FMO DATABASE

FMODB ID: GNLN1

Calculation Name: 3MJK-F-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: F

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-906342.467407
FMO2-HF: Nuclear repulsion	854951.66564
FMO2-HF: Total energy	-51390.801768
FMO2-MP2: Total energy	-51536.791551

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(F:22:ACE )

Summations of interaction energy for fragment #1(F: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.
-0.117	1.512	0.001	-0.832	-0.797	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.014

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	F	24	GLU	-1	-0.920	-0.953	3.607	-0.523	1.106	0.001	-0.832	-0.797	-0.002
4	F	25	ILE	0	-0.017	-0.005	5.501	0.301	0.301	0.000	0.000	0.000	0.000
5	F	26	PRO	0	0.006	-0.002	6.622	0.133	0.133	0.000	0.000	0.000	0.000
6	F	27	ARG	1	1.011	0.983	8.706	-0.334	-0.334	0.000	0.000	0.000	0.000
7	F	28	GLU	-1	-0.804	-0.889	11.941	0.196	0.196	0.000	0.000	0.000	0.000
8	F	29	VAL	0	-0.029	-0.003	10.906	-0.023	-0.023	0.000	0.000	0.000	0.000
9	F	30	ILE	0	0.030	0.014	11.885	-0.010	-0.010	0.000	0.000	0.000	0.000
10	F	31	GLU	-1	-0.916	-0.962	14.602	0.060	0.060	0.000	0.000	0.000	0.000
11	F	32	ARG	1	0.922	0.945	14.451	0.026	0.026	0.000	0.000	0.000	0.000
12	F	33	LEU	0	0.020	-0.003	15.270	-0.005	-0.005	0.000	0.000	0.000	0.000
13	F	34	ALA	0	-0.041	-0.003	18.505	-0.003	-0.003	0.000	0.000	0.000	0.000
14	F	35	ARG	1	0.858	0.951	18.081	-0.017	-0.017	0.000	0.000	0.000	0.000
15	F	36	SER	0	0.024	0.004	21.236	0.006	0.006	0.000	0.000	0.000	0.000
16	F	37	GLN	0	-0.045	-0.014	23.365	-0.006	-0.006	0.000	0.000	0.000	0.000
17	F	38	ILE	0	0.000	0.006	20.270	-0.003	-0.003	0.000	0.000	0.000	0.000
18	F	39	HIS	0	-0.051	-0.031	24.431	0.000	0.000	0.000	0.000	0.000	0.000
19	F	40	SER	0	-0.008	0.001	25.454	-0.001	-0.001	0.000	0.000	0.000	0.000
20	F	41	ILE	0	0.060	0.028	21.088	-0.006	-0.006	0.000	0.000	0.000	0.000
21	F	42	ARG	1	0.947	0.988	22.022	0.075	0.075	0.000	0.000	0.000	0.000
22	F	43	ASP	-1	-0.878	-0.960	23.500	-0.066	-0.066	0.000	0.000	0.000	0.000
23	F	44	LEU	0	0.030	0.013	17.571	0.002	0.002	0.000	0.000	0.000	0.000
24	F	45	GLN	0	-0.059	-0.050	18.324	0.004	0.004	0.000	0.000	0.000	0.000
25	F	46	ARG	1	0.966	0.994	18.710	0.072	0.072	0.000	0.000	0.000	0.000
26	F	47	LEU	0	-0.014	-0.003	18.943	0.010	0.010	0.000	0.000	0.000	0.000
27	F	48	LEU	0	-0.113	-0.038	13.367	0.002	0.002	0.000	0.000	0.000	0.000
28	F	49	GLU	-1	-0.877	-0.936	13.713	-0.028	-0.028	0.000	0.000	0.000	0.000
29	F	50	ILE	0	-0.049	-0.015	15.060	-0.010	-0.010	0.000	0.000	0.000	0.000
30	F	51	NME	0	-0.055	-0.027	17.298	0.021	0.021	0.000	0.000	0.000	0.000
31	F	86	ACE	0	0.004	-0.012	29.608	-0.002	-0.002	0.000	0.000	0.000	0.000
32	F	87	SER	0	-0.051	-0.029	30.230	0.007	0.007	0.000	0.000	0.000	0.000
33	F	88	ILE	0	0.000	0.011	28.438	0.005	0.005	0.000	0.000	0.000	0.000
34	F	89	GLU	-1	-0.936	-0.967	30.649	-0.080	-0.080	0.000	0.000	0.000	0.000
35	F	90	GLU	-1	-0.857	-0.931	26.506	-0.114	-0.114	0.000	0.000	0.000	0.000
36	F	91	ALA	0	-0.008	-0.006	26.052	0.006	0.006	0.000	0.000	0.000	0.000
37	F	92	VAL	0	0.049	0.022	27.685	0.000	0.000	0.000	0.000	0.000	0.000
38	F	93	PRO	0	-0.001	0.010	26.265	-0.001	-0.001	0.000	0.000	0.000	0.000
39	F	94	ALA	0	0.024	0.006	28.094	0.009	0.009	0.000	0.000	0.000	0.000
40	F	95	VAL	0	0.036	0.001	29.319	0.000	0.000	0.000	0.000	0.000	0.000
41	F	140	CYS	0	-0.009	0.037	26.580	0.008	0.008	0.000	0.000	0.000	0.000
42	F	97	LYS	1	0.968	0.971	31.189	0.045	0.045	0.000	0.000	0.000	0.000
43	F	98	THR	0	0.039	0.023	34.930	-0.002	-0.002	0.000	0.000	0.000	0.000
44	F	99	ARG	1	0.784	0.858	32.901	0.048	0.048	0.000	0.000	0.000	0.000
45	F	100	THR	0	-0.025	-0.007	39.406	0.001	0.001	0.000	0.000	0.000	0.000
46	F	101	VAL	0	0.058	0.034	38.152	-0.002	-0.002	0.000	0.000	0.000	0.000
47	F	102	ILE	0	0.032	0.007	41.487	0.002	0.002	0.000	0.000	0.000	0.000
48	F	103	TYR	0	-0.037	-0.015	42.669	-0.001	-0.001	0.000	0.000	0.000	0.000
49	F	104	GLU	-1	-0.890	-0.958	44.909	-0.027	-0.027	0.000	0.000	0.000	0.000
50	F	105	ILE	0	-0.049	-0.023	46.902	0.001	0.001	0.000	0.000	0.000	0.000
51	F	106	PRO	0	0.035	0.016	46.423	0.000	0.000	0.000	0.000	0.000	0.000
52	F	107	ARG	1	0.955	0.983	48.727	0.020	0.020	0.000	0.000	0.000	0.000
53	F	108	SER	0	0.020	-0.009	48.273	0.001	0.001	0.000	0.000	0.000	0.000
54	F	109	GLN	0	0.030	0.000	47.494	0.001	0.001	0.000	0.000	0.000	0.000
55	F	110	VAL	0	-0.026	0.000	51.474	0.001	0.001	0.000	0.000	0.000	0.000
56	F	111	ASP	-1	-0.790	-0.887	54.868	-0.010	-0.010	0.000	0.000	0.000	0.000
57	F	112	PRO	0	-0.016	-0.009	52.957	-0.001	-0.001	0.000	0.000	0.000	0.000
58	F	113	THR	0	-0.058	-0.027	54.480	0.000	0.000	0.000	0.000	0.000	0.000
59	F	114	SER	0	-0.056	-0.030	57.589	-0.001	-0.001	0.000	0.000	0.000	0.000
60	F	115	ALA	0	0.042	0.011	55.395	-0.001	-0.001	0.000	0.000	0.000	0.000
61	F	116	ASN	0	-0.031	-0.019	56.928	0.000	0.000	0.000	0.000	0.000	0.000
62	F	117	PHE	0	-0.063	-0.021	55.351	0.000	0.000	0.000	0.000	0.000	0.000
63	F	118	LEU	0	-0.024	-0.011	56.603	-0.001	-0.001	0.000	0.000	0.000	0.000
64	F	119	ILE	0	0.009	0.018	52.777	0.001	0.001	0.000	0.000	0.000	0.000
65	F	120	TRP	0	0.038	0.030	55.817	-0.001	-0.001	0.000	0.000	0.000	0.000
66	F	121	PRO	0	0.063	0.017	53.755	0.001	0.001	0.000	0.000	0.000	0.000
67	F	122	PRO	0	0.032	-0.002	51.726	0.000	0.000	0.000	0.000	0.000	0.000
68	F	123	CYS	0	-0.048	-0.011	47.909	-0.001	-0.001	0.000	0.000	0.000	0.000
69	F	124	VAL	0	-0.009	0.003	48.125	0.001	0.001	0.000	0.000	0.000	0.000
70	F	125	GLU	-1	-0.911	-0.954	46.084	-0.028	-0.028	0.000	0.000	0.000	0.000
71	F	126	VAL	0	-0.019	0.000	42.690	0.002	0.002	0.000	0.000	0.000	0.000
72	F	127	LYS	1	0.873	0.948	42.136	0.025	0.025	0.000	0.000	0.000	0.000
73	F	128	ARG	1	0.914	0.934	37.915	0.026	0.026	0.000	0.000	0.000	0.000
74	F	177	CYS	0	-0.048	0.003	33.826	-0.001	-0.001	0.000	0.000	0.000	0.000
75	F	130	THR	0	0.020	0.008	33.135	-0.002	-0.002	0.000	0.000	0.000	0.000
76	F	131	GLY	0	0.035	0.019	30.593	0.002	0.002	0.000	0.000	0.000	0.000
77	F	132	CYS	0	-0.056	-0.035	25.160	-0.001	-0.001	0.000	0.000	0.000	0.000
78	F	179	CYS	0	-0.032	0.025	23.996	0.002	0.002	0.000	0.000	0.000	0.000
79	F	134	ASN	0	-0.015	-0.024	20.567	-0.012	-0.012	0.000	0.000	0.000	0.000
80	F	135	THR	0	0.040	0.043	16.997	-0.014	-0.014	0.000	0.000	0.000	0.000
81	F	136	SER	0	0.035	0.007	18.667	0.011	0.011	0.000	0.000	0.000	0.000
82	F	137	SER	0	-0.050	-0.026	17.923	0.015	0.015	0.000	0.000	0.000	0.000
83	F	138	VAL	0	-0.045	-0.029	20.024	0.016	0.016	0.000	0.000	0.000	0.000
84	F	139	LYS	1	0.898	0.952	23.363	0.024	0.024	0.000	0.000	0.000	0.000
85	F	141	GLN	0	0.029	0.009	29.673	-0.002	-0.002	0.000	0.000	0.000	0.000
86	F	142	PRO	0	0.021	-0.006	32.355	0.000	0.000	0.000	0.000	0.000	0.000
87	F	143	SER	0	-0.006	-0.011	35.657	0.001	0.001	0.000	0.000	0.000	0.000
88	F	144	ARG	1	0.895	0.951	37.204	0.012	0.012	0.000	0.000	0.000	0.000
89	F	145	VAL	0	0.024	0.004	39.939	-0.002	-0.002	0.000	0.000	0.000	0.000
90	F	146	HIS	0	-0.003	-0.003	42.553	0.001	0.001	0.000	0.000	0.000	0.000
91	F	147	HIS	0	0.029	0.024	44.047	-0.002	-0.002	0.000	0.000	0.000	0.000
92	F	148	ARG	1	0.881	0.908	48.093	0.018	0.018	0.000	0.000	0.000	0.000
93	F	149	SER	0	-0.001	0.004	51.161	-0.001	-0.001	0.000	0.000	0.000	0.000
94	F	150	VAL	0	-0.011	0.003	52.798	0.000	0.000	0.000	0.000	0.000	0.000
95	F	151	LYS	1	0.874	0.917	55.359	0.012	0.012	0.000	0.000	0.000	0.000
96	F	152	VAL	0	0.008	0.015	54.187	-0.001	-0.001	0.000	0.000	0.000	0.000
97	F	153	ALA	0	0.004	-0.016	57.631	0.001	0.001	0.000	0.000	0.000	0.000
98	F	154	LYS	1	0.828	0.941	59.065	0.011	0.011	0.000	0.000	0.000	0.000
99	F	155	VAL	0	0.010	-0.010	60.383	0.001	0.001	0.000	0.000	0.000	0.000
100	F	156	GLU	-1	-0.824	-0.936	61.450	-0.012	-0.012	0.000	0.000	0.000	0.000
101	F	157	TYR	0	0.021	0.011	63.869	0.001	0.001	0.000	0.000	0.000	0.000
102	F	158	VAL	0	0.029	0.028	66.080	0.000	0.000	0.000	0.000	0.000	0.000
103	F	159	ARG	1	0.931	0.939	68.341	0.009	0.009	0.000	0.000	0.000	0.000
104	F	160	LYS	1	0.986	0.988	69.537	0.011	0.011	0.000	0.000	0.000	0.000
105	F	161	LYS	1	0.985	1.003	70.520	0.010	0.010	0.000	0.000	0.000	0.000
106	F	162	PRO	0	0.014	0.015	67.935	0.000	0.000	0.000	0.000	0.000	0.000
107	F	163	LYS	1	0.920	0.952	67.297	0.010	0.010	0.000	0.000	0.000	0.000
108	F	164	LEU	0	0.020	0.021	63.603	0.000	0.000	0.000	0.000	0.000	0.000
109	F	165	LYS	1	0.926	0.970	62.733	0.011	0.011	0.000	0.000	0.000	0.000
110	F	166	GLU	-1	-0.833	-0.899	61.778	-0.012	-0.012	0.000	0.000	0.000	0.000
111	F	167	VAL	0	-0.023	-0.002	56.890	0.001	0.001	0.000	0.000	0.000	0.000
112	F	168	GLN	0	-0.022	-0.011	56.337	0.000	0.000	0.000	0.000	0.000	0.000
113	F	169	VAL	0	0.021	0.010	51.003	0.000	0.000	0.000	0.000	0.000	0.000
114	F	170	ARG	1	0.944	0.966	49.553	0.010	0.010	0.000	0.000	0.000	0.000
115	F	171	LEU	0	-0.012	0.000	47.575	-0.001	-0.001	0.000	0.000	0.000	0.000
116	F	172	GLU	-1	-0.858	-0.919	40.477	-0.018	-0.018	0.000	0.000	0.000	0.000
117	F	173	GLU	-1	-0.822	-0.896	43.339	-0.022	-0.022	0.000	0.000	0.000	0.000
118	F	174	HIS	0	-0.005	-0.001	37.433	0.000	0.000	0.000	0.000	0.000	0.000
119	F	175	LEU	0	-0.033	-0.022	41.104	-0.001	-0.001	0.000	0.000	0.000	0.000
120	F	176	GLU	-1	-0.904	-0.945	37.312	-0.014	-0.014	0.000	0.000	0.000	0.000
121	F	178	ALA	0	0.041	0.015	31.530	0.001	0.001	0.000	0.000	0.000	0.000
122	F	180	ALA	0	0.032	0.009	26.970	0.004	0.004	0.000	0.000	0.000	0.000
123	F	181	THR	0	0.020	0.004	24.391	-0.007	-0.007	0.000	0.000	0.000	0.000
124	F	182	THR	0	0.000	-0.021	25.646	0.000	0.000	0.000	0.000	0.000	0.000
125	F	183	SER	0	-0.007	0.003	26.858	0.003	0.003	0.000	0.000	0.000	0.000
126	F	184	NME	0	0.022	0.025	29.482	-0.001	-0.001	0.000	0.000	0.000	0.000

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