FMO DATABASE

FMODB ID: LVMV9

Calculation Name: 1H4B-A-Other547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1H4B

Chain ID: A

ChEMBL ID:

UniProt ID: Q39419

Base Structure: SolutionNMR

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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-543871.791152
FMO2-HF: Nuclear repulsion	511168.692203
FMO2-HF: Total energy	-32703.098949
FMO2-MP2: Total energy	-32798.80397

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:1:ALA)

Summations of interaction energy for fragment #1(A:1: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.
-48.78	-45.969	0.026	-1.184	-1.654	-0.006

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.798 / q_NPA : 0.883

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	A	3	ASP	-1	-0.833	-0.875	2.949	-44.404	-41.800	0.027	-1.132	-1.499	-0.006
4	A	4	HIS	0	0.004	0.013	4.338	-5.557	-5.350	-0.001	-0.052	-0.155	0.000
5	A	5	PRO	0	-0.030	-0.041	6.564	2.615	2.615	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.005	-0.002	9.215	1.286	1.286	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.811	-0.903	8.266	-31.655	-31.655	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.913	0.950	7.907	35.186	35.186	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.048	0.034	12.009	1.574	1.574	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.845	-0.922	14.481	-16.428	-16.428	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.904	0.945	8.738	29.563	29.563	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.916	-0.960	15.314	-17.551	-17.551	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.847	0.921	17.463	17.152	17.152	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.020	-0.006	17.017	0.655	0.655	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.012	0.007	18.573	0.351	0.351	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.919	0.948	19.837	15.678	15.678	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.801	0.912	22.618	13.540	13.540	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.022	-0.008	21.639	0.385	0.385	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.841	-0.918	24.251	-11.840	-11.840	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.007	0.008	26.087	0.072	0.072	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.106	-0.068	29.733	0.061	0.061	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.015	0.008	26.716	0.136	0.136	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.871	-0.916	27.156	-11.136	-11.136	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.033	-0.018	23.475	-0.196	-0.196	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.808	0.892	22.946	10.225	10.225	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.025	-0.009	22.456	0.439	0.439	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.019	-0.016	26.205	0.043	0.043	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.067	-0.005	29.171	-0.110	-0.110	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.051	-0.021	30.838	0.077	0.077	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.742	-0.843	29.122	-10.687	-10.687	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.041	0.015	24.548	-0.082	-0.082	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.030	0.003	28.045	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-1.024	-1.027	31.249	-8.987	-8.987	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.000	0.011	27.384	0.099	0.099	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.025	-0.003	25.991	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.921	0.964	29.401	8.955	8.955	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.036	-0.005	28.213	0.306	0.306	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.012	0.000	27.559	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.051	-0.012	31.358	0.161	0.161	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.108	-0.076	33.781	0.397	0.397	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.025	0.036	29.129	-0.217	-0.217	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.017	-0.001	33.378	0.294	0.294	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.033	-0.001	33.158	-0.282	-0.282	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.864	-0.931	33.420	-8.817	-8.817	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.876	-0.947	30.352	-9.921	-9.921	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.018	0.006	28.846	-0.386	-0.386	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.892	0.933	28.525	8.709	8.709	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.086	-0.044	27.372	0.177	0.177	0.000	0.000	0.000	0.000
49	A	49	MET	0	0.006	-0.008	24.741	-0.427	-0.427	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.029	0.010	24.414	-0.360	-0.360	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.013	-0.002	25.277	-0.305	-0.305	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.930	-0.943	22.902	-12.709	-12.709	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.102	-0.061	19.461	-0.853	-0.853	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.829	-0.919	20.739	-12.841	-12.841	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.121	-0.099	18.266	-0.234	-0.234	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.954	-0.988	21.720	-12.452	-12.452	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.027	-0.001	24.541	0.450	0.450	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.927	-0.963	26.715	-11.204	-11.204	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.051	-0.022	28.019	0.491	0.491	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.118	-0.085	26.806	0.443	0.443	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.007	0.032	20.785	-0.523	-0.523	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.060	0.023	20.164	0.172	0.172	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.072	-0.038	13.993	-1.104	-1.104	0.000	0.000	0.000	0.000
64	A	64	GLN	0	-0.048	-0.039	14.379	-2.563	-2.563	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.690	-0.794	14.772	-16.187	-16.187	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.059	0.025	16.555	-0.754	-0.754	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.048	-0.024	10.725	-1.803	-1.803	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.869	-0.916	12.193	-25.070	-25.070	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.097	0.048	13.295	-0.823	-0.823	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.012	-0.006	13.881	0.127	0.127	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.744	0.846	7.850	27.629	27.629	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.033	0.022	11.047	-0.937	-0.937	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.006	0.005	13.935	1.007	1.007	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.842	0.893	6.256	39.283	39.283	0.000	0.000	0.000	0.000
75	A	75	GLY	0	-0.090	-0.049	14.001	0.414	0.414	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.093	0.045	17.210	0.427	0.427	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.018	0.026	14.103	0.389	0.389	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.889	0.939	14.614	20.409	20.409	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.946	-0.948	18.510	-12.454	-12.454	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.083	0.029	20.966	0.387	0.387	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.056	-0.033	19.056	0.378	0.378	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.826	0.899	21.220	14.421	14.421	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.042	-0.006	24.410	0.448	0.448	0.000	0.000	0.000	0.000
84	A	84	PHE	-1	-0.864	-0.905	24.737	-11.847	-11.847	0.000	0.000	0.000	0.000

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