FMO DATABASE

FMODB ID: 654JZ

Calculation Name: 6XII-9-Other547

Preferred Name:

Target Type:

Ligand Name: magnesium ion | zinc ion

Ligand 3-letter code: MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6XII

Chain ID: 9

ChEMBL ID:

UniProt ID:

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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1216492.59964
FMO2-HF: Nuclear repulsion	1159946.719641
FMO2-HF: Total energy	-56545.879999
FMO2-MP2: Total energy	-56708.209522

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.
30.036	33.35	2.904	-0.634	-5.583	-0.02

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 : 0.857 / q_NPA : 0.943

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	LEU	0	0.048	0.006	3.337	0.909	1.407	0.590	0.729	-1.817	-0.002
4	A	4	ASN	0	-0.022	-0.010	4.362	1.166	1.795	0.019	-0.182	-0.467	-0.002
6	A	6	GLN	0	0.016	0.012	3.612	2.683	3.038	0.009	-0.069	-0.295	0.000
7	A	7	ASP	-1	-0.848	-0.937	2.307	-39.639	-38.043	2.187	-1.243	-2.539	-0.015
8	A	8	LYS	1	0.953	0.964	3.310	27.795	27.719	0.092	0.218	-0.233	-0.001
62	A	62	ARG	1	0.791	0.881	3.454	30.630	30.942	0.007	-0.087	-0.232	0.000
5	A	5	LEU	0	0.052	0.030	5.320	2.442	2.442	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.036	0.036	6.365	2.589	2.589	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.046	-0.020	6.383	1.525	1.525	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.054	0.038	7.012	1.103	1.103	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.005	0.003	9.965	1.625	1.625	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.044	-0.019	11.434	1.304	1.304	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.775	-0.893	10.054	-21.896	-21.896	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.055	0.031	13.549	0.943	0.943	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.167	-0.096	15.499	1.086	1.086	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.796	-0.912	16.270	-15.035	-15.035	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.016	-0.018	16.481	0.541	0.541	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.020	0.015	19.069	0.552	0.552	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.844	0.932	19.337	13.514	13.514	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.067	0.029	22.762	-0.158	-0.158	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.014	-0.005	23.599	0.474	0.474	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.048	-0.017	25.104	-0.232	-0.232	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.020	0.010	22.110	-0.206	-0.206	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.064	-0.036	23.103	0.416	0.416	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.037	0.028	20.644	-0.483	-0.483	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.003	0.002	19.918	0.646	0.646	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.002	0.006	19.527	-0.765	-0.765	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.838	-0.911	17.649	-15.675	-15.675	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.056	-0.055	17.977	-1.143	-1.143	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.900	0.930	18.747	14.733	14.733	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.054	0.042	19.412	0.631	0.631	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.014	0.017	19.679	-0.654	-0.654	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.011	-0.011	20.933	-0.398	-0.398	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.034	-0.004	22.943	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.802	-0.891	23.354	-12.450	-12.450	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.936	0.965	16.474	17.002	17.002	0.000	0.000	0.000	0.000
38	A	38	MET	0	0.018	0.012	22.310	0.356	0.356	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.082	-0.042	24.853	0.529	0.529	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.847	-0.934	22.479	-12.896	-12.896	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.003	-0.005	20.612	0.207	0.207	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.889	0.939	24.386	11.003	11.003	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.842	0.955	26.208	11.342	11.342	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.022	-0.006	23.614	0.267	0.267	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.009	0.011	25.669	0.096	0.096	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.808	0.882	27.260	9.628	9.628	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.812	-0.879	27.603	-9.119	-9.119	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.012	0.014	28.016	-0.296	-0.296	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.021	-0.005	27.463	0.181	0.181	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.061	-0.026	20.967	-0.191	-0.191	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.066	-0.061	21.981	-0.462	-0.462	0.000	0.000	0.000	0.000
52	A	52	MET	0	-0.007	0.021	21.277	-0.277	-0.277	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.862	0.926	15.672	15.299	15.299	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.061	0.032	17.633	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.014	0.007	11.030	-0.585	-0.585	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.851	0.922	12.621	20.705	20.705	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.061	-0.037	8.049	-3.843	-3.843	0.000	0.000	0.000	0.000
58	A	58	THR	0	0.104	0.053	10.924	1.291	1.291	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.069	-0.028	6.621	-0.105	-0.105	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.065	0.019	10.452	0.145	0.145	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.961	0.991	6.786	24.818	24.818	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.102	0.075	8.849	0.918	0.918	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.000	0.011	12.216	0.776	0.776	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.957	-0.991	9.422	-21.819	-21.819	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.005	-0.020	12.589	0.402	0.402	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.020	0.000	14.651	0.443	0.443	0.000	0.000	0.000	0.000
68	A	68	PRO	0	-0.083	-0.047	16.183	0.685	0.685	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.078	-0.009	18.365	0.400	0.400	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.849	-0.929	19.942	-11.320	-11.320	0.000	0.000	0.000	0.000
71	A	71	CYS	0	-0.003	-0.010	19.977	-0.238	-0.238	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.085	0.063	20.891	-0.304	-0.304	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.880	0.905	22.016	10.695	10.695	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.809	-0.910	18.098	-13.469	-13.469	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.038	-0.017	18.745	-0.564	-0.564	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.082	-0.034	19.774	-0.028	-0.028	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.038	0.037	20.305	-0.163	-0.163	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.083	0.051	16.872	-0.548	-0.548	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.063	-0.012	16.139	-1.101	-1.101	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.070	-0.050	17.432	0.494	0.494	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.046	-0.044	14.164	-1.336	-1.336	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.017	0.022	16.102	0.966	0.966	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.052	-0.018	15.555	-1.039	-1.039	0.000	0.000	0.000	0.000
84	A	84	TYR	0	0.031	-0.017	14.498	0.216	0.216	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.070	-0.060	17.648	-0.326	-0.326	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.030	0.043	17.879	0.547	0.547	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.798	-0.897	20.695	-10.259	-10.259	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.044	-0.031	20.712	-0.670	-0.670	0.000	0.000	0.000	0.000
89	A	89	PRO	0	-0.041	-0.008	24.619	0.291	0.291	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.002	0.017	28.190	-0.070	-0.070	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.024	-0.011	30.191	0.172	0.172	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.060	0.032	29.088	-0.248	-0.248	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.008	0.016	30.352	-0.041	-0.041	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.853	0.904	32.028	9.148	9.148	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.067	0.056	25.386	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.159	0.057	26.904	-0.117	-0.117	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.856	0.945	29.834	8.238	8.238	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.824	-0.927	30.027	-9.367	-9.367	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.043	0.020	22.518	0.134	0.134	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.011	0.003	28.380	-0.084	-0.084	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.926	0.950	31.366	8.285	8.285	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.011	0.030	28.241	0.183	0.183	0.000	0.000	0.000	0.000
103	A	103	ASN	0	0.046	0.006	25.777	-0.247	-0.247	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.065	-0.026	29.220	0.070	0.070	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.813	0.896	31.751	9.663	9.663	0.000	0.000	0.000	0.000
106	A	106	PHE	0	-0.027	-0.011	30.310	0.028	0.028	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.891	-0.941	26.318	-10.817	-10.817	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.064	-0.023	22.039	-0.215	-0.215	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.961	0.975	24.688	11.856	11.856	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.067	0.046	23.736	-0.454	-0.454	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.022	0.016	22.530	0.159	0.159	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.036	-0.021	24.661	0.183	0.183	0.000	0.000	0.000	0.000
113	A	113	PHE	0	-0.029	-0.020	26.624	0.445	0.445	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.874	-0.939	22.575	-12.263	-12.263	0.000	0.000	0.000	0.000
115	A	115	GLY	0	-0.028	-0.016	24.931	0.349	0.349	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.818	-0.914	20.707	-13.493	-13.493	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.059	-0.024	23.190	0.450	0.450	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.012	-0.007	26.145	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.010	0.008	29.237	0.237	0.237	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.013	0.003	31.294	-0.166	-0.166	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.063	-0.044	31.529	0.301	0.301	0.000	0.000	0.000	0.000
122	A	122	GLN	0	0.024	0.008	28.528	-0.216	-0.216	0.000	0.000	0.000	0.000
123	A	123	ILE	0	0.007	0.027	29.289	0.023	0.023	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.852	-0.939	30.337	-8.029	-8.029	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.739	0.908	29.719	9.358	9.358	0.000	0.000	0.000	0.000
126	A	126	LEU	0	0.027	0.016	33.988	0.228	0.228	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.025	-0.047	34.777	-0.200	-0.200	0.000	0.000	0.000	0.000
128	A	128	THR	0	-0.011	-0.009	37.290	0.101	0.101	0.000	0.000	0.000	0.000
129	A	129	LEU	0	0.008	0.000	32.233	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	130	PRO	0	-0.053	-0.014	35.864	-0.043	-0.043	0.000	0.000	0.000	0.000
131	A	131	THR	0	-0.037	-0.010	37.109	-0.019	-0.019	0.000	0.000	0.000	0.000
132	A	132	TYR	0	-0.015	-0.023	37.031	0.055	0.055	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.902	-0.960	39.130	-7.264	-7.264	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.843	-0.904	41.593	-6.351	-6.351	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.009	0.010	44.636	0.063	0.063	0.000	0.000	0.000	0.000
136	A	136	ILE	0	-0.036	-0.016	47.887	0.147	0.147	0.000	0.000	0.000	0.000
137	A	137	ALA	0	-0.005	-0.009	49.574	0.146	0.146	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.909	0.943	49.293	6.123	6.123	0.000	0.000	0.000	0.000
139	A	139	LEU	0	0.007	0.010	53.371	0.109	0.109	0.000	0.000	0.000	0.000
140	A	140	MET	0	-0.021	0.009	54.784	0.124	0.124	0.000	0.000	0.000	0.000
141	A	141	ALA	0	-0.005	-0.013	56.769	0.067	0.067	0.000	0.000	0.000	0.000
142	A	142	THR	0	0.060	0.026	59.503	0.019	0.019	0.000	0.000	0.000	0.000
143	A	143	MET	0	-0.017	-0.003	62.052	0.086	0.086	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.839	0.901	59.396	5.190	5.190	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.923	-0.943	62.554	-4.918	-4.918	0.000	0.000	0.000	0.000
146	A	146	ALA	0	0.001	-0.007	66.360	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	147	SER	0	-0.049	-0.027	69.077	0.035	0.035	0.000	0.000	0.000	0.000
148	A	148	ALA	-1	-0.951	-0.952	70.199	-4.374	-4.374	0.000	0.000	0.000	0.000

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