FMO DATABASE

FMODB ID: JVGZ9

Calculation Name: 4NHF-B-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4NHF

Chain ID: B

ChEMBL ID:

UniProt ID: C6AAT5

Base Structure: X-ray

Registration Date: 2025-10-05

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1288101.616634
FMO2-HF: Nuclear repulsion	1232877.148378
FMO2-HF: Total energy	-55224.468255
FMO2-MP2: Total energy	-55388.666532

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:92:SER)

Summations of interaction energy for fragment #1(A:92:SER)

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.
-76.963	-79.947	33.014	-17.844	-12.178	-0.092

Interaction energy analysis for fragmet #1(A:92:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.759 / q_NPA : 0.847

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	94	GLY	0	0.041	0.030	2.063	5.608	7.123	4.446	-2.914	-3.047	0.026
4	A	95	GLU	-1	-0.825	-0.903	3.676	-29.606	-29.359	0.002	0.139	-0.387	0.000
5	A	96	VAL	0	0.017	0.000	5.241	0.717	0.758	-0.001	0.000	-0.039	0.000
7	A	98	ASP	-1	-0.682	-0.779	1.555	-108.347	-116.469	26.368	-12.322	-5.923	-0.099
8	A	99	ARG	1	0.807	0.878	4.942	28.198	28.246	-0.001	-0.008	-0.038	0.000
74	A	165	LEU	0	0.018	0.019	4.394	-0.686	-0.632	-0.001	-0.003	-0.049	0.000
78	A	169	GLY	0	0.044	0.039	4.676	1.133	1.169	-0.001	-0.012	-0.022	0.000
108	A	199	TYR	0	-0.094	-0.082	2.833	3.362	4.839	0.036	-0.738	-0.774	-0.002
109	A	200	THR	0	-0.003	-0.006	4.515	-9.170	-9.055	-0.001	-0.008	-0.105	0.000
110	A	201	TYR	0	-0.058	-0.065	2.175	-1.503	0.077	2.168	-1.978	-1.770	-0.017
111	A	202	VAL	0	-0.032	-0.010	5.279	-1.021	-0.996	-0.001	0.000	-0.024	0.000
6	A	97	VAL	0	0.022	0.013	5.706	1.800	1.800	0.000	0.000	0.000	0.000
9	A	100	TYR	0	-0.007	0.013	8.172	3.082	3.082	0.000	0.000	0.000	0.000
10	A	101	TRP	0	0.043	0.010	7.035	3.131	3.131	0.000	0.000	0.000	0.000
11	A	102	LEU	0	-0.002	0.004	7.076	2.380	2.380	0.000	0.000	0.000	0.000
12	A	103	ASN	0	-0.020	-0.014	10.422	2.675	2.675	0.000	0.000	0.000	0.000
13	A	104	GLN	0	-0.013	-0.006	12.963	2.002	2.002	0.000	0.000	0.000	0.000
14	A	105	TYR	0	0.003	0.013	12.289	1.423	1.423	0.000	0.000	0.000	0.000
15	A	106	VAL	0	0.008	0.005	14.265	1.276	1.276	0.000	0.000	0.000	0.000
16	A	107	LEU	0	-0.047	-0.037	16.680	1.188	1.188	0.000	0.000	0.000	0.000
17	A	108	ASN	0	-0.049	-0.022	17.110	1.573	1.573	0.000	0.000	0.000	0.000
18	A	109	ARG	1	0.932	0.978	17.563	17.299	17.299	0.000	0.000	0.000	0.000
19	A	110	GLU	-1	-0.820	-0.893	19.748	-13.962	-13.962	0.000	0.000	0.000	0.000
20	A	111	ASN	0	-0.072	-0.036	22.020	0.858	0.858	0.000	0.000	0.000	0.000
21	A	112	TYR	0	-0.055	-0.053	24.020	-0.142	-0.142	0.000	0.000	0.000	0.000
22	A	113	ASP	-1	-0.831	-0.932	27.272	-9.944	-9.944	0.000	0.000	0.000	0.000
23	A	114	TYR	0	0.011	0.017	29.059	-0.171	-0.171	0.000	0.000	0.000	0.000
24	A	115	ASP	-1	-0.851	-0.932	31.296	-9.322	-9.322	0.000	0.000	0.000	0.000
25	A	116	THR	0	-0.066	-0.047	25.946	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	117	ILE	0	-0.002	0.020	25.990	-0.578	-0.578	0.000	0.000	0.000	0.000
27	A	118	GLN	0	0.041	0.013	25.496	-0.546	-0.546	0.000	0.000	0.000	0.000
28	A	119	LEU	0	0.039	0.031	21.739	-0.489	-0.489	0.000	0.000	0.000	0.000
29	A	120	ASN	0	0.016	0.009	21.294	-0.274	-0.274	0.000	0.000	0.000	0.000
30	A	121	TYR	0	0.040	0.034	20.743	-0.978	-0.978	0.000	0.000	0.000	0.000
31	A	122	ASP	-1	-0.884	-0.949	21.182	-13.677	-13.677	0.000	0.000	0.000	0.000
32	A	123	THR	0	-0.068	-0.047	16.484	-1.064	-1.064	0.000	0.000	0.000	0.000
33	A	124	THR	0	-0.019	-0.028	16.581	-1.510	-1.510	0.000	0.000	0.000	0.000
34	A	125	ALA	0	0.007	0.020	16.712	-1.022	-1.022	0.000	0.000	0.000	0.000
35	A	126	LEU	0	-0.043	0.003	15.232	-0.888	-0.888	0.000	0.000	0.000	0.000
36	A	127	LEU	0	-0.033	-0.021	11.496	-1.720	-1.720	0.000	0.000	0.000	0.000
37	A	128	SER	0	-0.035	-0.027	12.335	-1.911	-1.911	0.000	0.000	0.000	0.000
38	A	129	ALA	0	0.032	0.025	13.049	0.454	0.454	0.000	0.000	0.000	0.000
39	A	130	ALA	0	0.032	0.001	14.875	0.929	0.929	0.000	0.000	0.000	0.000
40	A	131	SER	0	-0.004	0.001	17.158	0.624	0.624	0.000	0.000	0.000	0.000
41	A	132	VAL	0	0.025	0.010	15.047	0.815	0.815	0.000	0.000	0.000	0.000
42	A	133	GLN	0	-0.057	-0.026	17.679	1.186	1.186	0.000	0.000	0.000	0.000
43	A	134	GLN	0	0.012	0.007	19.977	1.061	1.061	0.000	0.000	0.000	0.000
44	A	135	GLU	-1	-0.954	-0.981	19.266	-16.001	-16.001	0.000	0.000	0.000	0.000
45	A	136	TYR	0	-0.056	-0.016	20.082	0.402	0.402	0.000	0.000	0.000	0.000
46	A	137	TYR	0	0.014	-0.001	22.157	0.350	0.350	0.000	0.000	0.000	0.000
47	A	138	LYS	1	1.016	1.012	25.137	11.026	11.026	0.000	0.000	0.000	0.000
48	A	139	ILE	0	-0.063	-0.024	23.333	0.382	0.382	0.000	0.000	0.000	0.000
49	A	140	TYR	0	-0.027	-0.028	24.626	0.469	0.469	0.000	0.000	0.000	0.000
50	A	141	ASP	-1	-0.851	-0.905	28.976	-10.776	-10.776	0.000	0.000	0.000	0.000
51	A	142	GLY	0	-0.045	-0.029	31.449	0.105	0.105	0.000	0.000	0.000	0.000
52	A	143	GLU	-1	-0.852	-0.928	35.047	-8.273	-8.273	0.000	0.000	0.000	0.000
53	A	144	ASN	0	-0.056	-0.029	33.472	0.287	0.287	0.000	0.000	0.000	0.000
54	A	145	ALA	0	0.005	0.043	31.645	-0.250	-0.250	0.000	0.000	0.000	0.000
55	A	146	ARG	1	0.944	0.963	25.206	12.101	12.101	0.000	0.000	0.000	0.000
56	A	147	ASP	-1	-0.816	-0.926	30.764	-9.826	-9.826	0.000	0.000	0.000	0.000
57	A	148	LYS	1	0.785	0.874	32.459	8.977	8.977	0.000	0.000	0.000	0.000
58	A	149	VAL	0	-0.018	0.006	34.798	0.299	0.299	0.000	0.000	0.000	0.000
59	A	150	LEU	0	-0.040	-0.019	31.402	0.294	0.294	0.000	0.000	0.000	0.000
60	A	151	SER	0	0.014	0.011	35.170	0.299	0.299	0.000	0.000	0.000	0.000
61	A	152	ASN	0	-0.007	-0.004	34.623	-0.350	-0.350	0.000	0.000	0.000	0.000
62	A	153	LYS	1	0.859	0.935	36.506	8.240	8.240	0.000	0.000	0.000	0.000
63	A	154	ALA	0	-0.020	-0.002	35.098	0.139	0.139	0.000	0.000	0.000	0.000
64	A	155	ARG	1	0.905	0.965	30.610	9.469	9.469	0.000	0.000	0.000	0.000
65	A	156	ILE	0	-0.013	-0.008	26.788	0.174	0.174	0.000	0.000	0.000	0.000
66	A	157	THR	0	-0.001	0.017	26.298	-0.447	-0.447	0.000	0.000	0.000	0.000
67	A	158	VAL	0	0.060	0.026	20.118	0.075	0.075	0.000	0.000	0.000	0.000
68	A	159	LYS	1	0.852	0.923	22.152	12.167	12.167	0.000	0.000	0.000	0.000
69	A	160	VAL	0	0.073	0.039	15.511	0.208	0.208	0.000	0.000	0.000	0.000
70	A	161	ARG	1	0.827	0.911	18.721	13.548	13.548	0.000	0.000	0.000	0.000
71	A	162	SER	0	-0.020	-0.026	16.181	0.574	0.574	0.000	0.000	0.000	0.000
72	A	163	ILE	0	0.034	0.024	9.989	-0.151	-0.151	0.000	0.000	0.000	0.000
73	A	164	GLN	0	0.007	0.017	11.460	0.108	0.108	0.000	0.000	0.000	0.000
75	A	166	ASN	0	-0.038	-0.037	8.229	1.625	1.625	0.000	0.000	0.000	0.000
76	A	167	GLY	0	0.061	0.038	6.461	1.367	1.367	0.000	0.000	0.000	0.000
77	A	168	LEU	0	0.000	-0.019	6.307	-1.148	-1.148	0.000	0.000	0.000	0.000
79	A	170	GLN	0	-0.023	-0.003	5.500	5.420	5.420	0.000	0.000	0.000	0.000
80	A	171	ALA	0	-0.007	-0.007	8.021	-1.761	-1.761	0.000	0.000	0.000	0.000
81	A	172	THR	0	0.031	0.030	9.995	2.024	2.024	0.000	0.000	0.000	0.000
82	A	173	VAL	0	-0.024	-0.007	12.522	-0.517	-0.517	0.000	0.000	0.000	0.000
83	A	174	ARG	1	0.956	1.002	14.727	14.332	14.332	0.000	0.000	0.000	0.000
84	A	175	PHE	0	-0.026	-0.031	18.230	-0.151	-0.151	0.000	0.000	0.000	0.000
85	A	176	THR	0	-0.004	0.004	20.480	0.560	0.560	0.000	0.000	0.000	0.000
86	A	177	THR	0	0.019	0.006	23.557	-0.154	-0.154	0.000	0.000	0.000	0.000
87	A	178	GLN	0	-0.052	-0.039	25.785	0.107	0.107	0.000	0.000	0.000	0.000
88	A	179	GLN	0	0.005	0.011	29.410	-0.350	-0.350	0.000	0.000	0.000	0.000
89	A	180	LEU	0	-0.045	-0.029	30.077	0.152	0.152	0.000	0.000	0.000	0.000
90	A	181	ASP	-1	-0.755	-0.873	33.708	-8.197	-8.197	0.000	0.000	0.000	0.000
91	A	182	SER	0	0.019	0.007	35.592	-0.356	-0.356	0.000	0.000	0.000	0.000
92	A	183	SER	0	-0.044	-0.035	37.243	0.231	0.231	0.000	0.000	0.000	0.000
93	A	184	GLY	0	0.014	0.029	38.893	0.153	0.153	0.000	0.000	0.000	0.000
94	A	185	ALA	0	-0.042	-0.036	36.064	-0.151	-0.151	0.000	0.000	0.000	0.000
95	A	186	THR	0	-0.021	-0.009	33.079	-0.232	-0.232	0.000	0.000	0.000	0.000
96	A	187	THR	0	-0.001	0.006	35.506	0.135	0.135	0.000	0.000	0.000	0.000
97	A	188	GLY	0	0.017	0.006	35.060	0.072	0.072	0.000	0.000	0.000	0.000
98	A	189	PRO	0	0.020	0.019	33.697	-0.109	-0.109	0.000	0.000	0.000	0.000
99	A	190	LYS	1	0.900	0.948	27.331	10.442	10.442	0.000	0.000	0.000	0.000
100	A	191	GLN	0	0.025	0.025	27.369	0.388	0.388	0.000	0.000	0.000	0.000
101	A	192	HIS	0	0.026	-0.001	25.143	-0.741	-0.741	0.000	0.000	0.000	0.000
102	A	193	GLN	0	-0.003	0.012	21.951	0.707	0.707	0.000	0.000	0.000	0.000
103	A	194	ILE	0	0.015	-0.001	17.746	-0.517	-0.517	0.000	0.000	0.000	0.000
104	A	195	ALA	0	-0.005	0.020	16.058	0.215	0.215	0.000	0.000	0.000	0.000
105	A	196	THR	0	-0.034	-0.029	15.046	-0.720	-0.720	0.000	0.000	0.000	0.000
106	A	197	ILE	0	-0.035	-0.021	10.877	0.575	0.575	0.000	0.000	0.000	0.000
107	A	198	GLY	0	0.050	0.046	9.907	-1.460	-1.460	0.000	0.000	0.000	0.000
112	A	203	GLY	0	0.009	0.021	7.822	2.342	2.342	0.000	0.000	0.000	0.000
113	A	204	ALA	0	0.005	-0.003	9.363	1.180	1.180	0.000	0.000	0.000	0.000
114	A	205	PRO	0	0.018	0.022	12.547	1.249	1.249	0.000	0.000	0.000	0.000
115	A	206	MET	0	0.049	0.029	15.244	0.597	0.597	0.000	0.000	0.000	0.000
116	A	207	LYS	1	0.874	0.927	18.713	15.068	15.068	0.000	0.000	0.000	0.000
117	A	208	SER	0	0.013	-0.008	19.419	-0.857	-0.857	0.000	0.000	0.000	0.000
118	A	209	SER	0	0.037	-0.013	20.438	-0.219	-0.219	0.000	0.000	0.000	0.000
119	A	210	ASP	-1	-0.784	-0.853	17.367	-15.856	-15.856	0.000	0.000	0.000	0.000
120	A	211	ARG	1	0.870	0.915	15.371	15.453	15.453	0.000	0.000	0.000	0.000
121	A	212	LEU	0	-0.028	-0.010	16.105	-0.711	-0.711	0.000	0.000	0.000	0.000
122	A	213	LEU	0	0.018	0.013	16.920	-0.119	-0.119	0.000	0.000	0.000	0.000
123	A	214	ASN	0	-0.029	-0.010	11.078	-2.736	-2.736	0.000	0.000	0.000	0.000
124	A	215	PRO	0	0.017	0.011	12.280	-0.928	-0.928	0.000	0.000	0.000	0.000
125	A	216	LEU	0	-0.031	-0.023	7.177	-0.272	-0.272	0.000	0.000	0.000	0.000
126	A	217	GLY	0	0.041	0.031	7.664	-3.742	-3.742	0.000	0.000	0.000	0.000
127	A	218	PHE	0	-0.010	-0.013	5.776	-2.860	-2.860	0.000	0.000	0.000	0.000
128	A	219	GLN	0	-0.033	-0.019	7.890	5.476	5.476	0.000	0.000	0.000	0.000
129	A	220	ILE	0	0.012	0.007	9.022	-3.396	-3.396	0.000	0.000	0.000	0.000
130	A	221	THR	0	-0.021	-0.024	9.494	2.035	2.035	0.000	0.000	0.000	0.000
131	A	222	SER	0	-0.006	-0.008	12.175	1.998	1.998	0.000	0.000	0.000	0.000
132	A	223	TYR	0	-0.039	-0.058	13.874	-1.722	-1.722	0.000	0.000	0.000	0.000
133	A	224	ARG	1	0.893	0.949	16.340	16.876	16.876	0.000	0.000	0.000	0.000
134	A	225	SER	0	0.009	-0.016	18.456	-0.657	-0.657	0.000	0.000	0.000	0.000
135	A	226	ASP	-1	-0.833	-0.892	20.949	-13.727	-13.727	0.000	0.000	0.000	0.000
136	A	227	PRO	0	0.008	-0.006	23.041	-0.242	-0.242	0.000	0.000	0.000	0.000
137	A	228	GLU	-1	-0.923	-0.973	23.011	-12.941	-12.941	0.000	0.000	0.000	0.000
138	A	229	ILE	0	-0.034	-0.020	25.239	0.426	0.426	0.000	0.000	0.000	0.000
139	A	230	LEU	0	-0.042	-0.023	26.521	0.019	0.019	0.000	0.000	0.000	0.000
140	A	231	LEU	0	-0.034	-0.011	29.374	0.293	0.293	0.000	0.000	0.000	0.000
141	A	232	ASN	-1	-0.945	-0.961	31.811	-8.762	-8.762	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:92:SER)