FMO DATABASE

FMODB ID: GRYG1

Calculation Name: 3P3K-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3P3K

Chain ID: A

ChEMBL ID:

UniProt ID: Q8I3Z5

Base Structure: X-ray

Registration Date: 2025-10-04

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1750113.846664
FMO2-HF: Nuclear repulsion	1682937.694849
FMO2-HF: Total energy	-67176.151815
FMO2-MP2: Total energy	-67372.204654

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-74.011	-67.874	2.872	-3.562	-5.448	-0.035

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.807 / q_NPA : 0.900

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 ES EX CT+mix DI(MP2)

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].
3	A	3	PHE	0	-0.021	0.004	2.569	-0.392	2.759	2.637	-1.901	-3.887	-0.016
155	A	178	HIS	0	-0.017	-0.033	2.941	-25.641	-22.991	0.236	-1.510	-1.376	-0.018
156	A	179	HIS	0	-0.045	-0.028	3.951	-6.468	-6.132	-0.001	-0.151	-0.185	-0.001
4	A	4	ARG	1	0.850	0.893	5.432	35.020	35.020	0.000	0.000	0.000	0.000
5	A	5	MET	0	0.012	0.020	8.968	0.625	0.625	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.805	0.904	12.244	14.790	14.790	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.006	0.014	15.620	0.528	0.528	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.029	-0.028	18.132	0.304	0.304	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.868	0.931	19.183	15.950	15.950	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.711	-0.855	23.882	-10.064	-10.064	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.069	-0.034	27.491	-0.267	-0.267	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.076	-0.046	29.614	0.255	0.255	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.005	-0.020	28.099	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.063	-0.029	24.325	-0.441	-0.441	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.751	-0.834	23.421	-12.149	-12.149	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.827	-0.924	17.082	-17.728	-17.728	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.019	0.010	21.322	0.169	0.169	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.031	0.007	20.980	0.494	0.494	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.020	0.002	15.580	-0.141	-0.141	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.840	-0.944	15.030	-18.679	-18.679	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.066	-0.024	14.004	0.013	0.013	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.004	0.014	16.191	0.493	0.493	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.004	-0.007	19.983	0.137	0.137	0.000	0.000	0.000	0.000
24	A	24	GLN	0	0.012	0.015	22.323	0.715	0.715	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.051	-0.029	25.259	0.402	0.402	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.800	-0.892	28.846	-9.549	-9.549	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.040	-0.013	32.144	0.096	0.096	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.013	-0.007	33.724	0.247	0.247	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.888	-0.914	34.532	-8.163	-8.163	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.003	0.010	35.983	0.192	0.192	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.022	0.004	35.815	-0.191	-0.191	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.942	-0.978	36.427	-7.821	-7.821	0.000	0.000	0.000	0.000
33	A	33	PHE	0	-0.025	-0.027	36.281	0.046	0.046	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.863	0.925	26.930	10.392	10.392	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.917	-0.938	32.305	-9.250	-9.250	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.036	-0.017	33.782	-0.053	-0.053	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.009	0.006	31.622	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.006	-0.003	24.751	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.758	-0.843	29.041	-9.241	-9.241	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.020	0.007	23.277	-0.338	-0.338	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.774	0.885	25.166	10.241	10.241	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.012	0.002	23.905	-0.436	-0.436	0.000	0.000	0.000	0.000
43	A	43	ASN	0	-0.029	-0.021	22.003	0.737	0.737	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.942	0.978	24.175	9.474	9.474	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.855	0.928	16.745	14.362	14.362	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.041	-0.025	19.718	0.540	0.540	0.000	0.000	0.000	0.000
47	A	47	LYS	0	0.095	0.054	20.891	-2.840	-2.840	0.000	0.000	0.000	0.000
48	A	71	HIS	0	-0.062	-0.053	25.074	-0.142	-0.142	0.000	0.000	0.000	0.000
49	A	72	VAL	0	0.023	0.027	23.021	0.395	0.395	0.000	0.000	0.000	0.000
50	A	73	ILE	0	0.017	0.007	24.906	-0.071	-0.071	0.000	0.000	0.000	0.000
51	A	74	ASP	-1	-0.798	-0.904	19.848	-12.639	-12.639	0.000	0.000	0.000	0.000
52	A	75	ILE	0	0.009	0.001	20.867	-0.424	-0.424	0.000	0.000	0.000	0.000
53	A	76	VAL	0	-0.008	-0.005	22.657	-0.147	-0.147	0.000	0.000	0.000	0.000
54	A	77	ASP	-1	-0.857	-0.922	20.197	-13.403	-13.403	0.000	0.000	0.000	0.000
55	A	78	SER	0	-0.044	-0.031	16.759	-0.501	-0.501	0.000	0.000	0.000	0.000
56	A	79	PHE	0	-0.040	-0.011	17.710	-0.804	-0.804	0.000	0.000	0.000	0.000
57	A	80	GLN	0	-0.055	-0.026	20.954	-0.179	-0.179	0.000	0.000	0.000	0.000
58	A	81	LEU	0	-0.023	0.008	23.636	0.415	0.415	0.000	0.000	0.000	0.000
59	A	82	THR	0	-0.008	-0.009	26.488	0.164	0.164	0.000	0.000	0.000	0.000
60	A	83	SER	0	-0.021	-0.001	29.953	0.093	0.093	0.000	0.000	0.000	0.000
61	A	84	THR	0	-0.040	-0.029	32.798	0.184	0.184	0.000	0.000	0.000	0.000
62	A	85	ALA	0	0.007	0.004	36.016	0.050	0.050	0.000	0.000	0.000	0.000
63	A	86	PHE	0	0.022	0.002	37.237	0.060	0.060	0.000	0.000	0.000	0.000
64	A	87	SER	0	-0.025	-0.036	41.810	0.111	0.111	0.000	0.000	0.000	0.000
65	A	88	LYS	1	0.942	0.974	44.665	6.489	6.489	0.000	0.000	0.000	0.000
66	A	89	LYS	1	0.926	0.971	45.971	5.951	5.951	0.000	0.000	0.000	0.000
67	A	90	GLU	-1	-0.810	-0.873	43.946	-6.886	-6.886	0.000	0.000	0.000	0.000
68	A	91	TYR	0	0.066	0.029	38.321	0.013	0.013	0.000	0.000	0.000	0.000
69	A	92	SER	0	-0.032	-0.037	42.726	-0.063	-0.063	0.000	0.000	0.000	0.000
70	A	93	ALA	0	-0.063	-0.031	45.393	0.013	0.013	0.000	0.000	0.000	0.000
71	A	94	TYR	0	-0.007	0.001	35.327	0.070	0.070	0.000	0.000	0.000	0.000
72	A	95	ILE	0	0.010	0.014	38.482	-0.080	-0.080	0.000	0.000	0.000	0.000
73	A	96	LYS	1	0.937	0.973	41.261	6.431	6.431	0.000	0.000	0.000	0.000
74	A	97	ASN	0	-0.051	-0.039	42.578	0.026	0.026	0.000	0.000	0.000	0.000
75	A	98	TYR	0	0.059	0.042	32.354	-0.040	-0.040	0.000	0.000	0.000	0.000
76	A	99	MET	0	-0.009	-0.001	36.986	-0.141	-0.141	0.000	0.000	0.000	0.000
77	A	100	GLN	0	-0.035	-0.028	40.257	0.104	0.104	0.000	0.000	0.000	0.000
78	A	101	LYS	1	0.827	0.926	36.197	8.589	8.589	0.000	0.000	0.000	0.000
79	A	102	VAL	0	0.026	0.017	34.629	-0.137	-0.137	0.000	0.000	0.000	0.000
80	A	103	ALA	0	-0.009	-0.013	37.037	-0.080	-0.080	0.000	0.000	0.000	0.000
81	A	104	LYS	1	0.968	0.997	39.688	7.561	7.561	0.000	0.000	0.000	0.000
82	A	105	TYR	0	0.047	0.016	30.101	-0.105	-0.105	0.000	0.000	0.000	0.000
83	A	106	LEU	0	-0.031	-0.018	34.061	-0.176	-0.176	0.000	0.000	0.000	0.000
84	A	107	GLU	-1	-0.883	-0.946	36.789	-7.522	-7.522	0.000	0.000	0.000	0.000
85	A	108	GLU	-1	-0.953	-0.976	37.191	-8.027	-8.027	0.000	0.000	0.000	0.000
86	A	109	LYS	1	0.826	0.912	32.912	9.255	9.255	0.000	0.000	0.000	0.000
87	A	110	LYS	1	0.904	0.969	28.502	10.614	10.614	0.000	0.000	0.000	0.000
88	A	111	PRO	0	0.078	0.039	34.860	0.124	0.124	0.000	0.000	0.000	0.000
89	A	112	ASP	-1	-0.938	-0.976	34.608	-9.121	-9.121	0.000	0.000	0.000	0.000
90	A	113	ARG	1	0.773	0.830	33.138	9.454	9.454	0.000	0.000	0.000	0.000
91	A	114	VAL	0	-0.027	0.013	36.874	0.120	0.120	0.000	0.000	0.000	0.000
92	A	115	GLU	-1	-0.856	-0.950	39.979	-7.085	-7.085	0.000	0.000	0.000	0.000
93	A	116	ILE	0	-0.031	0.006	37.075	0.164	0.164	0.000	0.000	0.000	0.000
94	A	117	PHE	0	0.044	0.009	36.090	0.097	0.097	0.000	0.000	0.000	0.000
95	A	118	LYS	1	0.846	0.930	38.799	7.493	7.493	0.000	0.000	0.000	0.000
96	A	119	THR	0	-0.036	-0.026	42.458	0.222	0.222	0.000	0.000	0.000	0.000
97	A	120	LYS	1	0.926	0.952	38.903	7.801	7.801	0.000	0.000	0.000	0.000
98	A	121	ALA	0	0.068	0.047	39.349	-0.043	-0.043	0.000	0.000	0.000	0.000
99	A	122	GLN	0	-0.100	-0.041	40.374	0.200	0.200	0.000	0.000	0.000	0.000
100	A	123	PRO	0	-0.055	-0.037	42.202	0.110	0.110	0.000	0.000	0.000	0.000
101	A	124	PHE	0	0.085	0.052	34.564	0.065	0.065	0.000	0.000	0.000	0.000
102	A	125	ILE	0	0.051	0.017	38.439	0.011	0.011	0.000	0.000	0.000	0.000
103	A	126	LYS	1	0.915	0.960	41.417	6.698	6.698	0.000	0.000	0.000	0.000
104	A	127	HIS	0	0.025	0.037	39.295	0.271	0.271	0.000	0.000	0.000	0.000
105	A	128	ILE	0	0.020	0.019	36.703	0.066	0.066	0.000	0.000	0.000	0.000
106	A	129	LEU	0	-0.046	-0.024	40.895	0.107	0.107	0.000	0.000	0.000	0.000
107	A	130	THR	0	-0.087	-0.064	44.345	0.210	0.210	0.000	0.000	0.000	0.000
108	A	131	ASN	0	-0.044	-0.023	41.762	0.229	0.229	0.000	0.000	0.000	0.000
109	A	132	PHE	0	-0.022	-0.014	41.669	-0.112	-0.112	0.000	0.000	0.000	0.000
110	A	133	ASP	-1	-0.901	-0.967	41.594	-6.784	-6.784	0.000	0.000	0.000	0.000
111	A	134	ASP	-1	-0.926	-0.945	39.651	-7.221	-7.221	0.000	0.000	0.000	0.000
112	A	135	PHE	0	-0.106	-0.058	35.855	-0.280	-0.280	0.000	0.000	0.000	0.000
113	A	136	GLU	-1	-0.892	-0.941	33.932	-8.567	-8.567	0.000	0.000	0.000	0.000
114	A	137	PHE	0	-0.017	-0.028	34.141	-0.210	-0.210	0.000	0.000	0.000	0.000
115	A	138	TYR	0	-0.013	-0.007	29.333	-0.063	-0.063	0.000	0.000	0.000	0.000
116	A	139	MET	0	-0.007	0.007	30.839	0.078	0.078	0.000	0.000	0.000	0.000
117	A	140	GLY	0	0.063	0.024	26.801	-0.233	-0.233	0.000	0.000	0.000	0.000
118	A	141	GLU	-1	-0.871	-0.925	23.175	-12.630	-12.630	0.000	0.000	0.000	0.000
119	A	142	SER	0	-0.038	-0.058	26.545	0.291	0.291	0.000	0.000	0.000	0.000
120	A	143	LEU	0	-0.121	-0.055	29.239	0.424	0.424	0.000	0.000	0.000	0.000
121	A	144	ASP	-1	-0.845	-0.912	31.916	-8.701	-8.701	0.000	0.000	0.000	0.000
122	A	145	MET	0	-0.008	-0.019	33.950	0.001	0.001	0.000	0.000	0.000	0.000
123	A	146	GLU	-1	-0.945	-0.965	36.576	-7.844	-7.844	0.000	0.000	0.000	0.000
124	A	147	ALA	0	-0.015	-0.002	31.561	0.003	0.003	0.000	0.000	0.000	0.000
125	A	148	GLY	0	-0.021	-0.016	31.171	0.287	0.287	0.000	0.000	0.000	0.000
126	A	149	ILE	0	-0.053	-0.018	30.987	-0.152	-0.152	0.000	0.000	0.000	0.000
127	A	150	ILE	0	-0.044	-0.010	27.015	-0.024	-0.024	0.000	0.000	0.000	0.000
128	A	151	TYR	0	0.029	0.011	30.422	0.391	0.391	0.000	0.000	0.000	0.000
129	A	152	SER	0	-0.016	-0.003	30.526	-0.341	-0.341	0.000	0.000	0.000	0.000
130	A	153	TYR	0	0.024	-0.016	32.374	0.328	0.328	0.000	0.000	0.000	0.000
131	A	154	TYR	0	0.002	0.009	32.872	-0.359	-0.359	0.000	0.000	0.000	0.000
132	A	155	LYS	1	0.855	0.915	33.078	9.006	9.006	0.000	0.000	0.000	0.000
133	A	156	GLY	0	0.004	0.001	35.743	-0.044	-0.044	0.000	0.000	0.000	0.000
134	A	157	GLU	-1	-0.934	-0.970	37.635	-7.255	-7.255	0.000	0.000	0.000	0.000
135	A	158	GLU	-1	-0.834	-0.876	31.265	-9.468	-9.468	0.000	0.000	0.000	0.000
136	A	159	ILE	0	-0.026	-0.029	31.201	-0.036	-0.036	0.000	0.000	0.000	0.000
137	A	160	THR	0	-0.084	-0.059	27.260	0.052	0.052	0.000	0.000	0.000	0.000
138	A	161	PRO	0	0.077	0.055	28.918	0.026	0.026	0.000	0.000	0.000	0.000
139	A	162	ARG	1	0.746	0.857	28.607	9.137	9.137	0.000	0.000	0.000	0.000
140	A	163	PHE	0	0.054	0.015	26.701	0.227	0.227	0.000	0.000	0.000	0.000
141	A	164	VAL	0	-0.035	-0.028	28.549	-0.158	-0.158	0.000	0.000	0.000	0.000
142	A	165	TYR	0	0.008	-0.012	24.083	0.166	0.166	0.000	0.000	0.000	0.000
143	A	166	ILE	0	0.016	0.004	29.651	0.128	0.128	0.000	0.000	0.000	0.000
144	A	167	SER	0	0.020	-0.004	29.069	-0.088	-0.088	0.000	0.000	0.000	0.000
145	A	168	ASP	-1	-0.774	-0.871	29.551	-9.700	-9.700	0.000	0.000	0.000	0.000
146	A	169	GLY	0	-0.019	-0.002	31.799	0.063	0.063	0.000	0.000	0.000	0.000
147	A	170	LEU	0	-0.026	-0.008	25.822	-0.226	-0.226	0.000	0.000	0.000	0.000
148	A	171	PHE	0	-0.089	-0.046	22.839	0.241	0.241	0.000	0.000	0.000	0.000
149	A	172	GLU	-1	-0.829	-0.909	20.955	-14.282	-14.282	0.000	0.000	0.000	0.000
150	A	173	GLU	-1	-0.813	-0.869	18.308	-16.500	-16.500	0.000	0.000	0.000	0.000
151	A	174	LYS	1	0.904	0.947	15.390	15.966	15.966	0.000	0.000	0.000	0.000
152	A	175	TYR	0	-0.007	-0.014	11.917	-0.173	-0.173	0.000	0.000	0.000	0.000
153	A	176	LEU	0	-0.033	-0.027	7.708	-0.380	-0.380	0.000	0.000	0.000	0.000
154	A	177	GLU	-1	-0.793	-0.876	8.006	-28.116	-28.116	0.000	0.000	0.000	0.000
157	A	180	HIS	0	-0.010	-0.005	6.101	2.701	2.701	0.000	0.000	0.000	0.000
158	A	181	HIS	1	0.853	0.907	7.031	22.954	22.954	0.000	0.000	0.000	0.000
159	A	182	HIS	0	-0.007	0.005	10.618	4.977	4.977	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)