FMO DATABASE

FMODB ID: 82V8Y

Calculation Name: 3MJK-Y-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: Y

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-926457.322856
FMO2-HF: Nuclear repulsion	874122.726917
FMO2-HF: Total energy	-52334.595939
FMO2-MP2: Total energy	-52483.060796

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:23:ALA)

Summations of interaction energy for fragment #1(Y: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.
0.723	2.699	-0.013	-1.173	-0.79	0.004

Interaction energy analysis for fragmet #1(Y:23:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	Y	25	ILE	0	-0.012	-0.009	3.893	-0.713	1.263	-0.013	-1.173	-0.790	0.004
4	Y	26	PRO	0	0.041	0.019	6.010	0.329	0.329	0.000	0.000	0.000	0.000
5	Y	27	ARG	1	0.898	0.922	8.043	0.456	0.456	0.000	0.000	0.000	0.000
6	Y	28	GLU	-1	-0.813	-0.892	11.436	-0.249	-0.249	0.000	0.000	0.000	0.000
7	Y	29	VAL	0	0.040	0.026	10.226	0.050	0.050	0.000	0.000	0.000	0.000
8	Y	30	ILE	0	0.012	0.002	10.765	0.058	0.058	0.000	0.000	0.000	0.000
9	Y	31	GLU	-1	-0.842	-0.919	13.419	-0.281	-0.281	0.000	0.000	0.000	0.000
10	Y	32	ARG	1	0.757	0.852	15.427	0.324	0.324	0.000	0.000	0.000	0.000
11	Y	33	LEU	0	0.036	0.026	13.275	0.036	0.036	0.000	0.000	0.000	0.000
12	Y	34	ALA	0	-0.051	-0.015	17.295	0.039	0.039	0.000	0.000	0.000	0.000
13	Y	35	ARG	1	0.788	0.894	17.569	0.307	0.307	0.000	0.000	0.000	0.000
14	Y	36	SER	0	-0.012	-0.015	19.863	0.025	0.025	0.000	0.000	0.000	0.000
15	Y	37	GLN	0	-0.054	-0.031	22.667	-0.014	-0.014	0.000	0.000	0.000	0.000
16	Y	38	ILE	0	0.013	0.003	18.573	-0.007	-0.007	0.000	0.000	0.000	0.000
17	Y	39	HIS	0	-0.076	-0.055	22.827	0.008	0.008	0.000	0.000	0.000	0.000
18	Y	40	SER	0	-0.065	-0.056	23.244	0.012	0.012	0.000	0.000	0.000	0.000
19	Y	41	ILE	0	0.031	0.013	18.319	-0.023	-0.023	0.000	0.000	0.000	0.000
20	Y	42	ARG	0	0.044	0.024	19.214	-0.034	-0.034	0.000	0.000	0.000	0.000
21	Y	43	ASP	-1	-0.829	-0.891	20.938	-0.178	-0.178	0.000	0.000	0.000	0.000
22	Y	44	LEU	0	0.014	-0.001	15.069	-0.011	-0.011	0.000	0.000	0.000	0.000
23	Y	45	GLN	0	-0.048	-0.034	16.214	-0.029	-0.029	0.000	0.000	0.000	0.000
24	Y	46	ARG	1	0.876	0.937	17.003	0.154	0.154	0.000	0.000	0.000	0.000
25	Y	47	LEU	0	0.005	0.009	18.026	0.007	0.007	0.000	0.000	0.000	0.000
26	Y	48	LEU	0	-0.070	-0.026	11.614	-0.052	-0.052	0.000	0.000	0.000	0.000
27	Y	49	GLU	-1	-0.835	-0.895	13.399	-0.181	-0.181	0.000	0.000	0.000	0.000
28	Y	50	ILE	0	-0.034	-0.010	12.256	0.032	0.032	0.000	0.000	0.000	0.000
29	Y	51	ASP	-1	-0.892	-0.955	14.980	0.018	0.018	0.000	0.000	0.000	0.000
30	Y	52	SER	0	-0.059	-0.031	17.852	0.007	0.007	0.000	0.000	0.000	0.000
31	Y	53	VAL	0	0.000	0.000	19.892	-0.021	-0.021	0.000	0.000	0.000	0.000
32	Y	54	GLY	0	0.022	0.031	16.530	0.007	0.007	0.000	0.000	0.000	0.000
33	Y	55	SER	0	-0.037	-0.015	16.976	0.016	0.016	0.000	0.000	0.000	0.000
34	Y	87	SER	0	-0.025	-0.027	28.487	-0.002	-0.002	0.000	0.000	0.000	0.000
35	Y	88	ILE	0	-0.015	-0.011	24.524	0.003	0.003	0.000	0.000	0.000	0.000
36	Y	89	GLU	-1	-0.947	-0.964	27.485	-0.131	-0.131	0.000	0.000	0.000	0.000
37	Y	90	GLU	-1	-0.762	-0.859	23.579	-0.196	-0.196	0.000	0.000	0.000	0.000
38	Y	91	ALA	0	0.004	-0.010	22.747	0.007	0.007	0.000	0.000	0.000	0.000
39	Y	92	VAL	0	0.022	0.017	24.099	-0.017	-0.017	0.000	0.000	0.000	0.000
40	Y	93	PRO	0	0.033	0.029	23.551	-0.005	-0.005	0.000	0.000	0.000	0.000
41	Y	94	ALA	0	0.020	0.004	25.309	0.019	0.019	0.000	0.000	0.000	0.000
42	Y	95	VAL	0	0.004	-0.004	27.001	-0.010	-0.010	0.000	0.000	0.000	0.000
43	Y	96	CYS	0	0.019	0.033	24.639	0.034	0.034	0.000	0.000	0.000	0.000
44	Y	97	LYS	1	0.961	0.980	28.810	0.139	0.139	0.000	0.000	0.000	0.000
45	Y	98	THR	0	0.045	0.016	32.666	-0.005	-0.005	0.000	0.000	0.000	0.000
46	Y	99	ARG	1	0.781	0.891	30.420	0.167	0.167	0.000	0.000	0.000	0.000
47	Y	100	THR	0	-0.017	-0.016	36.907	0.000	0.000	0.000	0.000	0.000	0.000
48	Y	101	VAL	0	-0.019	0.011	35.029	-0.005	-0.005	0.000	0.000	0.000	0.000
49	Y	102	ILE	0	0.031	0.009	38.352	0.006	0.006	0.000	0.000	0.000	0.000
50	Y	103	TYR	0	-0.001	-0.001	39.430	-0.004	-0.004	0.000	0.000	0.000	0.000
51	Y	104	GLU	-1	-0.904	-0.959	41.496	-0.087	-0.087	0.000	0.000	0.000	0.000
52	Y	105	ILE	0	-0.025	-0.014	43.752	-0.002	-0.002	0.000	0.000	0.000	0.000
53	Y	106	PRO	0	0.002	0.005	43.237	0.002	0.002	0.000	0.000	0.000	0.000
54	Y	107	ARG	1	0.942	0.949	45.729	0.068	0.068	0.000	0.000	0.000	0.000
55	Y	108	SER	0	0.034	0.005	45.146	0.003	0.003	0.000	0.000	0.000	0.000
56	Y	109	GLN	0	-0.040	-0.026	45.264	0.003	0.003	0.000	0.000	0.000	0.000
57	Y	110	VAL	0	-0.043	-0.006	48.791	0.002	0.002	0.000	0.000	0.000	0.000
58	Y	111	ASP	-1	-0.771	-0.886	51.839	-0.049	-0.049	0.000	0.000	0.000	0.000
59	Y	112	PRO	0	-0.006	-0.002	50.113	0.000	0.000	0.000	0.000	0.000	0.000
60	Y	113	THR	0	-0.041	-0.016	51.791	0.000	0.000	0.000	0.000	0.000	0.000
61	Y	114	SER	0	-0.043	-0.015	54.430	0.003	0.003	0.000	0.000	0.000	0.000
62	Y	115	ALA	0	0.017	0.007	53.072	-0.002	-0.002	0.000	0.000	0.000	0.000
63	Y	116	ASN	0	-0.046	-0.023	52.799	-0.002	-0.002	0.000	0.000	0.000	0.000
64	Y	117	PHE	0	0.006	0.002	51.891	0.002	0.002	0.000	0.000	0.000	0.000
65	Y	118	LEU	0	0.012	0.009	52.528	-0.003	-0.003	0.000	0.000	0.000	0.000
66	Y	119	ILE	0	0.013	0.008	49.361	0.002	0.002	0.000	0.000	0.000	0.000
67	Y	120	TRP	0	0.019	0.027	52.616	-0.001	-0.001	0.000	0.000	0.000	0.000
68	Y	121	PRO	0	0.057	0.023	50.541	0.002	0.002	0.000	0.000	0.000	0.000
69	Y	122	PRO	0	0.008	-0.004	48.461	-0.001	-0.001	0.000	0.000	0.000	0.000
70	Y	123	CYS	0	-0.009	-0.001	44.653	-0.003	-0.003	0.000	0.000	0.000	0.000
71	Y	124	VAL	0	-0.015	-0.001	45.038	0.004	0.004	0.000	0.000	0.000	0.000
72	Y	125	GLU	-1	-0.827	-0.908	42.778	-0.093	-0.093	0.000	0.000	0.000	0.000
73	Y	126	VAL	0	-0.070	-0.027	39.902	0.003	0.003	0.000	0.000	0.000	0.000
74	Y	127	LYS	1	0.903	0.924	39.845	0.090	0.090	0.000	0.000	0.000	0.000
75	Y	128	ARG	1	0.870	0.921	35.630	0.115	0.115	0.000	0.000	0.000	0.000
76	Y	129	CYS	0	-0.070	-0.031	32.083	0.000	0.000	0.000	0.000	0.000	0.000
77	Y	130	THR	0	0.011	0.010	30.839	-0.004	-0.004	0.000	0.000	0.000	0.000
78	Y	131	GLY	0	0.021	0.015	27.870	0.005	0.005	0.000	0.000	0.000	0.000
79	Y	132	CYS	0	-0.048	-0.032	22.720	-0.005	-0.005	0.000	0.000	0.000	0.000
80	Y	133	CYS	0	-0.002	-0.001	22.411	0.025	0.025	0.000	0.000	0.000	0.000
81	Y	134	ASN	0	-0.006	-0.007	18.719	-0.014	-0.014	0.000	0.000	0.000	0.000
82	Y	135	THR	0	0.018	0.015	14.714	-0.042	-0.042	0.000	0.000	0.000	0.000
83	Y	136	SER	0	0.039	0.018	16.336	0.055	0.055	0.000	0.000	0.000	0.000
84	Y	137	SER	0	-0.020	-0.002	16.429	0.024	0.024	0.000	0.000	0.000	0.000
85	Y	138	VAL	0	-0.025	-0.008	18.259	0.044	0.044	0.000	0.000	0.000	0.000
86	Y	139	LYS	1	0.903	0.949	20.380	0.348	0.348	0.000	0.000	0.000	0.000
87	Y	141	GLN	0	-0.045	-0.030	27.797	0.006	0.006	0.000	0.000	0.000	0.000
88	Y	142	PRO	0	0.046	0.004	30.629	0.003	0.003	0.000	0.000	0.000	0.000
89	Y	143	SER	0	-0.017	-0.018	34.412	-0.002	-0.002	0.000	0.000	0.000	0.000
90	Y	144	ARG	1	0.818	0.888	35.721	0.105	0.105	0.000	0.000	0.000	0.000
91	Y	145	VAL	0	0.008	0.011	37.805	-0.002	-0.002	0.000	0.000	0.000	0.000
92	Y	146	HIS	0	0.019	0.005	40.226	0.003	0.003	0.000	0.000	0.000	0.000
93	Y	147	HIS	0	0.023	0.010	40.842	0.002	0.002	0.000	0.000	0.000	0.000
94	Y	148	ARG	1	0.844	0.914	45.692	0.080	0.080	0.000	0.000	0.000	0.000
95	Y	149	SER	0	0.007	-0.006	48.753	-0.003	-0.003	0.000	0.000	0.000	0.000
96	Y	150	VAL	0	-0.022	-0.004	50.070	0.000	0.000	0.000	0.000	0.000	0.000
97	Y	151	LYS	1	0.863	0.902	52.559	0.049	0.049	0.000	0.000	0.000	0.000
98	Y	152	VAL	0	0.005	0.016	51.241	-0.001	-0.001	0.000	0.000	0.000	0.000
99	Y	153	ALA	0	0.023	0.010	54.686	0.002	0.002	0.000	0.000	0.000	0.000
100	Y	154	LYS	1	0.799	0.890	55.566	0.049	0.049	0.000	0.000	0.000	0.000
101	Y	155	VAL	0	-0.013	-0.021	56.880	0.003	0.003	0.000	0.000	0.000	0.000
102	Y	156	GLU	-1	-0.759	-0.863	57.900	-0.046	-0.046	0.000	0.000	0.000	0.000
103	Y	157	TYR	0	0.039	0.008	60.543	0.001	0.001	0.000	0.000	0.000	0.000
104	Y	158	VAL	0	0.026	0.023	62.917	0.001	0.001	0.000	0.000	0.000	0.000
105	Y	159	ARG	1	0.947	0.950	65.023	0.035	0.035	0.000	0.000	0.000	0.000
106	Y	160	LYS	1	0.975	0.989	66.594	0.032	0.032	0.000	0.000	0.000	0.000
107	Y	161	LYS	1	0.990	1.008	67.171	0.032	0.032	0.000	0.000	0.000	0.000
108	Y	162	PRO	0	0.042	0.031	64.327	-0.001	-0.001	0.000	0.000	0.000	0.000
109	Y	163	LYS	1	0.842	0.917	63.659	0.041	0.041	0.000	0.000	0.000	0.000
110	Y	164	LEU	0	0.051	0.030	60.583	-0.001	-0.001	0.000	0.000	0.000	0.000
111	Y	165	LYS	1	0.826	0.897	59.626	0.047	0.047	0.000	0.000	0.000	0.000
112	Y	166	GLU	-1	-0.805	-0.875	58.767	-0.049	-0.049	0.000	0.000	0.000	0.000
113	Y	167	VAL	0	-0.030	-0.009	54.325	0.001	0.001	0.000	0.000	0.000	0.000
114	Y	168	GLN	0	0.024	0.017	53.330	-0.001	-0.001	0.000	0.000	0.000	0.000
115	Y	169	VAL	0	0.005	0.006	48.491	-0.001	-0.001	0.000	0.000	0.000	0.000
116	Y	170	ARG	1	0.905	0.946	43.781	0.084	0.084	0.000	0.000	0.000	0.000
117	Y	171	LEU	0	-0.008	0.003	45.104	-0.002	-0.002	0.000	0.000	0.000	0.000
118	Y	172	GLU	-1	-0.803	-0.890	38.178	-0.115	-0.115	0.000	0.000	0.000	0.000
119	Y	173	GLU	-1	-0.787	-0.873	40.917	-0.089	-0.089	0.000	0.000	0.000	0.000
120	Y	174	HIS	0	-0.016	-0.024	35.018	-0.004	-0.004	0.000	0.000	0.000	0.000
121	Y	175	LEU	0	-0.022	-0.014	39.170	0.001	0.001	0.000	0.000	0.000	0.000
122	Y	176	GLU	-1	-0.788	-0.850	36.779	-0.104	-0.104	0.000	0.000	0.000	0.000
123	Y	178	ALA	0	0.050	0.033	30.120	0.004	0.004	0.000	0.000	0.000	0.000
124	Y	180	ALA	0	0.023	0.017	26.414	0.004	0.004	0.000	0.000	0.000	0.000
125	Y	181	THR	0	0.030	0.006	22.456	-0.028	-0.028	0.000	0.000	0.000	0.000
126	Y	182	THR	0	-0.009	0.002	22.721	0.003	0.003	0.000	0.000	0.000	0.000

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