FMO DATABASE

FMODB ID: Q1G7Y

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	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	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-886227.322314
FMO2-HF: Nuclear repulsion	835497.459571
FMO2-HF: Total energy	-50729.862743
FMO2-MP2: Total energy	-50873.656372

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.
1.303	3.306	-0.006	-1.102	-0.895	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 : 0.013 / q_NPA : 0.004

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	B	25	ILE	0	-0.017	-0.009	3.897	0.022	2.025	-0.006	-1.102	-0.895	0.004
4	B	26	PRO	0	0.038	0.018	5.615	0.219	0.219	0.000	0.000	0.000	0.000
5	B	27	ARG	1	0.950	0.965	7.951	0.334	0.334	0.000	0.000	0.000	0.000
6	B	28	GLU	-1	-0.799	-0.899	11.313	-0.281	-0.281	0.000	0.000	0.000	0.000
7	B	29	VAL	0	-0.011	0.004	9.691	0.057	0.057	0.000	0.000	0.000	0.000
8	B	30	ILE	0	-0.001	-0.005	10.718	0.043	0.043	0.000	0.000	0.000	0.000
9	B	31	GLU	-1	-0.821	-0.909	13.390	-0.220	-0.220	0.000	0.000	0.000	0.000
10	B	32	ARG	1	0.752	0.849	14.739	0.261	0.261	0.000	0.000	0.000	0.000
11	B	33	LEU	0	0.026	0.007	13.173	0.033	0.033	0.000	0.000	0.000	0.000
12	B	34	ALA	0	-0.062	-0.023	17.051	0.033	0.033	0.000	0.000	0.000	0.000
13	B	35	ARG	1	0.805	0.891	18.714	0.264	0.264	0.000	0.000	0.000	0.000
14	B	36	SER	0	0.011	0.015	20.116	0.033	0.033	0.000	0.000	0.000	0.000
15	B	37	GLN	0	-0.025	-0.017	21.983	-0.009	-0.009	0.000	0.000	0.000	0.000
16	B	38	ILE	0	-0.004	-0.015	18.671	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	39	HIS	0	-0.018	0.003	22.928	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	40	SER	0	-0.028	-0.020	23.594	0.007	0.007	0.000	0.000	0.000	0.000
19	B	41	ILE	0	0.040	0.008	18.381	-0.020	-0.020	0.000	0.000	0.000	0.000
20	B	42	ARG	1	0.873	0.906	19.473	0.134	0.134	0.000	0.000	0.000	0.000
21	B	43	ASP	-1	-0.802	-0.874	21.050	-0.155	-0.155	0.000	0.000	0.000	0.000
22	B	44	LEU	0	0.020	0.009	15.038	-0.002	-0.002	0.000	0.000	0.000	0.000
23	B	45	GLN	0	0.005	-0.003	16.050	-0.014	-0.014	0.000	0.000	0.000	0.000
24	B	46	ARG	1	0.854	0.917	16.531	0.150	0.150	0.000	0.000	0.000	0.000
25	B	47	LEU	0	-0.021	-0.002	17.496	0.015	0.015	0.000	0.000	0.000	0.000
26	B	48	LEU	0	-0.063	-0.032	11.409	-0.050	-0.050	0.000	0.000	0.000	0.000
27	B	49	GLU	-1	-0.826	-0.878	12.949	-0.125	-0.125	0.000	0.000	0.000	0.000
28	B	50	ILE	0	-0.044	-0.012	13.292	0.032	0.032	0.000	0.000	0.000	0.000
29	B	87	SER	0	-0.019	-0.022	28.927	0.001	0.001	0.000	0.000	0.000	0.000
30	B	88	ILE	0	-0.014	-0.011	25.730	0.002	0.002	0.000	0.000	0.000	0.000
31	B	89	GLU	-1	-0.939	-0.960	27.305	-0.140	-0.140	0.000	0.000	0.000	0.000
32	B	90	GLU	-1	-0.799	-0.875	23.446	-0.195	-0.195	0.000	0.000	0.000	0.000
33	B	91	ALA	0	0.007	-0.005	23.334	0.006	0.006	0.000	0.000	0.000	0.000
34	B	92	VAL	0	0.048	0.028	24.522	-0.015	-0.015	0.000	0.000	0.000	0.000
35	B	93	PRO	0	0.016	0.020	23.893	-0.009	-0.009	0.000	0.000	0.000	0.000
36	B	94	ALA	0	0.026	0.009	25.584	0.019	0.019	0.000	0.000	0.000	0.000
37	B	95	VAL	0	-0.005	-0.009	27.048	-0.010	-0.010	0.000	0.000	0.000	0.000
38	B	96	CYS	0	-0.010	0.007	25.013	0.034	0.034	0.000	0.000	0.000	0.000
39	B	97	LYS	1	0.958	0.976	28.939	0.144	0.144	0.000	0.000	0.000	0.000
40	B	98	THR	0	0.048	0.016	32.793	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	99	ARG	1	0.784	0.896	30.749	0.172	0.172	0.000	0.000	0.000	0.000
42	B	100	THR	0	-0.017	-0.018	37.191	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	101	VAL	0	-0.021	0.009	35.320	-0.005	-0.005	0.000	0.000	0.000	0.000
44	B	102	ILE	0	0.031	0.008	38.685	0.006	0.006	0.000	0.000	0.000	0.000
45	B	103	TYR	0	-0.003	-0.003	39.628	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	104	GLU	-1	-0.904	-0.960	41.529	-0.094	-0.094	0.000	0.000	0.000	0.000
47	B	105	ILE	0	-0.027	-0.017	43.914	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	106	PRO	0	0.004	0.007	43.463	0.002	0.002	0.000	0.000	0.000	0.000
49	B	107	ARG	1	0.957	0.959	45.794	0.074	0.074	0.000	0.000	0.000	0.000
50	B	108	SER	0	0.035	0.010	45.087	0.003	0.003	0.000	0.000	0.000	0.000
51	B	109	GLN	0	-0.036	-0.018	45.754	0.004	0.004	0.000	0.000	0.000	0.000
52	B	110	VAL	0	-0.044	-0.016	49.254	0.002	0.002	0.000	0.000	0.000	0.000
53	B	111	ASP	-1	-0.826	-0.918	51.974	-0.054	-0.054	0.000	0.000	0.000	0.000
54	B	112	PRO	0	-0.010	0.000	49.940	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	113	THR	0	-0.034	-0.018	51.362	0.000	0.000	0.000	0.000	0.000	0.000
56	B	114	SER	0	-0.024	-0.008	54.241	0.001	0.001	0.000	0.000	0.000	0.000
57	B	115	ALA	0	0.067	0.027	52.316	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	116	ASN	0	-0.057	-0.019	53.265	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	117	PHE	0	-0.051	-0.032	51.908	0.002	0.002	0.000	0.000	0.000	0.000
60	B	118	LEU	0	0.020	0.018	52.702	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	119	ILE	0	0.003	0.000	49.520	0.002	0.002	0.000	0.000	0.000	0.000
62	B	120	TRP	0	0.023	0.026	52.726	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	121	PRO	0	0.050	0.019	50.712	0.002	0.002	0.000	0.000	0.000	0.000
64	B	122	PRO	0	0.016	0.000	48.537	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	123	CYS	0	-0.009	-0.003	44.792	-0.003	-0.003	0.000	0.000	0.000	0.000
66	B	124	VAL	0	-0.017	-0.001	45.255	0.004	0.004	0.000	0.000	0.000	0.000
67	B	125	GLU	-1	-0.830	-0.907	43.185	-0.098	-0.098	0.000	0.000	0.000	0.000
68	B	126	VAL	0	-0.064	-0.024	40.127	0.003	0.003	0.000	0.000	0.000	0.000
69	B	127	LYS	1	0.898	0.922	40.045	0.094	0.094	0.000	0.000	0.000	0.000
70	B	128	ARG	1	0.872	0.925	35.821	0.122	0.122	0.000	0.000	0.000	0.000
71	B	129	CYS	0	-0.057	-0.020	32.171	0.000	0.000	0.000	0.000	0.000	0.000
72	B	130	THR	0	0.024	0.016	31.078	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	131	GLY	0	0.019	0.014	28.140	0.006	0.006	0.000	0.000	0.000	0.000
74	B	132	CYS	0	-0.038	-0.028	22.981	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	133	CYS	0	-0.025	-0.011	22.624	0.023	0.023	0.000	0.000	0.000	0.000
76	B	134	ASN	0	-0.010	-0.012	18.835	-0.021	-0.021	0.000	0.000	0.000	0.000
77	B	135	THR	0	0.039	0.036	15.062	-0.049	-0.049	0.000	0.000	0.000	0.000
78	B	136	SER	0	0.047	0.020	16.720	0.047	0.047	0.000	0.000	0.000	0.000
79	B	137	SER	0	-0.035	-0.013	16.748	0.042	0.042	0.000	0.000	0.000	0.000
80	B	138	VAL	0	-0.017	-0.002	18.682	0.048	0.048	0.000	0.000	0.000	0.000
81	B	139	LYS	1	0.873	0.918	21.579	0.328	0.328	0.000	0.000	0.000	0.000
82	B	141	GLN	0	0.020	0.014	28.082	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	142	PRO	0	0.042	-0.002	30.719	0.004	0.004	0.000	0.000	0.000	0.000
84	B	143	SER	0	-0.032	-0.031	34.458	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	144	ARG	1	0.813	0.894	35.947	0.101	0.101	0.000	0.000	0.000	0.000
86	B	145	VAL	0	0.018	0.006	38.222	-0.005	-0.005	0.000	0.000	0.000	0.000
87	B	146	HIS	0	0.002	0.000	40.663	0.004	0.004	0.000	0.000	0.000	0.000
88	B	147	HIS	0	-0.027	-0.024	41.297	0.001	0.001	0.000	0.000	0.000	0.000
89	B	148	ARG	1	0.833	0.899	45.948	0.085	0.085	0.000	0.000	0.000	0.000
90	B	149	SER	0	-0.014	-0.020	48.997	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	150	VAL	0	-0.016	0.002	50.357	0.001	0.001	0.000	0.000	0.000	0.000
92	B	151	LYS	1	0.853	0.898	52.875	0.052	0.052	0.000	0.000	0.000	0.000
93	B	152	VAL	0	0.006	0.014	51.403	-0.001	-0.001	0.000	0.000	0.000	0.000
94	B	153	ALA	0	0.028	0.014	54.871	0.002	0.002	0.000	0.000	0.000	0.000
95	B	154	LYS	1	0.821	0.909	55.584	0.053	0.053	0.000	0.000	0.000	0.000
96	B	155	VAL	0	-0.007	-0.016	56.988	0.003	0.003	0.000	0.000	0.000	0.000
97	B	156	GLU	-1	-0.774	-0.872	58.007	-0.051	-0.051	0.000	0.000	0.000	0.000
98	B	157	TYR	0	0.040	0.008	60.502	0.001	0.001	0.000	0.000	0.000	0.000
99	B	158	VAL	0	0.033	0.025	63.579	0.001	0.001	0.000	0.000	0.000	0.000
100	B	159	ARG	1	0.976	0.976	66.226	0.033	0.033	0.000	0.000	0.000	0.000
101	B	160	LYN	0	0.084	0.039	64.718	0.001	0.001	0.000	0.000	0.000	0.000
102	B	161	LYS	1	0.836	0.924	67.766	0.036	0.036	0.000	0.000	0.000	0.000
103	B	162	PRO	0	0.032	0.017	64.404	-0.001	-0.001	0.000	0.000	0.000	0.000
104	B	163	LYS	1	0.855	0.930	63.339	0.046	0.046	0.000	0.000	0.000	0.000
105	B	164	LEU	0	0.023	0.010	60.808	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	165	LYS	1	0.923	0.962	59.250	0.051	0.051	0.000	0.000	0.000	0.000
107	B	166	GLU	-1	-0.808	-0.875	58.816	-0.052	-0.052	0.000	0.000	0.000	0.000
108	B	167	VAL	0	-0.051	-0.024	54.461	0.001	0.001	0.000	0.000	0.000	0.000
109	B	168	GLN	0	0.024	0.019	53.751	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	169	VAL	0	0.004	0.009	48.739	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	170	ARG	1	0.960	0.974	47.179	0.077	0.077	0.000	0.000	0.000	0.000
112	B	171	LEU	0	0.012	0.013	45.336	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	172	GLU	-1	-0.784	-0.882	38.386	-0.121	-0.121	0.000	0.000	0.000	0.000
114	B	173	GLU	-1	-0.795	-0.860	41.146	-0.093	-0.093	0.000	0.000	0.000	0.000
115	B	174	HIS	0	-0.003	-0.019	35.213	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	175	LEU	0	-0.044	-0.025	39.323	0.001	0.001	0.000	0.000	0.000	0.000
117	B	176	GLU	-1	-0.792	-0.853	36.760	-0.102	-0.102	0.000	0.000	0.000	0.000
118	B	178	ALA	0	0.043	0.027	30.248	0.004	0.004	0.000	0.000	0.000	0.000
119	B	180	ALA	0	0.030	0.018	26.233	0.004	0.004	0.000	0.000	0.000	0.000
120	B	181	THR	0	0.002	0.004	20.410	-0.018	-0.018	0.000	0.000	0.000	0.000
121	B	182	THR	0	0.029	0.029	22.566	-0.008	-0.008	0.000	0.000	0.000	0.000

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