FMO DATABASE

FMODB ID: MZQ8Z

Calculation Name: 1NYK-A-Xray549

Preferred Name:

Target Type:

Ligand Name: fe2/s2 (inorganic) cluster | magnesium ion

Ligand 3-letter code: FES | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NYK

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SGZ9

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1402943.01647
FMO2-HF: Nuclear repulsion	1345430.930001
FMO2-HF: Total energy	-57512.08647
FMO2-MP2: Total energy	-57680.025532

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:46:THR)

Summations of interaction energy for fragment #1(A:46:THR)

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.
-146.077	-135.245	12.264	-11.358	-11.737	-0.109

Interaction energy analysis for fragmet #1(A:46:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.765 / q_NPA : 0.860

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	48	GLU	-1	-0.740	-0.869	1.834	-104.006	-96.968	10.448	-9.321	-8.165	-0.112
4	A	49	LYS	1	0.790	0.884	2.047	50.056	53.506	1.816	-1.998	-3.267	0.003
5	A	50	GLU	-1	-0.842	-0.888	4.055	-33.812	-33.468	0.000	-0.039	-0.305	0.000
6	A	51	PRO	0	-0.019	-0.001	5.959	3.409	3.409	0.000	0.000	0.000	0.000
7	A	52	LEU	0	0.033	0.003	9.439	-0.278	-0.278	0.000	0.000	0.000	0.000
8	A	53	LYS	1	0.829	0.907	9.564	28.715	28.715	0.000	0.000	0.000	0.000
9	A	54	PRO	0	0.005	0.010	14.517	0.458	0.458	0.000	0.000	0.000	0.000
10	A	55	GLY	0	-0.027	-0.017	17.648	-0.291	-0.291	0.000	0.000	0.000	0.000
11	A	56	ASP	-1	-0.792	-0.891	13.308	-24.712	-24.712	0.000	0.000	0.000	0.000
12	A	57	ILE	0	-0.012	-0.002	16.405	1.086	1.086	0.000	0.000	0.000	0.000
13	A	58	LEU	0	-0.002	-0.004	16.229	-1.244	-1.244	0.000	0.000	0.000	0.000
14	A	59	VAL	0	0.004	-0.003	13.917	0.794	0.794	0.000	0.000	0.000	0.000
15	A	60	TYR	0	-0.006	-0.037	17.028	-0.177	-0.177	0.000	0.000	0.000	0.000
16	A	61	ALA	0	-0.044	-0.017	15.256	-1.111	-1.111	0.000	0.000	0.000	0.000
17	A	62	GLN	0	-0.057	-0.040	14.392	1.362	1.362	0.000	0.000	0.000	0.000
18	A	63	GLY	0	-0.006	0.002	13.281	-1.140	-1.140	0.000	0.000	0.000	0.000
19	A	64	GLY	0	-0.004	-0.006	13.085	-1.061	-1.061	0.000	0.000	0.000	0.000
20	A	65	GLY	0	-0.012	-0.010	14.327	0.923	0.923	0.000	0.000	0.000	0.000
21	A	66	GLU	-1	-0.899	-0.952	14.898	-18.596	-18.596	0.000	0.000	0.000	0.000
22	A	67	PRO	0	-0.018	0.013	13.752	0.644	0.644	0.000	0.000	0.000	0.000
23	A	68	LYS	1	0.863	0.924	16.038	13.333	13.333	0.000	0.000	0.000	0.000
24	A	69	PRO	0	-0.013	-0.009	18.760	-0.397	-0.397	0.000	0.000	0.000	0.000
25	A	70	ILE	0	0.017	0.001	19.864	0.642	0.642	0.000	0.000	0.000	0.000
26	A	71	ARG	1	0.795	0.876	22.409	11.320	11.320	0.000	0.000	0.000	0.000
27	A	72	LEU	0	0.004	-0.003	25.898	0.106	0.106	0.000	0.000	0.000	0.000
28	A	73	GLU	-1	-0.880	-0.933	28.761	-10.031	-10.031	0.000	0.000	0.000	0.000
29	A	74	GLU	-1	-0.810	-0.871	25.108	-12.110	-12.110	0.000	0.000	0.000	0.000
30	A	75	LEU	0	-0.020	0.006	25.345	0.001	0.001	0.000	0.000	0.000	0.000
31	A	76	LYS	1	0.910	0.948	29.318	8.983	8.983	0.000	0.000	0.000	0.000
32	A	77	PRO	0	-0.008	-0.017	32.187	-0.234	-0.234	0.000	0.000	0.000	0.000
33	A	78	GLY	0	0.022	0.018	33.716	0.227	0.227	0.000	0.000	0.000	0.000
34	A	79	ASP	-1	-0.916	-0.939	31.217	-9.186	-9.186	0.000	0.000	0.000	0.000
35	A	80	PRO	0	-0.060	-0.034	28.865	-0.188	-0.188	0.000	0.000	0.000	0.000
36	A	81	PHE	0	-0.030	-0.004	23.349	-0.181	-0.181	0.000	0.000	0.000	0.000
37	A	82	VAL	0	-0.011	0.000	22.167	-0.083	-0.083	0.000	0.000	0.000	0.000
38	A	83	LEU	0	-0.005	-0.012	18.394	-0.264	-0.264	0.000	0.000	0.000	0.000
39	A	84	ALA	0	-0.007	-0.005	17.359	0.116	0.116	0.000	0.000	0.000	0.000
40	A	85	TYR	0	0.004	-0.002	11.841	-0.633	-0.633	0.000	0.000	0.000	0.000
41	A	86	PRO	0	0.005	0.028	11.794	0.984	0.984	0.000	0.000	0.000	0.000
42	A	87	MET	0	-0.033	-0.008	11.816	-2.103	-2.103	0.000	0.000	0.000	0.000
43	A	88	ASP	-1	-0.773	-0.864	10.938	-23.421	-23.421	0.000	0.000	0.000	0.000
44	A	89	PRO	0	0.035	0.023	12.891	0.503	0.503	0.000	0.000	0.000	0.000
45	A	90	LYS	1	0.883	0.948	14.833	19.300	19.300	0.000	0.000	0.000	0.000
46	A	91	THR	0	-0.058	-0.064	10.466	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	92	LYS	1	0.892	0.940	11.822	17.775	17.775	0.000	0.000	0.000	0.000
48	A	93	VAL	0	0.019	0.011	6.125	-0.506	-0.506	0.000	0.000	0.000	0.000
49	A	94	VAL	0	0.040	0.019	9.324	0.474	0.474	0.000	0.000	0.000	0.000
50	A	95	LYS	1	0.765	0.890	7.077	25.304	25.304	0.000	0.000	0.000	0.000
51	A	96	SER	0	0.057	0.023	7.956	-0.652	-0.652	0.000	0.000	0.000	0.000
52	A	97	GLY	0	0.000	0.013	4.895	1.465	1.465	0.000	0.000	0.000	0.000
53	A	98	GLU	-1	-0.915	-0.940	5.976	-32.891	-32.891	0.000	0.000	0.000	0.000
54	A	99	ALA	0	0.058	0.034	7.879	2.200	2.200	0.000	0.000	0.000	0.000
55	A	100	LYS	1	0.869	0.929	11.223	21.903	21.903	0.000	0.000	0.000	0.000
56	A	101	ASN	0	-0.032	-0.039	8.627	3.227	3.227	0.000	0.000	0.000	0.000
57	A	102	THR	0	-0.024	-0.029	12.390	0.441	0.441	0.000	0.000	0.000	0.000
58	A	103	LEU	0	-0.027	-0.004	14.769	0.761	0.761	0.000	0.000	0.000	0.000
59	A	104	LEU	0	-0.031	-0.006	17.998	0.062	0.062	0.000	0.000	0.000	0.000
60	A	105	VAL	0	0.001	-0.010	20.865	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	106	ALA	0	0.042	0.023	23.569	0.173	0.173	0.000	0.000	0.000	0.000
62	A	107	ARG	1	0.824	0.915	27.362	9.709	9.709	0.000	0.000	0.000	0.000
63	A	108	PHE	0	0.028	0.018	30.316	0.087	0.087	0.000	0.000	0.000	0.000
64	A	109	ASP	-1	-0.851	-0.918	33.962	-8.468	-8.468	0.000	0.000	0.000	0.000
65	A	110	PRO	0	-0.035	-0.043	35.570	-0.073	-0.073	0.000	0.000	0.000	0.000
66	A	111	GLU	-1	-0.933	-0.970	36.753	-8.060	-8.060	0.000	0.000	0.000	0.000
67	A	112	GLU	-1	-0.876	-0.932	37.635	-7.924	-7.924	0.000	0.000	0.000	0.000
68	A	113	LEU	0	-0.079	-0.026	32.545	-0.169	-0.169	0.000	0.000	0.000	0.000
69	A	114	ALA	0	0.010	0.006	34.593	0.259	0.259	0.000	0.000	0.000	0.000
70	A	115	PRO	0	0.014	-0.010	34.787	-0.264	-0.264	0.000	0.000	0.000	0.000
71	A	116	GLU	-1	-0.871	-0.916	31.277	-10.181	-10.181	0.000	0.000	0.000	0.000
72	A	117	VAL	0	-0.006	0.003	29.651	-0.340	-0.340	0.000	0.000	0.000	0.000
73	A	118	ALA	0	0.050	0.021	30.556	-0.337	-0.337	0.000	0.000	0.000	0.000
74	A	119	GLN	0	-0.048	-0.019	32.134	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	120	HIS	1	0.738	0.847	26.877	10.689	10.689	0.000	0.000	0.000	0.000
76	A	121	ALA	0	0.052	0.041	27.294	-0.516	-0.516	0.000	0.000	0.000	0.000
77	A	122	ALA	0	-0.013	-0.003	28.192	0.168	0.168	0.000	0.000	0.000	0.000
78	A	123	GLU	-1	-0.916	-0.966	30.082	-9.631	-9.631	0.000	0.000	0.000	0.000
79	A	124	GLY	0	0.081	0.046	32.841	0.118	0.118	0.000	0.000	0.000	0.000
80	A	125	VAL	0	-0.036	-0.014	26.204	-0.097	-0.097	0.000	0.000	0.000	0.000
81	A	126	VAL	0	0.001	-0.004	27.250	-0.069	-0.069	0.000	0.000	0.000	0.000
82	A	127	ALA	0	0.014	0.007	21.685	-0.206	-0.206	0.000	0.000	0.000	0.000
83	A	128	TYR	0	0.007	-0.008	22.455	0.259	0.259	0.000	0.000	0.000	0.000
84	A	129	SER	0	0.009	0.010	17.225	-0.515	-0.515	0.000	0.000	0.000	0.000
85	A	130	ALA	0	0.017	0.005	18.570	0.789	0.789	0.000	0.000	0.000	0.000
86	A	131	VAL	0	-0.056	-0.016	15.327	0.070	0.070	0.000	0.000	0.000	0.000
87	A	132	CYS	-1	-0.773	-0.782	18.785	-12.505	-12.505	0.000	0.000	0.000	0.000
88	A	133	THR	0	-0.041	-0.050	21.101	-0.527	-0.527	0.000	0.000	0.000	0.000
89	A	134	HIS	0	-0.021	-0.027	23.158	0.323	0.323	0.000	0.000	0.000	0.000
90	A	135	LEU	0	-0.023	-0.036	22.387	-0.097	-0.097	0.000	0.000	0.000	0.000
91	A	136	GLY	0	-0.028	-0.001	18.848	-0.388	-0.388	0.000	0.000	0.000	0.000
92	A	137	CYS	0	-0.111	-0.062	18.411	-0.505	-0.505	0.000	0.000	0.000	0.000
93	A	138	ILE	0	0.011	0.002	15.838	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	139	VAL	0	-0.008	-0.014	19.923	0.651	0.651	0.000	0.000	0.000	0.000
95	A	140	SER	0	-0.009	-0.011	21.646	0.102	0.102	0.000	0.000	0.000	0.000
96	A	141	GLN	0	-0.015	-0.001	23.358	0.316	0.316	0.000	0.000	0.000	0.000
97	A	142	TRP	0	0.063	0.022	27.190	-0.226	-0.226	0.000	0.000	0.000	0.000
98	A	143	VAL	0	-0.008	0.000	29.900	0.203	0.203	0.000	0.000	0.000	0.000
99	A	144	ALA	0	-0.008	-0.019	33.307	0.027	0.027	0.000	0.000	0.000	0.000
100	A	145	ASP	-1	-0.913	-0.955	35.241	-8.164	-8.164	0.000	0.000	0.000	0.000
101	A	146	GLU	-1	-0.919	-0.966	35.298	-8.248	-8.248	0.000	0.000	0.000	0.000
102	A	147	GLU	-1	-0.931	-0.971	33.755	-8.897	-8.897	0.000	0.000	0.000	0.000
103	A	148	ALA	0	-0.021	0.000	31.378	-0.290	-0.290	0.000	0.000	0.000	0.000
104	A	149	ALA	0	-0.010	-0.005	26.199	-0.063	-0.063	0.000	0.000	0.000	0.000
105	A	150	LEU	0	-0.004	-0.001	27.787	0.137	0.137	0.000	0.000	0.000	0.000
106	A	151	CYS	0	-0.053	-0.063	24.729	-0.509	-0.509	0.000	0.000	0.000	0.000
107	A	152	PRO	0	-0.015	-0.006	24.344	0.400	0.400	0.000	0.000	0.000	0.000
108	A	154	HIS	0	0.033	0.005	25.584	0.137	0.137	0.000	0.000	0.000	0.000
109	A	155	GLY	0	0.041	0.025	29.730	0.282	0.282	0.000	0.000	0.000	0.000
110	A	156	GLY	0	-0.015	0.002	28.720	0.243	0.243	0.000	0.000	0.000	0.000
111	A	157	VAL	0	-0.012	-0.009	28.923	-0.325	-0.325	0.000	0.000	0.000	0.000
112	A	158	TYR	0	-0.019	-0.067	25.021	0.059	0.059	0.000	0.000	0.000	0.000
113	A	159	ASP	-1	-0.740	-0.859	29.781	-9.344	-9.344	0.000	0.000	0.000	0.000
114	A	160	LEU	0	-0.009	-0.008	26.862	-0.163	-0.163	0.000	0.000	0.000	0.000
115	A	161	ARG	1	0.914	0.989	30.251	8.447	8.447	0.000	0.000	0.000	0.000
116	A	162	HIS	1	0.801	0.868	33.375	8.869	8.869	0.000	0.000	0.000	0.000
117	A	163	GLY	0	0.040	0.016	29.957	0.079	0.079	0.000	0.000	0.000	0.000
118	A	164	ALA	0	-0.040	-0.015	27.049	-0.214	-0.214	0.000	0.000	0.000	0.000
119	A	165	GLN	0	-0.017	-0.011	29.002	0.041	0.041	0.000	0.000	0.000	0.000
120	A	166	VAL	0	-0.007	0.002	29.383	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	167	ILE	0	0.009	0.009	32.010	0.248	0.248	0.000	0.000	0.000	0.000
122	A	168	ALA	0	-0.020	-0.007	33.446	0.307	0.307	0.000	0.000	0.000	0.000
123	A	169	GLY	0	0.034	0.020	32.073	-0.353	-0.353	0.000	0.000	0.000	0.000
124	A	170	PRO	0	-0.012	-0.015	29.212	0.116	0.116	0.000	0.000	0.000	0.000
125	A	171	PRO	0	-0.032	-0.007	27.079	-0.151	-0.151	0.000	0.000	0.000	0.000
126	A	172	PRO	0	0.014	0.020	26.421	0.318	0.318	0.000	0.000	0.000	0.000
127	A	173	ARG	1	0.828	0.897	21.323	13.768	13.768	0.000	0.000	0.000	0.000
128	A	174	PRO	0	0.059	0.038	26.818	-0.297	-0.297	0.000	0.000	0.000	0.000
129	A	175	VAL	0	-0.008	0.010	22.217	-0.334	-0.334	0.000	0.000	0.000	0.000
130	A	176	PRO	0	-0.050	-0.011	20.099	0.356	0.356	0.000	0.000	0.000	0.000
131	A	177	GLN	0	0.048	0.007	22.022	-0.271	-0.271	0.000	0.000	0.000	0.000
132	A	178	LEU	0	-0.020	-0.018	18.435	-0.419	-0.419	0.000	0.000	0.000	0.000
133	A	179	PRO	0	-0.015	-0.003	21.799	0.508	0.508	0.000	0.000	0.000	0.000
134	A	180	VAL	0	-0.023	0.008	22.544	-0.727	-0.727	0.000	0.000	0.000	0.000
135	A	181	ARG	1	0.827	0.892	22.745	14.029	14.029	0.000	0.000	0.000	0.000
136	A	182	VAL	0	0.020	0.013	25.176	-0.418	-0.418	0.000	0.000	0.000	0.000
137	A	183	GLU	-1	-0.880	-0.913	24.060	-13.115	-13.115	0.000	0.000	0.000	0.000
138	A	184	ASP	-1	-0.878	-0.947	25.973	-12.435	-12.435	0.000	0.000	0.000	0.000
139	A	185	GLY	0	0.021	0.019	28.248	0.099	0.099	0.000	0.000	0.000	0.000
140	A	186	VAL	0	-0.034	-0.014	21.629	0.014	0.014	0.000	0.000	0.000	0.000
141	A	187	LEU	0	0.025	0.013	22.755	0.210	0.210	0.000	0.000	0.000	0.000
142	A	188	VAL	0	-0.033	-0.015	20.303	-0.850	-0.850	0.000	0.000	0.000	0.000
143	A	189	ALA	0	0.043	0.024	18.328	0.649	0.649	0.000	0.000	0.000	0.000
144	A	190	ALA	0	-0.035	-0.039	20.327	-0.043	-0.043	0.000	0.000	0.000	0.000
145	A	191	GLY	0	-0.013	-0.018	21.160	0.432	0.432	0.000	0.000	0.000	0.000
146	A	192	GLU	-1	-0.879	-0.941	16.687	-19.022	-19.022	0.000	0.000	0.000	0.000
147	A	193	PHE	0	0.000	-0.016	14.683	0.727	0.727	0.000	0.000	0.000	0.000
148	A	194	LEU	0	-0.026	-0.009	19.883	0.090	0.090	0.000	0.000	0.000	0.000
149	A	195	GLY	0	0.010	0.005	21.625	0.689	0.689	0.000	0.000	0.000	0.000
150	A	196	PRO	0	-0.012	-0.005	19.248	-0.740	-0.740	0.000	0.000	0.000	0.000
151	A	197	VAL	0	0.044	0.038	15.548	0.679	0.679	0.000	0.000	0.000	0.000
152	A	198	GLY	0	0.018	0.025	17.586	-0.628	-0.628	0.000	0.000	0.000	0.000
153	A	199	VAL	0	0.030	0.019	18.822	0.601	0.601	0.000	0.000	0.000	0.000
154	A	200	GLN	0	-0.125	-0.073	18.007	-0.774	-0.774	0.000	0.000	0.000	0.000
155	A	201	ALA	-1	-0.898	-0.931	21.492	-11.829	-11.829	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:46:THR)