FMO DATABASE

FMODB ID: 8282Y

Calculation Name: 3MJK-E-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-873999.6381
FMO2-HF: Nuclear repulsion	823648.498881
FMO2-HF: Total energy	-50351.139219
FMO2-MP2: Total energy	-50494.079447

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:22:ACE )

Summations of interaction energy for fragment #1(E:22:ACE )

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.
0.432	2.123	0.004	-0.807	-0.888	-0.002

Interaction energy analysis for fragmet #1(E:22:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.009

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	24	GLU	-1	-0.925	-0.951	3.640	0.425	2.116	0.004	-0.807	-0.888	-0.002
4	E	25	ILE	0	-0.018	-0.018	5.722	-0.134	-0.134	0.000	0.000	0.000	0.000
5	E	26	PRO	0	0.004	0.020	6.974	0.144	0.144	0.000	0.000	0.000	0.000
6	E	27	ARG	1	1.015	0.971	8.805	-0.280	-0.280	0.000	0.000	0.000	0.000
7	E	28	GLU	-1	-0.901	-0.936	11.776	0.041	0.041	0.000	0.000	0.000	0.000
8	E	29	VAL	0	0.051	0.026	10.814	-0.018	-0.018	0.000	0.000	0.000	0.000
9	E	30	ILE	0	0.014	0.002	12.097	0.000	0.000	0.000	0.000	0.000	0.000
10	E	31	GLU	-1	-0.848	-0.936	15.031	0.061	0.061	0.000	0.000	0.000	0.000
11	E	32	ARG	1	0.936	0.974	15.193	0.078	0.078	0.000	0.000	0.000	0.000
12	E	33	LEU	0	-0.010	0.025	15.437	0.001	0.001	0.000	0.000	0.000	0.000
13	E	34	ALA	0	-0.043	-0.008	18.778	0.005	0.005	0.000	0.000	0.000	0.000
14	E	35	ARG	1	0.828	0.938	18.743	0.006	0.006	0.000	0.000	0.000	0.000
15	E	36	SER	0	-0.001	-0.038	21.521	0.006	0.006	0.000	0.000	0.000	0.000
16	E	37	GLN	0	-0.056	-0.040	24.009	-0.001	-0.001	0.000	0.000	0.000	0.000
17	E	38	ILE	0	0.025	0.026	20.869	-0.002	-0.002	0.000	0.000	0.000	0.000
18	E	39	HIS	1	0.820	0.897	25.079	0.064	0.064	0.000	0.000	0.000	0.000
19	E	40	SER	0	0.074	0.047	26.092	0.001	0.001	0.000	0.000	0.000	0.000
20	E	41	ILE	0	0.077	0.045	21.888	-0.006	-0.006	0.000	0.000	0.000	0.000
21	E	42	ARG	1	0.956	0.987	22.640	0.082	0.082	0.000	0.000	0.000	0.000
22	E	43	ASP	-1	-0.887	-0.962	23.474	-0.079	-0.079	0.000	0.000	0.000	0.000
23	E	44	LEU	0	0.006	0.006	17.870	0.002	0.002	0.000	0.000	0.000	0.000
24	E	45	GLN	0	0.035	0.004	18.838	0.009	0.009	0.000	0.000	0.000	0.000
25	E	46	ARG	1	0.939	0.978	19.374	0.065	0.065	0.000	0.000	0.000	0.000
26	E	47	LEU	0	-0.015	-0.017	19.919	0.004	0.004	0.000	0.000	0.000	0.000
27	E	48	LEU	0	-0.127	-0.043	14.467	0.004	0.004	0.000	0.000	0.000	0.000
28	E	49	GLU	-1	-0.905	-0.968	15.421	-0.072	-0.072	0.000	0.000	0.000	0.000
29	E	50	ILE	0	-0.047	-0.027	16.638	0.012	0.012	0.000	0.000	0.000	0.000
30	E	51	NME	0	-0.008	0.020	18.950	0.007	0.007	0.000	0.000	0.000	0.000
31	E	86	ACE	0	0.025	0.003	31.363	-0.001	-0.001	0.000	0.000	0.000	0.000
32	E	87	SER	0	-0.071	-0.050	32.123	0.007	0.007	0.000	0.000	0.000	0.000
33	E	88	ILE	0	0.014	0.034	29.169	0.003	0.003	0.000	0.000	0.000	0.000
34	E	89	GLU	-1	-0.946	-0.978	32.024	-0.079	-0.079	0.000	0.000	0.000	0.000
35	E	90	GLU	-1	-0.921	-0.968	27.072	-0.115	-0.115	0.000	0.000	0.000	0.000
36	E	91	ALA	0	0.012	0.002	26.467	0.006	0.006	0.000	0.000	0.000	0.000
37	E	92	VAL	0	0.051	0.022	28.179	0.000	0.000	0.000	0.000	0.000	0.000
38	E	93	PRO	0	-0.028	-0.001	26.410	0.000	0.000	0.000	0.000	0.000	0.000
39	E	94	ALA	0	0.017	0.009	28.244	0.009	0.009	0.000	0.000	0.000	0.000
40	E	95	VAL	0	0.053	0.006	28.957	-0.001	-0.001	0.000	0.000	0.000	0.000
41	E	140	CYS	0	-0.024	0.012	26.005	0.009	0.009	0.000	0.000	0.000	0.000
42	E	97	LYS	1	0.953	0.969	30.989	0.047	0.047	0.000	0.000	0.000	0.000
43	E	98	THR	0	0.065	0.031	34.756	-0.002	-0.002	0.000	0.000	0.000	0.000
44	E	99	ARG	1	0.758	0.862	32.911	0.051	0.051	0.000	0.000	0.000	0.000
45	E	100	THR	0	0.038	-0.001	38.950	0.002	0.002	0.000	0.000	0.000	0.000
46	E	101	VAL	0	-0.030	0.007	37.108	-0.003	-0.003	0.000	0.000	0.000	0.000
47	E	102	ILE	0	0.046	0.009	40.423	0.002	0.002	0.000	0.000	0.000	0.000
48	E	103	TYR	0	-0.043	-0.019	41.485	-0.001	-0.001	0.000	0.000	0.000	0.000
49	E	104	GLU	-1	-0.887	-0.951	42.939	-0.027	-0.027	0.000	0.000	0.000	0.000
50	E	105	ILE	0	-0.046	-0.023	45.280	0.001	0.001	0.000	0.000	0.000	0.000
51	E	106	PRO	0	0.013	0.007	44.649	0.000	0.000	0.000	0.000	0.000	0.000
52	E	107	ARG	1	0.974	0.987	47.055	0.019	0.019	0.000	0.000	0.000	0.000
53	E	108	SER	0	0.017	0.004	46.427	0.001	0.001	0.000	0.000	0.000	0.000
54	E	109	GLN	0	0.025	-0.005	45.074	0.001	0.001	0.000	0.000	0.000	0.000
55	E	110	VAL	0	-0.041	-0.001	50.126	0.001	0.001	0.000	0.000	0.000	0.000
56	E	111	ASP	-1	-0.881	-0.963	52.818	-0.009	-0.009	0.000	0.000	0.000	0.000
57	E	112	PRO	0	-0.008	-0.002	50.987	-0.001	-0.001	0.000	0.000	0.000	0.000
58	E	113	THR	0	-0.028	0.007	52.413	0.000	0.000	0.000	0.000	0.000	0.000
59	E	114	SER	0	-0.047	-0.016	55.641	0.000	0.000	0.000	0.000	0.000	0.000
60	E	115	ALA	0	0.024	-0.015	52.778	-0.001	-0.001	0.000	0.000	0.000	0.000
61	E	116	ASN	0	-0.037	-0.006	54.544	-0.001	-0.001	0.000	0.000	0.000	0.000
62	E	117	PHE	0	-0.016	-0.009	53.552	0.000	0.000	0.000	0.000	0.000	0.000
63	E	118	LEU	0	0.000	-0.007	54.909	-0.001	-0.001	0.000	0.000	0.000	0.000
64	E	119	ILE	0	-0.002	0.010	51.402	0.001	0.001	0.000	0.000	0.000	0.000
65	E	120	TRP	0	-0.009	0.018	54.240	-0.001	-0.001	0.000	0.000	0.000	0.000
66	E	121	PRO	0	0.077	0.019	52.489	0.001	0.001	0.000	0.000	0.000	0.000
67	E	122	PRO	0	0.009	0.003	50.302	0.000	0.000	0.000	0.000	0.000	0.000
68	E	123	CYS	0	-0.015	-0.003	46.525	-0.001	-0.001	0.000	0.000	0.000	0.000
69	E	124	VAL	0	-0.010	-0.008	46.965	0.001	0.001	0.000	0.000	0.000	0.000
70	E	125	GLU	-1	-0.900	-0.936	45.090	-0.029	-0.029	0.000	0.000	0.000	0.000
71	E	126	VAL	0	-0.016	-0.011	41.692	0.002	0.002	0.000	0.000	0.000	0.000
72	E	127	LYS	1	0.908	0.972	41.356	0.027	0.027	0.000	0.000	0.000	0.000
73	E	128	ARG	1	0.941	0.968	37.074	0.027	0.027	0.000	0.000	0.000	0.000
74	E	177	CYS	0	-0.063	0.004	33.523	-0.001	-0.001	0.000	0.000	0.000	0.000
75	E	130	THR	0	0.023	0.028	32.537	-0.003	-0.003	0.000	0.000	0.000	0.000
76	E	131	GLY	0	0.014	0.005	30.313	0.002	0.002	0.000	0.000	0.000	0.000
77	E	132	CYS	0	-0.048	-0.030	24.801	-0.001	-0.001	0.000	0.000	0.000	0.000
78	E	179	CYS	0	-0.027	0.014	23.725	0.005	0.005	0.000	0.000	0.000	0.000
79	E	134	ASN	0	-0.010	-0.021	21.010	-0.010	-0.010	0.000	0.000	0.000	0.000
80	E	135	THR	0	-0.013	0.010	17.403	-0.018	-0.018	0.000	0.000	0.000	0.000
81	E	136	SER	0	0.046	0.017	17.768	0.018	0.018	0.000	0.000	0.000	0.000
82	E	137	SER	0	0.003	-0.001	17.353	0.006	0.006	0.000	0.000	0.000	0.000
83	E	138	VAL	0	-0.047	-0.012	19.380	0.018	0.018	0.000	0.000	0.000	0.000
84	E	139	LYS	1	0.961	0.985	22.820	0.017	0.017	0.000	0.000	0.000	0.000
85	E	141	GLN	0	0.035	0.007	28.725	-0.001	-0.001	0.000	0.000	0.000	0.000
86	E	142	PRO	0	0.057	-0.009	31.624	-0.001	-0.001	0.000	0.000	0.000	0.000
87	E	143	SER	0	-0.033	-0.023	35.362	0.002	0.002	0.000	0.000	0.000	0.000
88	E	144	ARG	1	0.898	0.947	36.903	0.013	0.013	0.000	0.000	0.000	0.000
89	E	145	VAL	0	0.032	0.017	39.159	-0.002	-0.002	0.000	0.000	0.000	0.000
90	E	146	HIS	0	-0.011	0.002	41.733	0.002	0.002	0.000	0.000	0.000	0.000
91	E	147	HIS	0	0.004	0.000	42.733	0.000	0.000	0.000	0.000	0.000	0.000
92	E	148	ARG	1	0.941	0.976	47.083	0.018	0.018	0.000	0.000	0.000	0.000
93	E	149	SER	0	-0.002	-0.007	50.121	-0.001	-0.001	0.000	0.000	0.000	0.000
94	E	150	VAL	0	-0.010	0.006	51.798	0.000	0.000	0.000	0.000	0.000	0.000
95	E	151	LYS	1	0.919	0.966	54.378	0.012	0.012	0.000	0.000	0.000	0.000
96	E	152	VAL	0	-0.005	0.014	52.955	-0.001	-0.001	0.000	0.000	0.000	0.000
97	E	153	ALA	0	0.004	-0.010	56.388	0.001	0.001	0.000	0.000	0.000	0.000
98	E	154	LYS	1	0.855	0.947	57.469	0.010	0.010	0.000	0.000	0.000	0.000
99	E	155	VAL	0	-0.016	-0.029	58.827	0.001	0.001	0.000	0.000	0.000	0.000
100	E	156	GLU	-1	-0.842	-0.947	60.083	-0.011	-0.011	0.000	0.000	0.000	0.000
101	E	157	TYR	0	0.012	0.001	62.678	0.000	0.000	0.000	0.000	0.000	0.000
102	E	158	VAL	0	0.020	0.022	65.564	0.000	0.000	0.000	0.000	0.000	0.000
103	E	159	ARG	1	0.958	0.955	68.022	0.008	0.008	0.000	0.000	0.000	0.000
104	E	160	LYS	1	0.997	0.985	67.632	0.012	0.012	0.000	0.000	0.000	0.000
105	E	161	LYS	1	0.957	0.996	70.093	0.009	0.009	0.000	0.000	0.000	0.000
106	E	162	PRO	0	0.038	0.019	66.816	0.000	0.000	0.000	0.000	0.000	0.000
107	E	163	LYS	1	0.889	0.947	65.786	0.010	0.010	0.000	0.000	0.000	0.000
108	E	164	LEU	0	0.042	0.042	62.114	0.000	0.000	0.000	0.000	0.000	0.000
109	E	165	LYS	1	0.964	0.996	61.404	0.010	0.010	0.000	0.000	0.000	0.000
110	E	166	GLU	-1	-0.845	-0.935	60.310	-0.012	-0.012	0.000	0.000	0.000	0.000
111	E	167	VAL	0	-0.028	-0.011	55.716	0.001	0.001	0.000	0.000	0.000	0.000
112	E	168	GLN	0	-0.004	-0.004	54.869	-0.001	-0.001	0.000	0.000	0.000	0.000
113	E	169	VAL	0	0.020	0.005	49.753	0.000	0.000	0.000	0.000	0.000	0.000
114	E	170	ARG	1	0.959	0.976	48.230	0.009	0.009	0.000	0.000	0.000	0.000
115	E	171	LEU	0	-0.015	-0.002	46.588	-0.001	-0.001	0.000	0.000	0.000	0.000
116	E	172	GLU	-1	-0.849	-0.931	39.620	-0.017	-0.017	0.000	0.000	0.000	0.000
117	E	173	GLU	-1	-0.925	-0.967	42.615	-0.023	-0.023	0.000	0.000	0.000	0.000
118	E	174	HIS	0	0.003	-0.008	36.193	0.000	0.000	0.000	0.000	0.000	0.000
119	E	175	LEU	0	-0.035	-0.035	40.419	-0.001	-0.001	0.000	0.000	0.000	0.000
120	E	176	GLU	-1	-0.880	-0.926	38.239	-0.016	-0.016	0.000	0.000	0.000	0.000
121	E	178	ALA	0	0.024	0.013	31.518	0.000	0.000	0.000	0.000	0.000	0.000
122	E	180	ALA	0	0.033	0.017	26.662	0.003	0.003	0.000	0.000	0.000	0.000
123	E	181	NME	0	0.010	0.001	24.784	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:22:ACE )