FMO DATABASE

FMODB ID: VR8R1

Calculation Name: 3MJK-Y-Xray317

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: Y

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:

Apendix: None

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
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-936813.454808
FMO2-HF: Nuclear repulsion	884139.07587
FMO2-HF: Total energy	-52674.378938
FMO2-MP2: Total energy	-52824.083817

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(Y:22:ACE )

Summations of interaction energy for fragment #1(Y: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.
0.807	1.639	-0.005	-0.383	-0.443	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.008

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	Y	24	GLU	-1	-0.928	-0.949	3.843	0.152	0.984	-0.005	-0.383	-0.443
4	Y	25	ILE	0	-0.008	-0.002	7.042	0.108	0.108	0.000	0.000	0.000
5	Y	26	PRO	0	0.019	0.001	8.560	0.007	0.007	0.000	0.000	0.000
6	Y	27	ARG	1	1.005	0.985	11.592	0.246	0.246	0.000	0.000	0.000
7	Y	28	GLU	-1	-0.854	-0.917	14.964	-0.102	-0.102	0.000	0.000	0.000
8	Y	29	VAL	0	-0.006	-0.006	11.955	0.034	0.034	0.000	0.000	0.000
9	Y	30	ILE	0	0.004	0.003	12.875	0.033	0.033	0.000	0.000	0.000
10	Y	31	GLU	-1	-0.931	-0.971	15.892	-0.086	-0.086	0.000	0.000	0.000
11	Y	32	ARG	1	0.946	0.976	15.502	0.028	0.028	0.000	0.000	0.000
12	Y	33	LEU	0	-0.001	-0.002	14.519	0.011	0.011	0.000	0.000	0.000
13	Y	34	ALA	0	-0.025	-0.002	19.063	0.009	0.009	0.000	0.000	0.000
14	Y	35	ARG	1	0.876	0.954	21.285	0.054	0.054	0.000	0.000	0.000
15	Y	36	SER	0	-0.031	-0.031	21.245	0.007	0.007	0.000	0.000	0.000
16	Y	37	GLN	0	-0.023	-0.013	23.906	-0.002	-0.002	0.000	0.000	0.000
17	Y	38	ILE	0	0.002	0.009	19.316	0.005	0.005	0.000	0.000	0.000
18	Y	39	HIS	0	-0.085	-0.053	23.461	-0.006	-0.006	0.000	0.000	0.000
19	Y	40	SER	0	-0.079	-0.047	23.404	-0.002	-0.002	0.000	0.000	0.000
20	Y	41	ILE	0	0.058	0.038	17.955	0.003	0.003	0.000	0.000	0.000
21	Y	42	ARG	0	0.089	0.055	19.321	0.013	0.013	0.000	0.000	0.000
22	Y	43	ASP	-1	-0.866	-0.954	20.889	0.060	0.060	0.000	0.000	0.000
23	Y	44	LEU	0	-0.014	-0.005	15.712	-0.006	-0.006	0.000	0.000	0.000
24	Y	45	GLN	0	-0.040	-0.025	16.259	-0.012	-0.012	0.000	0.000	0.000
25	Y	46	ARG	1	0.977	1.005	16.999	-0.086	-0.086	0.000	0.000	0.000
26	Y	47	LEU	0	-0.022	0.000	18.394	-0.006	-0.006	0.000	0.000	0.000
27	Y	48	LEU	0	-0.103	-0.064	12.308	-0.019	-0.019	0.000	0.000	0.000
28	Y	49	GLU	-1	-0.974	-0.974	14.115	0.058	0.058	0.000	0.000	0.000
29	Y	50	ILE	0	-0.100	-0.035	11.814	0.030	0.030	0.000	0.000	0.000
30	Y	51	ASP	-1	-0.860	-0.951	14.206	0.173	0.173	0.000	0.000	0.000
31	Y	52	SER	0	-0.095	-0.044	16.722	-0.029	-0.029	0.000	0.000	0.000
32	Y	53	VAL	0	-0.004	-0.005	18.133	-0.013	-0.013	0.000	0.000	0.000
33	Y	54	GLY	0	-0.012	0.016	15.405	0.000	0.000	0.000	0.000	0.000
34	Y	55	SER	0	-0.013	-0.014	16.047	0.007	0.007	0.000	0.000	0.000
35	Y	56	NME	0	0.010	0.014	17.732	-0.023	-0.023	0.000	0.000	0.000
36	Y	86	ACE	0	0.011	-0.006	27.453	0.001	0.001	0.000	0.000	0.000
37	Y	87	SER	0	-0.053	-0.034	27.631	-0.002	-0.002	0.000	0.000	0.000
38	Y	88	ILE	0	-0.004	0.008	23.517	-0.006	-0.006	0.000	0.000	0.000
39	Y	89	GLU	-1	-0.950	-0.971	26.378	0.072	0.072	0.000	0.000	0.000
40	Y	90	GLU	-1	-0.823	-0.920	23.048	0.114	0.114	0.000	0.000	0.000
41	Y	91	ALA	0	-0.004	-0.005	22.825	-0.010	-0.010	0.000	0.000	0.000
42	Y	92	VAL	0	0.034	0.014	24.533	0.001	0.001	0.000	0.000	0.000
43	Y	93	PRO	0	0.018	0.015	24.380	-0.005	-0.005	0.000	0.000	0.000
44	Y	94	ALA	0	0.020	0.009	26.004	-0.005	-0.005	0.000	0.000	0.000
45	Y	95	VAL	0	0.040	-0.001	27.832	-0.005	-0.005	0.000	0.000	0.000
46	Y	140	CYS	0	-0.026	0.022	26.605	-0.001	-0.001	0.000	0.000	0.000
47	Y	97	LYS	1	0.960	0.974	30.429	-0.017	-0.017	0.000	0.000	0.000
48	Y	98	THR	0	0.059	0.022	34.196	-0.001	-0.001	0.000	0.000	0.000
49	Y	99	ARG	1	0.744	0.859	31.337	-0.012	-0.012	0.000	0.000	0.000
50	Y	100	THR	0	-0.042	-0.014	37.863	-0.002	-0.002	0.000	0.000	0.000
51	Y	101	VAL	0	0.042	0.025	36.236	0.001	0.001	0.000	0.000	0.000
52	Y	102	ILE	0	0.049	0.019	39.270	-0.001	-0.001	0.000	0.000	0.000
53	Y	103	TYR	0	-0.022	-0.005	40.478	-0.001	-0.001	0.000	0.000	0.000
54	Y	104	GLU	-1	-0.891	-0.968	42.492	-0.001	-0.001	0.000	0.000	0.000
55	Y	105	ILE	0	-0.048	-0.030	44.506	-0.002	-0.002	0.000	0.000	0.000
56	Y	106	PRO	0	0.015	0.003	44.434	0.000	0.000	0.000	0.000	0.000
57	Y	107	ARG	1	0.963	0.970	46.840	0.005	0.005	0.000	0.000	0.000
58	Y	108	SER	0	0.024	0.002	46.398	0.000	0.000	0.000	0.000	0.000
59	Y	109	GLN	0	-0.008	-0.007	46.863	-0.001	-0.001	0.000	0.000	0.000
60	Y	110	VAL	0	-0.037	0.004	50.249	0.000	0.000	0.000	0.000	0.000
61	Y	111	ASP	-1	-0.812	-0.907	53.430	-0.008	-0.008	0.000	0.000	0.000
62	Y	112	PRO	0	0.036	0.020	52.354	0.000	0.000	0.000	0.000	0.000
63	Y	113	THR	0	-0.067	-0.021	53.633	0.000	0.000	0.000	0.000	0.000
64	Y	114	SER	0	-0.048	-0.042	55.934	0.001	0.001	0.000	0.000	0.000
65	Y	115	ALA	0	0.023	0.020	54.549	0.000	0.000	0.000	0.000	0.000
66	Y	116	ASN	0	-0.050	-0.018	54.396	0.000	0.000	0.000	0.000	0.000
67	Y	117	PHE	0	0.017	-0.002	53.427	0.000	0.000	0.000	0.000	0.000
68	Y	118	LEU	0	-0.031	-0.023	53.473	0.000	0.000	0.000	0.000	0.000
69	Y	119	ILE	0	0.012	0.042	50.313	0.000	0.000	0.000	0.000	0.000
70	Y	120	TRP	0	0.040	0.029	53.375	0.001	0.001	0.000	0.000	0.000
71	Y	121	PRO	0	0.059	0.016	51.195	0.000	0.000	0.000	0.000	0.000
72	Y	122	PRO	0	0.012	-0.009	48.836	-0.001	-0.001	0.000	0.000	0.000
73	Y	123	CYS	0	-0.032	0.002	45.224	-0.001	-0.001	0.000	0.000	0.000
74	Y	124	VAL	0	-0.006	0.005	46.044	0.001	0.001	0.000	0.000	0.000
75	Y	125	GLU	-1	-0.900	-0.945	43.984	0.007	0.007	0.000	0.000	0.000
76	Y	126	VAL	0	-0.046	-0.012	41.248	-0.001	-0.001	0.000	0.000	0.000
77	Y	127	LYS	1	0.945	0.965	40.748	-0.005	-0.005	0.000	0.000	0.000
78	Y	128	ARG	1	0.885	0.937	36.652	0.006	0.006	0.000	0.000	0.000
79	Y	177	CYS	0	-0.066	0.005	33.573	0.001	0.001	0.000	0.000	0.000
80	Y	130	THR	0	0.019	0.002	31.747	0.000	0.000	0.000	0.000	0.000
81	Y	131	GLY	0	0.033	0.010	28.922	0.002	0.002	0.000	0.000	0.000
82	Y	132	CYS	0	-0.073	-0.033	23.828	-0.005	-0.005	0.000	0.000	0.000
83	Y	179	CYS	0	-0.028	0.018	23.851	0.004	0.004	0.000	0.000	0.000
84	Y	134	ASN	0	0.014	-0.003	20.041	0.009	0.009	0.000	0.000	0.000
85	Y	135	THR	0	0.028	0.020	16.809	0.009	0.009	0.000	0.000	0.000
86	Y	136	SER	0	-0.010	-0.021	18.141	0.003	0.003	0.000	0.000	0.000
87	Y	137	SER	0	-0.004	0.010	19.116	-0.005	-0.005	0.000	0.000	0.000
88	Y	138	VAL	0	-0.006	0.005	20.924	-0.002	-0.002	0.000	0.000	0.000
89	Y	139	LYN	0	0.030	0.022	23.236	0.004	0.004	0.000	0.000	0.000
90	Y	141	GLN	0	-0.003	-0.014	29.453	-0.005	-0.005	0.000	0.000	0.000
91	Y	142	PRO	0	0.045	-0.009	32.513	0.002	0.002	0.000	0.000	0.000
92	Y	143	SER	0	-0.009	-0.013	36.227	-0.002	-0.002	0.000	0.000	0.000
93	Y	144	ARG	1	0.924	0.961	37.877	0.009	0.009	0.000	0.000	0.000
94	Y	145	VAL	0	0.005	0.007	39.943	0.001	0.001	0.000	0.000	0.000
95	Y	146	HIS	0	-0.004	0.002	42.549	-0.001	-0.001	0.000	0.000	0.000
96	Y	147	HIS	0	0.023	0.002	43.655	0.001	0.001	0.000	0.000	0.000
97	Y	148	ARG	1	0.879	0.922	47.603	0.003	0.003	0.000	0.000	0.000
98	Y	149	SER	0	0.024	0.007	50.357	0.000	0.000	0.000	0.000	0.000
99	Y	150	VAL	0	-0.020	0.002	51.205	0.001	0.001	0.000	0.000	0.000
100	Y	151	LYS	1	0.952	0.970	54.158	0.002	0.002	0.000	0.000	0.000
101	Y	152	VAL	0	0.008	0.023	52.119	0.001	0.001	0.000	0.000	0.000
102	Y	153	ALA	0	0.001	-0.009	55.516	0.000	0.000	0.000	0.000	0.000
103	Y	154	LYS	1	0.810	0.916	56.680	0.006	0.006	0.000	0.000	0.000
104	Y	155	VAL	0	-0.002	-0.023	57.790	0.000	0.000	0.000	0.000	0.000
105	Y	156	GLU	-1	-0.844	-0.944	59.006	-0.005	-0.005	0.000	0.000	0.000
106	Y	157	TYR	0	0.016	0.003	61.517	0.001	0.001	0.000	0.000	0.000
107	Y	158	VAL	0	0.017	0.032	63.891	0.000	0.000	0.000	0.000	0.000
108	Y	159	ARG	1	0.946	0.950	66.128	0.004	0.004	0.000	0.000	0.000
109	Y	160	LYS	1	0.962	0.962	67.711	0.002	0.002	0.000	0.000	0.000
110	Y	161	LYS	1	1.023	1.012	67.930	0.002	0.002	0.000	0.000	0.000
111	Y	162	PRO	0	0.015	0.024	65.288	0.000	0.000	0.000	0.000	0.000
112	Y	163	LYS	1	0.913	0.967	64.479	0.003	0.003	0.000	0.000	0.000
113	Y	164	LEU	0	0.028	0.023	61.392	0.000	0.000	0.000	0.000	0.000
114	Y	165	LYS	1	0.895	0.949	60.986	0.005	0.005	0.000	0.000	0.000
115	Y	166	GLU	-1	-0.880	-0.946	59.984	-0.002	-0.002	0.000	0.000	0.000
116	Y	167	VAL	0	-0.006	0.002	55.659	0.000	0.000	0.000	0.000	0.000
117	Y	168	GLN	0	-0.026	-0.011	55.088	0.001	0.001	0.000	0.000	0.000
118	Y	169	VAL	0	0.009	0.005	49.701	-0.001	-0.001	0.000	0.000	0.000
119	Y	170	ARG	1	0.923	0.966	46.290	0.014	0.014	0.000	0.000	0.000
120	Y	171	LEU	0	-0.020	-0.011	46.492	0.000	0.000	0.000	0.000	0.000
121	Y	172	GLU	-1	-0.866	-0.933	39.878	-0.014	-0.014	0.000	0.000	0.000
122	Y	173	GLU	-1	-0.806	-0.884	42.376	0.000	0.000	0.000	0.000	0.000
123	Y	174	HIS	0	0.022	0.011	36.276	0.000	0.000	0.000	0.000	0.000
124	Y	175	LEU	0	-0.042	-0.023	40.583	0.002	0.002	0.000	0.000	0.000
125	Y	176	GLU	-1	-0.902	-0.959	38.511	-0.005	-0.005	0.000	0.000	0.000
126	Y	178	ALA	0	0.029	0.017	32.058	0.002	0.002	0.000	0.000	0.000
127	Y	180	ALA	0	0.027	0.000	28.507	-0.001	-0.001	0.000	0.000	0.000
128	Y	181	THR	0	0.001	-0.001	25.441	-0.004	-0.004	0.000	0.000	0.000
129	Y	182	THR	0	-0.019	-0.014	25.847	0.002	0.002	0.000	0.000	0.000
130	Y	183	NME	0	0.012	0.023	23.404	-0.005	-0.005	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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