FMO DATABASE

FMODB ID: 14L2Z

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	OptH
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	-927706.03695
FMO2-HF: Nuclear repulsion	875373.176124
FMO2-HF: Total energy	-52332.860826
FMO2-MP2: Total energy	-52481.486945

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.
0.104	2.682	-0.015	-1.479	-1.085	0.005

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 : 0.014 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	Y	25	ILE	0	-0.011	-0.004	3.742	-1.391	1.187	-0.015	-1.479	-1.085	0.005
4	Y	26	PRO	0	0.022	0.004	5.524	0.368	0.368	0.000	0.000	0.000	0.000
5	Y	27	ARG	1	0.998	0.982	7.947	0.466	0.466	0.000	0.000	0.000	0.000
6	Y	28	GLU	-1	-0.850	-0.916	11.264	-0.248	-0.248	0.000	0.000	0.000	0.000
7	Y	29	VAL	0	-0.002	-0.004	9.761	0.062	0.062	0.000	0.000	0.000	0.000
8	Y	30	ILE	0	0.003	0.002	10.654	0.068	0.068	0.000	0.000	0.000	0.000
9	Y	31	GLU	-1	-0.938	-0.975	13.335	-0.266	-0.266	0.000	0.000	0.000	0.000
10	Y	32	ARG	1	0.950	0.977	13.570	0.416	0.416	0.000	0.000	0.000	0.000
11	Y	33	LEU	0	0.006	0.002	13.217	0.036	0.036	0.000	0.000	0.000	0.000
12	Y	34	ALA	0	-0.034	-0.010	17.296	0.041	0.041	0.000	0.000	0.000	0.000
13	Y	35	ARG	1	0.873	0.951	18.241	0.313	0.313	0.000	0.000	0.000	0.000
14	Y	36	SER	0	-0.027	-0.028	19.540	0.023	0.023	0.000	0.000	0.000	0.000
15	Y	37	GLN	0	-0.022	-0.011	22.245	-0.020	-0.020	0.000	0.000	0.000	0.000
16	Y	38	ILE	0	0.000	0.007	18.359	-0.002	-0.002	0.000	0.000	0.000	0.000
17	Y	39	HIS	0	-0.081	-0.052	22.618	0.010	0.010	0.000	0.000	0.000	0.000
18	Y	40	SER	0	-0.076	-0.044	22.935	0.013	0.013	0.000	0.000	0.000	0.000
19	Y	41	ILE	0	0.055	0.037	18.018	-0.025	-0.025	0.000	0.000	0.000	0.000
20	Y	42	ARG	0	0.093	0.056	19.277	-0.038	-0.038	0.000	0.000	0.000	0.000
21	Y	43	ASP	-1	-0.867	-0.954	20.884	-0.219	-0.219	0.000	0.000	0.000	0.000
22	Y	44	LEU	0	-0.018	-0.007	15.179	-0.012	-0.012	0.000	0.000	0.000	0.000
23	Y	45	GLN	0	-0.038	-0.023	16.277	-0.009	-0.009	0.000	0.000	0.000	0.000
24	Y	46	ARG	1	0.978	1.005	16.933	0.175	0.175	0.000	0.000	0.000	0.000
25	Y	47	LEU	0	-0.024	-0.001	17.561	-0.003	-0.003	0.000	0.000	0.000	0.000
26	Y	48	LEU	0	-0.104	-0.065	11.721	-0.032	-0.032	0.000	0.000	0.000	0.000
27	Y	49	GLU	-1	-0.973	-0.973	13.869	-0.220	-0.220	0.000	0.000	0.000	0.000
28	Y	50	ILE	0	-0.098	-0.034	12.081	0.016	0.016	0.000	0.000	0.000	0.000
29	Y	51	ASP	-1	-0.857	-0.949	14.633	-0.050	-0.050	0.000	0.000	0.000	0.000
30	Y	52	SER	0	-0.092	-0.044	17.509	0.010	0.010	0.000	0.000	0.000	0.000
31	Y	53	VAL	0	-0.009	-0.005	19.263	-0.013	-0.013	0.000	0.000	0.000	0.000
32	Y	54	GLY	0	-0.010	0.018	16.786	0.016	0.016	0.000	0.000	0.000	0.000
33	Y	55	SER	0	-0.002	0.000	17.505	0.016	0.016	0.000	0.000	0.000	0.000
34	Y	87	SER	0	-0.030	-0.027	28.285	-0.001	-0.001	0.000	0.000	0.000	0.000
35	Y	88	ILE	0	-0.010	-0.006	24.260	0.005	0.005	0.000	0.000	0.000	0.000
36	Y	89	GLU	-1	-0.956	-0.973	27.009	-0.151	-0.151	0.000	0.000	0.000	0.000
37	Y	90	GLU	-1	-0.820	-0.919	23.137	-0.230	-0.230	0.000	0.000	0.000	0.000
38	Y	91	ALA	0	-0.005	-0.005	22.718	0.008	0.008	0.000	0.000	0.000	0.000
39	Y	92	VAL	0	0.034	0.015	24.313	-0.011	-0.011	0.000	0.000	0.000	0.000
40	Y	93	PRO	0	0.017	0.015	23.561	-0.002	-0.002	0.000	0.000	0.000	0.000
41	Y	94	ALA	0	0.021	0.010	25.320	0.022	0.022	0.000	0.000	0.000	0.000
42	Y	95	VAL	0	0.041	-0.001	26.858	-0.011	-0.011	0.000	0.000	0.000	0.000
43	Y	96	CYS	0	-0.009	0.031	24.624	0.027	0.027	0.000	0.000	0.000	0.000
44	Y	97	LYS	1	0.961	0.975	29.069	0.155	0.155	0.000	0.000	0.000	0.000
45	Y	98	THR	0	0.064	0.023	32.849	-0.006	-0.006	0.000	0.000	0.000	0.000
46	Y	99	ARG	1	0.744	0.860	30.375	0.179	0.179	0.000	0.000	0.000	0.000
47	Y	100	THR	0	-0.037	-0.012	36.773	-0.002	-0.002	0.000	0.000	0.000	0.000
48	Y	101	VAL	0	0.037	0.023	35.042	-0.005	-0.005	0.000	0.000	0.000	0.000
49	Y	102	ILE	0	0.052	0.021	38.158	0.006	0.006	0.000	0.000	0.000	0.000
50	Y	103	TYR	0	-0.023	-0.006	39.283	-0.003	-0.003	0.000	0.000	0.000	0.000
51	Y	104	GLU	-1	-0.889	-0.967	41.284	-0.088	-0.088	0.000	0.000	0.000	0.000
52	Y	105	ILE	0	-0.047	-0.030	43.259	-0.001	-0.001	0.000	0.000	0.000	0.000
53	Y	106	PRO	0	0.013	0.003	42.988	0.002	0.002	0.000	0.000	0.000	0.000
54	Y	107	ARG	1	0.964	0.970	45.412	0.066	0.066	0.000	0.000	0.000	0.000
55	Y	108	SER	0	0.023	0.000	44.590	0.003	0.003	0.000	0.000	0.000	0.000
56	Y	109	GLN	0	-0.009	-0.008	45.273	0.004	0.004	0.000	0.000	0.000	0.000
57	Y	110	VAL	0	-0.036	0.004	48.536	0.002	0.002	0.000	0.000	0.000	0.000
58	Y	111	ASP	-1	-0.810	-0.906	51.843	-0.049	-0.049	0.000	0.000	0.000	0.000
59	Y	112	PRO	0	0.036	0.020	50.299	0.000	0.000	0.000	0.000	0.000	0.000
60	Y	113	THR	0	-0.067	-0.021	51.705	0.001	0.001	0.000	0.000	0.000	0.000
61	Y	114	SER	0	-0.048	-0.042	54.140	0.003	0.003	0.000	0.000	0.000	0.000
62	Y	115	ALA	0	0.024	0.021	52.964	-0.002	-0.002	0.000	0.000	0.000	0.000
63	Y	116	ASN	0	-0.050	-0.019	52.979	-0.001	-0.001	0.000	0.000	0.000	0.000
64	Y	117	PHE	0	0.016	-0.001	51.970	0.002	0.002	0.000	0.000	0.000	0.000
65	Y	118	LEU	0	-0.031	-0.023	52.346	-0.002	-0.002	0.000	0.000	0.000	0.000
66	Y	119	ILE	0	0.014	0.042	49.132	0.002	0.002	0.000	0.000	0.000	0.000
67	Y	120	TRP	0	0.038	0.029	52.220	-0.001	-0.001	0.000	0.000	0.000	0.000
68	Y	121	PRO	0	0.058	0.017	50.081	0.002	0.002	0.000	0.000	0.000	0.000
69	Y	122	PRO	0	0.016	-0.009	47.739	-0.001	-0.001	0.000	0.000	0.000	0.000
70	Y	123	CYS	0	-0.037	0.000	44.118	-0.004	-0.004	0.000	0.000	0.000	0.000
71	Y	124	VAL	0	0.000	0.008	44.852	0.004	0.004	0.000	0.000	0.000	0.000
72	Y	125	GLU	-1	-0.902	-0.946	42.865	-0.093	-0.093	0.000	0.000	0.000	0.000
73	Y	126	VAL	0	-0.048	-0.011	39.954	0.003	0.003	0.000	0.000	0.000	0.000
74	Y	127	LYS	1	0.948	0.965	39.519	0.100	0.100	0.000	0.000	0.000	0.000
75	Y	128	ARG	1	0.886	0.938	35.252	0.122	0.122	0.000	0.000	0.000	0.000
76	Y	129	CYS	0	-0.075	0.001	31.960	0.002	0.002	0.000	0.000	0.000	0.000
77	Y	130	THR	0	0.022	0.004	30.455	-0.004	-0.004	0.000	0.000	0.000	0.000
78	Y	131	GLY	0	0.038	0.012	27.853	0.008	0.008	0.000	0.000	0.000	0.000
79	Y	132	CYS	0	-0.078	-0.036	22.595	-0.003	-0.003	0.000	0.000	0.000	0.000
80	Y	133	CYS	0	-0.023	0.017	22.152	0.023	0.023	0.000	0.000	0.000	0.000
81	Y	134	ASN	0	0.021	0.002	18.787	-0.008	-0.008	0.000	0.000	0.000	0.000
82	Y	135	THR	0	0.042	0.035	15.161	-0.037	-0.037	0.000	0.000	0.000	0.000
83	Y	136	SER	0	0.005	-0.011	16.420	0.059	0.059	0.000	0.000	0.000	0.000
84	Y	137	SER	0	-0.032	-0.017	16.384	0.007	0.007	0.000	0.000	0.000	0.000
85	Y	138	VAL	0	-0.024	0.002	18.432	0.040	0.040	0.000	0.000	0.000	0.000
86	Y	139	LYS	1	0.966	0.989	20.776	0.331	0.331	0.000	0.000	0.000	0.000
87	Y	141	GLN	0	-0.017	-0.021	27.742	0.002	0.002	0.000	0.000	0.000	0.000
88	Y	142	PRO	0	0.056	-0.001	30.515	0.001	0.001	0.000	0.000	0.000	0.000
89	Y	143	SER	0	-0.014	-0.018	33.989	0.000	0.000	0.000	0.000	0.000	0.000
90	Y	144	ARG	1	0.931	0.965	35.506	0.107	0.107	0.000	0.000	0.000	0.000
91	Y	145	VAL	0	0.004	0.006	37.944	-0.003	-0.003	0.000	0.000	0.000	0.000
92	Y	146	HIS	0	-0.002	0.004	40.551	0.004	0.004	0.000	0.000	0.000	0.000
93	Y	147	HIS	0	0.024	0.001	41.525	0.000	0.000	0.000	0.000	0.000	0.000
94	Y	148	ARG	1	0.880	0.923	45.677	0.081	0.081	0.000	0.000	0.000	0.000
95	Y	149	SER	0	0.025	0.008	48.635	-0.003	-0.003	0.000	0.000	0.000	0.000
96	Y	150	VAL	0	-0.021	0.001	49.810	0.001	0.001	0.000	0.000	0.000	0.000
97	Y	151	LYS	1	0.953	0.971	52.692	0.050	0.050	0.000	0.000	0.000	0.000
98	Y	152	VAL	0	0.007	0.023	50.767	-0.001	-0.001	0.000	0.000	0.000	0.000
99	Y	153	ALA	0	0.002	-0.009	54.178	0.002	0.002	0.000	0.000	0.000	0.000
100	Y	154	LYS	1	0.808	0.915	55.401	0.048	0.048	0.000	0.000	0.000	0.000
101	Y	155	VAL	0	0.000	-0.023	56.530	0.002	0.002	0.000	0.000	0.000	0.000
102	Y	156	GLU	-1	-0.847	-0.945	57.775	-0.045	-0.045	0.000	0.000	0.000	0.000
103	Y	157	TYR	0	0.018	0.003	60.259	0.001	0.001	0.000	0.000	0.000	0.000
104	Y	158	VAL	0	0.017	0.031	62.702	0.001	0.001	0.000	0.000	0.000	0.000
105	Y	159	ARG	1	0.948	0.952	64.881	0.033	0.033	0.000	0.000	0.000	0.000
106	Y	160	LYS	1	0.962	0.962	66.624	0.031	0.031	0.000	0.000	0.000	0.000
107	Y	161	LYS	1	1.023	1.012	66.785	0.031	0.031	0.000	0.000	0.000	0.000
108	Y	162	PRO	0	0.015	0.024	64.129	-0.001	-0.001	0.000	0.000	0.000	0.000
109	Y	163	LYS	1	0.912	0.966	63.125	0.040	0.040	0.000	0.000	0.000	0.000
110	Y	164	LEU	0	0.026	0.022	60.135	-0.001	-0.001	0.000	0.000	0.000	0.000
111	Y	165	LYS	1	0.898	0.951	59.559	0.045	0.045	0.000	0.000	0.000	0.000
112	Y	166	GLU	-1	-0.881	-0.946	58.595	-0.049	-0.049	0.000	0.000	0.000	0.000
113	Y	167	VAL	0	-0.005	0.003	54.046	0.001	0.001	0.000	0.000	0.000	0.000
114	Y	168	GLN	0	-0.026	-0.011	53.315	-0.001	-0.001	0.000	0.000	0.000	0.000
115	Y	169	VAL	0	0.009	0.004	48.105	-0.001	-0.001	0.000	0.000	0.000	0.000
116	Y	170	ARG	1	0.922	0.966	44.020	0.084	0.084	0.000	0.000	0.000	0.000
117	Y	171	LEU	0	-0.018	-0.010	44.905	-0.003	-0.003	0.000	0.000	0.000	0.000
118	Y	172	GLU	-1	-0.868	-0.934	37.992	-0.116	-0.116	0.000	0.000	0.000	0.000
119	Y	173	GLU	-1	-0.805	-0.884	40.872	-0.094	-0.094	0.000	0.000	0.000	0.000
120	Y	174	HIS	0	0.019	0.010	34.578	-0.004	-0.004	0.000	0.000	0.000	0.000
121	Y	175	LEU	0	-0.039	-0.021	38.957	0.002	0.002	0.000	0.000	0.000	0.000
122	Y	176	GLU	-1	-0.896	-0.956	36.526	-0.110	-0.110	0.000	0.000	0.000	0.000
123	Y	178	ALA	0	0.034	0.020	29.965	0.004	0.004	0.000	0.000	0.000	0.000
124	Y	180	ALA	0	0.030	0.002	26.041	0.005	0.005	0.000	0.000	0.000	0.000
125	Y	181	THR	0	0.012	0.009	22.028	-0.026	-0.026	0.000	0.000	0.000	0.000
126	Y	182	THR	0	-0.003	0.002	21.760	0.013	0.013	0.000	0.000	0.000	0.000

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