FMO DATABASE

FMODB ID: N79NQ

Calculation Name: 3D1M-A-Xray549

Preferred Name:

Target Type:

Ligand Name: calcium ion | zinc ion

Ligand 3-letter code: CA | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3D1M

Chain ID: A

ChEMBL ID:

UniProt ID: Q4KMG0

Base Structure: X-ray

Registration Date: 2025-10-12

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1497072.343015
FMO2-HF: Nuclear repulsion	1437512.21409
FMO2-HF: Total energy	-59560.128925
FMO2-MP2: Total energy	-59733.696141

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:41:THR)

Summations of interaction energy for fragment #1(A:41: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.
5.633	9.706	0.698	-1.996	-2.777	-0.01

Interaction energy analysis for fragmet #1(A:41:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.874 / q_NPA : 0.927

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	43	LEU	0	-0.036	-0.002	3.357	-3.736	-1.910	0.025	-0.901	-0.951	-0.003
121	A	161	MET	0	-0.022	-0.013	4.168	-10.779	-10.666	0.000	-0.060	-0.054	0.000
124	A	164	ARG	1	0.874	0.942	2.269	57.439	59.442	0.674	-1.005	-1.672	-0.007
128	A	168	GLU	-1	-0.948	-0.986	4.344	-54.940	-54.809	-0.001	-0.030	-0.100	0.000
4	A	44	ALA	0	0.026	0.009	6.154	2.450	2.450	0.000	0.000	0.000	0.000
5	A	45	TYR	0	0.012	-0.021	8.535	1.039	1.039	0.000	0.000	0.000	0.000
6	A	46	LYS	1	0.811	0.894	12.295	16.766	16.766	0.000	0.000	0.000	0.000
7	A	47	GLN	0	0.054	0.046	5.351	-0.436	-0.436	0.000	0.000	0.000	0.000
8	A	48	PHE	0	-0.007	-0.008	10.882	0.060	0.060	0.000	0.000	0.000	0.000
9	A	49	ILE	0	-0.066	-0.018	6.452	-1.976	-1.976	0.000	0.000	0.000	0.000
10	A	50	PRO	0	0.092	0.033	10.163	0.389	0.389	0.000	0.000	0.000	0.000
11	A	51	ASN	0	-0.020	-0.002	10.124	0.964	0.964	0.000	0.000	0.000	0.000
12	A	52	VAL	0	-0.009	-0.010	12.041	1.223	1.223	0.000	0.000	0.000	0.000
13	A	53	ALA	0	0.056	0.026	15.817	-0.523	-0.523	0.000	0.000	0.000	0.000
14	A	54	GLU	-1	-0.718	-0.829	18.205	-15.083	-15.083	0.000	0.000	0.000	0.000
15	A	55	LYS	1	0.939	0.971	19.082	13.183	13.183	0.000	0.000	0.000	0.000
16	A	56	THR	0	-0.063	-0.032	19.039	0.628	0.628	0.000	0.000	0.000	0.000
17	A	57	LEU	0	0.050	0.010	21.166	-0.304	-0.304	0.000	0.000	0.000	0.000
18	A	58	GLY	0	-0.014	0.003	18.257	-0.090	-0.090	0.000	0.000	0.000	0.000
19	A	59	ALA	0	-0.016	0.013	16.702	-0.805	-0.805	0.000	0.000	0.000	0.000
20	A	60	SER	0	0.023	0.003	17.681	0.205	0.205	0.000	0.000	0.000	0.000
21	A	61	GLY	0	-0.007	0.012	19.964	0.702	0.702	0.000	0.000	0.000	0.000
22	A	62	ARG	1	0.895	0.926	23.201	11.744	11.744	0.000	0.000	0.000	0.000
23	A	63	TYR	0	0.032	0.034	26.528	-0.041	-0.041	0.000	0.000	0.000	0.000
24	A	64	GLU	-1	-0.933	-0.976	28.358	-10.390	-10.390	0.000	0.000	0.000	0.000
25	A	65	GLY	0	-0.002	-0.002	31.085	0.413	0.413	0.000	0.000	0.000	0.000
26	A	66	LYS	1	0.871	0.951	32.414	9.489	9.489	0.000	0.000	0.000	0.000
27	A	67	ILE	0	-0.018	0.023	30.666	0.306	0.306	0.000	0.000	0.000	0.000
28	A	68	THR	0	0.019	0.001	33.763	-0.107	-0.107	0.000	0.000	0.000	0.000
29	A	69	ARG	1	0.918	0.941	35.233	8.904	8.904	0.000	0.000	0.000	0.000
30	A	70	ASN	0	-0.029	-0.015	37.831	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	71	SER	0	-0.056	-0.026	37.091	0.107	0.107	0.000	0.000	0.000	0.000
32	A	72	GLU	-1	-0.816	-0.932	38.620	-7.705	-7.705	0.000	0.000	0.000	0.000
33	A	73	ARG	1	0.898	0.942	31.346	9.666	9.666	0.000	0.000	0.000	0.000
34	A	74	PHE	0	-0.003	-0.001	33.581	-0.312	-0.312	0.000	0.000	0.000	0.000
35	A	75	LYS	1	0.852	0.934	34.642	7.754	7.754	0.000	0.000	0.000	0.000
36	A	76	GLU	-1	-0.893	-0.945	31.561	-9.161	-9.161	0.000	0.000	0.000	0.000
37	A	77	LEU	0	-0.105	-0.027	28.734	-0.488	-0.488	0.000	0.000	0.000	0.000
38	A	78	THR	0	0.049	0.025	29.974	0.201	0.201	0.000	0.000	0.000	0.000
39	A	79	PRO	0	-0.017	-0.006	29.179	-0.400	-0.400	0.000	0.000	0.000	0.000
40	A	80	ASN	0	-0.030	-0.018	22.828	0.309	0.309	0.000	0.000	0.000	0.000
41	A	81	TYR	0	0.029	-0.007	27.022	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	82	ASN	0	0.019	0.015	21.434	0.440	0.440	0.000	0.000	0.000	0.000
43	A	83	PRO	0	0.031	0.020	25.218	-0.147	-0.147	0.000	0.000	0.000	0.000
44	A	84	ASP	-1	-0.867	-0.947	20.942	-13.382	-13.382	0.000	0.000	0.000	0.000
45	A	85	ILE	0	-0.056	-0.027	19.955	-0.934	-0.934	0.000	0.000	0.000	0.000
46	A	86	ILE	0	-0.053	-0.021	21.850	0.643	0.643	0.000	0.000	0.000	0.000
47	A	87	PHE	0	0.010	-0.012	22.881	-0.561	-0.561	0.000	0.000	0.000	0.000
48	A	88	LYS	1	0.750	0.875	25.198	11.714	11.714	0.000	0.000	0.000	0.000
49	A	89	ASP	-1	-0.796	-0.901	26.954	-9.590	-9.590	0.000	0.000	0.000	0.000
50	A	90	GLU	-1	-0.787	-0.877	28.834	-11.036	-11.036	0.000	0.000	0.000	0.000
51	A	91	GLU	0	0.027	0.018	28.723	0.397	0.397	0.000	0.000	0.000	0.000
52	A	92	ASN	0	-0.113	-0.048	33.534	0.407	0.407	0.000	0.000	0.000	0.000
53	A	93	THR	0	-0.030	-0.018	34.001	0.195	0.195	0.000	0.000	0.000	0.000
54	A	94	GLY	0	-0.024	-0.015	31.648	0.075	0.075	0.000	0.000	0.000	0.000
55	A	95	ALA	0	0.003	0.008	30.574	-0.277	-0.277	0.000	0.000	0.000	0.000
56	A	96	ASP	-1	-0.752	-0.894	25.607	-12.164	-12.164	0.000	0.000	0.000	0.000
57	A	97	ARG	1	0.850	0.921	25.554	10.617	10.617	0.000	0.000	0.000	0.000
58	A	98	LEU	0	-0.032	-0.003	27.394	-0.068	-0.068	0.000	0.000	0.000	0.000
59	A	99	MET	0	-0.001	0.001	23.165	-0.592	-0.592	0.000	0.000	0.000	0.000
60	A	100	THR	0	0.078	0.035	24.838	0.178	0.178	0.000	0.000	0.000	0.000
61	A	101	GLN	0	-0.038	-0.036	24.895	-0.054	-0.054	0.000	0.000	0.000	0.000
62	A	102	ARG	1	0.873	0.905	18.621	14.886	14.886	0.000	0.000	0.000	0.000
63	A	103	CYS	0	0.005	0.002	20.468	-1.027	-1.027	0.000	0.000	0.000	0.000
64	A	104	LYS	1	0.868	0.925	20.159	10.516	10.516	0.000	0.000	0.000	0.000
65	A	105	ASP	-1	-0.868	-0.923	20.705	-13.940	-13.940	0.000	0.000	0.000	0.000
66	A	106	LYS	1	0.891	0.960	15.671	17.133	17.133	0.000	0.000	0.000	0.000
67	A	107	LEU	0	0.032	0.019	15.942	-1.136	-1.136	0.000	0.000	0.000	0.000
68	A	108	ASN	0	0.042	0.019	17.688	-0.245	-0.245	0.000	0.000	0.000	0.000
69	A	109	ALA	0	0.014	0.019	15.137	-0.085	-0.085	0.000	0.000	0.000	0.000
70	A	110	LEU	0	-0.015	-0.001	11.605	-0.818	-0.818	0.000	0.000	0.000	0.000
71	A	111	ALA	0	0.002	0.003	14.092	-0.793	-0.793	0.000	0.000	0.000	0.000
72	A	112	ILE	0	0.011	0.011	16.023	-0.081	-0.081	0.000	0.000	0.000	0.000
73	A	113	SER	0	-0.044	-0.030	10.880	-0.980	-0.980	0.000	0.000	0.000	0.000
74	A	114	VAL	0	-0.005	-0.021	12.262	-1.183	-1.183	0.000	0.000	0.000	0.000
75	A	115	MET	0	-0.031	0.000	13.451	0.216	0.216	0.000	0.000	0.000	0.000
76	A	116	ASN	0	-0.025	-0.011	13.614	1.258	1.258	0.000	0.000	0.000	0.000
77	A	117	GLN	0	-0.065	-0.009	8.119	-3.118	-3.118	0.000	0.000	0.000	0.000
78	A	118	TRP	0	-0.018	-0.036	9.656	-0.702	-0.702	0.000	0.000	0.000	0.000
79	A	119	PRO	0	0.071	0.037	14.771	0.823	0.823	0.000	0.000	0.000	0.000
80	A	120	GLY	0	0.003	0.009	18.251	0.374	0.374	0.000	0.000	0.000	0.000
81	A	121	VAL	0	-0.087	-0.032	15.991	0.462	0.462	0.000	0.000	0.000	0.000
82	A	122	LYS	1	0.888	0.926	17.778	12.948	12.948	0.000	0.000	0.000	0.000
83	A	123	LEU	0	0.023	0.009	15.174	-0.665	-0.665	0.000	0.000	0.000	0.000
84	A	124	ARG	1	0.883	0.936	17.674	15.323	15.323	0.000	0.000	0.000	0.000
85	A	125	VAL	0	0.020	0.013	19.198	-0.848	-0.848	0.000	0.000	0.000	0.000
86	A	126	THR	0	-0.091	-0.079	21.227	0.318	0.318	0.000	0.000	0.000	0.000
87	A	127	GLU	-1	-0.741	-0.835	22.674	-11.411	-11.411	0.000	0.000	0.000	0.000
88	A	128	GLY	0	0.004	0.005	22.902	-0.766	-0.766	0.000	0.000	0.000	0.000
89	A	129	TRP	0	-0.048	-0.032	25.012	-0.155	-0.155	0.000	0.000	0.000	0.000
90	A	130	ASP	-1	-0.811	-0.914	27.903	-10.493	-10.493	0.000	0.000	0.000	0.000
91	A	131	GLU	-1	-0.864	-0.922	30.036	-8.753	-8.753	0.000	0.000	0.000	0.000
92	A	132	ASP	-1	-0.915	-0.954	32.298	-9.401	-9.401	0.000	0.000	0.000	0.000
93	A	133	GLY	0	-0.064	-0.031	32.465	0.209	0.209	0.000	0.000	0.000	0.000
94	A	134	HIS	0	-0.031	-0.010	27.010	-0.028	-0.028	0.000	0.000	0.000	0.000
95	A	135	HIS	1	0.762	0.871	24.486	12.222	12.222	0.000	0.000	0.000	0.000
96	A	136	SER	0	0.045	0.029	27.154	0.210	0.210	0.000	0.000	0.000	0.000
97	A	137	GLU	-1	-0.856	-0.943	28.880	-10.127	-10.127	0.000	0.000	0.000	0.000
98	A	138	GLU	-1	-0.975	-0.995	28.159	-11.035	-11.035	0.000	0.000	0.000	0.000
99	A	139	SER	0	-0.034	-0.008	25.425	-0.732	-0.732	0.000	0.000	0.000	0.000
100	A	140	LEU	0	0.015	-0.007	21.533	0.326	0.326	0.000	0.000	0.000	0.000
101	A	141	HIS	0	-0.003	-0.005	22.213	-0.358	-0.358	0.000	0.000	0.000	0.000
102	A	142	TYR	0	-0.028	-0.038	25.927	0.376	0.376	0.000	0.000	0.000	0.000
103	A	143	GLU	-1	-0.717	-0.857	27.056	-10.893	-10.893	0.000	0.000	0.000	0.000
104	A	144	GLY	0	0.030	0.022	26.368	0.029	0.029	0.000	0.000	0.000	0.000
105	A	145	ARG	1	0.775	0.878	23.084	12.383	12.383	0.000	0.000	0.000	0.000
106	A	146	ALA	0	-0.036	-0.036	20.521	-0.838	-0.838	0.000	0.000	0.000	0.000
107	A	147	VAL	0	0.002	0.011	17.968	0.579	0.579	0.000	0.000	0.000	0.000
108	A	148	ASP	-1	-0.826	-0.894	18.882	-16.212	-16.212	0.000	0.000	0.000	0.000
109	A	149	ILE	0	0.009	-0.007	13.584	0.447	0.447	0.000	0.000	0.000	0.000
110	A	150	THR	0	-0.051	-0.030	16.237	-0.297	-0.297	0.000	0.000	0.000	0.000
111	A	151	THR	0	0.038	0.004	13.917	-0.218	-0.218	0.000	0.000	0.000	0.000
112	A	152	SER	0	0.034	0.031	16.603	0.569	0.569	0.000	0.000	0.000	0.000
113	A	153	ASP	-1	-0.765	-0.859	17.601	-17.341	-17.341	0.000	0.000	0.000	0.000
114	A	154	ARG	1	0.861	0.928	18.844	14.004	14.004	0.000	0.000	0.000	0.000
115	A	155	ASP	-1	-0.767	-0.857	15.433	-19.727	-19.727	0.000	0.000	0.000	0.000
116	A	156	ARG	1	0.928	0.948	14.768	14.482	14.482	0.000	0.000	0.000	0.000
117	A	157	SER	0	-0.042	-0.026	12.371	-1.379	-1.379	0.000	0.000	0.000	0.000
118	A	158	LYS	1	0.777	0.878	10.472	17.197	17.197	0.000	0.000	0.000	0.000
119	A	159	TYR	0	-0.002	0.010	10.242	-2.239	-2.239	0.000	0.000	0.000	0.000
120	A	160	GLY	0	0.071	0.035	8.187	-0.714	-0.714	0.000	0.000	0.000	0.000
122	A	162	LEU	0	0.022	0.019	6.901	-1.568	-1.568	0.000	0.000	0.000	0.000
123	A	163	ALA	0	0.029	0.010	8.520	0.850	0.850	0.000	0.000	0.000	0.000
125	A	165	LEU	0	0.044	0.017	5.676	1.728	1.728	0.000	0.000	0.000	0.000
126	A	166	ALA	0	0.006	0.010	7.943	2.683	2.683	0.000	0.000	0.000	0.000
127	A	167	VAL	0	-0.025	-0.020	7.057	1.688	1.688	0.000	0.000	0.000	0.000
129	A	169	ALA	0	-0.026	0.000	8.874	2.253	2.253	0.000	0.000	0.000	0.000
130	A	170	GLY	0	-0.015	-0.007	11.640	2.167	2.167	0.000	0.000	0.000	0.000
131	A	171	PHE	0	-0.026	-0.031	12.958	1.828	1.828	0.000	0.000	0.000	0.000
132	A	172	ASP	-1	-0.791	-0.851	13.281	-18.037	-18.037	0.000	0.000	0.000	0.000
133	A	173	TRP	0	-0.029	-0.027	13.953	-0.144	-0.144	0.000	0.000	0.000	0.000
134	A	174	VAL	0	0.015	0.016	10.469	0.459	0.459	0.000	0.000	0.000	0.000
135	A	175	TYR	0	0.035	0.018	12.140	-0.707	-0.707	0.000	0.000	0.000	0.000
136	A	176	TYR	0	-0.003	0.014	9.777	1.720	1.720	0.000	0.000	0.000	0.000
137	A	177	GLU	-1	-0.855	-0.925	13.050	-15.368	-15.368	0.000	0.000	0.000	0.000
138	A	178	SER	0	0.063	0.044	16.791	1.028	1.028	0.000	0.000	0.000	0.000
139	A	179	LYS	1	0.942	0.961	16.312	15.263	15.263	0.000	0.000	0.000	0.000
140	A	180	ALA	0	-0.041	-0.028	17.393	-0.131	-0.131	0.000	0.000	0.000	0.000
141	A	181	HIS	0	0.002	-0.008	17.560	0.328	0.328	0.000	0.000	0.000	0.000
142	A	182	ILE	0	-0.030	-0.003	11.904	-0.618	-0.618	0.000	0.000	0.000	0.000
143	A	183	HIS	1	0.832	0.916	15.092	17.243	17.243	0.000	0.000	0.000	0.000
144	A	184	CYS	0	-0.057	-0.027	13.913	-2.046	-2.046	0.000	0.000	0.000	0.000
145	A	185	SER	0	0.014	-0.007	16.021	0.978	0.978	0.000	0.000	0.000	0.000
146	A	186	VAL	0	-0.021	-0.013	17.046	-1.151	-1.151	0.000	0.000	0.000	0.000
147	A	187	LYS	1	0.804	0.884	18.513	16.581	16.581	0.000	0.000	0.000	0.000
148	A	188	ALA	-1	-0.907	-0.939	21.928	-12.460	-12.460	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:41:THR)