FMO DATABASE

FMODB ID: KV633

Calculation Name: 5VT2-A-Xray547

Preferred Name: Growth/differentiation factor 15

Target Type: SINGLE PROTEIN

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5VT2

Chain ID: A

ChEMBL ID: CHEMBL3120039

UniProt ID: Q99988

Base Structure: X-ray

Registration Date: 2025-10-06

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-719511.098839
FMO2-HF: Nuclear repulsion	675384.689286
FMO2-HF: Total energy	-44126.409553
FMO2-MP2: Total energy	-44246.248518

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:5:ASP)

Summations of interaction energy for fragment #1(A:5:ASP)

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.
-2.17	2.779	1.521	-3.123	-3.348	-0.022

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.028

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	7	CYS	0	-0.073	0.003	3.373	-12.957	-10.885	0.020	-1.255	-0.837	0.002
47	A	52	PHE	0	-0.040	-0.017	2.665	-10.255	-8.212	1.167	-1.537	-1.674	-0.021
48	A	53	ARG	1	0.869	0.920	2.859	15.577	16.356	0.335	-0.329	-0.785	-0.003
49	A	54	ALA	0	0.022	0.020	5.194	2.233	2.288	-0.001	-0.002	-0.052	0.000
4	A	8	PRO	0	-0.001	-0.005	5.729	3.176	3.176	0.000	0.000	0.000	0.000
5	A	9	LEU	0	0.029	0.000	8.648	0.951	0.951	0.000	0.000	0.000	0.000
6	A	10	GLY	0	0.039	0.028	9.792	0.610	0.610	0.000	0.000	0.000	0.000
7	A	11	PRO	0	0.032	-0.014	8.277	-1.426	-1.426	0.000	0.000	0.000	0.000
8	A	12	GLY	0	0.022	0.011	7.654	0.282	0.282	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.924	0.973	8.892	2.580	2.580	0.000	0.000	0.000	0.000
10	A	15	CYS	0	-0.086	-0.024	6.990	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	16	ARG	1	0.890	0.931	6.071	1.013	1.013	0.000	0.000	0.000	0.000
12	A	17	LEU	0	0.057	0.025	8.112	0.900	0.900	0.000	0.000	0.000	0.000
13	A	18	HIS	0	-0.089	-0.041	11.244	0.494	0.494	0.000	0.000	0.000	0.000
14	A	19	THR	0	0.017	-0.007	14.310	0.138	0.138	0.000	0.000	0.000	0.000
15	A	20	VAL	0	-0.021	-0.010	17.888	0.038	0.038	0.000	0.000	0.000	0.000
16	A	21	ARG	1	0.819	0.905	21.030	0.689	0.689	0.000	0.000	0.000	0.000
17	A	22	ALA	0	0.010	0.009	24.490	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	23	SER	0	-0.025	-0.041	26.817	0.058	0.058	0.000	0.000	0.000	0.000
19	A	24	LEU	0	0.026	-0.002	30.178	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.923	-0.945	32.430	-0.569	-0.569	0.000	0.000	0.000	0.000
21	A	26	ASP	-1	-0.857	-0.908	28.843	-0.816	-0.816	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.048	-0.028	26.190	-0.071	-0.071	0.000	0.000	0.000	0.000
23	A	28	GLY	0	-0.009	0.017	29.791	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	29	TRP	0	-0.006	-0.041	26.985	0.014	0.014	0.000	0.000	0.000	0.000
25	A	30	ALA	0	0.010	0.012	33.964	0.032	0.032	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.922	-0.944	36.990	-0.479	-0.479	0.000	0.000	0.000	0.000
27	A	32	TRP	0	-0.050	-0.029	31.547	0.036	0.036	0.000	0.000	0.000	0.000
28	A	33	VAL	0	-0.013	0.004	32.175	0.014	0.014	0.000	0.000	0.000	0.000
29	A	34	LEU	0	-0.038	-0.024	35.500	0.018	0.018	0.000	0.000	0.000	0.000
30	A	35	SER	0	-0.066	-0.031	34.483	0.016	0.016	0.000	0.000	0.000	0.000
31	A	36	PRO	0	0.062	0.038	29.030	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.966	0.959	32.030	0.368	0.368	0.000	0.000	0.000	0.000
33	A	38	GLU	-1	-0.859	-0.898	27.806	-0.601	-0.601	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.019	0.009	24.331	0.025	0.025	0.000	0.000	0.000	0.000
35	A	40	GLN	0	0.018	-0.003	22.009	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	41	VAL	0	0.054	0.024	20.344	-0.043	-0.043	0.000	0.000	0.000	0.000
37	A	42	THR	0	-0.040	-0.027	16.261	-0.070	-0.070	0.000	0.000	0.000	0.000
38	A	43	MET	0	0.039	0.017	16.084	-0.050	-0.050	0.000	0.000	0.000	0.000
39	A	44	CYS	0	-0.039	0.013	8.508	0.174	0.174	0.000	0.000	0.000	0.000
40	A	45	ILE	0	0.056	0.022	11.816	0.269	0.269	0.000	0.000	0.000	0.000
41	A	46	GLY	0	0.031	0.016	10.075	-0.683	-0.683	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.003	0.002	10.619	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	48	CYS	0	-0.003	0.008	8.421	-1.412	-1.412	0.000	0.000	0.000	0.000
44	A	49	PRO	0	0.020	0.021	7.322	1.056	1.056	0.000	0.000	0.000	0.000
45	A	50	SER	0	0.045	0.002	8.375	-1.135	-1.135	0.000	0.000	0.000	0.000
46	A	51	GLN	0	-0.016	-0.016	7.338	-0.088	-0.088	0.000	0.000	0.000	0.000
50	A	55	ALA	0	0.037	0.022	8.924	0.332	0.332	0.000	0.000	0.000	0.000
51	A	56	ASN	0	0.017	0.000	10.772	0.749	0.749	0.000	0.000	0.000	0.000
52	A	57	MET	0	0.070	0.024	13.690	-0.303	-0.303	0.000	0.000	0.000	0.000
53	A	58	HIS	0	0.043	0.028	16.181	0.099	0.099	0.000	0.000	0.000	0.000
54	A	59	ALA	0	0.060	0.043	12.214	0.035	0.035	0.000	0.000	0.000	0.000
55	A	60	GLN	0	-0.003	-0.001	12.514	-0.328	-0.328	0.000	0.000	0.000	0.000
56	A	61	ILE	0	0.024	0.017	14.297	0.192	0.192	0.000	0.000	0.000	0.000
57	A	62	LYS	1	0.850	0.917	16.069	3.258	3.258	0.000	0.000	0.000	0.000
58	A	63	THR	0	-0.063	-0.041	12.403	-0.146	-0.146	0.000	0.000	0.000	0.000
59	A	64	SER	0	-0.094	-0.059	15.012	0.201	0.201	0.000	0.000	0.000	0.000
60	A	65	LEU	0	0.012	-0.002	17.877	0.205	0.205	0.000	0.000	0.000	0.000
61	A	66	HIS	0	-0.037	-0.009	16.847	0.006	0.006	0.000	0.000	0.000	0.000
62	A	67	ARG	1	0.924	0.956	14.490	2.325	2.325	0.000	0.000	0.000	0.000
63	A	68	LEU	0	-0.045	-0.021	19.584	0.164	0.164	0.000	0.000	0.000	0.000
64	A	69	LYS	1	0.940	0.977	22.754	1.195	1.195	0.000	0.000	0.000	0.000
65	A	70	PRO	0	0.004	0.015	21.145	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	71	ASP	-1	-0.860	-0.920	22.588	-1.299	-1.299	0.000	0.000	0.000	0.000
67	A	72	THR	0	-0.058	-0.038	25.621	0.041	0.041	0.000	0.000	0.000	0.000
68	A	73	VAL	0	-0.014	-0.011	20.682	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	74	PRO	0	0.010	0.023	19.138	-0.085	-0.085	0.000	0.000	0.000	0.000
70	A	75	ALA	0	0.050	0.012	14.419	-0.041	-0.041	0.000	0.000	0.000	0.000
71	A	76	PRO	0	-0.076	-0.044	11.759	0.188	0.188	0.000	0.000	0.000	0.000
72	A	77	CYS	0	0.003	-0.004	13.533	-0.200	-0.200	0.000	0.000	0.000	0.000
73	A	79	VAL	0	0.035	0.017	11.788	0.683	0.683	0.000	0.000	0.000	0.000
74	A	80	PRO	0	0.065	-0.003	11.893	-0.879	-0.879	0.000	0.000	0.000	0.000
75	A	81	ALA	0	-0.110	-0.032	10.372	0.055	0.055	0.000	0.000	0.000	0.000
76	A	82	SER	0	-0.013	-0.041	12.463	0.701	0.701	0.000	0.000	0.000	0.000
77	A	83	TYR	0	0.059	0.013	14.984	-0.353	-0.353	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.053	-0.036	16.963	0.237	0.237	0.000	0.000	0.000	0.000
79	A	85	PRO	0	0.030	0.033	20.005	-0.049	-0.049	0.000	0.000	0.000	0.000
80	A	86	MET	0	-0.037	-0.010	23.845	0.048	0.048	0.000	0.000	0.000	0.000
81	A	87	VAL	0	-0.010	-0.012	25.670	0.021	0.021	0.000	0.000	0.000	0.000
82	A	88	LEU	0	-0.003	0.005	28.885	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	89	ILE	0	-0.026	-0.013	31.864	0.036	0.036	0.000	0.000	0.000	0.000
84	A	90	GLN	0	0.079	0.049	33.737	-0.046	-0.046	0.000	0.000	0.000	0.000
85	A	91	LYS	1	0.840	0.907	37.256	0.370	0.370	0.000	0.000	0.000	0.000
86	A	92	THR	0	0.000	-0.008	40.445	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.817	-0.906	42.928	-0.339	-0.339	0.000	0.000	0.000	0.000
88	A	94	THR	0	-0.057	-0.026	46.222	0.006	0.006	0.000	0.000	0.000	0.000
89	A	95	GLY	0	-0.043	-0.024	45.845	0.018	0.018	0.000	0.000	0.000	0.000
90	A	96	VAL	0	0.005	0.010	40.605	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.026	0.002	37.175	0.016	0.016	0.000	0.000	0.000	0.000
92	A	98	LEU	0	0.014	0.005	34.479	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	99	GLN	0	-0.001	-0.005	32.989	0.003	0.003	0.000	0.000	0.000	0.000
94	A	100	THR	0	0.008	-0.004	27.297	0.006	0.006	0.000	0.000	0.000	0.000
95	A	101	TYR	0	-0.034	-0.026	26.462	0.004	0.004	0.000	0.000	0.000	0.000
96	A	102	ASP	-1	-0.900	-0.956	23.149	-0.808	-0.808	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.928	-0.975	21.805	-1.205	-1.205	0.000	0.000	0.000	0.000
98	A	104	LEU	0	-0.025	0.003	22.497	-0.103	-0.103	0.000	0.000	0.000	0.000
99	A	105	LEU	0	0.023	0.008	20.231	-0.070	-0.070	0.000	0.000	0.000	0.000
100	A	106	ALA	0	-0.002	0.008	14.844	-0.037	-0.037	0.000	0.000	0.000	0.000
101	A	107	LYS	1	0.859	0.962	13.398	1.605	1.605	0.000	0.000	0.000	0.000
102	A	108	ASP	-1	-0.837	-0.907	9.352	-2.888	-2.888	0.000	0.000	0.000	0.000
103	A	110	HIS	0	-0.043	-0.027	7.473	-2.138	-2.138	0.000	0.000	0.000	0.000
104	A	112	ILE	-1	-0.761	-0.850	10.069	-3.498	-3.498	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)