FMO DATABASE

FMODB ID: 2GRGR

Calculation Name: 6ZM3-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6ZM3

Chain ID: A

ChEMBL ID:

UniProt ID:

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1431263.206193
FMO2-HF: Nuclear repulsion	1371932.328951
FMO2-HF: Total energy	-59330.877242
FMO2-MP2: Total energy	-59503.527735

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:2:LEU)

Summations of interaction energy for fragment #1(A:2:LEU)

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.
64.755	70.145	3.417	-2.184	-6.624	-0.01

Interaction energy analysis for fragmet #1(A:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.883 / q_NPA : 0.930

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	4	THR	0	0.083	0.028	3.839	-0.052	1.426	-0.019	-0.602	-0.857	0.001
5	A	6	ILE	0	0.045	0.032	2.768	0.631	1.734	0.287	-0.257	-1.133	-0.001
6	A	7	ILE	0	-0.008	0.013	2.382	1.904	3.252	1.015	-0.411	-1.952	-0.004
7	A	8	LYS	1	0.890	0.924	4.553	28.796	28.904	-0.001	-0.019	-0.088	0.000
29	A	30	PRO	0	0.034	0.020	2.277	-0.249	0.095	2.094	-0.534	-1.904	-0.004
30	A	31	ARG	1	0.834	0.915	3.483	41.313	42.331	0.042	-0.359	-0.702	-0.002
31	A	32	TYR	0	-0.077	-0.052	5.327	2.539	2.530	-0.001	-0.002	0.012	0.000
4	A	5	ARG	1	0.824	0.891	6.544	27.590	27.590	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.746	-0.837	7.807	-24.204	-24.204	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.002	-0.021	5.293	1.966	1.966	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.826	-0.885	7.713	-20.237	-20.237	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.879	0.924	9.877	19.421	19.421	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.014	-0.008	9.033	1.195	1.195	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.009	0.003	10.622	0.919	0.919	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.844	0.902	12.215	20.390	20.390	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.893	-0.933	15.210	-15.402	-15.402	0.000	0.000	0.000	0.000
16	A	17	CYS	0	-0.064	-0.009	14.520	0.014	0.014	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.001	0.005	17.081	0.670	0.670	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.048	0.013	20.325	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.059	0.046	23.204	0.191	0.191	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.050	-0.017	17.173	-0.043	-0.043	0.000	0.000	0.000	0.000
21	A	22	THR	0	0.011	0.007	16.378	-0.141	-0.141	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.026	-0.001	11.929	0.005	0.005	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.017	-0.008	10.553	-0.249	-0.249	0.000	0.000	0.000	0.000
24	A	25	PRO	0	-0.038	-0.003	5.967	0.681	0.681	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.000	-0.006	7.920	1.374	1.374	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.910	0.948	7.704	18.581	18.581	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.836	-0.922	8.315	-22.895	-22.895	0.000	0.000	0.000	0.000
28	A	29	ASN	0	0.015	0.001	6.528	-4.773	-4.773	0.000	0.000	0.000	0.000
32	A	33	PHE	0	0.001	-0.007	5.534	-0.676	-0.676	0.000	0.000	0.000	0.000
33	A	34	MET	0	0.017	0.019	10.051	1.603	1.603	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.010	-0.018	13.166	-0.663	-0.663	0.000	0.000	0.000	0.000
35	A	36	THR	0	-0.063	-0.033	15.512	0.916	0.916	0.000	0.000	0.000	0.000
36	A	37	ILE	0	0.031	0.008	19.059	-0.388	-0.388	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.009	-0.008	21.633	0.478	0.478	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.004	-0.003	25.067	-0.105	-0.105	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.008	-0.002	27.232	0.178	0.178	0.000	0.000	0.000	0.000
40	A	41	PRO	0	0.050	0.026	29.473	0.240	0.240	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.031	-0.005	32.669	0.008	0.008	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.016	-0.021	32.016	0.145	0.145	0.000	0.000	0.000	0.000
43	A	44	CYS	0	-0.049	-0.025	33.256	0.115	0.115	0.000	0.000	0.000	0.000
44	A	45	TYR	0	-0.048	-0.066	29.725	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.883	-0.914	30.716	-8.531	-8.531	0.000	0.000	0.000	0.000
46	A	47	GLY	0	-0.015	-0.017	31.671	0.152	0.152	0.000	0.000	0.000	0.000
47	A	48	GLY	0	-0.011	0.002	29.410	0.036	0.036	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.054	-0.027	22.496	-0.225	-0.225	0.000	0.000	0.000	0.000
49	A	50	PHE	0	-0.011	-0.011	23.811	-0.041	-0.041	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.971	0.981	20.032	11.753	11.753	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.008	-0.004	17.773	0.388	0.388	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.773	-0.842	14.630	-16.702	-16.702	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.015	-0.002	10.312	0.460	0.460	0.000	0.000	0.000	0.000
54	A	55	PHE	0	0.001	-0.004	8.317	-1.306	-1.306	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.004	0.007	5.340	0.919	0.919	0.000	0.000	0.000	0.000
56	A	57	PRO	0	0.009	0.008	8.044	-2.679	-2.679	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.896	-0.956	8.159	-29.606	-29.606	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.899	-0.954	8.410	-22.560	-22.560	0.000	0.000	0.000	0.000
59	A	60	TYR	0	-0.101	-0.033	7.522	2.328	2.328	0.000	0.000	0.000	0.000
60	A	61	PRO	0	-0.043	-0.030	8.704	-3.284	-3.284	0.000	0.000	0.000	0.000
61	A	62	MET	0	0.064	0.013	11.699	1.738	1.738	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.893	0.953	13.597	18.980	18.980	0.000	0.000	0.000	0.000
63	A	64	PRO	0	0.054	0.030	13.420	-1.559	-1.559	0.000	0.000	0.000	0.000
64	A	65	PRO	0	-0.049	-0.029	11.599	-0.739	-0.739	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.931	0.976	12.970	20.226	20.226	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.006	-0.001	14.230	-0.909	-0.909	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.772	0.878	16.593	14.665	14.665	0.000	0.000	0.000	0.000
68	A	69	PHE	0	0.046	0.007	18.890	-0.491	-0.491	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.068	-0.029	18.046	0.014	0.014	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.020	0.006	22.106	0.255	0.255	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.875	0.938	24.923	9.886	9.886	0.000	0.000	0.000	0.000
72	A	73	ILE	0	0.032	0.012	26.388	0.168	0.168	0.000	0.000	0.000	0.000
73	A	74	TYR	0	-0.019	-0.024	29.171	-0.151	-0.151	0.000	0.000	0.000	0.000
74	A	75	HIS	0	0.046	0.011	29.234	0.073	0.073	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.052	0.044	31.197	-0.132	-0.132	0.000	0.000	0.000	0.000
76	A	77	ASN	0	0.001	0.005	28.109	0.063	0.063	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.010	-0.007	25.172	-0.594	-0.594	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.705	-0.819	26.682	-10.874	-10.874	0.000	0.000	0.000	0.000
79	A	80	LYS	1	1.003	0.990	27.862	9.172	9.172	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.095	-0.048	25.205	0.123	0.123	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.046	0.038	23.639	-0.557	-0.557	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.844	0.892	22.266	11.108	11.108	0.000	0.000	0.000	0.000
83	A	84	ILE	0	0.033	0.017	20.213	0.457	0.457	0.000	0.000	0.000	0.000
84	A	85	CYS	0	-0.058	-0.016	23.189	-0.420	-0.420	0.000	0.000	0.000	0.000
85	A	86	LEU	0	0.046	0.019	20.692	0.257	0.257	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.765	-0.888	23.211	-12.281	-12.281	0.000	0.000	0.000	0.000
87	A	88	ILE	0	-0.059	-0.035	19.563	-0.440	-0.440	0.000	0.000	0.000	0.000
88	A	89	ILE	0	-0.061	-0.042	17.428	-0.989	-0.989	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.816	0.908	19.590	11.060	11.060	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.895	-0.957	22.231	-11.925	-11.925	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.937	0.972	23.600	11.004	11.004	0.000	0.000	0.000	0.000
92	A	93	TRP	0	-0.019	-0.011	13.672	-0.268	-0.268	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.041	0.008	18.704	0.215	0.215	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.024	0.017	14.853	-0.493	-0.493	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.003	0.008	14.741	-1.344	-1.344	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.041	0.003	16.815	0.026	0.026	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.009	0.003	12.551	-1.402	-1.402	0.000	0.000	0.000	0.000
98	A	99	ILE	0	0.041	0.007	8.414	1.324	1.324	0.000	0.000	0.000	0.000
99	A	100	ASN	0	0.033	0.008	13.025	1.040	1.040	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.959	0.992	15.356	14.004	14.004	0.000	0.000	0.000	0.000
101	A	102	VAL	0	0.010	0.020	15.530	0.850	0.850	0.000	0.000	0.000	0.000
102	A	103	LEU	0	0.017	0.004	13.860	0.703	0.703	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.050	0.028	17.945	0.631	0.631	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.036	-0.042	20.633	0.793	0.793	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.003	0.008	18.567	0.463	0.463	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.007	-0.009	22.222	0.351	0.351	0.000	0.000	0.000	0.000
107	A	108	ILE	0	-0.014	-0.010	24.078	0.457	0.457	0.000	0.000	0.000	0.000
108	A	109	LEU	0	-0.007	0.007	25.089	0.358	0.358	0.000	0.000	0.000	0.000
109	A	110	MET	0	-0.065	-0.018	24.810	0.166	0.166	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.012	-0.009	27.996	0.358	0.358	0.000	0.000	0.000	0.000
111	A	112	SER	0	-0.037	-0.009	30.064	0.417	0.417	0.000	0.000	0.000	0.000
112	A	113	PRO	0	-0.015	-0.004	30.839	-0.281	-0.281	0.000	0.000	0.000	0.000
113	A	114	ASN	0	-0.002	0.000	29.435	0.366	0.366	0.000	0.000	0.000	0.000
114	A	115	PRO	0	0.050	0.026	32.875	-0.167	-0.167	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.838	-0.911	35.567	-7.715	-7.715	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.850	-0.916	29.917	-10.177	-10.177	0.000	0.000	0.000	0.000
117	A	118	PRO	0	-0.029	-0.024	32.387	0.154	0.154	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.083	-0.035	29.407	0.115	0.115	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.032	0.018	33.467	-0.106	-0.106	0.000	0.000	0.000	0.000
120	A	121	ASN	0	-0.047	-0.038	32.922	-0.063	-0.063	0.000	0.000	0.000	0.000
121	A	122	ASP	-1	-0.799	-0.901	36.028	-7.890	-7.890	0.000	0.000	0.000	0.000
122	A	123	VAL	0	-0.061	-0.016	33.645	0.141	0.141	0.000	0.000	0.000	0.000
123	A	124	ALA	0	-0.011	-0.024	34.700	0.094	0.094	0.000	0.000	0.000	0.000
124	A	125	GLU	-1	-0.953	-0.960	36.546	-7.418	-7.418	0.000	0.000	0.000	0.000
125	A	126	HIS	0	0.048	0.041	39.208	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	127	TRP	0	-0.053	-0.057	34.363	0.013	0.013	0.000	0.000	0.000	0.000
127	A	128	LYS	1	0.778	0.880	38.384	7.916	7.916	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.957	-0.959	42.156	-6.461	-6.461	0.000	0.000	0.000	0.000
129	A	130	ASP	-1	-0.862	-0.949	43.451	-6.544	-6.544	0.000	0.000	0.000	0.000
130	A	131	GLU	-1	-0.844	-0.923	38.850	-7.821	-7.821	0.000	0.000	0.000	0.000
131	A	132	ALA	0	-0.035	-0.011	40.997	-0.134	-0.134	0.000	0.000	0.000	0.000
132	A	133	SER	0	0.002	0.007	42.487	-0.152	-0.152	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.004	0.028	38.346	-0.127	-0.127	0.000	0.000	0.000	0.000
134	A	135	LEU	0	0.029	-0.005	36.599	-0.237	-0.237	0.000	0.000	0.000	0.000
135	A	136	GLN	0	-0.074	-0.053	37.943	-0.184	-0.184	0.000	0.000	0.000	0.000
136	A	137	THR	0	0.008	-0.008	37.085	-0.069	-0.069	0.000	0.000	0.000	0.000
137	A	138	ALA	0	-0.002	0.003	33.950	-0.178	-0.178	0.000	0.000	0.000	0.000
138	A	139	ARG	1	0.965	1.006	34.244	7.346	7.346	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.911	-0.928	36.409	-7.316	-7.316	0.000	0.000	0.000	0.000
140	A	141	TRP	0	-0.027	-0.028	31.160	-0.248	-0.248	0.000	0.000	0.000	0.000
141	A	142	THR	0	0.004	-0.012	30.840	-0.321	-0.321	0.000	0.000	0.000	0.000
142	A	143	ARG	1	0.864	0.921	32.149	7.481	7.481	0.000	0.000	0.000	0.000
143	A	144	LYS	1	0.890	0.959	34.531	8.344	8.344	0.000	0.000	0.000	0.000
144	A	145	TYR	0	-0.024	-0.020	29.475	0.029	0.029	0.000	0.000	0.000	0.000
145	A	146	ALA	0	0.007	0.011	27.859	-0.311	-0.311	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.925	0.972	28.827	8.619	8.619	0.000	0.000	0.000	0.000
147	A	148	PRO	-1	-0.896	-0.935	26.515	-10.586	-10.586	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LEU)