Manual

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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: XRY88

Calculation Name: 4GZC-A-Xray29

Preferred Name:

Target Type:

Ligand Name: chloride ion

ligand 3-letter code: CL

PDB ID: 4GZC

Chain ID: A

ChEMBL ID:

UniProt ID: Q05785

Base Structure: X-ray

Registration Date: 2018-09-06

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 211
LigandCharge CL-=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1495588.316641
FMO2-HF: Nuclear repulsion 1434160.754151
FMO2-HF: Total energy -61427.562489
FMO2-MP2: Total energy -61602.614308


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:14:ACE)


Summations of interaction energy for fragment #1(A:14:ACE)
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.
-1.8780.1081.155-1.67-1.472-0.01
Interaction energy analysis for fragmet #1(A:14:ACE)
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 : -0.031
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].
3A16TYR0-0.086-0.0273.838-0.1361.593-0.015-0.840-0.875-0.003
4A17SER00.0810.0245.4520.1020.1020.0000.0000.0000.000
5A18SER0-0.011-0.0178.1300.1270.1270.0000.0000.0000.000
6A19THR00.030-0.0269.8050.0670.0670.0000.0000.0000.000
7A20GLN00.0220.0059.359-0.117-0.1170.0000.0000.0000.000
8A21VAL0-0.048-0.0207.3880.0400.0400.0000.0000.0000.000
9A22LEU00.0660.03910.0600.0360.0360.0000.0000.0000.000
10A23VAL00.0420.02213.7190.0150.0150.0000.0000.0000.000
11A24ARG10.8960.96210.0380.1230.1230.0000.0000.0000.000
12A25ASP-1-0.878-0.94613.3550.1250.1250.0000.0000.0000.000
13A26ALA00.0260.02314.7160.0040.0040.0000.0000.0000.000
14A27THR0-0.025-0.03216.898-0.004-0.0040.0000.0000.0000.000
15A28ALA0-0.030-0.00715.842-0.011-0.0110.0000.0000.0000.000
16A29ASN0-0.036-0.02417.5150.0010.0010.0000.0000.0000.000
17A30ASP-1-0.851-0.92518.7740.0660.0660.0000.0000.0000.000
18A31SER00.006-0.01321.582-0.006-0.0060.0000.0000.0000.000
19A32ARG10.8080.91316.601-0.089-0.0890.0000.0000.0000.000
20A33THR0-0.008-0.01323.517-0.011-0.0110.0000.0000.0000.000
21A34PRO0-0.007-0.00421.7950.0090.0090.0000.0000.0000.000
22A35SER00.0410.02521.417-0.006-0.0060.0000.0000.0000.000
23A36ILE00.0500.00223.554-0.005-0.0050.0000.0000.0000.000
24A37ASP-1-0.920-0.95021.3510.0590.0590.0000.0000.0000.000
25A38THR00.0170.01218.271-0.001-0.0010.0000.0000.0000.000
26A39LEU0-0.031-0.01820.501-0.014-0.0140.0000.0000.0000.000
27A40ASP-1-0.761-0.84623.043-0.007-0.0070.0000.0000.0000.000
28A41ASP-1-0.842-0.90318.4720.0320.0320.0000.0000.0000.000
29A42LEU0-0.065-0.04716.790-0.017-0.0170.0000.0000.0000.000
30A43ALA00.0110.00320.162-0.014-0.0140.0000.0000.0000.000
31A44GLN00.0300.02122.152-0.005-0.0050.0000.0000.0000.000
32A45ARG10.9070.93113.3210.0080.0080.0000.0000.0000.000
33A46SER0-0.034-0.01019.969-0.015-0.0150.0000.0000.0000.000
34A47TYR0-0.018-0.01121.855-0.008-0.0080.0000.0000.0000.000
35A48ASP-1-0.905-0.92619.035-0.122-0.1220.0000.0000.0000.000
36A49SER0-0.018-0.02720.350-0.014-0.0140.0000.0000.0000.000
37A50VAL00.0280.02515.322-0.012-0.0120.0000.0000.0000.000
38A51ASP-1-0.760-0.86015.527-0.183-0.1830.0000.0000.0000.000
39A52PHE0-0.023-0.01517.007-0.005-0.0050.0000.0000.0000.000
40A53PHE0-0.027-0.01218.8540.0020.0020.0000.0000.0000.000
41A54GLU-1-0.765-0.82912.742-0.411-0.4110.0000.0000.0000.000
42A55ILE00.003-0.01215.748-0.007-0.0070.0000.0000.0000.000
43A56MET0-0.0130.00017.5460.0090.0090.0000.0000.0000.000
44A57ASP-1-0.712-0.79816.901-0.244-0.2440.0000.0000.0000.000
45A58MET0-0.120-0.04111.785-0.010-0.0100.0000.0000.0000.000
46A59LEU0-0.008-0.01616.7020.0220.0220.0000.0000.0000.000
47A60ASP-1-0.811-0.89320.085-0.122-0.1220.0000.0000.0000.000
48A61LYS10.9430.99114.3270.2550.2550.0000.0000.0000.000
49A62ARG10.8250.91414.4290.1010.1010.0000.0000.0000.000
50A63LEU00.0250.01020.5560.0170.0170.0000.0000.0000.000
51A64ASN0-0.0130.01523.2240.0190.0190.0000.0000.0000.000
52A65ASP-1-0.831-0.89421.234-0.082-0.0820.0000.0000.0000.000
53A66LYS10.8990.92823.9680.0690.0690.0000.0000.0000.000
54A67GLY00.0180.01226.1080.0010.0010.0000.0000.0000.000
55A68LYS10.9800.97624.8330.0160.0160.0000.0000.0000.000
56A69TYR0-0.069-0.03020.4380.0080.0080.0000.0000.0000.000
57A70TRP00.0680.04023.622-0.006-0.0060.0000.0000.0000.000
58A71ARG10.8980.94523.289-0.006-0.0060.0000.0000.0000.000
59A72HIS0-0.026-0.00518.0950.0080.0080.0000.0000.0000.000
60A73VAL00.0090.02421.677-0.005-0.0050.0000.0000.0000.000
61A74ALA00.009-0.00324.7250.0000.0000.0000.0000.0000.000
62A75LYS10.8180.92420.425-0.016-0.0160.0000.0000.0000.000
63A76SER00.0340.00221.187-0.004-0.0040.0000.0000.0000.000
64A77LEU0-0.009-0.00122.873-0.002-0.0020.0000.0000.0000.000
65A78THR0-0.036-0.00225.2740.0040.0040.0000.0000.0000.000
66A79VAL00.0430.02220.6980.0030.0030.0000.0000.0000.000
67A80LEU0-0.0020.00023.9620.0000.0000.0000.0000.0000.000
68A81ASP-1-0.781-0.86225.863-0.024-0.0240.0000.0000.0000.000
69A82TYR0-0.016-0.03825.6960.0010.0010.0000.0000.0000.000
70A83LEU0-0.001-0.01221.9890.0000.0000.0000.0000.0000.000
71A84VAL0-0.033-0.01326.401-0.001-0.0010.0000.0000.0000.000
72A85ARG10.8030.89429.8030.0220.0220.0000.0000.0000.000
73A86PHE00.0500.02427.9880.0020.0020.0000.0000.0000.000
74A87GLY00.0180.01326.0890.0010.0010.0000.0000.0000.000
75A88SER00.0070.00124.8060.0040.0040.0000.0000.0000.000
76A89GLU-1-0.731-0.86727.452-0.046-0.0460.0000.0000.0000.000
77A90ASN00.0220.01225.3100.0020.0020.0000.0000.0000.000
78A91CYS00.0010.01425.140-0.007-0.0070.0000.0000.0000.000
79A92VAL00.0070.00926.9840.0000.0000.0000.0000.0000.000
80A93LEU0-0.060-0.03429.3340.0010.0010.0000.0000.0000.000
81A94TRP00.0820.03823.7810.0110.0110.0000.0000.0000.000
82A95CYS0-0.024-0.00728.0330.0000.0000.0000.0000.0000.000
83A96ARG10.8470.90330.0860.0490.0490.0000.0000.0000.000
84A97GLU-1-0.831-0.89528.739-0.100-0.1000.0000.0000.0000.000
85A98ASN0-0.050-0.01126.925-0.002-0.0020.0000.0000.0000.000
86A99PHE00.0290.01830.1230.0040.0040.0000.0000.0000.000
87A100TYR0-0.026-0.02432.8240.0060.0060.0000.0000.0000.000
88A101VAL00.0720.03527.4970.0050.0050.0000.0000.0000.000
89A102ILE00.0500.03729.3110.0050.0050.0000.0000.0000.000
90A103LYS10.8260.89431.2940.0490.0490.0000.0000.0000.000
91A104THR0-0.0020.01031.8470.0030.0030.0000.0000.0000.000
92A105LEU00.0200.02727.9470.0040.0040.0000.0000.0000.000
93A106ARG10.7840.85732.3410.0410.0410.0000.0000.0000.000
94A107GLU-1-0.906-0.95335.254-0.036-0.0360.0000.0000.0000.000
95A108PHE0-0.0140.01328.2650.0010.0010.0000.0000.0000.000
96A109ARG10.9430.96433.5070.0350.0350.0000.0000.0000.000
97A110HIS0-0.008-0.00930.674-0.007-0.0070.0000.0000.0000.000
98A111GLU-1-0.957-0.96733.293-0.011-0.0110.0000.0000.0000.000
99A112ASN0-0.082-0.05732.636-0.001-0.0010.0000.0000.0000.000
100A113GLU-1-0.885-0.96332.466-0.004-0.0040.0000.0000.0000.000
101A114SER0-0.095-0.04035.5310.0010.0010.0000.0000.0000.000
102A115GLY00.0270.02037.4320.0000.0000.0000.0000.0000.000
103A116PHE0-0.057-0.00734.425-0.001-0.0010.0000.0000.0000.000
104A117ASP-1-0.696-0.81635.850-0.018-0.0180.0000.0000.0000.000
105A118GLU-1-0.835-0.91531.0260.0000.0000.0000.0000.0000.000
106A119GLY00.0270.01032.101-0.001-0.0010.0000.0000.0000.000
107A120GLN0-0.0050.00033.255-0.003-0.0030.0000.0000.0000.000
108A121ILE00.0210.00530.745-0.002-0.0020.0000.0000.0000.000
109A122ILE00.0000.00328.179-0.001-0.0010.0000.0000.0000.000
110A123ARG10.7970.90431.7010.0190.0190.0000.0000.0000.000
111A124VAL0-0.032-0.01635.075-0.001-0.0010.0000.0000.0000.000
112A125LYS10.9490.98428.8750.0140.0140.0000.0000.0000.000
113A126ALA00.0400.03032.248-0.002-0.0020.0000.0000.0000.000
114A127LYS10.9140.95533.4170.0210.0210.0000.0000.0000.000
115A128GLU-1-0.883-0.90535.445-0.016-0.0160.0000.0000.0000.000
116A129LEU00.0970.05730.0420.0000.0000.0000.0000.0000.000
117A130VAL0-0.050-0.03334.243-0.002-0.0020.0000.0000.0000.000
118A131SER0-0.068-0.02836.4020.0010.0010.0000.0000.0000.000
119A132LEU00.0450.02434.1410.0000.0000.0000.0000.0000.000
120A133LEU00.0140.00432.162-0.001-0.0010.0000.0000.0000.000
121A134ASN0-0.020-0.01236.595-0.004-0.0040.0000.0000.0000.000
122A135ASP-1-0.878-0.91739.853-0.022-0.0220.0000.0000.0000.000
123A136GLU-1-0.932-0.98339.821-0.031-0.0310.0000.0000.0000.000
124A137GLU-1-0.908-0.94940.423-0.020-0.0200.0000.0000.0000.000
125A138ARG10.9390.96638.8430.0220.0220.0000.0000.0000.000
126A139LEU0-0.059-0.03033.9890.0000.0000.0000.0000.0000.000
127A140ARG10.7940.86034.3460.0400.0400.0000.0000.0000.000
128A141GLU-1-0.892-0.94038.666-0.016-0.0160.0000.0000.0000.000
129A142GLU-1-0.874-0.94036.405-0.014-0.0140.0000.0000.0000.000
130A143ARG10.7540.86429.9200.0420.0420.0000.0000.0000.000
131A144SER0-0.066-0.02434.9930.0000.0000.0000.0000.0000.000
132A145MET0-0.093-0.04237.5910.0020.0020.0000.0000.0000.000
133A146ASN0-0.083-0.04532.7470.0050.0050.0000.0000.0000.000
134A147NME0-0.0430.00033.1870.0010.0010.0000.0000.0000.000
135A201CL--1-0.866-0.9249.855-0.248-0.2480.0000.0000.0000.000
136A301HOH0-0.025-0.01726.368-0.001-0.0010.0000.0000.0000.000
137A302HOH0-0.049-0.04919.282-0.004-0.0040.0000.0000.0000.000
138A303HOH0-0.031-0.01610.8420.0300.0300.0000.0000.0000.000
139A304HOH0-0.051-0.03427.081-0.002-0.0020.0000.0000.0000.000
140A305HOH0-0.071-0.05113.861-0.014-0.0140.0000.0000.0000.000
141A306HOH0-0.061-0.04228.1510.0020.0020.0000.0000.0000.000
142A307HOH00.0060.00241.2850.0000.0000.0000.0000.0000.000
143A308HOH0-0.025-0.01214.115-0.026-0.0260.0000.0000.0000.000
144A310HOH0-0.022-0.02223.8160.0000.0000.0000.0000.0000.000
145A311HOH00.0070.00316.889-0.007-0.0070.0000.0000.0000.000
146A312HOH0-0.040-0.03313.228-0.008-0.0080.0000.0000.0000.000
147A313HOH0-0.040-0.02630.2620.0000.0000.0000.0000.0000.000
148A315HOH00.002-0.00237.7710.0000.0000.0000.0000.0000.000
149A316HOH00.0520.03716.370-0.004-0.0040.0000.0000.0000.000
150A317HOH00.0130.01018.899-0.005-0.0050.0000.0000.0000.000
151A318HOH0-0.032-0.03232.404-0.001-0.0010.0000.0000.0000.000
152A319HOH00.0390.02630.114-0.002-0.0020.0000.0000.0000.000
153A320HOH0-0.024-0.01418.576-0.001-0.0010.0000.0000.0000.000
154A321HOH00.0570.0342.816-1.193-0.9361.170-0.830-0.597-0.007
155A322HOH0-0.029-0.01723.717-0.001-0.0010.0000.0000.0000.000
156A323HOH00.0100.00626.3500.0010.0010.0000.0000.0000.000
157A324HOH00.0490.03320.618-0.004-0.0040.0000.0000.0000.000
158A325HOH0-0.001-0.00440.511-0.001-0.0010.0000.0000.0000.000
159A326HOH00.0120.00334.950-0.001-0.0010.0000.0000.0000.000
160A328HOH00.0040.00520.7230.0000.0000.0000.0000.0000.000
161A331HOH0-0.0050.00031.6980.0000.0000.0000.0000.0000.000
162A332HOH00.0340.02029.731-0.001-0.0010.0000.0000.0000.000
163A333HOH0-0.004-0.00726.6220.0000.0000.0000.0000.0000.000
164A334HOH0-0.052-0.04532.002-0.001-0.0010.0000.0000.0000.000
165A335HOH0-0.033-0.02221.5150.0040.0040.0000.0000.0000.000
166A336HOH0-0.014-0.01128.835-0.001-0.0010.0000.0000.0000.000
167A337HOH0-0.049-0.02912.153-0.015-0.0150.0000.0000.0000.000
168A338HOH00.0140.00230.827-0.001-0.0010.0000.0000.0000.000
169A339HOH0-0.060-0.06019.8910.0090.0090.0000.0000.0000.000
170A340HOH0-0.020-0.01928.529-0.003-0.0030.0000.0000.0000.000
171A342HOH00.0000.00723.4870.0040.0040.0000.0000.0000.000
172A343HOH0-0.009-0.01715.352-0.016-0.0160.0000.0000.0000.000
173A344HOH0-0.007-0.01332.0060.0010.0010.0000.0000.0000.000
174A347HOH0-0.014-0.01324.5050.0010.0010.0000.0000.0000.000
175A348HOH00.0630.04641.1240.0000.0000.0000.0000.0000.000
176A349HOH0-0.013-0.00639.3700.0000.0000.0000.0000.0000.000
177A350HOH00.0240.01927.0190.0000.0000.0000.0000.0000.000
178A351HOH0-0.011-0.00437.519-0.001-0.0010.0000.0000.0000.000
179A353HOH0-0.031-0.02128.9880.0020.0020.0000.0000.0000.000
180A354HOH0-0.013-0.00224.951-0.001-0.0010.0000.0000.0000.000
181A355HOH0-0.022-0.01935.0330.0000.0000.0000.0000.0000.000
182A356HOH00.0020.01340.262-0.001-0.0010.0000.0000.0000.000
183A357HOH0-0.0070.00137.8510.0000.0000.0000.0000.0000.000
184A358HOH00.0150.01842.3880.0000.0000.0000.0000.0000.000
185A360HOH0-0.039-0.02918.540-0.005-0.0050.0000.0000.0000.000
186A361HOH0-0.052-0.03833.679-0.001-0.0010.0000.0000.0000.000
187A363HOH0-0.017-0.00125.7770.0010.0010.0000.0000.0000.000
188A366HOH0-0.020-0.02533.693-0.001-0.0010.0000.0000.0000.000
189A367HOH0-0.052-0.04327.1000.0010.0010.0000.0000.0000.000
190A369HOH0-0.047-0.02718.1910.0060.0060.0000.0000.0000.000
191A370HOH00.0010.00944.4360.0000.0000.0000.0000.0000.000
192A371HOH0-0.0070.00521.660-0.004-0.0040.0000.0000.0000.000
193A372HOH0-0.052-0.03737.219-0.001-0.0010.0000.0000.0000.000
194A373HOH0-0.027-0.01710.722-0.005-0.0050.0000.0000.0000.000
195A376HOH00.0580.03434.785-0.001-0.0010.0000.0000.0000.000
196A382HOH00.014-0.00122.0620.0010.0010.0000.0000.0000.000
197A383HOH0-0.024-0.01732.6060.0010.0010.0000.0000.0000.000
198A386HOH00.0010.00130.900-0.003-0.0030.0000.0000.0000.000
199A388HOH00.0410.02222.8220.0010.0010.0000.0000.0000.000
200A389HOH0-0.014-0.01341.8220.0000.0000.0000.0000.0000.000
201A390HOH0-0.058-0.03226.9790.0020.0020.0000.0000.0000.000
202A391HOH0-0.016-0.00921.4020.0070.0070.0000.0000.0000.000
203A392HOH00.0190.01014.206-0.016-0.0160.0000.0000.0000.000
204A394HOH0-0.0040.00224.540-0.002-0.0020.0000.0000.0000.000
205A397HOH0-0.026-0.01920.905-0.002-0.0020.0000.0000.0000.000
206A398HOH0-0.051-0.03833.0980.0000.0000.0000.0000.0000.000
207A399HOH0-0.059-0.04624.752-0.001-0.0010.0000.0000.0000.000
208A402HOH0-0.014-0.03536.103-0.001-0.0010.0000.0000.0000.000
209A404HOH00.000-0.00226.2630.0000.0000.0000.0000.0000.000
210A406HOH0-0.032-0.03127.7720.0010.0010.0000.0000.0000.000
211A407HOH00.0460.03228.2700.0030.0030.0000.0000.0000.000