FMO DATABASE

FMODB ID: M316Z

Calculation Name: 3MJK-F-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: F

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	OptAll
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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-895594.330023
FMO2-HF: Nuclear repulsion	844543.694388
FMO2-HF: Total energy	-51050.635636
FMO2-MP2: Total energy	-51195.340057

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(F:23:ALA)

Summations of interaction energy for fragment #1(F: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.
1.797	3.093	-0.016	-0.634	-0.645	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.033

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].
3	F	25	ILE	0	-0.035	-0.018	3.875	1.804	3.100	-0.016	-0.634	-0.645
4	F	26	PRO	0	0.011	0.008	6.937	-0.161	-0.161	0.000	0.000	0.000
5	F	27	ARG	1	0.994	0.996	9.255	-0.407	-0.407	0.000	0.000	0.000
6	F	28	GLU	-1	-0.807	-0.920	12.104	0.537	0.537	0.000	0.000	0.000
7	F	29	VAL	0	0.001	0.002	10.804	-0.052	-0.052	0.000	0.000	0.000
8	F	30	ILE	0	0.005	-0.004	10.319	-0.077	-0.077	0.000	0.000	0.000
9	F	31	GLU	-1	-0.832	-0.904	13.822	0.096	0.096	0.000	0.000	0.000
10	F	32	ARG	1	0.738	0.842	15.098	-0.360	-0.360	0.000	0.000	0.000
11	F	33	LEU	0	0.026	0.025	13.230	-0.024	-0.024	0.000	0.000	0.000
12	F	34	ALA	0	-0.036	-0.009	17.380	-0.021	-0.021	0.000	0.000	0.000
13	F	35	ARG	1	0.776	0.872	19.371	-0.147	-0.147	0.000	0.000	0.000
14	F	36	SER	0	0.009	-0.002	20.330	0.014	0.014	0.000	0.000	0.000
15	F	37	GLN	0	-0.053	-0.026	22.563	-0.015	-0.015	0.000	0.000	0.000
16	F	38	ILE	0	0.020	0.003	18.383	0.010	0.010	0.000	0.000	0.000
17	F	39	HIS	0	-0.063	-0.045	22.600	-0.017	-0.017	0.000	0.000	0.000
18	F	40	SER	0	-0.014	-0.002	23.257	-0.004	-0.004	0.000	0.000	0.000
19	F	41	ILE	0	0.031	0.005	17.983	0.010	0.010	0.000	0.000	0.000
20	F	42	ARG	1	0.957	0.974	19.273	-0.018	-0.018	0.000	0.000	0.000
21	F	43	ASP	-1	-0.844	-0.899	21.702	0.076	0.076	0.000	0.000	0.000
22	F	44	LEU	0	0.013	0.000	14.779	0.016	0.016	0.000	0.000	0.000
23	F	45	GLN	0	-0.024	-0.028	16.372	0.025	0.025	0.000	0.000	0.000
24	F	46	ARG	1	0.899	0.956	17.310	-0.055	-0.055	0.000	0.000	0.000
25	F	47	LEU	0	0.017	0.012	17.881	0.017	0.017	0.000	0.000	0.000
26	F	48	LEU	0	-0.041	-0.005	11.867	0.033	0.033	0.000	0.000	0.000
27	F	49	GLU	-1	-0.778	-0.851	12.728	0.404	0.404	0.000	0.000	0.000
28	F	50	ILE	0	-0.061	-0.028	12.603	-0.007	-0.007	0.000	0.000	0.000
29	F	87	SER	0	-0.006	-0.022	27.304	0.000	0.000	0.000	0.000	0.000
30	F	88	ILE	0	-0.034	-0.003	24.233	0.000	0.000	0.000	0.000	0.000
31	F	89	GLU	-1	-0.941	-0.969	27.305	-0.037	-0.037	0.000	0.000	0.000
32	F	90	GLU	-1	-0.858	-0.925	23.047	-0.013	-0.013	0.000	0.000	0.000
33	F	91	ALA	0	0.007	-0.008	22.428	0.002	0.002	0.000	0.000	0.000
34	F	92	VAL	0	0.039	0.023	23.883	0.003	0.003	0.000	0.000	0.000
35	F	93	PRO	0	0.018	0.023	23.402	-0.009	-0.009	0.000	0.000	0.000
36	F	94	ALA	0	0.024	0.006	25.137	0.007	0.007	0.000	0.000	0.000
37	F	95	VAL	0	-0.005	-0.008	26.815	-0.004	-0.004	0.000	0.000	0.000
38	F	96	CYS	0	-0.003	0.017	24.742	0.011	0.011	0.000	0.000	0.000
39	F	97	LYS	1	0.964	0.983	28.825	0.024	0.024	0.000	0.000	0.000
40	F	98	THR	0	0.029	0.003	32.691	-0.006	-0.006	0.000	0.000	0.000
41	F	99	ARG	1	0.786	0.881	30.302	0.038	0.038	0.000	0.000	0.000
42	F	100	THR	0	-0.039	-0.049	36.939	0.000	0.000	0.000	0.000	0.000
43	F	101	VAL	0	0.006	0.008	35.252	-0.003	-0.003	0.000	0.000	0.000
44	F	102	ILE	0	0.008	0.000	38.569	0.003	0.003	0.000	0.000	0.000
45	F	103	TYR	0	-0.035	-0.029	39.662	-0.003	-0.003	0.000	0.000	0.000
46	F	104	GLU	-1	-0.901	-0.960	41.426	-0.044	-0.044	0.000	0.000	0.000
47	F	105	ILE	0	-0.029	-0.017	43.952	0.000	0.000	0.000	0.000	0.000
48	F	106	PRO	0	0.023	0.017	43.741	-0.001	-0.001	0.000	0.000	0.000
49	F	107	ARG	1	0.920	0.949	46.077	0.036	0.036	0.000	0.000	0.000
50	F	108	SER	0	0.035	0.002	45.924	0.002	0.002	0.000	0.000	0.000
51	F	109	GLN	0	0.019	0.024	45.392	0.001	0.001	0.000	0.000	0.000
52	F	110	VAL	0	-0.034	-0.010	49.174	0.002	0.002	0.000	0.000	0.000
53	F	111	ASP	-1	-0.764	-0.858	52.325	-0.024	-0.024	0.000	0.000	0.000
54	F	112	PRO	0	-0.011	-0.011	50.879	-0.001	-0.001	0.000	0.000	0.000
55	F	113	THR	0	-0.076	-0.042	52.164	-0.001	-0.001	0.000	0.000	0.000
56	F	114	SER	0	-0.033	-0.022	54.971	0.000	0.000	0.000	0.000	0.000
57	F	115	ALA	0	0.030	0.002	52.663	-0.001	-0.001	0.000	0.000	0.000
58	F	116	ASN	0	-0.028	-0.012	53.969	-0.001	-0.001	0.000	0.000	0.000
59	F	117	PHE	0	-0.037	-0.017	52.964	0.001	0.001	0.000	0.000	0.000
60	F	118	LEU	0	0.032	0.021	52.557	-0.002	-0.002	0.000	0.000	0.000
61	F	119	ILE	0	0.011	0.003	49.430	0.001	0.001	0.000	0.000	0.000
62	F	120	TRP	0	0.023	0.027	52.451	-0.001	-0.001	0.000	0.000	0.000
63	F	121	PRO	0	0.055	0.019	50.616	0.001	0.001	0.000	0.000	0.000
64	F	122	PRO	0	0.007	-0.001	48.414	0.000	0.000	0.000	0.000	0.000
65	F	123	CYS	0	-0.014	-0.002	44.758	-0.002	-0.002	0.000	0.000	0.000
66	F	124	VAL	0	-0.012	-0.003	45.390	0.002	0.002	0.000	0.000	0.000
67	F	125	GLU	-1	-0.776	-0.865	43.361	-0.027	-0.027	0.000	0.000	0.000
68	F	126	VAL	0	-0.050	-0.017	40.087	0.002	0.002	0.000	0.000	0.000
69	F	127	LYS	1	0.844	0.921	39.924	0.020	0.020	0.000	0.000	0.000
70	F	128	ARG	1	0.838	0.897	35.741	0.034	0.034	0.000	0.000	0.000
71	F	129	CYS	0	-0.066	-0.017	32.286	-0.002	-0.002	0.000	0.000	0.000
72	F	130	THR	0	0.031	0.018	30.904	-0.005	-0.005	0.000	0.000	0.000
73	F	131	GLY	0	0.013	0.012	27.843	0.006	0.006	0.000	0.000	0.000
74	F	132	CYS	0	-0.044	-0.030	22.694	-0.008	-0.008	0.000	0.000	0.000
75	F	133	CYS	0	-0.008	-0.001	22.541	0.005	0.005	0.000	0.000	0.000
76	F	134	ASN	0	-0.027	-0.021	18.854	-0.028	-0.028	0.000	0.000	0.000
77	F	135	THR	0	0.032	0.030	14.831	-0.023	-0.023	0.000	0.000	0.000
78	F	136	SER	0	0.059	0.028	16.849	0.010	0.010	0.000	0.000	0.000
79	F	137	SER	0	-0.017	-0.005	16.727	0.006	0.006	0.000	0.000	0.000
80	F	138	VAL	0	-0.042	-0.013	18.528	0.010	0.010	0.000	0.000	0.000
81	F	139	LYS	1	0.850	0.912	20.978	0.065	0.065	0.000	0.000	0.000
82	F	141	GLN	0	0.030	0.010	27.880	-0.006	-0.006	0.000	0.000	0.000
83	F	142	PRO	0	0.010	-0.013	30.854	0.005	0.005	0.000	0.000	0.000
84	F	143	SER	0	-0.031	-0.046	34.654	0.000	0.000	0.000	0.000	0.000
85	F	144	ARG	1	0.809	0.881	36.043	0.000	0.000	0.000	0.000	0.000
86	F	145	VAL	0	0.027	0.016	38.355	-0.002	-0.002	0.000	0.000	0.000
87	F	146	HIS	0	-0.014	-0.014	40.625	0.002	0.002	0.000	0.000	0.000
88	F	147	HIS	0	0.032	0.012	42.258	-0.003	-0.003	0.000	0.000	0.000
89	F	148	ARG	1	0.861	0.926	46.434	0.021	0.021	0.000	0.000	0.000
90	F	149	SER	0	-0.011	-0.019	49.306	-0.002	-0.002	0.000	0.000	0.000
91	F	150	VAL	0	-0.009	0.001	50.392	0.001	0.001	0.000	0.000	0.000
92	F	151	LYS	1	0.816	0.882	53.115	0.016	0.016	0.000	0.000	0.000
93	F	152	VAL	0	0.015	0.021	51.539	0.000	0.000	0.000	0.000	0.000
94	F	153	ALA	0	0.026	0.011	54.995	0.001	0.001	0.000	0.000	0.000
95	F	154	LYS	1	0.797	0.903	55.927	0.023	0.023	0.000	0.000	0.000
96	F	155	VAL	0	0.012	-0.012	57.113	0.001	0.001	0.000	0.000	0.000
97	F	156	GLU	-1	-0.787	-0.880	58.082	-0.024	-0.024	0.000	0.000	0.000
98	F	157	TYR	0	0.070	0.025	60.434	0.001	0.001	0.000	0.000	0.000
99	F	158	VAL	0	0.036	0.024	62.939	0.000	0.000	0.000	0.000	0.000
100	F	159	ARG	1	0.922	0.940	65.137	0.018	0.018	0.000	0.000	0.000
101	F	160	LYS	1	0.980	0.996	66.241	0.021	0.021	0.000	0.000	0.000
102	F	161	LYS	1	0.963	0.993	67.304	0.016	0.016	0.000	0.000	0.000
103	F	162	PRO	0	0.029	0.027	64.188	0.000	0.000	0.000	0.000	0.000
104	F	163	LYS	1	0.912	0.947	64.053	0.018	0.018	0.000	0.000	0.000
105	F	164	LEU	0	0.004	0.005	60.880	-0.001	-0.001	0.000	0.000	0.000
106	F	165	LYS	1	0.868	0.928	60.098	0.021	0.021	0.000	0.000	0.000
107	F	166	GLU	-1	-0.798	-0.876	59.197	-0.017	-0.017	0.000	0.000	0.000
108	F	167	VAL	0	-0.026	-0.009	54.976	0.000	0.000	0.000	0.000	0.000
109	F	168	GLN	0	0.037	0.027	54.032	0.000	0.000	0.000	0.000	0.000
110	F	169	VAL	0	0.027	0.019	48.927	-0.001	-0.001	0.000	0.000	0.000
111	F	170	ARG	1	0.879	0.926	47.949	0.021	0.021	0.000	0.000	0.000
112	F	171	LEU	0	-0.002	0.008	45.400	-0.002	-0.002	0.000	0.000	0.000
113	F	172	GLU	-1	-0.779	-0.854	38.500	-0.031	-0.031	0.000	0.000	0.000
114	F	173	GLU	-1	-0.793	-0.877	41.022	-0.024	-0.024	0.000	0.000	0.000
115	F	174	HIS	0	-0.018	-0.030	35.342	0.001	0.001	0.000	0.000	0.000
116	F	175	LEU	0	-0.009	0.003	39.306	0.000	0.000	0.000	0.000	0.000
117	F	176	GLU	-1	-0.798	-0.842	36.310	0.004	0.004	0.000	0.000	0.000
118	F	178	ALA	0	0.045	0.031	30.519	0.005	0.005	0.000	0.000	0.000
119	F	180	ALA	0	0.028	0.016	26.432	0.010	0.010	0.000	0.000	0.000
120	F	181	THR	0	0.035	0.012	23.439	-0.016	-0.016	0.000	0.000	0.000
121	F	182	THR	0	0.003	-0.015	24.901	0.002	0.002	0.000	0.000	0.000
122	F	183	SER	0	-0.001	0.020	26.029	-0.005	-0.005	0.000	0.000	0.000

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