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: YVV12

Calculation Name: 4R3O-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: N

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptH
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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2536703.512153
FMO2-HF: Nuclear repulsion 2450585.868606
FMO2-HF: Total energy -86117.643547
FMO2-MP2: Total energy -86363.537791


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(N:1:THR)


Summations of interaction energy for fragment #1(N:1:THR)
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.
-36.055-44.12145.57-20.074-17.428-0.12
Interaction energy analysis for fragmet #1(N:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.047
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].
3N3ASN0-0.016-0.0133.092-3.681-0.1110.256-1.789-2.0380.007
4N4PRO00.0180.0232.641-0.4790.9500.776-0.645-1.560-0.003
5N5MET00.000-0.0033.5650.3870.2590.0240.259-0.1550.000
6N6VAL0-0.049-0.0216.291-0.162-0.1620.0000.0000.0000.000
7N7THR0-0.035-0.0156.280-0.242-0.2420.0000.0000.0000.000
8N8GLY00.0330.0298.7080.2330.2330.0000.0000.0000.000
9N9THR00.0100.01411.215-0.207-0.2070.0000.0000.0000.000
10N10SER00.0090.01313.854-0.078-0.0780.0000.0000.0000.000
11N11VAL0-0.0170.00714.9020.0350.0350.0000.0000.0000.000
12N12LEU0-0.018-0.01417.573-0.012-0.0120.0000.0000.0000.000
13N13GLY00.0340.01321.2330.0040.0040.0000.0000.0000.000
14N14VAL00.000-0.00323.145-0.007-0.0070.0000.0000.0000.000
15N15LYS10.9210.97726.7510.2540.2540.0000.0000.0000.000
16N16PHE0-0.036-0.02129.0430.0000.0000.0000.0000.0000.000
17N17GLU-1-0.937-0.98532.464-0.122-0.1220.0000.0000.0000.000
18N18GLY00.0310.03334.3550.0050.0050.0000.0000.0000.000
19N19GLY00.005-0.01830.5700.0080.0080.0000.0000.0000.000
20N20VAL0-0.042-0.01524.615-0.014-0.0140.0000.0000.0000.000
21N21VAL0-0.0060.01326.1620.0090.0090.0000.0000.0000.000
22N22ILE0-0.012-0.00719.540-0.025-0.0250.0000.0000.0000.000
23N23ALA00.0020.00621.8650.0290.0290.0000.0000.0000.000
24N24ALA00.013-0.00917.195-0.055-0.0550.0000.0000.0000.000
25N25ASP-1-0.791-0.90717.147-0.347-0.3470.0000.0000.0000.000
26N26MET0-0.044-0.01117.349-0.037-0.0370.0000.0000.0000.000
27N27LEU0-0.053-0.00815.5410.0610.0610.0000.0000.0000.000
28N28GLY00.0300.01412.454-0.084-0.0840.0000.0000.0000.000
29N29SER0-0.036-0.03412.1370.1200.1200.0000.0000.0000.000
30N30TYR0-0.017-0.0189.867-0.090-0.0900.0000.0000.0000.000
31N31GLY00.0560.02610.9810.0490.0490.0000.0000.0000.000
32N32SER0-0.002-0.01412.626-0.053-0.0530.0000.0000.0000.000
33N33LEU00.0020.01615.4650.0110.0110.0000.0000.0000.000
34N34ALA00.0840.03315.349-0.023-0.0230.0000.0000.0000.000
35N35ARG10.8970.96213.093-0.226-0.2260.0000.0000.0000.000
36N36PHE0-0.011-0.01912.6430.0500.0500.0000.0000.0000.000
37N37ARG10.9690.98116.533-0.003-0.0030.0000.0000.0000.000
38N38ASN0-0.007-0.01218.448-0.020-0.0200.0000.0000.0000.000
39N39ILE0-0.0060.02413.0810.0390.0390.0000.0000.0000.000
40N40SER00.008-0.00917.090-0.043-0.0430.0000.0000.0000.000
41N41ARG10.7950.89413.1290.5800.5800.0000.0000.0000.000
42N42ILE00.0360.01314.962-0.083-0.0830.0000.0000.0000.000
43N43MET0-0.0600.01114.0960.0740.0740.0000.0000.0000.000
44N44ARG10.9450.97017.5910.0450.0450.0000.0000.0000.000
45N45VAL0-0.044-0.02617.5560.0220.0220.0000.0000.0000.000
46N46ASN00.1290.05220.370-0.018-0.0180.0000.0000.0000.000
47N47ASN00.0500.00823.962-0.015-0.0150.0000.0000.0000.000
48N48SER00.0200.03225.952-0.004-0.0040.0000.0000.0000.000
49N49THR0-0.023-0.01921.064-0.036-0.0360.0000.0000.0000.000
50N50MET0-0.0250.01120.2620.0250.0250.0000.0000.0000.000
51N51LEU0-0.005-0.00513.185-0.036-0.0360.0000.0000.0000.000
52N52GLY00.0610.03415.8110.0460.0460.0000.0000.0000.000
53N53ALA0-0.016-0.01510.342-0.083-0.0830.0000.0000.0000.000
54N54SER0-0.021-0.01411.3790.1340.1340.0000.0000.0000.000
55N55GLY0-0.0010.0037.506-0.274-0.2740.0000.0000.0000.000
56N56ASP-1-0.806-0.9373.249-1.668-0.9050.055-0.241-0.577-0.001
57N57TYR0-0.019-0.0355.215-0.087-0.069-0.0010.000-0.0160.000
58N58ALA0-0.0150.0014.9810.2020.2020.0000.0000.0000.000
59N59ASP-1-0.765-0.8561.599-22.715-33.36325.266-9.975-4.644-0.073
60N60PHE00.0020.0034.6650.6280.682-0.001-0.024-0.0290.000
61N61GLN0-0.034-0.0268.1400.1730.1730.0000.0000.0000.000
62N62TYR0-0.021-0.0026.8140.2360.2360.0000.0000.0000.000
63N63LEU00.027-0.0017.9020.0680.0680.0000.0000.0000.000
64N64LYS10.9530.97210.1380.1150.1150.0000.0000.0000.000
65N65GLN0-0.037-0.01612.1250.1010.1010.0000.0000.0000.000
66N66VAL0-0.025-0.01011.575-0.008-0.0080.0000.0000.0000.000
67N67LEU00.021-0.00113.942-0.024-0.0240.0000.0000.0000.000
68N68GLY00.0030.01115.930-0.003-0.0030.0000.0000.0000.000
69N69GLN0-0.033-0.02717.3200.0090.0090.0000.0000.0000.000
70N70MET0-0.0200.00717.466-0.019-0.0190.0000.0000.0000.000
71N71VAL0-0.012-0.00919.983-0.014-0.0140.0000.0000.0000.000
72N72ILE0-0.004-0.00221.842-0.001-0.0010.0000.0000.0000.000
73N73ASP-1-0.904-0.96421.9130.1450.1450.0000.0000.0000.000
74N74GLU-1-0.871-0.93724.203-0.057-0.0570.0000.0000.0000.000
75N75GLU-1-0.988-1.00726.069-0.016-0.0160.0000.0000.0000.000
76N76LEU0-0.093-0.03427.0740.0030.0030.0000.0000.0000.000
77N77LEU0-0.065-0.01828.7460.0030.0030.0000.0000.0000.000
78N78GLY0-0.0050.00831.232-0.001-0.0010.0000.0000.0000.000
79N79ASP-1-0.887-0.95731.795-0.007-0.0070.0000.0000.0000.000
80N80GLY0-0.054-0.02034.078-0.005-0.0050.0000.0000.0000.000
81N81HIS0-0.109-0.05230.567-0.010-0.0100.0000.0000.0000.000
82N82SER00.0460.02427.6190.0070.0070.0000.0000.0000.000
83N83TYR0-0.072-0.03722.478-0.016-0.0160.0000.0000.0000.000
84N84SER00.0510.03125.174-0.014-0.0140.0000.0000.0000.000
85N85PRO00.0720.01722.863-0.016-0.0160.0000.0000.0000.000
86N86ARG10.9560.98621.9630.1870.1870.0000.0000.0000.000
87N87ALA00.0050.01322.488-0.026-0.0260.0000.0000.0000.000
88N88ILE00.0510.02817.840-0.016-0.0160.0000.0000.0000.000
89N89HIS0-0.0060.00117.768-0.019-0.0190.0000.0000.0000.000
90N90SER0-0.0180.01317.889-0.072-0.0720.0000.0000.0000.000
91N91TRP00.0290.00912.982-0.072-0.0720.0000.0000.0000.000
92N92LEU00.0440.00811.694-0.021-0.0210.0000.0000.0000.000
93N93THR0-0.017-0.02913.111-0.144-0.1440.0000.0000.0000.000
94N94ARG10.8970.94713.8230.3360.3360.0000.0000.0000.000
95N95ALA00.0050.01511.105-0.005-0.0050.0000.0000.0000.000
96N96MET0-0.0020.0197.6780.0140.0140.0000.0000.0000.000
97N97TYR00.0260.0089.284-0.194-0.1940.0000.0000.0000.000
98N98SER0-0.032-0.00611.1140.0080.0080.0000.0000.0000.000
99N99ARG10.8860.9202.991-3.471-2.9090.018-0.214-0.3660.002
100N100ARG10.9500.9976.9000.6490.6490.0000.0000.0000.000
101N101SER0-0.066-0.0438.3620.0460.0460.0000.0000.0000.000
102N102LYS10.8970.9617.921-0.027-0.0270.0000.0000.0000.000
103N103MET0-0.0110.0047.3860.1370.1370.0000.0000.0000.000
104N104ASN00.0110.0031.8390.184-6.93912.977-3.516-2.337-0.022
105N105PRO00.0200.0313.3740.7671.8740.040-0.359-0.7890.000
106N106LEU00.0250.0151.993-6.558-6.6755.525-2.629-2.778-0.029
107N107TRP00.0390.0182.6490.3332.6420.634-0.922-2.020-0.001
108N108ASN0-0.058-0.0594.1810.5550.6930.001-0.019-0.1190.000
109N109THR0-0.0010.0077.6990.0760.0760.0000.0000.0000.000
110N110MET0-0.057-0.0289.9520.1140.1140.0000.0000.0000.000
111N111VAL00.0270.01713.4580.0430.0430.0000.0000.0000.000
112N112ILE0-0.007-0.00316.3640.0220.0220.0000.0000.0000.000
113N113GLY00.0330.01318.9790.0080.0080.0000.0000.0000.000
114N114GLY0-0.018-0.03022.5120.0090.0090.0000.0000.0000.000
115N115TYR0-0.025-0.00325.231-0.004-0.0040.0000.0000.0000.000
116N116ALA00.009-0.01428.9590.0090.0090.0000.0000.0000.000
117N117ASP-1-0.915-0.95130.765-0.111-0.1110.0000.0000.0000.000
118N118GLY0-0.0140.00334.2150.0000.0000.0000.0000.0000.000
119N119GLU-1-0.902-0.93131.920-0.143-0.1430.0000.0000.0000.000
120N120SER0-0.044-0.02329.141-0.002-0.0020.0000.0000.0000.000
121N121PHE0-0.068-0.04521.438-0.006-0.0060.0000.0000.0000.000
122N122LEU0-0.009-0.02022.038-0.004-0.0040.0000.0000.0000.000
123N123GLY00.0110.01720.7320.0070.0070.0000.0000.0000.000
124N124TYR0-0.006-0.00714.678-0.032-0.0320.0000.0000.0000.000
125N125VAL00.005-0.00412.7600.0440.0440.0000.0000.0000.000
126N126ASP-1-0.879-0.93411.988-1.386-1.3860.0000.0000.0000.000
127N127MET0-0.007-0.0066.590-0.264-0.2640.0000.0000.0000.000
128N128LEU0-0.031-0.0398.582-0.126-0.1260.0000.0000.0000.000
129N129GLY0-0.001-0.00511.1580.1890.1890.0000.0000.0000.000
130N130VAL0-0.035-0.00713.4080.1390.1390.0000.0000.0000.000
131N131ALA00.0310.00515.621-0.060-0.0600.0000.0000.0000.000
132N132TYR0-0.066-0.02917.9660.0590.0590.0000.0000.0000.000
133N133GLU-1-0.847-0.93621.236-0.292-0.2920.0000.0000.0000.000
134N134ALA0-0.021-0.01823.9930.0070.0070.0000.0000.0000.000
135N135PRO00.0180.00925.733-0.004-0.0040.0000.0000.0000.000
136N136SER00.0420.02025.9220.0090.0090.0000.0000.0000.000
137N137LEU0-0.031-0.00619.795-0.029-0.0290.0000.0000.0000.000
138N138ALA00.0320.01320.1900.0210.0210.0000.0000.0000.000
139N139THR00.001-0.01214.6120.0120.0120.0000.0000.0000.000
140N140GLY00.0160.00115.2900.0410.0410.0000.0000.0000.000
141N141TYR00.0320.00815.8200.0360.0360.0000.0000.0000.000
142N142GLY00.0440.03318.6610.0540.0540.0000.0000.0000.000
143N143ALA0-0.034-0.01619.1060.0430.0430.0000.0000.0000.000
144N144TYR0-0.036-0.02718.0620.0340.0340.0000.0000.0000.000
145N145LEU0-0.054-0.02122.1990.0350.0350.0000.0000.0000.000
146N146ALA00.0350.01223.2880.0220.0220.0000.0000.0000.000
147N147GLN00.018-0.01123.5100.0270.0270.0000.0000.0000.000
148N148PRO0-0.031-0.01625.4730.0170.0170.0000.0000.0000.000
149N149LEU00.0340.02728.4800.0170.0170.0000.0000.0000.000
150N150LEU00.015-0.00425.2450.0130.0130.0000.0000.0000.000
151N151ARG10.9480.97024.8430.3350.3350.0000.0000.0000.000
152N152GLU-1-0.897-0.94130.591-0.164-0.1640.0000.0000.0000.000
153N153VAL0-0.010-0.01432.9680.0130.0130.0000.0000.0000.000
154N154LEU00.014-0.00529.7550.0080.0080.0000.0000.0000.000
155N155GLU-1-0.978-0.97832.585-0.213-0.2130.0000.0000.0000.000
156N156LYS10.7950.90635.8340.1680.1680.0000.0000.0000.000
157N157GLN0-0.088-0.04437.2960.0100.0100.0000.0000.0000.000
158N158PRO0-0.0170.00235.224-0.005-0.0050.0000.0000.0000.000
159N159VAL0-0.0080.00734.776-0.008-0.0080.0000.0000.0000.000
160N160LEU00.0470.02832.1540.0050.0050.0000.0000.0000.000
161N161SER00.0680.03535.5990.0020.0020.0000.0000.0000.000
162N162GLN00.0720.02232.279-0.005-0.0050.0000.0000.0000.000
163N163THR0-0.047-0.03033.271-0.006-0.0060.0000.0000.0000.000
164N164GLU-1-0.793-0.89334.904-0.134-0.1340.0000.0000.0000.000
165N165ALA00.0250.02130.380-0.009-0.0090.0000.0000.0000.000
166N166ARG10.8160.88930.1830.1200.1200.0000.0000.0000.000
167N167ASP-1-0.872-0.94030.647-0.152-0.1520.0000.0000.0000.000
168N168LEU0-0.004-0.00729.982-0.008-0.0080.0000.0000.0000.000
169N169VAL0-0.003-0.00625.734-0.015-0.0150.0000.0000.0000.000
170N170GLU-1-0.877-0.94026.977-0.162-0.1620.0000.0000.0000.000
171N171ARG10.8820.94228.7320.1620.1620.0000.0000.0000.000
172N172CYS0-0.040-0.00825.426-0.008-0.0080.0000.0000.0000.000
173N173MET00.000-0.00120.906-0.029-0.0290.0000.0000.0000.000
174N174ARG10.9220.97824.9410.1490.1490.0000.0000.0000.000
175N175VAL0-0.031-0.01626.2300.0030.0030.0000.0000.0000.000
176N176LEU0-0.013-0.02220.516-0.009-0.0090.0000.0000.0000.000
177N177TYR00.0070.01222.909-0.001-0.0010.0000.0000.0000.000
178N178TYR0-0.0230.00224.4280.0160.0160.0000.0000.0000.000
179N179ARG10.8940.93824.7730.2070.2070.0000.0000.0000.000
180N180ASP-1-0.788-0.88618.181-0.458-0.4580.0000.0000.0000.000
181N181ALA0-0.015-0.00419.8340.0140.0140.0000.0000.0000.000
182N182ARG10.8560.93410.2890.5920.5920.0000.0000.0000.000
183N183SER00.0190.02816.393-0.028-0.0280.0000.0000.0000.000
184N184TYR0-0.027-0.03418.9980.0470.0470.0000.0000.0000.000
185N185ASN00.0810.11521.168-0.021-0.0210.0000.0000.0000.000
186N186ARG10.9060.94822.6610.1030.1030.0000.0000.0000.000
187N187PHE0-0.0100.00021.661-0.027-0.0270.0000.0000.0000.000
188N188GLN00.0670.05520.2660.0020.0020.0000.0000.0000.000
189N189ILE00.0540.02522.785-0.034-0.0340.0000.0000.0000.000
190N190ALA0-0.032-0.00322.4460.0210.0210.0000.0000.0000.000
191N191THR00.024-0.00224.368-0.022-0.0220.0000.0000.0000.000
192N192VAL0-0.018-0.00125.3930.0120.0120.0000.0000.0000.000
193N193THR00.0500.02727.8200.0000.0000.0000.0000.0000.000
194N194GLU-1-0.832-0.91730.911-0.082-0.0820.0000.0000.0000.000
195N195LYS10.8020.89333.4550.0820.0820.0000.0000.0000.000
196N196GLY00.0220.03129.6690.0100.0100.0000.0000.0000.000
197N197VAL0-0.050-0.03323.477-0.012-0.0120.0000.0000.0000.000
198N198GLU-1-0.936-0.95526.934-0.083-0.0830.0000.0000.0000.000
199N199ILE0-0.052-0.04521.360-0.021-0.0210.0000.0000.0000.000
200N200GLU-1-0.810-0.87525.372-0.105-0.1050.0000.0000.0000.000
201N201GLY0-0.036-0.02825.813-0.012-0.0120.0000.0000.0000.000
202N202PRO0-0.042-0.03725.184-0.010-0.0100.0000.0000.0000.000
203N203LEU00.0510.04625.9400.0150.0150.0000.0000.0000.000
204N204SER0-0.050-0.03326.356-0.008-0.0080.0000.0000.0000.000
205N205THR0-0.027-0.07126.825-0.004-0.0040.0000.0000.0000.000
206N206GLU-1-0.888-0.94529.270-0.113-0.1130.0000.0000.0000.000
207N207THR0-0.055-0.03329.562-0.008-0.0080.0000.0000.0000.000
208N208ASN00.003-0.01532.6120.0120.0120.0000.0000.0000.000
209N209TRP0-0.005-0.01529.198-0.010-0.0100.0000.0000.0000.000
210N210ASP-1-0.815-0.90436.033-0.085-0.0850.0000.0000.0000.000
211N211ILE0-0.056-0.04134.2210.0030.0030.0000.0000.0000.000
212N212ALA0-0.023-0.00536.891-0.001-0.0010.0000.0000.0000.000
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