FMO DATABASE

FMODB ID: 1VK4Z

Calculation Name: 1J1D-C-Xray549

Preferred Name: Troponin, cardiac muscle

Target Type: PROTEIN COMPLEX

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1J1D

Chain ID: C

ChEMBL ID: CHEMBL2095202

UniProt ID: P63316

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-740993.65696
FMO2-HF: Nuclear repulsion	691356.118363
FMO2-HF: Total energy	-49637.538597
FMO2-MP2: Total energy	-49784.081565

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(C:35:ALA)

Summations of interaction energy for fragment #1(C:35:ALA)

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.
199.08	201.31	0.202	-0.917	-1.514	-0.001

Interaction energy analysis for fragmet #1(C:35:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.915 / q_NPA : 0.947

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

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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	C	37	LYS	1	0.985	1.016	2.574	47.522	49.420	0.201	-0.858	-1.241	-0.001
4	C	38	LYS	1	1.025	1.000	4.255	30.379	30.549	0.001	-0.023	-0.149	0.000
5	C	39	SER	0	-0.035	-0.028	4.052	0.551	0.713	0.000	-0.036	-0.124	0.000
6	C	40	LYS	1	0.940	0.982	5.880	29.361	29.361	0.000	0.000	0.000	0.000
7	C	41	ILE	0	0.058	0.027	6.630	1.258	1.258	0.000	0.000	0.000	0.000
8	C	42	SER	0	0.070	0.037	10.108	-0.686	-0.686	0.000	0.000	0.000	0.000
9	C	43	ALA	0	0.011	-0.007	12.619	0.359	0.359	0.000	0.000	0.000	0.000
10	C	44	SER	0	0.078	0.035	15.012	0.342	0.342	0.000	0.000	0.000	0.000
11	C	45	ARG	1	0.956	0.983	14.468	16.768	16.768	0.000	0.000	0.000	0.000
12	C	46	LYS	1	0.933	0.964	11.654	21.957	21.957	0.000	0.000	0.000	0.000
13	C	47	LEU	0	0.032	0.015	16.398	0.358	0.358	0.000	0.000	0.000	0.000
14	C	48	GLN	0	0.080	0.058	19.257	-0.127	-0.127	0.000	0.000	0.000	0.000
15	C	49	LEU	0	0.010	-0.002	17.089	0.390	0.390	0.000	0.000	0.000	0.000
16	C	50	LYS	1	0.937	0.965	18.039	15.660	15.660	0.000	0.000	0.000	0.000
17	C	51	THR	0	0.016	-0.001	21.891	0.472	0.472	0.000	0.000	0.000	0.000
18	C	52	LEU	0	0.017	0.008	23.338	0.368	0.368	0.000	0.000	0.000	0.000
19	C	53	LEU	0	-0.011	-0.001	20.986	0.228	0.228	0.000	0.000	0.000	0.000
20	C	54	LEU	0	-0.001	-0.002	25.310	0.309	0.309	0.000	0.000	0.000	0.000
21	C	55	GLN	0	-0.001	0.004	27.860	0.358	0.358	0.000	0.000	0.000	0.000
22	C	56	ILE	0	0.020	0.012	27.212	0.264	0.264	0.000	0.000	0.000	0.000
23	C	57	ALA	0	0.041	0.021	28.856	0.262	0.262	0.000	0.000	0.000	0.000
24	C	58	LYS	1	0.932	0.969	30.775	8.989	8.989	0.000	0.000	0.000	0.000
25	C	59	GLN	0	0.031	0.012	33.300	0.031	0.031	0.000	0.000	0.000	0.000
26	C	60	GLU	-1	-0.962	-0.990	31.338	-9.359	-9.359	0.000	0.000	0.000	0.000
27	C	61	LEU	0	-0.002	0.012	34.974	0.206	0.206	0.000	0.000	0.000	0.000
28	C	62	GLU	-1	-0.951	-0.987	36.757	-7.693	-7.693	0.000	0.000	0.000	0.000
29	C	63	ARG	1	0.933	0.975	34.146	8.676	8.676	0.000	0.000	0.000	0.000
30	C	64	GLU	-1	-0.855	-0.911	38.454	-7.740	-7.740	0.000	0.000	0.000	0.000
31	C	65	ALA	0	-0.045	-0.029	40.449	0.201	0.201	0.000	0.000	0.000	0.000
32	C	66	GLU	-1	-0.842	-0.892	42.774	-6.502	-6.502	0.000	0.000	0.000	0.000
33	C	67	GLU	-1	-0.794	-0.874	43.330	-6.537	-6.537	0.000	0.000	0.000	0.000
34	C	68	ARG	1	0.893	0.922	41.046	7.443	7.443	0.000	0.000	0.000	0.000
35	C	69	ARG	1	0.816	0.890	44.829	6.868	6.868	0.000	0.000	0.000	0.000
36	C	70	GLY	0	0.039	0.025	48.461	0.156	0.156	0.000	0.000	0.000	0.000
37	C	71	GLU	-1	-0.999	-1.004	46.176	-6.584	-6.584	0.000	0.000	0.000	0.000
38	C	72	LYS	1	0.961	0.983	49.783	6.018	6.018	0.000	0.000	0.000	0.000
39	C	73	GLY	0	0.022	0.014	52.150	0.126	0.126	0.000	0.000	0.000	0.000
40	C	74	ARG	1	0.835	0.890	47.750	6.467	6.467	0.000	0.000	0.000	0.000
41	C	75	ALA	0	-0.004	0.000	53.071	0.097	0.097	0.000	0.000	0.000	0.000
42	C	76	LEU	0	-0.034	-0.031	55.064	0.087	0.087	0.000	0.000	0.000	0.000
43	C	77	SER	0	-0.002	0.006	57.780	0.127	0.127	0.000	0.000	0.000	0.000
44	C	78	THR	0	0.005	0.004	57.578	0.082	0.082	0.000	0.000	0.000	0.000
45	C	79	ARG	1	0.908	0.944	53.103	5.801	5.801	0.000	0.000	0.000	0.000
46	C	80	ALA	0	-0.050	-0.023	60.575	0.071	0.071	0.000	0.000	0.000	0.000
47	C	81	GLN	0	-0.009	0.013	63.025	-0.010	-0.010	0.000	0.000	0.000	0.000
48	C	82	PRO	0	-0.013	-0.002	64.091	0.047	0.047	0.000	0.000	0.000	0.000
49	C	83	LEU	0	-0.022	-0.019	66.884	0.026	0.026	0.000	0.000	0.000	0.000
50	C	84	GLU	-1	-0.872	-0.933	70.664	-4.303	-4.303	0.000	0.000	0.000	0.000
51	C	85	LEU	0	-0.015	-0.028	73.127	0.033	0.033	0.000	0.000	0.000	0.000
52	C	86	ALA	0	-0.033	-0.004	76.405	0.063	0.063	0.000	0.000	0.000	0.000
53	C	87	GLY	0	-0.005	-0.006	78.372	0.051	0.051	0.000	0.000	0.000	0.000
54	C	88	LEU	0	-0.051	-0.002	76.739	0.029	0.029	0.000	0.000	0.000	0.000
55	C	89	GLY	0	0.055	0.028	81.116	0.036	0.036	0.000	0.000	0.000	0.000
56	C	90	PHE	0	-0.029	-0.033	83.181	-0.038	-0.038	0.000	0.000	0.000	0.000
57	C	91	ALA	0	0.015	0.004	83.941	-0.026	-0.026	0.000	0.000	0.000	0.000
58	C	92	GLU	-1	-0.806	-0.898	80.242	-3.936	-3.936	0.000	0.000	0.000	0.000
59	C	93	LEU	0	0.010	0.009	78.239	-0.065	-0.065	0.000	0.000	0.000	0.000
60	C	94	GLN	0	-0.017	-0.009	79.225	-0.033	-0.033	0.000	0.000	0.000	0.000
61	C	95	ASP	-1	-0.909	-0.961	79.036	-3.979	-3.979	0.000	0.000	0.000	0.000
62	C	96	LEU	0	-0.027	-0.006	73.023	-0.063	-0.063	0.000	0.000	0.000	0.000
63	C	97	ALA	0	0.002	-0.005	75.056	-0.065	-0.065	0.000	0.000	0.000	0.000
64	C	98	ARG	1	0.930	0.962	75.909	3.909	3.909	0.000	0.000	0.000	0.000
65	C	99	GLN	0	-0.016	-0.010	72.966	-0.092	-0.092	0.000	0.000	0.000	0.000
66	C	100	LEU	0	-0.048	-0.028	70.212	-0.080	-0.080	0.000	0.000	0.000	0.000
67	C	101	HIS	0	-0.021	0.000	71.137	-0.023	-0.023	0.000	0.000	0.000	0.000
68	C	102	ALA	0	0.042	0.021	71.966	-0.043	-0.043	0.000	0.000	0.000	0.000
69	C	103	ARG	1	0.920	0.956	66.435	4.603	4.603	0.000	0.000	0.000	0.000
70	C	104	VAL	0	-0.023	-0.012	67.082	-0.094	-0.094	0.000	0.000	0.000	0.000
71	C	105	ASP	-1	-0.879	-0.939	67.089	-4.524	-4.524	0.000	0.000	0.000	0.000
72	C	106	LYS	1	0.806	0.902	63.226	4.938	4.938	0.000	0.000	0.000	0.000
73	C	107	VAL	0	-0.038	-0.028	61.711	-0.088	-0.088	0.000	0.000	0.000	0.000
74	C	108	ASP	-1	-0.843	-0.907	62.071	-5.135	-5.135	0.000	0.000	0.000	0.000
75	C	109	GLU	-1	-0.911	-0.942	62.449	-4.942	-4.942	0.000	0.000	0.000	0.000
76	C	110	GLU	-1	-0.821	-0.912	59.704	-5.245	-5.245	0.000	0.000	0.000	0.000
77	C	111	ARG	1	0.740	0.848	58.029	5.141	5.141	0.000	0.000	0.000	0.000
78	C	112	TYR	0	0.025	0.016	57.633	-0.122	-0.122	0.000	0.000	0.000	0.000
79	C	113	ASP	-1	-0.842	-0.922	58.017	-5.420	-5.420	0.000	0.000	0.000	0.000
80	C	114	ILE	0	-0.141	-0.069	51.094	-0.147	-0.147	0.000	0.000	0.000	0.000
81	C	115	GLU	-1	-0.855	-0.922	53.319	-5.630	-5.630	0.000	0.000	0.000	0.000
82	C	116	ALA	0	0.049	0.038	54.077	-0.112	-0.112	0.000	0.000	0.000	0.000
83	C	117	LYS	1	0.913	0.959	51.308	5.702	5.702	0.000	0.000	0.000	0.000
84	C	118	VAL	0	0.003	0.005	48.865	-0.154	-0.154	0.000	0.000	0.000	0.000
85	C	119	THR	0	-0.007	-0.023	49.527	-0.124	-0.124	0.000	0.000	0.000	0.000
86	C	120	LYS	1	0.894	0.956	50.724	6.061	6.061	0.000	0.000	0.000	0.000
87	C	121	ASN	0	0.072	0.014	46.020	-0.041	-0.041	0.000	0.000	0.000	0.000
88	C	122	ILE	0	-0.006	0.006	45.945	-0.182	-0.182	0.000	0.000	0.000	0.000
89	C	123	THR	0	-0.050	-0.024	46.646	-0.038	-0.038	0.000	0.000	0.000	0.000
90	C	124	GLU	-1	-0.925	-0.957	44.220	-7.145	-7.145	0.000	0.000	0.000	0.000
91	C	125	ILE	0	0.018	0.004	41.040	-0.197	-0.197	0.000	0.000	0.000	0.000
92	C	126	ALA	0	-0.012	0.016	42.022	-0.214	-0.214	0.000	0.000	0.000	0.000
93	C	127	ASP	-1	-0.879	-0.944	43.365	-7.304	-7.304	0.000	0.000	0.000	0.000
94	C	128	LEU	0	0.006	-0.003	39.654	-0.227	-0.227	0.000	0.000	0.000	0.000
95	C	129	THR	0	-0.027	-0.027	38.098	-0.331	-0.331	0.000	0.000	0.000	0.000
96	C	130	GLN	0	0.026	0.043	38.746	-0.277	-0.277	0.000	0.000	0.000	0.000
97	C	131	LYS	1	0.965	0.982	39.767	7.621	7.621	0.000	0.000	0.000	0.000
98	C	132	ILE	0	0.015	0.007	33.560	-0.228	-0.228	0.000	0.000	0.000	0.000
99	C	133	PHE	0	-0.007	-0.006	35.158	-0.302	-0.302	0.000	0.000	0.000	0.000
100	C	134	ASP	0	-0.042	-0.063	36.466	-0.164	-0.164	0.000	0.000	0.000	0.000
101	C	135	LEU	0	0.025	0.020	36.337	-0.001	-0.001	0.000	0.000	0.000	0.000
102	C	136	ARG	1	0.883	0.933	30.455	9.684	9.684	0.000	0.000	0.000	0.000
103	C	137	GLY	0	-0.009	0.017	31.688	-0.301	-0.301	0.000	0.000	0.000	0.000
104	C	138	LYS	1	0.837	0.927	32.916	8.380	8.380	0.000	0.000	0.000	0.000
105	C	139	PHE	0	0.052	0.014	31.457	-0.126	-0.126	0.000	0.000	0.000	0.000
106	C	140	LYS	1	0.951	0.996	34.128	8.346	8.346	0.000	0.000	0.000	0.000
107	C	141	ARG	1	0.916	0.946	28.755	10.575	10.575	0.000	0.000	0.000	0.000
108	C	142	PRO	0	0.022	0.023	33.566	0.245	0.245	0.000	0.000	0.000	0.000
109	C	143	THR	0	-0.038	-0.044	34.281	-0.450	-0.450	0.000	0.000	0.000	0.000
110	C	144	LEU	0	0.091	0.070	36.284	0.178	0.178	0.000	0.000	0.000	0.000
111	C	145	ARG	1	0.971	0.983	37.362	7.348	7.348	0.000	0.000	0.000	0.000
112	C	146	ARG	1	0.906	0.949	33.874	9.413	9.413	0.000	0.000	0.000	0.000
113	C	147	VAL	0	0.071	0.039	36.999	0.162	0.162	0.000	0.000	0.000	0.000
114	C	148	ARG	1	0.908	0.944	28.220	10.129	10.129	0.000	0.000	0.000	0.000
115	C	149	ILE	0	0.055	0.032	31.342	0.208	0.208	0.000	0.000	0.000	0.000
116	C	150	SER	0	-0.001	-0.003	34.215	-0.179	-0.179	0.000	0.000	0.000	0.000
117	C	151	ALA	0	0.024	0.006	33.030	0.025	0.025	0.000	0.000	0.000	0.000
118	C	152	ASP	-1	-0.835	-0.923	34.675	-8.345	-8.345	0.000	0.000	0.000	0.000
119	C	153	ALA	0	-0.024	-0.009	37.953	0.136	0.136	0.000	0.000	0.000	0.000
120	C	154	MET	0	-0.019	-0.003	34.280	-0.036	-0.036	0.000	0.000	0.000	0.000
121	C	155	MET	0	-0.022	-0.019	34.566	-0.046	-0.046	0.000	0.000	0.000	0.000
122	C	156	GLN	0	-0.003	-0.004	37.509	0.200	0.200	0.000	0.000	0.000	0.000
123	C	157	ALA	0	-0.020	0.004	40.027	0.162	0.162	0.000	0.000	0.000	0.000
124	C	158	LEU	0	-0.081	-0.047	35.181	0.019	0.019	0.000	0.000	0.000	0.000
125	C	159	LEU	0	-0.063	-0.030	36.631	-0.031	-0.031	0.000	0.000	0.000	0.000
126	C	160	GLY	-1	-0.910	-0.937	40.696	-7.116	-7.116	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:35:ALA)