000
180A445GLY 00.02028.6740.0000.0000.0000.0000.0000.000
181A446ILE 0-0.03627.618-0.012-0.0120.0000.0000.0000.000
182A447SER 00.05031.810-0.006-0.0060.0000.0000.0000.000
183A448SER 00.10232.1560.0110.0110.0000.0000.0000.000
184A449GLN 00.00232.0260.0280.0280.0000.0000.0000.000
185A450GLN 00.03829.7280.0120.0120.0000.0000.0000.000
186A451GLN 0-0.03528.0200.0280.0280.0000.0000.0000.000
187A452SER 00.00227.0340.0200.0200.0000.0000.0000.000
188A453MET 0-0.03026.5100.0280.0280.0000.0000.0000.000
189A454ARG 10.78320.644-0.536-0.5360.0000.0000.0000.000
190A455LEU 00.02722.2770.0550.0550.0000.0000.0000.000
191A456ALA 00.02721.9900.0380.0380.0000.0000.0000.000
192A457ASN 0-0.04621.3290.0310.0310.0000.0000.0000.000
193A458LEU 00.00117.3360.0830.0830.0000.0000.0000.000
194A459LEU 00.01917.1190.0830.0830.0000.0000.0000.000
195A460MET 0-0.02618.1430.0320.0320.0000.0000.0000.000
196A461LEU 0-0.00914.5010.0450.0450.0000.0000.0000.000
197A462LEU 00.01913.5640.1840.1840.0000.0000.0000.000
198A463SER 0-0.00713.7090.0350.0350.0000.0000.0000.000
199A464HIS 0-0.02113.4590.0690.0690.0000.0000.0000.000
200A465VAL 00.0038.1130.2670.2670.0000.0000.0000.000
201A466ARG 10.8869.332-0.464-0.4640.0000.0000.0000.000
202A467HIS 0-0.02610.9800.1260.1260.0000.0000.0000.000
203A468ALA 00.0646.755-0.098-0.0980.0000.0000.0000.000
204A469SER 00.0446.3640.5990.5990.0000.0000.0000.000
205A470ASN 0-0.0107.553-0.303-0.3030.0000.0000.0000.000
206A471LYS 10.9256.799-0.938-0.9380.0000.0000.0000.000
207A472GLY 00.0263.266-1.560-0.8670.097-0.269-0.5210.001
208A473MET 0-0.0373.918-3.233-2.3200.072-0.250-0.736-0.001
209A474GLU -1-0.9486.205-0.993-0.9930.0000.0000.0000.000
210A475HIS 0-0.0151.741-27.054-34.62420.568-7.386-5.612-0.065
211A476LEU 00.0122.225-2.999-0.4063.601-1.435-4.7600.005
212A477LEU 0-0.0233.2170.659-0.2870.2811.242-0.5780.003
213A478ASN 0-0.0175.8980.6010.6010.0000.0000.0000.000
214A479MET 0-0.0653.527-0.5260.0400.021-0.148-0.4400.001
215A480LYS 10.9196.4351.1241.1240.0000.0000.0000.000
216A481CYS 00.0629.3480.0200.0200.0000.0000.0000.000
217A482LYS 10.95810.4380.5580.5580.0000.0000.0000.000
218A483ASN 0-0.0698.8890.1250.1250.0000.0000.0000.000
219A484VAL 0-0.0254.497-0.1380.025-0.001-0.014-0.1480.000
220A485VAL 00.0666.7140.1150.1150.0000.0000.0000.000
221A486PRO 00.0276.662-0.136-0.1360.0000.0000.0000.000
222A487VAL 00.0064.166-0.2000.0020.000-0.013-0.1890.000
223A488TYR 0-0.0847.5770.0560.0560.0000.0000.0000.000
224A489ASP -1-0.8649.787-0.646-0.6460.0000.0000.0000.000
225A490LEU 00.0089.7640.0500.0500.0000.0000.0000.000
226A491LEU 0-0.0429.9200.0360.0360.0000.0000.0000.000
227A492LEU 0-0.04611.8090.1140.1140.0000.0000.0000.000
228A493GLU -1-0.98314.969-0.674-0.6740.0000.0000.0000.000
229A494MET 0-0.14610.3780.0360.0360.0000.0000.0000.000
230A495LEU -1-0.99814.619-0.341-0.3410.0000.0000.0000.000
232A2026HOH 0-0.0292.605-1.717-0.6880.787-0.790-1.0260.005