FMO DATABASE

FMODB ID: 7GV3K

Calculation Name: 3MJK-E-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

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:

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864752.294259
FMO2-HF: Nuclear repulsion	814743.07451
FMO2-HF: Total energy	-50009.219748
FMO2-MP2: Total energy	-50151.080667

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(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.
0.464	1.569	-0.009	-0.567	-0.53	0.003

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 : -0.012 / q_NPA : -0.015

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	-0.020	-0.020	3.807	0.609	1.714	-0.009	-0.567	-0.530	0.003
4	E	26	PRO	0	0.006	0.021	6.821	-0.079	-0.079	0.000	0.000	0.000	0.000
5	E	27	ARG	1	1.012	0.969	8.999	-0.582	-0.582	0.000	0.000	0.000	0.000
6	E	28	GLU	-1	-0.899	-0.935	12.006	0.432	0.432	0.000	0.000	0.000	0.000
7	E	29	VAL	0	0.051	0.026	9.777	-0.097	-0.097	0.000	0.000	0.000	0.000
8	E	30	ILE	0	0.013	0.001	10.387	-0.076	-0.076	0.000	0.000	0.000	0.000
9	E	31	GLU	-1	-0.852	-0.937	13.782	0.156	0.156	0.000	0.000	0.000	0.000
10	E	32	ARG	1	0.938	0.974	14.245	-0.281	-0.281	0.000	0.000	0.000	0.000
11	E	33	LEU	0	-0.008	0.025	13.119	-0.024	-0.024	0.000	0.000	0.000	0.000
12	E	34	ALA	0	-0.045	-0.011	17.328	-0.017	-0.017	0.000	0.000	0.000	0.000
13	E	35	ARG	1	0.831	0.939	18.524	-0.147	-0.147	0.000	0.000	0.000	0.000
14	E	36	SER	0	-0.004	-0.038	20.163	0.019	0.019	0.000	0.000	0.000	0.000
15	E	37	GLN	0	-0.052	-0.038	22.426	-0.016	-0.016	0.000	0.000	0.000	0.000
16	E	38	ILE	0	0.024	0.025	18.223	0.007	0.007	0.000	0.000	0.000	0.000
17	E	39	HIS	1	0.821	0.897	22.469	-0.019	-0.019	0.000	0.000	0.000	0.000
18	E	40	SER	0	0.075	0.049	23.045	-0.002	-0.002	0.000	0.000	0.000	0.000
19	E	41	ILE	0	0.079	0.047	18.226	0.004	0.004	0.000	0.000	0.000	0.000
20	E	42	ARG	1	0.956	0.986	19.405	-0.029	-0.029	0.000	0.000	0.000	0.000
21	E	43	ASP	-1	-0.889	-0.964	20.615	0.047	0.047	0.000	0.000	0.000	0.000
22	E	44	LEU	0	0.007	0.008	14.928	0.015	0.015	0.000	0.000	0.000	0.000
23	E	45	GLN	0	0.035	0.004	16.021	0.021	0.021	0.000	0.000	0.000	0.000
24	E	46	ARG	1	0.936	0.975	17.048	-0.041	-0.041	0.000	0.000	0.000	0.000
25	E	47	LEU	0	-0.017	-0.018	18.093	0.020	0.020	0.000	0.000	0.000	0.000
26	E	48	LEU	0	-0.125	-0.042	12.002	0.024	0.024	0.000	0.000	0.000	0.000
27	E	49	GLU	-1	-0.912	-0.959	14.020	0.388	0.388	0.000	0.000	0.000	0.000
28	E	50	ILE	0	-0.046	-0.012	13.676	-0.044	-0.044	0.000	0.000	0.000	0.000
29	E	87	SER	0	-0.017	-0.029	28.621	0.001	0.001	0.000	0.000	0.000	0.000
30	E	88	ILE	0	-0.012	0.017	24.339	0.000	0.000	0.000	0.000	0.000	0.000
31	E	89	GLU	-1	-0.954	-0.982	27.605	-0.052	-0.052	0.000	0.000	0.000	0.000
32	E	90	GLU	-1	-0.914	-0.965	23.136	-0.038	-0.038	0.000	0.000	0.000	0.000
33	E	91	ALA	0	0.011	0.001	22.110	0.002	0.002	0.000	0.000	0.000	0.000
34	E	92	VAL	0	0.050	0.022	24.214	0.006	0.006	0.000	0.000	0.000	0.000
35	E	93	PRO	0	-0.028	-0.001	23.046	-0.008	-0.008	0.000	0.000	0.000	0.000
36	E	94	ALA	0	0.015	0.008	24.686	0.010	0.010	0.000	0.000	0.000	0.000
37	E	95	VAL	0	0.053	0.006	25.720	-0.005	-0.005	0.000	0.000	0.000	0.000
38	E	96	CYS	0	-0.023	0.012	23.890	0.013	0.013	0.000	0.000	0.000	0.000
39	E	97	LYS	1	0.949	0.968	28.429	0.042	0.042	0.000	0.000	0.000	0.000
40	E	98	THR	0	0.070	0.033	32.207	-0.006	-0.006	0.000	0.000	0.000	0.000
41	E	99	ARG	1	0.756	0.862	29.689	0.056	0.056	0.000	0.000	0.000	0.000
42	E	100	THR	0	0.039	0.000	35.664	0.000	0.000	0.000	0.000	0.000	0.000
43	E	101	VAL	0	-0.031	0.006	33.527	-0.003	-0.003	0.000	0.000	0.000	0.000
44	E	102	ILE	0	0.050	0.010	36.689	0.003	0.003	0.000	0.000	0.000	0.000
45	E	103	TYR	0	-0.043	-0.019	37.790	-0.004	-0.004	0.000	0.000	0.000	0.000
46	E	104	GLU	-1	-0.887	-0.951	39.236	-0.053	-0.053	0.000	0.000	0.000	0.000
47	E	105	ILE	0	-0.045	-0.023	41.735	0.000	0.000	0.000	0.000	0.000	0.000
48	E	106	PRO	0	0.011	0.007	41.614	0.000	0.000	0.000	0.000	0.000	0.000
49	E	107	ARG	1	0.976	0.988	43.973	0.043	0.043	0.000	0.000	0.000	0.000
50	E	108	SER	0	0.015	0.002	43.685	0.002	0.002	0.000	0.000	0.000	0.000
51	E	109	GLN	0	0.025	-0.006	42.392	0.003	0.003	0.000	0.000	0.000	0.000
52	E	110	VAL	0	-0.042	-0.001	47.372	0.002	0.002	0.000	0.000	0.000	0.000
53	E	111	ASP	-1	-0.878	-0.962	49.931	-0.028	-0.028	0.000	0.000	0.000	0.000
54	E	112	PRO	0	-0.007	-0.001	48.374	-0.001	-0.001	0.000	0.000	0.000	0.000
55	E	113	THR	0	-0.028	0.007	49.682	-0.001	-0.001	0.000	0.000	0.000	0.000
56	E	114	SER	0	-0.047	-0.016	52.784	0.000	0.000	0.000	0.000	0.000	0.000
57	E	115	ALA	0	0.022	-0.015	49.545	-0.001	-0.001	0.000	0.000	0.000	0.000
58	E	116	ASN	0	-0.038	-0.006	51.356	-0.001	-0.001	0.000	0.000	0.000	0.000
59	E	117	PHE	0	-0.017	-0.009	50.493	0.001	0.001	0.000	0.000	0.000	0.000
60	E	118	LEU	0	0.001	-0.006	51.130	-0.002	-0.002	0.000	0.000	0.000	0.000
61	E	119	ILE	0	0.002	0.011	48.039	0.002	0.002	0.000	0.000	0.000	0.000
62	E	120	TRP	0	-0.012	0.017	50.507	-0.001	-0.001	0.000	0.000	0.000	0.000
63	E	121	PRO	0	0.074	0.019	48.664	0.002	0.002	0.000	0.000	0.000	0.000
64	E	122	PRO	0	0.012	0.003	46.450	0.000	0.000	0.000	0.000	0.000	0.000
65	E	123	CYS	0	-0.016	-0.004	42.652	-0.003	-0.003	0.000	0.000	0.000	0.000
66	E	124	VAL	0	-0.007	-0.006	43.284	0.003	0.003	0.000	0.000	0.000	0.000
67	E	125	GLU	-1	-0.902	-0.937	41.400	-0.038	-0.038	0.000	0.000	0.000	0.000
68	E	126	VAL	0	-0.019	-0.011	38.476	0.002	0.002	0.000	0.000	0.000	0.000
69	E	127	LYS	1	0.911	0.972	38.223	0.028	0.028	0.000	0.000	0.000	0.000
70	E	128	ARG	1	0.941	0.967	34.135	0.049	0.049	0.000	0.000	0.000	0.000
71	E	129	CYS	0	-0.069	0.001	31.146	-0.002	-0.002	0.000	0.000	0.000	0.000
72	E	130	THR	0	0.027	0.029	29.398	-0.005	-0.005	0.000	0.000	0.000	0.000
73	E	131	GLY	0	0.013	0.003	26.913	0.007	0.007	0.000	0.000	0.000	0.000
74	E	132	CYS	0	-0.041	-0.026	21.713	-0.009	-0.009	0.000	0.000	0.000	0.000
75	E	133	CYS	0	-0.017	0.015	21.511	0.008	0.008	0.000	0.000	0.000	0.000
76	E	134	ASN	0	-0.014	-0.023	18.460	-0.023	-0.023	0.000	0.000	0.000	0.000
77	E	135	THR	0	-0.011	0.012	15.257	-0.019	-0.019	0.000	0.000	0.000	0.000
78	E	136	SER	0	0.047	0.018	15.216	0.022	0.022	0.000	0.000	0.000	0.000
79	E	137	SER	0	0.003	0.000	15.761	0.001	0.001	0.000	0.000	0.000	0.000
80	E	138	VAL	0	-0.046	-0.014	17.589	0.025	0.025	0.000	0.000	0.000	0.000
81	E	139	LYS	1	0.967	0.987	21.021	0.053	0.053	0.000	0.000	0.000	0.000
82	E	141	GLN	0	0.034	0.006	27.037	-0.009	-0.009	0.000	0.000	0.000	0.000
83	E	142	PRO	0	0.058	-0.007	29.667	0.004	0.004	0.000	0.000	0.000	0.000
84	E	143	SER	0	-0.035	-0.025	33.418	0.000	0.000	0.000	0.000	0.000	0.000
85	E	144	ARG	1	0.899	0.948	35.287	0.011	0.011	0.000	0.000	0.000	0.000
86	E	145	VAL	0	0.030	0.017	37.287	-0.003	-0.003	0.000	0.000	0.000	0.000
87	E	146	HIS	0	-0.009	0.003	39.780	0.003	0.003	0.000	0.000	0.000	0.000
88	E	147	HIS	0	0.006	0.000	40.627	-0.001	-0.001	0.000	0.000	0.000	0.000
89	E	148	ARG	1	0.940	0.975	44.981	0.028	0.028	0.000	0.000	0.000	0.000
90	E	149	SER	0	-0.001	-0.006	47.617	-0.002	-0.002	0.000	0.000	0.000	0.000
91	E	150	VAL	0	-0.011	0.005	48.639	0.001	0.001	0.000	0.000	0.000	0.000
92	E	151	LYS	1	0.919	0.966	51.441	0.019	0.019	0.000	0.000	0.000	0.000
93	E	152	VAL	0	-0.004	0.014	49.646	0.000	0.000	0.000	0.000	0.000	0.000
94	E	153	ALA	0	0.002	-0.010	53.055	0.001	0.001	0.000	0.000	0.000	0.000
95	E	154	LYS	1	0.852	0.946	54.020	0.027	0.027	0.000	0.000	0.000	0.000
96	E	155	VAL	0	-0.008	-0.028	55.333	0.001	0.001	0.000	0.000	0.000	0.000
97	E	156	GLU	-1	-0.847	-0.948	56.597	-0.028	-0.028	0.000	0.000	0.000	0.000
98	E	157	TYR	0	0.012	0.001	59.243	0.001	0.001	0.000	0.000	0.000	0.000
99	E	158	VAL	0	0.019	0.022	62.064	0.000	0.000	0.000	0.000	0.000	0.000
100	E	159	ARG	1	0.959	0.956	64.709	0.020	0.020	0.000	0.000	0.000	0.000
101	E	160	LYS	1	0.997	0.984	63.780	0.025	0.025	0.000	0.000	0.000	0.000
102	E	161	LYS	1	0.956	0.996	66.535	0.018	0.018	0.000	0.000	0.000	0.000
103	E	162	PRO	0	0.038	0.018	63.161	-0.001	-0.001	0.000	0.000	0.000	0.000
104	E	163	LYS	1	0.889	0.947	62.246	0.021	0.021	0.000	0.000	0.000	0.000
105	E	164	LEU	0	0.042	0.042	58.538	-0.001	-0.001	0.000	0.000	0.000	0.000
106	E	165	LYS	1	0.962	0.997	58.441	0.025	0.025	0.000	0.000	0.000	0.000
107	E	166	GLU	-1	-0.844	-0.935	57.122	-0.022	-0.022	0.000	0.000	0.000	0.000
108	E	167	VAL	0	-0.028	-0.011	52.921	0.001	0.001	0.000	0.000	0.000	0.000
109	E	168	GLN	0	-0.005	-0.005	52.346	0.000	0.000	0.000	0.000	0.000	0.000
110	E	169	VAL	0	0.021	0.006	46.865	-0.001	-0.001	0.000	0.000	0.000	0.000
111	E	170	ARG	1	0.957	0.975	45.790	0.028	0.028	0.000	0.000	0.000	0.000
112	E	171	LEU	0	-0.013	-0.002	43.750	-0.002	-0.002	0.000	0.000	0.000	0.000
113	E	172	GLU	-1	-0.851	-0.932	37.369	-0.039	-0.039	0.000	0.000	0.000	0.000
114	E	173	GLU	-1	-0.924	-0.967	39.963	-0.032	-0.032	0.000	0.000	0.000	0.000
115	E	174	HIS	0	0.004	-0.008	33.799	0.001	0.001	0.000	0.000	0.000	0.000
116	E	175	LEU	0	-0.036	-0.035	38.138	0.000	0.000	0.000	0.000	0.000	0.000
117	E	176	GLU	-1	-0.879	-0.926	36.411	-0.008	-0.008	0.000	0.000	0.000	0.000
118	E	178	ALA	0	0.023	0.014	29.913	0.005	0.005	0.000	0.000	0.000	0.000
119	E	180	ALA	0	0.024	0.013	24.664	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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