FMO DATABASE

FMODB ID: 8GLGY

Calculation Name: 1Z2M-A-Xray547

Preferred Name:

Target Type:

Ligand Name: osmium 4+ ion

Ligand 3-letter code: OS4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1Z2M

Chain ID: A

ChEMBL ID:

UniProt ID: P05161

Base Structure: X-ray

Registration Date: 2025-10-03

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1301665.581817
FMO2-HF: Nuclear repulsion	1243789.936254
FMO2-HF: Total energy	-57875.645563
FMO2-MP2: Total energy	-58046.317028

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:3:TRP)

Summations of interaction energy for fragment #1(A:3:TRP)

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.
-47.852	-40.044	26.743	-11.881	-22.667	-0.078

Interaction energy analysis for fragmet #1(A:3:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.890

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	5	LEU	0	-0.042	-0.015	3.573	0.196	2.314	0.040	-0.911	-1.247	-0.003
4	A	6	THR	0	0.023	0.003	5.371	1.872	1.925	-0.001	-0.002	-0.050	0.000
16	A	18	SER	0	0.040	0.001	4.134	-4.224	-4.070	-0.001	-0.076	-0.077	0.000
17	A	19	LEU	0	-0.062	-0.027	2.037	3.351	4.706	1.628	-1.115	-1.868	-0.007
18	A	20	SER	0	0.014	-0.009	1.841	-34.864	-36.855	10.752	-5.211	-3.550	-0.061
19	A	21	SER	0	-0.015	0.005	4.581	4.657	4.751	-0.001	-0.025	-0.068	0.000
21	A	23	MET	0	-0.034	-0.019	2.738	-15.531	-14.900	8.000	-2.484	-6.146	-0.008
58	A	60	LEU	0	0.038	0.013	3.672	0.921	1.256	0.004	-0.050	-0.289	0.000
59	A	61	ALA	0	0.046	0.032	2.319	0.459	1.314	0.690	-0.439	-1.107	-0.002
60	A	62	SER	0	-0.045	-0.028	3.989	2.243	2.372	0.005	-0.052	-0.082	0.000
64	A	66	GLY	0	0.030	-0.006	2.668	-4.279	-2.503	1.910	-1.516	-2.168	0.004
65	A	67	PRO	0	-0.040	-0.028	2.231	-8.556	-5.559	3.579	-0.971	-5.604	0.001
66	A	68	GLY	0	0.014	0.012	3.053	6.476	5.778	0.138	0.971	-0.411	-0.002
5	A	7	VAL	0	-0.001	-0.003	9.133	0.382	0.382	0.000	0.000	0.000	0.000
6	A	8	LYS	1	0.924	0.957	11.840	18.327	18.327	0.000	0.000	0.000	0.000
7	A	9	MET	0	-0.029	-0.013	15.225	0.036	0.036	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.006	-0.002	18.390	0.457	0.457	0.000	0.000	0.000	0.000
9	A	11	ALA	0	-0.031	-0.008	21.473	0.594	0.594	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.008	-0.003	21.119	0.321	0.321	0.000	0.000	0.000	0.000
11	A	13	ASN	0	0.007	0.015	18.363	0.668	0.668	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.896	-0.952	14.228	-18.987	-18.987	0.000	0.000	0.000	0.000
13	A	15	PHE	0	-0.037	-0.026	12.101	1.035	1.035	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.075	0.048	8.413	-0.506	-0.506	0.000	0.000	0.000	0.000
15	A	17	VAL	0	-0.007	0.002	6.241	2.444	2.444	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.044	-0.029	6.854	-0.850	-0.850	0.000	0.000	0.000	0.000
22	A	24	SER	0	0.042	0.030	5.345	2.039	2.039	0.000	0.000	0.000	0.000
23	A	25	VAL	0	0.061	0.009	8.203	-1.909	-1.909	0.000	0.000	0.000	0.000
24	A	26	SER	0	0.015	0.008	10.194	0.415	0.415	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.781	-0.879	7.142	-38.293	-38.293	0.000	0.000	0.000	0.000
26	A	28	LEU	0	0.008	0.000	7.455	-0.294	-0.294	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.924	0.956	8.971	19.563	19.563	0.000	0.000	0.000	0.000
28	A	30	ALA	0	0.048	0.039	11.879	1.256	1.256	0.000	0.000	0.000	0.000
29	A	31	GLN	0	-0.025	-0.014	7.601	1.694	1.694	0.000	0.000	0.000	0.000
30	A	32	ILE	0	-0.031	-0.011	11.002	1.112	1.112	0.000	0.000	0.000	0.000
31	A	33	THR	0	-0.043	-0.036	13.558	0.954	0.954	0.000	0.000	0.000	0.000
32	A	34	GLN	0	-0.023	-0.012	12.877	2.105	2.105	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.886	0.968	13.539	20.555	20.555	0.000	0.000	0.000	0.000
34	A	36	ILE	0	-0.052	-0.045	15.538	0.973	0.973	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.038	0.029	18.396	0.868	0.868	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.043	-0.010	18.837	0.649	0.649	0.000	0.000	0.000	0.000
37	A	39	HIS	0	0.086	0.056	18.547	-1.593	-1.593	0.000	0.000	0.000	0.000
38	A	40	ALA	0	0.027	0.009	16.818	-0.195	-0.195	0.000	0.000	0.000	0.000
39	A	41	PHE	0	0.010	0.007	18.259	-0.100	-0.100	0.000	0.000	0.000	0.000
40	A	42	GLN	0	-0.008	0.007	21.195	0.193	0.193	0.000	0.000	0.000	0.000
41	A	43	GLN	0	-0.045	-0.026	15.124	-0.828	-0.828	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.775	0.867	18.687	14.079	14.079	0.000	0.000	0.000	0.000
43	A	45	LEU	0	0.031	0.005	12.287	-0.349	-0.349	0.000	0.000	0.000	0.000
44	A	46	ALA	0	0.019	0.012	14.484	0.570	0.570	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.049	0.033	10.109	-1.183	-1.183	0.000	0.000	0.000	0.000
46	A	48	HIS	0	0.005	0.021	12.208	1.879	1.879	0.000	0.000	0.000	0.000
47	A	49	PRO	0	-0.013	-0.022	12.540	-1.195	-1.195	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.044	-0.039	14.440	0.909	0.909	0.000	0.000	0.000	0.000
49	A	51	GLY	0	0.046	0.025	16.395	0.774	0.774	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.032	-0.005	15.188	0.607	0.607	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.013	0.004	14.809	-1.054	-1.054	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.011	-0.009	9.694	-0.288	-0.288	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.003	-0.009	12.097	1.626	1.626	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.877	-0.945	12.092	-18.950	-18.950	0.000	0.000	0.000	0.000
55	A	57	ARG	1	0.881	0.934	13.664	16.028	16.028	0.000	0.000	0.000	0.000
56	A	58	VAL	0	0.004	0.023	9.329	0.001	0.001	0.000	0.000	0.000	0.000
57	A	59	PRO	0	0.032	0.020	6.530	-1.116	-1.116	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.025	-0.019	6.720	2.992	2.992	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.004	0.011	7.339	1.033	1.033	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.041	-0.014	5.186	0.131	0.131	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.029	0.007	5.549	4.379	4.379	0.000	0.000	0.000	0.000
68	A	70	THR	0	0.009	-0.003	7.430	-1.225	-1.225	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.013	0.001	8.976	0.938	0.938	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.018	-0.005	11.562	0.504	0.504	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.006	-0.005	15.033	-0.205	-0.205	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.021	-0.020	16.708	0.811	0.811	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.002	-0.007	19.752	-0.405	-0.405	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.816	-0.886	21.873	-11.188	-11.188	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.912	0.939	24.768	11.934	11.934	0.000	0.000	0.000	0.000
76	A	78	SER	0	-0.055	-0.020	27.416	0.301	0.301	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.741	-0.866	28.844	-10.768	-10.768	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.922	-0.951	31.163	-8.619	-8.619	0.000	0.000	0.000	0.000
79	A	81	PRO	0	-0.048	0.000	34.318	-0.196	-0.196	0.000	0.000	0.000	0.000
80	A	82	LEU	0	-0.011	-0.013	33.069	0.127	0.127	0.000	0.000	0.000	0.000
81	A	83	SER	0	0.015	0.013	37.213	0.089	0.089	0.000	0.000	0.000	0.000
82	A	84	ILE	0	-0.032	-0.011	34.893	-0.043	-0.043	0.000	0.000	0.000	0.000
83	A	85	LEU	0	-0.021	-0.011	38.339	0.238	0.238	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.039	0.026	37.600	-0.238	-0.238	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.833	0.914	40.027	7.563	7.563	0.000	0.000	0.000	0.000
86	A	88	ASN	0	0.042	-0.002	41.484	-0.102	-0.102	0.000	0.000	0.000	0.000
87	A	89	ASN	0	0.083	0.030	44.058	0.001	0.001	0.000	0.000	0.000	0.000
88	A	90	LYS	1	0.882	0.949	45.530	6.391	6.391	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.032	0.017	45.247	0.142	0.142	0.000	0.000	0.000	0.000
90	A	92	ARG	1	0.887	0.948	46.314	6.266	6.266	0.000	0.000	0.000	0.000
91	A	93	SER	0	-0.011	-0.001	43.390	-0.123	-0.123	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.042	0.028	43.978	0.213	0.213	0.000	0.000	0.000	0.000
93	A	95	THR	0	-0.016	-0.020	42.528	-0.184	-0.184	0.000	0.000	0.000	0.000
94	A	96	TYR	0	0.006	0.006	39.197	0.107	0.107	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.936	-0.963	38.871	-7.986	-7.986	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.031	-0.012	34.157	-0.040	-0.040	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.915	0.949	31.984	9.074	9.074	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.015	-0.003	28.087	-0.125	-0.125	0.000	0.000	0.000	0.000
99	A	101	THR	0	-0.061	-0.066	26.612	-0.405	-0.405	0.000	0.000	0.000	0.000
100	A	102	GLN	0	0.010	0.023	27.567	-0.183	-0.183	0.000	0.000	0.000	0.000
101	A	103	THR	0	0.033	0.009	26.964	-0.067	-0.067	0.000	0.000	0.000	0.000
102	A	104	VAL	0	0.022	0.012	28.364	0.474	0.474	0.000	0.000	0.000	0.000
103	A	105	ALA	0	0.008	0.006	30.398	0.373	0.373	0.000	0.000	0.000	0.000
104	A	106	HIS	0	-0.010	0.006	32.119	0.147	0.147	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.017	0.007	33.301	0.328	0.328	0.000	0.000	0.000	0.000
106	A	108	LYS	1	0.847	0.930	33.379	9.692	9.692	0.000	0.000	0.000	0.000
107	A	109	GLN	0	-0.002	0.000	36.433	0.127	0.127	0.000	0.000	0.000	0.000
108	A	110	GLN	0	-0.015	-0.009	37.091	0.060	0.060	0.000	0.000	0.000	0.000
109	A	111	VAL	0	-0.006	-0.013	38.378	0.215	0.215	0.000	0.000	0.000	0.000
110	A	112	SER	0	-0.082	-0.045	40.397	0.219	0.219	0.000	0.000	0.000	0.000
111	A	113	GLY	0	-0.007	-0.004	42.235	0.186	0.186	0.000	0.000	0.000	0.000
112	A	114	LEU	0	-0.070	-0.021	44.027	0.193	0.193	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.860	-0.948	44.130	-6.960	-6.960	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.016	0.009	46.153	0.118	0.118	0.000	0.000	0.000	0.000
115	A	117	VAL	0	-0.066	-0.023	43.269	0.071	0.071	0.000	0.000	0.000	0.000
116	A	118	GLN	0	0.061	0.044	41.687	0.031	0.031	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.840	-0.936	37.264	-8.483	-8.483	0.000	0.000	0.000	0.000
118	A	120	ASP	-1	-0.875	-0.945	37.116	-8.229	-8.229	0.000	0.000	0.000	0.000
119	A	121	LEU	0	0.004	0.007	38.196	-0.119	-0.119	0.000	0.000	0.000	0.000
120	A	122	PHE	0	-0.064	-0.027	37.751	0.051	0.051	0.000	0.000	0.000	0.000
121	A	123	TRP	0	-0.029	-0.014	32.785	-0.220	-0.220	0.000	0.000	0.000	0.000
122	A	124	LEU	0	0.047	0.021	33.311	0.269	0.269	0.000	0.000	0.000	0.000
123	A	125	THR	0	-0.011	-0.020	32.156	-0.306	-0.306	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.023	0.003	29.338	0.366	0.366	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.906	-0.958	28.284	-10.904	-10.904	0.000	0.000	0.000	0.000
126	A	128	GLY	0	-0.014	0.002	30.042	-0.191	-0.191	0.000	0.000	0.000	0.000
127	A	129	LYS	1	0.889	0.959	25.244	11.499	11.499	0.000	0.000	0.000	0.000
128	A	130	PRO	0	0.009	-0.010	27.709	0.279	0.279	0.000	0.000	0.000	0.000
129	A	131	LEU	0	-0.037	-0.014	28.020	-0.368	-0.368	0.000	0.000	0.000	0.000
130	A	132	GLU	-1	-0.915	-0.969	23.401	-13.375	-13.375	0.000	0.000	0.000	0.000
131	A	133	ASP	-1	-0.846	-0.938	27.142	-10.352	-10.352	0.000	0.000	0.000	0.000
132	A	134	GLN	0	0.002	-0.012	24.361	0.520	0.520	0.000	0.000	0.000	0.000
133	A	135	LEU	0	-0.011	0.010	20.797	-0.362	-0.362	0.000	0.000	0.000	0.000
134	A	136	PRO	0	-0.005	-0.002	23.042	0.586	0.586	0.000	0.000	0.000	0.000
135	A	137	LEU	0	0.018	0.000	25.797	-0.201	-0.201	0.000	0.000	0.000	0.000
136	A	138	GLY	0	0.006	-0.001	26.186	0.119	0.119	0.000	0.000	0.000	0.000
137	A	139	GLU	-1	-0.878	-0.952	20.308	-15.490	-15.490	0.000	0.000	0.000	0.000
138	A	140	TYR	0	-0.009	0.001	23.351	-0.182	-0.182	0.000	0.000	0.000	0.000
139	A	141	GLY	0	-0.044	-0.011	25.910	0.267	0.267	0.000	0.000	0.000	0.000
140	A	142	LEU	0	-0.034	-0.010	26.828	0.401	0.401	0.000	0.000	0.000	0.000
141	A	143	LYS	1	0.963	0.981	28.808	10.102	10.102	0.000	0.000	0.000	0.000
142	A	144	PRO	0	0.059	0.022	33.075	0.110	0.110	0.000	0.000	0.000	0.000
143	A	145	LEU	0	-0.031	-0.021	36.886	0.027	0.027	0.000	0.000	0.000	0.000
144	A	146	SER	0	-0.020	-0.007	33.960	0.001	0.001	0.000	0.000	0.000	0.000
145	A	147	THR	0	-0.034	-0.020	36.065	0.176	0.176	0.000	0.000	0.000	0.000
146	A	148	VAL	0	0.018	0.017	33.695	-0.150	-0.150	0.000	0.000	0.000	0.000
147	A	149	PHE	0	-0.020	-0.023	35.901	0.387	0.387	0.000	0.000	0.000	0.000
148	A	150	MET	0	0.026	0.024	36.872	-0.176	-0.176	0.000	0.000	0.000	0.000
149	A	151	ASN	0	-0.043	-0.002	36.386	0.021	0.021	0.000	0.000	0.000	0.000
150	A	152	LEU	0	0.047	0.013	38.791	-0.111	-0.111	0.000	0.000	0.000	0.000
151	A	153	ARG	1	0.836	0.911	33.233	9.007	9.007	0.000	0.000	0.000	0.000
152	A	154	LEU	-1	-0.930	-0.944	40.532	-7.371	-7.371	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:TRP)