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: 85NZY

Calculation Name: 4TZO-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TZO

Chain ID: G

ChEMBL ID:

UniProt ID: G5EBG0

Base Structure: X-ray

Registration Date: 2023-06-22

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3112517.534471
FMO2-HF: Nuclear repulsion 3016993.875315
FMO2-HF: Total energy -95523.659157
FMO2-MP2: Total energy -95797.836848


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(G:17:ASP)


Summations of interaction energy for fragment #1(G:17:ASP)
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.
-58.419-104.437102.477-48.588-7.8730.152
Interaction energy analysis for fragmet #1(G:17:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.830 / q_NPA : -0.863
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].
3G19ILE00.0070.0243.800-4.387-2.516-0.033-0.902-0.9370.003
4G20ASP-1-0.904-0.9716.45229.35329.3530.0000.0000.0000.000
5G21ASP-1-0.794-0.8998.92017.22917.2290.0000.0000.0000.000
6G22LYS10.9240.94711.999-16.617-16.6170.0000.0000.0000.000
7G23LYS10.8080.91415.031-15.141-15.1410.0000.0000.0000.000
8G24TRP00.0620.0259.461-1.713-1.7130.0000.0000.0000.000
9G25SER0-0.041-0.01412.846-0.289-0.2890.0000.0000.0000.000
10G26LYS10.9100.97613.711-14.519-14.5190.0000.0000.0000.000
11G27LEU0-0.034-0.02216.456-0.511-0.5110.0000.0000.0000.000
12G28PHE00.0180.00211.819-0.362-0.3620.0000.0000.0000.000
13G29PRO00.0240.0169.764-0.441-0.4410.0000.0000.0000.000
14G30ARG10.9750.9858.280-24.715-24.7150.0000.0000.0000.000
15G31ILE00.0020.0104.7211.1951.316-0.001-0.041-0.0780.000
16G32VAL00.025-0.0014.730-6.650-6.528-0.001-0.016-0.1050.000
17G33SER00.0640.0402.870-13.478-10.6790.293-1.434-1.6580.015
18G34ASP-1-0.807-0.9094.77328.78428.849-0.001-0.017-0.0470.000
19G35PRO00.0880.0148.355-0.301-0.3010.0000.0000.0000.000
20G36ASP-1-0.857-0.92311.53320.39320.3930.0000.0000.0000.000
21G37ARG10.8570.9148.778-34.977-34.9770.0000.0000.0000.000
22G38SER0-0.041-0.0438.6270.5870.5870.0000.0000.0000.000
23G39SER00.0410.0289.940-1.697-1.6970.0000.0000.0000.000
24G40ASN00.016-0.00713.266-1.988-1.9880.0000.0000.0000.000
25G41PHE0-0.011-0.01510.581-1.189-1.1890.0000.0000.0000.000
26G42MET00.0170.03512.536-1.408-1.4080.0000.0000.0000.000
27G43THR00.0320.03514.671-1.569-1.5690.0000.0000.0000.000
28G44ARG10.8580.92915.100-17.857-17.8570.0000.0000.0000.000
29G45ALA0-0.023-0.01214.527-0.836-0.8360.0000.0000.0000.000
30G46ILE00.0570.02416.504-0.843-0.8430.0000.0000.0000.000
31G47TYR0-0.042-0.02119.829-0.663-0.6630.0000.0000.0000.000
32G48VAL0-0.030-0.00918.012-0.838-0.8380.0000.0000.0000.000
33G49ALA00.0320.00919.547-0.647-0.6470.0000.0000.0000.000
34G50PHE00.0440.01221.317-0.597-0.5970.0000.0000.0000.000
35G51SER0-0.069-0.04123.784-0.806-0.8060.0000.0000.0000.000
36G52ALA0-0.012-0.01123.266-0.523-0.5230.0000.0000.0000.000
37G53VAL00.0330.03125.164-0.445-0.4450.0000.0000.0000.000
38G54LEU00.0250.00727.384-0.462-0.4620.0000.0000.0000.000
39G55ARG10.8360.93128.242-10.080-10.0800.0000.0000.0000.000
40G56ASN0-0.064-0.05626.8880.1130.1130.0000.0000.0000.000
41G57ARG10.8510.88230.263-9.426-9.4260.0000.0000.0000.000
42G58ASN0-0.086-0.03032.799-0.131-0.1310.0000.0000.0000.000
43G59ILE00.0670.05932.418-0.192-0.1920.0000.0000.0000.000
44G60LEU0-0.050-0.01931.709-0.185-0.1850.0000.0000.0000.000
45G61GLY00.0550.02634.2170.0990.0990.0000.0000.0000.000
46G62GLN0-0.016-0.03532.5410.5800.5800.0000.0000.0000.000
47G63GLU-1-0.862-0.93533.1738.7678.7670.0000.0000.0000.000
48G64TYR0-0.043-0.01432.721-0.005-0.0050.0000.0000.0000.000
49G65PHE0-0.007-0.00627.7580.4300.4300.0000.0000.0000.000
50G66THR0-0.042-0.02326.424-0.110-0.1100.0000.0000.0000.000
51G67LYS10.9680.96226.187-10.879-10.8790.0000.0000.0000.000
52G68ASN0-0.030-0.01821.2160.6550.6550.0000.0000.0000.000
53G69TYR0-0.028-0.02618.845-0.691-0.6910.0000.0000.0000.000
54G70ILE00.0530.05014.8670.2650.2650.0000.0000.0000.000
55G71THR00.0450.01613.1500.8950.8950.0000.0000.0000.000
56G72GLU-1-0.924-0.98915.41616.66716.6670.0000.0000.0000.000
57G73LYS10.9300.97016.730-17.089-17.0890.0000.0000.0000.000
58G74LEU0-0.0230.01318.038-0.800-0.8000.0000.0000.0000.000
59G75LYS10.8850.94019.518-11.886-11.8860.0000.0000.0000.000
60G76CYS00.0450.01021.2850.0260.0260.0000.0000.0000.000
61G77MET0-0.046-0.00223.1090.0220.0220.0000.0000.0000.000
62G78THR00.0320.01221.6630.2700.2700.0000.0000.0000.000
63G79LEU00.0660.05525.055-0.428-0.4280.0000.0000.0000.000
64G80CYS0-0.0490.00026.8820.3380.3380.0000.0000.0000.000
65G81PHE00.0510.05423.484-0.148-0.1480.0000.0000.0000.000
66G82ARG10.9300.95128.811-10.822-10.8220.0000.0000.0000.000
67G83ASN00.0430.02232.488-0.309-0.3090.0000.0000.0000.000
68G84LEU00.0380.01933.6840.2420.2420.0000.0000.0000.000
69G85ARG11.0351.01534.834-8.409-8.4090.0000.0000.0000.000
70G86SER00.009-0.04430.8170.0530.0530.0000.0000.0000.000
71G87ASN00.0000.00429.9570.6600.6600.0000.0000.0000.000
72G88GLN00.0120.00229.9330.2920.2920.0000.0000.0000.000
73G89ILE00.0500.03328.8130.1740.1740.0000.0000.0000.000
74G90ALA0-0.019-0.02025.9240.3710.3710.0000.0000.0000.000
75G91GLN0-0.076-0.04225.7610.5540.5540.0000.0000.0000.000
76G92LEU00.0420.03427.2210.2440.2440.0000.0000.0000.000
77G93LEU00.001-0.00123.5500.3050.3050.0000.0000.0000.000
78G94ARG10.8700.93821.001-13.696-13.6960.0000.0000.0000.000
79G95ASN00.0440.02722.8610.6580.6580.0000.0000.0000.000
80G96ALA00.0280.01523.9160.1270.1270.0000.0000.0000.000
81G97GLY0-0.044-0.04220.1370.3770.3770.0000.0000.0000.000
82G98ASP-1-0.889-0.94319.10315.87115.8710.0000.0000.0000.000
83G99ALA00.0050.00721.0350.1730.1730.0000.0000.0000.000
84G100THR0-0.044-0.01615.9500.2400.2400.0000.0000.0000.000
85G101LYS10.9090.95317.081-15.462-15.4620.0000.0000.0000.000
86G102ASP-1-0.934-0.96718.02915.20315.2030.0000.0000.0000.000
87G103GLY0-0.059-0.03219.613-0.244-0.2440.0000.0000.0000.000
88G104PHE00.0340.01720.370-0.605-0.6050.0000.0000.0000.000
89G105LEU0-0.0020.00821.074-0.652-0.6520.0000.0000.0000.000
90G106LYS10.8720.94721.911-10.952-10.9520.0000.0000.0000.000
91G107GLU-1-0.751-0.83423.10411.97311.9730.0000.0000.0000.000
92G108VAL0-0.032-0.00323.858-0.364-0.3640.0000.0000.0000.000
93G109SER0-0.051-0.09924.8950.5570.5570.0000.0000.0000.000
94G110LEU0-0.077-0.02427.563-0.259-0.2590.0000.0000.0000.000
95G111VAL00.014-0.00129.7380.0170.0170.0000.0000.0000.000
96G112ILE0-0.007-0.00233.128-0.149-0.1490.0000.0000.0000.000
97G113THR0-0.011-0.01635.9470.0350.0350.0000.0000.0000.000
98G114ASN00.0520.01439.4620.0070.0070.0000.0000.0000.000
99G115ASN0-0.0280.00243.062-0.139-0.1390.0000.0000.0000.000
100G116GLU-1-0.983-0.95440.6877.7827.7820.0000.0000.0000.000
101G117GLY00.0810.00840.514-0.130-0.1300.0000.0000.0000.000
102G118ASP-1-0.899-0.94441.3407.2777.2770.0000.0000.0000.000
103G119LEU00.024-0.00739.4270.2500.2500.0000.0000.0000.000
104G120GLU-1-0.927-0.95838.3887.8397.8390.0000.0000.0000.000
105G121ALA0-0.050-0.03235.729-0.070-0.0700.0000.0000.0000.000
106G122ILE0-0.006-0.00137.682-0.034-0.0340.0000.0000.0000.000
107G123GLU-1-0.758-0.85132.7319.5179.5170.0000.0000.0000.000
108G124VAL0-0.009-0.00429.2830.0340.0340.0000.0000.0000.000
109G125PHE0-0.041-0.01326.5210.3250.3250.0000.0000.0000.000
110G126SER00.0580.02825.2860.0220.0220.0000.0000.0000.000
111G127MET0-0.063-0.03218.3760.5380.5380.0000.0000.0000.000
112G128LYS10.9621.00321.529-11.992-11.9920.0000.0000.0000.000
113G129PHE00.024-0.01916.8591.0381.0380.0000.0000.0000.000
114G130ILE0-0.0100.03517.326-0.759-0.7590.0000.0000.0000.000
115G131TYR0-0.017-0.01515.8761.5061.5060.0000.0000.0000.000
116G132PHE00.000-0.00313.230-0.273-0.2730.0000.0000.0000.000
117G133GLU-1-0.923-0.95715.36116.02416.0240.0000.0000.0000.000
118G134ASN00.019-0.01114.8881.1091.1090.0000.0000.0000.000
119G135GLY0-0.053-0.00911.688-0.379-0.3790.0000.0000.0000.000
120G136GLY00.0100.00310.3452.2372.2370.0000.0000.0000.000
121G137VAL0-0.0190.00610.9761.1151.1150.0000.0000.0000.000
122G138VAL00.0320.01713.131-0.585-0.5850.0000.0000.0000.000
123G139ALA00.002-0.00216.7520.2920.2920.0000.0000.0000.000
124G140ARG10.9430.96917.741-16.801-16.8010.0000.0000.0000.000
125G141LEU0-0.018-0.01620.5050.1020.1020.0000.0000.0000.000
126G142SER0-0.184-0.14022.850-0.151-0.1510.0000.0000.0000.000
127G143THR00.016-0.00224.706-0.221-0.2210.0000.0000.0000.000
128G144ASP-1-0.816-0.90928.4739.9789.9780.0000.0000.0000.000
129G145LYS10.9250.94731.701-9.083-9.0830.0000.0000.0000.000
130G146ASN0-0.043-0.02834.603-0.365-0.3650.0000.0000.0000.000
131G147GLY0-0.0020.00932.548-0.153-0.1530.0000.0000.0000.000
132G148GLN0-0.065-0.02632.015-0.085-0.0850.0000.0000.0000.000
133G149GLU-1-0.902-0.95926.20512.27712.2770.0000.0000.0000.000
134G150ASP-1-0.660-0.74225.38911.66911.6690.0000.0000.0000.000
135G151PRO00.025-0.00126.0760.3840.3840.0000.0000.0000.000
136G152HIS0-0.027-0.01620.992-0.133-0.1330.0000.0000.0000.000
137G153PHE00.008-0.02720.8211.0181.0180.0000.0000.0000.000
138G154ALA00.0810.03920.6780.8430.8430.0000.0000.0000.000
139G155LYS10.9050.94419.162-14.570-14.5700.0000.0000.0000.000
140G156LEU0-0.047-0.03116.5180.9720.9720.0000.0000.0000.000
141G157ALA00.0040.00615.8581.4651.4650.0000.0000.0000.000
142G158GLN0-0.044-0.01716.794-0.009-0.0090.0000.0000.0000.000
143G159LEU0-0.066-0.01113.0260.6840.6840.0000.0000.0000.000
144G160VAL00.0220.0039.7320.3520.3520.0000.0000.0000.000
145G161TYR0-0.138-0.1301.248-18.830-70.00494.712-42.350-1.1890.112
146G162GLU-1-0.930-0.9636.84929.85929.8590.0000.0000.0000.000
147G163GLY00.0140.0272.675-3.060-1.2181.069-1.583-1.3290.015
148G164GLY00.0340.0221.649-12.317-13.9856.412-2.487-2.2570.007
149G165ASP-1-0.849-0.9523.36326.60926.6130.0270.242-0.2730.000
150G166SER0-0.017-0.0315.754-5.557-5.5570.0000.0000.0000.000
151G167VAL00.0130.0176.411-4.145-4.1450.0000.0000.0000.000
152G168ARG10.7850.8817.651-30.748-30.7480.0000.0000.0000.000
153G169ASP-1-0.829-0.9069.55121.13621.1360.0000.0000.0000.000
154G170GLN00.0550.0399.995-2.123-2.1230.0000.0000.0000.000
155G171MET0-0.0010.01912.426-2.295-2.2950.0000.0000.0000.000
156G172VAL0-0.071-0.04413.934-1.835-1.8350.0000.0000.0000.000
157G173THR0-0.036-0.02415.493-1.556-1.5560.0000.0000.0000.000
158G174ILE00.0230.02816.463-1.104-1.1040.0000.0000.0000.000
159G175VAL0-0.001-0.00518.525-0.994-0.9940.0000.0000.0000.000
160G176ARG10.9120.94818.523-15.513-15.5130.0000.0000.0000.000
161G177SER00.0170.03521.453-0.935-0.9350.0000.0000.0000.000
162G178VAL00.0430.03423.051-0.605-0.6050.0000.0000.0000.000
163G179GLN0-0.030-0.01923.160-0.496-0.4960.0000.0000.0000.000
164G180PHE0-0.009-0.01025.821-0.565-0.5650.0000.0000.0000.000
165G181LEU00.0290.00826.808-0.446-0.4460.0000.0000.0000.000
166G182CYS0-0.041-0.01328.579-0.377-0.3770.0000.0000.0000.000
167G183THR0-0.080-0.02430.092-0.374-0.3740.0000.0000.0000.000
168G184LYS10.8660.90830.989-9.745-9.7450.0000.0000.0000.000
169G185VAL0-0.0170.01230.765-0.158-0.1580.0000.0000.0000.000
170G186LEU0-0.033-0.02030.978-0.170-0.1700.0000.0000.0000.000
171G187GLU-1-0.895-0.94234.7087.7157.7150.0000.0000.0000.000
172G188PRO0-0.068-0.03937.5690.2110.2110.0000.0000.0000.000
173G189LEU00.003-0.00335.441-0.066-0.0660.0000.0000.0000.000
174G190PRO00.0050.00139.542-0.126-0.1260.0000.0000.0000.000
175G191GLU-1-0.954-0.97942.3746.7726.7720.0000.0000.0000.000
176G192GLU-1-0.976-0.97744.3056.7136.7130.0000.0000.0000.000
177G193PHE0-0.032-0.01437.3040.1470.1470.0000.0000.0000.000
178G194THR0-0.014-0.00538.677-0.054-0.0540.0000.0000.0000.000
179G195ALA0-0.012-0.00134.0580.1300.1300.0000.0000.0000.000
180G196ASN00.0340.03234.1850.0650.0650.0000.0000.0000.000
181G197PHE0-0.020-0.01326.8480.2050.2050.0000.0000.0000.000
182G198ARG10.8190.89530.421-9.008-9.0080.0000.0000.0000.000
183G199LEU0-0.028-0.01126.8240.3760.3760.0000.0000.0000.000
184G200GLU-1-0.891-0.93627.49510.37910.3790.0000.0000.0000.000
185G201TYR00.0210.00126.7440.6290.6290.0000.0000.0000.000
186G202THR0-0.027-0.02623.122-0.338-0.3380.0000.0000.0000.000
187G203ASN00.014-0.01426.570-0.301-0.3010.0000.0000.0000.000
188G204ASP-1-0.935-0.95623.90212.72312.7230.0000.0000.0000.000
189G205ALA0-0.068-0.02126.743-0.076-0.0760.0000.0000.0000.000
190G206PRO0-0.0050.00427.838-0.426-0.4260.0000.0000.0000.000
191G207SER00.010-0.00531.0890.0600.0600.0000.0000.0000.000
192G208ASN0-0.056-0.03531.6970.0540.0540.0000.0000.0000.000
193G209PHE00.0050.01325.3890.0300.0300.0000.0000.0000.000
194G210ARG10.8930.92830.622-9.238-9.2380.0000.0000.0000.000
195G211ILE0-0.027-0.00325.9030.2140.2140.0000.0000.0000.000
196G212ASP-1-0.875-0.93729.2569.8829.8820.0000.0000.0000.000
197G213GLY0-0.065-0.05030.1660.2890.2890.0000.0000.0000.000
198G214PHE0-0.047-0.03228.075-0.057-0.0570.0000.0000.0000.000
199G215GLU-1-0.939-0.95932.7668.2968.2960.0000.0000.0000.000
200G216ASP-1-0.850-0.91535.2949.1649.1640.0000.0000.0000.000
201G217SER00.030-0.00836.005-0.355-0.3550.0000.0000.0000.000
202G218SER0-0.071-0.03036.4190.1220.1220.0000.0000.0000.000
203G219THR0-0.071-0.02737.989-0.026-0.0260.0000.0000.0000.000
204G220PHE00.0560.03828.8710.0350.0350.0000.0000.0000.000
205G221TYR0-0.027-0.04129.160-0.181-0.1810.0000.0000.0000.000
206G222THR0-0.029-0.01035.3110.0190.0190.0000.0000.0000.000
207G223LEU0-0.013-0.01132.3740.0460.0460.0000.0000.0000.000
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209G225ASP-1-0.929-0.97138.6257.7957.7950.0000.0000.0000.000
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