FMO DATABASE

FMODB ID: 2237R

Calculation Name: 3MJK-E-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: E

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	OptHSide
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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864821.020528
FMO2-HF: Nuclear repulsion	814810.875812
FMO2-HF: Total energy	-50010.144717
FMO2-MP2: Total energy	-50151.909417

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(E:23:ALA)

Summations of interaction energy for fragment #1(E: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.
0.263	1.347	-0.008	-0.557	-0.518	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.020

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	E	25	ILE	0	-0.026	-0.023	3.807	0.486	1.570	-0.008	-0.557	-0.518	0.003
4	E	26	PRO	0	0.040	0.026	6.812	-0.117	-0.117	0.000	0.000	0.000	0.000
5	E	27	ARG	1	0.908	0.921	8.999	-0.535	-0.535	0.000	0.000	0.000	0.000
6	E	28	GLU	-1	-0.920	-0.947	12.040	0.414	0.414	0.000	0.000	0.000	0.000
7	E	29	VAL	0	0.068	0.033	10.194	-0.104	-0.104	0.000	0.000	0.000	0.000
8	E	30	ILE	0	0.006	0.002	10.202	-0.078	-0.078	0.000	0.000	0.000	0.000
9	E	31	GLU	-1	-0.799	-0.907	13.776	0.183	0.183	0.000	0.000	0.000	0.000
10	E	32	ARG	1	0.896	0.957	14.175	-0.280	-0.280	0.000	0.000	0.000	0.000
11	E	33	LEU	0	0.007	0.015	13.381	-0.026	-0.026	0.000	0.000	0.000	0.000
12	E	34	ALA	0	-0.036	-0.009	17.326	-0.017	-0.017	0.000	0.000	0.000	0.000
13	E	35	ARG	1	0.843	0.939	18.610	-0.151	-0.151	0.000	0.000	0.000	0.000
14	E	36	SER	0	0.015	-0.004	20.342	0.016	0.016	0.000	0.000	0.000	0.000
15	E	37	GLN	0	-0.041	-0.028	22.422	-0.015	-0.015	0.000	0.000	0.000	0.000
16	E	38	ILE	0	0.023	0.022	18.160	0.007	0.007	0.000	0.000	0.000	0.000
17	E	39	HIS	1	0.811	0.879	22.473	-0.021	-0.021	0.000	0.000	0.000	0.000
18	E	40	SER	0	0.053	0.037	23.081	-0.002	-0.002	0.000	0.000	0.000	0.000
19	E	41	ILE	0	0.046	0.023	18.271	0.005	0.005	0.000	0.000	0.000	0.000
20	E	42	ARG	1	0.953	0.988	19.414	-0.026	-0.026	0.000	0.000	0.000	0.000
21	E	43	ASP	-1	-0.814	-0.912	20.620	0.046	0.046	0.000	0.000	0.000	0.000
22	E	44	LEU	0	-0.014	-0.001	15.012	0.015	0.015	0.000	0.000	0.000	0.000
23	E	45	GLN	0	0.030	0.003	16.024	0.021	0.021	0.000	0.000	0.000	0.000
24	E	46	ARG	1	0.898	0.942	17.046	-0.032	-0.032	0.000	0.000	0.000	0.000
25	E	47	LEU	0	-0.031	-0.013	18.317	0.018	0.018	0.000	0.000	0.000	0.000
26	E	48	LEU	0	-0.103	-0.037	12.002	0.026	0.026	0.000	0.000	0.000	0.000
27	E	49	GLU	-1	-0.875	-0.935	14.052	0.368	0.368	0.000	0.000	0.000	0.000
28	E	50	ILE	0	-0.077	-0.030	13.556	-0.053	-0.053	0.000	0.000	0.000	0.000
29	E	87	SER	0	-0.022	-0.030	28.780	0.001	0.001	0.000	0.000	0.000	0.000
30	E	88	ILE	0	-0.008	0.016	24.632	0.000	0.000	0.000	0.000	0.000	0.000
31	E	89	GLU	-1	-0.950	-0.979	27.657	-0.050	-0.050	0.000	0.000	0.000	0.000
32	E	90	GLU	-1	-0.864	-0.929	23.040	-0.038	-0.038	0.000	0.000	0.000	0.000
33	E	91	ALA	0	0.008	-0.002	22.166	0.002	0.002	0.000	0.000	0.000	0.000
34	E	92	VAL	0	0.047	0.018	24.285	0.006	0.006	0.000	0.000	0.000	0.000
35	E	93	PRO	0	-0.012	0.001	22.969	-0.007	-0.007	0.000	0.000	0.000	0.000
36	E	94	ALA	0	0.011	0.011	24.766	0.009	0.009	0.000	0.000	0.000	0.000
37	E	95	VAL	0	0.039	0.002	25.805	-0.004	-0.004	0.000	0.000	0.000	0.000
38	E	96	CYS	0	-0.012	0.013	23.890	0.012	0.012	0.000	0.000	0.000	0.000
39	E	97	LYS	1	0.964	0.971	28.439	0.037	0.037	0.000	0.000	0.000	0.000
40	E	98	THR	0	0.036	0.020	32.222	-0.005	-0.005	0.000	0.000	0.000	0.000
41	E	99	ARG	1	0.780	0.880	29.655	0.051	0.051	0.000	0.000	0.000	0.000
42	E	100	THR	0	-0.028	-0.026	35.751	0.000	0.000	0.000	0.000	0.000	0.000
43	E	101	VAL	0	-0.020	-0.001	33.550	-0.003	-0.003	0.000	0.000	0.000	0.000
44	E	102	ILE	0	0.029	-0.001	36.777	0.003	0.003	0.000	0.000	0.000	0.000
45	E	103	TYR	0	-0.036	-0.017	37.875	-0.003	-0.003	0.000	0.000	0.000	0.000
46	E	104	GLU	-1	-0.898	-0.950	39.308	-0.050	-0.050	0.000	0.000	0.000	0.000
47	E	105	ILE	0	-0.038	-0.021	41.819	0.000	0.000	0.000	0.000	0.000	0.000
48	E	106	PRO	0	0.019	0.012	41.673	-0.001	-0.001	0.000	0.000	0.000	0.000
49	E	107	ARG	1	0.951	0.959	44.055	0.039	0.039	0.000	0.000	0.000	0.000
50	E	108	SER	0	0.021	0.008	43.568	0.002	0.002	0.000	0.000	0.000	0.000
51	E	109	GLN	0	0.018	-0.008	42.716	0.003	0.003	0.000	0.000	0.000	0.000
52	E	110	VAL	0	-0.050	-0.008	47.482	0.002	0.002	0.000	0.000	0.000	0.000
53	E	111	ASP	-1	-0.827	-0.908	50.042	-0.026	-0.026	0.000	0.000	0.000	0.000
54	E	112	PRO	0	0.009	0.009	48.397	-0.001	-0.001	0.000	0.000	0.000	0.000
55	E	113	THR	0	-0.041	-0.008	49.788	-0.001	-0.001	0.000	0.000	0.000	0.000
56	E	114	SER	0	-0.053	-0.032	52.902	0.000	0.000	0.000	0.000	0.000	0.000
57	E	115	ALA	0	0.044	-0.002	49.629	-0.001	-0.001	0.000	0.000	0.000	0.000
58	E	116	ASN	0	-0.055	-0.014	51.461	-0.001	-0.001	0.000	0.000	0.000	0.000
59	E	117	PHE	0	-0.018	-0.008	50.794	0.001	0.001	0.000	0.000	0.000	0.000
60	E	118	LEU	0	0.016	0.009	50.987	-0.002	-0.002	0.000	0.000	0.000	0.000
61	E	119	ILE	0	0.008	0.012	47.996	0.002	0.002	0.000	0.000	0.000	0.000
62	E	120	TRP	0	-0.009	0.021	50.590	-0.001	-0.001	0.000	0.000	0.000	0.000
63	E	121	PRO	0	0.084	0.020	48.644	0.002	0.002	0.000	0.000	0.000	0.000
64	E	122	PRO	0	0.004	0.004	46.415	0.000	0.000	0.000	0.000	0.000	0.000
65	E	123	CYS	0	-0.007	-0.006	42.693	-0.002	-0.002	0.000	0.000	0.000	0.000
66	E	124	VAL	0	-0.005	-0.005	43.373	0.002	0.002	0.000	0.000	0.000	0.000
67	E	125	GLU	-1	-0.847	-0.903	41.480	-0.036	-0.036	0.000	0.000	0.000	0.000
68	E	126	VAL	0	-0.046	-0.023	38.691	0.002	0.002	0.000	0.000	0.000	0.000
69	E	127	LYS	1	0.926	0.972	38.342	0.025	0.025	0.000	0.000	0.000	0.000
70	E	128	ARG	1	0.893	0.937	34.215	0.043	0.043	0.000	0.000	0.000	0.000
71	E	129	CYS	0	-0.060	-0.003	31.192	-0.002	-0.002	0.000	0.000	0.000	0.000
72	E	130	THR	0	0.043	0.027	29.484	-0.005	-0.005	0.000	0.000	0.000	0.000
73	E	131	GLY	0	0.010	0.001	27.001	0.007	0.007	0.000	0.000	0.000	0.000
74	E	132	CYS	0	-0.048	-0.031	21.818	-0.009	-0.009	0.000	0.000	0.000	0.000
75	E	133	CYS	0	-0.018	0.012	21.532	0.008	0.008	0.000	0.000	0.000	0.000
76	E	134	ASN	0	-0.018	-0.027	18.480	-0.023	-0.023	0.000	0.000	0.000	0.000
77	E	135	THR	0	-0.004	0.007	15.390	-0.019	-0.019	0.000	0.000	0.000	0.000
78	E	136	SER	0	0.068	0.027	15.304	-0.002	-0.002	0.000	0.000	0.000	0.000
79	E	137	SER	0	-0.023	-0.006	15.719	0.000	0.000	0.000	0.000	0.000	0.000
80	E	138	VAL	0	-0.043	-0.019	17.589	0.024	0.024	0.000	0.000	0.000	0.000
81	E	139	LYS	1	0.945	0.976	21.021	0.040	0.040	0.000	0.000	0.000	0.000
82	E	141	GLN	0	0.020	0.010	27.037	-0.010	-0.010	0.000	0.000	0.000	0.000
83	E	142	PRO	0	0.068	0.004	29.667	0.004	0.004	0.000	0.000	0.000	0.000
84	E	143	SER	0	-0.037	-0.030	33.418	0.000	0.000	0.000	0.000	0.000	0.000
85	E	144	ARG	1	0.844	0.905	35.287	0.008	0.008	0.000	0.000	0.000	0.000
86	E	145	VAL	0	-0.001	0.003	37.070	-0.003	-0.003	0.000	0.000	0.000	0.000
87	E	146	HIS	0	0.004	0.005	39.780	0.002	0.002	0.000	0.000	0.000	0.000
88	E	147	HIS	0	-0.007	-0.018	40.556	0.000	0.000	0.000	0.000	0.000	0.000
89	E	148	ARG	1	0.847	0.906	44.981	0.026	0.026	0.000	0.000	0.000	0.000
90	E	149	SER	0	-0.013	-0.032	47.704	-0.002	-0.002	0.000	0.000	0.000	0.000
91	E	150	VAL	0	-0.022	-0.001	48.786	0.001	0.001	0.000	0.000	0.000	0.000
92	E	151	LYS	1	0.855	0.906	51.528	0.018	0.018	0.000	0.000	0.000	0.000
93	E	152	VAL	0	-0.005	0.014	49.675	0.000	0.000	0.000	0.000	0.000	0.000
94	E	153	ALA	0	-0.002	-0.008	53.140	0.001	0.001	0.000	0.000	0.000	0.000
95	E	154	LYS	1	0.812	0.911	54.060	0.025	0.025	0.000	0.000	0.000	0.000
96	E	155	VAL	0	-0.003	-0.025	55.417	0.001	0.001	0.000	0.000	0.000	0.000
97	E	156	GLU	-1	-0.765	-0.889	56.677	-0.025	-0.025	0.000	0.000	0.000	0.000
98	E	157	TYR	0	0.044	0.013	59.322	0.001	0.001	0.000	0.000	0.000	0.000
99	E	158	VAL	0	0.018	0.014	62.141	0.000	0.000	0.000	0.000	0.000	0.000
100	E	159	ARG	1	0.970	0.968	64.786	0.019	0.019	0.000	0.000	0.000	0.000
101	E	160	LYS	1	0.998	0.986	63.996	0.023	0.023	0.000	0.000	0.000	0.000
102	E	161	LYS	1	0.962	0.998	66.610	0.017	0.017	0.000	0.000	0.000	0.000
103	E	162	PRO	0	0.042	0.022	63.183	-0.001	-0.001	0.000	0.000	0.000	0.000
104	E	163	LYS	1	0.889	0.948	62.327	0.020	0.020	0.000	0.000	0.000	0.000
105	E	164	LEU	0	0.018	0.029	58.701	-0.001	-0.001	0.000	0.000	0.000	0.000
106	E	165	LYS	1	0.853	0.932	58.506	0.023	0.023	0.000	0.000	0.000	0.000
107	E	166	GLU	-1	-0.802	-0.884	57.212	-0.020	-0.020	0.000	0.000	0.000	0.000
108	E	167	VAL	0	-0.023	-0.007	52.989	0.001	0.001	0.000	0.000	0.000	0.000
109	E	168	GLN	0	0.029	0.019	52.285	0.000	0.000	0.000	0.000	0.000	0.000
110	E	169	VAL	0	0.018	0.009	46.828	-0.001	-0.001	0.000	0.000	0.000	0.000
111	E	170	ARG	1	0.945	0.974	45.883	0.024	0.024	0.000	0.000	0.000	0.000
112	E	171	LEU	0	-0.007	0.004	43.842	-0.002	-0.002	0.000	0.000	0.000	0.000
113	E	172	GLU	-1	-0.802	-0.885	37.273	-0.035	-0.035	0.000	0.000	0.000	0.000
114	E	173	GLU	-1	-0.802	-0.870	39.986	-0.029	-0.029	0.000	0.000	0.000	0.000
115	E	174	HIS	0	0.009	-0.012	34.022	0.001	0.001	0.000	0.000	0.000	0.000
116	E	175	LEU	0	-0.037	-0.033	38.138	0.000	0.000	0.000	0.000	0.000	0.000
117	E	176	GLU	-1	-0.821	-0.884	36.354	-0.005	-0.005	0.000	0.000	0.000	0.000
118	E	178	ALA	0	0.029	0.021	29.924	0.005	0.005	0.000	0.000	0.000	0.000
119	E	180	ALA	0	0.045	0.028	24.845	-0.002	-0.002	0.000	0.000	0.000	0.000

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