FMO DATABASE

FMODB ID: N1V1Q

Calculation Name: 3MJK-B-Xray317

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: B

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-896128.586441
FMO2-HF: Nuclear repulsion	845058.693198
FMO2-HF: Total energy	-51069.893242
FMO2-MP2: Total energy	-51214.97333

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(B:22:ACE )

Summations of interaction energy for fragment #1(B: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.
0.77	1.481	-0.005	-0.313	-0.392	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / 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].
3	B	24	GLU	-1	-0.924	-0.952	3.839	0.365	1.076	-0.005	-0.313	-0.392
4	B	25	ILE	0	-0.018	-0.012	6.833	0.079	0.079	0.000	0.000	0.000
5	B	26	PRO	0	0.059	0.028	8.595	0.029	0.029	0.000	0.000	0.000
6	B	27	ARG	1	0.991	0.993	11.611	0.270	0.270	0.000	0.000	0.000
7	B	28	GLU	-1	-0.876	-0.938	14.501	-0.145	-0.145	0.000	0.000	0.000
8	B	29	VAL	0	-0.012	-0.020	12.010	0.038	0.038	0.000	0.000	0.000
9	B	30	ILE	0	-0.007	0.003	12.689	0.041	0.041	0.000	0.000	0.000
10	B	31	GLU	-1	-0.898	-0.957	15.832	-0.085	-0.085	0.000	0.000	0.000
11	B	32	ARG	1	0.920	0.966	15.160	0.047	0.047	0.000	0.000	0.000
12	B	33	LEU	0	0.024	-0.001	14.574	0.013	0.013	0.000	0.000	0.000
13	B	34	ALA	0	-0.061	-0.027	18.996	0.011	0.011	0.000	0.000	0.000
14	B	35	ARG	1	0.894	0.969	21.307	0.062	0.062	0.000	0.000	0.000
15	B	36	SER	0	-0.024	-0.007	21.532	0.001	0.001	0.000	0.000	0.000
16	B	37	GLN	0	-0.002	-0.004	23.602	0.007	0.007	0.000	0.000	0.000
17	B	38	ILE	0	-0.022	-0.015	19.310	0.004	0.004	0.000	0.000	0.000
18	B	39	HIS	0	-0.004	-0.001	23.466	0.004	0.004	0.000	0.000	0.000
19	B	40	SER	0	-0.025	-0.007	23.328	0.006	0.006	0.000	0.000	0.000
20	B	41	ILE	0	0.024	0.000	17.707	-0.001	-0.001	0.000	0.000	0.000
21	B	42	ARG	1	0.925	0.973	18.956	-0.096	-0.096	0.000	0.000	0.000
22	B	43	ASP	-1	-0.838	-0.923	20.389	0.056	0.056	0.000	0.000	0.000
23	B	44	LEU	0	0.013	0.019	15.073	-0.006	-0.006	0.000	0.000	0.000
24	B	45	GLN	0	0.031	0.011	15.710	-0.021	-0.021	0.000	0.000	0.000
25	B	46	ARG	1	0.880	0.934	17.064	-0.077	-0.077	0.000	0.000	0.000
26	B	47	LEU	0	-0.043	-0.024	18.157	-0.013	-0.013	0.000	0.000	0.000
27	B	48	LEU	0	-0.131	-0.073	12.269	-0.026	-0.026	0.000	0.000	0.000
28	B	49	GLU	-1	-0.926	-0.933	14.004	0.012	0.012	0.000	0.000	0.000
29	B	50	ILE	0	-0.019	-0.018	13.705	0.018	0.018	0.000	0.000	0.000
30	B	51	NME	0	-0.053	-0.020	12.176	0.011	0.011	0.000	0.000	0.000
31	B	86	ACE	0	0.007	-0.009	27.248	0.000	0.000	0.000	0.000	0.000
32	B	87	SER	0	-0.048	-0.033	27.405	0.001	0.001	0.000	0.000	0.000
33	B	88	ILE	0	-0.004	0.006	24.494	-0.008	-0.008	0.000	0.000	0.000
34	B	89	GLU	-1	-0.932	-0.965	25.746	0.090	0.090	0.000	0.000	0.000
35	B	90	GLU	-1	-0.801	-0.898	22.729	0.127	0.127	0.000	0.000	0.000
36	B	91	ALA	0	-0.006	-0.006	22.607	-0.010	-0.010	0.000	0.000	0.000
37	B	92	VAL	0	0.041	0.020	24.111	0.000	0.000	0.000	0.000	0.000
38	B	93	PRO	0	-0.002	0.009	23.873	-0.001	-0.001	0.000	0.000	0.000
39	B	94	ALA	0	0.018	0.008	25.614	-0.007	-0.007	0.000	0.000	0.000
40	B	95	VAL	0	0.027	-0.006	27.385	-0.003	-0.003	0.000	0.000	0.000
41	B	140	CYS	0	-0.024	0.004	26.351	-0.003	-0.003	0.000	0.000	0.000
42	B	97	LYS	1	0.973	0.970	30.011	-0.029	-0.029	0.000	0.000	0.000
43	B	98	THR	0	0.071	0.041	33.775	0.001	0.001	0.000	0.000	0.000
44	B	99	ARG	1	0.782	0.886	31.160	-0.030	-0.030	0.000	0.000	0.000
45	B	100	THR	0	-0.028	-0.011	37.553	-0.001	-0.001	0.000	0.000	0.000
46	B	101	VAL	0	0.038	0.015	35.816	0.002	0.002	0.000	0.000	0.000
47	B	102	ILE	0	0.045	0.012	39.044	-0.002	-0.002	0.000	0.000	0.000
48	B	103	TYR	0	-0.026	-0.008	40.042	-0.001	-0.001	0.000	0.000	0.000
49	B	104	GLU	-1	-0.884	-0.950	41.882	0.016	0.016	0.000	0.000	0.000
50	B	105	ILE	0	-0.069	-0.035	44.151	-0.001	-0.001	0.000	0.000	0.000
51	B	106	PRO	0	0.012	0.008	44.076	0.000	0.000	0.000	0.000	0.000
52	B	107	ARG	1	0.980	0.977	46.163	-0.009	-0.009	0.000	0.000	0.000
53	B	108	SER	0	0.011	-0.005	46.153	0.000	0.000	0.000	0.000	0.000
54	B	109	GLN	0	0.009	-0.001	46.652	-0.002	-0.002	0.000	0.000	0.000
55	B	110	VAL	0	-0.037	0.002	49.786	0.000	0.000	0.000	0.000	0.000
56	B	111	ASP	-1	-0.843	-0.959	52.792	0.002	0.002	0.000	0.000	0.000
57	B	112	PRO	0	-0.039	-0.009	50.835	0.001	0.001	0.000	0.000	0.000
58	B	113	THR	0	-0.008	0.003	52.098	0.000	0.000	0.000	0.000	0.000
59	B	114	SER	0	-0.038	-0.005	54.335	0.000	0.000	0.000	0.000	0.000
60	B	115	ALA	0	0.068	0.021	52.931	0.000	0.000	0.000	0.000	0.000
61	B	116	ASN	0	-0.049	-0.017	54.167	0.001	0.001	0.000	0.000	0.000
62	B	117	PHE	0	-0.053	-0.030	52.262	0.000	0.000	0.000	0.000	0.000
63	B	118	LEU	0	-0.014	-0.006	53.650	0.001	0.001	0.000	0.000	0.000
64	B	119	ILE	0	0.008	0.014	50.229	-0.001	-0.001	0.000	0.000	0.000
65	B	120	TRP	0	0.040	0.044	53.064	0.001	0.001	0.000	0.000	0.000
66	B	121	PRO	0	0.056	0.011	51.144	-0.001	-0.001	0.000	0.000	0.000
67	B	122	PRO	0	0.026	-0.013	48.411	-0.001	-0.001	0.000	0.000	0.000
68	B	123	CYS	0	-0.021	0.004	44.868	0.000	0.000	0.000	0.000	0.000
69	B	124	VAL	0	-0.020	-0.004	45.703	0.000	0.000	0.000	0.000	0.000
70	B	125	GLU	-1	-0.899	-0.947	43.772	0.018	0.018	0.000	0.000	0.000
71	B	126	VAL	0	-0.030	-0.001	40.730	-0.002	-0.002	0.000	0.000	0.000
72	B	127	LYS	1	0.917	0.968	40.406	-0.014	-0.014	0.000	0.000	0.000
73	B	128	ARG	1	0.883	0.933	36.349	-0.009	-0.009	0.000	0.000	0.000
74	B	177	CYS	0	-0.072	0.006	33.227	0.002	0.002	0.000	0.000	0.000
75	B	130	THR	0	0.010	0.008	31.501	0.001	0.001	0.000	0.000	0.000
76	B	131	GLY	0	0.034	0.015	28.628	0.000	0.000	0.000	0.000	0.000
77	B	132	CYS	0	-0.049	-0.031	23.639	-0.002	-0.002	0.000	0.000	0.000
78	B	179	CYS	0	-0.020	0.011	23.478	0.001	0.001	0.000	0.000	0.000
79	B	134	ASN	0	0.006	0.001	19.748	0.013	0.013	0.000	0.000	0.000
80	B	135	THR	0	0.033	0.021	16.741	0.004	0.004	0.000	0.000	0.000
81	B	136	SER	0	0.036	0.012	17.661	0.000	0.000	0.000	0.000	0.000
82	B	137	SER	0	-0.047	-0.019	18.817	-0.009	-0.009	0.000	0.000	0.000
83	B	138	VAL	0	0.009	-0.002	20.625	-0.005	-0.005	0.000	0.000	0.000
84	B	139	LYS	1	0.868	0.952	23.730	0.044	0.044	0.000	0.000	0.000
85	B	141	GLN	0	0.020	0.007	29.112	0.003	0.003	0.000	0.000	0.000
86	B	142	PRO	0	0.061	-0.009	32.149	0.001	0.001	0.000	0.000	0.000
87	B	143	SER	0	-0.021	-0.019	35.781	-0.002	-0.002	0.000	0.000	0.000
88	B	144	ARG	1	0.921	0.961	37.633	0.002	0.002	0.000	0.000	0.000
89	B	145	VAL	0	0.028	0.020	39.746	0.002	0.002	0.000	0.000	0.000
90	B	146	HIS	0	-0.009	-0.001	42.262	-0.001	-0.001	0.000	0.000	0.000
91	B	147	HIS	0	-0.001	0.007	43.105	0.001	0.001	0.000	0.000	0.000
92	B	148	ARG	1	0.894	0.923	47.297	-0.006	-0.006	0.000	0.000	0.000
93	B	149	SER	0	0.000	-0.014	49.978	0.000	0.000	0.000	0.000	0.000
94	B	150	VAL	0	-0.014	0.006	50.909	0.000	0.000	0.000	0.000	0.000
95	B	151	LYS	1	0.909	0.969	53.781	-0.005	-0.005	0.000	0.000	0.000
96	B	152	VAL	0	0.003	0.010	51.894	0.001	0.001	0.000	0.000	0.000
97	B	153	ALA	0	0.003	-0.015	55.283	-0.001	-0.001	0.000	0.000	0.000
98	B	154	LYS	1	0.878	0.971	56.209	-0.003	-0.003	0.000	0.000	0.000
99	B	155	VAL	0	-0.007	-0.032	57.474	0.000	0.000	0.000	0.000	0.000
100	B	156	GLU	-1	-0.801	-0.902	58.630	0.004	0.004	0.000	0.000	0.000
101	B	157	TYR	0	0.023	0.017	60.966	0.000	0.000	0.000	0.000	0.000
102	B	158	VAL	0	0.019	0.041	64.135	0.000	0.000	0.000	0.000	0.000
103	B	159	ARG	1	0.984	0.970	66.722	-0.004	-0.004	0.000	0.000	0.000
104	B	160	LYN	0	0.071	0.007	64.915	0.000	0.000	0.000	0.000	0.000
105	B	161	LYS	1	0.887	0.965	68.110	-0.005	-0.005	0.000	0.000	0.000
106	B	162	PRO	0	0.014	-0.007	64.684	0.000	0.000	0.000	0.000	0.000
107	B	163	LYS	1	0.856	0.948	63.036	-0.004	-0.004	0.000	0.000	0.000
108	B	164	LEU	0	0.027	-0.003	60.804	0.000	0.000	0.000	0.000	0.000
109	B	165	LYS	1	0.891	0.950	60.124	-0.003	-0.003	0.000	0.000	0.000
110	B	166	GLU	-1	-0.844	-0.929	59.432	0.005	0.005	0.000	0.000	0.000
111	B	167	VAL	0	-0.027	0.003	54.848	-0.001	-0.001	0.000	0.000	0.000
112	B	168	GLN	0	-0.014	-0.012	54.686	0.001	0.001	0.000	0.000	0.000
113	B	169	VAL	0	0.015	0.001	49.191	-0.001	-0.001	0.000	0.000	0.000
114	B	170	ARG	1	0.959	0.982	48.078	0.003	0.003	0.000	0.000	0.000
115	B	171	LEU	0	-0.006	-0.003	45.956	0.001	0.001	0.000	0.000	0.000
116	B	172	GLU	-1	-0.842	-0.914	39.400	-0.002	-0.002	0.000	0.000	0.000
117	B	173	GLU	-1	-0.847	-0.895	41.984	0.010	0.010	0.000	0.000	0.000
118	B	174	HIS	0	0.008	-0.018	36.007	0.000	0.000	0.000	0.000	0.000
119	B	175	LEU	0	-0.059	-0.038	40.308	0.001	0.001	0.000	0.000	0.000
120	B	176	GLU	-1	-0.900	-0.952	38.184	0.000	0.000	0.000	0.000	0.000
121	B	178	ALA	0	0.030	0.021	31.847	0.000	0.000	0.000	0.000	0.000
122	B	180	ALA	0	0.041	0.015	28.109	-0.004	-0.004	0.000	0.000	0.000
123	B	181	THR	0	-0.011	-0.004	23.418	0.002	0.002	0.000	0.000	0.000
124	B	182	THR	0	0.014	-0.008	25.454	-0.001	-0.001	0.000	0.000	0.000
125	B	183	NME	0	0.043	0.032	25.008	-0.003	-0.003	0.000	0.000	0.000

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