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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: J3Q49

Calculation Name: 7XVZ-BDFW-Xray333

Preferred Name:

Target Type:

Ligand Name: (2~{r})-3-(2-chloranyl-4-oxidanyl-phenyl)-2-(4-hydroxyphenyl)propanenitrile

ligand 3-letter code: I1D

PDB ID: 7XVZ

Chain ID: BDFW

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2022-08-10

Reference: Chiaki Handa et al., Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives, J. Steroid Biochem. Mol. Biol. 222, 106152, (2022).

DOI: 10.1016/j.jsbmb.2022.106152


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSide
Protonation MOE:Protonate 3D + manually
Complement MOE:manually
Water Water(s) essential for molecular recognition.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2954225.183878
FMO2-HF: Nuclear repulsion 2860856.413696
FMO2-HF: Total energy -93368.770182
FMO2-MP2: Total energy -93632.695259


3D Structure
Snapshot
 
Ligand structure

DRG

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.
-106.281-91.51779.763-35.163-59.3670.109


Interactive mode: IFIE and PIEDA for fragment #228(F:1:DRG)


Summations of interaction energy for fragment #228(F:1:DRG)
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.
-106.281-91.51779.763-35.163-59.367-0.109
Interaction energy analysis for fragmet #228(F:1:DRG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.108 / q_NPA : -0.136
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].
1B263LEU0-0.029-0.02228.841-0.001-0.0010.0000.0000.0000.000
2B264SER0-0.004-0.01729.3110.0060.0060.0000.0000.0000.000
3B265PRO00.0940.04026.153-0.005-0.0050.0000.0000.0000.000
4B266GLU-1-0.828-0.93025.0780.0420.0420.0000.0000.0000.000
5B267GLN00.0720.04525.268-0.001-0.0010.0000.0000.0000.000
6B268LEU00.0100.03521.585-0.013-0.0130.0000.0000.0000.000
7B269VAL00.012-0.00920.651-0.007-0.0070.0000.0000.0000.000
8B270LEU0-0.045-0.03420.368-0.001-0.0010.0000.0000.0000.000
9B271THR0-0.011-0.01320.820-0.016-0.0160.0000.0000.0000.000
10B272LEU0-0.024-0.02216.463-0.025-0.0250.0000.0000.0000.000
11B273LEU0-0.049-0.02016.190-0.006-0.0060.0000.0000.0000.000
12B274GLU-1-0.993-0.99117.101-0.205-0.2050.0000.0000.0000.000
13B275ALA00.0260.01015.986-0.036-0.0360.0000.0000.0000.000
14B276GLU-1-0.791-0.86011.298-0.138-0.1380.0000.0000.0000.000
15B277PRO0-0.027-0.0018.515-0.025-0.0250.0000.0000.0000.000
16B278PRO0-0.010-0.00110.5320.0490.0490.0000.0000.0000.000
17B279HIS0-0.001-0.0198.589-0.343-0.3430.0000.0000.0000.000
18B280VAL0-0.0010.0026.3180.2130.2130.0000.0000.0000.000
19B281LEU0-0.005-0.0038.203-0.032-0.0320.0000.0000.0000.000
20B282ILE0-0.044-0.0356.839-0.096-0.0960.0000.0000.0000.000
21B283SER00.0150.0269.7280.0700.0700.0000.0000.0000.000
22B291GLU-1-0.811-0.9087.956-0.440-0.4400.0000.0000.0000.000
23B292ALA00.0310.0028.5470.1730.1730.0000.0000.0000.000
24B293SER0-0.0020.0049.1760.0710.0710.0000.0000.0000.000
25B294MET00.0580.0536.7290.0980.0980.0000.0000.0000.000
26B295MET00.0490.0282.352-3.093-1.5672.031-0.925-2.6320.012
27B296MET0-0.0150.0275.046-0.0890.073-0.001-0.003-0.1600.000
28B297SER0-0.020-0.0347.559-0.277-0.2770.0000.0000.0000.000
29B298LEU00.0190.0072.560-3.820-1.1161.691-0.820-3.5760.002
30B299THR0-0.024-0.0393.056-6.041-3.0151.200-1.430-2.796-0.013
31B300LYS10.9150.9594.213-0.486-0.4290.0110.097-0.1650.000
32B301LEU00.0150.0222.580-0.8200.5740.885-0.469-1.8100.002
33B302ALA00.0550.0242.807-2.071-0.5630.448-0.542-1.4150.002
34B303ASP-1-0.849-0.9383.983-0.178-0.0210.005-0.036-0.1260.000
35B304LYS10.8810.9376.9441.6031.6030.0000.0000.0000.000
36B305GLU-1-0.717-0.8161.510-34.955-48.79731.548-12.760-4.947-0.101
37B306LEU00.0010.0175.7750.8530.8530.0000.0000.0000.000
38B307VAL0-0.007-0.0048.2910.3010.3010.0000.0000.0000.000
39B308HIS0-0.021-0.0198.5270.3120.3120.0000.0000.0000.000
40B309MET0-0.0280.0126.9830.2760.2760.0000.0000.0000.000
41B310ILE00.0210.0069.9040.1830.1830.0000.0000.0000.000
42B311SER0-0.012-0.01013.1250.1090.1090.0000.0000.0000.000
43B312TRP00.0070.01911.5610.0650.0650.0000.0000.0000.000
44B313ALA00.0450.01713.4880.0720.0720.0000.0000.0000.000
45B314LYS10.7870.88415.2090.3090.3090.0000.0000.0000.000
46B315LYS10.8810.94715.8750.3720.3720.0000.0000.0000.000
47B316ILE0-0.0030.01315.0850.0330.0330.0000.0000.0000.000
48B317PRO00.003-0.01219.217-0.003-0.0030.0000.0000.0000.000
49B318GLY00.0370.01822.9360.0070.0070.0000.0000.0000.000
50B319PHE00.0100.00417.3700.0010.0010.0000.0000.0000.000
51B320VAL00.004-0.01121.264-0.004-0.0040.0000.0000.0000.000
52B321GLU-1-0.902-0.93123.151-0.073-0.0730.0000.0000.0000.000
53B322LEU0-0.042-0.00821.4320.0110.0110.0000.0000.0000.000
54B323SER00.0130.00125.253-0.010-0.0100.0000.0000.0000.000
55B324LEU00.0310.02422.154-0.006-0.0060.0000.0000.0000.000
56B325PHE00.047-0.00122.360-0.011-0.0110.0000.0000.0000.000
57B326ASP-1-0.804-0.85321.849-0.099-0.0990.0000.0000.0000.000
58B327GLN0-0.043-0.02619.565-0.022-0.0220.0000.0000.0000.000
59B328VAL0-0.013-0.01017.914-0.018-0.0180.0000.0000.0000.000
60B329ARG10.8990.94116.7890.1010.1010.0000.0000.0000.000
61B330LEU0-0.027-0.00716.594-0.002-0.0020.0000.0000.0000.000
62B331LEU00.0010.01512.603-0.002-0.0020.0000.0000.0000.000
63B332GLU-1-0.905-0.97912.215-0.191-0.1910.0000.0000.0000.000
64B333SER0-0.088-0.04312.115-0.017-0.0170.0000.0000.0000.000
65B334SER0-0.030-0.02811.584-0.012-0.0120.0000.0000.0000.000
66B335TRP00.0250.0004.127-0.3560.0010.000-0.013-0.3440.000
67B336MET00.0280.0222.884-2.838-1.6972.749-0.692-3.197-0.004
68B337GLU-1-0.784-0.8745.2160.1940.1940.0000.0000.0000.000
69B338VAL0-0.025-0.0146.5780.2480.2480.0000.0000.0000.000
70B339LEU0-0.0200.0012.735-3.399-0.3992.631-1.485-4.1460.012
71B340MET0-0.0210.0012.604-2.6291.2311.899-1.557-4.202-0.009
72B341MET0-0.0050.0073.4080.6490.6220.0060.181-0.1600.000
73B342GLY00.0190.0085.431-0.142-0.1420.0000.0000.0000.000
74B343LEU0-0.0090.0072.468-2.986-1.0892.437-0.941-3.3940.008
75B344MET0-0.0190.0004.427-0.731-0.5750.000-0.024-0.1320.000
76B345TRP0-0.0040.0037.321-0.193-0.1930.0000.0000.0000.000
77B346ARG10.7760.8712.5851.5072.3680.212-0.339-0.7340.001
78B347SER00.016-0.0087.484-0.069-0.0690.0000.0000.0000.000
79B348ILE00.0060.02310.158-0.060-0.0600.0000.0000.0000.000
80B349ASP-1-0.925-0.96312.9170.4660.4660.0000.0000.0000.000
81B350HIS10.8000.89912.443-0.776-0.7760.0000.0000.0000.000
82B351PRO00.0460.01013.7230.1790.1790.0000.0000.0000.000
83B352GLY0-0.0090.00114.022-0.073-0.0730.0000.0000.0000.000
84B353LYS10.7830.87511.859-0.826-0.8260.0000.0000.0000.000
85B354LEU0-0.0100.0025.1900.0960.204-0.001-0.001-0.1060.000
86B355ILE0-0.030-0.0158.304-0.231-0.2310.0000.0000.0000.000
87B356PHE00.0500.0202.756-5.019-1.6452.924-1.225-5.0730.016
88B357ALA00.0250.0104.754-2.175-2.086-0.001-0.006-0.0820.000
89B358PRO0-0.036-0.0277.4930.4370.4370.0000.0000.0000.000
90B359ASP-1-0.911-0.94811.0780.0720.0720.0000.0000.0000.000
91B360LEU0-0.041-0.0046.164-0.003-0.0030.0000.0000.0000.000
92B361VAL0-0.015-0.0148.7960.2940.2940.0000.0000.0000.000
93B362LEU00.0120.0156.878-0.028-0.0280.0000.0000.0000.000
94B363ASP-1-0.788-0.88610.4961.1421.1420.0000.0000.0000.000
95B364ARG10.8130.87310.083-0.808-0.8080.0000.0000.0000.000
96B365ASP-1-0.875-0.96610.6630.8890.8890.0000.0000.0000.000
97B366GLU-1-0.822-0.90310.6750.9240.9240.0000.0000.0000.000
98B367GLY00.0170.0148.520-0.001-0.0010.0000.0000.0000.000
99B368LYS10.8370.9159.306-0.965-0.9650.0000.0000.0000.000
100B369SER0-0.076-0.04010.806-0.205-0.2050.0000.0000.0000.000
101B370VAL00.006-0.0054.711-0.172-0.074-0.001-0.004-0.0930.000
102B371GLU-1-0.900-0.9467.995-0.784-0.7840.0000.0000.0000.000
103B372GLY00.0240.0076.416-0.954-0.9540.0000.0000.0000.000
104B373ILE0-0.0150.0063.504-1.484-0.1050.159-0.369-1.1690.003
105B374LEU00.000-0.0065.9791.8501.8500.0000.0000.0000.000
106B375GLU-1-0.865-0.9307.809-0.448-0.4480.0000.0000.0000.000
107B376ILE00.014-0.0033.094-0.8300.3330.158-0.286-1.0350.001
108B377PHE00.013-0.0053.6650.1910.8640.017-0.141-0.5490.001
109B378ASP-1-0.753-0.8346.3850.8770.8770.0000.0000.0000.000
110B379MET0-0.024-0.0067.928-0.214-0.2140.0000.0000.0000.000
111B380LEU00.0220.0222.967-1.494-0.6120.372-0.287-0.9680.004
112B381LEU00.0260.0297.637-0.634-0.6340.0000.0000.0000.000
113B382ALA00.0020.01610.469-0.339-0.3390.0000.0000.0000.000
114B383THR0-0.014-0.02810.155-0.289-0.2890.0000.0000.0000.000
115B384THR0-0.032-0.0379.304-0.174-0.1740.0000.0000.0000.000
116B385SER0-0.039-0.03211.426-0.201-0.2010.0000.0000.0000.000
117B386ARG10.9420.98415.112-0.516-0.5160.0000.0000.0000.000
118B387PHE00.0460.00110.856-0.117-0.1170.0000.0000.0000.000
119B388ARG10.8540.93113.636-1.012-1.0120.0000.0000.0000.000
120B389GLU-1-0.947-0.97716.7590.4600.4600.0000.0000.0000.000
121B390LEU0-0.053-0.02117.606-0.062-0.0620.0000.0000.0000.000
122B391LYS10.9220.96819.142-0.336-0.3360.0000.0000.0000.000
123B392LEU0-0.0040.02313.245-0.050-0.0500.0000.0000.0000.000
124B393GLN0-0.035-0.03317.358-0.017-0.0170.0000.0000.0000.000
125B394HIS00.0730.03014.0690.0520.0520.0000.0000.0000.000
126B395LYS10.9630.97416.483-0.070-0.0700.0000.0000.0000.000
127B396GLU-1-0.733-0.82917.8030.2330.2330.0000.0000.0000.000
128B397TYR0-0.005-0.0209.3520.0330.0330.0000.0000.0000.000
129B398LEU0-0.0190.00813.5450.0020.0020.0000.0000.0000.000
130B399CYS0-0.022-0.00615.227-0.034-0.0340.0000.0000.0000.000
131B400VAL00.0050.00012.351-0.020-0.0200.0000.0000.0000.000
132B401LYS10.8080.8868.5180.0350.0350.0000.0000.0000.000
133B402ALA00.0250.01112.117-0.047-0.0470.0000.0000.0000.000
134B403MET0-0.029-0.02415.156-0.023-0.0230.0000.0000.0000.000
135B404ILE0-0.026-0.0049.921-0.019-0.0190.0000.0000.0000.000
136B405LEU00.0160.01613.161-0.035-0.0350.0000.0000.0000.000
137B406LEU0-0.0030.01114.069-0.023-0.0230.0000.0000.0000.000
138B407ASN0-0.003-0.01316.985-0.022-0.0220.0000.0000.0000.000
139B408SER0-0.030-0.00914.303-0.013-0.0130.0000.0000.0000.000
140B409SER0-0.0200.00616.290-0.029-0.0290.0000.0000.0000.000
141B421ASP-1-0.774-0.89031.496-0.058-0.0580.0000.0000.0000.000
142B422SER0-0.006-0.02226.3500.0010.0010.0000.0000.0000.000
143B423SER00.0000.00827.1070.0020.0020.0000.0000.0000.000
144B424ARG10.8820.90427.5950.0480.0480.0000.0000.0000.000
145B425LYS10.8690.93627.0150.0750.0750.0000.0000.0000.000
146B426LEU00.0240.02020.8080.0030.0030.0000.0000.0000.000
147B427ALA00.0060.00524.0020.0080.0080.0000.0000.0000.000
148B428HIS0-0.014-0.00726.1420.0110.0110.0000.0000.0000.000
149B429LEU00.0000.00621.2490.0080.0080.0000.0000.0000.000
150B430LEU00.0250.01019.6340.0090.0090.0000.0000.0000.000
151B431ASN00.0140.01222.4370.0200.0200.0000.0000.0000.000
152B432ALA00.0110.01524.9230.0100.0100.0000.0000.0000.000
153B433VAL00.006-0.00718.3570.0070.0070.0000.0000.0000.000
154B434THR0-0.023-0.02521.3800.0240.0240.0000.0000.0000.000
155B435ASP-1-0.946-0.97222.8900.0460.0460.0000.0000.0000.000
156B436ALA00.008-0.00122.4070.0070.0070.0000.0000.0000.000
157B437LEU00.0050.00618.8050.0110.0110.0000.0000.0000.000
158B438VAL00.0060.00222.1790.0130.0130.0000.0000.0000.000
159B439TRP0-0.009-0.00125.0840.0050.0050.0000.0000.0000.000
160B440VAL0-0.032-0.02321.4010.0010.0010.0000.0000.0000.000
161B441ILE0-0.0170.00021.8290.0070.0070.0000.0000.0000.000
162B442ALA0-0.0030.01925.2590.0020.0020.0000.0000.0000.000
163B443LYS10.8030.91726.970-0.059-0.0590.0000.0000.0000.000
164B444SER0-0.061-0.04526.0520.0030.0030.0000.0000.0000.000
165B445GLY00.0010.00328.1110.0030.0030.0000.0000.0000.000
166B446ILE0-0.0220.00626.945-0.004-0.0040.0000.0000.0000.000
167B447SER00.0510.01731.130-0.006-0.0060.0000.0000.0000.000
168B448SER00.0650.02431.6240.0080.0080.0000.0000.0000.000
169B449GLN00.0560.03631.3580.0080.0080.0000.0000.0000.000
170B450GLN00.027-0.00629.2230.0160.0160.0000.0000.0000.000
171B451GLN0-0.029-0.01927.2820.0110.0110.0000.0000.0000.000
172B452SER00.0080.00526.2630.0070.0070.0000.0000.0000.000
173B453MET0-0.022-0.01326.2360.0040.0040.0000.0000.0000.000
174B454ARG10.7580.85120.555-0.239-0.2390.0000.0000.0000.000
175B455LEU00.0400.01721.7000.0250.0250.0000.0000.0000.000
176B456ALA00.0180.00721.3900.0120.0120.0000.0000.0000.000
177B457ASN0-0.028-0.03420.8430.0350.0350.0000.0000.0000.000
178B458LEU00.0020.00816.7330.0410.0410.0000.0000.0000.000
179B459LEU00.007-0.00716.6910.0310.0310.0000.0000.0000.000
180B460MET0-0.0060.00117.676-0.008-0.0080.0000.0000.0000.000
181B461LEU00.0110.02113.9950.0010.0010.0000.0000.0000.000
182B462LEU00.0130.01412.7470.0710.0710.0000.0000.0000.000
183B463SER0-0.054-0.03013.004-0.016-0.0160.0000.0000.0000.000
184B464HIS00.006-0.00112.792-0.016-0.0160.0000.0000.0000.000
185B465VAL0-0.004-0.0087.4680.0930.0930.0000.0000.0000.000
186B466ARG10.8300.8968.7070.0220.0220.0000.0000.0000.000
187B467HIS00.0000.00410.146-0.198-0.1980.0000.0000.0000.000
188B468ALA00.0460.0147.012-0.231-0.2310.0000.0000.0000.000
189B469SER00.013-0.0035.632-0.609-0.6090.0000.0000.0000.000
190B470ASN0-0.016-0.0186.094-0.420-0.4200.0000.0000.0000.000
191B471LYS10.8570.9396.9041.0881.0880.0000.0000.0000.000
192B472GLY00.0340.0082.838-2.059-1.4960.383-0.394-0.5510.000
193B473MET0-0.0030.0023.016-2.046-0.8730.680-0.358-1.494-0.006
194B474GLU-1-0.880-0.9425.829-1.143-1.1430.0000.0000.0000.000
195B475HIS0-0.0040.0201.728-24.184-32.67022.287-7.877-5.925-0.063
196B476LEU00.0260.0142.240-3.2840.3783.944-1.765-5.8410.012
197B477LEU00.0310.0063.4560.3570.2730.1060.456-0.4770.002
198B478ASN0-0.0240.0025.9370.6680.6680.0000.0000.0000.000
199B479MET00.0220.0113.159-0.2040.6750.070-0.288-0.6610.002
200B480LYS10.9020.9615.6580.0350.106-0.001-0.001-0.0700.000
201B481SER0-0.052-0.0408.023-0.003-0.0030.0000.0000.0000.000
202B482LYS10.8780.9437.9871.0241.0240.0000.0000.0000.000
203B483ASN0-0.075-0.03610.5000.0280.0280.0000.0000.0000.000
204B484VAL00.0430.0267.2240.0230.0230.0000.0000.0000.000
205B485VAL0-0.067-0.0155.1790.1830.1830.0000.0000.0000.000
206B486PRO0-0.005-0.0026.953-0.196-0.1960.0000.0000.0000.000
207B487VAL0-0.008-0.0049.2680.0780.0780.0000.0000.0000.000
208B488TYR00.017-0.0038.095-0.134-0.1340.0000.0000.0000.000
209B489ASP-1-0.847-0.91511.061-0.188-0.1880.0000.0000.0000.000
210B490LEU0-0.010-0.00411.1040.0530.0530.0000.0000.0000.000
211B491LEU00.0250.0034.283-0.2710.0570.009-0.056-0.2800.000
212B492LEU0-0.028-0.0128.4600.1660.1660.0000.0000.0000.000
213B493GLU-1-0.773-0.86110.697-0.224-0.2240.0000.0000.0000.000
214B494MET00.009-0.0119.386-0.002-0.0020.0000.0000.0000.000
215B495LEU0-0.0250.0036.8280.0090.0090.0000.0000.0000.000
216B496ASN0-0.043-0.02710.038-0.057-0.0570.0000.0000.0000.000
217B497ALA0-0.0310.01112.757-0.040-0.0400.0000.0000.0000.000
218D604HIS0-0.006-0.02117.6100.0030.0030.0000.0000.0000.000
219D605LYS10.8190.89515.0750.2920.2920.0000.0000.0000.000
220D606LEU00.0230.00614.812-0.038-0.0380.0000.0000.0000.000
221D607VAL00.0350.00817.143-0.003-0.0030.0000.0000.0000.000
222D608GLN00.0010.00919.833-0.015-0.0150.0000.0000.0000.000
223D609LEU00.0120.01014.3540.0010.0010.0000.0000.0000.000
224D610LEU0-0.006-0.00217.503-0.007-0.0070.0000.0000.0000.000
225D611THR0-0.084-0.05719.6520.0180.0180.0000.0000.0000.000
226D612THR0-0.0010.01022.1300.0190.0190.0000.0000.0000.000
227D613THR0-0.0130.00618.576-0.012-0.0120.0000.0000.0000.000
229W7HOH0-0.022-0.0182.486-2.556-1.6010.906-0.803-1.0570.007