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: 4GNKN

Calculation Name: 3GNU-P-Xray547

Preferred Name:

Target Type:

Ligand Name: guanidine

Ligand 3-letter code: GAI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3GNU

Chain ID: P

ChEMBL ID:

UniProt ID: Q9SPD4

Base Structure: X-ray

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 211
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2507405.416089
FMO2-HF: Nuclear repulsion 2425950.300681
FMO2-HF: Total energy -81455.115408
FMO2-MP2: Total energy -81693.657849


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(P:1:ALA)


Summations of interaction energy for fragment #1(P:1:ALA)
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.
-106.598-103.6313.034-8.564-7.439-0.097
Interaction energy analysis for fragmet #1(P:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.801 / q_NPA : 0.893
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].
3P3ILE00.0190.0153.4011.3812.8610.015-0.600-0.895-0.001
47P47GLY00.0120.0264.883-3.165-3.073-0.001-0.016-0.0760.000
48P48ASN0-0.118-0.0811.798-67.363-66.06112.959-8.257-6.004-0.094
49P49THR00.0200.0063.07313.18813.2510.0620.311-0.436-0.002
185P186ALA0-0.0140.0224.760-0.043-0.012-0.001-0.002-0.0280.000
4P4ASN00.0040.0015.7970.8000.8000.0000.0000.0000.000
5P5HIS00.009-0.0039.636-2.254-2.2540.0000.0000.0000.000
6P6ASP-1-0.889-0.96112.000-21.147-21.1470.0000.0000.0000.000
7P7ALA0-0.0030.0009.0681.1301.1300.0000.0000.0000.000
8P8VAL0-0.0170.0098.390-1.054-1.0540.0000.0000.0000.000
9P9PRO0-0.021-0.0059.3082.9352.9350.0000.0000.0000.000
10P10VAL00.0080.00212.351-0.899-0.8990.0000.0000.0000.000
11P11TRP0-0.0010.00110.392-0.406-0.4060.0000.0000.0000.000
12P12PRO0-0.014-0.01314.9660.9460.9460.0000.0000.0000.000
13P13GLN00.0560.03618.608-0.422-0.4220.0000.0000.0000.000
14P14PRO0-0.032-0.00819.0810.4900.4900.0000.0000.0000.000
15P15GLU-1-0.894-0.95121.876-11.209-11.2090.0000.0000.0000.000
16P16PRO0-0.084-0.03124.585-0.449-0.4490.0000.0000.0000.000
17P17ALA00.010-0.00224.8560.4050.4050.0000.0000.0000.000
18P18ASP-1-0.835-0.90925.979-11.886-11.8860.0000.0000.0000.000
19P19ALA00.0500.00328.734-0.061-0.0610.0000.0000.0000.000
20P20THR0-0.0060.00725.2860.2520.2520.0000.0000.0000.000
21P21GLN00.0100.00923.322-0.353-0.3530.0000.0000.0000.000
22P22ALA00.0320.00825.826-0.131-0.1310.0000.0000.0000.000
23P23LEU0-0.034-0.00829.0450.1440.1440.0000.0000.0000.000
24P24ALA00.0190.01724.1770.0770.0770.0000.0000.0000.000
25P25VAL00.001-0.00325.083-0.200-0.2000.0000.0000.0000.000
26P26ARG10.8900.96226.9429.2269.2260.0000.0000.0000.000
27P27PHE00.021-0.00829.3430.3250.3250.0000.0000.0000.000
28P28LYS10.8280.93524.23012.66912.6690.0000.0000.0000.000
29P29PRO0-0.011-0.00125.6100.3160.3160.0000.0000.0000.000
30P30GLN0-0.044-0.01427.340-0.280-0.2800.0000.0000.0000.000
31P31LEU0-0.005-0.01123.6560.0800.0800.0000.0000.0000.000
32P32ASP-1-0.871-0.94427.794-9.918-9.9180.0000.0000.0000.000
33P33VAL0-0.039-0.01825.139-0.078-0.0780.0000.0000.0000.000
34P34VAL00.0150.01328.0310.1540.1540.0000.0000.0000.000
35P35ASN0-0.036-0.02728.937-0.067-0.0670.0000.0000.0000.000
36P36GLY00.0370.01825.107-0.237-0.2370.0000.0000.0000.000
37P37CYS0-0.106-0.01718.823-0.520-0.5200.0000.0000.0000.000
38P38GLN00.0460.02021.6690.3340.3340.0000.0000.0000.000
39P39PRO0-0.026-0.00119.245-0.673-0.6730.0000.0000.0000.000
40P40TYR00.027-0.01114.7470.7400.7400.0000.0000.0000.000
41P41PRO0-0.0160.00411.898-0.013-0.0130.0000.0000.0000.000
42P42ALA00.0210.00510.827-1.350-1.3500.0000.0000.0000.000
43P43VAL0-0.045-0.0286.108-4.172-4.1720.0000.0000.0000.000
44P44ASP-1-0.747-0.8425.822-45.801-45.8010.0000.0000.0000.000
45P45PRO00.042-0.0047.952-1.754-1.7540.0000.0000.0000.000
46P46GLN0-0.0200.0035.7892.1072.1070.0000.0000.0000.000
50P50SER00.015-0.0055.495-1.845-1.8450.0000.0000.0000.000
51P51GLY00.0430.0048.4830.4640.4640.0000.0000.0000.000
52P52GLY0-0.0220.0059.1902.8562.8560.0000.0000.0000.000
53P53LEU0-0.066-0.03812.866-0.062-0.0620.0000.0000.0000.000
54P54LYS10.9750.98415.88014.93314.9330.0000.0000.0000.000
55P55PRO00.0080.01317.8480.3180.3180.0000.0000.0000.000
56P56SER0-0.025-0.02121.1220.4250.4250.0000.0000.0000.000
57P57GLY00.0320.01423.0520.3660.3660.0000.0000.0000.000
58P58SER00.0300.00824.886-0.092-0.0920.0000.0000.0000.000
59P59GLN00.0290.00425.244-0.687-0.6870.0000.0000.0000.000
60P60ALA00.0690.03424.009-0.499-0.4990.0000.0000.0000.000
61P61ALA0-0.085-0.04323.702-0.232-0.2320.0000.0000.0000.000
62P62ALA00.0380.00118.834-0.486-0.4860.0000.0000.0000.000
63P64ARG11.0010.98920.12112.43412.4340.0000.0000.0000.000
64P65ASP-1-0.819-0.87719.952-14.529-14.5290.0000.0000.0000.000
65P66MET00.005-0.01421.104-0.335-0.3350.0000.0000.0000.000
66P67SER0-0.072-0.04521.354-0.092-0.0920.0000.0000.0000.000
67P68LYS10.8630.92514.14820.57720.5770.0000.0000.0000.000
68P69ALA00.0060.00917.611-0.763-0.7630.0000.0000.0000.000
69P70GLN0-0.017-0.01315.055-1.484-1.4840.0000.0000.0000.000
70P71VAL0-0.048-0.02118.3700.3710.3710.0000.0000.0000.000
71P72TYR00.0600.03212.339-0.845-0.8450.0000.0000.0000.000
72P73SER00.0450.00418.0460.9240.9240.0000.0000.0000.000
73P74ARG10.7870.90918.44814.85214.8520.0000.0000.0000.000
74P75SER00.0050.00221.1550.6070.6070.0000.0000.0000.000
75P76GLY0-0.018-0.01424.345-0.415-0.4150.0000.0000.0000.000
76P77THR0-0.0330.00026.8860.4030.4030.0000.0000.0000.000
77P78TYR00.0230.01829.707-0.141-0.1410.0000.0000.0000.000
78P79ASN0-0.024-0.01631.6340.1270.1270.0000.0000.0000.000
79P80GLY0-0.013-0.00134.9490.2500.2500.0000.0000.0000.000
80P81TYR00.0070.01834.0450.1710.1710.0000.0000.0000.000
81P82TYR00.006-0.01128.785-0.272-0.2720.0000.0000.0000.000
82P83ASP-1-0.879-0.95226.770-11.443-11.4430.0000.0000.0000.000
83P84ILE00.0280.00725.145-0.274-0.2740.0000.0000.0000.000
84P85MET0-0.0330.01321.663-0.098-0.0980.0000.0000.0000.000
85P86TYR0-0.008-0.03522.089-0.462-0.4620.0000.0000.0000.000
86P87SER0-0.055-0.05718.505-0.070-0.0700.0000.0000.0000.000
87P88TRP0-0.012-0.01818.439-0.397-0.3970.0000.0000.0000.000
88P89TYR00.0550.02612.353-0.473-0.4730.0000.0000.0000.000
89P90MET00.0020.00716.2710.3390.3390.0000.0000.0000.000
90P91PRO00.007-0.01114.768-0.653-0.6530.0000.0000.0000.000
91P92LYS10.8450.93515.68513.82313.8230.0000.0000.0000.000
92P93ASP-1-0.716-0.82218.475-13.319-13.3190.0000.0000.0000.000
93P94SER0-0.006-0.01221.664-0.149-0.1490.0000.0000.0000.000
94P95PRO00.0410.03324.5750.2450.2450.0000.0000.0000.000
95P96SER0-0.015-0.01827.9420.5080.5080.0000.0000.0000.000
96P97ILE0-0.014-0.02727.565-0.558-0.5580.0000.0000.0000.000
97P98GLY0-0.048-0.00725.6930.2450.2450.0000.0000.0000.000
98P99ILE00.0080.01325.444-0.172-0.1720.0000.0000.0000.000
99P100GLY00.0340.00823.810-0.046-0.0460.0000.0000.0000.000
100P101HIS10.8190.90819.48713.90113.9010.0000.0000.0000.000
101P102ARG10.8780.93112.41623.18023.1800.0000.0000.0000.000
102P103HIS00.0010.02210.4690.6870.6870.0000.0000.0000.000
103P104ASP-1-0.800-0.88715.539-14.209-14.2090.0000.0000.0000.000
104P105TRP0-0.047-0.03411.830-0.910-0.9100.0000.0000.0000.000
105P106GLU-1-0.785-0.84217.906-12.895-12.8950.0000.0000.0000.000
106P107ASN0-0.033-0.00820.621-0.366-0.3660.0000.0000.0000.000
107P108VAL00.0410.01822.7870.5100.5100.0000.0000.0000.000
108P109VAL0-0.0040.00025.145-0.513-0.5130.0000.0000.0000.000
109P110VAL0-0.0110.00227.6170.4430.4430.0000.0000.0000.000
110P111TRP00.010-0.00729.820-0.205-0.2050.0000.0000.0000.000
111P112LEU00.002-0.00832.0710.2820.2820.0000.0000.0000.000
112P113ASP-1-0.772-0.88034.675-8.264-8.2640.0000.0000.0000.000
113P114ASN0-0.011-0.01635.792-0.023-0.0230.0000.0000.0000.000
114P115ALA00.0070.00132.8900.0250.0250.0000.0000.0000.000
115P116ALA0-0.0070.00034.436-0.061-0.0610.0000.0000.0000.000
116P117SER0-0.046-0.02337.6540.2180.2180.0000.0000.0000.000
117P118ALA0-0.036-0.01035.2560.0510.0510.0000.0000.0000.000
118P119ASN0-0.037-0.03336.7290.0140.0140.0000.0000.0000.000
119P120ILE0-0.020-0.01434.354-0.110-0.1100.0000.0000.0000.000
120P121VAL0-0.033-0.00636.3750.2370.2370.0000.0000.0000.000
121P122ALA00.018-0.00135.0840.2060.2060.0000.0000.0000.000
122P123LEU0-0.043-0.00731.724-0.272-0.2720.0000.0000.0000.000
123P124SER00.002-0.01629.5430.3240.3240.0000.0000.0000.000
124P125ALA00.004-0.00727.780-0.361-0.3610.0000.0000.0000.000
125P126SER0-0.029-0.02524.4090.2460.2460.0000.0000.0000.000
126P127ALA00.0400.00326.5340.0910.0910.0000.0000.0000.000
127P128HIS0-0.001-0.00625.6580.0190.0190.0000.0000.0000.000
128P129SER0-0.0130.00025.432-0.383-0.3830.0000.0000.0000.000
129P130GLY0-0.034-0.01927.2870.0740.0740.0000.0000.0000.000
130P131TYR0-0.026-0.03424.075-0.464-0.4640.0000.0000.0000.000
131P132LYS10.8060.89529.96210.53710.5370.0000.0000.0000.000
132P133LYS10.8370.89831.9599.4319.4310.0000.0000.0000.000
133P134SER0-0.0100.00534.5830.2560.2560.0000.0000.0000.000
134P135PHE00.0440.02336.812-0.148-0.1480.0000.0000.0000.000
135P136PRO00.033-0.00239.1450.1370.1370.0000.0000.0000.000
136P137ALA0-0.0150.01337.290-0.018-0.0180.0000.0000.0000.000
137P138ASP-1-0.868-0.91038.799-7.538-7.5380.0000.0000.0000.000
138P139LYS10.9750.96638.9377.0947.0940.0000.0000.0000.000
139P140SER0-0.052-0.02740.562-0.087-0.0870.0000.0000.0000.000
140P141TYR00.019-0.00635.491-0.116-0.1160.0000.0000.0000.000
141P142LEU0-0.025-0.00935.270-0.326-0.3260.0000.0000.0000.000
142P143ASP-1-0.884-0.92235.500-8.533-8.5330.0000.0000.0000.000
143P144GLY00.0250.00936.418-0.190-0.1900.0000.0000.0000.000
144P145ILE0-0.047-0.02633.4550.1410.1410.0000.0000.0000.000
145P146THR0-0.014-0.00731.313-0.341-0.3410.0000.0000.0000.000
146P147ALA00.0380.01530.3970.2230.2230.0000.0000.0000.000
147P148LYS10.8050.92530.9318.2228.2220.0000.0000.0000.000
148P149ILE0-0.003-0.00327.3320.1940.1940.0000.0000.0000.000
149P150SER0-0.032-0.00629.579-0.031-0.0310.0000.0000.0000.000
150P151TYR0-0.050-0.05421.9210.0490.0490.0000.0000.0000.000
151P152LYS10.9280.94927.3509.6389.6380.0000.0000.0000.000
152P153SER0-0.040-0.00927.700-0.107-0.1070.0000.0000.0000.000
153P154THR00.004-0.02029.4320.3800.3800.0000.0000.0000.000
154P155TRP00.0300.04231.025-0.152-0.1520.0000.0000.0000.000
155P156PRO0-0.026-0.02433.6050.2750.2750.0000.0000.0000.000
156P157LEU00.012-0.00130.266-0.219-0.2190.0000.0000.0000.000
157P158ASP-1-0.843-0.91425.017-12.625-12.6250.0000.0000.0000.000
158P159HIS10.7300.84323.75513.08013.0800.0000.0000.0000.000
159P160GLU-1-0.803-0.85525.484-10.543-10.5430.0000.0000.0000.000
160P161LEU00.0000.00524.2350.0810.0810.0000.0000.0000.000
161P162GLY0-0.019-0.00827.9100.3550.3550.0000.0000.0000.000
162P163PHE0-0.0040.01831.198-0.223-0.2230.0000.0000.0000.000
163P164THR0-0.030-0.01132.9780.2950.2950.0000.0000.0000.000
164P165THR00.0440.01135.445-0.041-0.0410.0000.0000.0000.000
165P166SER0-0.027-0.00934.8030.2220.2220.0000.0000.0000.000
166P167ALA00.0390.02934.994-0.167-0.1670.0000.0000.0000.000
167P168GLY00.016-0.00230.909-0.050-0.0500.0000.0000.0000.000
168P169LYS10.8950.93527.50410.76510.7650.0000.0000.0000.000
169P170GLN00.0150.01626.414-0.265-0.2650.0000.0000.0000.000
170P171GLN00.0130.01321.303-0.071-0.0710.0000.0000.0000.000
171P172PRO00.003-0.00519.5180.4460.4460.0000.0000.0000.000
172P173LEU0-0.0090.01119.833-0.715-0.7150.0000.0000.0000.000
173P174ILE0-0.014-0.00114.6960.0900.0900.0000.0000.0000.000
174P175GLN00.0090.00317.519-0.196-0.1960.0000.0000.0000.000
175P176TRP00.0620.00512.926-1.158-1.1580.0000.0000.0000.000
176P177GLU-1-0.804-0.91516.745-15.791-15.7910.0000.0000.0000.000
177P178GLN00.000-0.01618.415-0.401-0.4010.0000.0000.0000.000
178P179MET0-0.094-0.00312.763-1.000-1.0000.0000.0000.0000.000
179P180THR00.006-0.02610.2461.0151.0150.0000.0000.0000.000
180P181GLN00.005-0.01111.8920.4660.4660.0000.0000.0000.000
181P182ALA00.0530.0307.144-0.151-0.1510.0000.0000.0000.000
182P183ALA00.0000.0077.163-4.461-4.4610.0000.0000.0000.000
183P184ARG10.8470.9128.61420.12420.1240.0000.0000.0000.000
184P185ASP-1-0.816-0.8998.472-26.756-26.7560.0000.0000.0000.000
186P187LEU0-0.013-0.0066.4280.7060.7060.0000.0000.0000.000
187P188GLU-1-0.814-0.8889.472-18.249-18.2490.0000.0000.0000.000
188P189SER0-0.067-0.0637.7260.0760.0760.0000.0000.0000.000
189P190THR0-0.050-0.0276.082-3.316-3.3160.0000.0000.0000.000
190P191ASP-1-0.879-0.9298.122-19.789-19.7890.0000.0000.0000.000
191P192PHE0-0.015-0.0278.959-1.902-1.9020.0000.0000.0000.000
192P193GLY00.0170.00012.7031.3341.3340.0000.0000.0000.000
193P194ASN0-0.034-0.02115.5541.1381.1380.0000.0000.0000.000
194P195ALA0-0.0150.01615.4980.7660.7660.0000.0000.0000.000
195P196ASN0-0.032-0.03315.738-1.124-1.1240.0000.0000.0000.000
196P197VAL00.0260.02612.0070.9960.9960.0000.0000.0000.000
197P198PRO0-0.027-0.00715.4170.4000.4000.0000.0000.0000.000
198P199PHE00.0790.02114.3690.7680.7680.0000.0000.0000.000
199P200LYS10.8930.98612.99021.99021.9900.0000.0000.0000.000
200P201SER0-0.034-0.06216.2841.4211.4210.0000.0000.0000.000
201P202ASN0-0.036-0.02517.9040.6770.6770.0000.0000.0000.000
202P203PHE00.0150.00720.0960.4720.4720.0000.0000.0000.000
203P204GLN00.0510.01521.5730.7980.7980.0000.0000.0000.000
204P205ASP-1-0.857-0.92323.677-12.406-12.4060.0000.0000.0000.000
205P206LYS10.8600.93620.52414.93714.9370.0000.0000.0000.000
206P207LEU00.0100.01524.5510.4100.4100.0000.0000.0000.000
207P208VAL00.0010.00127.0970.4510.4510.0000.0000.0000.000
208P209LYS10.8380.91225.97512.13712.1370.0000.0000.0000.000
209P210ALA0-0.008-0.00527.4610.3280.3280.0000.0000.0000.000
210P211PHE00.0230.02729.4930.2420.2420.0000.0000.0000.000
211P212PHE-1-0.908-0.93632.506-8.566-8.5660.0000.0000.0000.000