FMO DATABASE

FMODB ID: R5GN8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-886697.128399
FMO2-HF: Nuclear repulsion	835967.92193
FMO2-HF: Total energy	-50729.206469
FMO2-MP2: Total energy	-50873.070247

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.
1.069	3.504	-0.021	-1.325	-1.088	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 : 0.004 / q_NPA : 0.001

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	-0.022	-0.013	3.806	-0.429	2.006	-0.021	-1.325	-1.088	0.004
4	B	26	PRO	0	0.066	0.032	5.470	0.254	0.254	0.000	0.000	0.000	0.000
5	B	27	ARG	1	0.926	0.962	8.010	0.426	0.426	0.000	0.000	0.000	0.000
6	B	28	GLU	-1	-0.812	-0.913	10.870	-0.237	-0.237	0.000	0.000	0.000	0.000
7	B	29	VAL	0	-0.023	-0.020	9.904	0.062	0.062	0.000	0.000	0.000	0.000
8	B	30	ILE	0	-0.003	0.004	10.775	0.051	0.051	0.000	0.000	0.000	0.000
9	B	31	GLU	-1	-0.816	-0.900	13.418	-0.233	-0.233	0.000	0.000	0.000	0.000
10	B	32	ARG	1	0.807	0.905	13.733	0.260	0.260	0.000	0.000	0.000	0.000
11	B	33	LEU	0	0.044	0.010	13.497	0.036	0.036	0.000	0.000	0.000	0.000
12	B	34	ALA	0	-0.071	-0.027	17.286	0.031	0.031	0.000	0.000	0.000	0.000
13	B	35	ARG	1	0.819	0.913	18.201	0.269	0.269	0.000	0.000	0.000	0.000
14	B	36	SER	0	-0.008	0.004	20.095	0.036	0.036	0.000	0.000	0.000	0.000
15	B	37	GLN	0	-0.018	-0.013	21.946	-0.009	-0.009	0.000	0.000	0.000	0.000
16	B	38	ILE	0	-0.027	-0.023	18.522	0.002	0.002	0.000	0.000	0.000	0.000
17	B	39	HIS	0	0.003	0.001	22.785	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	40	SER	0	-0.036	-0.006	23.068	0.009	0.009	0.000	0.000	0.000	0.000
19	B	41	ILE	0	0.050	0.009	18.009	-0.019	-0.019	0.000	0.000	0.000	0.000
20	B	42	ARG	1	0.868	0.921	19.148	0.098	0.098	0.000	0.000	0.000	0.000
21	B	43	ASP	-1	-0.799	-0.890	20.470	-0.130	-0.130	0.000	0.000	0.000	0.000
22	B	44	LEU	0	0.029	0.019	14.885	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	45	GLN	0	0.020	0.010	16.121	-0.012	-0.012	0.000	0.000	0.000	0.000
24	B	46	ARG	1	0.853	0.917	17.071	0.116	0.116	0.000	0.000	0.000	0.000
25	B	47	LEU	0	-0.057	-0.028	17.407	0.006	0.006	0.000	0.000	0.000	0.000
26	B	48	LEU	0	-0.085	-0.056	11.509	-0.020	-0.020	0.000	0.000	0.000	0.000
27	B	49	GLU	-1	-0.872	-0.902	13.266	-0.088	-0.088	0.000	0.000	0.000	0.000
28	B	50	ILE	0	-0.045	-0.019	13.850	0.014	0.014	0.000	0.000	0.000	0.000
29	B	87	SER	0	-0.029	-0.026	28.544	0.002	0.002	0.000	0.000	0.000	0.000
30	B	88	ILE	0	-0.019	-0.017	25.547	0.000	0.000	0.000	0.000	0.000	0.000
31	B	89	GLU	-1	-0.943	-0.960	26.598	-0.109	-0.109	0.000	0.000	0.000	0.000
32	B	90	GLU	-1	-0.781	-0.867	22.962	-0.144	-0.144	0.000	0.000	0.000	0.000
33	B	91	ALA	0	0.011	0.000	22.668	0.003	0.003	0.000	0.000	0.000	0.000
34	B	92	VAL	0	0.040	0.019	24.132	-0.008	-0.008	0.000	0.000	0.000	0.000
35	B	93	PRO	0	0.008	0.009	23.310	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	94	ALA	0	0.006	0.008	25.152	0.018	0.018	0.000	0.000	0.000	0.000
37	B	95	VAL	0	0.026	-0.005	26.546	-0.013	-0.013	0.000	0.000	0.000	0.000
38	B	96	CYS	0	-0.002	0.019	24.742	0.030	0.030	0.000	0.000	0.000	0.000
39	B	97	LYS	1	0.976	0.973	28.862	0.132	0.132	0.000	0.000	0.000	0.000
40	B	98	THR	0	0.051	0.021	32.622	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	99	ARG	1	0.782	0.892	30.233	0.157	0.157	0.000	0.000	0.000	0.000
42	B	100	THR	0	-0.022	-0.022	36.606	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	101	VAL	0	-0.025	-0.005	35.028	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	102	ILE	0	0.034	0.005	38.329	0.005	0.005	0.000	0.000	0.000	0.000
45	B	103	TYR	0	-0.013	-0.002	39.288	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	104	GLU	-1	-0.902	-0.955	41.242	-0.087	-0.087	0.000	0.000	0.000	0.000
47	B	105	ILE	0	-0.047	-0.027	43.367	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	106	PRO	0	0.006	0.006	43.050	0.001	0.001	0.000	0.000	0.000	0.000
49	B	107	ARG	1	0.975	0.965	45.192	0.069	0.069	0.000	0.000	0.000	0.000
50	B	108	SER	0	0.025	-0.003	44.903	0.003	0.003	0.000	0.000	0.000	0.000
51	B	109	GLN	0	0.008	0.005	45.405	0.004	0.004	0.000	0.000	0.000	0.000
52	B	110	VAL	0	-0.045	-0.004	48.649	0.002	0.002	0.000	0.000	0.000	0.000
53	B	111	ASP	-1	-0.781	-0.898	51.765	-0.052	-0.052	0.000	0.000	0.000	0.000
54	B	112	PRO	0	-0.042	-0.012	49.539	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	113	THR	0	-0.041	-0.018	51.011	0.000	0.000	0.000	0.000	0.000	0.000
56	B	114	SER	0	-0.027	-0.004	53.378	0.000	0.000	0.000	0.000	0.000	0.000
57	B	115	ALA	0	0.066	0.021	52.216	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	116	ASN	0	-0.059	-0.021	53.400	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	117	PHE	0	-0.028	-0.020	51.840	0.002	0.002	0.000	0.000	0.000	0.000
60	B	118	LEU	0	-0.013	0.007	52.730	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	119	ILE	0	0.016	0.014	49.031	0.002	0.002	0.000	0.000	0.000	0.000
62	B	120	TRP	0	0.019	0.040	52.398	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	121	PRO	0	0.068	0.019	50.383	0.002	0.002	0.000	0.000	0.000	0.000
64	B	122	PRO	0	0.016	-0.010	47.783	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	123	CYS	0	-0.008	-0.002	44.205	-0.003	-0.003	0.000	0.000	0.000	0.000
66	B	124	VAL	0	-0.016	-0.002	44.947	0.004	0.004	0.000	0.000	0.000	0.000
67	B	125	GLU	-1	-0.848	-0.917	43.038	-0.087	-0.087	0.000	0.000	0.000	0.000
68	B	126	VAL	0	-0.054	-0.016	39.931	0.002	0.002	0.000	0.000	0.000	0.000
69	B	127	LYS	1	0.943	0.976	39.423	0.090	0.090	0.000	0.000	0.000	0.000
70	B	128	ARG	1	0.859	0.916	35.234	0.116	0.116	0.000	0.000	0.000	0.000
71	B	129	CYS	0	-0.071	0.005	31.917	0.001	0.001	0.000	0.000	0.000	0.000
72	B	130	THR	0	0.030	0.013	30.477	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	131	GLY	0	0.025	0.009	27.712	0.007	0.007	0.000	0.000	0.000	0.000
74	B	132	CYS	0	-0.046	-0.029	22.476	-0.009	-0.009	0.000	0.000	0.000	0.000
75	B	133	CYS	0	-0.026	0.004	22.053	0.021	0.021	0.000	0.000	0.000	0.000
76	B	134	ASN	0	-0.003	-0.009	18.670	-0.014	-0.014	0.000	0.000	0.000	0.000
77	B	135	THR	0	0.031	0.029	15.681	-0.051	-0.051	0.000	0.000	0.000	0.000
78	B	136	SER	0	0.047	0.019	16.249	0.041	0.041	0.000	0.000	0.000	0.000
79	B	137	SER	0	-0.044	-0.028	16.657	0.036	0.036	0.000	0.000	0.000	0.000
80	B	138	VAL	0	0.011	0.009	18.613	0.042	0.042	0.000	0.000	0.000	0.000
81	B	139	LYS	1	0.866	0.931	21.518	0.328	0.328	0.000	0.000	0.000	0.000
82	B	141	GLN	0	-0.001	0.001	27.630	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	142	PRO	0	0.076	0.002	30.520	0.003	0.003	0.000	0.000	0.000	0.000
84	B	143	SER	0	-0.030	-0.031	34.181	-0.004	-0.004	0.000	0.000	0.000	0.000
85	B	144	ARG	1	0.875	0.925	35.774	0.095	0.095	0.000	0.000	0.000	0.000
86	B	145	VAL	0	0.006	0.009	38.016	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	146	HIS	0	-0.005	0.001	40.689	0.003	0.003	0.000	0.000	0.000	0.000
88	B	147	HIS	0	-0.033	-0.025	41.421	0.001	0.001	0.000	0.000	0.000	0.000
89	B	148	ARG	1	0.857	0.906	45.927	0.079	0.079	0.000	0.000	0.000	0.000
90	B	149	SER	0	-0.003	-0.013	48.737	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	150	VAL	0	-0.007	0.004	49.995	0.002	0.002	0.000	0.000	0.000	0.000
92	B	151	LYS	1	0.843	0.914	52.694	0.047	0.047	0.000	0.000	0.000	0.000
93	B	152	VAL	0	0.001	0.008	50.888	0.000	0.000	0.000	0.000	0.000	0.000
94	B	153	ALA	0	0.003	-0.012	54.370	0.002	0.002	0.000	0.000	0.000	0.000
95	B	154	LYS	1	0.778	0.891	55.253	0.051	0.051	0.000	0.000	0.000	0.000
96	B	155	VAL	0	-0.002	-0.026	56.706	0.002	0.002	0.000	0.000	0.000	0.000
97	B	156	GLU	-1	-0.750	-0.851	57.918	-0.048	-0.048	0.000	0.000	0.000	0.000
98	B	157	TYR	0	0.027	0.005	60.229	0.001	0.001	0.000	0.000	0.000	0.000
99	B	158	VAL	0	0.020	0.037	63.450	0.000	0.000	0.000	0.000	0.000	0.000
100	B	159	ARG	1	1.001	0.982	65.977	0.031	0.031	0.000	0.000	0.000	0.000
101	B	160	LYN	0	0.082	0.021	64.585	0.001	0.001	0.000	0.000	0.000	0.000
102	B	161	LYS	1	0.850	0.944	67.555	0.033	0.033	0.000	0.000	0.000	0.000
103	B	162	PRO	0	0.027	0.009	63.979	-0.001	-0.001	0.000	0.000	0.000	0.000
104	B	163	LYS	1	0.839	0.918	62.557	0.044	0.044	0.000	0.000	0.000	0.000
105	B	164	LEU	0	0.033	0.005	60.139	-0.001	-0.001	0.000	0.000	0.000	0.000
106	B	165	LYS	1	0.913	0.960	59.140	0.048	0.048	0.000	0.000	0.000	0.000
107	B	166	GLU	-1	-0.803	-0.882	58.467	-0.049	-0.049	0.000	0.000	0.000	0.000
108	B	167	VAL	0	-0.036	-0.004	53.945	0.001	0.001	0.000	0.000	0.000	0.000
109	B	168	GLN	0	0.000	-0.007	53.412	-0.001	-0.001	0.000	0.000	0.000	0.000
110	B	169	VAL	0	-0.001	-0.004	48.193	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	170	ARG	1	0.970	0.980	46.906	0.075	0.075	0.000	0.000	0.000	0.000
112	B	171	LEU	0	-0.001	0.001	44.803	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	172	GLU	-1	-0.810	-0.888	38.109	-0.116	-0.116	0.000	0.000	0.000	0.000
114	B	173	GLU	-1	-0.787	-0.852	40.765	-0.088	-0.088	0.000	0.000	0.000	0.000
115	B	174	HIS	0	0.009	-0.017	34.926	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	175	LEU	0	-0.055	-0.033	38.902	0.003	0.003	0.000	0.000	0.000	0.000
117	B	176	GLU	-1	-0.844	-0.907	36.604	-0.099	-0.099	0.000	0.000	0.000	0.000
118	B	178	ALA	0	0.029	0.022	30.122	0.005	0.005	0.000	0.000	0.000	0.000
119	B	180	ALA	0	0.030	0.014	26.080	0.002	0.002	0.000	0.000	0.000	0.000
120	B	181	THR	0	0.009	0.001	20.595	-0.014	-0.014	0.000	0.000	0.000	0.000
121	B	182	THR	0	0.036	0.026	22.459	-0.013	-0.013	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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