FMO DATABASE

FMODB ID: K9LY3

Calculation Name: 3MJG-A-Xray372

Preferred Name: Platelet-derived growth factor subunit B

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJG

Chain ID: A

ChEMBL ID: CHEMBL3108633

UniProt ID: P01127

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-626083.706107
FMO2-HF: Nuclear repulsion	585411.442352
FMO2-HF: Total energy	-40672.263755
FMO2-MP2: Total energy	-40784.999413

3D Structure

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:6:THR)

Summations of interaction energy for fragment #1(A:6:THR)

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.
0.687	2.552	0.073	-0.748	-1.191	-0.002

Interaction energy analysis for fragmet #1(A:6:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / 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	8	ALA	0	-0.028	-0.008	3.329	-0.651	1.124	0.074	-0.741	-1.109	-0.002
4	A	9	GLU	-1	-0.906	-0.959	4.510	1.235	1.325	-0.001	-0.007	-0.082	0.000
5	A	10	PRO	0	-0.038	-0.013	7.184	-0.151	-0.151	0.000	0.000	0.000	0.000
6	A	11	ALA	0	0.009	0.003	10.574	0.083	0.083	0.000	0.000	0.000	0.000
7	A	12	MET	0	0.000	0.000	11.800	0.046	0.046	0.000	0.000	0.000	0.000
8	A	13	ILE	0	-0.002	0.007	14.694	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	14	ALA	0	0.004	0.009	17.869	0.038	0.038	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.892	-0.969	19.162	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	16	CYS	0	-0.026	0.010	22.396	0.011	0.011	0.000	0.000	0.000	0.000
12	A	17	LYS	1	0.963	0.975	20.997	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	18	THR	0	-0.011	-0.010	26.510	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	19	ARG	1	0.802	0.883	20.326	0.025	0.025	0.000	0.000	0.000	0.000
15	A	20	THR	0	0.036	0.017	24.485	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	21	GLU	-1	-0.943	-0.959	24.309	-0.050	-0.050	0.000	0.000	0.000	0.000
17	A	22	VAL	0	0.007	-0.006	25.993	0.010	0.010	0.000	0.000	0.000	0.000
18	A	23	PHE	0	-0.014	-0.004	28.459	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	24	GLU	-1	-0.901	-0.963	32.052	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	25	ILE	0	-0.026	-0.003	33.978	0.000	0.000	0.000	0.000	0.000	0.000
21	A	26	SER	0	0.020	-0.017	37.501	0.000	0.000	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.996	0.976	39.174	0.027	0.027	0.000	0.000	0.000	0.000
23	A	28	ARG	1	0.963	0.996	41.772	0.035	0.035	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.042	-0.011	39.240	0.000	0.000	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.027	0.000	42.703	0.003	0.003	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.843	-0.895	45.783	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	32	ARG	1	0.909	0.954	44.535	0.033	0.033	0.000	0.000	0.000	0.000
28	A	33	THR	0	-0.053	-0.061	48.394	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	34	ASN	0	0.068	0.055	50.626	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	35	ALA	0	-0.008	-0.019	46.817	0.000	0.000	0.000	0.000	0.000	0.000
31	A	36	ASN	0	-0.020	-0.015	47.848	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	37	PHE	0	-0.056	-0.051	44.949	0.003	0.003	0.000	0.000	0.000	0.000
33	A	38	LEU	0	-0.015	0.005	41.881	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.018	0.013	39.634	0.002	0.002	0.000	0.000	0.000	0.000
35	A	40	TRP	0	-0.002	0.035	35.605	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	41	PRO	0	0.035	0.001	35.314	0.002	0.002	0.000	0.000	0.000	0.000
37	A	42	PRO	0	0.054	0.004	33.750	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	43	CYS	0	-0.036	-0.010	31.372	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	44	VAL	0	-0.033	-0.008	32.434	0.007	0.007	0.000	0.000	0.000	0.000
40	A	45	GLU	-1	-0.878	-0.940	26.585	0.046	0.046	0.000	0.000	0.000	0.000
41	A	46	VAL	0	-0.057	-0.018	29.581	0.000	0.000	0.000	0.000	0.000	0.000
42	A	47	GLN	0	0.011	0.021	27.250	0.000	0.000	0.000	0.000	0.000	0.000
43	A	48	ARG	1	0.917	0.946	28.411	0.014	0.014	0.000	0.000	0.000	0.000
44	A	49	CYS	0	-0.053	-0.010	27.670	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	50	SER	0	0.062	0.057	24.244	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.036	0.016	22.277	0.014	0.014	0.000	0.000	0.000	0.000
47	A	52	CYS	0	-0.074	-0.038	22.264	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	53	CYS	0	-0.016	0.007	24.237	0.010	0.010	0.000	0.000	0.000	0.000
49	A	54	ASN	0	0.038	0.016	25.161	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	55	ASN	0	-0.005	0.006	26.160	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	56	ARG	1	1.015	0.997	26.519	0.146	0.146	0.000	0.000	0.000	0.000
52	A	57	ASN	0	-0.013	-0.002	30.889	0.007	0.007	0.000	0.000	0.000	0.000
53	A	58	VAL	0	0.020	0.012	29.838	0.009	0.009	0.000	0.000	0.000	0.000
54	A	59	GLN	0	0.022	0.012	30.449	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.884	0.947	29.978	0.047	0.047	0.000	0.000	0.000	0.000
56	A	62	PRO	0	0.036	-0.001	33.128	0.005	0.005	0.000	0.000	0.000	0.000
57	A	63	THR	0	-0.038	-0.030	34.474	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	64	GLN	0	-0.014	-0.019	36.215	0.006	0.006	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.042	0.038	36.464	0.002	0.002	0.000	0.000	0.000	0.000
60	A	66	GLN	0	-0.009	-0.004	37.897	0.001	0.001	0.000	0.000	0.000	0.000
61	A	67	LEU	0	0.012	0.016	38.815	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.974	0.984	35.411	-0.023	-0.023	0.000	0.000	0.000	0.000
63	A	69	PRO	0	-0.033	0.005	41.484	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	70	VAL	0	0.041	0.016	38.600	0.004	0.004	0.000	0.000	0.000	0.000
65	A	71	GLN	0	-0.006	-0.018	41.908	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	72	VAL	0	0.023	0.019	40.311	0.002	0.002	0.000	0.000	0.000	0.000
67	A	73	ARG	1	0.910	0.930	42.448	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	74	LYS	1	0.945	0.994	43.785	0.007	0.007	0.000	0.000	0.000	0.000
69	A	75	ILE	0	-0.035	-0.039	43.195	0.002	0.002	0.000	0.000	0.000	0.000
70	A	76	GLU	-1	-0.849	-0.925	47.042	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	77	ILE	0	-0.020	-0.013	48.445	0.003	0.003	0.000	0.000	0.000	0.000
72	A	78	VAL	0	0.025	-0.003	51.140	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	79	ARG	1	1.055	1.033	54.694	0.004	0.004	0.000	0.000	0.000	0.000
74	A	80	LYS	1	0.971	1.005	49.974	0.000	0.000	0.000	0.000	0.000	0.000
75	A	81	LYS	1	0.924	0.952	51.408	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	82	PRO	0	0.019	0.005	48.286	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	83	ILE	0	-0.008	-0.007	50.710	0.002	0.002	0.000	0.000	0.000	0.000
78	A	84	PHE	0	-0.031	-0.010	45.541	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	85	LYS	1	0.973	0.994	48.769	0.002	0.002	0.000	0.000	0.000	0.000
80	A	86	LYS	1	0.938	0.975	47.540	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	87	ALA	0	0.024	0.014	46.055	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	88	THR	0	-0.010	0.008	45.134	0.003	0.003	0.000	0.000	0.000	0.000
83	A	89	VAL	0	-0.016	0.005	40.250	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	90	THR	0	0.018	-0.010	41.684	0.004	0.004	0.000	0.000	0.000	0.000
85	A	91	LEU	0	-0.006	0.012	35.671	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	92	GLU	-1	-0.899	-0.954	36.382	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.844	-0.922	33.933	0.020	0.020	0.000	0.000	0.000	0.000
88	A	94	HIS	0	-0.027	-0.022	31.830	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	95	LEU	0	0.000	-0.014	32.616	0.004	0.004	0.000	0.000	0.000	0.000
90	A	96	ALA	0	0.011	0.004	31.968	0.006	0.006	0.000	0.000	0.000	0.000
91	A	98	LYS	1	0.968	0.995	31.030	0.017	0.017	0.000	0.000	0.000	0.000
92	A	100	GLU	-1	-0.921	-0.974	31.084	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	101	THR	0	0.036	0.010	34.309	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	102	VAL	0	-0.041	-0.024	34.688	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:THR)