FMO DATABASE

FMODB ID: GN2L1

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	OptHSide
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	-927462.754432
FMO2-HF: Nuclear repulsion	875128.774048
FMO2-HF: Total energy	-52333.980384
FMO2-MP2: Total energy	-52482.474356

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.
-0.018	2.614	-0.022	-1.534	-1.076	0.006

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 : 0.009 / q_NPA : 0.002

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	-0.015	-0.008	3.815	-1.387	1.245	-0.022	-1.534	-1.076	0.006
4	Y	26	PRO	0	0.034	0.012	5.882	0.343	0.343	0.000	0.000	0.000	0.000
5	Y	27	ARG	1	0.895	0.923	8.123	0.435	0.435	0.000	0.000	0.000	0.000
6	Y	28	GLU	-1	-0.905	-0.944	11.383	-0.240	-0.240	0.000	0.000	0.000	0.000
7	Y	29	VAL	0	0.036	0.012	10.068	0.052	0.052	0.000	0.000	0.000	0.000
8	Y	30	ILE	0	0.013	0.008	10.957	0.068	0.068	0.000	0.000	0.000	0.000
9	Y	31	GLU	-1	-0.852	-0.924	13.546	-0.274	-0.274	0.000	0.000	0.000	0.000
10	Y	32	ARG	1	0.818	0.897	15.622	0.355	0.355	0.000	0.000	0.000	0.000
11	Y	33	LEU	0	0.029	0.019	13.377	0.034	0.034	0.000	0.000	0.000	0.000
12	Y	34	ALA	0	-0.044	-0.009	17.505	0.037	0.037	0.000	0.000	0.000	0.000
13	Y	35	ARG	1	0.878	0.950	18.213	0.310	0.310	0.000	0.000	0.000	0.000
14	Y	36	SER	0	-0.020	-0.029	19.746	0.023	0.023	0.000	0.000	0.000	0.000
15	Y	37	GLN	0	-0.046	-0.024	22.449	-0.015	-0.015	0.000	0.000	0.000	0.000
16	Y	38	ILE	0	0.015	0.012	18.431	-0.002	-0.002	0.000	0.000	0.000	0.000
17	Y	39	HIS	0	-0.071	-0.055	22.632	0.008	0.008	0.000	0.000	0.000	0.000
18	Y	40	SER	0	-0.061	-0.055	22.936	0.012	0.012	0.000	0.000	0.000	0.000
19	Y	41	ILE	0	0.056	0.035	18.042	-0.024	-0.024	0.000	0.000	0.000	0.000
20	Y	42	ARG	0	0.026	0.025	19.290	-0.036	-0.036	0.000	0.000	0.000	0.000
21	Y	43	ASP	-1	-0.826	-0.902	20.894	-0.203	-0.203	0.000	0.000	0.000	0.000
22	Y	44	LEU	0	-0.014	-0.013	15.094	-0.013	-0.013	0.000	0.000	0.000	0.000
23	Y	45	GLN	0	-0.023	-0.016	16.282	-0.016	-0.016	0.000	0.000	0.000	0.000
24	Y	46	ARG	1	0.932	0.960	16.939	0.167	0.167	0.000	0.000	0.000	0.000
25	Y	47	LEU	0	-0.018	0.005	17.869	-0.003	-0.003	0.000	0.000	0.000	0.000
26	Y	48	LEU	0	-0.061	-0.042	11.673	-0.028	-0.028	0.000	0.000	0.000	0.000
27	Y	49	GLU	-1	-0.911	-0.931	13.871	-0.227	-0.227	0.000	0.000	0.000	0.000
28	Y	50	ILE	0	-0.078	-0.024	11.962	0.019	0.019	0.000	0.000	0.000	0.000
29	Y	51	ASP	-1	-0.885	-0.963	14.636	-0.038	-0.038	0.000	0.000	0.000	0.000
30	Y	52	SER	0	-0.062	-0.031	17.509	0.009	0.009	0.000	0.000	0.000	0.000
31	Y	53	VAL	0	-0.006	-0.005	19.271	-0.014	-0.014	0.000	0.000	0.000	0.000
32	Y	54	GLY	0	-0.018	0.017	16.793	0.015	0.015	0.000	0.000	0.000	0.000
33	Y	55	SER	0	-0.002	0.001	17.509	-0.001	-0.001	0.000	0.000	0.000	0.000
34	Y	87	SER	0	-0.033	-0.025	28.695	-0.004	-0.004	0.000	0.000	0.000	0.000
35	Y	88	ILE	0	-0.011	-0.011	24.375	0.004	0.004	0.000	0.000	0.000	0.000
36	Y	89	GLU	-1	-0.959	-0.970	26.996	-0.142	-0.142	0.000	0.000	0.000	0.000
37	Y	90	GLU	-1	-0.753	-0.861	23.213	-0.220	-0.220	0.000	0.000	0.000	0.000
38	Y	91	ALA	0	-0.010	-0.007	22.680	0.008	0.008	0.000	0.000	0.000	0.000
39	Y	92	VAL	0	0.037	0.014	24.333	-0.011	-0.011	0.000	0.000	0.000	0.000
40	Y	93	PRO	0	0.025	0.018	23.496	-0.002	-0.002	0.000	0.000	0.000	0.000
41	Y	94	ALA	0	0.002	0.006	25.340	0.022	0.022	0.000	0.000	0.000	0.000
42	Y	95	VAL	0	0.032	-0.004	26.853	-0.012	-0.012	0.000	0.000	0.000	0.000
43	Y	96	CYS	0	0.022	0.042	24.624	0.026	0.026	0.000	0.000	0.000	0.000
44	Y	97	LYS	1	0.980	0.979	29.089	0.148	0.148	0.000	0.000	0.000	0.000
45	Y	98	THR	0	0.038	0.014	32.868	-0.006	-0.006	0.000	0.000	0.000	0.000
46	Y	99	ARG	1	0.775	0.880	30.281	0.173	0.173	0.000	0.000	0.000	0.000
47	Y	100	THR	0	-0.044	-0.032	36.762	-0.002	-0.002	0.000	0.000	0.000	0.000
48	Y	101	VAL	0	-0.007	0.004	34.914	-0.004	-0.004	0.000	0.000	0.000	0.000
49	Y	102	ILE	0	0.040	0.014	38.149	0.006	0.006	0.000	0.000	0.000	0.000
50	Y	103	TYR	0	-0.002	0.002	39.276	-0.003	-0.003	0.000	0.000	0.000	0.000
51	Y	104	GLU	-1	-0.917	-0.967	41.088	-0.086	-0.086	0.000	0.000	0.000	0.000
52	Y	105	ILE	0	-0.037	-0.026	43.254	-0.001	-0.001	0.000	0.000	0.000	0.000
53	Y	106	PRO	0	0.024	0.009	42.992	0.002	0.002	0.000	0.000	0.000	0.000
54	Y	107	ARG	1	0.928	0.940	45.409	0.066	0.066	0.000	0.000	0.000	0.000
55	Y	108	SER	0	0.020	-0.002	44.588	0.003	0.003	0.000	0.000	0.000	0.000
56	Y	109	GLN	0	-0.021	-0.017	44.971	0.004	0.004	0.000	0.000	0.000	0.000
57	Y	110	VAL	0	-0.033	0.001	48.517	0.002	0.002	0.000	0.000	0.000	0.000
58	Y	111	ASP	-1	-0.791	-0.889	51.822	-0.048	-0.048	0.000	0.000	0.000	0.000
59	Y	112	PRO	0	0.021	0.015	50.238	0.000	0.000	0.000	0.000	0.000	0.000
60	Y	113	THR	0	-0.067	-0.025	51.687	0.001	0.001	0.000	0.000	0.000	0.000
61	Y	114	SER	0	-0.031	-0.030	54.105	0.003	0.003	0.000	0.000	0.000	0.000
62	Y	115	ALA	0	0.016	0.015	52.940	-0.002	-0.002	0.000	0.000	0.000	0.000
63	Y	116	ASN	0	-0.051	-0.019	52.952	-0.001	-0.001	0.000	0.000	0.000	0.000
64	Y	117	PHE	0	0.006	-0.002	51.843	0.002	0.002	0.000	0.000	0.000	0.000
65	Y	118	LEU	0	-0.009	-0.001	52.282	-0.002	-0.002	0.000	0.000	0.000	0.000
66	Y	119	ILE	0	0.025	0.037	48.835	0.002	0.002	0.000	0.000	0.000	0.000
67	Y	120	TRP	0	0.022	0.026	52.215	-0.001	-0.001	0.000	0.000	0.000	0.000
68	Y	121	PRO	0	0.067	0.019	50.031	0.002	0.002	0.000	0.000	0.000	0.000
69	Y	122	PRO	0	0.000	-0.002	47.705	-0.001	-0.001	0.000	0.000	0.000	0.000
70	Y	123	CYS	0	0.000	0.001	44.081	-0.003	-0.003	0.000	0.000	0.000	0.000
71	Y	124	VAL	0	-0.010	0.001	44.849	0.003	0.003	0.000	0.000	0.000	0.000
72	Y	125	GLU	-1	-0.846	-0.907	42.852	-0.094	-0.094	0.000	0.000	0.000	0.000
73	Y	126	VAL	0	-0.067	-0.024	39.778	0.003	0.003	0.000	0.000	0.000	0.000
74	Y	127	LYS	1	0.957	0.975	39.534	0.093	0.093	0.000	0.000	0.000	0.000
75	Y	128	ARG	1	0.861	0.921	35.324	0.116	0.116	0.000	0.000	0.000	0.000
76	Y	129	CYS	0	-0.065	0.012	32.035	0.002	0.002	0.000	0.000	0.000	0.000
77	Y	130	THR	0	0.024	0.006	30.449	-0.004	-0.004	0.000	0.000	0.000	0.000
78	Y	131	GLY	0	0.041	0.015	27.843	0.007	0.007	0.000	0.000	0.000	0.000
79	Y	132	CYS	0	-0.077	-0.035	22.557	-0.004	-0.004	0.000	0.000	0.000	0.000
80	Y	133	CYS	0	-0.032	0.007	22.214	0.022	0.022	0.000	0.000	0.000	0.000
81	Y	134	ASN	0	0.006	-0.007	18.756	-0.007	-0.007	0.000	0.000	0.000	0.000
82	Y	135	THR	0	0.034	0.034	15.124	-0.036	-0.036	0.000	0.000	0.000	0.000
83	Y	136	SER	0	0.027	0.010	16.430	0.061	0.061	0.000	0.000	0.000	0.000
84	Y	137	SER	0	-0.004	-0.012	16.525	0.007	0.007	0.000	0.000	0.000	0.000
85	Y	138	VAL	0	-0.031	-0.001	18.470	0.039	0.039	0.000	0.000	0.000	0.000
86	Y	139	LYS	1	0.928	0.965	20.345	0.345	0.345	0.000	0.000	0.000	0.000
87	Y	141	GLN	0	-0.047	-0.028	27.742	0.006	0.006	0.000	0.000	0.000	0.000
88	Y	142	PRO	0	0.070	0.003	30.515	0.001	0.001	0.000	0.000	0.000	0.000
89	Y	143	SER	0	-0.012	-0.015	34.187	-0.002	-0.002	0.000	0.000	0.000	0.000
90	Y	144	ARG	1	0.838	0.893	35.718	0.107	0.107	0.000	0.000	0.000	0.000
91	Y	145	VAL	0	-0.016	-0.005	37.899	-0.003	-0.003	0.000	0.000	0.000	0.000
92	Y	146	HIS	0	0.005	0.006	40.551	0.003	0.003	0.000	0.000	0.000	0.000
93	Y	147	HIS	0	0.040	0.019	41.149	0.001	0.001	0.000	0.000	0.000	0.000
94	Y	148	ARG	1	0.862	0.913	45.677	0.081	0.081	0.000	0.000	0.000	0.000
95	Y	149	SER	0	0.023	0.010	48.635	-0.003	-0.003	0.000	0.000	0.000	0.000
96	Y	150	VAL	0	-0.018	-0.001	50.013	0.001	0.001	0.000	0.000	0.000	0.000
97	Y	151	LYS	1	0.868	0.906	52.692	0.048	0.048	0.000	0.000	0.000	0.000
98	Y	152	VAL	0	0.005	0.022	50.707	-0.001	-0.001	0.000	0.000	0.000	0.000
99	Y	153	ALA	0	0.003	-0.007	54.172	0.002	0.002	0.000	0.000	0.000	0.000
100	Y	154	LYS	1	0.787	0.886	55.396	0.047	0.047	0.000	0.000	0.000	0.000
101	Y	155	VAL	0	-0.010	-0.029	56.527	0.002	0.002	0.000	0.000	0.000	0.000
102	Y	156	GLU	-1	-0.759	-0.866	57.771	-0.045	-0.045	0.000	0.000	0.000	0.000
103	Y	157	TYR	0	0.042	0.004	60.256	0.001	0.001	0.000	0.000	0.000	0.000
104	Y	158	VAL	0	0.014	0.026	62.700	0.001	0.001	0.000	0.000	0.000	0.000
105	Y	159	ARG	1	0.956	0.958	64.879	0.033	0.033	0.000	0.000	0.000	0.000
106	Y	160	LYS	1	0.965	0.973	66.596	0.030	0.030	0.000	0.000	0.000	0.000
107	Y	161	LYS	1	1.007	1.014	66.799	0.031	0.031	0.000	0.000	0.000	0.000
108	Y	162	PRO	0	0.036	0.030	64.114	-0.001	-0.001	0.000	0.000	0.000	0.000
109	Y	163	LYS	1	0.860	0.934	63.320	0.040	0.040	0.000	0.000	0.000	0.000
110	Y	164	LEU	0	0.033	0.023	60.000	-0.001	-0.001	0.000	0.000	0.000	0.000
111	Y	165	LYS	1	0.835	0.901	59.497	0.045	0.045	0.000	0.000	0.000	0.000
112	Y	166	GLU	-1	-0.805	-0.882	58.588	-0.048	-0.048	0.000	0.000	0.000	0.000
113	Y	167	VAL	0	-0.005	0.005	53.964	0.001	0.001	0.000	0.000	0.000	0.000
114	Y	168	GLN	0	-0.005	-0.003	53.203	-0.001	-0.001	0.000	0.000	0.000	0.000
115	Y	169	VAL	0	-0.007	-0.001	48.159	-0.001	-0.001	0.000	0.000	0.000	0.000
116	Y	170	ARG	1	0.920	0.953	43.404	0.083	0.083	0.000	0.000	0.000	0.000
117	Y	171	LEU	0	-0.009	-0.002	44.904	-0.003	-0.003	0.000	0.000	0.000	0.000
118	Y	172	GLU	-1	-0.836	-0.904	37.889	-0.116	-0.116	0.000	0.000	0.000	0.000
119	Y	173	GLU	-1	-0.778	-0.872	40.827	-0.092	-0.092	0.000	0.000	0.000	0.000
120	Y	174	HIS	0	-0.013	-0.023	34.801	-0.004	-0.004	0.000	0.000	0.000	0.000
121	Y	175	LEU	0	-0.031	-0.016	38.957	0.002	0.002	0.000	0.000	0.000	0.000
122	Y	176	GLU	-1	-0.813	-0.891	36.679	-0.107	-0.107	0.000	0.000	0.000	0.000
123	Y	178	ALA	0	0.043	0.026	30.167	0.004	0.004	0.000	0.000	0.000	0.000
124	Y	180	ALA	0	0.027	0.004	26.276	0.005	0.005	0.000	0.000	0.000	0.000
125	Y	181	THR	0	0.007	-0.001	22.233	-0.023	-0.023	0.000	0.000	0.000	0.000
126	Y	182	THR	0	0.003	0.008	22.340	0.016	0.016	0.000	0.000	0.000	0.000

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