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: P4L3N

Calculation Name: 1L7M-B-Xray28

Preferred Name:

Target Type:

Ligand Name: phosphate ion

ligand 3-letter code: PO4

PDB ID: 1L7M

Chain ID: B

ChEMBL ID:

UniProt ID: Q58989

Base Structure: X-ray

Registration Date: 2018-07-26

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 224
LigandCharge MG2=2,PO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2572907.531474
FMO2-HF: Nuclear repulsion 2489322.904844
FMO2-HF: Total energy -83584.62663
FMO2-MP2: Total energy -83829.16419


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(B:501:ACE)


Summations of interaction energy for fragment #1(B:501: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.
0.5721.929-0.014-0.724-0.62-0.002
Interaction energy analysis for fragmet #1(B:501:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.024
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].
3B503LYS10.8460.9473.8370.3501.707-0.014-0.724-0.620-0.002
4B504LYS10.9581.0056.0910.1650.1650.0000.0000.0000.000
5B505LYS10.9260.9499.6400.5850.5850.0000.0000.0000.000
6B506LYS10.9130.96111.6150.0270.0270.0000.0000.0000.000
7B507LEU0-0.0040.00214.812-0.010-0.0100.0000.0000.0000.000
8B508ILE0-0.023-0.01116.3020.0140.0140.0000.0000.0000.000
9B509LEU0-0.019-0.00820.165-0.003-0.0030.0000.0000.0000.000
10B510PHE00.009-0.00321.6410.0080.0080.0000.0000.0000.000
11B511ASP-1-0.781-0.89626.380-0.023-0.0230.0000.0000.0000.000
12B512PHE0-0.068-0.05929.7740.0020.0020.0000.0000.0000.000
13B513ASP-1-0.780-0.87831.744-0.011-0.0110.0000.0000.0000.000
14B514SER00.0180.03034.6870.0010.0010.0000.0000.0000.000
15B515THR00.0200.01428.6740.0040.0040.0000.0000.0000.000
16B516LEU0-0.028-0.01125.7340.0040.0040.0000.0000.0000.000
17B517VAL0-0.078-0.02029.6390.0030.0030.0000.0000.0000.000
18B518ASN0-0.021-0.02433.0260.0010.0010.0000.0000.0000.000
19B519ASN0-0.045-0.02735.8610.0010.0010.0000.0000.0000.000
20B520GLU-1-0.789-0.88337.356-0.010-0.0100.0000.0000.0000.000
21B521THR0-0.059-0.07437.5900.0000.0000.0000.0000.0000.000
22B522ILE0-0.031-0.02940.2300.0000.0000.0000.0000.0000.000
23B523ASP-1-0.762-0.89043.034-0.006-0.0060.0000.0000.0000.000
24B524GLU-1-0.825-0.89341.5300.0000.0000.0000.0000.0000.000
25B525ILE0-0.021-0.03542.4540.0000.0000.0000.0000.0000.000
26B526ALA00.0200.01546.0740.0000.0000.0000.0000.0000.000
27B527ARG10.9000.96748.1340.0020.0020.0000.0000.0000.000
28B528GLU-1-0.927-0.96148.077-0.003-0.0030.0000.0000.0000.000
29B529ALA0-0.043-0.02450.6820.0000.0000.0000.0000.0000.000
30B530GLY0-0.0360.00052.5110.0000.0000.0000.0000.0000.000
31B531VAL00.0340.01751.2100.0000.0000.0000.0000.0000.000
32B532GLU-1-0.890-0.96248.513-0.001-0.0010.0000.0000.0000.000
33B533GLU-1-0.963-0.98250.199-0.002-0.0020.0000.0000.0000.000
34B534GLU-1-0.871-0.93851.740-0.008-0.0080.0000.0000.0000.000
35B535VAL00.009-0.00746.808-0.001-0.0010.0000.0000.0000.000
36B536LYS10.9790.99646.372-0.001-0.0010.0000.0000.0000.000
37B537LYS10.9180.97247.0730.0030.0030.0000.0000.0000.000
38B538ILE00.008-0.00247.1350.0000.0000.0000.0000.0000.000
39B539THR00.014-0.00342.280-0.002-0.0020.0000.0000.0000.000
40B540LYS10.8570.94143.5000.0010.0010.0000.0000.0000.000
41B541GLU-1-0.871-0.94744.359-0.007-0.0070.0000.0000.0000.000
42B542ALA0-0.0070.00343.056-0.001-0.0010.0000.0000.0000.000
43B543MET0-0.0030.00238.797-0.001-0.0010.0000.0000.0000.000
44B544GLU-1-0.919-0.96940.218-0.002-0.0020.0000.0000.0000.000
45B545GLY0-0.003-0.01742.5480.0000.0000.0000.0000.0000.000
46B546LYS10.8670.95743.0260.0070.0070.0000.0000.0000.000
47B547LEU0-0.080-0.04545.7730.0000.0000.0000.0000.0000.000
48B548ASN0-0.004-0.00944.6100.0000.0000.0000.0000.0000.000
49B549PHE00.023-0.00839.5640.0010.0010.0000.0000.0000.000
50B550GLU-1-0.753-0.85742.823-0.027-0.0270.0000.0000.0000.000
51B551GLN0-0.024-0.01643.9700.0020.0020.0000.0000.0000.000
52B552SER0-0.029-0.01944.4730.0010.0010.0000.0000.0000.000
53B553LEU0-0.0090.00241.1360.0010.0010.0000.0000.0000.000
54B554ARG10.8410.91045.0600.0260.0260.0000.0000.0000.000
55B555LYS10.9320.96847.7000.0110.0110.0000.0000.0000.000
56B556ARG10.8550.93042.5280.0140.0140.0000.0000.0000.000
57B557VAL00.012-0.00144.8230.0010.0010.0000.0000.0000.000
58B558SER0-0.044-0.02348.0320.0010.0010.0000.0000.0000.000
59B559LEU0-0.067-0.02351.3530.0000.0000.0000.0000.0000.000
60B560LEU0-0.061-0.02446.7250.0010.0010.0000.0000.0000.000
61B561LYS10.9340.96751.1230.0130.0130.0000.0000.0000.000
62B562ASP-1-0.925-0.96353.265-0.011-0.0110.0000.0000.0000.000
63B563LEU0-0.0290.00048.7090.0010.0010.0000.0000.0000.000
64B564PRO0-0.017-0.02050.980-0.001-0.0010.0000.0000.0000.000
65B565ILE00.0880.02844.7780.0000.0000.0000.0000.0000.000
66B566GLU-1-0.938-0.97546.933-0.006-0.0060.0000.0000.0000.000
67B567LYS10.9430.96847.9200.0070.0070.0000.0000.0000.000
68B568VAL00.0360.02743.5990.0010.0010.0000.0000.0000.000
69B569GLU-1-0.900-0.97041.487-0.014-0.0140.0000.0000.0000.000
70B570LYS10.8930.96143.3510.0040.0040.0000.0000.0000.000
71B571ALA00.0130.00544.4220.0010.0010.0000.0000.0000.000
72B572ILE0-0.004-0.00638.5680.0010.0010.0000.0000.0000.000
73B573LYS10.8670.92939.3380.0080.0080.0000.0000.0000.000
74B574ARG10.8000.90540.2330.0040.0040.0000.0000.0000.000
75B575ILE0-0.038-0.00435.3180.0010.0010.0000.0000.0000.000
76B576THR0-0.030-0.00735.3000.0010.0010.0000.0000.0000.000
77B577PRO0-0.013-0.01929.843-0.001-0.0010.0000.0000.0000.000
78B578THR0-0.029-0.02729.9380.0030.0030.0000.0000.0000.000
79B579GLU-1-0.887-0.94329.6690.0400.0400.0000.0000.0000.000
80B580GLY00.0630.02326.4410.0000.0000.0000.0000.0000.000
81B581ALA0-0.0030.01124.7500.0030.0030.0000.0000.0000.000
82B582GLU-1-0.898-0.95723.4370.0140.0140.0000.0000.0000.000
83B583GLU-1-0.892-0.95321.3590.0830.0830.0000.0000.0000.000
84B584THR00.019-0.01220.1060.0110.0110.0000.0000.0000.000
85B585ILE0-0.0050.00719.1290.0000.0000.0000.0000.0000.000
86B586LYS10.9110.95418.028-0.016-0.0160.0000.0000.0000.000
87B587GLU-1-0.789-0.87414.2100.2010.2010.0000.0000.0000.000
88B588LEU0-0.012-0.01414.2750.0100.0100.0000.0000.0000.000
89B589LYS10.8350.90013.6860.0570.0570.0000.0000.0000.000
90B590ASN0-0.051-0.00111.742-0.032-0.0320.0000.0000.0000.000
91B591ARG10.7340.8729.568-0.096-0.0960.0000.0000.0000.000
92B592GLY0-0.032-0.0229.098-0.069-0.0690.0000.0000.0000.000
93B593TYR0-0.117-0.10710.335-0.074-0.0740.0000.0000.0000.000
94B594VAL00.0390.04113.4590.0090.0090.0000.0000.0000.000
95B595VAL0-0.026-0.00416.7270.0180.0180.0000.0000.0000.000
96B596ALA00.012-0.00819.857-0.005-0.0050.0000.0000.0000.000
97B597VAL0-0.0020.01923.4490.0080.0080.0000.0000.0000.000
98B598VAL00.000-0.00826.958-0.005-0.0050.0000.0000.0000.000
99B599SER00.0270.00329.6370.0050.0050.0000.0000.0000.000
100B600GLY00.0370.01533.141-0.002-0.0020.0000.0000.0000.000
101B601GLY00.0430.02835.9960.0020.0020.0000.0000.0000.000
102B602PHE00.008-0.02937.640-0.002-0.0020.0000.0000.0000.000
103B603ASP-1-0.804-0.90334.839-0.037-0.0370.0000.0000.0000.000
104B604ILE0-0.082-0.03035.6590.0000.0000.0000.0000.0000.000
105B605ALA0-0.024-0.01336.4440.0020.0020.0000.0000.0000.000
106B606VAL00.018-0.00230.8740.0010.0010.0000.0000.0000.000
107B607ASN00.0120.00231.155-0.004-0.0040.0000.0000.0000.000
108B608LYS10.9150.95531.1040.0140.0140.0000.0000.0000.000
109B609ILE00.0000.00528.7480.0010.0010.0000.0000.0000.000
110B610LYS11.0011.01825.9900.0660.0660.0000.0000.0000.000
111B611GLU-1-0.920-0.95925.978-0.046-0.0460.0000.0000.0000.000
112B612LYS10.8590.93326.5620.0080.0080.0000.0000.0000.000
113B613LEU00.0170.00024.7170.0050.0050.0000.0000.0000.000
114B614GLY0-0.0150.00822.2150.0040.0040.0000.0000.0000.000
115B615LEU0-0.035-0.02821.135-0.007-0.0070.0000.0000.0000.000
116B616ASP-1-0.810-0.89918.359-0.115-0.1150.0000.0000.0000.000
117B617TYR0-0.110-0.09020.4240.0050.0050.0000.0000.0000.000
118B618ALA0-0.001-0.01624.6470.0080.0080.0000.0000.0000.000
119B619PHE0-0.025-0.00126.520-0.005-0.0050.0000.0000.0000.000
120B620ALA00.0160.00230.8970.0030.0030.0000.0000.0000.000
121B621ASN0-0.0150.00434.353-0.004-0.0040.0000.0000.0000.000
122B622ARG10.9730.98537.9840.0360.0360.0000.0000.0000.000
123B623LEU00.0200.00740.4400.0010.0010.0000.0000.0000.000
124B624ILE0-0.030-0.01143.764-0.001-0.0010.0000.0000.0000.000
125B625VAL00.005-0.00245.5830.0020.0020.0000.0000.0000.000
126B626LYS10.9480.96948.3200.0160.0160.0000.0000.0000.000
127B627ASP-1-0.882-0.93451.742-0.015-0.0150.0000.0000.0000.000
128B628GLY0-0.027-0.01950.4940.0010.0010.0000.0000.0000.000
129B629LYS10.9220.96651.2290.0130.0130.0000.0000.0000.000
130B630LEU00.0390.03546.261-0.001-0.0010.0000.0000.0000.000
131B631THR0-0.004-0.01249.7850.0010.0010.0000.0000.0000.000
132B632GLY00.0310.01549.9800.0010.0010.0000.0000.0000.000
133B633ASH0-0.078-0.08047.6290.0000.0000.0000.0000.0000.000
134B634VAL0-0.006-0.00942.3930.0000.0000.0000.0000.0000.000
135B635GLU-1-0.831-0.87042.878-0.028-0.0280.0000.0000.0000.000
136B636GLY0-0.019-0.02838.9630.0000.0000.0000.0000.0000.000
137B637GLU-1-0.892-0.93435.147-0.045-0.0450.0000.0000.0000.000
138B638VAL0-0.041-0.01833.751-0.002-0.0020.0000.0000.0000.000
139B639LEU0-0.033-0.01236.1620.0040.0040.0000.0000.0000.000
140B640LYS11.0881.03438.7160.0430.0430.0000.0000.0000.000
141B641GLU-1-0.914-0.94638.274-0.031-0.0310.0000.0000.0000.000
142B642ASN0-0.053-0.05633.1550.0030.0030.0000.0000.0000.000
143B643ALA0-0.030-0.00334.306-0.004-0.0040.0000.0000.0000.000
144B644LYS10.8620.92030.7770.0230.0230.0000.0000.0000.000
145B645GLY00.0040.00729.723-0.005-0.0050.0000.0000.0000.000
146B646GLU-1-0.933-0.95829.386-0.063-0.0630.0000.0000.0000.000
147B647ILE00.000-0.00527.692-0.008-0.0080.0000.0000.0000.000
148B648LEU0-0.011-0.00324.393-0.009-0.0090.0000.0000.0000.000
149B649GLU-1-0.907-0.96424.734-0.086-0.0860.0000.0000.0000.000
150B650LYS10.8960.96125.4440.0800.0800.0000.0000.0000.000
151B651ILE0-0.036-0.02221.472-0.010-0.0100.0000.0000.0000.000
152B652ALA00.0340.01620.712-0.017-0.0170.0000.0000.0000.000
153B653LYS10.9210.95920.6850.0960.0960.0000.0000.0000.000
154B654ILE0-0.053-0.02321.437-0.010-0.0100.0000.0000.0000.000
155B655GLU-1-0.829-0.90117.309-0.240-0.2400.0000.0000.0000.000
156B656GLY0-0.0370.00916.869-0.041-0.0410.0000.0000.0000.000
157B657ILE0-0.074-0.02815.245-0.029-0.0290.0000.0000.0000.000
158B658ASN00.0250.01217.5100.0420.0420.0000.0000.0000.000
159B659LEU00.0710.02119.3970.0040.0040.0000.0000.0000.000
160B660GLU-1-0.941-0.94318.209-0.110-0.1100.0000.0000.0000.000
161B661ASP-1-0.946-0.98115.731-0.162-0.1620.0000.0000.0000.000
162B662THR0-0.045-0.05217.450-0.003-0.0030.0000.0000.0000.000
163B663VAL0-0.005-0.00518.8480.0120.0120.0000.0000.0000.000
164B664ALA0-0.0030.00421.626-0.006-0.0060.0000.0000.0000.000
165B665VAL0-0.021-0.00723.8070.0070.0070.0000.0000.0000.000
166B666GLY00.004-0.01326.587-0.004-0.0040.0000.0000.0000.000
167B667ASP-1-0.801-0.90230.322-0.001-0.0010.0000.0000.0000.000
168B668GLY00.0760.02733.7230.0020.0020.0000.0000.0000.000
169B669ALA00.013-0.00635.604-0.002-0.0020.0000.0000.0000.000
170B670ASN0-0.019-0.00536.416-0.001-0.0010.0000.0000.0000.000
171B671ASP-1-0.713-0.84931.533-0.025-0.0250.0000.0000.0000.000
172B672ILE0-0.013-0.00931.978-0.002-0.0020.0000.0000.0000.000
173B673SER0-0.039-0.01732.983-0.003-0.0030.0000.0000.0000.000
174B674MET00.0310.02327.481-0.006-0.0060.0000.0000.0000.000
175B675PHE00.0400.00128.199-0.004-0.0040.0000.0000.0000.000
176B676LYS10.8710.93228.9470.0280.0280.0000.0000.0000.000
177B677LYS10.8760.94727.4040.0570.0570.0000.0000.0000.000
178B678ALA00.0000.01724.355-0.007-0.0070.0000.0000.0000.000
179B679GLY0-0.0040.01121.8910.0050.0050.0000.0000.0000.000
180B680LEU0-0.059-0.01120.7810.0090.0090.0000.0000.0000.000
181B681LYS10.8500.93223.4680.0260.0260.0000.0000.0000.000
182B682ILE00.0380.01622.7090.0070.0070.0000.0000.0000.000
183B683ALA0-0.005-0.00527.160-0.004-0.0040.0000.0000.0000.000
184B684PHE0-0.007-0.02128.6330.0060.0060.0000.0000.0000.000
185B685CYS0-0.043-0.01230.773-0.001-0.0010.0000.0000.0000.000
186B686ALA00.0120.02833.491-0.002-0.0020.0000.0000.0000.000
187B687LYS10.9330.96635.4630.0030.0030.0000.0000.0000.000
188B688PRO0-0.006-0.02737.5710.0000.0000.0000.0000.0000.000
189B689ILE00.0310.02738.7870.0000.0000.0000.0000.0000.000
190B690LEU0-0.0230.00732.046-0.001-0.0010.0000.0000.0000.000
191B691LYS10.9400.95934.205-0.009-0.0090.0000.0000.0000.000
192B692GLU-1-0.994-0.98234.828-0.005-0.0050.0000.0000.0000.000
193B693LYS10.8860.93433.6970.0150.0150.0000.0000.0000.000
194B694ALA0-0.038-0.00830.368-0.003-0.0030.0000.0000.0000.000
195B695ASP-1-0.823-0.89226.434-0.009-0.0090.0000.0000.0000.000
196B696ILE0-0.054-0.03225.1800.0060.0060.0000.0000.0000.000
197B697CYS0-0.0230.00328.535-0.005-0.0050.0000.0000.0000.000
198B698ILE0-0.022-0.00225.9890.0050.0050.0000.0000.0000.000
199B699GLU-1-0.858-0.95630.5990.0120.0120.0000.0000.0000.000
200B700LYS10.8940.96430.774-0.046-0.0460.0000.0000.0000.000
201B701ARG10.8760.90931.073-0.011-0.0110.0000.0000.0000.000
202B702ASP-1-0.782-0.88627.2830.0500.0500.0000.0000.0000.000
203B703LEU0-0.002-0.00625.1710.0020.0020.0000.0000.0000.000
204B704ARG10.8520.93323.001-0.061-0.0610.0000.0000.0000.000
205B705GLU-1-0.962-0.98922.9590.0680.0680.0000.0000.0000.000
206B706ILE0-0.008-0.01421.2260.0020.0020.0000.0000.0000.000
207B707LEU0-0.033-0.01517.6560.0010.0010.0000.0000.0000.000
208B708LYS10.8840.94718.658-0.061-0.0610.0000.0000.0000.000
209B709TYR0-0.0090.00120.3150.0070.0070.0000.0000.0000.000
210B710ILE0-0.0270.00815.610-0.013-0.0130.0000.0000.0000.000
211B711LYS00.1840.13610.930-0.052-0.0520.0000.0000.0000.000
212A230PO4-2-1.714-1.83743.772-0.051-0.0510.0000.0000.0000.000
213B220PO4-2-1.212-1.55275.664-0.017-0.0170.0000.0000.0000.000
214B221MG221.1811.58877.2090.0170.0170.0000.0000.0000.000
215A807HOH0-0.021-0.02054.6470.0000.0000.0000.0000.0000.000
216A815HOH0-0.073-0.04447.4810.0010.0010.0000.0000.0000.000
217A871HOH00.0370.02541.6180.0010.0010.0000.0000.0000.000
218A968HOH00.0410.03551.2950.0000.0000.0000.0000.0000.000
219A1035HOH0-0.030-0.01552.8840.0000.0000.0000.0000.0000.000
220A1100HOH0-0.031-0.02138.1510.0000.0000.0000.0000.0000.000
221B857HOH0-0.054-0.03879.2090.0000.0000.0000.0000.0000.000
222B901HOH0-0.010-0.01355.1420.0000.0000.0000.0000.0000.000
223B904HOH0-0.024-0.01352.8450.0000.0000.0000.0000.0000.000
224B960HOH00.0850.00275.7370.0000.0000.0000.0000.0000.000