Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: J3JL9

Calculation Name: 3NCV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NCV

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F8M6

Base Structure: X-ray

Registration Date: 2023-06-20

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1929677.979115
FMO2-HF: Nuclear repulsion 1855047.759459
FMO2-HF: Total energy -74630.219656
FMO2-MP2: Total energy -74843.670583


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:463:GLU)


Summations of interaction energy for fragment #1(A:463:GLU)
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.
58.96560.257-0.006-0.608-0.6780.003
Interaction energy analysis for fragmet #1(A:463:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.950 / q_NPA : -0.989
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].
3A465PRO0-0.0130.0123.859-2.770-1.558-0.005-0.604-0.6030.003
4A466PRO00.0150.0046.803-0.734-0.7340.0000.0000.0000.000
5A467LEU0-0.045-0.0319.335-1.387-1.3870.0000.0000.0000.000
6A468GLY0-0.0010.0068.643-1.145-1.1450.0000.0000.0000.000
7A469PHE0-0.001-0.0135.954-0.768-0.7680.0000.0000.0000.000
8A470ALA0-0.015-0.01411.011-0.909-0.9090.0000.0000.0000.000
9A471ILE0-0.026-0.01713.8260.2960.2960.0000.0000.0000.000
10A472ALA0-0.006-0.00816.428-0.736-0.7360.0000.0000.0000.000
11A473GLN00.0310.01420.1190.3230.3230.0000.0000.0000.000
12A474LEU00.0080.00822.923-0.421-0.4210.0000.0000.0000.000
13A475LEU00.019-0.01824.904-0.141-0.1410.0000.0000.0000.000
14A476GLY0-0.028-0.00427.344-0.342-0.3420.0000.0000.0000.000
15A477ILE0-0.017-0.00927.541-0.015-0.0150.0000.0000.0000.000
16A478TYR00.0130.00422.8160.0040.0040.0000.0000.0000.000
17A479ILE00.0180.01317.637-0.130-0.1300.0000.0000.0000.000
18A480LEU0-0.021-0.00218.3940.0070.0070.0000.0000.0000.000
19A481ALA00.0380.00613.2440.2130.2130.0000.0000.0000.000
20A482GLN0-0.0170.00210.691-1.826-1.8260.0000.0000.0000.000
21A483ALA00.0370.0178.2601.7071.7070.0000.0000.0000.000
22A484GLU-1-0.891-0.9454.89137.09737.177-0.001-0.004-0.0750.000
23A485ASP-1-0.928-0.9537.53121.12421.1240.0000.0000.0000.000
24A486SER0-0.071-0.05110.807-2.224-2.2240.0000.0000.0000.000
25A487LEU00.0130.02712.4790.9470.9470.0000.0000.0000.000
26A488LEU0-0.004-0.01012.555-0.584-0.5840.0000.0000.0000.000
27A489LEU0-0.010-0.01016.360-0.263-0.2630.0000.0000.0000.000
28A490ILE00.0320.00515.998-0.316-0.3160.0000.0000.0000.000
29A491ASP-1-0.821-0.90020.34910.77410.7740.0000.0000.0000.000
30A492MET0-0.014-0.00623.0120.2100.2100.0000.0000.0000.000
31A493HIS0-0.013-0.00424.015-0.118-0.1180.0000.0000.0000.000
32A494ALA00.0260.01425.634-0.083-0.0830.0000.0000.0000.000
33A495ALA00.012-0.00821.3140.0410.0410.0000.0000.0000.000
34A496ALA0-0.026-0.00823.2540.1250.1250.0000.0000.0000.000
35A497GLU-1-0.855-0.90925.0129.7409.7400.0000.0000.0000.000
36A498ARG10.8080.89623.186-11.295-11.2950.0000.0000.0000.000
37A499VAL00.006-0.00920.641-0.017-0.0170.0000.0000.0000.000
38A500ASN0-0.021-0.01923.4080.2790.2790.0000.0000.0000.000
39A501TYR00.0140.00826.617-0.266-0.2660.0000.0000.0000.000
40A502GLU-1-0.765-0.84723.83710.93010.9300.0000.0000.0000.000
41A503LYS10.8000.90922.003-13.028-13.0280.0000.0000.0000.000
42A504MET0-0.0020.00425.600-0.215-0.2150.0000.0000.0000.000
43A505LYS10.8490.91828.828-9.114-9.1140.0000.0000.0000.000
44A506ARG10.8120.90920.374-13.064-13.0640.0000.0000.0000.000
45A507GLN00.0780.03127.893-0.220-0.2200.0000.0000.0000.000
46A508ARG10.8620.91029.374-8.330-8.3300.0000.0000.0000.000
47A509GLN0-0.076-0.03730.879-0.265-0.2650.0000.0000.0000.000
48A510GLU-1-0.960-0.97526.72510.97910.9790.0000.0000.0000.000
49A511ASN0-0.061-0.03429.805-0.176-0.1760.0000.0000.0000.000
50A512GLY0-0.0160.00633.685-0.232-0.2320.0000.0000.0000.000
51A513ASN0-0.075-0.04835.060-0.154-0.1540.0000.0000.0000.000
52A514LEU0-0.036-0.02031.5040.3510.3510.0000.0000.0000.000
53A515GLN00.0420.02831.442-0.378-0.3780.0000.0000.0000.000
54A516SER0-0.0010.00033.0660.2550.2550.0000.0000.0000.000
55A517GLN0-0.035-0.02630.0150.1450.1450.0000.0000.0000.000
56A518HIS0-0.034-0.03734.822-0.156-0.1560.0000.0000.0000.000
57A519LEU0-0.043-0.01436.7060.2040.2040.0000.0000.0000.000
58A520LEU0-0.025-0.02636.150-0.192-0.1920.0000.0000.0000.000
59A521ILE0-0.031-0.01239.623-0.207-0.2070.0000.0000.0000.000
60A522PRO00.0020.00241.2910.1080.1080.0000.0000.0000.000
61A523VAL0-0.0050.00839.759-0.110-0.1100.0000.0000.0000.000
62A524THR00.001-0.00243.062-0.047-0.0470.0000.0000.0000.000
63A525PHE0-0.079-0.04744.8240.0910.0910.0000.0000.0000.000
64A526ALA00.0290.02747.610-0.080-0.0800.0000.0000.0000.000
65A527ALA00.0040.01149.3800.1420.1420.0000.0000.0000.000
66A528SER0-0.016-0.04450.598-0.182-0.1820.0000.0000.0000.000
67A529HIS0-0.017-0.02052.8050.0030.0030.0000.0000.0000.000
68A530GLU-1-0.849-0.93551.6985.7365.7360.0000.0000.0000.000
69A531GLU-1-0.782-0.85847.4896.6256.6250.0000.0000.0000.000
70A532CYS0-0.025-0.01549.8050.0680.0680.0000.0000.0000.000
71A533ALA0-0.021-0.00352.3300.0150.0150.0000.0000.0000.000
72A534ALA00.0590.02647.9040.0130.0130.0000.0000.0000.000
73A535LEU0-0.057-0.03147.5120.1460.1460.0000.0000.0000.000
74A536ALA0-0.081-0.05049.1560.0270.0270.0000.0000.0000.000
75A537ASP-1-0.933-0.95451.6445.7875.7870.0000.0000.0000.000
76A538HIS-1-0.848-0.92646.6166.4346.4340.0000.0000.0000.000
77A539ALA00.0120.00646.0040.2040.2040.0000.0000.0000.000
78A540GLU-1-0.849-0.91445.0316.7916.7910.0000.0000.0000.000
79A541THR0-0.027-0.03642.7060.2490.2490.0000.0000.0000.000
80A542LEU0-0.052-0.02341.4280.2510.2510.0000.0000.0000.000
81A543ALA00.0270.02340.2350.2390.2390.0000.0000.0000.000
82A544GLY00.0360.01939.1010.2310.2310.0000.0000.0000.000
83A545PHE0-0.053-0.03936.3450.2470.2470.0000.0000.0000.000
84A546GLY00.0400.01735.5880.2150.2150.0000.0000.0000.000
85A547LEU0-0.042-0.02836.6600.1160.1160.0000.0000.0000.000
86A548GLU-1-0.805-0.87739.2907.4827.4820.0000.0000.0000.000
87A549LEU00.0470.01542.1970.0710.0710.0000.0000.0000.000
88A550SER0-0.019-0.01745.208-0.034-0.0340.0000.0000.0000.000
89A551ASP-1-0.776-0.90148.6615.9735.9730.0000.0000.0000.000
90A552MET0-0.074-0.04050.1450.0250.0250.0000.0000.0000.000
91A553GLY00.0390.04653.517-0.107-0.1070.0000.0000.0000.000
92A554GLY0-0.029-0.03055.2560.0630.0630.0000.0000.0000.000
93A555ASN0-0.053-0.03554.422-0.057-0.0570.0000.0000.0000.000
94A556THR0-0.055-0.02551.0840.1010.1010.0000.0000.0000.000
95A557LEU00.0590.05147.9440.0160.0160.0000.0000.0000.000
96A558ALA0-0.006-0.01446.1310.0520.0520.0000.0000.0000.000
97A559VAL0-0.0010.00339.758-0.030-0.0300.0000.0000.0000.000
98A560ARG10.8210.89442.093-7.025-7.0250.0000.0000.0000.000
99A561ALA00.0010.00537.9820.1580.1580.0000.0000.0000.000
100A562ALA00.0310.01835.298-0.154-0.1540.0000.0000.0000.000
101A563PRO00.0360.01832.0900.1500.1500.0000.0000.0000.000
102A564VAL0-0.013-0.00927.6960.2130.2130.0000.0000.0000.000
103A565MET0-0.064-0.00926.5670.2380.2380.0000.0000.0000.000
104A566LEU00.0260.02327.1300.2970.2970.0000.0000.0000.000
105A567GLY00.0020.00528.164-0.006-0.0060.0000.0000.0000.000
106A568LYN0-0.013-0.00528.799-0.082-0.0820.0000.0000.0000.000
107A569SER0-0.010-0.03131.890-0.160-0.1600.0000.0000.0000.000
108A570ASP-1-0.873-0.92933.2087.8127.8120.0000.0000.0000.000
109A571VAL00.0550.01135.7900.0080.0080.0000.0000.0000.000
110A572VAL0-0.021-0.00137.789-0.128-0.1280.0000.0000.0000.000
111A573SER0-0.047-0.02437.622-0.166-0.1660.0000.0000.0000.000
112A574LEU00.0090.01634.540-0.072-0.0720.0000.0000.0000.000
113A575ALA00.009-0.00238.074-0.077-0.0770.0000.0000.0000.000
114A576ARG10.8330.91341.198-7.043-7.0430.0000.0000.0000.000
115A577ASP-1-0.836-0.90038.9697.7527.7520.0000.0000.0000.000
116A578VAL0-0.022-0.02038.510-0.086-0.0860.0000.0000.0000.000
117A579LEU0-0.022-0.00641.390-0.113-0.1130.0000.0000.0000.000
118A580GLY00.0330.01244.723-0.163-0.1630.0000.0000.0000.000
119A581GLU-1-0.845-0.89240.5847.3617.3610.0000.0000.0000.000
120A582LEU0-0.038-0.02243.345-0.049-0.0490.0000.0000.0000.000
121A583ALA00.0360.01445.901-0.133-0.1330.0000.0000.0000.000
122A584GLN0-0.133-0.05644.505-0.157-0.1570.0000.0000.0000.000
123A585VAL0-0.079-0.02846.133-0.056-0.0560.0000.0000.0000.000
124A586GLY00.1010.04249.406-0.053-0.0530.0000.0000.0000.000
125A587SER0-0.069-0.04051.6930.0000.0000.0000.0000.0000.000
126A588SER0-0.063-0.02547.6110.0200.0200.0000.0000.0000.000
127A589GLN00.0080.01447.9420.1760.1760.0000.0000.0000.000
128A590THR00.0140.00046.6970.1180.1180.0000.0000.0000.000
129A591ILE00.0490.03042.0430.1950.1950.0000.0000.0000.000
130A592ALA0-0.014-0.00242.5200.1060.1060.0000.0000.0000.000
131A593SER0-0.034-0.04541.5890.1740.1740.0000.0000.0000.000
132A594HIS00.0630.04741.8610.1290.1290.0000.0000.0000.000
133A595GLU-1-0.765-0.85935.9508.5658.5650.0000.0000.0000.000
134A596ASN00.003-0.00234.9550.2270.2270.0000.0000.0000.000
135A597ARG10.8030.88935.533-7.001-7.0010.0000.0000.0000.000
136A598ILE00.0850.04737.3710.1400.1400.0000.0000.0000.000
137A599LEU0-0.001-0.00732.6080.1910.1910.0000.0000.0000.000
138A600ALA0-0.029-0.01732.7820.2960.2960.0000.0000.0000.000
139A601THR00.0100.00233.5810.2790.2790.0000.0000.0000.000
140A602MET0-0.015-0.00733.8820.0740.0740.0000.0000.0000.000
141A603SER0-0.107-0.05829.4340.3030.3030.0000.0000.0000.000
142A604CYS0-0.033-0.01930.0170.3480.3480.0000.0000.0000.000
143A605HIS0-0.060-0.02032.2540.1620.1620.0000.0000.0000.000
144A606GLY00.0580.02128.1860.1150.1150.0000.0000.0000.000
145A607SER0-0.008-0.00925.314-0.216-0.2160.0000.0000.0000.000
146A608ILE0-0.032-0.03122.938-0.247-0.2470.0000.0000.0000.000
147A609ARG10.9330.98826.574-9.639-9.6390.0000.0000.0000.000
148A610ALA00.0750.02929.631-0.082-0.0820.0000.0000.0000.000
149A611GLY0-0.023-0.00731.086-0.184-0.1840.0000.0000.0000.000
150A612ARG10.8870.95628.828-9.449-9.4490.0000.0000.0000.000
151A613ARG10.8910.94127.200-10.011-10.0110.0000.0000.0000.000
152A614LEU00.0280.02922.924-0.148-0.1480.0000.0000.0000.000
153A615THR0-0.008-0.03521.8480.4050.4050.0000.0000.0000.000
154A616LEU00.0570.01116.8510.2040.2040.0000.0000.0000.000
155A617PRO00.0190.00716.8570.7920.7920.0000.0000.0000.000
156A618GLU-1-0.798-0.86117.68613.29013.2900.0000.0000.0000.000
157A619MET0-0.057-0.01418.0750.1940.1940.0000.0000.0000.000
158A620ASN00.010-0.01412.7701.5451.5450.0000.0000.0000.000
159A621ALA00.0030.01114.7130.8000.8000.0000.0000.0000.000
160A622LEU00.0310.01316.7890.0850.0850.0000.0000.0000.000
161A623LEU0-0.021-0.00813.476-0.244-0.2440.0000.0000.0000.000
162A624ARG10.7910.85110.481-23.888-23.8880.0000.0000.0000.000
163A625ASP-1-0.806-0.89313.95314.33914.3390.0000.0000.0000.000
164A626MET0-0.074-0.02516.447-0.614-0.6140.0000.0000.0000.000
165A627GLU-1-0.742-0.83510.74324.09124.0910.0000.0000.0000.000
166A628ASN0-0.043-0.00314.0880.0650.0650.0000.0000.0000.000
167A629THR0-0.027-0.02516.061-1.193-1.1930.0000.0000.0000.000
168A630PRO00.0310.01018.8240.1970.1970.0000.0000.0000.000
169A631ARG10.8260.87020.619-11.345-11.3450.0000.0000.0000.000
170A632SER00.0160.01117.605-0.401-0.4010.0000.0000.0000.000
171A633ASN00.0030.00218.808-0.396-0.3960.0000.0000.0000.000
172A634GLN00.0260.01720.514-0.131-0.1310.0000.0000.0000.000
173A635CYS00.0500.04324.407-0.184-0.1840.0000.0000.0000.000
174A636ASN00.0450.00827.2710.0040.0040.0000.0000.0000.000
175A637HIS0-0.034-0.01930.863-0.239-0.2390.0000.0000.0000.000
176A638GLY0-0.0050.01028.590-0.182-0.1820.0000.0000.0000.000
177A639ARG10.8220.90527.415-10.356-10.3560.0000.0000.0000.000
178A640PRO00.0190.01123.3500.1100.1100.0000.0000.0000.000
179A641THR0-0.040-0.02421.443-0.486-0.4860.0000.0000.0000.000
180A642TRP00.004-0.00615.8600.2620.2620.0000.0000.0000.000
181A643VAL00.0060.01120.069-0.311-0.3110.0000.0000.0000.000
182A644LYS10.8610.90413.736-16.077-16.0770.0000.0000.0000.000
183A645LEU0-0.0220.00716.789-0.635-0.6350.0000.0000.0000.000
184A646THR00.025-0.03913.6340.5570.5570.0000.0000.0000.000
185A647LEU00.009-0.00213.362-1.052-1.0520.0000.0000.0000.000
186A648LYS10.9790.99515.509-17.652-17.6520.0000.0000.0000.000
187A649GLU-1-0.773-0.82817.65414.74014.7400.0000.0000.0000.000
188A650LEU0-0.014-0.01617.207-0.598-0.5980.0000.0000.0000.000
189A651ASP-1-0.900-0.94520.61911.91011.9100.0000.0000.0000.000
190A652THR0-0.054-0.03322.582-0.679-0.6790.0000.0000.0000.000
191A653LEU0-0.079-0.03223.556-0.460-0.4600.0000.0000.0000.000
192A654PHE0-0.104-0.04223.407-0.813-0.8130.0000.0000.0000.000