FMO DATABASE

FMODB ID: JVMK9

Calculation Name: 1M5X-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1M5X

Chain ID: A

ChEMBL ID:

UniProt ID: C0JWR6

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	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1602268.570729
FMO2-HF: Nuclear repulsion	1539373.631161
FMO2-HF: Total energy	-62894.939568
FMO2-MP2: Total energy	-63084.664978

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:6:THR)

Summations of interaction energy for fragment #1(A:6: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.
27.116	30.465	0.547	-1.637	-2.26	-0.009

Interaction energy analysis for fragmet #1(A:6:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / q_NPA : 0.906

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	8	GLN	0	0.001	-0.006	2.801	5.069	8.329	0.548	-1.632	-2.177	-0.009
4	A	9	PRO	0	0.038	0.008	4.834	4.217	4.306	-0.001	-0.005	-0.083	0.000
5	A	10	THR	0	0.039	0.014	7.830	1.881	1.881	0.000	0.000	0.000	0.000
6	A	11	GLU	-1	-0.831	-0.894	6.166	-45.831	-45.831	0.000	0.000	0.000	0.000
7	A	12	ALA	0	0.019	0.012	7.874	2.407	2.407	0.000	0.000	0.000	0.000
8	A	13	ALA	0	-0.010	-0.014	9.665	2.448	2.448	0.000	0.000	0.000	0.000
9	A	14	TYR	0	-0.008	0.005	12.434	1.920	1.920	0.000	0.000	0.000	0.000
10	A	15	ILE	0	0.015	0.003	9.661	1.702	1.702	0.000	0.000	0.000	0.000
11	A	16	ALA	0	-0.007	-0.002	13.706	1.406	1.406	0.000	0.000	0.000	0.000
12	A	17	GLY	0	0.006	0.000	15.372	1.240	1.240	0.000	0.000	0.000	0.000
13	A	18	PHE	0	-0.017	-0.011	16.868	0.909	0.909	0.000	0.000	0.000	0.000
14	A	19	LEU	0	-0.042	-0.014	16.004	0.823	0.823	0.000	0.000	0.000	0.000
15	A	20	ASP	-1	-0.756	-0.898	18.686	-13.745	-13.745	0.000	0.000	0.000	0.000
16	A	21	GLY	0	-0.008	0.005	21.297	0.757	0.757	0.000	0.000	0.000	0.000
17	A	22	ASP	-1	-0.851	-0.897	22.200	-12.354	-12.354	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.035	0.003	20.820	-0.326	-0.326	0.000	0.000	0.000	0.000
19	A	24	SER	0	-0.060	-0.025	21.371	0.687	0.687	0.000	0.000	0.000	0.000
20	A	25	ILE	0	0.033	0.017	18.348	-0.633	-0.633	0.000	0.000	0.000	0.000
21	A	26	TYR	0	-0.015	-0.009	21.774	0.587	0.587	0.000	0.000	0.000	0.000
22	A	27	ALA	0	0.047	0.027	23.604	-0.400	-0.400	0.000	0.000	0.000	0.000
23	A	28	LYS	1	0.947	0.970	25.999	11.053	11.053	0.000	0.000	0.000	0.000
24	A	29	LEU	0	0.044	0.036	28.948	-0.277	-0.277	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.044	-0.023	28.159	0.089	0.089	0.000	0.000	0.000	0.000
26	A	31	PRO	0	0.044	0.014	32.403	-0.034	-0.034	0.000	0.000	0.000	0.000
27	A	32	ARG	1	0.871	0.932	29.239	9.720	9.720	0.000	0.000	0.000	0.000
28	A	33	PRO	0	0.040	0.009	36.048	0.086	0.086	0.000	0.000	0.000	0.000
29	A	34	ASP	-1	-0.861	-0.929	35.162	-8.600	-8.600	0.000	0.000	0.000	0.000
30	A	35	TYR	0	-0.096	-0.043	30.611	-0.191	-0.191	0.000	0.000	0.000	0.000
31	A	36	LYS	1	0.941	0.965	34.253	8.874	8.874	0.000	0.000	0.000	0.000
32	A	37	ASP	-1	-0.855	-0.923	38.673	-7.402	-7.402	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.021	-0.013	34.415	0.122	0.122	0.000	0.000	0.000	0.000
34	A	39	LYS	1	0.911	0.970	36.217	7.169	7.169	0.000	0.000	0.000	0.000
35	A	40	TYR	0	-0.028	-0.051	33.888	-0.094	-0.094	0.000	0.000	0.000	0.000
36	A	41	GLN	0	-0.012	0.003	26.086	0.072	0.072	0.000	0.000	0.000	0.000
37	A	42	VAL	0	0.017	0.017	26.389	0.029	0.029	0.000	0.000	0.000	0.000
38	A	43	SER	0	-0.054	-0.018	25.239	-0.519	-0.519	0.000	0.000	0.000	0.000
39	A	44	LEU	0	0.022	0.005	21.379	0.240	0.240	0.000	0.000	0.000	0.000
40	A	45	ALA	0	0.012	-0.010	19.992	-0.390	-0.390	0.000	0.000	0.000	0.000
41	A	46	ILE	0	0.016	0.017	14.359	0.292	0.292	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.046	-0.017	18.862	0.073	0.073	0.000	0.000	0.000	0.000
43	A	48	PHE	0	0.060	0.032	14.246	-0.047	-0.047	0.000	0.000	0.000	0.000
44	A	49	ILE	0	-0.014	-0.005	19.910	0.197	0.197	0.000	0.000	0.000	0.000
45	A	50	GLN	0	-0.028	-0.043	22.325	0.171	0.171	0.000	0.000	0.000	0.000
46	A	51	ARG	1	0.885	0.910	24.398	10.771	10.771	0.000	0.000	0.000	0.000
47	A	52	LYS	1	0.874	0.915	25.790	10.499	10.499	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.813	-0.866	25.362	-11.672	-11.672	0.000	0.000	0.000	0.000
49	A	54	LYS	1	0.931	0.968	22.580	12.275	12.275	0.000	0.000	0.000	0.000
50	A	55	PHE	0	0.003	0.001	20.026	-0.644	-0.644	0.000	0.000	0.000	0.000
51	A	56	PRO	0	0.020	0.003	18.737	-0.686	-0.686	0.000	0.000	0.000	0.000
52	A	57	TYR	0	0.065	0.038	16.760	-0.469	-0.469	0.000	0.000	0.000	0.000
53	A	58	LEU	0	-0.057	-0.022	16.146	-0.880	-0.880	0.000	0.000	0.000	0.000
54	A	59	GLN	0	-0.030	-0.018	14.982	-0.191	-0.191	0.000	0.000	0.000	0.000
55	A	60	ASP	-1	-0.834	-0.921	12.477	-21.691	-21.691	0.000	0.000	0.000	0.000
56	A	61	ILE	0	0.003	-0.001	10.909	-2.678	-2.678	0.000	0.000	0.000	0.000
57	A	62	TYR	0	-0.020	-0.009	10.680	-1.933	-1.933	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.891	-0.958	9.218	-26.306	-26.306	0.000	0.000	0.000	0.000
59	A	64	GLN	0	-0.071	-0.044	6.568	-1.984	-1.984	0.000	0.000	0.000	0.000
60	A	65	LEU	0	-0.049	-0.021	5.830	-4.887	-4.887	0.000	0.000	0.000	0.000
61	A	66	GLY	0	-0.025	-0.019	6.907	1.354	1.354	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.896	0.950	7.346	26.738	26.738	0.000	0.000	0.000	0.000
63	A	68	ARG	1	0.920	0.976	8.241	29.322	29.322	0.000	0.000	0.000	0.000
64	A	69	GLY	0	-0.006	0.002	12.417	0.268	0.268	0.000	0.000	0.000	0.000
65	A	70	ASN	0	-0.034	-0.026	16.040	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	71	LEU	0	0.026	0.028	15.976	0.307	0.307	0.000	0.000	0.000	0.000
67	A	72	ARG	1	0.805	0.871	19.399	12.169	12.169	0.000	0.000	0.000	0.000
68	A	73	LYS	1	0.985	0.989	23.105	12.400	12.400	0.000	0.000	0.000	0.000
69	A	74	ASP	-1	-0.758	-0.878	24.819	-10.104	-10.104	0.000	0.000	0.000	0.000
70	A	75	ARG	1	0.756	0.870	26.767	10.715	10.715	0.000	0.000	0.000	0.000
71	A	76	GLY	0	-0.010	0.001	29.132	0.206	0.206	0.000	0.000	0.000	0.000
72	A	77	ASP	-1	-0.783	-0.876	30.897	-9.898	-9.898	0.000	0.000	0.000	0.000
73	A	78	GLY	0	0.015	0.017	31.405	0.114	0.114	0.000	0.000	0.000	0.000
74	A	79	ILE	0	-0.086	-0.043	26.770	-0.334	-0.334	0.000	0.000	0.000	0.000
75	A	80	ALA	0	0.001	0.004	23.556	0.096	0.096	0.000	0.000	0.000	0.000
76	A	81	ASP	-1	-0.784	-0.881	22.245	-12.403	-12.403	0.000	0.000	0.000	0.000
77	A	82	TYR	0	-0.031	-0.018	12.875	-0.415	-0.415	0.000	0.000	0.000	0.000
78	A	83	THR	0	0.025	0.007	18.904	0.035	0.035	0.000	0.000	0.000	0.000
79	A	84	ILE	0	-0.011	0.001	13.050	0.065	0.065	0.000	0.000	0.000	0.000
80	A	85	ILE	0	0.007	-0.002	17.235	0.498	0.498	0.000	0.000	0.000	0.000
81	A	86	GLY	0	0.028	0.011	18.447	-0.412	-0.412	0.000	0.000	0.000	0.000
82	A	87	SER	0	0.045	0.009	17.635	-0.849	-0.849	0.000	0.000	0.000	0.000
83	A	88	THR	0	0.008	0.016	15.038	-0.519	-0.519	0.000	0.000	0.000	0.000
84	A	89	HIS	0	0.057	0.046	12.897	-2.234	-2.234	0.000	0.000	0.000	0.000
85	A	90	LEU	0	0.014	0.014	12.485	-1.278	-1.278	0.000	0.000	0.000	0.000
86	A	91	SER	0	-0.048	-0.047	13.833	-0.607	-0.607	0.000	0.000	0.000	0.000
87	A	92	ILE	0	-0.026	0.000	7.923	-0.356	-0.356	0.000	0.000	0.000	0.000
88	A	93	ILE	0	0.041	0.015	9.091	-0.888	-0.888	0.000	0.000	0.000	0.000
89	A	94	LEU	0	-0.015	-0.012	10.360	0.021	0.021	0.000	0.000	0.000	0.000
90	A	95	PRO	0	-0.039	-0.022	9.625	0.472	0.472	0.000	0.000	0.000	0.000
91	A	96	ASP	-1	-0.865	-0.911	6.080	-34.977	-34.977	0.000	0.000	0.000	0.000
92	A	97	LEU	0	-0.020	-0.022	8.837	0.661	0.661	0.000	0.000	0.000	0.000
93	A	98	VAL	0	0.002	0.001	12.198	1.310	1.310	0.000	0.000	0.000	0.000
94	A	99	PRO	0	-0.034	-0.010	11.435	1.571	1.571	0.000	0.000	0.000	0.000
95	A	100	TYR	0	0.010	-0.005	9.809	0.693	0.693	0.000	0.000	0.000	0.000
96	A	101	LEU	0	-0.028	0.003	15.335	0.925	0.925	0.000	0.000	0.000	0.000
97	A	102	ARG	1	0.883	0.926	17.685	14.963	14.963	0.000	0.000	0.000	0.000
98	A	103	ILE	0	-0.042	-0.019	21.384	0.508	0.508	0.000	0.000	0.000	0.000
99	A	104	LYS	1	0.860	0.940	20.832	13.294	13.294	0.000	0.000	0.000	0.000
100	A	105	LYS	1	0.869	0.948	17.756	15.489	15.489	0.000	0.000	0.000	0.000
101	A	106	LYS	1	0.936	0.969	20.452	11.032	11.032	0.000	0.000	0.000	0.000
102	A	107	GLN	0	0.089	0.030	22.546	-0.192	-0.192	0.000	0.000	0.000	0.000
103	A	108	ALA	0	0.018	0.014	17.246	-0.054	-0.054	0.000	0.000	0.000	0.000
104	A	109	ASN	0	0.041	0.002	18.628	-0.758	-0.758	0.000	0.000	0.000	0.000
105	A	110	ARG	1	0.798	0.903	20.243	11.458	11.458	0.000	0.000	0.000	0.000
106	A	111	ILE	0	0.009	0.011	18.818	0.273	0.273	0.000	0.000	0.000	0.000
107	A	112	LEU	0	0.033	0.008	14.933	0.076	0.076	0.000	0.000	0.000	0.000
108	A	113	HIS	0	0.008	0.016	19.185	-0.115	-0.115	0.000	0.000	0.000	0.000
109	A	114	ILE	0	0.010	-0.007	22.740	0.241	0.241	0.000	0.000	0.000	0.000
110	A	115	ILE	0	-0.038	-0.028	17.574	0.230	0.230	0.000	0.000	0.000	0.000
111	A	116	ASN	0	-0.036	-0.022	18.764	0.013	0.013	0.000	0.000	0.000	0.000
112	A	117	LEU	0	0.005	0.015	22.318	0.384	0.384	0.000	0.000	0.000	0.000
113	A	118	TYR	0	0.001	-0.007	24.302	0.328	0.328	0.000	0.000	0.000	0.000
114	A	119	PRO	0	-0.033	-0.022	23.556	0.428	0.428	0.000	0.000	0.000	0.000
115	A	120	GLN	0	-0.005	-0.001	26.592	0.568	0.568	0.000	0.000	0.000	0.000
116	A	121	ALA	0	0.018	0.010	29.064	0.367	0.367	0.000	0.000	0.000	0.000
117	A	122	GLN	0	0.004	0.007	29.098	0.309	0.309	0.000	0.000	0.000	0.000
118	A	123	LYS	1	0.885	0.922	31.143	9.357	9.357	0.000	0.000	0.000	0.000
119	A	124	ASN	0	0.035	0.027	34.186	0.247	0.247	0.000	0.000	0.000	0.000
120	A	125	PRO	0	0.086	0.044	35.222	-0.211	-0.211	0.000	0.000	0.000	0.000
121	A	126	SER	0	0.064	0.041	37.022	-0.100	-0.100	0.000	0.000	0.000	0.000
122	A	127	LYS	1	0.986	0.988	32.064	8.842	8.842	0.000	0.000	0.000	0.000
123	A	128	PHE	0	-0.032	-0.010	31.174	-0.329	-0.329	0.000	0.000	0.000	0.000
124	A	129	LEU	0	0.028	0.025	33.186	-0.193	-0.193	0.000	0.000	0.000	0.000
125	A	130	ASP	-1	-0.857	-0.929	32.578	-8.646	-8.646	0.000	0.000	0.000	0.000
126	A	131	LEU	0	-0.047	-0.016	26.990	-0.247	-0.247	0.000	0.000	0.000	0.000
127	A	132	VAL	0	-0.001	-0.014	29.776	-0.275	-0.275	0.000	0.000	0.000	0.000
128	A	133	LYS	1	0.893	0.949	32.151	8.330	8.330	0.000	0.000	0.000	0.000
129	A	134	ILE	0	-0.029	-0.002	26.371	-0.078	-0.078	0.000	0.000	0.000	0.000
130	A	135	VAL	0	-0.030	-0.017	27.830	-0.319	-0.319	0.000	0.000	0.000	0.000
131	A	136	ASP	-1	-0.737	-0.855	29.354	-8.855	-8.855	0.000	0.000	0.000	0.000
132	A	137	ASP	-1	-0.839	-0.905	29.032	-10.153	-10.153	0.000	0.000	0.000	0.000
133	A	138	VAL	0	-0.047	-0.025	25.096	-0.144	-0.144	0.000	0.000	0.000	0.000
134	A	139	GLN	0	-0.029	-0.015	27.647	0.171	0.171	0.000	0.000	0.000	0.000
135	A	140	ASN	0	0.011	0.006	30.379	0.265	0.265	0.000	0.000	0.000	0.000
136	A	141	LEU	0	-0.043	-0.025	26.281	0.060	0.060	0.000	0.000	0.000	0.000
137	A	142	ASN	0	-0.106	-0.042	25.668	-0.407	-0.407	0.000	0.000	0.000	0.000
138	A	143	LYS	1	0.878	0.963	29.568	8.900	8.900	0.000	0.000	0.000	0.000
139	A	144	ARG	1	0.812	0.889	33.385	8.178	8.178	0.000	0.000	0.000	0.000
140	A	145	ALA	0	-0.013	-0.022	36.030	0.053	0.053	0.000	0.000	0.000	0.000
141	A	146	ASP	-1	-0.845	-0.902	38.500	-7.703	-7.703	0.000	0.000	0.000	0.000
142	A	147	GLU	-1	-0.848	-0.910	35.869	-8.596	-8.596	0.000	0.000	0.000	0.000
143	A	148	LEU	0	0.008	0.000	39.437	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	149	LYS	1	0.978	0.984	36.282	8.106	8.106	0.000	0.000	0.000	0.000
145	A	150	SER	0	-0.082	-0.052	33.812	0.176	0.176	0.000	0.000	0.000	0.000
146	A	151	THR	0	0.059	0.016	36.282	0.063	0.063	0.000	0.000	0.000	0.000
147	A	152	ASN	0	-0.093	-0.074	34.317	0.262	0.262	0.000	0.000	0.000	0.000
148	A	153	TYR	0	0.012	-0.001	36.024	0.046	0.046	0.000	0.000	0.000	0.000
149	A	154	ASP	-1	-0.839	-0.919	37.496	-7.444	-7.444	0.000	0.000	0.000	0.000
150	A	155	ARG	1	0.888	0.939	37.233	8.101	8.101	0.000	0.000	0.000	0.000
151	A	156	LEU	0	0.001	0.004	35.855	0.077	0.077	0.000	0.000	0.000	0.000
152	A	157	LEU	0	0.016	0.016	40.178	0.061	0.061	0.000	0.000	0.000	0.000
153	A	158	GLU	-1	-0.835	-0.921	42.054	-6.417	-6.417	0.000	0.000	0.000	0.000
154	A	159	GLU	-1	-0.893	-0.927	41.308	-7.467	-7.467	0.000	0.000	0.000	0.000
155	A	160	PHE	0	-0.089	-0.064	37.282	0.004	0.004	0.000	0.000	0.000	0.000
156	A	161	LEU	0	0.063	0.045	43.416	0.088	0.088	0.000	0.000	0.000	0.000
157	A	162	LYS	1	0.828	0.908	46.671	6.520	6.520	0.000	0.000	0.000	0.000
158	A	163	ALA	0	-0.062	-0.028	45.213	0.099	0.099	0.000	0.000	0.000	0.000
159	A	164	GLY	0	0.014	0.016	46.762	-0.031	-0.031	0.000	0.000	0.000	0.000
160	A	165	LYS	1	0.825	0.919	41.329	7.327	7.327	0.000	0.000	0.000	0.000
161	A	166	ILE	-1	-0.904	-0.945	41.225	-7.005	-7.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:THR)