FMO DATABASE

FMODB ID: J3639

Calculation Name: 3MJK-A-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: A

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-959477.113453
FMO2-HF: Nuclear repulsion	905579.614989
FMO2-HF: Total energy	-53897.498464
FMO2-MP2: Total energy	-54051.259044

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:21:ACE )

Summations of interaction energy for fragment #1(A:21: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.
0.826	1.86	-0.005	-0.504	-0.524	-0.002

Interaction energy analysis for fragmet #1(A:21:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.027

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	23	ALA	0	-0.010	0.013	3.844	0.771	1.805	-0.005	-0.504	-0.524	-0.002
4	A	24	GLU	-1	-0.945	-0.970	5.712	0.011	0.011	0.000	0.000	0.000	0.000
5	A	25	ILE	0	-0.030	-0.034	7.682	0.099	0.099	0.000	0.000	0.000	0.000
6	A	26	PRO	0	-0.016	0.006	11.489	-0.006	-0.006	0.000	0.000	0.000	0.000
7	A	27	ARG	1	1.039	1.009	14.299	0.232	0.232	0.000	0.000	0.000	0.000
8	A	28	GLU	-1	-0.838	-0.916	16.862	-0.162	-0.162	0.000	0.000	0.000	0.000
9	A	29	VAL	0	0.014	0.014	16.110	0.019	0.019	0.000	0.000	0.000	0.000
10	A	30	ILE	0	0.009	0.009	15.244	0.023	0.023	0.000	0.000	0.000	0.000
11	A	31	GLU	-1	-0.879	-0.961	19.111	-0.058	-0.058	0.000	0.000	0.000	0.000
12	A	32	ARG	1	0.842	0.919	20.529	0.078	0.078	0.000	0.000	0.000	0.000
13	A	33	LEU	0	0.011	-0.005	19.575	0.008	0.008	0.000	0.000	0.000	0.000
14	A	34	ALA	0	-0.001	0.017	23.437	0.008	0.008	0.000	0.000	0.000	0.000
15	A	35	ARG	1	0.853	0.950	23.832	0.063	0.063	0.000	0.000	0.000	0.000
16	A	36	SER	0	-0.013	-0.024	26.545	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	37	GLN	0	-0.023	-0.019	28.469	0.008	0.008	0.000	0.000	0.000	0.000
18	A	38	ILE	0	-0.011	0.003	25.112	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	39	HIS	0	-0.039	-0.027	28.774	0.005	0.005	0.000	0.000	0.000	0.000
20	A	40	SER	0	-0.003	-0.003	29.210	0.002	0.002	0.000	0.000	0.000	0.000
21	A	41	ILE	0	0.022	0.015	23.749	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	42	ARG	1	0.983	0.992	25.419	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	43	ASP	-1	-0.858	-0.918	27.183	0.001	0.001	0.000	0.000	0.000	0.000
24	A	44	LEU	0	0.019	0.006	20.935	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	45	GLN	0	-0.025	-0.037	22.575	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	46	ARG	1	1.052	1.038	23.424	0.008	0.008	0.000	0.000	0.000	0.000
27	A	47	LEU	0	-0.171	-0.069	24.001	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	48	LEU	0	-0.080	-0.063	18.698	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	49	GLU	-1	-0.904	-0.939	21.872	-0.065	-0.065	0.000	0.000	0.000	0.000
30	A	50	ILE	0	-0.066	-0.023	18.756	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	51	ASP	-1	-0.893	-0.926	21.272	-0.031	-0.031	0.000	0.000	0.000	0.000
32	A	52	SER	0	-0.090	-0.060	23.151	0.008	0.008	0.000	0.000	0.000	0.000
33	A	53	VAL	0	0.040	0.017	17.620	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	54	NME	0	-0.038	-0.008	19.234	0.015	0.015	0.000	0.000	0.000	0.000
35	A	82	ACE	0	0.062	0.024	23.508	0.001	0.001	0.000	0.000	0.000	0.000
36	A	83	ARG	0	-0.022	-0.030	24.083	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	84	ARG	1	0.998	0.992	23.245	-0.091	-0.091	0.000	0.000	0.000	0.000
38	A	85	LYS	1	1.011	1.048	27.727	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	86	ARG	0	0.001	0.219	31.492	0.004	0.004	0.000	0.000	0.000	0.000
40	A	87	SER	0	0.053	-0.134	30.240	0.000	0.000	0.000	0.000	0.000	0.000
41	A	88	ILE	0	-0.163	-0.118	29.416	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	89	GLU	-1	-0.937	-1.004	32.129	0.044	0.044	0.000	0.000	0.000	0.000
43	A	90	GLU	-1	-0.906	-0.960	28.543	0.043	0.043	0.000	0.000	0.000	0.000
44	A	91	ALA	0	0.013	0.006	27.698	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	92	VAL	0	0.044	0.020	29.632	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	93	PRO	0	-0.005	0.013	28.671	0.003	0.003	0.000	0.000	0.000	0.000
47	A	94	ALA	0	0.010	0.002	30.188	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	95	VAL	0	0.056	0.005	31.348	0.000	0.000	0.000	0.000	0.000	0.000
49	A	140	CYS	0	-0.006	0.015	28.177	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	97	LYS	1	0.956	0.985	33.560	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	98	THR	0	0.042	0.023	37.012	0.003	0.003	0.000	0.000	0.000	0.000
52	A	99	ARG	1	0.764	0.864	35.035	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	100	THR	0	0.045	0.021	40.387	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	101	VAL	0	0.008	0.014	37.589	0.002	0.002	0.000	0.000	0.000	0.000
55	A	102	ILE	0	0.040	0.008	40.675	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	103	TYR	0	-0.041	-0.016	41.142	0.002	0.002	0.000	0.000	0.000	0.000
57	A	104	GLU	-1	-0.878	-0.958	42.804	0.033	0.033	0.000	0.000	0.000	0.000
58	A	105	ILE	0	-0.074	-0.038	44.634	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	106	PRO	0	0.015	0.007	43.749	0.001	0.001	0.000	0.000	0.000	0.000
60	A	107	ARG	1	1.012	0.994	45.731	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	108	SER	0	0.044	0.021	44.643	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	109	GLN	0	-0.019	-0.008	46.861	0.000	0.000	0.000	0.000	0.000	0.000
63	A	110	VAL	0	-0.084	-0.031	48.818	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	111	ASP	-1	-0.836	-0.914	51.592	0.017	0.017	0.000	0.000	0.000	0.000
65	A	112	PRO	0	-0.021	0.004	49.305	0.001	0.001	0.000	0.000	0.000	0.000
66	A	113	THR	0	-0.065	-0.048	50.522	0.001	0.001	0.000	0.000	0.000	0.000
67	A	114	SER	0	-0.036	-0.020	53.090	0.001	0.001	0.000	0.000	0.000	0.000
68	A	115	ALA	0	0.049	0.024	51.395	0.000	0.000	0.000	0.000	0.000	0.000
69	A	116	ASN	0	-0.093	-0.045	52.910	0.001	0.001	0.000	0.000	0.000	0.000
70	A	117	PHE	0	-0.007	-0.012	51.965	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	118	LEU	0	-0.035	-0.016	54.224	0.001	0.001	0.000	0.000	0.000	0.000
72	A	119	ILE	0	0.026	0.020	50.257	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	120	TRP	0	0.024	0.030	53.285	0.001	0.001	0.000	0.000	0.000	0.000
74	A	121	PRO	0	0.033	0.011	52.109	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	122	PRO	0	0.030	-0.003	49.099	0.000	0.000	0.000	0.000	0.000	0.000
76	A	123	CYS	0	0.004	0.019	45.369	0.001	0.001	0.000	0.000	0.000	0.000
77	A	124	VAL	0	-0.015	0.000	46.588	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	125	GLU	-1	-0.915	-0.950	45.219	0.024	0.024	0.000	0.000	0.000	0.000
79	A	126	VAL	0	-0.052	-0.027	42.222	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	127	LYS	1	0.867	0.923	42.583	-0.018	-0.018	0.000	0.000	0.000	0.000
81	A	128	ARG	1	0.933	0.960	37.793	-0.024	-0.024	0.000	0.000	0.000	0.000
82	A	177	CYS	0	-0.049	0.018	35.195	0.001	0.001	0.000	0.000	0.000	0.000
83	A	130	THR	0	0.016	0.013	33.672	0.003	0.003	0.000	0.000	0.000	0.000
84	A	131	GLY	0	0.036	0.010	31.694	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	132	CYS	0	-0.065	-0.036	26.471	0.004	0.004	0.000	0.000	0.000	0.000
86	A	179	CYS	0	-0.022	0.020	26.337	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	134	ASN	0	-0.003	-0.012	24.693	0.011	0.011	0.000	0.000	0.000	0.000
88	A	135	THR	0	0.014	0.026	20.447	0.006	0.006	0.000	0.000	0.000	0.000
89	A	136	SER	0	0.040	0.002	19.692	0.004	0.004	0.000	0.000	0.000	0.000
90	A	137	SER	0	-0.027	-0.003	19.944	0.003	0.003	0.000	0.000	0.000	0.000
91	A	138	VAL	0	-0.029	-0.008	21.742	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	139	LYS	1	0.978	0.985	25.409	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	141	GLN	0	0.015	-0.002	31.354	0.005	0.005	0.000	0.000	0.000	0.000
94	A	142	PRO	0	0.033	-0.011	33.816	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	143	SER	0	-0.025	-0.034	37.608	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	144	ARG	1	0.895	0.948	39.721	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	145	VAL	0	0.035	0.015	41.030	0.002	0.002	0.000	0.000	0.000	0.000
98	A	146	HIS	0	-0.021	-0.013	43.540	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	147	HIS	0	0.039	0.032	43.339	0.002	0.002	0.000	0.000	0.000	0.000
100	A	148	ARG	1	0.872	0.924	47.891	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	149	SER	0	-0.023	-0.033	50.166	0.001	0.001	0.000	0.000	0.000	0.000
102	A	150	VAL	0	-0.007	0.005	51.474	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	151	LYS	1	0.907	0.956	53.885	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	152	VAL	0	0.010	0.017	52.080	0.000	0.000	0.000	0.000	0.000	0.000
105	A	153	ALA	0	-0.017	-0.018	55.467	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	154	LYS	1	0.924	0.982	56.295	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	155	VAL	0	-0.001	-0.020	57.614	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	156	GLU	-1	-0.839	-0.924	58.629	0.017	0.017	0.000	0.000	0.000	0.000
109	A	157	TYR	0	-0.002	-0.014	60.858	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	158	VAL	0	0.004	0.011	63.889	0.000	0.000	0.000	0.000	0.000	0.000
111	A	159	ARG	1	1.002	1.005	65.780	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	160	LYS	1	1.002	1.006	67.138	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	161	LYS	1	0.943	0.944	68.080	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	162	PRO	0	0.050	0.031	65.198	0.000	0.000	0.000	0.000	0.000	0.000
115	A	163	LYS	1	0.859	0.938	64.067	-0.014	-0.014	0.000	0.000	0.000	0.000
116	A	164	LEU	0	0.063	0.033	61.160	0.001	0.001	0.000	0.000	0.000	0.000
117	A	165	LYS	1	0.931	0.976	59.821	-0.015	-0.015	0.000	0.000	0.000	0.000
118	A	166	GLU	-1	-0.846	-0.932	59.342	0.013	0.013	0.000	0.000	0.000	0.000
119	A	167	VAL	0	-0.001	0.003	54.026	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	168	GLN	0	-0.031	-0.014	53.932	0.000	0.000	0.000	0.000	0.000	0.000
121	A	169	VAL	0	0.017	0.006	48.786	0.000	0.000	0.000	0.000	0.000	0.000
122	A	170	ARG	1	0.952	0.978	47.378	-0.012	-0.012	0.000	0.000	0.000	0.000
123	A	171	LEU	0	-0.025	-0.003	46.060	0.001	0.001	0.000	0.000	0.000	0.000
124	A	172	GLU	-1	-0.846	-0.927	40.051	0.015	0.015	0.000	0.000	0.000	0.000
125	A	173	GLU	-1	-0.846	-0.900	43.069	0.018	0.018	0.000	0.000	0.000	0.000
126	A	174	HIS	0	0.015	0.002	37.076	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	175	LEU	0	-0.044	-0.036	41.957	0.001	0.001	0.000	0.000	0.000	0.000
128	A	176	GLU	-1	-0.879	-0.920	40.583	0.002	0.002	0.000	0.000	0.000	0.000
129	A	178	ALA	0	0.059	0.026	34.864	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	180	ALA	0	0.026	0.016	30.466	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	181	NME	0	0.001	-0.002	26.857	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:ACE )