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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: XMMYZ

Calculation Name: 1Z6M-A-Xray13

Preferred Name:

Target Type:

Ligand Name: phosphate ion

ligand 3-letter code: PO4

PDB ID: 1Z6M

Chain ID: A

ChEMBL ID:

UniProt ID: Q837R1

Base Structure: X-ray

Registration Date: 2018-03-01

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 No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 176
LigandCharge PO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1917864.018357
FMO2-HF: Nuclear repulsion 1847581.248344
FMO2-HF: Total energy -70282.770014
FMO2-MP2: Total energy -70486.443859


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-227.294-224.4280.331-1.167-2.03-0.008
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.894
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].
3A0ALA00.005-0.0102.8023.7245.3410.121-0.601-1.138-0.003
4A1MET0-0.018-0.0024.4876.8716.9810.000-0.017-0.0920.000
5A2ASP-1-0.823-0.8627.913-20.672-20.6720.0000.0000.0000.000
6A3ILE00.0400.01310.6021.5471.5470.0000.0000.0000.000
7A4SER0-0.087-0.07912.8471.9301.9300.0000.0000.0000.000
8A5VAL0-0.056-0.01712.5381.4721.4720.0000.0000.0000.000
9A6ILE0-0.042-0.02611.1811.0821.0820.0000.0000.0000.000
10A7ASP-1-0.845-0.90715.307-13.754-13.7540.0000.0000.0000.000
11A8ALA00.0470.01718.3820.1960.1960.0000.0000.0000.000
12A9THR0-0.064-0.04919.7340.7480.7480.0000.0000.0000.000
13A10LYS10.8250.91621.02913.91513.9150.0000.0000.0000.000
14A11VAL00.0030.01818.289-0.013-0.0130.0000.0000.0000.000
15A12ASN0-0.013-0.00721.7110.7540.7540.0000.0000.0000.000
16A13THR00.0580.01323.205-0.487-0.4870.0000.0000.0000.000
17A14GLU-1-0.952-0.97425.348-10.271-10.2710.0000.0000.0000.000
18A15THR0-0.035-0.01424.0720.3010.3010.0000.0000.0000.000
19A16GLY00.0480.02223.186-0.655-0.6550.0000.0000.0000.000
20A17LEU0-0.030-0.00122.6380.6800.6800.0000.0000.0000.000
21A18HIS10.8290.92223.72711.21611.2160.0000.0000.0000.000
22A19ILE00.0040.00723.6910.3870.3870.0000.0000.0000.000
23A20GLY00.0720.02025.999-0.299-0.2990.0000.0000.0000.000
24A21GLU-1-0.970-0.98228.574-9.382-9.3820.0000.0000.0000.000
25A22SER00.0540.01930.213-0.102-0.1020.0000.0000.0000.000
26A23ASN0-0.074-0.04031.480-0.122-0.1220.0000.0000.0000.000
27A24ALA00.0050.02928.5560.1260.1260.0000.0000.0000.000
28A25PRO0-0.048-0.02329.345-0.155-0.1550.0000.0000.0000.000
29A26VAL0-0.0070.00923.301-0.146-0.1460.0000.0000.0000.000
30A27LYS10.8080.90024.12411.24811.2480.0000.0000.0000.000
31A28MET00.0080.01418.248-0.589-0.5890.0000.0000.0000.000
32A29ILE00.0020.00117.6520.3860.3860.0000.0000.0000.000
33A30GLU-1-0.726-0.82815.306-18.951-18.9510.0000.0000.0000.000
34A31PHE0-0.0060.00513.5070.9030.9030.0000.0000.0000.000
35A32ILE00.0600.00212.506-2.452-2.4520.0000.0000.0000.000
36A33ASN0-0.023-0.03212.6571.0961.0960.0000.0000.0000.000
37A34VAL00.0570.02313.295-1.487-1.4870.0000.0000.0000.000
38A35ARG10.8270.92813.76120.79920.7990.0000.0000.0000.000
39A36CYS0-0.109-0.0088.460-1.727-1.7270.0000.0000.0000.000
40A37PRO00.0160.0148.1170.5790.5790.0000.0000.0000.000
41A38TYR0-0.004-0.0152.8500.6821.6950.211-0.495-0.729-0.005
42A39CYS00.0150.0127.5821.6021.6020.0000.0000.0000.000
43A40ARG10.9130.96710.61723.53423.5340.0000.0000.0000.000
44A41LYS10.8520.9468.84029.62729.6270.0000.0000.0000.000
45A42TRP00.0780.02410.5280.9300.9300.0000.0000.0000.000
46A43PHE0-0.071-0.04411.9462.0302.0300.0000.0000.0000.000
47A44GLU-1-0.964-0.98614.182-19.256-19.2560.0000.0000.0000.000
48A45GLU-1-0.801-0.89811.248-26.351-26.3510.0000.0000.0000.000
49A46SER00.0120.01015.4431.2771.2770.0000.0000.0000.000
50A47GLU-1-0.987-0.98717.213-13.835-13.8350.0000.0000.0000.000
51A48GLU-1-0.966-0.99920.104-12.775-12.7750.0000.0000.0000.000
52A49LEU00.0290.02219.5300.8710.8710.0000.0000.0000.000
53A50LEU00.0270.00517.8300.8510.8510.0000.0000.0000.000
54A51ALA0-0.0080.00822.2070.6630.6630.0000.0000.0000.000
55A52GLN0-0.025-0.01325.1750.4950.4950.0000.0000.0000.000
56A53SER0-0.021-0.03324.0760.5360.5360.0000.0000.0000.000
57A54VAL0-0.0250.00024.5230.3710.3710.0000.0000.0000.000
58A55LYS10.8890.95227.1669.9369.9360.0000.0000.0000.000
59A56SER0-0.106-0.06029.1120.4070.4070.0000.0000.0000.000
60A57GLY00.0780.04730.5920.2510.2510.0000.0000.0000.000
61A58LYS10.8780.95726.95611.44611.4460.0000.0000.0000.000
62A59VAL00.014-0.00722.663-0.121-0.1210.0000.0000.0000.000
63A60GLU-1-0.837-0.90925.582-11.065-11.0650.0000.0000.0000.000
64A61ARG10.8410.87818.07415.79715.7970.0000.0000.0000.000
65A62ILE0-0.047-0.01921.3840.6250.6250.0000.0000.0000.000
66A63ILE00.0020.00218.095-0.783-0.7830.0000.0000.0000.000
67A64LYS10.7470.85717.97815.43815.4380.0000.0000.0000.000
68A65LEU00.0010.00017.185-1.257-1.2570.0000.0000.0000.000
69A66PHE00.0500.01713.3340.5870.5870.0000.0000.0000.000
70A67ASP-1-0.770-0.88015.959-16.160-16.1600.0000.0000.0000.000
71A68LYS10.7970.90611.24823.52723.5270.0000.0000.0000.000
72A69GLU-1-0.848-0.92715.069-15.557-15.5570.0000.0000.0000.000
73A70LYS10.9160.9758.87527.58727.5870.0000.0000.0000.000
74A71GLU-1-0.868-0.93713.484-16.035-16.0350.0000.0000.0000.000
75A72SER00.0350.00212.3680.2250.2250.0000.0000.0000.000
76A73LEU0-0.019-0.01610.4250.4020.4020.0000.0000.0000.000
77A74GLN00.0020.00714.7371.2561.2560.0000.0000.0000.000
78A75ARG10.8700.92717.79516.72416.7240.0000.0000.0000.000
79A76GLY00.0080.00516.8820.5590.5590.0000.0000.0000.000
80A77ASN00.0220.00417.877-0.249-0.2490.0000.0000.0000.000
81A78VAL0-0.0030.01719.9280.5540.5540.0000.0000.0000.000
82A79MET00.0100.00720.3800.7010.7010.0000.0000.0000.000
83A80HIS0-0.020-0.01116.711-0.317-0.3170.0000.0000.0000.000
84A81HIS0-0.090-0.06521.9580.7440.7440.0000.0000.0000.000
85A82TYR0-0.057-0.05225.0940.4710.4710.0000.0000.0000.000
86A83ILE0-0.043-0.01322.8180.1760.1760.0000.0000.0000.000
87A84ASP-1-0.805-0.87026.230-9.725-9.7250.0000.0000.0000.000
88A85TYR00.007-0.02923.566-0.241-0.2410.0000.0000.0000.000
89A86SER0-0.124-0.07229.1360.1640.1640.0000.0000.0000.000
90A87ALA00.0230.02131.1570.2830.2830.0000.0000.0000.000
91A88PRO00.0450.01728.085-0.329-0.3290.0000.0000.0000.000
92A89GLU-1-0.862-0.94927.323-10.433-10.4330.0000.0000.0000.000
93A90GLN0-0.033-0.02428.193-0.279-0.2790.0000.0000.0000.000
94A91ALA00.0060.01225.554-0.271-0.2710.0000.0000.0000.000
95A92LEU00.0170.00821.693-0.539-0.5390.0000.0000.0000.000
96A93SER0-0.037-0.01523.462-0.371-0.3710.0000.0000.0000.000
97A94ALA0-0.001-0.00724.936-0.209-0.2090.0000.0000.0000.000
98A95LEU00.0230.00519.272-0.413-0.4130.0000.0000.0000.000
99A96HIS00.0730.03420.178-1.018-1.0180.0000.0000.0000.000
100A97LYS10.9290.96921.33511.10811.1080.0000.0000.0000.000
101A98MET0-0.0170.00920.033-0.339-0.3390.0000.0000.0000.000
102A99PHE00.0320.00713.878-0.717-0.7170.0000.0000.0000.000
103A100ALA0-0.021-0.00517.991-0.568-0.5680.0000.0000.0000.000
104A101THR00.007-0.00320.4600.0500.0500.0000.0000.0000.000
105A102GLN0-0.044-0.02813.290-0.623-0.6230.0000.0000.0000.000
106A103ASP-1-0.930-0.97915.847-19.341-19.3410.0000.0000.0000.000
107A104GLU-1-0.947-0.93318.362-12.301-12.3010.0000.0000.0000.000
108A105TRP00.0300.00617.5620.0550.0550.0000.0000.0000.000
109A106GLY00.0010.00017.5790.0090.0090.0000.0000.0000.000
110A107ASN0-0.077-0.05517.254-1.545-1.5450.0000.0000.0000.000
111A108LEU00.0180.04619.7180.5030.5030.0000.0000.0000.000
112A109THR00.0350.00521.978-0.605-0.6050.0000.0000.0000.000
113A110LEU00.0290.00120.867-0.008-0.0080.0000.0000.0000.000
114A111GLU-1-0.928-0.95824.423-9.986-9.9860.0000.0000.0000.000
115A112GLU-1-0.916-0.97826.546-10.356-10.3560.0000.0000.0000.000
116A113VAL0-0.059-0.01121.886-0.026-0.0260.0000.0000.0000.000
117A114ALA00.0480.02524.9920.0140.0140.0000.0000.0000.000
118A115THR00.0090.01127.7270.3960.3960.0000.0000.0000.000
119A116TYR0-0.052-0.05524.8910.1970.1970.0000.0000.0000.000
120A117ALA00.011-0.00625.9810.0990.0990.0000.0000.0000.000
121A118GLU-1-0.880-0.91027.507-9.766-9.7660.0000.0000.0000.000
122A119LYS10.8750.92231.2559.3619.3610.0000.0000.0000.000
123A120ASN0-0.044-0.02428.2500.3250.3250.0000.0000.0000.000
124A121LEU0-0.044-0.01624.159-0.039-0.0390.0000.0000.0000.000
125A122GLY0-0.0310.01128.8850.0920.0920.0000.0000.0000.000
126A123LEU0-0.036-0.01426.2150.1460.1460.0000.0000.0000.000
127A124LYS10.8990.93430.6029.5199.5190.0000.0000.0000.000
128A125GLU-1-0.891-0.94329.272-10.549-10.5490.0000.0000.0000.000
129A126GLN0-0.046-0.04229.4920.5940.5940.0000.0000.0000.000
130A127LYS10.9721.00625.76311.71111.7110.0000.0000.0000.000
131A128ASP-1-0.835-0.89927.721-10.355-10.3550.0000.0000.0000.000
132A129ALA0-0.031-0.04027.445-0.423-0.4230.0000.0000.0000.000
133A130THR0-0.008-0.01127.421-0.310-0.3100.0000.0000.0000.000
134A131LEU00.0300.03323.858-0.307-0.3070.0000.0000.0000.000
135A132VAL00.002-0.00122.347-0.467-0.4670.0000.0000.0000.000
136A133SER0-0.050-0.02822.549-0.701-0.7010.0000.0000.0000.000
137A134ALA00.0250.01623.620-0.322-0.3220.0000.0000.0000.000
138A135VAL00.0190.01418.778-0.348-0.3480.0000.0000.0000.000
139A136ILE0-0.011-0.00218.847-0.732-0.7320.0000.0000.0000.000
140A137ALA0-0.039-0.02419.491-0.448-0.4480.0000.0000.0000.000
141A138GLU-1-0.759-0.86520.498-14.744-14.7440.0000.0000.0000.000
142A139ALA00.0340.01815.589-0.274-0.2740.0000.0000.0000.000
143A140ASN0-0.043-0.02116.859-1.023-1.0230.0000.0000.0000.000
144A141ALA0-0.079-0.03618.544-0.024-0.0240.0000.0000.0000.000
145A142ALA00.0250.01517.6440.2580.2580.0000.0000.0000.000
146A143HIS10.8500.93115.54416.04716.0470.0000.0000.0000.000
147A144ILE00.0530.05312.250-1.559-1.5590.0000.0000.0000.000
148A145GLN0-0.013-0.0179.9940.3950.3950.0000.0000.0000.000
149A146PHE0-0.045-0.0416.575-0.911-0.9110.0000.0000.0000.000
150A147VAL0-0.0400.0138.1612.7992.7990.0000.0000.0000.000
151A148PRO00.031-0.0106.563-3.774-3.7740.0000.0000.0000.000
152A149THR0-0.009-0.0148.525-3.131-3.1310.0000.0000.0000.000
153A150ILE0-0.046-0.00911.0882.2662.2660.0000.0000.0000.000
154A151ILE00.0180.00013.707-0.565-0.5650.0000.0000.0000.000
155A152ILE00.0100.01416.6100.9520.9520.0000.0000.0000.000
156A153GLY0-0.014-0.01219.6920.0810.0810.0000.0000.0000.000
157A154GLU-1-0.928-0.99120.405-15.244-15.2440.0000.0000.0000.000
158A155TYR0-0.0720.00017.311-0.811-0.8110.0000.0000.0000.000
159A156ILE0-0.018-0.01512.037-0.067-0.0670.0000.0000.0000.000
160A157PHE0-0.006-0.01310.893-0.539-0.5390.0000.0000.0000.000
161A158ASP-1-0.822-0.9135.788-48.175-48.1750.0000.0000.0000.000
162A159GLU-1-0.874-0.9774.242-59.808-59.682-0.001-0.054-0.0710.000
163A160SER0-0.150-0.0695.8041.7021.7020.0000.0000.0000.000
164A161VAL0-0.064-0.0177.7002.0742.0740.0000.0000.0000.000
165A162THR00.1040.06811.3700.9150.9150.0000.0000.0000.000
166A163GLU-1-0.783-0.93913.993-17.585-17.5850.0000.0000.0000.000
167A164GLU-1-1.106-1.06617.219-13.957-13.9570.0000.0000.0000.000
168A165GLU-1-0.900-0.95013.287-22.192-22.1920.0000.0000.0000.000
169A166LEU0-0.0060.00516.0890.6630.6630.0000.0000.0000.000
170A167ARG10.8980.94317.63215.15915.1590.0000.0000.0000.000
171A168GLY0-0.020-0.00520.3760.6980.6980.0000.0000.0000.000
172A169TYR00.0240.00414.1750.7750.7750.0000.0000.0000.000
173A170ILE0-0.065-0.02020.3870.6080.6080.0000.0000.0000.000
174A171GLU-1-1.005-1.01922.801-10.985-10.9850.0000.0000.0000.000
175A172LYS0-0.0190.01123.519-1.748-1.7480.0000.0000.0000.000
176A312PO4-2-1.817-1.91113.854-41.003-41.0030.0000.0000.0000.000