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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: N1NZQ

Calculation Name: 7XWP-ACEW-Xray333

Preferred Name:

Target Type:

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

ligand 3-letter code: I1I

PDB ID: 7XWP

Chain ID: ACEW

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 -2952002.253014
FMO2-HF: Nuclear repulsion 2858634.089324
FMO2-HF: Total energy -93368.16369
FMO2-MP2: Total energy -93632.049296


3D Structure
Snapshot
 
Ligand structure

LIG

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.
-104.774-91.43981.632-35.341-59.6260.105


Interactive mode: IFIE and PIEDA for fragment #228(E:1:LIG)


Summations of interaction energy for fragment #228(E:1:LIG)
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.
-104.774-91.43981.632-35.341-59.626-0.105
Interaction energy analysis for fragmet #228(E:1:LIG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.103 / q_NPA : -0.134
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].
1A263LEU00.016-0.00726.015-0.003-0.0030.0000.0000.0000.000
2A264SER00.0130.01730.0640.0110.0110.0000.0000.0000.000
3A265PRO00.0890.02726.857-0.009-0.0090.0000.0000.0000.000
4A266GLU-1-0.946-0.96825.5750.1030.1030.0000.0000.0000.000
5A267GLN00.028-0.00125.367-0.011-0.0110.0000.0000.0000.000
6A268LEU00.0090.03922.563-0.027-0.0270.0000.0000.0000.000
7A269VAL00.000-0.01620.645-0.010-0.0100.0000.0000.0000.000
8A270LEU0-0.033-0.02620.510-0.004-0.0040.0000.0000.0000.000
9A271THR0-0.002-0.00921.194-0.035-0.0350.0000.0000.0000.000
10A272LEU0-0.030-0.02517.191-0.041-0.0410.0000.0000.0000.000
11A273LEU0-0.021-0.00216.392-0.014-0.0140.0000.0000.0000.000
12A274GLU-1-0.917-0.95716.878-0.223-0.2230.0000.0000.0000.000
13A275ALA0-0.035-0.02016.016-0.079-0.0790.0000.0000.0000.000
14A276GLU-1-0.786-0.86111.510-0.206-0.2060.0000.0000.0000.000
15A277PRO0-0.035-0.0068.466-0.056-0.0560.0000.0000.0000.000
16A278PRO0-0.010-0.00310.9200.1330.1330.0000.0000.0000.000
17A279HIS00.003-0.0149.282-0.398-0.3980.0000.0000.0000.000
18A280VAL0-0.0200.0005.9750.1470.1470.0000.0000.0000.000
19A281LEU00.0340.0247.518-0.021-0.0210.0000.0000.0000.000
20A282ILE0-0.003-0.0026.555-0.451-0.4510.0000.0000.0000.000
21A283SER0-0.091-0.0399.0640.1350.1350.0000.0000.0000.000
22A291GLU-1-0.872-0.94310.747-0.055-0.0550.0000.0000.0000.000
23A292ALA00.016-0.0048.8380.0230.0230.0000.0000.0000.000
24A293SER0-0.0060.0028.759-0.227-0.2270.0000.0000.0000.000
25A294MET00.0630.0476.629-0.187-0.1870.0000.0000.0000.000
26A295MET00.0280.0232.708-2.534-1.7993.570-0.855-3.4490.010
27A296MET00.0010.0124.568-1.401-1.197-0.001-0.009-0.1940.000
28A297SER0-0.031-0.0197.155-0.678-0.6780.0000.0000.0000.000
29A298LEU00.0110.0032.277-4.685-1.8672.902-1.136-4.5840.002
30A299THR0-0.027-0.0322.648-8.324-5.2400.788-1.378-2.494-0.018
31A300LYS10.8960.9414.4991.8101.9720.000-0.012-0.1500.000
32A301LEU0-0.052-0.0182.491-0.6841.0070.918-0.619-1.9910.003
33A302ALA00.0420.0242.345-1.588-0.1860.979-0.725-1.6560.002
34A303ASP-1-0.858-0.9343.842-0.850-0.6380.016-0.049-0.1790.000
35A304LYS10.8950.9316.9693.1743.1740.0000.0000.0000.000
36A305GLU-1-0.736-0.8221.476-37.785-53.45835.044-14.568-4.803-0.103
37A306LEU00.0110.0155.9391.1961.1960.0000.0000.0000.000
38A307VAL00.0080.0058.5330.5550.5550.0000.0000.0000.000
39A308HIS0-0.019-0.0128.6170.5750.5750.0000.0000.0000.000
40A309MET0-0.0260.0097.2960.4440.4440.0000.0000.0000.000
41A310ILE00.0200.01010.1580.3090.3090.0000.0000.0000.000
42A311SER0-0.048-0.03213.2590.2010.2010.0000.0000.0000.000
43A312TRP0-0.0180.00111.9120.0980.0980.0000.0000.0000.000
44A313ALA00.0340.00313.8760.1210.1210.0000.0000.0000.000
45A314LYS10.8410.92315.6280.5920.5920.0000.0000.0000.000
46A315LYS10.8450.95415.7840.5390.5390.0000.0000.0000.000
47A316ILE0-0.0100.01015.5610.0590.0590.0000.0000.0000.000
48A317PRO00.000-0.01119.766-0.007-0.0070.0000.0000.0000.000
49A318GLY00.0320.01523.6520.0300.0300.0000.0000.0000.000
50A319PHE0-0.008-0.01317.7640.0050.0050.0000.0000.0000.000
51A320VAL00.014-0.00221.624-0.014-0.0140.0000.0000.0000.000
52A321GLU-1-0.913-0.95023.662-0.128-0.1280.0000.0000.0000.000
53A322LEU0-0.065-0.02421.8580.0250.0250.0000.0000.0000.000
54A323SER0-0.034-0.04025.680-0.032-0.0320.0000.0000.0000.000
55A324LEU00.0600.02022.5090.0000.0000.0000.0000.0000.000
56A325PHE00.0310.01322.860-0.021-0.0210.0000.0000.0000.000
57A326ASP-1-0.762-0.82722.168-0.053-0.0530.0000.0000.0000.000
58A327GLN0-0.032-0.01620.034-0.025-0.0250.0000.0000.0000.000
59A328VAL00.0020.00018.314-0.030-0.0300.0000.0000.0000.000
60A329ARG10.9150.95317.3690.0000.0000.0000.0000.0000.000
61A330LEU0-0.0390.00016.9590.0380.0380.0000.0000.0000.000
62A331LEU00.0360.03712.7770.0680.0680.0000.0000.0000.000
63A332GLU-1-0.898-0.97212.686-0.280-0.2800.0000.0000.0000.000
64A333SER0-0.086-0.05012.5090.0640.0640.0000.0000.0000.000
65A334SER0-0.032-0.03911.3180.1210.1210.0000.0000.0000.000
66A335TRP00.0400.0074.6450.0970.341-0.001-0.003-0.2400.000
67A336MET00.0160.0223.226-0.8730.4931.144-0.326-2.184-0.001
68A337GLU-1-0.839-0.9134.7892.5552.7680.001-0.019-0.1950.000
69A338VAL0-0.012-0.0097.0490.3350.3350.0000.0000.0000.000
70A339LEU0-0.0180.0032.720-3.202-0.4162.095-1.157-3.7240.009
71A340MET0-0.0200.0042.755-1.706-1.6876.242-1.530-4.730-0.004
72A341MET00.0050.0073.970-0.406-0.2660.010-0.003-0.1460.000
73A342GLY00.0010.0005.909-0.278-0.2780.0000.0000.0000.000
74A343LEU00.0000.0122.535-2.665-0.4620.959-0.691-2.4710.004
75A344MET0-0.021-0.0014.620-0.971-0.826-0.001-0.015-0.1290.000
76A345TRP00.0040.0007.663-0.378-0.3780.0000.0000.0000.000
77A346ARG10.7610.8602.6600.9241.7720.259-0.333-0.7740.001
78A347SER00.002-0.0117.489-0.127-0.1270.0000.0000.0000.000
79A348ILE0-0.0160.01210.173-0.065-0.0650.0000.0000.0000.000
80A349ASP-1-0.917-0.95613.0280.7250.7250.0000.0000.0000.000
81A350HIS0-0.033-0.01612.773-0.114-0.1140.0000.0000.0000.000
82A351PRO0-0.001-0.01713.7380.2620.2620.0000.0000.0000.000
83A352GLY0-0.022-0.00413.907-0.114-0.1140.0000.0000.0000.000
84A353LYS10.8940.95711.522-0.940-0.9400.0000.0000.0000.000
85A354LEU00.0090.0075.0130.1380.280-0.001-0.003-0.1380.000
86A355ILE0-0.035-0.0198.095-0.482-0.4820.0000.0000.0000.000
87A356PHE00.0540.0182.822-6.670-2.4083.627-1.515-6.3740.016
88A357ALA00.0280.0144.532-2.015-1.896-0.001-0.013-0.1060.000
89A358PRO0-0.026-0.0227.1890.4880.4880.0000.0000.0000.000
90A359ASP-1-0.765-0.87610.118-1.305-1.3050.0000.0000.0000.000
91A360LEU0-0.027-0.0105.406-0.200-0.2000.0000.0000.0000.000
92A361VAL0-0.018-0.0068.2320.4080.4080.0000.0000.0000.000
93A362LEU00.0160.0126.261-0.166-0.1660.0000.0000.0000.000
94A363ASP-1-0.794-0.8919.9191.7911.7910.0000.0000.0000.000
95A364ARG10.8580.8999.806-1.266-1.2660.0000.0000.0000.000
96A365ASP-1-0.877-0.93111.0830.7160.7160.0000.0000.0000.000
97A366GLU-1-0.835-0.92710.9670.9970.9970.0000.0000.0000.000
98A367GLY0-0.008-0.0078.602-0.117-0.1170.0000.0000.0000.000
99A368LYS10.7790.8839.287-1.095-1.0950.0000.0000.0000.000
100A369SER0-0.086-0.04311.352-0.273-0.2730.0000.0000.0000.000
101A370VAL0-0.013-0.0165.627-0.194-0.1940.0000.0000.0000.000
102A371GLU-1-0.887-0.9418.337-0.399-0.3990.0000.0000.0000.000
103A372GLY00.0230.0096.434-0.864-0.8640.0000.0000.0000.000
104A373ILE0-0.024-0.0053.013-1.3940.0080.749-0.461-1.6900.003
105A374LEU00.0100.0085.8011.6261.6260.0000.0000.0000.000
106A375GLU-1-0.922-0.9518.1440.9320.9320.0000.0000.0000.000
107A376ILE00.0260.0042.840-0.9890.5370.353-0.335-1.5430.000
108A377PHE00.017-0.0103.2000.2551.3420.125-0.302-0.9100.004
109A378ASP-1-0.786-0.8726.4221.6831.6830.0000.0000.0000.000
110A379MET0-0.057-0.0097.961-0.203-0.2030.0000.0000.0000.000
111A380LEU00.0240.0193.053-1.674-0.6540.346-0.293-1.0740.003
112A381LEU00.0260.0337.619-0.902-0.9020.0000.0000.0000.000
113A382ALA0-0.0080.01610.410-0.530-0.5300.0000.0000.0000.000
114A383THR0-0.017-0.02910.120-0.465-0.4650.0000.0000.0000.000
115A384THR0-0.024-0.0319.443-0.316-0.3160.0000.0000.0000.000
116A385SER0-0.048-0.04211.656-0.411-0.4110.0000.0000.0000.000
117A386ARG10.8930.94815.229-1.124-1.1240.0000.0000.0000.000
118A387PHE00.037-0.00411.131-0.227-0.2270.0000.0000.0000.000
119A388ARG10.8830.94513.741-1.703-1.7030.0000.0000.0000.000
120A389GLU-1-0.931-0.95017.0120.8740.8740.0000.0000.0000.000
121A390LEU0-0.052-0.02417.938-0.115-0.1150.0000.0000.0000.000
122A391LYS10.9490.98419.221-0.694-0.6940.0000.0000.0000.000
123A392LEU00.0020.02213.374-0.086-0.0860.0000.0000.0000.000
124A393GLN0-0.020-0.02417.397-0.055-0.0550.0000.0000.0000.000
125A394HIS00.0250.01814.054-0.035-0.0350.0000.0000.0000.000
126A395LYS11.0030.98816.560-0.167-0.1670.0000.0000.0000.000
127A396GLU-1-0.724-0.82017.8540.5450.5450.0000.0000.0000.000
128A397TYR0-0.012-0.0269.4320.0580.0580.0000.0000.0000.000
129A398LEU0-0.0180.00413.6660.0290.0290.0000.0000.0000.000
130A399CYS0-0.031-0.00215.508-0.052-0.0520.0000.0000.0000.000
131A400VAL00.008-0.00913.023-0.021-0.0210.0000.0000.0000.000
132A401LYS10.8050.8939.1090.1060.1060.0000.0000.0000.000
133A402ALA00.0330.01312.304-0.055-0.0550.0000.0000.0000.000
134A403MET0-0.039-0.02215.291-0.014-0.0140.0000.0000.0000.000
135A404ILE0-0.023-0.01110.220-0.017-0.0170.0000.0000.0000.000
136A405LEU0-0.0050.01413.484-0.026-0.0260.0000.0000.0000.000
137A406LEU0-0.012-0.00314.523-0.048-0.0480.0000.0000.0000.000
138A407ASN0-0.042-0.01317.229-0.080-0.0800.0000.0000.0000.000
139A408SER0-0.034-0.01214.6740.0440.0440.0000.0000.0000.000
140A409SER0-0.019-0.01516.447-0.094-0.0940.0000.0000.0000.000
141A421ASP-1-0.807-0.91231.662-0.048-0.0480.0000.0000.0000.000
142A422SER0-0.015-0.01726.5600.0090.0090.0000.0000.0000.000
143A423SER00.0430.02426.9890.0050.0050.0000.0000.0000.000
144A424ARG10.9310.95227.7380.0150.0150.0000.0000.0000.000
145A425LYS10.8790.93828.0350.0740.0740.0000.0000.0000.000
146A426LEU00.0540.03121.0710.0020.0020.0000.0000.0000.000
147A427ALA0-0.007-0.00324.3160.0240.0240.0000.0000.0000.000
148A428HIS0-0.004-0.00426.4110.0260.0260.0000.0000.0000.000
149A429LEU0-0.0020.00321.6060.0150.0150.0000.0000.0000.000
150A430LEU00.0180.01019.9130.0180.0180.0000.0000.0000.000
151A431ASN0-0.047-0.00622.6890.0240.0240.0000.0000.0000.000
152A432ALA00.0700.03425.1620.0180.0180.0000.0000.0000.000
153A433VAL00.002-0.00818.5800.0070.0070.0000.0000.0000.000
154A434THR0-0.058-0.04521.5790.0570.0570.0000.0000.0000.000
155A435ASP-1-0.932-0.96723.1770.1800.1800.0000.0000.0000.000
156A436ALA00.0000.00122.5480.0060.0060.0000.0000.0000.000
157A437LEU00.005-0.00219.1810.0120.0120.0000.0000.0000.000
158A438VAL00.0040.00322.3170.0180.0180.0000.0000.0000.000
159A439TRP00.0070.00524.8790.0000.0000.0000.0000.0000.000
160A440VAL0-0.030-0.02621.287-0.007-0.0070.0000.0000.0000.000
161A441ILE0-0.0110.00722.1560.0050.0050.0000.0000.0000.000
162A442ALA00.0070.02325.310-0.004-0.0040.0000.0000.0000.000
163A443LYS10.8820.94126.904-0.175-0.1750.0000.0000.0000.000
164A444SER0-0.063-0.03926.027-0.005-0.0050.0000.0000.0000.000
165A445GLY0-0.0030.00328.0160.0000.0000.0000.0000.0000.000
166A446ILE0-0.0290.00127.139-0.008-0.0080.0000.0000.0000.000
167A447SER00.0480.01531.295-0.006-0.0060.0000.0000.0000.000
168A448SER00.0630.02031.8990.0220.0220.0000.0000.0000.000
169A449GLN00.0520.03331.780-0.001-0.0010.0000.0000.0000.000
170A450GLN00.021-0.00529.3390.0170.0170.0000.0000.0000.000
171A451GLN0-0.024-0.01527.5520.0300.0300.0000.0000.0000.000
172A452SER00.0320.01826.6590.0250.0250.0000.0000.0000.000
173A453MET0-0.020-0.01326.7580.0220.0220.0000.0000.0000.000
174A454ARG10.7420.84220.630-0.521-0.5210.0000.0000.0000.000
175A455LEU00.0400.01622.2750.0590.0590.0000.0000.0000.000
176A456ALA00.0200.00621.9140.0450.0450.0000.0000.0000.000
177A457ASN0-0.062-0.05821.1980.0900.0900.0000.0000.0000.000
178A458LEU0-0.0010.00717.1950.1000.1000.0000.0000.0000.000
179A459LEU00.010-0.00117.0810.0960.0960.0000.0000.0000.000
180A460MET0-0.0070.00117.9620.0330.0330.0000.0000.0000.000
181A461LEU0-0.0020.01414.2660.0570.0570.0000.0000.0000.000
182A462LEU00.0250.01913.1900.2330.2330.0000.0000.0000.000
183A463SER0-0.044-0.02812.9070.1100.1100.0000.0000.0000.000
184A464HIS00.0140.00612.5110.1060.1060.0000.0000.0000.000
185A465VAL00.0150.0057.6580.3280.3280.0000.0000.0000.000
186A466ARG10.8950.9368.336-0.429-0.4290.0000.0000.0000.000
187A467HIS0-0.0130.00210.5460.0380.0380.0000.0000.0000.000
188A468ALA00.0650.0136.610-0.219-0.2190.0000.0000.0000.000
189A469SER00.024-0.0055.8070.0550.0550.0000.0000.0000.000
190A470ASN0-0.055-0.0406.855-0.671-0.6710.0000.0000.0000.000
191A471LYS10.8820.9367.075-0.697-0.6970.0000.0000.0000.000
192A472GLY00.0330.0103.370-1.803-1.3630.038-0.161-0.3170.000
193A473MET0-0.005-0.0043.710-2.073-1.4530.035-0.159-0.497-0.001
194A474GLU-1-0.863-0.9126.531-0.649-0.6490.0000.0000.0000.000
195A475HIS00.0120.0181.797-22.592-28.38317.442-6.177-5.475-0.060
196A476LEU00.0250.0152.254-4.133-0.6183.344-1.717-5.1410.015
197A477LEU00.013-0.0013.5630.1970.3170.0610.187-0.3680.002
198A478ASN0-0.0180.0095.9310.2990.2990.0000.0000.0000.000
199A479MET00.0110.0112.656-1.259-0.0420.522-0.541-1.1980.005
200A480LYS10.9120.9555.6080.5930.5930.0000.0000.0000.000
201A481SER0-0.109-0.0597.940-0.005-0.0050.0000.0000.0000.000
202A482LYS10.9200.9488.5020.9920.9920.0000.0000.0000.000
203A483ASN0-0.042-0.01810.1710.0210.0210.0000.0000.0000.000
204A484VAL0-0.020-0.0016.837-0.028-0.0280.0000.0000.0000.000
205A485VAL0-0.018-0.0103.599-0.1630.1150.003-0.043-0.2390.000
206A486PRO0-0.0140.0036.8490.0300.0300.0000.0000.0000.000
207A487VAL00.0190.0028.102-0.229-0.2290.0000.0000.0000.000
208A488TYR0-0.0070.0047.8760.0610.0610.0000.0000.0000.000
209A489ASP-1-0.829-0.91310.987-0.988-0.9880.0000.0000.0000.000
210A490LEU0-0.0120.00111.1370.1620.1620.0000.0000.0000.000
211A491LEU00.020-0.0055.1000.0690.0690.0000.0000.0000.000
212A492LEU0-0.032-0.0149.1150.2840.2840.0000.0000.0000.000
213A493GLU-1-0.798-0.88810.991-0.591-0.5910.0000.0000.0000.000
214A494MET0-0.001-0.0099.7160.1550.1550.0000.0000.0000.000
215A495LEU0-0.024-0.0106.2120.1930.1930.0000.0000.0000.000
216A496ASN0-0.049-0.01610.4610.1000.1000.0000.0000.0000.000
217A497ALA0-0.0080.02513.7470.0830.0830.0000.0000.0000.000
218C604HIS0-0.034-0.02918.8510.0030.0030.0000.0000.0000.000
219C605LYS10.8960.92815.2811.0551.0550.0000.0000.0000.000
220C606LEU00.0340.01114.934-0.036-0.0360.0000.0000.0000.000
221C607VAL00.0290.01117.1040.0380.0380.0000.0000.0000.000
222C608GLN0-0.0130.00619.7480.0050.0050.0000.0000.0000.000
223C609LEU00.0190.02914.5090.0280.0280.0000.0000.0000.000
224C610LEU0-0.0010.00317.7050.0260.0260.0000.0000.0000.000
225C611THR0-0.062-0.04819.7410.0420.0420.0000.0000.0000.000
226C612THR0-0.077-0.03821.6700.0210.0210.0000.0000.0000.000
227C613THR00.004-0.00520.407-0.024-0.0240.0000.0000.0000.000
229W11HOH0-0.024-0.0173.127-0.4540.3250.065-0.380-0.4630.003