FMO DATABASE

FMODB ID: 53VZZ

Calculation Name: 3MJK-A-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: 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:

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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-948155.42611
FMO2-HF: Nuclear repulsion	894595.546783
FMO2-HF: Total energy	-53559.879327
FMO2-MP2: Total energy	-53712.122388

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: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.
-56.89	-54.115	0.051	-1.511	-1.314	0.009

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 : -0.907 / q_NPA : -0.953

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	-0.944	-0.971	3.681	18.967	21.742	0.051	-1.511	-1.314	0.009
4	A	25	ILE	0	-0.045	-0.032	5.990	-0.658	-0.658	0.000	0.000	0.000	0.000
5	A	26	PRO	0	0.006	0.012	9.636	-1.342	-1.342	0.000	0.000	0.000	0.000
6	A	27	ARG	1	0.938	0.952	11.909	-21.095	-21.095	0.000	0.000	0.000	0.000
7	A	28	GLU	-1	-0.794	-0.887	13.815	19.731	19.731	0.000	0.000	0.000	0.000
8	A	29	VAL	0	-0.004	0.001	13.428	-1.171	-1.171	0.000	0.000	0.000	0.000
9	A	30	ILE	0	-0.002	0.006	14.461	-1.228	-1.228	0.000	0.000	0.000	0.000
10	A	31	GLU	-1	-0.834	-0.955	17.380	14.554	14.554	0.000	0.000	0.000	0.000
11	A	32	ARG	1	0.679	0.798	17.859	-17.392	-17.392	0.000	0.000	0.000	0.000
12	A	33	LEU	0	0.020	0.008	18.311	-0.730	-0.730	0.000	0.000	0.000	0.000
13	A	34	ALA	0	-0.030	-0.004	21.551	-0.779	-0.779	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.870	0.949	21.280	-14.382	-14.382	0.000	0.000	0.000	0.000
15	A	36	SER	0	0.029	0.015	25.028	-0.457	-0.457	0.000	0.000	0.000	0.000
16	A	37	GLN	0	-0.043	-0.021	26.963	-0.552	-0.552	0.000	0.000	0.000	0.000
17	A	38	ILE	0	-0.011	0.000	23.501	0.309	0.309	0.000	0.000	0.000	0.000
18	A	39	HIS	0	-0.058	-0.040	27.460	-0.312	-0.312	0.000	0.000	0.000	0.000
19	A	40	SER	0	-0.053	-0.040	28.494	-0.239	-0.239	0.000	0.000	0.000	0.000
20	A	41	ILE	0	0.009	-0.013	23.004	0.406	0.406	0.000	0.000	0.000	0.000
21	A	42	ARG	1	0.961	0.981	23.894	-9.941	-9.941	0.000	0.000	0.000	0.000
22	A	43	ASP	-1	-0.812	-0.877	25.285	11.115	11.115	0.000	0.000	0.000	0.000
23	A	44	LEU	0	0.030	0.005	19.554	0.309	0.309	0.000	0.000	0.000	0.000
24	A	45	GLN	0	-0.043	-0.033	20.447	0.130	0.130	0.000	0.000	0.000	0.000
25	A	46	ARG	1	0.968	1.002	21.440	-11.473	-11.473	0.000	0.000	0.000	0.000
26	A	47	LEU	0	-0.066	-0.027	21.393	0.012	0.012	0.000	0.000	0.000	0.000
27	A	48	LEU	0	-0.027	-0.012	15.960	0.760	0.760	0.000	0.000	0.000	0.000
28	A	49	GLU	-1	-0.759	-0.836	17.105	16.765	16.765	0.000	0.000	0.000	0.000
29	A	50	ILE	0	-0.010	-0.003	15.156	1.020	1.020	0.000	0.000	0.000	0.000
30	A	51	ASP	-1	-0.860	-0.930	17.537	14.802	14.802	0.000	0.000	0.000	0.000
31	A	52	SER	0	-0.085	-0.025	20.342	-0.263	-0.263	0.000	0.000	0.000	0.000
32	A	53	VAL	0	-0.086	-0.044	15.156	-0.077	-0.077	0.000	0.000	0.000	0.000
33	A	83	ARG	1	0.992	0.986	24.144	-11.293	-11.293	0.000	0.000	0.000	0.000
34	A	84	ARG	1	0.989	0.989	24.326	-12.010	-12.010	0.000	0.000	0.000	0.000
35	A	85	LYS	1	0.942	0.968	28.005	-9.254	-9.254	0.000	0.000	0.000	0.000
36	A	86	ARG	1	0.932	0.968	31.819	-8.684	-8.684	0.000	0.000	0.000	0.000
37	A	87	SER	0	0.046	0.010	34.637	-0.105	-0.105	0.000	0.000	0.000	0.000
38	A	88	ILE	0	-0.032	0.002	29.542	-0.062	-0.062	0.000	0.000	0.000	0.000
39	A	89	GLU	-1	-0.875	-0.942	32.488	8.686	8.686	0.000	0.000	0.000	0.000
40	A	90	GLU	-1	-0.872	-0.929	27.784	11.332	11.332	0.000	0.000	0.000	0.000
41	A	91	ALA	0	0.002	-0.003	26.953	-0.311	-0.311	0.000	0.000	0.000	0.000
42	A	92	VAL	0	0.031	0.019	28.471	0.271	0.271	0.000	0.000	0.000	0.000
43	A	93	PRO	0	0.032	0.030	27.913	-0.051	-0.051	0.000	0.000	0.000	0.000
44	A	94	ALA	0	0.012	0.003	29.615	-0.379	-0.379	0.000	0.000	0.000	0.000
45	A	95	VAL	0	0.012	0.000	30.889	0.100	0.100	0.000	0.000	0.000	0.000
46	A	96	CYS	0	0.005	0.025	27.236	-0.541	-0.541	0.000	0.000	0.000	0.000
47	A	97	LYS	1	0.961	0.982	32.523	-8.016	-8.016	0.000	0.000	0.000	0.000
48	A	98	THR	0	0.027	-0.002	36.293	0.069	0.069	0.000	0.000	0.000	0.000
49	A	99	ARG	1	0.788	0.881	34.410	-8.614	-8.614	0.000	0.000	0.000	0.000
50	A	100	THR	0	-0.027	-0.020	40.097	0.017	0.017	0.000	0.000	0.000	0.000
51	A	101	VAL	0	-0.016	0.013	37.269	0.151	0.151	0.000	0.000	0.000	0.000
52	A	102	ILE	0	0.015	0.000	40.669	-0.176	-0.176	0.000	0.000	0.000	0.000
53	A	103	TYR	0	-0.013	-0.003	41.247	0.195	0.195	0.000	0.000	0.000	0.000
54	A	104	GLU	-1	-0.897	-0.956	43.265	6.584	6.584	0.000	0.000	0.000	0.000
55	A	105	ILE	0	-0.038	-0.022	45.012	0.048	0.048	0.000	0.000	0.000	0.000
56	A	106	PRO	0	0.024	0.013	43.997	-0.041	-0.041	0.000	0.000	0.000	0.000
57	A	107	ARG	1	0.943	0.968	46.089	-5.978	-5.978	0.000	0.000	0.000	0.000
58	A	108	SER	0	0.058	0.013	45.166	-0.124	-0.124	0.000	0.000	0.000	0.000
59	A	109	GLN	0	-0.019	-0.008	46.741	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	110	VAL	0	-0.050	-0.024	49.104	-0.102	-0.102	0.000	0.000	0.000	0.000
61	A	111	ASP	-1	-0.797	-0.894	51.842	5.239	5.239	0.000	0.000	0.000	0.000
62	A	112	PRO	0	-0.013	-0.004	49.921	0.059	0.059	0.000	0.000	0.000	0.000
63	A	113	THR	0	-0.036	-0.006	51.116	0.029	0.029	0.000	0.000	0.000	0.000
64	A	114	SER	0	-0.055	-0.028	53.965	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	115	ALA	0	0.076	0.020	52.131	0.067	0.067	0.000	0.000	0.000	0.000
66	A	116	ASN	0	-0.060	-0.023	53.388	0.052	0.052	0.000	0.000	0.000	0.000
67	A	117	PHE	0	-0.065	-0.036	52.171	-0.118	-0.118	0.000	0.000	0.000	0.000
68	A	118	LEU	0	0.002	0.018	54.676	0.106	0.106	0.000	0.000	0.000	0.000
69	A	119	ILE	0	0.023	0.002	50.719	-0.065	-0.065	0.000	0.000	0.000	0.000
70	A	120	TRP	0	0.012	0.020	53.948	0.049	0.049	0.000	0.000	0.000	0.000
71	A	121	PRO	0	0.041	0.013	52.182	-0.093	-0.093	0.000	0.000	0.000	0.000
72	A	122	PRO	0	0.016	0.001	49.874	0.028	0.028	0.000	0.000	0.000	0.000
73	A	123	CYS	0	-0.001	-0.003	46.348	0.120	0.120	0.000	0.000	0.000	0.000
74	A	124	VAL	0	-0.024	-0.005	46.807	-0.143	-0.143	0.000	0.000	0.000	0.000
75	A	125	GLU	-1	-0.823	-0.904	45.326	6.712	6.712	0.000	0.000	0.000	0.000
76	A	126	VAL	0	-0.045	-0.019	41.916	-0.103	-0.103	0.000	0.000	0.000	0.000
77	A	127	LYS	1	0.886	0.924	42.280	-6.581	-6.581	0.000	0.000	0.000	0.000
78	A	128	ARG	1	0.880	0.933	37.532	-7.484	-7.484	0.000	0.000	0.000	0.000
79	A	129	CYS	0	-0.045	-0.002	34.531	-0.047	-0.047	0.000	0.000	0.000	0.000
80	A	130	THR	0	0.023	0.015	33.300	0.094	0.094	0.000	0.000	0.000	0.000
81	A	131	GLY	0	0.011	0.010	31.191	-0.068	-0.068	0.000	0.000	0.000	0.000
82	A	132	CYS	0	-0.060	-0.041	25.976	0.153	0.153	0.000	0.000	0.000	0.000
83	A	133	CYS	0	-0.019	-0.004	25.557	-0.367	-0.367	0.000	0.000	0.000	0.000
84	A	134	ASN	0	-0.031	-0.028	23.600	-0.058	-0.058	0.000	0.000	0.000	0.000
85	A	135	THR	0	0.018	0.012	19.387	0.400	0.400	0.000	0.000	0.000	0.000
86	A	136	SER	0	0.041	0.012	18.895	-0.305	-0.305	0.000	0.000	0.000	0.000
87	A	137	SER	0	0.023	0.030	18.787	-0.405	-0.405	0.000	0.000	0.000	0.000
88	A	138	VAL	0	-0.028	0.005	20.647	-0.464	-0.464	0.000	0.000	0.000	0.000
89	A	139	LYS	1	0.918	0.945	23.654	-11.697	-11.697	0.000	0.000	0.000	0.000
90	A	141	GLN	0	0.032	0.019	29.967	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	142	PRO	0	0.028	-0.010	32.730	-0.060	-0.060	0.000	0.000	0.000	0.000
92	A	143	SER	0	-0.036	-0.045	36.588	0.090	0.090	0.000	0.000	0.000	0.000
93	A	144	ARG	1	0.817	0.882	38.502	-7.260	-7.260	0.000	0.000	0.000	0.000
94	A	145	VAL	0	0.017	0.002	39.832	0.086	0.086	0.000	0.000	0.000	0.000
95	A	146	HIS	0	0.009	0.002	42.716	-0.091	-0.091	0.000	0.000	0.000	0.000
96	A	147	HIS	0	0.016	0.003	42.260	-0.099	-0.099	0.000	0.000	0.000	0.000
97	A	148	ARG	1	0.859	0.924	47.007	-6.398	-6.398	0.000	0.000	0.000	0.000
98	A	149	SER	0	-0.009	-0.035	49.411	0.124	0.124	0.000	0.000	0.000	0.000
99	A	150	VAL	0	-0.009	0.008	51.072	-0.062	-0.062	0.000	0.000	0.000	0.000
100	A	151	LYS	1	0.822	0.889	53.622	-5.020	-5.020	0.000	0.000	0.000	0.000
101	A	152	VAL	0	0.014	0.016	52.426	0.013	0.013	0.000	0.000	0.000	0.000
102	A	153	ALA	0	0.027	0.013	55.766	-0.065	-0.065	0.000	0.000	0.000	0.000
103	A	154	LYS	1	0.838	0.925	56.025	-5.182	-5.182	0.000	0.000	0.000	0.000
104	A	155	VAL	0	0.002	-0.011	57.742	-0.117	-0.117	0.000	0.000	0.000	0.000
105	A	156	GLU	-1	-0.768	-0.879	58.982	5.080	5.080	0.000	0.000	0.000	0.000
106	A	157	TYR	0	0.035	0.004	61.225	-0.071	-0.071	0.000	0.000	0.000	0.000
107	A	158	VAL	0	0.012	0.014	64.279	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	159	ARG	1	0.946	0.978	66.114	-4.359	-4.359	0.000	0.000	0.000	0.000
109	A	160	LYS	1	1.022	1.007	67.632	-4.244	-4.244	0.000	0.000	0.000	0.000
110	A	161	LYS	1	0.948	0.959	68.666	-4.171	-4.171	0.000	0.000	0.000	0.000
111	A	162	PRO	0	0.051	0.045	65.618	0.025	0.025	0.000	0.000	0.000	0.000
112	A	163	LYS	1	0.868	0.931	64.640	-4.551	-4.551	0.000	0.000	0.000	0.000
113	A	164	LEU	0	0.048	0.023	61.674	0.067	0.067	0.000	0.000	0.000	0.000
114	A	165	LYS	1	0.838	0.917	59.792	-5.029	-5.029	0.000	0.000	0.000	0.000
115	A	166	GLU	-1	-0.792	-0.873	59.513	5.042	5.042	0.000	0.000	0.000	0.000
116	A	167	VAL	0	-0.013	-0.005	54.415	-0.040	-0.040	0.000	0.000	0.000	0.000
117	A	168	GLN	0	0.017	0.017	53.507	0.136	0.136	0.000	0.000	0.000	0.000
118	A	169	VAL	0	0.017	0.012	48.737	0.045	0.045	0.000	0.000	0.000	0.000
119	A	170	ARG	1	0.892	0.934	47.366	-6.087	-6.087	0.000	0.000	0.000	0.000
120	A	171	LEU	0	-0.022	-0.005	45.869	0.080	0.080	0.000	0.000	0.000	0.000
121	A	172	GLU	-1	-0.787	-0.879	39.495	7.458	7.458	0.000	0.000	0.000	0.000
122	A	173	GLU	-1	-0.811	-0.867	42.583	6.611	6.611	0.000	0.000	0.000	0.000
123	A	174	HIS	0	-0.010	-0.030	36.539	0.113	0.113	0.000	0.000	0.000	0.000
124	A	175	LEU	0	-0.036	-0.015	41.060	-0.015	-0.015	0.000	0.000	0.000	0.000
125	A	176	GLU	-1	-0.780	-0.829	39.483	7.405	7.405	0.000	0.000	0.000	0.000
126	A	178	ALA	0	0.046	0.029	33.547	-0.046	-0.046	0.000	0.000	0.000	0.000
127	A	180	ALA	0	0.026	0.015	26.578	0.163	0.163	0.000	0.000	0.000	0.000

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