FMO DATABASE

FMODB ID: K3L73

Calculation Name: 3MJK-A-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: A

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:

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-949159.751804
FMO2-HF: Nuclear repulsion	895602.080062
FMO2-HF: Total energy	-53557.671742
FMO2-MP2: Total energy	-53710.159223

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:22:GLU)

Summations of interaction energy for fragment #1(A:22:GLU)

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.
-48.548	-47.018	0.025	-0.485	-1.071	0.002

Interaction energy analysis for fragmet #1(A:22:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.965 / q_NPA : -0.999

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	24	GLU	-1	-0.934	-0.964	3.372	25.684	27.214	0.025	-0.485	-1.071	0.002
4	A	25	ILE	0	-0.036	-0.037	6.164	-1.292	-1.292	0.000	0.000	0.000	0.000
5	A	26	PRO	0	-0.014	0.007	9.172	-1.114	-1.114	0.000	0.000	0.000	0.000
6	A	27	ARG	1	1.039	1.009	11.075	-20.941	-20.941	0.000	0.000	0.000	0.000
7	A	28	GLU	-1	-0.835	-0.914	13.347	19.884	19.884	0.000	0.000	0.000	0.000
8	A	29	VAL	0	0.011	0.012	12.626	-1.195	-1.195	0.000	0.000	0.000	0.000
9	A	30	ILE	0	0.009	0.008	14.013	-1.181	-1.181	0.000	0.000	0.000	0.000
10	A	31	GLU	-1	-0.879	-0.961	17.188	14.711	14.711	0.000	0.000	0.000	0.000
11	A	32	ARG	1	0.845	0.920	16.562	-17.536	-17.536	0.000	0.000	0.000	0.000
12	A	33	LEU	0	0.006	-0.007	18.069	-0.742	-0.742	0.000	0.000	0.000	0.000
13	A	34	ALA	0	-0.001	0.016	21.302	-0.709	-0.709	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.860	0.954	19.985	-14.357	-14.357	0.000	0.000	0.000	0.000
15	A	36	SER	0	-0.014	-0.024	24.089	-0.376	-0.376	0.000	0.000	0.000	0.000
16	A	37	GLN	0	-0.018	-0.016	25.954	-0.253	-0.253	0.000	0.000	0.000	0.000
17	A	38	ILE	0	-0.011	0.003	23.205	0.162	0.162	0.000	0.000	0.000	0.000
18	A	39	HIS	0	-0.034	-0.024	27.142	-0.358	-0.358	0.000	0.000	0.000	0.000
19	A	40	SER	0	-0.016	-0.010	27.816	-0.225	-0.225	0.000	0.000	0.000	0.000
20	A	41	ILE	0	0.019	0.013	22.678	0.420	0.420	0.000	0.000	0.000	0.000
21	A	42	ARG	1	0.974	0.987	24.118	-9.895	-9.895	0.000	0.000	0.000	0.000
22	A	43	ASP	-1	-0.851	-0.914	25.260	11.186	11.186	0.000	0.000	0.000	0.000
23	A	44	LEU	0	0.024	0.008	19.406	0.364	0.364	0.000	0.000	0.000	0.000
24	A	45	GLN	0	-0.042	-0.041	20.721	0.106	0.106	0.000	0.000	0.000	0.000
25	A	46	ARG	1	1.049	1.036	20.885	-11.017	-11.017	0.000	0.000	0.000	0.000
26	A	47	LEU	0	-0.164	-0.065	21.205	0.074	0.074	0.000	0.000	0.000	0.000
27	A	48	LEU	0	-0.075	-0.058	16.176	0.702	0.702	0.000	0.000	0.000	0.000
28	A	49	GLU	-1	-0.901	-0.938	17.967	16.325	16.325	0.000	0.000	0.000	0.000
29	A	50	ILE	0	-0.057	-0.022	15.914	1.077	1.077	0.000	0.000	0.000	0.000
30	A	51	ASP	-1	-0.898	-0.927	18.183	14.267	14.267	0.000	0.000	0.000	0.000
31	A	52	SER	0	-0.098	-0.060	20.331	-0.137	-0.137	0.000	0.000	0.000	0.000
32	A	53	VAL	0	0.018	0.010	15.539	0.457	0.457	0.000	0.000	0.000	0.000
33	A	83	ARG	1	0.989	0.984	24.522	-10.990	-10.990	0.000	0.000	0.000	0.000
34	A	84	ARG	1	0.987	0.975	23.503	-11.616	-11.616	0.000	0.000	0.000	0.000
35	A	85	LYS	1	0.912	0.962	27.634	-9.321	-9.321	0.000	0.000	0.000	0.000
36	A	86	ARG	1	1.052	1.013	31.343	-8.605	-8.605	0.000	0.000	0.000	0.000
37	A	87	SER	0	-0.006	-0.010	34.004	-0.068	-0.068	0.000	0.000	0.000	0.000
38	A	88	ILE	0	0.005	0.028	29.321	-0.045	-0.045	0.000	0.000	0.000	0.000
39	A	89	GLU	-1	-0.977	-0.978	31.784	8.887	8.887	0.000	0.000	0.000	0.000
40	A	90	GLU	-1	-0.897	-0.956	27.848	11.176	11.176	0.000	0.000	0.000	0.000
41	A	91	ALA	0	0.023	0.011	27.050	-0.276	-0.276	0.000	0.000	0.000	0.000
42	A	92	VAL	0	0.041	0.019	28.798	0.203	0.203	0.000	0.000	0.000	0.000
43	A	93	PRO	0	0.002	0.017	27.763	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	94	ALA	0	0.009	0.002	29.420	-0.369	-0.369	0.000	0.000	0.000	0.000
45	A	95	VAL	0	0.056	0.006	30.738	0.148	0.148	0.000	0.000	0.000	0.000
46	A	96	CYS	0	-0.005	0.015	27.789	-0.463	-0.463	0.000	0.000	0.000	0.000
47	A	97	LYS	1	0.954	0.985	32.902	-8.079	-8.079	0.000	0.000	0.000	0.000
48	A	98	THR	0	0.052	0.027	36.599	0.109	0.109	0.000	0.000	0.000	0.000
49	A	99	ARG	1	0.753	0.860	34.488	-8.593	-8.593	0.000	0.000	0.000	0.000
50	A	100	THR	0	0.049	0.024	40.152	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	101	VAL	0	0.005	0.012	37.743	0.120	0.120	0.000	0.000	0.000	0.000
52	A	102	ILE	0	0.042	0.009	40.879	-0.146	-0.146	0.000	0.000	0.000	0.000
53	A	103	TYR	0	-0.042	-0.016	41.658	0.174	0.174	0.000	0.000	0.000	0.000
54	A	104	GLU	-1	-0.877	-0.957	43.515	6.503	6.503	0.000	0.000	0.000	0.000
55	A	105	ILE	0	-0.072	-0.037	45.399	0.043	0.043	0.000	0.000	0.000	0.000
56	A	106	PRO	0	0.012	0.006	44.604	-0.041	-0.041	0.000	0.000	0.000	0.000
57	A	107	ARG	1	1.014	0.995	46.687	-5.967	-5.967	0.000	0.000	0.000	0.000
58	A	108	SER	0	0.044	0.020	45.846	-0.125	-0.125	0.000	0.000	0.000	0.000
59	A	109	GLN	0	-0.021	-0.010	47.661	0.027	0.027	0.000	0.000	0.000	0.000
60	A	110	VAL	0	-0.082	-0.031	49.827	-0.105	-0.105	0.000	0.000	0.000	0.000
61	A	111	ASP	-1	-0.834	-0.913	52.758	5.286	5.286	0.000	0.000	0.000	0.000
62	A	112	PRO	0	-0.019	0.006	50.647	0.038	0.038	0.000	0.000	0.000	0.000
63	A	113	THR	0	-0.065	-0.048	51.864	0.031	0.031	0.000	0.000	0.000	0.000
64	A	114	SER	0	-0.034	-0.019	54.586	0.016	0.016	0.000	0.000	0.000	0.000
65	A	115	ALA	0	0.045	0.021	52.863	0.077	0.077	0.000	0.000	0.000	0.000
66	A	116	ASN	0	-0.092	-0.046	54.334	0.046	0.046	0.000	0.000	0.000	0.000
67	A	117	PHE	0	-0.008	-0.011	53.144	-0.111	-0.111	0.000	0.000	0.000	0.000
68	A	118	LEU	0	-0.035	-0.016	55.285	0.102	0.102	0.000	0.000	0.000	0.000
69	A	119	ILE	0	0.028	0.020	51.273	-0.083	-0.083	0.000	0.000	0.000	0.000
70	A	120	TRP	0	0.023	0.030	54.174	0.049	0.049	0.000	0.000	0.000	0.000
71	A	121	PRO	0	0.030	0.010	52.694	-0.091	-0.091	0.000	0.000	0.000	0.000
72	A	122	PRO	0	0.035	-0.002	49.968	0.026	0.026	0.000	0.000	0.000	0.000
73	A	123	CYS	0	0.000	0.017	46.098	0.111	0.111	0.000	0.000	0.000	0.000
74	A	124	VAL	0	-0.010	0.003	47.115	-0.142	-0.142	0.000	0.000	0.000	0.000
75	A	125	GLU	-1	-0.918	-0.952	45.479	6.539	6.539	0.000	0.000	0.000	0.000
76	A	126	VAL	0	-0.054	-0.026	42.437	-0.106	-0.106	0.000	0.000	0.000	0.000
77	A	127	LYS	1	0.869	0.922	42.498	-6.686	-6.686	0.000	0.000	0.000	0.000
78	A	128	ARG	1	0.933	0.960	37.811	-7.510	-7.510	0.000	0.000	0.000	0.000
79	A	129	CYS	0	-0.054	0.016	34.868	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	130	THR	0	0.019	0.015	33.534	0.097	0.097	0.000	0.000	0.000	0.000
81	A	131	GLY	0	0.036	0.009	31.341	-0.118	-0.118	0.000	0.000	0.000	0.000
82	A	132	CYS	0	-0.063	-0.036	26.007	0.097	0.097	0.000	0.000	0.000	0.000
83	A	133	CYS	0	-0.013	0.024	25.572	-0.312	-0.312	0.000	0.000	0.000	0.000
84	A	134	ASN	0	-0.013	-0.017	23.439	-0.085	-0.085	0.000	0.000	0.000	0.000
85	A	135	THR	0	0.016	0.027	19.338	0.294	0.294	0.000	0.000	0.000	0.000
86	A	136	SER	0	0.040	0.002	19.422	-0.308	-0.308	0.000	0.000	0.000	0.000
87	A	137	SER	0	-0.023	-0.001	19.318	-0.456	-0.456	0.000	0.000	0.000	0.000
88	A	138	VAL	0	-0.030	-0.009	21.239	-0.414	-0.414	0.000	0.000	0.000	0.000
89	A	139	LYS	1	0.983	0.987	24.794	-11.122	-11.122	0.000	0.000	0.000	0.000
90	A	141	GLN	0	0.016	-0.003	30.949	-0.098	-0.098	0.000	0.000	0.000	0.000
91	A	142	PRO	0	0.034	-0.009	33.433	-0.057	-0.057	0.000	0.000	0.000	0.000
92	A	143	SER	0	-0.027	-0.037	37.232	0.061	0.061	0.000	0.000	0.000	0.000
93	A	144	ARG	1	0.898	0.950	39.163	-7.186	-7.186	0.000	0.000	0.000	0.000
94	A	145	VAL	0	0.032	0.014	40.825	0.076	0.076	0.000	0.000	0.000	0.000
95	A	146	HIS	0	-0.012	-0.007	43.337	-0.076	-0.076	0.000	0.000	0.000	0.000
96	A	147	HIS	0	0.035	0.027	43.550	-0.061	-0.061	0.000	0.000	0.000	0.000
97	A	148	ARG	1	0.876	0.927	47.982	-6.268	-6.268	0.000	0.000	0.000	0.000
98	A	149	SER	0	-0.024	-0.035	50.448	0.108	0.108	0.000	0.000	0.000	0.000
99	A	150	VAL	0	-0.005	0.007	51.875	-0.074	-0.074	0.000	0.000	0.000	0.000
100	A	151	LYS	1	0.906	0.956	54.386	-4.970	-4.970	0.000	0.000	0.000	0.000
101	A	152	VAL	0	0.008	0.016	52.728	0.007	0.007	0.000	0.000	0.000	0.000
102	A	153	ALA	0	-0.015	-0.018	56.125	-0.079	-0.079	0.000	0.000	0.000	0.000
103	A	154	LYS	1	0.921	0.981	57.159	-5.128	-5.128	0.000	0.000	0.000	0.000
104	A	155	VAL	0	0.004	-0.019	58.582	-0.106	-0.106	0.000	0.000	0.000	0.000
105	A	156	GLU	-1	-0.844	-0.925	59.763	5.060	5.060	0.000	0.000	0.000	0.000
106	A	157	TYR	0	-0.001	-0.013	62.046	-0.074	-0.074	0.000	0.000	0.000	0.000
107	A	158	VAL	0	0.005	0.012	65.160	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	159	ARG	1	1.005	1.007	67.095	-4.326	-4.326	0.000	0.000	0.000	0.000
109	A	160	LYS	1	1.000	1.004	68.467	-4.239	-4.239	0.000	0.000	0.000	0.000
110	A	161	LYS	1	0.945	0.945	69.363	-4.151	-4.151	0.000	0.000	0.000	0.000
111	A	162	PRO	0	0.049	0.031	66.322	0.042	0.042	0.000	0.000	0.000	0.000
112	A	163	LYS	1	0.860	0.939	65.179	-4.536	-4.536	0.000	0.000	0.000	0.000
113	A	164	LEU	0	0.062	0.032	62.027	0.067	0.067	0.000	0.000	0.000	0.000
114	A	165	LYS	1	0.932	0.977	60.752	-4.978	-4.978	0.000	0.000	0.000	0.000
115	A	166	GLU	-1	-0.846	-0.933	60.088	5.008	5.008	0.000	0.000	0.000	0.000
116	A	167	VAL	0	-0.001	0.003	54.801	-0.034	-0.034	0.000	0.000	0.000	0.000
117	A	168	GLN	0	-0.029	-0.013	54.455	0.113	0.113	0.000	0.000	0.000	0.000
118	A	169	VAL	0	0.016	0.007	49.366	0.058	0.058	0.000	0.000	0.000	0.000
119	A	170	ARG	1	0.952	0.978	47.848	-6.116	-6.116	0.000	0.000	0.000	0.000
120	A	171	LEU	0	-0.020	0.000	46.441	0.104	0.104	0.000	0.000	0.000	0.000
121	A	172	GLU	-1	-0.863	-0.938	40.189	7.387	7.387	0.000	0.000	0.000	0.000
122	A	173	GLU	-1	-0.842	-0.896	43.217	6.618	6.618	0.000	0.000	0.000	0.000
123	A	174	HIS	0	0.019	0.004	37.077	0.086	0.086	0.000	0.000	0.000	0.000
124	A	175	LEU	0	-0.046	-0.037	41.742	-0.064	-0.064	0.000	0.000	0.000	0.000
125	A	176	GLU	-1	-0.876	-0.919	39.820	7.427	7.427	0.000	0.000	0.000	0.000
126	A	178	ALA	0	0.059	0.027	34.034	-0.038	-0.038	0.000	0.000	0.000	0.000
127	A	180	ALA	0	0.017	0.009	27.222	0.114	0.114	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:GLU)