FMO DATABASE

FMODB ID: 66VLZ

Calculation Name: 3MJK-E-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3MJK

Chain ID: E

ChEMBL ID: CHEMBL3137294

UniProt ID: P04085

Base Structure: X-ray

Registration Date: 2023-06-19

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

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864674.798074
FMO2-HF: Nuclear repulsion	814664.021145
FMO2-HF: Total energy	-50010.776929
FMO2-MP2: Total energy	-50152.508492

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(E:23:ALA)

Summations of interaction energy for fragment #1(E:23: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.
0.527	1.611	-0.011	-0.536	-0.537	0.002

Interaction energy analysis for fragmet #1(E:23:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.021

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	E	25	ILE	0	-0.017	-0.011	3.868	0.523	1.607	-0.011	-0.536	-0.537	0.002
4	E	26	PRO	0	0.043	0.026	6.730	0.057	0.057	0.000	0.000	0.000	0.000
5	E	27	ARG	1	0.928	0.917	9.138	-0.445	-0.445	0.000	0.000	0.000	0.000
6	E	28	GLU	-1	-0.826	-0.898	12.424	0.260	0.260	0.000	0.000	0.000	0.000
7	E	29	VAL	0	0.069	0.043	10.628	-0.068	-0.068	0.000	0.000	0.000	0.000
8	E	30	ILE	0	-0.008	0.000	10.278	-0.067	-0.067	0.000	0.000	0.000	0.000
9	E	31	GLU	-1	-0.833	-0.921	13.887	0.137	0.137	0.000	0.000	0.000	0.000
10	E	32	ARG	1	0.815	0.898	14.444	-0.218	-0.218	0.000	0.000	0.000	0.000
11	E	33	LEU	0	0.034	0.026	13.483	-0.017	-0.017	0.000	0.000	0.000	0.000
12	E	34	ALA	0	-0.058	-0.022	17.506	-0.011	-0.011	0.000	0.000	0.000	0.000
13	E	35	ARG	1	0.864	0.949	19.158	-0.100	-0.100	0.000	0.000	0.000	0.000
14	E	36	SER	0	0.002	-0.004	20.169	0.013	0.013	0.000	0.000	0.000	0.000
15	E	37	GLN	0	-0.022	-0.023	22.330	-0.013	-0.013	0.000	0.000	0.000	0.000
16	E	38	ILE	0	0.007	0.016	18.656	0.007	0.007	0.000	0.000	0.000	0.000
17	E	39	HIS	1	0.778	0.857	22.932	0.011	0.011	0.000	0.000	0.000	0.000
18	E	40	SER	0	0.049	0.031	23.300	0.001	0.001	0.000	0.000	0.000	0.000
19	E	41	ILE	0	0.037	0.015	17.995	0.002	0.002	0.000	0.000	0.000	0.000
20	E	42	ARG	1	0.967	0.989	19.305	0.002	0.002	0.000	0.000	0.000	0.000
21	E	43	ASP	-1	-0.781	-0.877	21.035	0.007	0.007	0.000	0.000	0.000	0.000
22	E	44	LEU	0	0.027	0.011	15.111	0.012	0.012	0.000	0.000	0.000	0.000
23	E	45	GLN	0	0.000	-0.007	16.204	0.020	0.020	0.000	0.000	0.000	0.000
24	E	46	ARG	1	0.888	0.936	17.083	0.002	0.002	0.000	0.000	0.000	0.000
25	E	47	LEU	0	-0.023	-0.013	18.755	0.017	0.017	0.000	0.000	0.000	0.000
26	E	48	LEU	0	-0.070	-0.019	11.899	0.016	0.016	0.000	0.000	0.000	0.000
27	E	49	GLU	-1	-0.867	-0.930	14.102	0.277	0.277	0.000	0.000	0.000	0.000
28	E	50	ILE	0	-0.123	-0.046	13.439	-0.026	-0.026	0.000	0.000	0.000	0.000
29	E	87	SER	0	-0.009	-0.028	28.182	0.001	0.001	0.000	0.000	0.000	0.000
30	E	88	ILE	0	-0.017	0.010	24.488	0.001	0.001	0.000	0.000	0.000	0.000
31	E	89	GLU	-1	-0.946	-0.969	27.411	-0.069	-0.069	0.000	0.000	0.000	0.000
32	E	90	GLU	-1	-0.839	-0.925	22.892	-0.075	-0.075	0.000	0.000	0.000	0.000
33	E	91	ALA	0	0.007	-0.006	21.706	0.004	0.004	0.000	0.000	0.000	0.000
34	E	92	VAL	0	0.016	0.013	23.274	-0.003	-0.003	0.000	0.000	0.000	0.000
35	E	93	PRO	0	0.015	0.019	22.837	-0.006	-0.006	0.000	0.000	0.000	0.000
36	E	94	ALA	0	0.028	0.008	24.492	0.011	0.011	0.000	0.000	0.000	0.000
37	E	95	VAL	0	-0.005	-0.008	26.169	-0.004	-0.004	0.000	0.000	0.000	0.000
38	E	96	CYS	0	-0.001	0.017	24.358	0.015	0.015	0.000	0.000	0.000	0.000
39	E	97	LYS	1	0.959	0.979	28.373	0.050	0.050	0.000	0.000	0.000	0.000
40	E	98	THR	0	0.040	0.008	32.216	-0.006	-0.006	0.000	0.000	0.000	0.000
41	E	99	ARG	1	0.789	0.881	29.666	0.065	0.065	0.000	0.000	0.000	0.000
42	E	100	THR	0	-0.026	-0.016	35.861	0.001	0.001	0.000	0.000	0.000	0.000
43	E	101	VAL	0	-0.015	0.012	33.525	-0.004	-0.004	0.000	0.000	0.000	0.000
44	E	102	ILE	0	0.027	0.005	36.875	0.004	0.004	0.000	0.000	0.000	0.000
45	E	103	TYR	0	-0.022	-0.007	37.873	-0.003	-0.003	0.000	0.000	0.000	0.000
46	E	104	GLU	-1	-0.904	-0.966	39.298	-0.053	-0.053	0.000	0.000	0.000	0.000
47	E	105	ILE	0	-0.036	-0.020	42.101	0.000	0.000	0.000	0.000	0.000	0.000
48	E	106	PRO	0	0.006	0.008	41.785	0.000	0.000	0.000	0.000	0.000	0.000
49	E	107	ARG	1	0.941	0.957	44.138	0.041	0.041	0.000	0.000	0.000	0.000
50	E	108	SER	0	0.030	0.006	44.036	0.002	0.002	0.000	0.000	0.000	0.000
51	E	109	GLN	0	0.007	-0.005	42.753	0.002	0.002	0.000	0.000	0.000	0.000
52	E	110	VAL	0	-0.047	-0.013	47.654	0.002	0.002	0.000	0.000	0.000	0.000
53	E	111	ASP	-1	-0.800	-0.885	50.311	-0.026	-0.026	0.000	0.000	0.000	0.000
54	E	112	PRO	0	-0.003	0.002	48.930	-0.001	-0.001	0.000	0.000	0.000	0.000
55	E	113	THR	0	-0.036	-0.016	50.072	-0.001	-0.001	0.000	0.000	0.000	0.000
56	E	114	SER	0	-0.073	-0.052	52.351	0.000	0.000	0.000	0.000	0.000	0.000
57	E	115	ALA	0	0.050	0.009	49.873	-0.001	-0.001	0.000	0.000	0.000	0.000
58	E	116	ASN	0	-0.029	0.002	51.596	-0.001	-0.001	0.000	0.000	0.000	0.000
59	E	117	PHE	0	-0.048	-0.030	50.903	0.002	0.002	0.000	0.000	0.000	0.000
60	E	118	LEU	0	0.021	0.011	51.155	-0.002	-0.002	0.000	0.000	0.000	0.000
61	E	119	ILE	0	0.016	0.006	48.270	0.001	0.001	0.000	0.000	0.000	0.000
62	E	120	TRP	0	-0.001	0.018	50.988	-0.001	-0.001	0.000	0.000	0.000	0.000
63	E	121	PRO	0	0.058	0.022	48.761	0.002	0.002	0.000	0.000	0.000	0.000
64	E	122	PRO	0	0.017	0.004	46.749	0.000	0.000	0.000	0.000	0.000	0.000
65	E	123	CYS	0	0.006	0.002	42.863	-0.002	-0.002	0.000	0.000	0.000	0.000
66	E	124	VAL	0	-0.023	-0.004	43.613	0.002	0.002	0.000	0.000	0.000	0.000
67	E	125	GLU	-1	-0.827	-0.906	41.374	-0.042	-0.042	0.000	0.000	0.000	0.000
68	E	126	VAL	0	-0.064	-0.024	38.540	0.003	0.003	0.000	0.000	0.000	0.000
69	E	127	LYS	1	0.883	0.919	38.487	0.034	0.034	0.000	0.000	0.000	0.000
70	E	128	ARG	1	0.881	0.932	34.376	0.048	0.048	0.000	0.000	0.000	0.000
71	E	129	CYS	0	-0.056	-0.028	31.213	-0.002	-0.002	0.000	0.000	0.000	0.000
72	E	130	THR	0	0.024	0.017	29.523	-0.005	-0.005	0.000	0.000	0.000	0.000
73	E	131	GLY	0	0.005	0.008	26.750	0.006	0.006	0.000	0.000	0.000	0.000
74	E	132	CYS	0	-0.033	-0.025	21.804	-0.007	-0.007	0.000	0.000	0.000	0.000
75	E	133	CYS	0	-0.023	-0.008	22.013	0.010	0.010	0.000	0.000	0.000	0.000
76	E	134	ASN	0	-0.026	-0.022	18.887	-0.024	-0.024	0.000	0.000	0.000	0.000
77	E	135	THR	0	0.036	0.022	15.213	-0.021	-0.021	0.000	0.000	0.000	0.000
78	E	136	SER	0	0.043	0.017	15.788	0.012	0.012	0.000	0.000	0.000	0.000
79	E	137	SER	0	0.019	0.023	16.512	0.002	0.002	0.000	0.000	0.000	0.000
80	E	138	VAL	0	-0.082	-0.029	18.129	0.026	0.026	0.000	0.000	0.000	0.000
81	E	139	LYS	1	0.927	0.957	21.403	0.056	0.056	0.000	0.000	0.000	0.000
82	E	141	GLN	0	0.030	0.017	27.572	-0.007	-0.007	0.000	0.000	0.000	0.000
83	E	142	PRO	0	0.049	0.001	30.018	0.003	0.003	0.000	0.000	0.000	0.000
84	E	143	SER	0	-0.037	-0.029	33.816	0.001	0.001	0.000	0.000	0.000	0.000
85	E	144	ARG	1	0.818	0.889	35.530	0.017	0.017	0.000	0.000	0.000	0.000
86	E	145	VAL	0	0.010	0.007	37.420	-0.003	-0.003	0.000	0.000	0.000	0.000
87	E	146	HIS	0	0.007	0.003	39.883	0.003	0.003	0.000	0.000	0.000	0.000
88	E	147	HIS	0	-0.001	-0.012	40.420	0.000	0.000	0.000	0.000	0.000	0.000
89	E	148	ARG	1	0.837	0.904	45.038	0.031	0.031	0.000	0.000	0.000	0.000
90	E	149	SER	0	-0.008	-0.022	47.830	-0.002	-0.002	0.000	0.000	0.000	0.000
91	E	150	VAL	0	-0.013	0.000	48.915	0.001	0.001	0.000	0.000	0.000	0.000
92	E	151	LYS	1	0.847	0.896	51.596	0.021	0.021	0.000	0.000	0.000	0.000
93	E	152	VAL	0	0.006	0.016	49.923	-0.001	-0.001	0.000	0.000	0.000	0.000
94	E	153	ALA	0	0.029	0.012	53.385	0.001	0.001	0.000	0.000	0.000	0.000
95	E	154	LYS	1	0.832	0.932	54.013	0.026	0.026	0.000	0.000	0.000	0.000
96	E	155	VAL	0	-0.014	-0.016	55.538	0.001	0.001	0.000	0.000	0.000	0.000
97	E	156	GLU	-1	-0.755	-0.872	56.736	-0.026	-0.026	0.000	0.000	0.000	0.000
98	E	157	TYR	0	0.022	0.000	59.317	0.001	0.001	0.000	0.000	0.000	0.000
99	E	158	VAL	0	0.028	0.019	62.138	0.000	0.000	0.000	0.000	0.000	0.000
100	E	159	ARG	1	0.984	0.976	64.911	0.019	0.019	0.000	0.000	0.000	0.000
101	E	160	LYS	1	1.001	0.997	64.177	0.024	0.024	0.000	0.000	0.000	0.000
102	E	161	LYS	1	0.980	1.004	66.619	0.017	0.017	0.000	0.000	0.000	0.000
103	E	162	PRO	0	0.035	0.022	63.141	0.000	0.000	0.000	0.000	0.000	0.000
104	E	163	LYS	1	0.861	0.925	62.479	0.021	0.021	0.000	0.000	0.000	0.000
105	E	164	LEU	0	0.020	0.016	59.083	-0.001	-0.001	0.000	0.000	0.000	0.000
106	E	165	LYS	1	0.841	0.917	58.451	0.024	0.024	0.000	0.000	0.000	0.000
107	E	166	GLU	-1	-0.819	-0.886	57.473	-0.022	-0.022	0.000	0.000	0.000	0.000
108	E	167	VAL	0	-0.021	-0.007	53.124	0.001	0.001	0.000	0.000	0.000	0.000
109	E	168	GLN	0	0.044	0.027	52.540	-0.001	-0.001	0.000	0.000	0.000	0.000
110	E	169	VAL	0	0.036	0.022	47.389	0.000	0.000	0.000	0.000	0.000	0.000
111	E	170	ARG	1	0.889	0.936	46.224	0.026	0.026	0.000	0.000	0.000	0.000
112	E	171	LEU	0	-0.008	0.004	43.927	-0.002	-0.002	0.000	0.000	0.000	0.000
113	E	172	GLU	-1	-0.772	-0.872	37.299	-0.041	-0.041	0.000	0.000	0.000	0.000
114	E	173	GLU	-1	-0.795	-0.862	39.841	-0.035	-0.035	0.000	0.000	0.000	0.000
115	E	174	HIS	0	-0.006	-0.018	34.098	0.001	0.001	0.000	0.000	0.000	0.000
116	E	175	LEU	0	-0.022	-0.006	38.305	-0.001	-0.001	0.000	0.000	0.000	0.000
117	E	176	GLU	-1	-0.789	-0.854	36.550	-0.015	-0.015	0.000	0.000	0.000	0.000
118	E	178	ALA	0	0.036	0.024	30.253	0.004	0.004	0.000	0.000	0.000	0.000
119	E	180	ALA	0	0.026	0.016	24.640	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:23:ALA)