FMO DATABASE

FMODB ID: 4KJQN

Calculation Name: 3VWC-A-Xray549

Preferred Name:

Target Type:

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

Ligand 3-letter code: MPD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VWC

Chain ID: A

ChEMBL ID:

UniProt ID: D0EWJ0

Base Structure: X-ray

Registration Date: 2025-10-12

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1380550.674519
FMO2-HF: Nuclear repulsion	1324273.870749
FMO2-HF: Total energy	-56276.80377
FMO2-MP2: Total energy	-56443.835155

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-174.581	-169.154	12.591	-9.131	-8.885	-0.105

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.757 / q_NPA : 0.865

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	4	LYS	1	0.897	0.952	3.655	26.128	27.635	-0.002	-0.696	-0.809	-0.001
55	A	56	TYR	0	-0.039	-0.028	2.405	-13.571	-10.782	1.718	-2.050	-2.457	-0.022
85	A	86	ILE	0	0.031	-0.001	4.520	-4.937	-4.816	-0.001	-0.009	-0.111	0.000
86	A	87	VAL	0	0.022	0.027	4.122	2.117	2.785	0.000	-0.357	-0.310	-0.001
87	A	88	THR	0	-0.007	-0.013	1.849	-58.050	-58.120	10.840	-6.135	-4.634	-0.080
88	A	89	HIS	0	0.017	0.026	3.030	11.582	11.883	0.037	0.146	-0.484	-0.001
97	A	98	PHE	0	-0.004	-0.004	4.791	-2.836	-2.725	-0.001	-0.030	-0.080	0.000
4	A	5	PRO	0	0.047	0.030	5.660	1.558	1.558	0.000	0.000	0.000	0.000
5	A	6	GLY	0	0.008	0.009	8.334	1.387	1.387	0.000	0.000	0.000	0.000
6	A	7	THR	0	-0.013	-0.007	11.787	0.093	0.093	0.000	0.000	0.000	0.000
7	A	8	TYR	0	-0.012	-0.038	8.224	-0.631	-0.631	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.849	-0.903	14.093	-14.781	-14.781	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.032	-0.014	12.842	-1.330	-1.330	0.000	0.000	0.000	0.000
10	A	11	THR	0	0.025	0.018	15.114	0.817	0.817	0.000	0.000	0.000	0.000
11	A	12	SER	0	0.032	0.018	15.326	-1.677	-1.677	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.877	0.937	14.470	20.001	20.001	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.080	-0.012	17.472	0.555	0.555	0.000	0.000	0.000	0.000
14	A	15	ASN	0	0.033	-0.007	20.592	0.085	0.085	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.018	0.007	20.253	0.525	0.525	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.032	0.035	21.017	-0.279	-0.279	0.000	0.000	0.000	0.000
17	A	18	HIS	0	0.007	-0.018	19.431	-0.795	-0.795	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.009	-0.013	16.179	0.543	0.543	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.008	-0.011	18.242	-0.689	-0.689	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.839	0.888	20.017	13.790	13.790	0.000	0.000	0.000	0.000
21	A	22	PRO	0	0.033	0.032	23.366	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.010	-0.007	26.872	-0.120	-0.120	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.043	-0.016	29.377	0.213	0.213	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.776	-0.881	25.846	-12.491	-12.491	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.842	-0.891	30.769	-9.538	-9.538	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.957	0.950	31.362	9.034	9.034	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.059	-0.038	31.866	-0.049	-0.049	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.015	-0.006	28.654	-0.217	-0.217	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.020	0.013	28.153	-0.255	-0.255	0.000	0.000	0.000	0.000
30	A	31	PRO	0	0.046	0.017	23.683	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.809	0.937	24.155	11.305	11.305	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.916	0.963	22.873	10.783	10.783	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.022	0.021	17.366	0.205	0.205	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.847	0.922	20.779	12.091	12.091	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.044	0.034	20.293	-0.815	-0.815	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.066	-0.037	22.119	0.691	0.691	0.000	0.000	0.000	0.000
37	A	38	PRO	0	0.068	0.036	24.661	-0.182	-0.182	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.888	-0.954	24.886	-12.940	-12.940	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.962	-0.969	27.766	-9.992	-9.992	0.000	0.000	0.000	0.000
40	A	41	ASN	0	-0.034	-0.030	28.692	0.066	0.066	0.000	0.000	0.000	0.000
41	A	42	ASN	0	0.055	0.036	23.559	-0.035	-0.035	0.000	0.000	0.000	0.000
42	A	43	SER	0	0.023	0.020	23.816	-0.443	-0.443	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.017	-0.020	23.764	0.146	0.146	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.058	-0.048	19.856	-0.508	-0.508	0.000	0.000	0.000	0.000
45	A	46	SER	0	0.032	0.021	17.799	-0.466	-0.466	0.000	0.000	0.000	0.000
46	A	47	TRP	0	-0.045	-0.036	13.696	0.085	0.085	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.001	0.004	13.843	-0.472	-0.472	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.043	-0.022	7.488	-0.523	-0.523	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.852	-0.929	10.077	-22.554	-22.554	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.831	0.900	5.185	37.880	37.880	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.846	-0.938	8.369	-20.275	-20.275	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.855	-0.926	9.814	-23.271	-23.271	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.961	-0.979	6.616	-35.931	-35.931	0.000	0.000	0.000	0.000
54	A	55	ALA	0	-0.039	-0.010	5.817	-6.265	-6.265	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.030	0.031	7.548	1.709	1.709	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.027	-0.006	7.939	-0.749	-0.749	0.000	0.000	0.000	0.000
58	A	59	TYR	0	0.023	0.004	11.897	2.010	2.010	0.000	0.000	0.000	0.000
59	A	60	CYS	0	0.013	0.031	15.460	0.171	0.171	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.869	0.926	18.123	13.509	13.509	0.000	0.000	0.000	0.000
61	A	62	GLY	0	-0.006	-0.003	20.026	0.629	0.629	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.004	0.017	20.192	0.021	0.021	0.000	0.000	0.000	0.000
63	A	64	PRO	0	0.003	0.015	16.188	-0.709	-0.709	0.000	0.000	0.000	0.000
64	A	65	VAL	0	-0.024	-0.022	13.962	0.988	0.988	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.029	0.016	15.199	-1.209	-1.209	0.000	0.000	0.000	0.000
66	A	67	PRO	0	-0.009	0.004	16.138	0.503	0.503	0.000	0.000	0.000	0.000
67	A	68	GLN	0	0.008	-0.008	18.711	0.369	0.369	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.943	-0.977	22.470	-11.280	-11.280	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.038	0.032	21.120	0.297	0.297	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.837	0.930	20.895	12.394	12.394	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.045	0.029	15.480	-0.141	-0.141	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.002	-0.001	19.142	0.967	0.967	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.043	0.019	19.046	-0.937	-0.937	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.751	-0.886	20.003	-12.851	-12.851	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.042	-0.026	21.917	-0.103	-0.103	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.049	-0.013	24.977	0.445	0.445	0.000	0.000	0.000	0.000
77	A	78	GLY	0	-0.028	-0.014	22.871	0.262	0.262	0.000	0.000	0.000	0.000
78	A	79	ASN	0	-0.044	-0.033	23.012	-0.506	-0.506	0.000	0.000	0.000	0.000
79	A	80	MET	0	-0.043	0.000	20.780	0.108	0.108	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.873	-0.946	19.761	-15.231	-15.231	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.847	-0.898	16.149	-17.573	-17.573	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.847	0.925	14.726	14.554	14.554	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.834	0.949	10.690	22.646	22.646	0.000	0.000	0.000	0.000
84	A	85	TRP	0	-0.020	-0.013	8.661	0.424	0.424	0.000	0.000	0.000	0.000
89	A	90	GLN	0	-0.001	0.000	5.480	2.922	2.922	0.000	0.000	0.000	0.000
90	A	91	PRO	0	0.062	0.033	7.701	3.168	3.168	0.000	0.000	0.000	0.000
91	A	92	GLN	0	-0.021	-0.012	10.735	1.372	1.372	0.000	0.000	0.000	0.000
92	A	93	HIS	0	-0.002	-0.009	12.539	1.749	1.749	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.010	-0.007	13.080	1.354	1.354	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.936	-0.959	11.419	-22.794	-22.794	0.000	0.000	0.000	0.000
95	A	96	ASN	0	0.003	0.003	9.910	-4.019	-4.019	0.000	0.000	0.000	0.000
96	A	97	VAL	0	-0.016	-0.006	10.656	0.717	0.717	0.000	0.000	0.000	0.000
98	A	99	THR	0	0.020	0.023	6.827	2.570	2.570	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.014	-0.008	6.308	-6.773	-6.773	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.025	0.010	7.547	4.089	4.089	0.000	0.000	0.000	0.000
101	A	102	ASN	0	0.014	0.003	8.971	-2.022	-2.022	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.039	-0.037	9.577	-0.047	-0.047	0.000	0.000	0.000	0.000
103	A	104	SER	0	-0.048	-0.048	11.233	0.029	0.029	0.000	0.000	0.000	0.000
104	A	105	THR	0	-0.005	-0.013	15.018	0.931	0.931	0.000	0.000	0.000	0.000
105	A	106	GLU	-1	-0.953	-0.966	12.827	-19.357	-19.357	0.000	0.000	0.000	0.000
106	A	107	HIS	0	-0.085	-0.038	13.717	0.713	0.713	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.040	0.002	12.090	-1.533	-1.533	0.000	0.000	0.000	0.000
108	A	109	TRP	0	-0.031	-0.021	12.099	1.554	1.554	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.010	-0.015	14.010	-0.424	-0.424	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.004	0.004	16.884	0.685	0.685	0.000	0.000	0.000	0.000
111	A	112	PRO	0	-0.004	-0.013	19.445	-0.154	-0.154	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.016	-0.012	22.579	-0.072	-0.072	0.000	0.000	0.000	0.000
113	A	114	ASP	-1	-0.935	-0.967	23.821	-11.471	-11.471	0.000	0.000	0.000	0.000
114	A	115	ALA	0	-0.074	-0.022	23.709	0.309	0.309	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.898	-0.947	25.706	-9.972	-9.972	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.877	-0.960	26.366	-11.497	-11.497	0.000	0.000	0.000	0.000
117	A	118	LEU	0	-0.076	-0.043	26.214	0.351	0.351	0.000	0.000	0.000	0.000
118	A	119	GLN	0	0.033	0.038	24.832	0.282	0.282	0.000	0.000	0.000	0.000
119	A	120	GLN	0	-0.125	-0.088	22.257	0.174	0.174	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.011	0.001	16.364	0.115	0.115	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.818	-0.914	19.278	-13.190	-13.190	0.000	0.000	0.000	0.000
122	A	123	VAL	0	-0.032	-0.022	15.532	-1.117	-1.117	0.000	0.000	0.000	0.000
123	A	124	ARG	1	0.875	0.926	16.670	15.471	15.471	0.000	0.000	0.000	0.000
124	A	125	PRO	0	0.027	0.013	15.951	-1.337	-1.337	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.034	0.009	11.011	0.306	0.306	0.000	0.000	0.000	0.000
126	A	127	ILE	0	-0.040	-0.025	15.178	0.628	0.628	0.000	0.000	0.000	0.000
127	A	128	ALA	0	0.013	-0.010	14.624	-0.733	-0.733	0.000	0.000	0.000	0.000
128	A	129	ALA	0	-0.014	0.001	16.782	0.916	0.916	0.000	0.000	0.000	0.000
129	A	130	PRO	0	0.009	0.005	17.942	-0.959	-0.959	0.000	0.000	0.000	0.000
130	A	131	SER	0	-0.074	-0.060	17.450	0.766	0.766	0.000	0.000	0.000	0.000
131	A	132	TYR	0	-0.019	0.001	14.950	-0.852	-0.852	0.000	0.000	0.000	0.000
132	A	133	PRO	0	0.026	0.001	12.840	0.748	0.748	0.000	0.000	0.000	0.000
133	A	134	PRO	0	0.065	0.044	12.642	1.074	1.074	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.823	0.913	14.059	16.792	16.792	0.000	0.000	0.000	0.000
135	A	136	TYR	0	0.051	0.031	10.575	-0.014	-0.014	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.003	0.009	15.112	0.628	0.628	0.000	0.000	0.000	0.000
137	A	138	ALA	0	0.011	-0.015	16.166	-0.975	-0.975	0.000	0.000	0.000	0.000
138	A	139	THR	0	0.050	0.012	17.133	-0.178	-0.178	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.858	-0.918	13.465	-19.369	-19.369	0.000	0.000	0.000	0.000
140	A	141	LEU	0	-0.070	-0.021	11.066	-2.252	-2.252	0.000	0.000	0.000	0.000
141	A	142	PHE	0	0.013	0.000	11.013	1.859	1.859	0.000	0.000	0.000	0.000
142	A	143	THR	0	-0.017	-0.012	11.069	-2.548	-2.548	0.000	0.000	0.000	0.000
143	A	144	PHE	0	-0.019	0.003	9.606	0.531	0.531	0.000	0.000	0.000	0.000
144	A	145	THR	0	0.014	-0.001	11.704	-1.226	-1.226	0.000	0.000	0.000	0.000
145	A	146	GLN	0	-0.017	0.003	11.927	-1.098	-1.098	0.000	0.000	0.000	0.000
146	A	147	VAL	-1	-0.918	-0.953	14.030	-16.831	-16.831	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)