FMO DATABASE

FMODB ID: ZZ83N

Calculation Name: 4N2P-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: MPD | ACT | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4N2P

Chain ID: A

ChEMBL ID:

UniProt ID: O59205

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1358382.801378
FMO2-HF: Nuclear repulsion	1300062.473156
FMO2-HF: Total energy	-58320.328222
FMO2-MP2: Total energy	-58491.900611

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:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-42.229	-37.831	5.263	-3.454	-6.207	-0.028

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.917

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	LYS	1	0.983	0.986	2.411	21.133	24.561	2.769	-2.740	-3.458	-0.033
4	A	4	LYS	1	0.962	0.973	2.534	33.707	34.621	2.495	-0.711	-2.698	0.005
5	A	5	TRP	0	-0.004	-0.002	4.934	-0.365	-0.309	-0.001	-0.003	-0.051	0.000
6	A	6	GLU	-1	-0.947	-0.971	8.063	-21.636	-21.636	0.000	0.000	0.000	0.000
7	A	7	HIS	0	0.000	-0.003	10.792	0.458	0.458	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.029	-0.007	12.824	-0.437	-0.437	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.931	-0.960	15.559	-11.343	-11.343	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.070	-0.057	18.983	-0.499	-0.499	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.011	0.010	21.029	0.083	0.083	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.015	-0.006	24.051	-0.327	-0.327	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.844	-0.917	26.265	-9.015	-9.015	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.014	0.004	29.565	-0.123	-0.123	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.018	-0.004	32.342	0.138	0.138	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.025	-0.001	34.647	0.076	0.076	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.862	0.888	36.269	7.506	7.506	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.007	0.016	40.941	0.043	0.043	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.050	-0.055	41.908	-0.096	-0.096	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.049	0.026	47.125	0.040	0.040	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.838	-0.904	50.954	-5.488	-5.488	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.067	-0.061	54.233	0.029	0.029	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.012	-0.013	50.208	-0.110	-0.110	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.819	-0.930	51.225	-5.437	-5.437	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.789	-0.855	52.083	-5.476	-5.476	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.055	-0.019	47.637	-0.101	-0.101	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.019	-0.006	47.314	-0.146	-0.146	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.833	-0.918	48.210	-5.548	-5.548	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.007	0.000	46.827	-0.088	-0.088	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.001	-0.002	42.112	-0.114	-0.114	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.038	0.032	43.694	-0.132	-0.132	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.074	-0.043	45.576	-0.047	-0.047	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.023	-0.015	40.996	-0.079	-0.079	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.034	0.018	40.387	-0.146	-0.146	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.043	0.007	41.178	-0.080	-0.080	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.895	-0.958	40.723	-6.985	-6.985	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.016	0.014	35.805	-0.135	-0.135	0.000	0.000	0.000	0.000
38	A	38	MET	0	0.040	0.037	37.629	-0.104	-0.104	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.049	-0.023	40.054	0.028	0.028	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.011	0.001	41.754	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.026	0.015	43.210	0.184	0.184	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.085	-0.061	44.695	0.255	0.255	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.759	0.873	46.163	6.385	6.385	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.014	0.013	47.607	0.075	0.075	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.856	-0.935	50.367	-5.270	-5.270	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.826	0.898	54.209	5.329	5.329	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.753	0.871	55.480	5.425	5.425	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.863	-0.930	56.013	-5.223	-5.223	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.013	-0.007	56.761	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.710	0.825	54.422	5.356	5.356	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.877	-0.935	56.494	-4.896	-4.896	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.024	0.025	51.352	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.845	-0.925	55.686	-4.843	-4.843	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.039	0.042	51.725	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.831	-0.918	54.712	-5.018	-5.018	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.009	0.014	50.860	-0.085	-0.085	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.880	-0.952	51.963	-5.339	-5.339	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.920	-0.956	47.854	-6.127	-6.127	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.011	-0.008	49.049	0.052	0.052	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.838	-0.930	44.027	-6.382	-6.382	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.064	0.018	45.541	-0.064	-0.064	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.078	-0.023	47.112	0.044	0.044	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.002	-0.005	43.895	0.041	0.041	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.002	0.001	41.639	0.040	0.040	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.002	-0.017	44.938	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.022	-0.018	48.077	0.046	0.046	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.003	-0.003	43.162	0.030	0.030	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.821	-0.916	42.477	-6.952	-6.952	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.936	-0.976	45.297	-5.721	-5.721	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.056	-0.030	47.116	0.067	0.067	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.003	0.019	40.618	0.041	0.041	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.061	0.022	45.026	0.028	0.028	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.045	-0.026	47.053	0.075	0.075	0.000	0.000	0.000	0.000
74	A	74	HIS	1	0.765	0.860	42.283	6.738	6.738	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.873	-0.940	43.355	-6.752	-6.752	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.089	-0.042	45.913	0.052	0.052	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.851	-0.896	49.377	-5.353	-5.353	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.040	0.032	47.527	0.080	0.080	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.055	-0.022	48.608	0.025	0.025	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.009	0.007	45.420	-0.149	-0.149	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.000	-0.007	48.021	0.156	0.156	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.891	0.946	48.287	5.780	5.780	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.829	-0.913	49.949	-5.612	-5.612	0.000	0.000	0.000	0.000
84	A	84	PHE	0	-0.019	-0.016	48.339	0.036	0.036	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.846	-0.877	53.524	-4.962	-4.962	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.025	-0.020	52.115	0.014	0.014	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.859	0.932	55.593	4.874	4.874	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.002	0.009	52.549	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.872	-0.937	57.053	-4.748	-4.748	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.830	0.920	56.197	5.174	5.174	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.002	-0.004	60.394	0.110	0.110	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.042	-0.029	61.194	-0.033	-0.033	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.003	0.006	60.863	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.909	0.981	56.513	5.165	5.165	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.011	-0.009	53.579	0.095	0.095	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.751	0.861	56.190	4.937	4.937	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.018	0.028	51.815	0.035	0.035	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.814	0.890	55.873	4.947	4.947	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.030	0.012	54.309	-0.032	-0.032	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.832	0.923	56.251	4.952	4.952	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.031	0.027	52.208	-0.065	-0.065	0.000	0.000	0.000	0.000
102	A	102	TYR	0	-0.059	-0.073	53.850	0.080	0.080	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.029	0.000	52.448	-0.112	-0.112	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.743	-0.806	52.041	-5.451	-5.451	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.911	0.948	51.304	5.482	5.482	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.020	0.016	43.910	0.016	0.016	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.850	-0.927	48.350	-5.858	-5.858	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.006	-0.016	43.297	-0.073	-0.073	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.875	0.944	44.923	5.748	5.748	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.743	0.858	47.077	5.597	5.597	0.000	0.000	0.000	0.000
111	A	111	HIS	0	0.004	-0.018	45.716	-0.093	-0.093	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.839	-0.891	41.600	-6.640	-6.640	0.000	0.000	0.000	0.000
113	A	113	PRO	0	0.000	-0.007	40.399	-0.044	-0.044	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.764	0.897	36.559	7.119	7.119	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.961	-0.974	31.868	-8.759	-8.759	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.869	-0.928	35.689	-6.928	-6.928	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.011	-0.007	35.873	-0.168	-0.168	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.777	0.884	30.325	9.146	9.146	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.022	0.003	37.051	0.132	0.132	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.043	0.000	37.763	-0.151	-0.151	0.000	0.000	0.000	0.000
121	A	121	THR	0	-0.037	-0.029	34.887	0.020	0.020	0.000	0.000	0.000	0.000
122	A	122	TYR	0	0.037	-0.010	37.774	0.184	0.184	0.000	0.000	0.000	0.000
123	A	123	HIS	0	-0.007	0.003	32.482	0.077	0.077	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.899	-0.961	33.737	-8.009	-8.009	0.000	0.000	0.000	0.000
125	A	125	MET	0	-0.040	0.016	35.724	0.182	0.182	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.799	0.897	39.415	7.182	7.182	0.000	0.000	0.000	0.000
127	A	127	ILE	0	0.043	0.023	41.752	0.048	0.048	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.865	-0.929	42.861	-6.812	-6.812	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.902	0.976	46.882	5.601	5.601	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.025	0.015	44.727	-0.043	-0.043	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.009	-0.021	47.377	0.147	0.147	0.000	0.000	0.000	0.000
132	A	132	ASN	0	-0.025	-0.028	49.159	0.126	0.126	0.000	0.000	0.000	0.000
133	A	133	GLY	0	-0.042	-0.018	52.119	0.093	0.093	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.819	0.918	49.827	5.552	5.552	0.000	0.000	0.000	0.000
135	A	135	TRP	0	0.012	0.002	49.325	-0.070	-0.070	0.000	0.000	0.000	0.000
136	A	136	MET	0	-0.047	-0.017	41.079	-0.046	-0.046	0.000	0.000	0.000	0.000
137	A	137	ALA	0	0.023	0.017	44.428	0.040	0.040	0.000	0.000	0.000	0.000
138	A	138	GLN	0	-0.031	-0.013	37.015	0.041	0.041	0.000	0.000	0.000	0.000
139	A	139	LEU	0	0.044	0.022	37.934	0.099	0.099	0.000	0.000	0.000	0.000
140	A	140	VAL	0	0.010	0.011	31.480	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	141	PRO	0	-0.031	0.000	34.614	-0.065	-0.065	0.000	0.000	0.000	0.000
142	A	142	ASP	-1	-0.860	-0.930	32.057	-8.853	-8.853	0.000	0.000	0.000	0.000
143	A	143	ILE	-1	-0.840	-0.897	30.563	-8.798	-8.798	0.000	0.000	0.000	0.000

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