FMO DATABASE

FMODB ID: 1424Z

Calculation Name: 3MJK-X-Xray317

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: X

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-870778.072485
FMO2-HF: Nuclear repulsion	820751.593522
FMO2-HF: Total energy	-50026.478962
FMO2-MP2: Total energy	-50168.532196

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(X:22:ACE )

Summations of interaction energy for fragment #1(X: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.
0.309	1.835	0.027	-0.67	-0.882	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.013

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	X	24	GLU	-1	-0.912	-0.949	3.845	0.034	1.310	-0.005	-0.578	-0.693	-0.002
4	X	25	ILE	0	-0.039	-0.017	3.331	-0.045	0.205	0.032	-0.092	-0.189	0.000
5	X	26	PRO	0	0.094	0.053	5.893	-0.158	-0.158	0.000	0.000	0.000	0.000
6	X	27	ARG	1	0.989	0.987	9.388	0.350	0.350	0.000	0.000	0.000	0.000
7	X	28	GLU	-1	-0.871	-0.937	10.818	0.080	0.080	0.000	0.000	0.000	0.000
8	X	29	VAL	0	0.047	0.028	8.784	0.043	0.043	0.000	0.000	0.000	0.000
9	X	30	ILE	0	0.004	0.004	6.071	0.028	0.028	0.000	0.000	0.000	0.000
10	X	31	GLU	-1	-0.926	-0.982	10.234	-0.063	-0.063	0.000	0.000	0.000	0.000
11	X	32	ARG	1	0.942	0.983	13.610	-0.133	-0.133	0.000	0.000	0.000	0.000
12	X	33	LEU	0	0.014	0.030	9.855	0.001	0.001	0.000	0.000	0.000	0.000
13	X	34	ALA	0	-0.040	-0.008	13.750	-0.005	-0.005	0.000	0.000	0.000	0.000
14	X	35	ARG	1	0.839	0.936	15.203	-0.039	-0.039	0.000	0.000	0.000	0.000
15	X	36	SER	0	-0.026	-0.057	17.206	-0.012	-0.012	0.000	0.000	0.000	0.000
16	X	37	GLN	0	-0.023	-0.007	19.110	0.005	0.005	0.000	0.000	0.000	0.000
17	X	38	ILE	0	-0.002	-0.003	15.133	0.005	0.005	0.000	0.000	0.000	0.000
18	X	39	HIS	0	-0.046	-0.034	19.288	0.004	0.004	0.000	0.000	0.000	0.000
19	X	40	SER	0	-0.003	0.005	20.586	-0.008	-0.008	0.000	0.000	0.000	0.000
20	X	41	ILE	0	0.003	-0.006	16.989	0.017	0.017	0.000	0.000	0.000	0.000
21	X	42	ARG	1	0.899	0.920	18.453	-0.125	-0.125	0.000	0.000	0.000	0.000
22	X	43	ASP	-1	-0.871	-0.938	20.294	0.145	0.145	0.000	0.000	0.000	0.000
23	X	44	LEU	0	-0.047	-0.039	12.934	0.003	0.003	0.000	0.000	0.000	0.000
24	X	45	GLN	0	0.017	0.015	15.863	-0.001	-0.001	0.000	0.000	0.000	0.000
25	X	46	ARG	0	0.155	0.116	17.391	-0.015	-0.015	0.000	0.000	0.000	0.000
26	X	47	LEU	0	-0.084	-0.024	17.345	-0.010	-0.010	0.000	0.000	0.000	0.000
27	X	48	LEU	0	-0.120	-0.061	11.272	0.016	0.016	0.000	0.000	0.000	0.000
28	X	49	GLU	-1	-0.990	-0.987	15.280	0.175	0.175	0.000	0.000	0.000	0.000
29	X	50	NME	0	-0.040	-0.031	17.019	-0.027	-0.027	0.000	0.000	0.000	0.000
30	X	87	ACE	0	-0.003	-0.015	22.727	0.005	0.005	0.000	0.000	0.000	0.000
31	X	88	ILE	0	-0.006	-0.016	23.349	-0.015	-0.015	0.000	0.000	0.000	0.000
32	X	89	GLU	-1	-0.969	-0.958	26.058	0.126	0.126	0.000	0.000	0.000	0.000
33	X	90	GLU	-1	-0.847	-0.917	20.957	0.219	0.219	0.000	0.000	0.000	0.000
34	X	91	ALA	0	-0.021	-0.016	19.444	-0.012	-0.012	0.000	0.000	0.000	0.000
35	X	92	VAL	0	0.051	0.025	21.217	0.006	0.006	0.000	0.000	0.000	0.000
36	X	93	PRO	0	-0.003	0.012	18.950	0.001	0.001	0.000	0.000	0.000	0.000
37	X	94	ALA	0	0.003	-0.006	20.631	-0.023	-0.023	0.000	0.000	0.000	0.000
38	X	95	VAL	0	0.066	0.016	21.174	0.005	0.005	0.000	0.000	0.000	0.000
39	X	140	CYS	0	-0.006	0.020	18.371	-0.017	-0.017	0.000	0.000	0.000	0.000
40	X	97	LYS	1	0.967	0.980	23.362	-0.085	-0.085	0.000	0.000	0.000	0.000
41	X	98	THR	0	0.044	0.018	27.047	0.002	0.002	0.000	0.000	0.000	0.000
42	X	99	ARG	1	0.754	0.863	24.909	-0.097	-0.097	0.000	0.000	0.000	0.000
43	X	100	THR	0	0.059	0.002	30.495	-0.003	-0.003	0.000	0.000	0.000	0.000
44	X	101	VAL	0	-0.022	0.007	28.362	0.005	0.005	0.000	0.000	0.000	0.000
45	X	102	ILE	0	0.047	0.014	31.600	-0.004	-0.004	0.000	0.000	0.000	0.000
46	X	103	TYR	0	-0.023	-0.013	32.351	0.000	0.000	0.000	0.000	0.000	0.000
47	X	104	GLU	-1	-0.897	-0.965	34.179	0.026	0.026	0.000	0.000	0.000	0.000
48	X	105	ILE	0	-0.056	-0.022	36.044	-0.002	-0.002	0.000	0.000	0.000	0.000
49	X	106	PRO	0	0.038	0.019	35.849	-0.001	-0.001	0.000	0.000	0.000	0.000
50	X	107	ARG	1	0.988	0.986	38.113	-0.014	-0.014	0.000	0.000	0.000	0.000
51	X	108	SER	0	0.051	0.027	37.627	0.000	0.000	0.000	0.000	0.000	0.000
52	X	109	GLN	0	-0.005	0.003	38.681	-0.002	-0.002	0.000	0.000	0.000	0.000
53	X	110	VAL	0	-0.060	-0.033	41.272	0.000	0.000	0.000	0.000	0.000	0.000
54	X	111	ASP	-1	-0.836	-0.913	44.176	0.002	0.002	0.000	0.000	0.000	0.000
55	X	112	PRO	0	-0.033	-0.007	42.104	0.001	0.001	0.000	0.000	0.000	0.000
56	X	113	THR	0	-0.073	-0.021	43.668	-0.001	-0.001	0.000	0.000	0.000	0.000
57	X	114	SER	0	-0.041	-0.053	45.911	0.000	0.000	0.000	0.000	0.000	0.000
58	X	115	ALA	0	0.047	0.014	44.029	0.001	0.001	0.000	0.000	0.000	0.000
59	X	116	ASN	0	-0.024	0.001	45.723	0.001	0.001	0.000	0.000	0.000	0.000
60	X	117	PHE	0	-0.040	-0.020	44.540	0.000	0.000	0.000	0.000	0.000	0.000
61	X	118	LEU	0	0.008	-0.013	45.330	0.001	0.001	0.000	0.000	0.000	0.000
62	X	119	ILE	0	0.005	0.016	42.198	-0.001	-0.001	0.000	0.000	0.000	0.000
63	X	120	TRP	0	-0.015	0.024	44.912	0.001	0.001	0.000	0.000	0.000	0.000
64	X	121	PRO	0	0.051	0.014	43.343	-0.001	-0.001	0.000	0.000	0.000	0.000
65	X	122	PRO	0	0.027	0.002	40.605	-0.001	-0.001	0.000	0.000	0.000	0.000
66	X	123	CYS	0	-0.021	-0.008	37.227	0.000	0.000	0.000	0.000	0.000	0.000
67	X	124	VAL	0	-0.010	0.000	37.913	-0.001	-0.001	0.000	0.000	0.000	0.000
68	X	125	GLU	-1	-0.912	-0.942	36.212	0.042	0.042	0.000	0.000	0.000	0.000
69	X	126	VAL	0	-0.032	-0.008	32.848	-0.003	-0.003	0.000	0.000	0.000	0.000
70	X	127	LYS	1	0.868	0.943	32.882	-0.044	-0.044	0.000	0.000	0.000	0.000
71	X	128	ARG	1	0.912	0.944	28.482	-0.037	-0.037	0.000	0.000	0.000	0.000
72	X	177	CYS	0	-0.045	0.015	25.526	0.002	0.002	0.000	0.000	0.000	0.000
73	X	130	THR	0	0.005	0.010	23.959	0.003	0.003	0.000	0.000	0.000	0.000
74	X	131	GLY	0	0.041	0.017	21.786	-0.002	-0.002	0.000	0.000	0.000	0.000
75	X	132	CYS	0	-0.042	-0.029	16.372	-0.002	-0.002	0.000	0.000	0.000	0.000
76	X	179	CYS	0	-0.016	0.014	16.395	-0.014	-0.014	0.000	0.000	0.000	0.000
77	X	134	ASN	0	0.001	0.004	14.574	0.028	0.028	0.000	0.000	0.000	0.000
78	X	135	THR	0	0.027	0.027	10.266	0.064	0.064	0.000	0.000	0.000	0.000
79	X	136	SER	0	0.052	0.010	9.537	-0.045	-0.045	0.000	0.000	0.000	0.000
80	X	137	SER	0	-0.047	-0.015	10.779	-0.037	-0.037	0.000	0.000	0.000	0.000
81	X	138	VAL	0	-0.045	-0.018	12.334	-0.046	-0.046	0.000	0.000	0.000	0.000
82	X	139	LYS	1	0.885	0.953	15.766	0.009	0.009	0.000	0.000	0.000	0.000
83	X	141	GLN	0	0.022	0.000	21.522	-0.001	-0.001	0.000	0.000	0.000	0.000
84	X	142	PRO	0	0.045	-0.010	24.196	0.004	0.004	0.000	0.000	0.000	0.000
85	X	143	SER	0	-0.010	-0.016	27.995	-0.004	-0.004	0.000	0.000	0.000	0.000
86	X	144	ARG	1	0.866	0.913	30.113	-0.028	-0.028	0.000	0.000	0.000	0.000
87	X	145	VAL	0	0.005	0.009	32.247	0.004	0.004	0.000	0.000	0.000	0.000
88	X	146	HIS	0	-0.013	-0.001	34.196	-0.002	-0.002	0.000	0.000	0.000	0.000
89	X	147	HIS	0	-0.020	-0.016	34.819	0.000	0.000	0.000	0.000	0.000	0.000
90	X	148	ARG	1	0.909	0.958	39.148	-0.023	-0.023	0.000	0.000	0.000	0.000
91	X	149	SER	0	-0.005	-0.005	41.867	0.000	0.000	0.000	0.000	0.000	0.000
92	X	150	VAL	0	-0.024	-0.001	42.927	0.001	0.001	0.000	0.000	0.000	0.000
93	X	151	LYS	1	0.863	0.924	45.640	-0.013	-0.013	0.000	0.000	0.000	0.000
94	X	152	VAL	0	-0.001	0.018	43.824	0.001	0.001	0.000	0.000	0.000	0.000
95	X	153	ALA	0	0.000	-0.014	47.251	-0.001	-0.001	0.000	0.000	0.000	0.000
96	X	154	LYS	1	0.891	0.967	48.235	-0.005	-0.005	0.000	0.000	0.000	0.000
97	X	155	VAL	0	0.001	-0.023	49.580	-0.001	-0.001	0.000	0.000	0.000	0.000
98	X	156	GLU	-1	-0.857	-0.943	50.591	0.006	0.006	0.000	0.000	0.000	0.000
99	X	157	TYR	0	0.045	0.009	53.032	0.000	0.000	0.000	0.000	0.000	0.000
100	X	158	VAL	0	-0.020	-0.008	56.006	-0.001	-0.001	0.000	0.000	0.000	0.000
101	X	159	ARG	1	0.995	0.984	58.647	-0.004	-0.004	0.000	0.000	0.000	0.000
102	X	160	LYS	1	0.964	0.977	60.044	-0.006	-0.006	0.000	0.000	0.000	0.000
103	X	161	LYS	1	0.958	0.982	60.735	-0.006	-0.006	0.000	0.000	0.000	0.000
104	X	162	PRO	0	0.016	0.044	57.050	0.000	0.000	0.000	0.000	0.000	0.000
105	X	163	LYS	1	0.931	0.964	55.770	-0.006	-0.006	0.000	0.000	0.000	0.000
106	X	164	LEU	0	0.038	0.012	53.066	0.000	0.000	0.000	0.000	0.000	0.000
107	X	165	LYS	1	0.947	0.989	52.349	-0.006	-0.006	0.000	0.000	0.000	0.000
108	X	166	GLU	-1	-0.815	-0.909	51.365	0.012	0.012	0.000	0.000	0.000	0.000
109	X	167	VAL	0	-0.025	-0.011	46.690	-0.001	-0.001	0.000	0.000	0.000	0.000
110	X	168	GLN	0	0.026	0.014	46.175	0.002	0.002	0.000	0.000	0.000	0.000
111	X	169	VAL	0	0.006	0.002	40.941	-0.001	-0.001	0.000	0.000	0.000	0.000
112	X	170	ARG	1	0.933	0.959	37.182	-0.006	-0.006	0.000	0.000	0.000	0.000
113	X	171	LEU	0	-0.010	0.002	38.028	0.001	0.001	0.000	0.000	0.000	0.000
114	X	172	GLU	-1	-0.846	-0.938	31.433	0.017	0.017	0.000	0.000	0.000	0.000
115	X	173	GLU	-1	-0.831	-0.902	34.168	0.035	0.035	0.000	0.000	0.000	0.000
116	X	174	HIS	0	0.013	0.000	27.889	0.002	0.002	0.000	0.000	0.000	0.000
117	X	175	LEU	0	-0.044	-0.030	32.473	0.002	0.002	0.000	0.000	0.000	0.000
118	X	176	GLU	-1	-0.853	-0.902	31.247	0.031	0.031	0.000	0.000	0.000	0.000
119	X	178	ALA	0	0.029	0.015	25.004	0.001	0.001	0.000	0.000	0.000	0.000
120	X	180	ALA	0	0.041	0.027	20.854	-0.005	-0.005	0.000	0.000	0.000	0.000
121	X	181	THR	0	0.018	-0.012	17.204	0.005	0.005	0.000	0.000	0.000	0.000
122	X	182	NME	0	0.033	0.021	18.337	0.000	0.000	0.000	0.000	0.000	0.000

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