FMO DATABASE

FMODB ID: 3QV3L

Calculation Name: 3MJK-X-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: X

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:

Apendix: None

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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-860320.443633
FMO2-HF: Nuclear repulsion	810634.346344
FMO2-HF: Total energy	-49686.097289
FMO2-MP2: Total energy	-49826.859963

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(X:23:ALA)

Summations of interaction energy for fragment #1(X: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.
-1.694	0.268	0.132	-0.868	-1.226	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.030

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	X	25	ILE	0	-0.010	-0.019	2.779	-2.350	-0.446	0.133	-0.865	-1.173	0.001
4	X	26	PRO	0	0.082	0.060	4.916	-0.696	-0.638	-0.001	-0.003	-0.053	0.000
5	X	27	ARG	1	0.861	0.910	7.993	0.694	0.694	0.000	0.000	0.000	0.000
6	X	28	GLU	-1	-0.824	-0.915	9.381	-0.040	-0.040	0.000	0.000	0.000	0.000
7	X	29	VAL	0	0.064	0.044	9.085	0.054	0.054	0.000	0.000	0.000	0.000
8	X	30	ILE	0	-0.012	-0.001	5.475	0.083	0.083	0.000	0.000	0.000	0.000
9	X	31	GLU	-1	-0.815	-0.918	9.960	-0.369	-0.369	0.000	0.000	0.000	0.000
10	X	32	ARG	1	0.773	0.885	13.324	0.057	0.057	0.000	0.000	0.000	0.000
11	X	33	LEU	0	0.045	0.031	10.668	0.021	0.021	0.000	0.000	0.000	0.000
12	X	34	ALA	0	-0.056	-0.021	13.867	0.018	0.018	0.000	0.000	0.000	0.000
13	X	35	ARG	1	0.851	0.937	15.508	0.186	0.186	0.000	0.000	0.000	0.000
14	X	36	SER	0	0.008	-0.007	17.611	0.018	0.018	0.000	0.000	0.000	0.000
15	X	37	GLN	0	-0.053	-0.026	19.516	0.003	0.003	0.000	0.000	0.000	0.000
16	X	38	ILE	0	0.016	-0.002	16.259	0.007	0.007	0.000	0.000	0.000	0.000
17	X	39	HIS	0	-0.057	-0.032	20.532	-0.002	-0.002	0.000	0.000	0.000	0.000
18	X	40	SER	0	-0.021	-0.015	22.303	0.004	0.004	0.000	0.000	0.000	0.000
19	X	41	ILE	0	0.003	-0.019	17.918	0.002	0.002	0.000	0.000	0.000	0.000
20	X	42	ARG	1	0.891	0.923	19.308	-0.059	-0.059	0.000	0.000	0.000	0.000
21	X	43	ASP	-1	-0.823	-0.895	21.174	0.051	0.051	0.000	0.000	0.000	0.000
22	X	44	LEU	0	-0.033	-0.019	13.455	-0.007	-0.007	0.000	0.000	0.000	0.000
23	X	45	GLN	0	-0.065	-0.041	16.303	0.008	0.008	0.000	0.000	0.000	0.000
24	X	46	ARG	0	0.083	0.071	17.989	0.000	0.000	0.000	0.000	0.000	0.000
25	X	47	LEU	0	-0.039	-0.006	17.676	-0.010	-0.010	0.000	0.000	0.000	0.000
26	X	48	LEU	0	-0.040	-0.010	11.093	-0.025	-0.025	0.000	0.000	0.000	0.000
27	X	49	GLU	-1	-0.918	-0.952	15.266	0.159	0.159	0.000	0.000	0.000	0.000
28	X	88	ILE	0	0.000	0.002	26.193	0.002	0.002	0.000	0.000	0.000	0.000
29	X	89	GLU	-1	-0.975	-0.993	27.641	0.056	0.056	0.000	0.000	0.000	0.000
30	X	90	GLU	-1	-0.857	-0.925	22.862	0.105	0.105	0.000	0.000	0.000	0.000
31	X	91	ALA	0	-0.010	-0.015	20.985	-0.011	-0.011	0.000	0.000	0.000	0.000
32	X	92	VAL	0	0.036	0.022	22.024	0.000	0.000	0.000	0.000	0.000	0.000
33	X	93	PRO	0	0.024	0.026	20.352	-0.004	-0.004	0.000	0.000	0.000	0.000
34	X	94	ALA	0	0.007	-0.003	21.999	-0.008	-0.008	0.000	0.000	0.000	0.000
35	X	95	VAL	0	0.016	0.002	22.702	-0.011	-0.011	0.000	0.000	0.000	0.000
36	X	96	CYS	0	0.005	0.020	19.058	0.005	0.005	0.000	0.000	0.000	0.000
37	X	97	LYS	1	0.962	0.981	24.191	0.014	0.014	0.000	0.000	0.000	0.000
38	X	98	THR	0	0.034	0.001	27.953	-0.001	-0.001	0.000	0.000	0.000	0.000
39	X	99	ARG	1	0.796	0.883	26.245	0.022	0.022	0.000	0.000	0.000	0.000
40	X	100	THR	0	-0.026	-0.016	31.940	-0.004	-0.004	0.000	0.000	0.000	0.000
41	X	101	VAL	0	-0.015	0.013	29.570	0.002	0.002	0.000	0.000	0.000	0.000
42	X	102	ILE	0	0.026	0.005	33.026	-0.001	-0.001	0.000	0.000	0.000	0.000
43	X	103	TYR	0	-0.014	-0.007	33.738	-0.002	-0.002	0.000	0.000	0.000	0.000
44	X	104	GLU	-1	-0.904	-0.966	35.753	-0.017	-0.017	0.000	0.000	0.000	0.000
45	X	105	ILE	0	-0.031	-0.016	37.576	-0.003	-0.003	0.000	0.000	0.000	0.000
46	X	106	PRO	0	0.014	0.008	36.929	0.001	0.001	0.000	0.000	0.000	0.000
47	X	107	ARG	1	0.924	0.949	39.338	0.016	0.016	0.000	0.000	0.000	0.000
48	X	108	SER	0	0.041	0.010	38.921	0.001	0.001	0.000	0.000	0.000	0.000
49	X	109	GLN	0	-0.007	0.001	39.711	-0.001	-0.001	0.000	0.000	0.000	0.000
50	X	110	VAL	0	-0.019	-0.010	42.666	0.001	0.001	0.000	0.000	0.000	0.000
51	X	111	ASP	-1	-0.811	-0.881	45.431	-0.019	-0.019	0.000	0.000	0.000	0.000
52	X	112	PRO	0	-0.023	0.000	43.235	0.000	0.000	0.000	0.000	0.000	0.000
53	X	113	THR	0	-0.051	-0.029	44.686	-0.001	-0.001	0.000	0.000	0.000	0.000
54	X	114	SER	0	-0.060	-0.048	47.472	0.002	0.002	0.000	0.000	0.000	0.000
55	X	115	ALA	0	0.044	0.015	45.758	-0.001	-0.001	0.000	0.000	0.000	0.000
56	X	116	ASN	0	-0.008	0.001	47.353	0.000	0.000	0.000	0.000	0.000	0.000
57	X	117	PHE	0	-0.060	-0.037	45.627	0.001	0.001	0.000	0.000	0.000	0.000
58	X	118	LEU	0	0.048	0.028	46.517	0.000	0.000	0.000	0.000	0.000	0.000
59	X	119	ILE	0	0.012	0.002	43.507	-0.001	-0.001	0.000	0.000	0.000	0.000
60	X	120	TRP	0	0.000	0.020	46.632	0.001	0.001	0.000	0.000	0.000	0.000
61	X	121	PRO	0	0.053	0.018	44.718	0.000	0.000	0.000	0.000	0.000	0.000
62	X	122	PRO	0	0.026	0.009	42.552	-0.001	-0.001	0.000	0.000	0.000	0.000
63	X	123	CYS	0	-0.025	-0.009	38.781	-0.001	-0.001	0.000	0.000	0.000	0.000
64	X	124	VAL	0	-0.015	-0.001	39.130	0.001	0.001	0.000	0.000	0.000	0.000
65	X	125	GLU	-1	-0.826	-0.906	37.587	-0.012	-0.012	0.000	0.000	0.000	0.000
66	X	126	VAL	0	-0.068	-0.026	34.052	-0.002	-0.002	0.000	0.000	0.000	0.000
67	X	127	LYS	1	0.885	0.920	34.188	0.017	0.017	0.000	0.000	0.000	0.000
68	X	128	ARG	1	0.880	0.932	29.692	0.038	0.038	0.000	0.000	0.000	0.000
69	X	129	CYS	0	-0.060	-0.027	26.271	0.003	0.003	0.000	0.000	0.000	0.000
70	X	130	THR	0	0.020	0.014	25.192	0.000	0.000	0.000	0.000	0.000	0.000
71	X	131	GLY	0	0.014	0.014	23.182	0.002	0.002	0.000	0.000	0.000	0.000
72	X	132	CYS	0	-0.050	-0.035	17.781	-0.007	-0.007	0.000	0.000	0.000	0.000
73	X	133	CYS	0	-0.028	-0.010	17.308	0.005	0.005	0.000	0.000	0.000	0.000
74	X	134	ASN	0	-0.013	-0.011	15.611	0.008	0.008	0.000	0.000	0.000	0.000
75	X	135	THR	0	0.044	0.030	10.659	0.021	0.021	0.000	0.000	0.000	0.000
76	X	136	SER	0	0.035	0.013	10.788	0.000	0.000	0.000	0.000	0.000	0.000
77	X	137	SER	0	0.010	0.013	11.057	-0.025	-0.025	0.000	0.000	0.000	0.000
78	X	138	VAL	0	-0.080	-0.021	12.660	0.007	0.007	0.000	0.000	0.000	0.000
79	X	139	LYS	1	0.880	0.931	15.914	0.253	0.253	0.000	0.000	0.000	0.000
80	X	141	GLN	0	0.023	0.014	22.318	0.002	0.002	0.000	0.000	0.000	0.000
81	X	142	PRO	0	0.038	-0.005	24.816	0.005	0.005	0.000	0.000	0.000	0.000
82	X	143	SER	0	-0.018	-0.008	28.680	-0.005	-0.005	0.000	0.000	0.000	0.000
83	X	144	ARG	1	0.861	0.918	30.574	0.041	0.041	0.000	0.000	0.000	0.000
84	X	145	VAL	0	0.020	0.018	32.782	0.003	0.003	0.000	0.000	0.000	0.000
85	X	146	HIS	0	-0.007	-0.004	34.386	0.002	0.002	0.000	0.000	0.000	0.000
86	X	147	HIS	0	-0.034	-0.045	35.081	0.001	0.001	0.000	0.000	0.000	0.000
87	X	148	ARG	1	0.868	0.921	39.750	0.026	0.026	0.000	0.000	0.000	0.000
88	X	149	SER	0	-0.004	-0.014	42.746	-0.001	-0.001	0.000	0.000	0.000	0.000
89	X	150	VAL	0	-0.025	-0.004	44.171	0.001	0.001	0.000	0.000	0.000	0.000
90	X	151	LYS	1	0.849	0.898	46.630	0.014	0.014	0.000	0.000	0.000	0.000
91	X	152	VAL	0	0.010	0.016	45.312	0.001	0.001	0.000	0.000	0.000	0.000
92	X	153	ALA	0	0.034	0.013	48.741	0.000	0.000	0.000	0.000	0.000	0.000
93	X	154	LYS	1	0.823	0.921	49.173	0.017	0.017	0.000	0.000	0.000	0.000
94	X	155	VAL	0	-0.003	-0.016	50.821	0.001	0.001	0.000	0.000	0.000	0.000
95	X	156	GLU	-1	-0.770	-0.875	51.843	-0.014	-0.014	0.000	0.000	0.000	0.000
96	X	157	TYR	0	0.036	0.011	54.186	0.001	0.001	0.000	0.000	0.000	0.000
97	X	158	VAL	0	-0.013	-0.008	57.352	-0.001	-0.001	0.000	0.000	0.000	0.000
98	X	159	ARG	1	0.965	0.976	60.246	0.010	0.010	0.000	0.000	0.000	0.000
99	X	160	LYS	1	0.974	0.977	61.837	0.005	0.005	0.000	0.000	0.000	0.000
100	X	161	LYS	1	0.972	1.004	62.381	0.007	0.007	0.000	0.000	0.000	0.000
101	X	162	PRO	0	0.058	0.040	58.571	-0.001	-0.001	0.000	0.000	0.000	0.000
102	X	163	LYS	1	0.823	0.900	56.415	0.013	0.013	0.000	0.000	0.000	0.000
103	X	164	LEU	0	0.023	0.015	54.669	0.000	0.000	0.000	0.000	0.000	0.000
104	X	165	LYS	1	0.945	0.974	53.523	0.017	0.017	0.000	0.000	0.000	0.000
105	X	166	GLU	-1	-0.810	-0.879	52.651	-0.014	-0.014	0.000	0.000	0.000	0.000
106	X	167	VAL	0	-0.048	-0.024	48.201	0.000	0.000	0.000	0.000	0.000	0.000
107	X	168	GLN	0	0.027	0.024	46.984	0.000	0.000	0.000	0.000	0.000	0.000
108	X	169	VAL	0	0.019	0.012	42.272	-0.001	-0.001	0.000	0.000	0.000	0.000
109	X	170	ARG	1	0.929	0.972	36.811	0.044	0.044	0.000	0.000	0.000	0.000
110	X	171	LEU	0	-0.004	0.000	39.153	-0.001	-0.001	0.000	0.000	0.000	0.000
111	X	172	GLU	-1	-0.808	-0.910	32.212	-0.055	-0.055	0.000	0.000	0.000	0.000
112	X	173	GLU	-1	-0.790	-0.855	34.980	-0.023	-0.023	0.000	0.000	0.000	0.000
113	X	174	HIS	0	-0.011	-0.017	29.139	-0.002	-0.002	0.000	0.000	0.000	0.000
114	X	175	LEU	0	-0.023	-0.004	33.368	0.003	0.003	0.000	0.000	0.000	0.000
115	X	176	GLU	-1	-0.822	-0.892	31.813	-0.042	-0.042	0.000	0.000	0.000	0.000
116	X	178	ALA	0	0.043	0.027	25.520	0.005	0.005	0.000	0.000	0.000	0.000
117	X	180	ALA	0	0.037	0.027	21.055	-0.004	-0.004	0.000	0.000	0.000	0.000
118	X	181	THR	0	0.035	0.012	16.281	-0.007	-0.007	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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