FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 746ZK

Calculation Name: 5IT7-A-Other547

Preferred Name:

Target Type:

Ligand Name: phosphomethylphosphonic acid guanylate ester | (2s)-1-amino-n,n,n-trimethyl-1-oxobutan-2-aminium

Ligand 3-letter code: GCP | 6EM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5IT7

Chain ID: A

ChEMBL ID:

UniProt ID: P38665

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2570234.836663
FMO2-HF: Nuclear repulsion 2484577.090659
FMO2-HF: Total energy -85657.746004
FMO2-MP2: Total energy -85915.140232


3D Structure Molmil
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:20:GLN)


Summations of interaction energy for fragment #1(A:20:GLN)
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.
127.827129.6370.015-0.808-1.015-0.001
Interaction energy analysis for fragmet #1(A:20:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.880 / q_NPA : 0.926
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].
3A22THR00.0090.0063.494-9.104-7.7050.013-0.724-0.687-0.001
4A23ALA00.0290.0263.6573.9614.2440.003-0.081-0.2050.000
5A24GLU-1-0.860-0.9465.286-32.367-32.239-0.001-0.003-0.1230.000
6A25GLN0-0.014-0.0048.3142.2852.2850.0000.0000.0000.000
7A26VAL00.0460.0276.8322.7952.7950.0000.0000.0000.000
8A27ALA0-0.039-0.0219.4142.6722.6720.0000.0000.0000.000
9A28ALA00.0450.01511.5602.0112.0110.0000.0000.0000.000
10A29GLU-1-0.927-0.96011.535-24.083-24.0830.0000.0000.0000.000
11A30ARG10.8860.93411.36225.96625.9660.0000.0000.0000.000
12A31VAL0-0.017-0.00614.7161.1781.1780.0000.0000.0000.000
13A32ALA00.0390.03817.2091.0901.0900.0000.0000.0000.000
14A33ARG11.0221.00914.13520.80020.8000.0000.0000.0000.000
15A34LYS10.9020.94617.14618.15518.1550.0000.0000.0000.000
16A35ALA0-0.0120.00020.7990.7100.7100.0000.0000.0000.000
17A36GLU-1-0.885-0.94820.908-14.219-14.2190.0000.0000.0000.000
18A37LYS10.8540.90820.60915.08715.0870.0000.0000.0000.000
19A38ARG10.9360.95823.90712.58512.5850.0000.0000.0000.000
20A39ALA00.0270.03326.6800.4610.4610.0000.0000.0000.000
21A40ALA00.0770.03527.7720.3830.3830.0000.0000.0000.000
22A41ILE0-0.069-0.03126.5350.3130.3130.0000.0000.0000.000
23A42LEU0-0.0160.00630.3570.3470.3470.0000.0000.0000.000
24A43GLU-1-0.875-0.94232.162-9.510-9.5100.0000.0000.0000.000
25A44ARG10.9030.95429.75110.57210.5720.0000.0000.0000.000
26A45ASN0-0.048-0.03533.5720.1490.1490.0000.0000.0000.000
27A46ALA00.0150.01636.2320.2600.2600.0000.0000.0000.000
28A47ALA00.0240.01738.1420.2720.2720.0000.0000.0000.000
29A48TYR0-0.028-0.02735.4620.1110.1110.0000.0000.0000.000
30A49GLN00.0040.00540.2670.0990.0990.0000.0000.0000.000
31A50LYS10.9950.99942.2047.0927.0920.0000.0000.0000.000
32A51GLU-1-0.834-0.88343.159-7.342-7.3420.0000.0000.0000.000
33A52TYR0-0.028-0.03339.9180.1510.1510.0000.0000.0000.000
34A53GLU-1-0.920-0.94446.214-6.537-6.5370.0000.0000.0000.000
35A54THR0-0.003-0.03447.7380.1780.1780.0000.0000.0000.000
36A55ALA00.0050.00748.9380.1550.1550.0000.0000.0000.000
37A56GLU-1-0.992-0.99750.377-6.212-6.2120.0000.0000.0000.000
38A57ARG10.9130.95952.2376.0646.0640.0000.0000.0000.000
39A58ALA00.0730.03953.6210.1320.1320.0000.0000.0000.000
40A59VAL0-0.026-0.01154.2940.1260.1260.0000.0000.0000.000
41A60ILE0-0.067-0.03755.6770.1340.1340.0000.0000.0000.000
42A61ASP-1-0.872-0.94157.514-5.466-5.4660.0000.0000.0000.000
43A62ALA00.0820.05059.2070.1090.1090.0000.0000.0000.000
44A63LYS10.8760.93159.1425.5605.5600.0000.0000.0000.000
45A64ARG10.8470.92660.0305.4345.4340.0000.0000.0000.000
46A65GLU-1-0.883-0.94661.658-5.174-5.1740.0000.0000.0000.000
47A66ALA0-0.022-0.00765.0000.0830.0830.0000.0000.0000.000
48A67LYS10.9550.97666.8154.8274.8270.0000.0000.0000.000
49A68ALA0-0.0120.00068.5230.0780.0780.0000.0000.0000.000
50A69ASN00.0170.02068.3740.1120.1120.0000.0000.0000.000
51A70SER0-0.053-0.02471.3850.0410.0410.0000.0000.0000.000
52A71SER0-0.016-0.00168.9950.0180.0180.0000.0000.0000.000
53A72TYR0-0.021-0.02668.255-0.075-0.0750.0000.0000.0000.000
54A73TYR00.0260.01957.977-0.050-0.0500.0000.0000.0000.000
55A74VAL0-0.015-0.00462.458-0.004-0.0040.0000.0000.0000.000
56A75SER0-0.002-0.01057.650-0.035-0.0350.0000.0000.0000.000
57A76ALA0-0.011-0.00555.1930.0350.0350.0000.0000.0000.000
58A77GLU-1-0.929-0.96156.657-5.626-5.6260.0000.0000.0000.000
59A78ALA00.0140.00853.250-0.128-0.1280.0000.0000.0000.000
60A79LYS10.9490.97348.1056.6136.6130.0000.0000.0000.000
61A80LEU0-0.027-0.00345.116-0.093-0.0930.0000.0000.0000.000
62A81VAL00.0260.02148.9050.1040.1040.0000.0000.0000.000
63A82PHE0-0.005-0.02043.962-0.177-0.1770.0000.0000.0000.000
64A83VAL00.0050.00148.2510.1560.1560.0000.0000.0000.000
65A84VAL00.0420.01548.059-0.191-0.1910.0000.0000.0000.000
66A85ARG10.7940.89449.1046.6856.6850.0000.0000.0000.000
67A86ILE00.0080.01250.986-0.035-0.0350.0000.0000.0000.000
68A87LYS10.9080.95254.0945.5975.5970.0000.0000.0000.000
69A88GLY00.0470.02852.654-0.129-0.1290.0000.0000.0000.000
70A89ILE0-0.031-0.02450.0230.1040.1040.0000.0000.0000.000
71A90ASN00.0460.00753.1990.0410.0410.0000.0000.0000.000
72A91LYS10.9921.01055.9435.3215.3210.0000.0000.0000.000
73A92ILE0-0.037-0.00354.9490.0550.0550.0000.0000.0000.000
74A93PRO00.0640.03458.002-0.046-0.0460.0000.0000.0000.000
75A94PRO00.0690.01757.159-0.115-0.1150.0000.0000.0000.000
76A95LYS11.0071.01256.0295.3395.3390.0000.0000.0000.000
77A96PRO00.0390.02355.750-0.108-0.1080.0000.0000.0000.000
78A97ARG10.9830.99152.1316.0666.0660.0000.0000.0000.000
79A98LYS10.9110.95948.7266.5216.5210.0000.0000.0000.000
80A99VAL00.0180.00450.896-0.150-0.1500.0000.0000.0000.000
81A100LEU00.000-0.00550.425-0.131-0.1310.0000.0000.0000.000
82A101GLN00.0220.02346.895-0.178-0.1780.0000.0000.0000.000
83A102LEU0-0.046-0.02146.280-0.183-0.1830.0000.0000.0000.000
84A103LEU0-0.0080.00346.007-0.144-0.1440.0000.0000.0000.000
85A104ARG10.8440.91538.5807.9897.9890.0000.0000.0000.000
86A105LEU0-0.0120.01844.291-0.104-0.1040.0000.0000.0000.000
87A106ASN00.0300.00443.4640.3060.3060.0000.0000.0000.000
88A107GLN00.0180.00943.029-0.092-0.0920.0000.0000.0000.000
89A108ILE0-0.002-0.00647.0230.0840.0840.0000.0000.0000.000
90A109ASN00.006-0.01747.534-0.010-0.0100.0000.0000.0000.000
91A110SER0-0.0140.00444.408-0.098-0.0980.0000.0000.0000.000
92A111GLY00.0450.00944.2460.1880.1880.0000.0000.0000.000
93A112THR0-0.073-0.04543.610-0.126-0.1260.0000.0000.0000.000
94A113PHE00.0350.03940.684-0.157-0.1570.0000.0000.0000.000
95A114VAL0-0.021-0.02144.630-0.100-0.1000.0000.0000.0000.000
96A115LYS10.9821.01446.0216.7716.7710.0000.0000.0000.000
97A116VAL00.0430.04647.7370.0450.0450.0000.0000.0000.000
98A117THR0-0.057-0.05250.615-0.054-0.0540.0000.0000.0000.000
99A118LYS11.0000.98853.4585.4415.4410.0000.0000.0000.000
100A119ALA00.0370.01352.9170.0360.0360.0000.0000.0000.000
101A120THR0-0.016-0.03949.5680.0710.0710.0000.0000.0000.000
102A121SER00.0350.02052.9510.0080.0080.0000.0000.0000.000
103A122GLU-1-0.752-0.84956.238-5.368-5.3680.0000.0000.0000.000
104A123LEU0-0.037-0.01751.1190.0140.0140.0000.0000.0000.000
105A124LEU0-0.009-0.01851.897-0.009-0.0090.0000.0000.0000.000
106A125LYS10.8920.93755.5795.3615.3610.0000.0000.0000.000
107A126LEU0-0.0250.00256.8260.0550.0550.0000.0000.0000.000
108A127ILE0-0.044-0.03452.6570.0190.0190.0000.0000.0000.000
109A128GLU-1-0.859-0.92056.735-5.369-5.3690.0000.0000.0000.000
110A129PRO00.013-0.00258.748-0.016-0.0160.0000.0000.0000.000
111A130TYR0-0.064-0.04655.741-0.003-0.0030.0000.0000.0000.000
112A131VAL0-0.006-0.00452.590-0.151-0.1510.0000.0000.0000.000
113A132ALA00.0090.01953.4640.1430.1430.0000.0000.0000.000
114A133TYR0-0.024-0.02652.654-0.162-0.1620.0000.0000.0000.000
115A134GLY00.0950.04352.4530.1500.1500.0000.0000.0000.000
116A135TYR0-0.024-0.02051.088-0.210-0.2100.0000.0000.0000.000
117A136PRO0-0.074-0.02346.7580.0250.0250.0000.0000.0000.000
118A137SER00.0830.03348.005-0.047-0.0470.0000.0000.0000.000
119A138TYR00.0510.00738.955-0.089-0.0890.0000.0000.0000.000
120A139SER00.0390.02643.4780.0830.0830.0000.0000.0000.000
121A140THR0-0.078-0.06844.037-0.112-0.1120.0000.0000.0000.000
122A141VAL00.0150.00340.588-0.128-0.1280.0000.0000.0000.000
123A142ARG10.9621.00338.3928.0218.0210.0000.0000.0000.000
124A143GLN00.0440.02539.155-0.064-0.0640.0000.0000.0000.000
125A144LEU0-0.0220.00740.193-0.120-0.1200.0000.0000.0000.000
126A145VAL0-0.020-0.01735.306-0.184-0.1840.0000.0000.0000.000
127A146TYR0-0.001-0.01733.529-0.305-0.3050.0000.0000.0000.000
128A147LYS10.8270.92935.0597.6207.6200.0000.0000.0000.000
129A148ARG10.8020.85936.3157.6917.6910.0000.0000.0000.000
130A149GLY00.0190.02135.5950.0830.0830.0000.0000.0000.000
131A150TYR0-0.056-0.03732.236-0.260-0.2600.0000.0000.0000.000
132A151GLY00.0640.04030.5290.2730.2730.0000.0000.0000.000
133A152LYS10.7810.89431.5629.1089.1080.0000.0000.0000.000
134A153ILE00.0140.01825.5270.0510.0510.0000.0000.0000.000
135A154ASN00.0270.00626.2540.2200.2200.0000.0000.0000.000
136A155LYS10.9250.96128.7099.8919.8910.0000.0000.0000.000
137A156GLN00.0760.01826.5330.0120.0120.0000.0000.0000.000
138A157ARG10.9090.98630.6819.1869.1860.0000.0000.0000.000
139A158ILE00.0530.04225.3890.0440.0440.0000.0000.0000.000
140A159PRO00.011-0.00527.9660.2990.2990.0000.0000.0000.000
141A160LEU0-0.018-0.02728.294-0.366-0.3660.0000.0000.0000.000
142A161SER0-0.050-0.01925.337-0.190-0.1900.0000.0000.0000.000
143A162ASP-1-0.790-0.86922.685-13.650-13.6500.0000.0000.0000.000
144A163ASN0-0.040-0.02525.794-0.407-0.4070.0000.0000.0000.000
145A164SER0-0.011-0.02021.452-0.024-0.0240.0000.0000.0000.000
146A165ILE00.0070.00422.324-0.246-0.2460.0000.0000.0000.000
147A166VAL0-0.037-0.02224.4690.1560.1560.0000.0000.0000.000
148A167GLU-1-0.834-0.89723.173-13.476-13.4760.0000.0000.0000.000
149A168ALA0-0.003-0.00121.9460.0500.0500.0000.0000.0000.000
150A169ASN0-0.067-0.03923.7670.2450.2450.0000.0000.0000.000
151A170LEU0-0.017-0.02626.9230.4000.4000.0000.0000.0000.000
152A171GLY00.0880.06626.8920.3340.3340.0000.0000.0000.000
153A172ASN0-0.032-0.01427.709-0.074-0.0740.0000.0000.0000.000
154A173TYR0-0.074-0.04729.8940.4850.4850.0000.0000.0000.000
155A174GLY00.0160.01631.2200.3760.3760.0000.0000.0000.000
156A175ILE0-0.073-0.04930.477-0.226-0.2260.0000.0000.0000.000
157A176LEU00.0420.02326.899-0.249-0.2490.0000.0000.0000.000
158A177SER00.0630.04027.900-0.403-0.4030.0000.0000.0000.000
159A178VAL00.007-0.00229.8340.2300.2300.0000.0000.0000.000
160A179ASP-1-0.797-0.90132.185-8.382-8.3820.0000.0000.0000.000
161A180ASP-1-0.775-0.90332.021-9.640-9.6400.0000.0000.0000.000
162A181LEU0-0.031-0.01433.2650.2270.2270.0000.0000.0000.000
163A182ILE0-0.026-0.01735.3880.3220.3220.0000.0000.0000.000
164A183HIS10.8760.93737.8888.2288.2280.0000.0000.0000.000
165A184GLU-1-0.853-0.91437.478-8.069-8.0690.0000.0000.0000.000
166A185ILE0-0.052-0.04438.8230.2340.2340.0000.0000.0000.000
167A186VAL0-0.006-0.01441.3940.2030.2030.0000.0000.0000.000
168A187THR0-0.027-0.01842.3530.1930.1930.0000.0000.0000.000
169A188VAL0-0.119-0.06443.8110.1960.1960.0000.0000.0000.000
170A189GLY00.0530.04941.4930.1390.1390.0000.0000.0000.000
171A190PRO00.009-0.00439.8720.0320.0320.0000.0000.0000.000
172A191HIS10.8790.93436.4738.5918.5910.0000.0000.0000.000
173A192PHE00.0330.03038.046-0.185-0.1850.0000.0000.0000.000
174A193LYS10.9400.96439.8887.5337.5330.0000.0000.0000.000
175A194GLN00.0280.01534.8730.1240.1240.0000.0000.0000.000
176A195ALA00.0640.03235.192-0.159-0.1590.0000.0000.0000.000
177A196ASN00.018-0.01536.169-0.215-0.2150.0000.0000.0000.000
178A197ASN0-0.064-0.02937.5380.0080.0080.0000.0000.0000.000
179A198PHE00.0340.02528.988-0.063-0.0630.0000.0000.0000.000
180A199LEU00.0370.02733.894-0.168-0.1680.0000.0000.0000.000
181A200TRP0-0.025-0.01634.1030.2080.2080.0000.0000.0000.000
182A201PRO0-0.056-0.02136.9190.0500.0500.0000.0000.0000.000
183A202PHE00.0570.03938.601-0.081-0.0810.0000.0000.0000.000
184A203LYS10.9200.94639.0888.2908.2900.0000.0000.0000.000
185A204LEU0-0.0120.00441.856-0.146-0.1460.0000.0000.0000.000
186A205SER00.0090.01644.379-0.004-0.0040.0000.0000.0000.000
187A206ASN00.013-0.00746.2650.0070.0070.0000.0000.0000.000
188A207PRO0-0.014-0.00449.389-0.100-0.1000.0000.0000.0000.000
189A208SER00.0340.00849.2330.1490.1490.0000.0000.0000.000
190A209GLY00.0410.02951.2010.0630.0630.0000.0000.0000.000
191A210GLY00.0050.01654.2260.1320.1320.0000.0000.0000.000
192A211TRP0-0.037-0.06352.187-0.030-0.0300.0000.0000.0000.000
193A212GLY00.0300.02157.5000.0240.0240.0000.0000.0000.000
194A213VAL0-0.031-0.00160.2390.0750.0750.0000.0000.0000.000
195A214PRO00.0750.05562.692-0.044-0.0440.0000.0000.0000.000
196A215ARG10.9310.94763.4654.9544.9540.0000.0000.0000.000
197A216LYS10.8950.96553.9426.0346.0340.0000.0000.0000.000
198A217PHE0-0.051-0.04857.520-0.065-0.0650.0000.0000.0000.000
199A218LYS10.9250.94562.0004.8734.8730.0000.0000.0000.000
200A219HIS00.1160.10261.449-0.003-0.0030.0000.0000.0000.000
201A220PHE00.0640.02559.6090.0530.0530.0000.0000.0000.000
202A221ILE0-0.0060.00063.0630.0110.0110.0000.0000.0000.000
203A222GLN0-0.032-0.01166.6390.0210.0210.0000.0000.0000.000
204A223GLY00.0580.03065.4740.0050.0050.0000.0000.0000.000
205A224GLY0-0.029-0.02362.988-0.082-0.0820.0000.0000.0000.000
206A225SER00.027-0.00357.554-0.063-0.0630.0000.0000.0000.000
207A226PHE0-0.0330.00757.764-0.111-0.1110.0000.0000.0000.000
208A227GLY00.0670.04157.9080.0750.0750.0000.0000.0000.000
209A228ASN0-0.019-0.02157.248-0.163-0.1630.0000.0000.0000.000
210A229ARG10.8460.92455.1065.9165.9160.0000.0000.0000.000
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