FMO DATABASE

FMODB ID: YRY62

Calculation Name: 1P3H-A-Xray547

Preferred Name:

Target Type:

Ligand Name: (4s)-2-methyl-2,4-pentanediol | calcium ion

Ligand 3-letter code: MPD | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1P3H

Chain ID: A

ChEMBL ID:

UniProt ID: P9WPE5

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-632533.730022
FMO2-HF: Nuclear repulsion	595801.408856
FMO2-HF: Total energy	-36732.321166
FMO2-MP2: Total energy	-36841.905208

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.
-105.48	-102.806	0.03	-1.099	-1.604	-0.003

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 : 0.899 / q_NPA : 0.939

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	3	VAL	0	-0.017	-0.001	3.843	7.749	9.307	-0.014	-0.665	-0.879	0.000
4	A	4	ASN	0	0.016	-0.004	3.375	-5.213	-4.628	0.027	-0.253	-0.359	-0.002
80	A	80	TYR	0	-0.045	-0.034	3.240	-6.250	-5.794	0.018	-0.165	-0.309	-0.001
81	A	81	ASN	0	-0.040	-0.034	3.851	1.006	1.081	-0.001	-0.016	-0.057	0.000
5	A	5	ILE	0	0.033	0.024	5.900	3.186	3.186	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.972	0.990	8.582	22.829	22.829	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.005	0.017	11.578	1.092	1.092	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.002	-0.005	14.503	0.318	0.318	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.895	-0.966	17.994	-12.505	-12.505	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.888	-0.933	19.972	-12.987	-12.987	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.943	0.988	17.730	13.827	13.827	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.020	0.008	15.202	-0.512	-0.512	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.044	-0.017	8.280	0.262	0.262	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.028	0.008	12.460	-0.668	-0.668	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.040	-0.027	9.127	-2.061	-2.061	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.025	-0.001	12.296	0.995	0.995	0.000	0.000	0.000	0.000
17	A	17	ASN	0	0.014	0.015	14.853	-1.765	-1.765	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.892	-0.955	17.132	-15.461	-15.461	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.037	0.014	18.916	-0.500	-0.500	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.922	-0.960	21.178	-13.072	-13.072	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.056	-0.024	23.333	0.344	0.344	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.006	0.001	26.825	0.100	0.100	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.012	-0.017	29.658	0.215	0.215	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.022	-0.002	33.342	-0.072	-0.072	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.055	-0.027	36.012	0.122	0.122	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.005	0.014	32.521	0.053	0.053	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.040	-0.011	31.630	-0.164	-0.164	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.050	0.024	25.281	0.092	0.092	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.042	-0.022	28.622	0.136	0.136	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.030	0.017	23.746	0.021	0.021	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.839	-0.906	24.709	-11.034	-11.034	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.011	-0.028	24.330	-0.552	-0.552	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.018	-0.002	26.030	-0.051	-0.051	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.852	0.928	20.652	13.729	13.729	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.850	-0.933	25.467	-10.104	-10.104	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.873	0.950	26.849	10.806	10.806	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.034	0.011	25.127	-0.385	-0.385	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.086	-0.063	18.871	0.409	0.409	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.902	-0.948	20.006	-13.823	-13.823	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.026	0.004	16.728	-0.251	-0.251	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.014	-0.002	12.646	0.927	0.927	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.011	0.002	13.043	-1.207	-1.207	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.045	-0.021	7.114	-1.221	-1.221	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.011	-0.001	8.997	-2.070	-2.070	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.026	0.018	11.025	1.311	1.311	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.003	0.012	14.344	-0.727	-0.727	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.099	-0.048	16.670	0.309	0.309	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.090	0.052	19.207	0.578	0.578	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.918	0.948	22.143	10.134	10.134	0.000	0.000	0.000	0.000
50	A	50	TRP	0	0.010	0.005	25.150	-0.104	-0.104	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.791	-0.891	27.884	-9.763	-9.763	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.948	-0.981	31.208	-8.707	-8.707	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.873	-0.895	34.526	-8.362	-8.362	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.038	0.000	30.964	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	55	GLU	0	-0.085	-0.087	30.922	-0.247	-0.247	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.835	0.893	28.472	9.692	9.692	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.857	0.945	22.106	13.119	13.119	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.014	-0.002	25.949	0.198	0.198	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.027	-0.028	22.895	-0.385	-0.385	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.004	-0.001	18.661	0.441	0.441	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.947	-0.964	22.077	-11.842	-11.842	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.014	-0.015	18.577	0.061	0.061	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.030	-0.015	16.657	-0.205	-0.205	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.962	-0.996	10.102	-25.933	-25.933	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.031	-0.018	12.778	0.423	0.423	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.844	-0.904	13.780	-14.883	-14.883	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.055	-0.021	16.343	-0.587	-0.587	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.001	-0.002	17.526	0.785	0.785	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.025	0.012	20.209	-0.175	-0.175	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.017	-0.012	18.275	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	71	SER	0	0.011	-0.008	22.695	0.345	0.345	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.809	0.894	21.365	12.218	12.218	0.000	0.000	0.000	0.000
73	A	73	TYR	0	0.037	0.029	22.476	-0.263	-0.263	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.013	0.004	24.215	-0.132	-0.132	0.000	0.000	0.000	0.000
75	A	75	GLY	0	-0.005	0.001	20.173	-0.242	-0.242	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.070	-0.038	16.995	0.441	0.441	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.834	-0.919	16.311	-16.230	-16.230	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.051	-0.032	10.599	-0.109	-0.109	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.905	0.967	11.752	16.559	16.559	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.005	0.000	8.320	0.515	0.515	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.855	-0.891	8.739	-25.315	-25.315	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.874	-0.950	10.892	-17.038	-17.038	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.029	-0.018	6.725	-1.604	-1.604	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.004	0.009	12.494	1.063	1.063	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.042	-0.014	12.645	-0.849	-0.849	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.040	0.024	15.626	0.865	0.865	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.038	-0.025	18.656	-0.375	-0.375	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.020	0.003	20.840	0.027	0.027	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.827	0.889	21.947	12.281	12.281	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.810	-0.894	22.391	-12.055	-12.055	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.035	-0.022	20.427	-0.029	-0.029	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.058	-0.020	23.227	0.454	0.454	0.000	0.000	0.000	0.000
95	A	95	ALA	0	-0.010	-0.011	24.681	0.419	0.419	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.030	0.023	21.050	-0.487	-0.487	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.055	-0.027	22.052	0.616	0.616	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.033	-0.025	21.988	-0.452	-0.452	0.000	0.000	0.000	0.000
99	A	99	LYS	0	0.029	0.024	20.307	2.521	2.521	0.000	0.000	0.000	0.000

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