FMO DATABASE

FMODB ID: LJ3M9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-897243.214298
FMO2-HF: Nuclear repulsion	846194.252152
FMO2-HF: Total energy	-51048.962146
FMO2-MP2: Total energy	-51193.87127

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.
1.202	2.659	-0.025	-0.667	-0.765	-0.001

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 : -0.021 / q_NPA : -0.021

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	F	25	ILE	0	-0.018	-0.007	3.800	1.423	2.880	-0.025	-0.667	-0.765	-0.001
4	F	26	PRO	0	0.008	-0.001	6.647	-0.261	-0.261	0.000	0.000	0.000	0.000
5	F	27	ARG	1	1.010	0.983	8.844	-0.356	-0.356	0.000	0.000	0.000	0.000
6	F	28	GLU	-1	-0.805	-0.889	11.857	0.463	0.463	0.000	0.000	0.000	0.000
7	F	29	VAL	0	-0.032	-0.004	10.530	-0.085	-0.085	0.000	0.000	0.000	0.000
8	F	30	ILE	0	0.034	0.015	10.169	-0.087	-0.087	0.000	0.000	0.000	0.000
9	F	31	GLU	-1	-0.920	-0.963	13.604	0.128	0.128	0.000	0.000	0.000	0.000
10	F	32	ARG	1	0.920	0.944	14.204	-0.383	-0.383	0.000	0.000	0.000	0.000
11	F	33	LEU	0	0.024	-0.001	13.341	-0.025	-0.025	0.000	0.000	0.000	0.000
12	F	34	ALA	0	-0.040	-0.003	17.161	-0.028	-0.028	0.000	0.000	0.000	0.000
13	F	35	ARG	1	0.855	0.950	18.376	-0.169	-0.169	0.000	0.000	0.000	0.000
14	F	36	SER	0	0.021	0.003	19.986	0.015	0.015	0.000	0.000	0.000	0.000
15	F	37	GLN	0	-0.044	-0.014	22.138	-0.018	-0.018	0.000	0.000	0.000	0.000
16	F	38	ILE	0	0.000	0.005	18.050	0.011	0.011	0.000	0.000	0.000	0.000
17	F	39	HIS	0	-0.056	-0.033	22.205	-0.019	-0.019	0.000	0.000	0.000	0.000
18	F	40	SER	0	0.004	0.005	22.856	-0.005	-0.005	0.000	0.000	0.000	0.000
19	F	41	ILE	0	0.058	0.031	17.772	0.010	0.010	0.000	0.000	0.000	0.000
20	F	42	ARG	1	0.943	0.984	19.270	-0.021	-0.021	0.000	0.000	0.000	0.000
21	F	43	ASP	-1	-0.865	-0.952	21.193	0.084	0.084	0.000	0.000	0.000	0.000
22	F	44	LEU	0	0.032	0.015	15.052	0.017	0.017	0.000	0.000	0.000	0.000
23	F	45	GLN	0	-0.005	-0.028	16.016	0.028	0.028	0.000	0.000	0.000	0.000
24	F	46	ARG	1	0.925	1.024	16.943	-0.056	-0.056	0.000	0.000	0.000	0.000
25	F	47	LEU	0	-0.006	0.001	17.395	0.018	0.018	0.000	0.000	0.000	0.000
26	F	48	LEU	0	-0.097	-0.028	11.813	0.042	0.042	0.000	0.000	0.000	0.000
27	F	49	GLU	-1	-0.880	-0.934	13.374	0.390	0.390	0.000	0.000	0.000	0.000
28	F	50	ILE	0	-0.149	-0.117	12.722	-0.025	-0.025	0.000	0.000	0.000	0.000
29	F	87	SER	0	-0.032	-0.033	27.446	-0.001	-0.001	0.000	0.000	0.000	0.000
30	F	88	ILE	0	-0.008	0.007	24.251	0.000	0.000	0.000	0.000	0.000	0.000
31	F	89	GLU	-1	-0.943	-0.973	26.766	-0.040	-0.040	0.000	0.000	0.000	0.000
32	F	90	GLU	-1	-0.858	-0.931	22.873	-0.016	-0.016	0.000	0.000	0.000	0.000
33	F	91	ALA	0	-0.008	-0.006	22.294	0.001	0.001	0.000	0.000	0.000	0.000
34	F	92	VAL	0	0.047	0.021	24.145	0.008	0.008	0.000	0.000	0.000	0.000
35	F	93	PRO	0	0.001	0.011	23.175	-0.010	-0.010	0.000	0.000	0.000	0.000
36	F	94	ALA	0	0.023	0.006	24.881	0.008	0.008	0.000	0.000	0.000	0.000
37	F	95	VAL	0	0.036	0.002	26.392	-0.004	-0.004	0.000	0.000	0.000	0.000
38	F	96	CYS	0	-0.008	0.037	24.561	0.009	0.009	0.000	0.000	0.000	0.000
39	F	97	LYS	1	0.965	0.971	28.781	0.026	0.026	0.000	0.000	0.000	0.000
40	F	98	THR	0	0.042	0.024	32.547	-0.006	-0.006	0.000	0.000	0.000	0.000
41	F	99	ARG	1	0.783	0.859	30.033	0.040	0.040	0.000	0.000	0.000	0.000
42	F	100	THR	0	-0.021	-0.006	36.488	-0.001	-0.001	0.000	0.000	0.000	0.000
43	F	101	VAL	0	0.055	0.033	34.725	-0.003	-0.003	0.000	0.000	0.000	0.000
44	F	102	ILE	0	0.033	0.007	37.975	0.003	0.003	0.000	0.000	0.000	0.000
45	F	103	TYR	0	-0.036	-0.015	38.975	-0.003	-0.003	0.000	0.000	0.000	0.000
46	F	104	GLU	-1	-0.890	-0.957	41.063	-0.045	-0.045	0.000	0.000	0.000	0.000
47	F	105	ILE	0	-0.049	-0.023	43.100	0.000	0.000	0.000	0.000	0.000	0.000
48	F	106	PRO	0	0.034	0.016	43.018	-0.001	-0.001	0.000	0.000	0.000	0.000
49	F	107	ARG	1	0.955	0.983	45.238	0.038	0.038	0.000	0.000	0.000	0.000
50	F	108	SER	0	0.020	-0.010	45.194	0.002	0.002	0.000	0.000	0.000	0.000
51	F	109	GLN	0	0.030	0.000	44.604	0.002	0.002	0.000	0.000	0.000	0.000
52	F	110	VAL	0	-0.026	0.000	48.366	0.002	0.002	0.000	0.000	0.000	0.000
53	F	111	ASP	-1	-0.790	-0.887	51.581	-0.024	-0.024	0.000	0.000	0.000	0.000
54	F	112	PRO	0	-0.012	-0.006	49.980	-0.001	-0.001	0.000	0.000	0.000	0.000
55	F	113	THR	0	-0.061	-0.028	51.386	-0.001	-0.001	0.000	0.000	0.000	0.000
56	F	114	SER	0	-0.056	-0.030	54.340	-0.001	-0.001	0.000	0.000	0.000	0.000
57	F	115	ALA	0	0.041	0.009	51.754	-0.001	-0.001	0.000	0.000	0.000	0.000
58	F	116	ASN	0	-0.032	-0.020	53.312	-0.001	-0.001	0.000	0.000	0.000	0.000
59	F	117	PHE	0	-0.059	-0.019	51.860	0.001	0.001	0.000	0.000	0.000	0.000
60	F	118	LEU	0	-0.027	-0.012	52.488	-0.002	-0.002	0.000	0.000	0.000	0.000
61	F	119	ILE	0	0.014	0.020	48.799	0.002	0.002	0.000	0.000	0.000	0.000
62	F	120	TRP	0	0.034	0.030	51.789	-0.001	-0.001	0.000	0.000	0.000	0.000
63	F	121	PRO	0	0.061	0.017	49.925	0.001	0.001	0.000	0.000	0.000	0.000
64	F	122	PRO	0	0.036	-0.002	47.585	0.000	0.000	0.000	0.000	0.000	0.000
65	F	123	CYS	0	-0.051	-0.012	43.967	-0.002	-0.002	0.000	0.000	0.000	0.000
66	F	124	VAL	0	-0.005	0.005	44.695	0.002	0.002	0.000	0.000	0.000	0.000
67	F	125	GLU	-1	-0.913	-0.955	42.595	-0.029	-0.029	0.000	0.000	0.000	0.000
68	F	126	VAL	0	-0.021	0.000	39.629	0.002	0.002	0.000	0.000	0.000	0.000
69	F	127	LYS	1	0.875	0.948	39.303	0.019	0.019	0.000	0.000	0.000	0.000
70	F	128	ARG	1	0.915	0.935	35.160	0.036	0.036	0.000	0.000	0.000	0.000
71	F	129	CYS	0	-0.053	0.000	31.823	-0.002	-0.002	0.000	0.000	0.000	0.000
72	F	130	THR	0	0.024	0.009	30.247	-0.004	-0.004	0.000	0.000	0.000	0.000
73	F	131	GLY	0	0.036	0.019	27.510	0.007	0.007	0.000	0.000	0.000	0.000
74	F	132	CYS	0	-0.053	-0.034	22.328	-0.010	-0.010	0.000	0.000	0.000	0.000
75	F	133	CYS	0	-0.029	0.026	21.931	0.004	0.004	0.000	0.000	0.000	0.000
76	F	134	ASN	0	-0.018	-0.025	18.307	-0.026	-0.026	0.000	0.000	0.000	0.000
77	F	135	THR	0	0.044	0.045	15.304	-0.029	-0.029	0.000	0.000	0.000	0.000
78	F	136	SER	0	0.034	0.007	16.253	0.006	0.006	0.000	0.000	0.000	0.000
79	F	137	SER	0	-0.048	-0.026	16.378	0.004	0.004	0.000	0.000	0.000	0.000
80	F	138	VAL	0	-0.046	-0.030	18.338	0.020	0.020	0.000	0.000	0.000	0.000
81	F	139	LYS	1	0.900	0.954	21.692	0.052	0.052	0.000	0.000	0.000	0.000
82	F	141	GLN	0	0.025	0.007	27.559	-0.008	-0.008	0.000	0.000	0.000	0.000
83	F	142	PRO	0	0.023	-0.004	30.460	0.005	0.005	0.000	0.000	0.000	0.000
84	F	143	SER	0	-0.009	-0.014	34.238	-0.001	-0.001	0.000	0.000	0.000	0.000
85	F	144	ARG	1	0.898	0.952	35.711	0.000	0.000	0.000	0.000	0.000	0.000
86	F	145	VAL	0	0.024	0.004	38.113	-0.002	-0.002	0.000	0.000	0.000	0.000
87	F	146	HIS	0	-0.004	-0.002	40.694	0.001	0.001	0.000	0.000	0.000	0.000
88	F	147	HIS	0	0.032	0.025	42.046	-0.003	-0.003	0.000	0.000	0.000	0.000
89	F	148	ARG	1	0.881	0.906	46.019	0.021	0.021	0.000	0.000	0.000	0.000
90	F	149	SER	0	0.002	0.008	48.707	-0.002	-0.002	0.000	0.000	0.000	0.000
91	F	150	VAL	0	-0.017	-0.002	49.722	0.001	0.001	0.000	0.000	0.000	0.000
92	F	151	LYS	1	0.875	0.919	52.496	0.016	0.016	0.000	0.000	0.000	0.000
93	F	152	VAL	0	0.009	0.015	50.737	0.000	0.000	0.000	0.000	0.000	0.000
94	F	153	ALA	0	0.003	-0.016	54.203	0.001	0.001	0.000	0.000	0.000	0.000
95	F	154	LYS	1	0.828	0.941	55.299	0.023	0.023	0.000	0.000	0.000	0.000
96	F	155	VAL	0	0.015	-0.010	56.555	0.001	0.001	0.000	0.000	0.000	0.000
97	F	156	GLU	-1	-0.827	-0.937	57.569	-0.024	-0.024	0.000	0.000	0.000	0.000
98	F	157	TYR	0	0.022	0.011	60.016	0.001	0.001	0.000	0.000	0.000	0.000
99	F	158	VAL	0	0.028	0.028	62.368	0.000	0.000	0.000	0.000	0.000	0.000
100	F	159	ARG	1	0.932	0.940	64.525	0.019	0.019	0.000	0.000	0.000	0.000
101	F	160	LYS	1	0.986	0.987	65.426	0.022	0.022	0.000	0.000	0.000	0.000
102	F	161	LYS	1	0.984	1.002	66.499	0.017	0.017	0.000	0.000	0.000	0.000
103	F	162	PRO	0	0.015	0.015	63.872	0.000	0.000	0.000	0.000	0.000	0.000
104	F	163	LYS	1	0.919	0.951	63.394	0.019	0.019	0.000	0.000	0.000	0.000
105	F	164	LEU	0	0.021	0.021	59.800	-0.001	-0.001	0.000	0.000	0.000	0.000
106	F	165	LYS	1	0.925	0.970	59.319	0.021	0.021	0.000	0.000	0.000	0.000
107	F	166	GLU	-1	-0.832	-0.899	58.402	-0.018	-0.018	0.000	0.000	0.000	0.000
108	F	167	VAL	0	-0.024	-0.002	53.771	0.001	0.001	0.000	0.000	0.000	0.000
109	F	168	GLN	0	-0.023	-0.011	53.709	0.000	0.000	0.000	0.000	0.000	0.000
110	F	169	VAL	0	0.022	0.010	47.999	-0.001	-0.001	0.000	0.000	0.000	0.000
111	F	170	ARG	1	0.942	0.965	47.133	0.022	0.022	0.000	0.000	0.000	0.000
112	F	171	LEU	0	-0.010	0.001	44.808	-0.002	-0.002	0.000	0.000	0.000	0.000
113	F	172	GLU	-1	-0.859	-0.920	38.254	-0.031	-0.031	0.000	0.000	0.000	0.000
114	F	173	GLU	-1	-0.822	-0.896	40.866	-0.024	-0.024	0.000	0.000	0.000	0.000
115	F	174	HIS	0	-0.003	0.001	35.053	0.001	0.001	0.000	0.000	0.000	0.000
116	F	175	LEU	0	-0.036	-0.023	38.958	0.000	0.000	0.000	0.000	0.000	0.000
117	F	176	GLU	-1	-0.900	-0.943	35.733	0.004	0.004	0.000	0.000	0.000	0.000
118	F	178	ALA	0	0.038	0.015	30.215	0.005	0.005	0.000	0.000	0.000	0.000
119	F	180	ALA	0	0.028	0.007	25.850	0.011	0.011	0.000	0.000	0.000	0.000
120	F	181	THR	0	0.021	0.006	23.628	-0.017	-0.017	0.000	0.000	0.000	0.000
121	F	182	THR	0	0.002	-0.019	24.390	0.002	0.002	0.000	0.000	0.000	0.000
122	F	183	SER	0	0.014	0.026	25.711	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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