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: YZM72

Calculation Name: 4ZNC-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZNC

Chain ID: F

ChEMBL ID:

UniProt ID: P01860

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptHSide
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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2000543.511828
FMO2-HF: Nuclear repulsion 1922429.222646
FMO2-HF: Total energy -78114.289182
FMO2-MP2: Total energy -78340.426057


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(F:240:VAL)


Summations of interaction energy for fragment #1(F:240:VAL)
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.
-14.518-6.03712.131-7.28-13.3290.003
Interaction energy analysis for fragmet #1(F:240:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.001
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].
3F242LEU00.0130.0033.864-1.8410.461-0.027-1.184-1.0910.002
4F243PHE00.0030.0036.218-0.012-0.0120.0000.0000.0000.000
5F244PRO00.0290.0209.980-0.034-0.0340.0000.0000.0000.000
6F245PRO00.0030.01313.0070.0310.0310.0000.0000.0000.000
7F246LYS10.8580.92116.107-0.179-0.1790.0000.0000.0000.000
8F247PRO00.0770.03418.867-0.015-0.0150.0000.0000.0000.000
9F248LYS10.8820.91221.375-0.101-0.1010.0000.0000.0000.000
10F249ASP-1-0.808-0.89120.4050.1220.1220.0000.0000.0000.000
11F250THR0-0.058-0.02219.488-0.011-0.0110.0000.0000.0000.000
12F251LEU0-0.0120.01122.287-0.009-0.0090.0000.0000.0000.000
13F252MET0-0.0130.01225.843-0.006-0.0060.0000.0000.0000.000
14F253ILE00.0590.02426.6470.0030.0030.0000.0000.0000.000
15F254SER0-0.041-0.01528.2580.0000.0000.0000.0000.0000.000
16F255ARG10.8010.89022.424-0.105-0.1050.0000.0000.0000.000
17F256THR00.022-0.00520.513-0.008-0.0080.0000.0000.0000.000
18F257PRO0-0.0200.01818.7660.0160.0160.0000.0000.0000.000
19F258GLU-1-0.892-0.96214.7280.1460.1460.0000.0000.0000.000
20F259VAL00.0150.0169.8840.0230.0230.0000.0000.0000.000
21F260THR0-0.0080.0008.897-0.008-0.0080.0000.0000.0000.000
22F261CYS0-0.077-0.0344.460-0.326-0.1210.004-0.036-0.1720.000
23F262VAL00.007-0.0015.023-0.331-0.148-0.001-0.030-0.1520.000
24F263VAL0-0.009-0.0042.224-2.703-0.0203.501-2.901-3.283-0.014
25F264VAL0-0.005-0.0072.499-3.165-2.6752.854-1.109-2.2340.008
26F265ASP-1-0.915-0.9584.277-2.075-1.891-0.001-0.024-0.1590.000
27F266VAL0-0.034-0.0256.434-0.272-0.2720.0000.0000.0000.000
28F267SER0-0.0010.0098.778-0.029-0.0290.0000.0000.0000.000
29F268HIS0-0.023-0.02311.1710.0100.0100.0000.0000.0000.000
30F269GLU-1-0.928-0.96614.761-0.131-0.1310.0000.0000.0000.000
31F270ASP-1-0.786-0.87913.377-0.214-0.2140.0000.0000.0000.000
32F271PRO00.0050.02711.965-0.051-0.0510.0000.0000.0000.000
33F272GLU-1-0.981-0.99112.241-0.093-0.0930.0000.0000.0000.000
34F273VAL0-0.034-0.0157.053-0.096-0.0960.0000.0000.0000.000
35F274GLN0-0.039-0.0219.5540.0520.0520.0000.0000.0000.000
36F275PHE00.015-0.0105.145-0.176-0.1760.0000.0000.0000.000
37F276LYS10.8150.9038.6850.3160.3160.0000.0000.0000.000
38F277TRP00.0550.0178.917-0.070-0.0700.0000.0000.0000.000
39F278TYR0-0.094-0.07610.304-0.009-0.0090.0000.0000.0000.000
40F279VAL00.0270.00213.1820.0110.0110.0000.0000.0000.000
41F280ASP-1-0.793-0.88815.843-0.045-0.0450.0000.0000.0000.000
42F281GLY0-0.033-0.01615.230-0.002-0.0020.0000.0000.0000.000
43F282VAL0-0.013-0.00416.246-0.014-0.0140.0000.0000.0000.000
44F283GLU-1-0.807-0.87214.301-0.202-0.2020.0000.0000.0000.000
45F284VAL0-0.022-0.00314.5900.0190.0190.0000.0000.0000.000
46F285HIS00.033-0.00315.231-0.016-0.0160.0000.0000.0000.000
47F286ASN0-0.044-0.00516.906-0.007-0.0070.0000.0000.0000.000
48F287ALA0-0.0040.01212.1830.0180.0180.0000.0000.0000.000
49F288LYS10.9520.97013.373-0.049-0.0490.0000.0000.0000.000
50F289THR00.0340.00311.2490.0130.0130.0000.0000.0000.000
51F290LYS10.9580.98712.704-0.235-0.2350.0000.0000.0000.000
52F291PRO00.0490.03612.3990.0610.0610.0000.0000.0000.000
53F302VAL00.0450.0277.205-0.101-0.1010.0000.0000.0000.000
54F303VAL0-0.056-0.0396.5180.1510.1510.0000.0000.0000.000
55F304SER0-0.0140.0037.855-0.134-0.1340.0000.0000.0000.000
56F305VAL0-0.025-0.0159.2750.0370.0370.0000.0000.0000.000
57F306LEU00.0130.02211.971-0.027-0.0270.0000.0000.0000.000
58F307THR00.011-0.00113.5080.0100.0100.0000.0000.0000.000
59F308VAL0-0.019-0.01115.316-0.017-0.0170.0000.0000.0000.000
60F309LEU00.0160.00618.1310.0090.0090.0000.0000.0000.000
61F310HIS00.0080.00821.091-0.006-0.0060.0000.0000.0000.000
62F311GLN00.0500.01722.7800.0050.0050.0000.0000.0000.000
63F312ASP-1-0.841-0.93119.885-0.010-0.0100.0000.0000.0000.000
64F313TRP0-0.021-0.02013.713-0.004-0.0040.0000.0000.0000.000
65F314LEU0-0.007-0.00919.235-0.001-0.0010.0000.0000.0000.000
66F315ASN0-0.036-0.01522.4370.0000.0000.0000.0000.0000.000
67F316GLY0-0.036-0.00919.630-0.005-0.0050.0000.0000.0000.000
68F317LYS10.8600.94518.0700.0230.0230.0000.0000.0000.000
69F318GLU-1-0.883-0.91813.793-0.037-0.0370.0000.0000.0000.000
70F319TYR00.0180.00011.629-0.010-0.0100.0000.0000.0000.000
71F320LYS10.8570.9218.5970.2780.2780.0000.0000.0000.000
72F322LYS10.9440.9755.2670.3730.3730.0000.0000.0000.000
73F323VAL0-0.006-0.0062.523-0.5780.0350.474-0.202-0.885-0.001
74F324SER0-0.021-0.0205.243-0.215-0.178-0.001-0.001-0.0340.000
75F325ASN00.0340.0097.7290.1930.1930.0000.0000.0000.000
76F326LYS10.8450.9209.5170.2210.2210.0000.0000.0000.000
77F327ALA0-0.025-0.0049.7350.0200.0200.0000.0000.0000.000
78F328LEU00.016-0.0095.339-0.118-0.1180.0000.0000.0000.000
79F329PRO0-0.0150.0158.7890.0870.0870.0000.0000.0000.000
80F330ALA00.004-0.0059.1010.1130.1130.0000.0000.0000.000
81F331PRO00.0140.0146.848-0.166-0.1660.0000.0000.0000.000
82F332ILE0-0.026-0.0182.256-0.954-0.5422.837-0.700-2.5490.000
83F333GLU-1-0.806-0.9074.090-0.593-0.3340.001-0.054-0.2060.000
84F334LYS10.8780.9532.380-1.400-0.3462.491-1.038-2.5070.008
85F335THR00.0280.0015.126-0.102-0.043-0.001-0.001-0.0570.000
86F336ILE0-0.026-0.0098.5750.0210.0210.0000.0000.0000.000
87F337SER0-0.039-0.04810.661-0.005-0.0050.0000.0000.0000.000
88F338LYS10.8350.91314.415-0.019-0.0190.0000.0000.0000.000
89F339THR0-0.008-0.00817.520-0.012-0.0120.0000.0000.0000.000
90F340LYS10.9050.95617.4080.0130.0130.0000.0000.0000.000
91F341GLY00.0420.01921.6860.0050.0050.0000.0000.0000.000
92F342GLN0-0.036-0.02725.250-0.001-0.0010.0000.0000.0000.000
93F343PRO00.0250.02026.5070.0030.0030.0000.0000.0000.000
94F344ARG10.7900.88428.576-0.036-0.0360.0000.0000.0000.000
95F345GLU-1-0.861-0.93930.6170.0370.0370.0000.0000.0000.000
96F346PRO0-0.048-0.00630.2250.0000.0000.0000.0000.0000.000
97F347GLN0-0.033-0.00533.014-0.003-0.0030.0000.0000.0000.000
98F348VAL0-0.012-0.02134.5380.0030.0030.0000.0000.0000.000
99F349TYR00.003-0.00137.115-0.004-0.0040.0000.0000.0000.000
100F350THR0-0.013-0.00538.8390.0030.0030.0000.0000.0000.000
101F351LEU0-0.008-0.00939.753-0.003-0.0030.0000.0000.0000.000
102F352PRO00.0010.00342.0080.0030.0030.0000.0000.0000.000
103F353PRO00.0380.02543.9130.0000.0000.0000.0000.0000.000
104F354SER00.0130.00744.853-0.003-0.0030.0000.0000.0000.000
105F355ARG10.9990.98946.779-0.031-0.0310.0000.0000.0000.000
106F356GLU-1-0.871-0.94447.6370.0380.0380.0000.0000.0000.000
107F357GLU-1-0.841-0.89441.7290.0600.0600.0000.0000.0000.000
108F358MET0-0.023-0.00646.4760.0020.0020.0000.0000.0000.000
109F359THR0-0.023-0.00949.0980.0000.0000.0000.0000.0000.000
110F360LYS10.9320.97443.355-0.053-0.0530.0000.0000.0000.000
111F361ASN00.007-0.00244.184-0.003-0.0030.0000.0000.0000.000
112F362GLN0-0.012-0.01439.7020.0010.0010.0000.0000.0000.000
113F363VAL0-0.044-0.01443.096-0.001-0.0010.0000.0000.0000.000
114F364SER0-0.022-0.04839.2370.0060.0060.0000.0000.0000.000
115F365LEU0-0.0330.00239.333-0.004-0.0040.0000.0000.0000.000
116F366THR00.0010.00836.9390.0060.0060.0000.0000.0000.000
117F367CYS0-0.040-0.01235.087-0.005-0.0050.0000.0000.0000.000
118F368LEU0-0.0170.01334.7720.0050.0050.0000.0000.0000.000
119F369VAL00.0270.00731.324-0.004-0.0040.0000.0000.0000.000
120F370LYS10.9410.95532.277-0.040-0.0400.0000.0000.0000.000
121F371GLY00.0390.02832.608-0.002-0.0020.0000.0000.0000.000
122F372PHE0-0.050-0.01325.983-0.003-0.0030.0000.0000.0000.000
123F373TYR00.022-0.00223.2500.0040.0040.0000.0000.0000.000
124F374PRO00.0490.04022.102-0.004-0.0040.0000.0000.0000.000
125F375SER00.0360.00720.916-0.001-0.0010.0000.0000.0000.000
126F376ASP-1-0.942-0.98119.7950.0960.0960.0000.0000.0000.000
127F377ILE0-0.021-0.00622.155-0.009-0.0090.0000.0000.0000.000
128F378ALA0-0.053-0.01624.2820.0130.0130.0000.0000.0000.000
129F379VAL00.012-0.00626.461-0.009-0.0090.0000.0000.0000.000
130F380GLU-1-0.821-0.88228.4150.1030.1030.0000.0000.0000.000
131F381TRP00.024-0.00231.257-0.009-0.0090.0000.0000.0000.000
132F382GLU-1-0.806-0.87934.6240.0660.0660.0000.0000.0000.000
133F383SER0-0.025-0.03037.224-0.004-0.0040.0000.0000.0000.000
134F384SER0-0.021-0.01040.8560.0000.0000.0000.0000.0000.000
135F385GLY00.0080.00940.1400.0000.0000.0000.0000.0000.000
136F386GLN0-0.021-0.01938.1480.0030.0030.0000.0000.0000.000
137F387PRO00.0140.02033.2090.0000.0000.0000.0000.0000.000
138F388GLU-1-0.775-0.86534.6860.0650.0650.0000.0000.0000.000
139F389ASN0-0.018-0.01233.1590.0110.0110.0000.0000.0000.000
140F390ASN0-0.018-0.01932.7800.0000.0000.0000.0000.0000.000
141F391TYR00.0720.04028.892-0.007-0.0070.0000.0000.0000.000
142F392ASN0-0.052-0.02229.2250.0160.0160.0000.0000.0000.000
143F393THR00.0230.01427.275-0.012-0.0120.0000.0000.0000.000
144F394THR0-0.0040.01426.5090.0090.0090.0000.0000.0000.000
145F395PRO00.012-0.00122.387-0.002-0.0020.0000.0000.0000.000
146F396PRO0-0.0100.00222.975-0.009-0.0090.0000.0000.0000.000
147F397MET0-0.016-0.00424.9170.0070.0070.0000.0000.0000.000
148F398LEU0-0.030-0.00425.701-0.005-0.0050.0000.0000.0000.000
149F399ASP-1-0.788-0.88027.8660.0460.0460.0000.0000.0000.000
150F400SER0-0.072-0.04831.305-0.003-0.0030.0000.0000.0000.000
151F401ASP-1-0.774-0.85433.2900.0330.0330.0000.0000.0000.000
152F402GLY0-0.043-0.02229.498-0.002-0.0020.0000.0000.0000.000
153F403SER0-0.092-0.05428.5170.0020.0020.0000.0000.0000.000
154F404PHE00.008-0.01123.2580.0030.0030.0000.0000.0000.000
155F405PHE0-0.030-0.02528.645-0.003-0.0030.0000.0000.0000.000
156F406LEU0-0.022-0.01427.1460.0060.0060.0000.0000.0000.000
157F407TYR00.0500.00930.389-0.008-0.0080.0000.0000.0000.000
158F408SER0-0.042-0.02230.8980.0070.0070.0000.0000.0000.000
159F409LYS10.9020.93632.576-0.084-0.0840.0000.0000.0000.000
160F410LEU00.0170.01233.9810.0060.0060.0000.0000.0000.000
161F411THR0-0.059-0.03236.048-0.003-0.0030.0000.0000.0000.000
162F412VAL00.0340.02737.8720.0010.0010.0000.0000.0000.000
163F413ASP-1-0.877-0.95440.9790.0590.0590.0000.0000.0000.000
164F414LYS10.8780.95044.145-0.046-0.0460.0000.0000.0000.000
165F415SER0-0.017-0.01147.062-0.001-0.0010.0000.0000.0000.000
166F416ARG10.8860.91740.337-0.061-0.0610.0000.0000.0000.000
167F417TRP00.0520.03444.957-0.001-0.0010.0000.0000.0000.000
168F418GLN0-0.010-0.02947.215-0.001-0.0010.0000.0000.0000.000
169F419GLN0-0.043-0.02050.441-0.001-0.0010.0000.0000.0000.000
170F420GLY00.0110.02250.327-0.001-0.0010.0000.0000.0000.000
171F421ASN0-0.091-0.04346.158-0.001-0.0010.0000.0000.0000.000
172F422ILE00.0150.00244.5070.0000.0000.0000.0000.0000.000
173F423PHE0-0.033-0.00940.2920.0020.0020.0000.0000.0000.000
174F424SER0-0.040-0.05739.035-0.003-0.0030.0000.0000.0000.000
175F425CYS0-0.037-0.00134.3030.0040.0040.0000.0000.0000.000
176F426SER00.0240.00333.844-0.004-0.0040.0000.0000.0000.000
177F427VAL0-0.007-0.01030.4430.0060.0060.0000.0000.0000.000
178F428MET0-0.010-0.01328.156-0.004-0.0040.0000.0000.0000.000
179F429HIS00.034-0.01526.2100.0030.0030.0000.0000.0000.000
180F430GLU-1-0.788-0.88824.1390.0350.0350.0000.0000.0000.000
181F431ALA0-0.033-0.00727.681-0.004-0.0040.0000.0000.0000.000
182F432LEU0-0.0370.00130.685-0.002-0.0020.0000.0000.0000.000
183F433HIS00.0760.03432.7830.0000.0000.0000.0000.0000.000
184F434ASN0-0.043-0.03133.9890.0010.0010.0000.0000.0000.000
185F435HIS0-0.037-0.02728.2060.0000.0000.0000.0000.0000.000
186F436TYR0-0.052-0.02930.5690.0060.0060.0000.0000.0000.000
187F437THR00.0130.01833.163-0.004-0.0040.0000.0000.0000.000
188F438GLN0-0.024-0.01935.4580.0020.0020.0000.0000.0000.000
189F439LYS10.8920.96537.909-0.044-0.0440.0000.0000.0000.000
190F440SER00.0580.01439.9000.0040.0040.0000.0000.0000.000
191F441LEU0-0.041-0.01541.823-0.002-0.0020.0000.0000.0000.000
192F442SER00.0270.00144.2180.0020.0020.0000.0000.0000.000
193F443LEU0-0.0260.01147.129-0.001-0.0010.0000.0000.0000.000
194F444SER00.0110.01050.103-0.001-0.0010.0000.0000.0000.000