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: X16ZZ

Calculation Name: 4MMG-A-Xray40

Preferred Name:

Target Type:

Ligand Name: sulfate ion

ligand 3-letter code: SO4

PDB ID: 4MMG

Chain ID: A

ChEMBL ID:

UniProt ID: A0A140

Base Structure: X-ray

Registration Date: 2019-02-15

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 198
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -977529.489561
FMO2-HF: Nuclear repulsion 929849.404761
FMO2-HF: Total energy -47680.0848
FMO2-MP2: Total energy -47813.315989


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:1:ACE)


Summations of interaction energy for fragment #1(A:1: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.
0.4781.424-0.013-0.368-0.565-0.001
Interaction energy analysis for fragmet #1(A:1:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.010
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].
3A3GLN00.0040.0173.8180.8781.824-0.013-0.368-0.565-0.001
4A4ARG10.8830.9696.7220.4260.4260.0000.0000.0000.000
5A5ASH00.0250.00710.2290.1300.1300.0000.0000.0000.000
6A6ILE00.013-0.00912.6570.0450.0450.0000.0000.0000.000
7A7GLU-1-0.789-0.83715.934-0.369-0.3690.0000.0000.0000.000
8A8TYR00.0130.00118.9460.0180.0180.0000.0000.0000.000
9A9SER00.0190.02622.7400.0040.0040.0000.0000.0000.000
10A10GLY00.0310.00124.8840.0100.0100.0000.0000.0000.000
11A11GLN00.0190.00127.8810.0110.0110.0000.0000.0000.000
12A12TYR00.0460.00326.5360.0100.0100.0000.0000.0000.000
13A13SER00.0160.00327.4200.0080.0080.0000.0000.0000.000
14A14LYS10.8930.95529.6090.0940.0940.0000.0000.0000.000
15A15ASP-1-0.667-0.79031.261-0.089-0.0890.0000.0000.0000.000
16A16VAL0-0.0050.00529.0680.0070.0070.0000.0000.0000.000
17A17LYS10.8880.94032.4020.0840.0840.0000.0000.0000.000
18A18LEU00.0110.01435.1630.0060.0060.0000.0000.0000.000
19A19ALA00.0400.01434.8540.0040.0040.0000.0000.0000.000
20A20GLN00.0310.03534.5700.0010.0010.0000.0000.0000.000
21A21LYS10.9520.99237.6630.0530.0530.0000.0000.0000.000
22A22ARG10.8210.89140.1770.0600.0600.0000.0000.0000.000
23A23HIS00.0160.03441.0860.0010.0010.0000.0000.0000.000
24A24LYS10.8750.96237.2150.0580.0580.0000.0000.0000.000
25A25ASP-1-0.808-0.92037.047-0.050-0.0500.0000.0000.0000.000
26A26MET0-0.011-0.01132.701-0.003-0.0030.0000.0000.0000.000
27A27ASN00.0230.02532.334-0.008-0.0080.0000.0000.0000.000
28A28LYS10.9160.98131.8290.0470.0470.0000.0000.0000.000
29A29LEU00.0370.02928.757-0.003-0.0030.0000.0000.0000.000
30A30LYS10.9320.94127.8810.0600.0600.0000.0000.0000.000
31A31TYR00.0260.04026.865-0.005-0.0050.0000.0000.0000.000
32A32LEU00.0420.02426.083-0.003-0.0030.0000.0000.0000.000
33A33MET0-0.0040.02424.032-0.005-0.0050.0000.0000.0000.000
34A34THR0-0.0050.00222.362-0.014-0.0140.0000.0000.0000.000
35A35LEU0-0.031-0.00621.695-0.005-0.0050.0000.0000.0000.000
36A36LEU0-0.017-0.00820.489-0.007-0.0070.0000.0000.0000.000
37A37ILE0-0.0070.00417.660-0.024-0.0240.0000.0000.0000.000
38A38ASN00.0030.01316.797-0.031-0.0310.0000.0000.0000.000
39A39ASN00.0600.03014.711-0.007-0.0070.0000.0000.0000.000
40A40THR0-0.024-0.00817.5600.0150.0150.0000.0000.0000.000
41A41LEU0-0.058-0.00817.9690.0030.0030.0000.0000.0000.000
42A42PRO00.018-0.00220.5040.0040.0040.0000.0000.0000.000
43A43LEU00.0170.01123.0210.0110.0110.0000.0000.0000.000
44A44PRO00.0290.02525.5390.0050.0050.0000.0000.0000.000
45A45ALA00.0700.02329.013-0.004-0.0040.0000.0000.0000.000
46A46VAL0-0.017-0.00431.609-0.001-0.0010.0000.0000.0000.000
47A47TYR00.000-0.01328.7120.0000.0000.0000.0000.0000.000
48A48LYS10.9701.00531.3000.0520.0520.0000.0000.0000.000
49A49ASP-1-0.689-0.78525.136-0.133-0.1330.0000.0000.0000.000
50A50HIS10.8250.92227.6420.0930.0930.0000.0000.0000.000
51A51PRO0-0.0220.00425.224-0.006-0.0060.0000.0000.0000.000
52A52LEU00.0170.02526.8420.0110.0110.0000.0000.0000.000
53A53GLN00.0300.00827.932-0.010-0.0100.0000.0000.0000.000
54A54GLY00.0690.04230.5250.0010.0010.0000.0000.0000.000
55A55SER00.013-0.02230.577-0.008-0.0080.0000.0000.0000.000
56A56TRP00.0070.02527.460-0.014-0.0140.0000.0000.0000.000
57A57LYS10.9630.99525.8140.1230.1230.0000.0000.0000.000
58A58GLY00.0020.00722.994-0.009-0.0090.0000.0000.0000.000
59A59TYR00.0070.02022.065-0.027-0.0270.0000.0000.0000.000
60A60ARG10.7950.87621.8070.1580.1580.0000.0000.0000.000
61A61ASP-1-0.736-0.87325.572-0.095-0.0950.0000.0000.0000.000
62A62ALA00.0090.00727.4530.0030.0030.0000.0000.0000.000
63A63HIS10.8030.88329.3480.0750.0750.0000.0000.0000.000
64A64VAL0-0.0080.00130.9160.0020.0020.0000.0000.0000.000
65A65GLU-1-0.852-0.94833.249-0.049-0.0490.0000.0000.0000.000
66A66PRO00.0320.00936.676-0.003-0.0030.0000.0000.0000.000
67A67ASP-1-0.706-0.84938.737-0.060-0.0600.0000.0000.0000.000
68A68TRP0-0.079-0.03933.2040.0020.0020.0000.0000.0000.000
69A69ILE00.0310.02931.167-0.001-0.0010.0000.0000.0000.000
70A70LEU0-0.009-0.00125.196-0.001-0.0010.0000.0000.0000.000
71A71ILE00.0150.02026.401-0.003-0.0030.0000.0000.0000.000
72A72TYR0-0.044-0.05821.143-0.009-0.0090.0000.0000.0000.000
73A73LYS10.8970.95218.4690.2560.2560.0000.0000.0000.000
74A74LEU00.002-0.00115.962-0.010-0.0100.0000.0000.0000.000
75A75THR0-0.024-0.02113.9150.0060.0060.0000.0000.0000.000
76A76ASP-1-0.822-0.9119.635-0.481-0.4810.0000.0000.0000.000
77A77LYS10.9210.9677.5761.3181.3180.0000.0000.0000.000
78A78LEU00.0140.02110.547-0.013-0.0130.0000.0000.0000.000
79A79LEU00.0150.02713.7690.0420.0420.0000.0000.0000.000
80A80ARG10.7790.87716.8630.2360.2360.0000.0000.0000.000
81A81PHE00.009-0.00719.7490.0190.0190.0000.0000.0000.000
82A82GLH0-0.010-0.02623.239-0.008-0.0080.0000.0000.0000.000
83A83ARG10.8410.89025.5350.1010.1010.0000.0000.0000.000
84A84THR0-0.057-0.03829.015-0.001-0.0010.0000.0000.0000.000
85A85GLY00.0490.01231.4490.0030.0030.0000.0000.0000.000
86A86THR0-0.022-0.01735.187-0.002-0.0020.0000.0000.0000.000
87A87GLN00.0310.03436.5360.0000.0000.0000.0000.0000.000
88A88ALA00.0340.01237.608-0.002-0.0020.0000.0000.0000.000
89A89ALA0-0.0010.00037.373-0.001-0.0010.0000.0000.0000.000
90A90LEU0-0.077-0.03231.656-0.004-0.0040.0000.0000.0000.000
91A91PHE0-0.061-0.02931.955-0.006-0.0060.0000.0000.0000.000
92A92GLY-1-0.800-0.86236.266-0.068-0.0680.0000.0000.0000.000
93A101SO4-2-1.697-1.78734.700-0.144-0.1440.0000.0000.0000.000
94A102SO4-2-1.631-1.76739.723-0.124-0.1240.0000.0000.0000.000
95A103SO4-2-1.682-1.77824.926-0.328-0.3280.0000.0000.0000.000
96B102SO4-2-1.878-1.9218.313-1.826-1.8260.0000.0000.0000.000
97A201HOH0-0.012-0.01538.2910.0010.0010.0000.0000.0000.000
98A202HOH00.0420.02837.6420.0000.0000.0000.0000.0000.000
99A203HOH0-0.066-0.04734.0450.0020.0020.0000.0000.0000.000
100A204HOH0-0.0020.00333.8920.0000.0000.0000.0000.0000.000
101A205HOH00.0120.00921.1210.0030.0030.0000.0000.0000.000
102A206HOH00.0280.01732.945-0.002-0.0020.0000.0000.0000.000
103A207HOH0-0.014-0.01122.2830.0000.0000.0000.0000.0000.000
104A208HOH0-0.050-0.03235.0540.0020.0020.0000.0000.0000.000
105A209HOH0-0.024-0.01231.5160.0000.0000.0000.0000.0000.000
106A210HOH0-0.025-0.01726.0410.0020.0020.0000.0000.0000.000
107A211HOH0-0.033-0.02828.3730.0000.0000.0000.0000.0000.000
108A212HOH0-0.029-0.00931.3840.0030.0030.0000.0000.0000.000
109A213HOH00.013-0.00232.2940.0000.0000.0000.0000.0000.000
110A215HOH0-0.014-0.02025.599-0.001-0.0010.0000.0000.0000.000
111A216HOH0-0.041-0.02841.8750.0000.0000.0000.0000.0000.000
112A217HOH0-0.018-0.02327.4490.0020.0020.0000.0000.0000.000
113A218HOH0-0.017-0.01120.888-0.006-0.0060.0000.0000.0000.000
114A219HOH0-0.0030.00139.0410.0010.0010.0000.0000.0000.000
115A221HOH0-0.058-0.06834.0670.0020.0020.0000.0000.0000.000
116A222HOH0-0.016-0.00825.0370.0060.0060.0000.0000.0000.000
117A223HOH0-0.006-0.01140.914-0.001-0.0010.0000.0000.0000.000
118A224HOH0-0.030-0.02538.974-0.001-0.0010.0000.0000.0000.000
119A226HOH00.0230.01435.069-0.002-0.0020.0000.0000.0000.000
120A227HOH0-0.040-0.02936.0210.0010.0010.0000.0000.0000.000
121A228HOH0-0.036-0.02335.7330.0010.0010.0000.0000.0000.000
122A230HOH00.0160.01240.607-0.001-0.0010.0000.0000.0000.000
123A231HOH00.0180.01437.666-0.001-0.0010.0000.0000.0000.000
124A232HOH00.0580.03820.8670.0070.0070.0000.0000.0000.000
125A233HOH0-0.005-0.00917.9520.0100.0100.0000.0000.0000.000
126A235HOH0-0.003-0.01622.4300.0040.0040.0000.0000.0000.000
127A236HOH00.0240.02641.2730.0000.0000.0000.0000.0000.000
128A237HOH00.0060.00224.9040.0000.0000.0000.0000.0000.000
129A238HOH0-0.032-0.01744.2170.0000.0000.0000.0000.0000.000
130A239HOH0-0.037-0.02335.132-0.002-0.0020.0000.0000.0000.000
131A240HOH00.0050.00523.250-0.010-0.0100.0000.0000.0000.000
132A241HOH00.0230.01432.736-0.002-0.0020.0000.0000.0000.000
133A245HOH00.006-0.01337.171-0.002-0.0020.0000.0000.0000.000
134A246HOH0-0.037-0.02236.907-0.002-0.0020.0000.0000.0000.000
135A249HOH0-0.023-0.01527.0300.0010.0010.0000.0000.0000.000
136A250HOH0-0.068-0.04619.516-0.002-0.0020.0000.0000.0000.000
137A251HOH00.0050.02039.953-0.001-0.0010.0000.0000.0000.000
138A252HOH00.0310.02735.574-0.002-0.0020.0000.0000.0000.000
139A253HOH0-0.055-0.03817.4320.0130.0130.0000.0000.0000.000
140A254HOH0-0.026-0.02126.2920.0000.0000.0000.0000.0000.000
141A255HOH0-0.040-0.02437.4240.0010.0010.0000.0000.0000.000
142A256HOH0-0.029-0.01420.522-0.002-0.0020.0000.0000.0000.000
143A257HOH0-0.018-0.01726.9190.0010.0010.0000.0000.0000.000
144A258HOH0-0.028-0.02330.988-0.002-0.0020.0000.0000.0000.000
145A261HOH00.0410.03419.405-0.002-0.0020.0000.0000.0000.000
146A262HOH0-0.053-0.03526.687-0.003-0.0030.0000.0000.0000.000
147A263HOH00.0090.00933.868-0.002-0.0020.0000.0000.0000.000
148A264HOH0-0.050-0.03535.0300.0010.0010.0000.0000.0000.000
149A266HOH0-0.028-0.02312.6620.0240.0240.0000.0000.0000.000
150A267HOH00.001-0.04038.133-0.001-0.0010.0000.0000.0000.000
151A269HOH00.0390.03814.068-0.020-0.0200.0000.0000.0000.000
152A272HOH00.011-0.00641.1950.0000.0000.0000.0000.0000.000
153A273HOH0-0.024-0.02034.3650.0010.0010.0000.0000.0000.000
154A274HOH00.0290.01823.217-0.004-0.0040.0000.0000.0000.000
155A277HOH00.0400.01420.468-0.001-0.0010.0000.0000.0000.000
156A278HOH0-0.025-0.02224.964-0.001-0.0010.0000.0000.0000.000
157A279HOH0-0.024-0.01240.9610.0000.0000.0000.0000.0000.000
158A280HOH0-0.033-0.02038.9840.0010.0010.0000.0000.0000.000
159A281HOH0-0.024-0.02030.0940.0040.0040.0000.0000.0000.000
160A282HOH00.0110.00622.120-0.001-0.0010.0000.0000.0000.000
161A283HOH0-0.055-0.03440.1360.0000.0000.0000.0000.0000.000
162A285HOH0-0.033-0.02843.4720.0010.0010.0000.0000.0000.000
163A288HOH0-0.021-0.00823.1210.0010.0010.0000.0000.0000.000
164A289HOH00.0340.02623.556-0.002-0.0020.0000.0000.0000.000
165A291HOH0-0.026-0.03733.979-0.002-0.0020.0000.0000.0000.000
166A294HOH0-0.026-0.01830.1260.0020.0020.0000.0000.0000.000
167A295HOH0-0.030-0.03323.3120.0050.0050.0000.0000.0000.000
168A297HOH00.0330.02620.708-0.005-0.0050.0000.0000.0000.000
169A298HOH0-0.028-0.01730.882-0.001-0.0010.0000.0000.0000.000
170A299HOH0-0.071-0.03738.8190.0000.0000.0000.0000.0000.000
171A305HOH0-0.033-0.03810.3350.0020.0020.0000.0000.0000.000
172A306HOH0-0.040-0.03314.5120.0140.0140.0000.0000.0000.000
173A307HOH0-0.026-0.01617.7740.0020.0020.0000.0000.0000.000
174A309HOH0-0.019-0.01339.612-0.001-0.0010.0000.0000.0000.000
175A316HOH0-0.025-0.01118.7250.0070.0070.0000.0000.0000.000
176A318HOH00.011-0.01030.5450.0000.0000.0000.0000.0000.000
177A320HOH0-0.044-0.02443.2670.0010.0010.0000.0000.0000.000
178A322HOH0-0.037-0.02516.5950.0110.0110.0000.0000.0000.000
179A323HOH0-0.036-0.02714.779-0.008-0.0080.0000.0000.0000.000
180A326HOH0-0.025-0.0168.987-0.069-0.0690.0000.0000.0000.000
181A328HOH0-0.025-0.02917.552-0.002-0.0020.0000.0000.0000.000
182A330HOH0-0.019-0.02225.0640.0010.0010.0000.0000.0000.000
183A331HOH0-0.048-0.02940.2320.0000.0000.0000.0000.0000.000
184A332HOH0-0.039-0.02930.4430.0000.0000.0000.0000.0000.000
185A333HOH00.0200.01334.123-0.002-0.0020.0000.0000.0000.000
186A335HOH0-0.020-0.01541.6950.0000.0000.0000.0000.0000.000
187A337HOH0-0.0050.00240.2690.0000.0000.0000.0000.0000.000
188A338HOH0-0.030-0.02616.268-0.013-0.0130.0000.0000.0000.000
189A348HOH00.0180.02232.0900.0030.0030.0000.0000.0000.000
190A350HOH0-0.040-0.03228.046-0.003-0.0030.0000.0000.0000.000
191A368HOH00.0300.0188.334-0.062-0.0620.0000.0000.0000.000
192A373HOH00.0110.01614.353-0.017-0.0170.0000.0000.0000.000
193A376HOH0-0.009-0.00943.1330.0010.0010.0000.0000.0000.000
194A384HOH0-0.033-0.03013.553-0.001-0.0010.0000.0000.0000.000
195A385HOH0-0.049-0.03034.6220.0000.0000.0000.0000.0000.000
196A390HOH0-0.026-0.05032.875-0.002-0.0020.0000.0000.0000.000
197B233HOH0-0.052-0.0348.2240.0290.0290.0000.0000.0000.000
198B249HOH0-0.055-0.0509.0010.0910.0910.0000.0000.0000.000