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: 1NJVZ

Calculation Name: 3P0U-A-Xray372

Preferred Name: Nuclear receptor subfamily 2 group C member 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P0U

Chain ID: A

ChEMBL ID: CHEMBL5716

UniProt ID: P49116

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2717853.090485
FMO2-HF: Nuclear repulsion 2626186.134894
FMO2-HF: Total energy -91666.955591
FMO2-MP2: Total energy -91928.00882


3D Structure
Snapshot
 
Ligand structure

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.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:367:ARG)


Summations of interaction energy for fragment #1(A:367:ARG)
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.
-96.905-97.5016.35-2.82-2.9340.006
Interaction energy analysis for fragmet #1(A:367:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.921 / q_NPA : 0.942
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].
3A369GLN00.007-0.0102.1472.4971.9016.350-2.820-2.9340.006
4A370SER00.0500.0135.9541.7421.7420.0000.0000.0000.000
5A371THR0-0.068-0.0338.5192.5662.5660.0000.0000.0000.000
6A372PRO0-0.0380.0108.480-1.791-1.7910.0000.0000.0000.000
7A373ILE0-0.040-0.0338.5380.0340.0340.0000.0000.0000.000
8A374ILE00.0070.01110.9890.9840.9840.0000.0000.0000.000
9A375GLU-1-0.891-0.95013.611-16.366-16.3660.0000.0000.0000.000
10A376VAL0-0.075-0.04515.0960.7730.7730.0000.0000.0000.000
11A377GLU-1-0.827-0.88414.620-17.379-17.3790.0000.0000.0000.000
12A378GLY00.036-0.00313.561-0.807-0.8070.0000.0000.0000.000
13A379PRO0-0.0320.0059.9490.3800.3800.0000.0000.0000.000
14A380LEU00.0150.01610.381-2.828-2.8280.0000.0000.0000.000
15A381LEU0-0.024-0.0337.731-1.597-1.5970.0000.0000.0000.000
16A382SER00.0140.00212.0530.8770.8770.0000.0000.0000.000
17A383ASP-1-0.938-0.95414.784-17.110-17.1100.0000.0000.0000.000
18A384THR0-0.010-0.02317.4740.2730.2730.0000.0000.0000.000
19A385HIS0-0.079-0.01918.3530.5230.5230.0000.0000.0000.000
20A386VAL0-0.045-0.01820.0440.5900.5900.0000.0000.0000.000
21A387THR00.0500.00523.7510.1830.1830.0000.0000.0000.000
22A388PHE00.0190.00326.9090.0390.0390.0000.0000.0000.000
23A389LYS10.8420.93227.55710.92110.9210.0000.0000.0000.000
24A390LEU00.0520.04530.1950.0280.0280.0000.0000.0000.000
25A391THR0-0.074-0.02731.5480.2640.2640.0000.0000.0000.000
26A392MET00.0040.00232.714-0.129-0.1290.0000.0000.0000.000
27A393PRO00.0050.01936.2880.1390.1390.0000.0000.0000.000
28A394SER00.034-0.00540.002-0.117-0.1170.0000.0000.0000.000
29A395PRO0-0.0030.00242.0060.1250.1250.0000.0000.0000.000
30A396MET0-0.013-0.00745.737-0.125-0.1250.0000.0000.0000.000
31A397PRO0-0.043-0.01548.3040.0490.0490.0000.0000.0000.000
32A398GLU-1-0.837-0.92251.956-5.483-5.4830.0000.0000.0000.000
33A399TYR0-0.022-0.01453.911-0.080-0.0800.0000.0000.0000.000
34A400LEU0-0.007-0.00256.414-0.004-0.0040.0000.0000.0000.000
35A401ASN00.0280.03653.765-0.008-0.0080.0000.0000.0000.000
36A402VAL00.0160.00554.7000.0000.0000.0000.0000.0000.000
37A403HIS00.012-0.02149.020-0.034-0.0340.0000.0000.0000.000
38A404TYR00.0050.00250.342-0.146-0.1460.0000.0000.0000.000
39A405ILE00.0310.02446.996-0.141-0.1410.0000.0000.0000.000
40A406CYS0-0.0200.02845.380-0.167-0.1670.0000.0000.0000.000
41A407GLU-1-0.849-0.89245.179-6.603-6.6030.0000.0000.0000.000
42A408SER0-0.025-0.03245.373-0.122-0.1220.0000.0000.0000.000
43A409ALA00.0110.01441.952-0.155-0.1550.0000.0000.0000.000
44A410SER0-0.020-0.03141.007-0.247-0.2470.0000.0000.0000.000
45A411ARG10.7910.89540.8966.5666.5660.0000.0000.0000.000
46A412LEU00.0510.03536.925-0.172-0.1720.0000.0000.0000.000
47A413LEU00.0020.02135.360-0.292-0.2920.0000.0000.0000.000
48A414PHE00.012-0.02036.039-0.236-0.2360.0000.0000.0000.000
49A415LEU0-0.0120.00436.259-0.212-0.2120.0000.0000.0000.000
50A416SER0-0.002-0.01432.750-0.278-0.2780.0000.0000.0000.000
51A417MET0-0.031-0.01231.757-0.405-0.4050.0000.0000.0000.000
52A418HIS00.0080.00331.817-0.423-0.4230.0000.0000.0000.000
53A419TRP0-0.037-0.00626.213-0.189-0.1890.0000.0000.0000.000
54A420ALA00.0500.02427.791-0.285-0.2850.0000.0000.0000.000
55A421ARG10.8310.91827.1618.8358.8350.0000.0000.0000.000
56A422SER0-0.035-0.03129.1460.1550.1550.0000.0000.0000.000
57A423ILE0-0.018-0.00522.7950.0410.0410.0000.0000.0000.000
58A424PRO0-0.009-0.01322.917-0.044-0.0440.0000.0000.0000.000
59A425ALA00.0740.03819.018-0.010-0.0100.0000.0000.0000.000
60A426PHE00.0080.01420.611-0.236-0.2360.0000.0000.0000.000
61A427GLN0-0.034-0.02822.997-0.048-0.0480.0000.0000.0000.000
62A428ALA0-0.0210.00219.8210.1780.1780.0000.0000.0000.000
63A429LEU00.0010.00817.618-0.273-0.2730.0000.0000.0000.000
64A430GLY00.0390.03220.4590.1050.1050.0000.0000.0000.000
65A431GLN0-0.012-0.02323.6320.1030.1030.0000.0000.0000.000
66A432ASP-1-0.875-0.94223.974-10.828-10.8280.0000.0000.0000.000
67A433CYS0-0.0220.00519.637-0.124-0.1240.0000.0000.0000.000
68A434ASN0-0.060-0.03622.4900.3880.3880.0000.0000.0000.000
69A435THR00.003-0.01325.0310.2140.2140.0000.0000.0000.000
70A436SER0-0.017-0.02223.5290.3500.3500.0000.0000.0000.000
71A437LEU00.0190.01720.7640.1500.1500.0000.0000.0000.000
72A438VAL00.006-0.00423.9040.1570.1570.0000.0000.0000.000
73A439ARG10.8040.87427.4419.7499.7490.0000.0000.0000.000
74A440ALA0-0.0240.00124.3950.2840.2840.0000.0000.0000.000
75A441CYS0-0.0120.00525.3630.0420.0420.0000.0000.0000.000
76A442TRP00.0080.00927.4420.2410.2410.0000.0000.0000.000
77A443ASN00.0100.01530.9730.4170.4170.0000.0000.0000.000
78A444GLU-1-0.817-0.88126.715-11.270-11.2700.0000.0000.0000.000
79A445LEU00.0470.01327.1500.1420.1420.0000.0000.0000.000
80A446PHE0-0.015-0.00830.7390.2200.2200.0000.0000.0000.000
81A447THR0-0.008-0.01433.4770.3230.3230.0000.0000.0000.000
82A448LEU00.008-0.00528.2560.1890.1890.0000.0000.0000.000
83A449GLY0-0.039-0.02032.8240.0860.0860.0000.0000.0000.000
84A450LEU0-0.003-0.01035.2160.2110.2110.0000.0000.0000.000
85A451ALA00.0260.00135.1590.1880.1880.0000.0000.0000.000
86A452GLN00.0060.01933.288-0.020-0.0200.0000.0000.0000.000
87A453CYS0-0.064-0.02936.5900.1530.1530.0000.0000.0000.000
88A454ALA00.0560.02539.9060.2420.2420.0000.0000.0000.000
89A455GLN0-0.061-0.04042.0320.2760.2760.0000.0000.0000.000
90A456VAL00.0300.02144.5300.1580.1580.0000.0000.0000.000
91A457MET0-0.042-0.00241.6100.0770.0770.0000.0000.0000.000
92A458SER00.0160.00345.9530.0060.0060.0000.0000.0000.000
93A459LEU0-0.046-0.02246.1230.1580.1580.0000.0000.0000.000
94A460SER00.0200.01748.678-0.062-0.0620.0000.0000.0000.000
95A461THR0-0.032-0.01548.3370.1170.1170.0000.0000.0000.000
96A462ILE0-0.025-0.02049.841-0.076-0.0760.0000.0000.0000.000
97A463LEU0-0.0040.00351.7980.1370.1370.0000.0000.0000.000
98A464ALA0-0.001-0.01153.183-0.074-0.0740.0000.0000.0000.000
99A465ALA0-0.0060.00755.7110.0920.0920.0000.0000.0000.000
100A466ILE00.006-0.00455.932-0.095-0.0950.0000.0000.0000.000
101A467VAL0-0.022-0.00658.7140.0530.0530.0000.0000.0000.000
102A468ASN0-0.021-0.01060.366-0.078-0.0780.0000.0000.0000.000
103A469HIS00.012-0.01761.381-0.103-0.1030.0000.0000.0000.000
104A470LEU0-0.0140.00162.3960.0020.0020.0000.0000.0000.000
105A471GLN00.0350.02865.454-0.016-0.0160.0000.0000.0000.000
106A472ASN00.0130.01967.585-0.073-0.0730.0000.0000.0000.000
107A473SER0-0.014-0.01370.7180.0860.0860.0000.0000.0000.000
108A483ARG10.9740.97351.1715.8175.8170.0000.0000.0000.000
109A484ILE00.0330.02648.9580.0110.0110.0000.0000.0000.000
110A485LYS10.8090.88143.0546.9536.9530.0000.0000.0000.000
111A486GLN00.0070.00341.0090.1470.1470.0000.0000.0000.000
112A487VAL00.029-0.00244.191-0.148-0.1480.0000.0000.0000.000
113A488MET00.0210.00544.516-0.100-0.1000.0000.0000.0000.000
114A489GLU-1-0.830-0.89540.561-7.747-7.7470.0000.0000.0000.000
115A490HIS0-0.020-0.01237.110-0.151-0.1510.0000.0000.0000.000
116A491ILE00.0390.01641.067-0.115-0.1150.0000.0000.0000.000
117A492TRP0-0.0160.00242.234-0.035-0.0350.0000.0000.0000.000
118A493LYS10.8790.92237.1658.1108.1100.0000.0000.0000.000
119A494LEU00.0730.03038.478-0.184-0.1840.0000.0000.0000.000
120A495GLN0-0.068-0.03639.607-0.003-0.0030.0000.0000.0000.000
121A496GLU-1-0.783-0.88239.956-7.378-7.3780.0000.0000.0000.000
122A497PHE0-0.033-0.00331.821-0.143-0.1430.0000.0000.0000.000
123A498CYS0-0.009-0.00236.622-0.169-0.1690.0000.0000.0000.000
124A499ASN0-0.020-0.02638.524-0.032-0.0320.0000.0000.0000.000
125A500SER0-0.115-0.05635.575-0.130-0.1300.0000.0000.0000.000
126A501MET00.0080.00130.894-0.216-0.2160.0000.0000.0000.000
127A502ALA00.0130.00835.458-0.046-0.0460.0000.0000.0000.000
128A503LYS10.9240.96338.6897.7937.7930.0000.0000.0000.000
129A504LEU0-0.050-0.02832.412-0.006-0.0060.0000.0000.0000.000
130A505ASP-1-0.895-0.94134.761-8.204-8.2040.0000.0000.0000.000
131A506ILE0-0.0440.00230.846-0.182-0.1820.0000.0000.0000.000
132A507ASP-1-0.734-0.82931.876-9.531-9.5310.0000.0000.0000.000
133A508GLY0-0.009-0.01331.970-0.206-0.2060.0000.0000.0000.000
134A509TYR00.027-0.00727.312-0.073-0.0730.0000.0000.0000.000
135A510GLU-1-0.751-0.84027.362-10.611-10.6110.0000.0000.0000.000
136A511TYR00.0370.00427.575-0.358-0.3580.0000.0000.0000.000
137A512ALA0-0.047-0.01328.015-0.174-0.1740.0000.0000.0000.000
138A513TYR0-0.006-0.04221.397-0.004-0.0040.0000.0000.0000.000
139A514LEU0-0.0090.00023.627-0.461-0.4610.0000.0000.0000.000
140A515LYS10.8750.92525.2049.5049.5040.0000.0000.0000.000
141A516ALA00.0070.00822.151-0.127-0.1270.0000.0000.0000.000
142A517ILE00.004-0.00119.971-0.401-0.4010.0000.0000.0000.000
143A518VAL0-0.032-0.00721.305-0.331-0.3310.0000.0000.0000.000
144A519LEU0-0.050-0.03023.2900.0070.0070.0000.0000.0000.000
145A520PHE0-0.029-0.02518.2900.0800.0800.0000.0000.0000.000
146A521SER00.037-0.01218.422-0.744-0.7440.0000.0000.0000.000
147A522PRO00.0000.00714.6870.3980.3980.0000.0000.0000.000
148A523ASP-1-0.848-0.88516.695-14.685-14.6850.0000.0000.0000.000
149A524HIS0-0.012-0.00119.0030.0720.0720.0000.0000.0000.000
150A525PRO0-0.004-0.00419.657-0.392-0.3920.0000.0000.0000.000
151A526GLY0-0.003-0.01419.9730.4940.4940.0000.0000.0000.000
152A527LEU0-0.0170.00617.8990.2820.2820.0000.0000.0000.000
153A528THR00.0240.00417.630-0.503-0.5030.0000.0000.0000.000
154A529SER0-0.020-0.00614.443-0.450-0.4500.0000.0000.0000.000
155A530THR00.0250.0119.111-0.007-0.0070.0000.0000.0000.000
156A531SER00.021-0.0318.1670.4080.4080.0000.0000.0000.000
157A532GLN0-0.078-0.03110.433-1.853-1.8530.0000.0000.0000.000
158A533ILE00.0400.01113.4570.1710.1710.0000.0000.0000.000
159A534GLU-1-0.868-0.9109.672-25.379-25.3790.0000.0000.0000.000
160A535LYS10.8150.9087.76331.10831.1080.0000.0000.0000.000
161A536PHE00.0170.00711.9080.6790.6790.0000.0000.0000.000
162A537GLN0-0.029-0.02215.4250.2010.2010.0000.0000.0000.000
163A538GLU-1-0.880-0.92110.575-22.676-22.6760.0000.0000.0000.000
164A539ALA00.0110.00813.7870.7640.7640.0000.0000.0000.000
165A540ALA0-0.062-0.02315.5910.9580.9580.0000.0000.0000.000
166A541GLN0-0.050-0.05814.1941.9371.9370.0000.0000.0000.000
167A542MET0-0.0080.00613.0490.2300.2300.0000.0000.0000.000
168A543GLU-1-0.714-0.84217.065-14.428-14.4280.0000.0000.0000.000
169A544LEU0-0.033-0.00319.8760.8570.8570.0000.0000.0000.000
170A545GLN00.001-0.01318.6860.2790.2790.0000.0000.0000.000
171A546ASP-1-0.913-0.95719.051-14.946-14.9460.0000.0000.0000.000
172A547TYR0-0.089-0.06922.0440.6540.6540.0000.0000.0000.000
173A548VAL0-0.037-0.02824.9000.5040.5040.0000.0000.0000.000
174A549GLN0-0.072-0.03023.3740.0830.0830.0000.0000.0000.000
175A550ALA0-0.018-0.00325.7280.3060.3060.0000.0000.0000.000
176A551THR0-0.052-0.03027.9490.3770.3770.0000.0000.0000.000
177A552TYR0-0.045-0.05029.7030.5090.5090.0000.0000.0000.000
178A553SER00.0240.01729.7950.0050.0050.0000.0000.0000.000
179A554GLU-1-0.985-0.98130.842-8.616-8.6160.0000.0000.0000.000
180A555ASP-1-0.824-0.90331.456-9.734-9.7340.0000.0000.0000.000
181A556THR00.0420.01525.740-0.302-0.3020.0000.0000.0000.000
182A557TYR0-0.040-0.02226.490-0.511-0.5110.0000.0000.0000.000
183A558ARG10.7680.85228.1849.5979.5970.0000.0000.0000.000
184A559LEU00.0530.04021.2790.0600.0600.0000.0000.0000.000
185A560ALA00.0310.00824.534-0.183-0.1830.0000.0000.0000.000
186A561ARG10.7700.85925.4519.7429.7420.0000.0000.0000.000
187A562ILE00.0380.02426.2900.1620.1620.0000.0000.0000.000
188A563LEU00.0530.03221.0080.1040.1040.0000.0000.0000.000
189A564VAL0-0.045-0.01725.0620.0340.0340.0000.0000.0000.000
190A565ARG10.8400.90427.52610.22210.2220.0000.0000.0000.000
191A566LEU00.0430.02723.1170.2990.2990.0000.0000.0000.000
192A567PRO0-0.001-0.00926.2550.1780.1780.0000.0000.0000.000
193A568ALA0-0.028-0.01428.3730.2350.2350.0000.0000.0000.000
194A569LEU0-0.0050.00328.1050.3340.3340.0000.0000.0000.000
195A570ARG10.8150.87322.32212.89012.8900.0000.0000.0000.000
196A571LEU0-0.070-0.01629.6180.2180.2180.0000.0000.0000.000
197A572MET0-0.0420.00433.0100.4690.4690.0000.0000.0000.000
198A573SER00.0110.00234.059-0.208-0.2080.0000.0000.0000.000
199A574SER00.0970.04032.9830.1220.1220.0000.0000.0000.000
200A575ASN00.0160.00335.072-0.001-0.0010.0000.0000.0000.000
201A576ILE0-0.0060.00338.1190.2190.2190.0000.0000.0000.000
202A577THR00.011-0.00636.6770.2500.2500.0000.0000.0000.000
203A578GLU-1-0.861-0.93637.824-7.869-7.8690.0000.0000.0000.000
204A579GLU-1-0.834-0.90340.309-6.966-6.9660.0000.0000.0000.000
205A580LEU0-0.058-0.03243.1220.1840.1840.0000.0000.0000.000
206A581PHE0-0.025-0.00441.3290.1240.1240.0000.0000.0000.000
207A582PHE0-0.031-0.03039.1910.0430.0430.0000.0000.0000.000
208A583THR00.0750.02343.3390.0310.0310.0000.0000.0000.000
209A584GLY0-0.045-0.02146.4560.1000.1000.0000.0000.0000.000
210A585LEU00.010-0.00447.0800.1090.1090.0000.0000.0000.000
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212A587GLY00.0700.03742.376-0.132-0.1320.0000.0000.0000.000
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