FMO DATABASE

FMODB ID: ZY5RN

Calculation Name: 3MJK-B-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: B

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-887194.114183
FMO2-HF: Nuclear repulsion	836466.127087
FMO2-HF: Total energy	-50727.987096
FMO2-MP2: Total energy	-50871.997547

3D Structure

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(B:23:ALA)

Summations of interaction energy for fragment #1(B: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.
1.333	3.701	-0.017	-1.271	-1.08	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.007

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

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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	B	25	ILE	0	-0.021	-0.014	3.806	-0.303	2.065	-0.017	-1.271	-1.080	0.004
4	B	26	PRO	0	0.059	0.030	5.286	0.254	0.254	0.000	0.000	0.000	0.000
5	B	27	ARG	1	0.989	0.992	7.853	0.457	0.457	0.000	0.000	0.000	0.000
6	B	28	GLU	-1	-0.876	-0.938	10.715	-0.170	-0.170	0.000	0.000	0.000	0.000
7	B	29	VAL	0	-0.012	-0.020	9.377	0.067	0.067	0.000	0.000	0.000	0.000
8	B	30	ILE	0	-0.007	0.003	10.454	0.047	0.047	0.000	0.000	0.000	0.000
9	B	31	GLU	-1	-0.901	-0.958	13.230	-0.263	-0.263	0.000	0.000	0.000	0.000
10	B	32	ARG	1	0.918	0.965	13.180	0.294	0.294	0.000	0.000	0.000	0.000
11	B	33	LEU	0	0.026	0.000	13.303	0.037	0.037	0.000	0.000	0.000	0.000
12	B	34	ALA	0	-0.060	-0.028	17.107	0.031	0.031	0.000	0.000	0.000	0.000
13	B	35	ARG	1	0.893	0.969	18.079	0.263	0.263	0.000	0.000	0.000	0.000
14	B	36	SER	0	-0.026	-0.008	19.850	0.036	0.036	0.000	0.000	0.000	0.000
15	B	37	GLN	0	0.000	-0.002	21.774	-0.015	-0.015	0.000	0.000	0.000	0.000
16	B	38	ILE	0	-0.022	-0.016	18.524	0.001	0.001	0.000	0.000	0.000	0.000
17	B	39	HIS	0	-0.004	0.000	22.771	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	40	SER	0	-0.024	-0.005	23.040	0.010	0.010	0.000	0.000	0.000	0.000
19	B	41	ILE	0	0.023	0.001	17.968	-0.018	-0.018	0.000	0.000	0.000	0.000
20	B	42	ARG	1	0.927	0.974	19.139	0.097	0.097	0.000	0.000	0.000	0.000
21	B	43	ASP	-1	-0.839	-0.923	20.465	-0.134	-0.134	0.000	0.000	0.000	0.000
22	B	44	LEU	0	0.014	0.019	14.891	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	45	GLN	0	0.023	0.007	16.119	-0.015	-0.015	0.000	0.000	0.000	0.000
24	B	46	ARG	1	0.881	0.935	17.021	0.112	0.112	0.000	0.000	0.000	0.000
25	B	47	LEU	0	-0.040	-0.022	17.014	0.005	0.005	0.000	0.000	0.000	0.000
26	B	48	LEU	0	-0.134	-0.074	11.748	-0.022	-0.022	0.000	0.000	0.000	0.000
27	B	49	GLU	-1	-0.932	-0.934	13.175	-0.043	-0.043	0.000	0.000	0.000	0.000
28	B	50	ILE	0	-0.059	-0.036	13.921	0.013	0.013	0.000	0.000	0.000	0.000
29	B	87	SER	0	-0.028	-0.024	28.564	0.001	0.001	0.000	0.000	0.000	0.000
30	B	88	ILE	0	-0.015	-0.012	25.329	0.000	0.000	0.000	0.000	0.000	0.000
31	B	89	GLU	-1	-0.937	-0.966	26.582	-0.115	-0.115	0.000	0.000	0.000	0.000
32	B	90	GLU	-1	-0.801	-0.898	23.043	-0.156	-0.156	0.000	0.000	0.000	0.000
33	B	91	ALA	0	-0.006	-0.006	22.673	0.003	0.003	0.000	0.000	0.000	0.000
34	B	92	VAL	0	0.040	0.020	24.110	-0.008	-0.008	0.000	0.000	0.000	0.000
35	B	93	PRO	0	-0.001	0.009	23.332	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	94	ALA	0	0.018	0.008	25.127	0.018	0.018	0.000	0.000	0.000	0.000
37	B	95	VAL	0	0.027	-0.006	26.518	-0.014	-0.014	0.000	0.000	0.000	0.000
38	B	96	CYS	0	-0.020	0.005	24.713	0.029	0.029	0.000	0.000	0.000	0.000
39	B	97	LYS	1	0.970	0.969	28.834	0.135	0.135	0.000	0.000	0.000	0.000
40	B	98	THR	0	0.074	0.042	32.594	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	99	ARG	1	0.779	0.886	30.313	0.158	0.158	0.000	0.000	0.000	0.000
42	B	100	THR	0	-0.025	-0.010	36.576	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	101	VAL	0	0.034	0.014	35.054	-0.004	-0.004	0.000	0.000	0.000	0.000
44	B	102	ILE	0	0.048	0.013	38.353	0.005	0.005	0.000	0.000	0.000	0.000
45	B	103	TYR	0	-0.025	-0.007	39.314	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	104	GLU	-1	-0.884	-0.949	41.216	-0.088	-0.088	0.000	0.000	0.000	0.000
47	B	105	ILE	0	-0.067	-0.035	43.392	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	106	PRO	0	0.011	0.008	43.076	0.001	0.001	0.000	0.000	0.000	0.000
49	B	107	ARG	1	0.978	0.977	45.215	0.070	0.070	0.000	0.000	0.000	0.000
50	B	108	SER	0	0.011	-0.005	45.035	0.003	0.003	0.000	0.000	0.000	0.000
51	B	109	GLN	0	0.009	-0.002	45.561	0.004	0.004	0.000	0.000	0.000	0.000
52	B	110	VAL	0	-0.037	0.002	48.672	0.002	0.002	0.000	0.000	0.000	0.000
53	B	111	ASP	-1	-0.842	-0.958	51.784	-0.053	-0.053	0.000	0.000	0.000	0.000
54	B	112	PRO	0	-0.035	-0.007	49.701	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	113	THR	0	-0.012	0.001	51.030	0.000	0.000	0.000	0.000	0.000	0.000
56	B	114	SER	0	-0.036	-0.003	53.395	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	115	ALA	0	0.065	0.020	52.241	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	116	ASN	0	-0.048	-0.017	53.418	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	117	PHE	0	-0.053	-0.030	51.381	0.002	0.002	0.000	0.000	0.000	0.000
60	B	118	LEU	0	-0.016	-0.006	53.067	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	119	ILE	0	0.011	0.015	49.541	0.002	0.002	0.000	0.000	0.000	0.000
62	B	120	TRP	0	0.035	0.043	52.422	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	121	PRO	0	0.056	0.012	50.502	0.002	0.002	0.000	0.000	0.000	0.000
64	B	122	PRO	0	0.029	-0.013	47.830	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	123	CYS	0	-0.023	0.003	44.246	-0.004	-0.004	0.000	0.000	0.000	0.000
66	B	124	VAL	0	-0.017	-0.002	44.969	0.004	0.004	0.000	0.000	0.000	0.000
67	B	125	GLU	-1	-0.902	-0.948	43.071	-0.085	-0.085	0.000	0.000	0.000	0.000
68	B	126	VAL	0	-0.032	-0.001	39.821	0.002	0.002	0.000	0.000	0.000	0.000
69	B	127	LYS	1	0.919	0.969	39.366	0.094	0.094	0.000	0.000	0.000	0.000
70	B	128	ARG	1	0.884	0.933	35.250	0.119	0.119	0.000	0.000	0.000	0.000
71	B	129	CYS	0	-0.079	0.004	31.834	0.001	0.001	0.000	0.000	0.000	0.000
72	B	130	THR	0	0.014	0.010	30.438	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	131	GLY	0	0.035	0.014	27.681	0.008	0.008	0.000	0.000	0.000	0.000
74	B	132	CYS	0	-0.048	-0.031	22.494	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	133	CYS	0	-0.013	0.014	22.000	0.022	0.022	0.000	0.000	0.000	0.000
76	B	134	ASN	0	0.002	-0.001	18.612	-0.015	-0.015	0.000	0.000	0.000	0.000
77	B	135	THR	0	0.034	0.022	15.199	-0.046	-0.046	0.000	0.000	0.000	0.000
78	B	136	SER	0	0.037	0.013	16.222	0.040	0.040	0.000	0.000	0.000	0.000
79	B	137	SER	0	-0.050	-0.022	16.469	0.034	0.034	0.000	0.000	0.000	0.000
80	B	138	VAL	0	0.007	-0.004	18.488	0.043	0.043	0.000	0.000	0.000	0.000
81	B	139	LYS	1	0.895	0.960	21.698	0.315	0.315	0.000	0.000	0.000	0.000
82	B	141	GLN	0	0.016	0.005	27.601	0.007	0.007	0.000	0.000	0.000	0.000
83	B	142	PRO	0	0.064	-0.007	30.431	0.003	0.003	0.000	0.000	0.000	0.000
84	B	143	SER	0	-0.022	-0.021	34.068	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	144	ARG	1	0.923	0.962	35.577	0.096	0.096	0.000	0.000	0.000	0.000
86	B	145	VAL	0	0.029	0.020	38.022	-0.002	-0.002	0.000	0.000	0.000	0.000
87	B	146	HIS	0	-0.010	0.000	40.606	0.003	0.003	0.000	0.000	0.000	0.000
88	B	147	HIS	0	0.000	0.007	41.637	0.001	0.001	0.000	0.000	0.000	0.000
89	B	148	ARG	1	0.893	0.922	45.896	0.078	0.078	0.000	0.000	0.000	0.000
90	B	149	SER	0	0.001	-0.014	48.764	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	150	VAL	0	-0.015	0.006	49.923	0.002	0.002	0.000	0.000	0.000	0.000
92	B	151	LYS	1	0.909	0.969	52.721	0.048	0.048	0.000	0.000	0.000	0.000
93	B	152	VAL	0	0.003	0.010	50.989	0.000	0.000	0.000	0.000	0.000	0.000
94	B	153	ALA	0	0.003	-0.015	54.395	0.002	0.002	0.000	0.000	0.000	0.000
95	B	154	LYS	1	0.876	0.970	55.426	0.052	0.052	0.000	0.000	0.000	0.000
96	B	155	VAL	0	-0.002	-0.031	56.732	0.002	0.002	0.000	0.000	0.000	0.000
97	B	156	GLU	-1	-0.805	-0.903	57.940	-0.049	-0.049	0.000	0.000	0.000	0.000
98	B	157	TYR	0	0.024	0.017	60.250	0.001	0.001	0.000	0.000	0.000	0.000
99	B	158	VAL	0	0.019	0.042	63.471	0.000	0.000	0.000	0.000	0.000	0.000
100	B	159	ARG	1	0.984	0.971	65.996	0.032	0.032	0.000	0.000	0.000	0.000
101	B	160	LYN	0	0.069	0.006	64.405	0.001	0.001	0.000	0.000	0.000	0.000
102	B	161	LYS	1	0.887	0.965	67.574	0.032	0.032	0.000	0.000	0.000	0.000
103	B	162	PRO	0	0.015	-0.007	64.091	-0.001	-0.001	0.000	0.000	0.000	0.000
104	B	163	LYS	1	0.854	0.946	62.125	0.045	0.045	0.000	0.000	0.000	0.000
105	B	164	LEU	0	0.029	-0.003	60.038	-0.001	-0.001	0.000	0.000	0.000	0.000
106	B	165	LYS	1	0.890	0.950	59.175	0.049	0.049	0.000	0.000	0.000	0.000
107	B	166	GLU	-1	-0.843	-0.928	58.498	-0.049	-0.049	0.000	0.000	0.000	0.000
108	B	167	VAL	0	-0.029	0.003	53.774	0.001	0.001	0.000	0.000	0.000	0.000
109	B	168	GLN	0	-0.013	-0.012	53.479	0.000	0.000	0.000	0.000	0.000	0.000
110	B	169	VAL	0	0.015	0.001	48.100	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	170	ARG	1	0.958	0.982	46.802	0.077	0.077	0.000	0.000	0.000	0.000
112	B	171	LEU	0	-0.005	-0.003	44.834	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	172	GLU	-1	-0.844	-0.915	38.092	-0.118	-0.118	0.000	0.000	0.000	0.000
114	B	173	GLU	-1	-0.846	-0.895	40.758	-0.089	-0.089	0.000	0.000	0.000	0.000
115	B	174	HIS	0	0.011	-0.016	34.702	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	175	LEU	0	-0.061	-0.039	38.872	0.003	0.003	0.000	0.000	0.000	0.000
117	B	176	GLU	-1	-0.898	-0.951	36.409	-0.100	-0.100	0.000	0.000	0.000	0.000
118	B	178	ALA	0	0.029	0.021	29.890	0.005	0.005	0.000	0.000	0.000	0.000
119	B	180	ALA	0	0.037	0.014	25.885	0.002	0.002	0.000	0.000	0.000	0.000
120	B	181	THR	0	0.003	-0.001	20.495	-0.015	-0.015	0.000	0.000	0.000	0.000
121	B	182	THR	0	0.019	0.013	22.287	0.011	0.011	0.000	0.000	0.000	0.000

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