FMO DATABASE

FMODB ID: 43VRN

Calculation Name: 3MJK-A-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: A

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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-948243.212194
FMO2-HF: Nuclear repulsion	894684.244534
FMO2-HF: Total energy	-53558.96766
FMO2-MP2: Total energy	-53711.299165

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(A:22:GLU)

Summations of interaction energy for fragment #1(A:22:GLU)

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.
-52.333	-50.084	-0.011	-1.1	-1.138	0.005

Interaction energy analysis for fragmet #1(A:22:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.957 / q_NPA : -0.974

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	A	24	GLU	-1	-0.938	-0.971	3.820	21.389	23.638	-0.011	-1.100	-1.138	0.005
4	A	25	ILE	0	-0.033	-0.032	6.252	-0.861	-0.861	0.000	0.000	0.000	0.000
5	A	26	PRO	0	-0.011	0.007	9.497	-1.185	-1.185	0.000	0.000	0.000	0.000
6	A	27	ARG	1	0.980	0.982	11.364	-20.514	-20.514	0.000	0.000	0.000	0.000
7	A	28	GLU	-1	-0.810	-0.907	13.312	19.398	19.398	0.000	0.000	0.000	0.000
8	A	29	VAL	0	0.019	0.021	13.479	-1.174	-1.174	0.000	0.000	0.000	0.000
9	A	30	ILE	0	0.013	0.011	14.813	-1.179	-1.179	0.000	0.000	0.000	0.000
10	A	31	GLU	-1	-0.879	-0.966	17.524	14.199	14.199	0.000	0.000	0.000	0.000
11	A	32	ARG	1	0.688	0.824	17.490	-17.177	-17.177	0.000	0.000	0.000	0.000
12	A	33	LEU	0	0.024	0.001	18.567	-0.728	-0.728	0.000	0.000	0.000	0.000
13	A	34	ALA	0	0.003	0.021	21.704	-0.714	-0.714	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.876	0.961	20.766	-14.039	-14.039	0.000	0.000	0.000	0.000
15	A	36	SER	0	-0.008	-0.024	24.567	-0.367	-0.367	0.000	0.000	0.000	0.000
16	A	37	GLN	0	-0.005	-0.002	26.351	-0.325	-0.325	0.000	0.000	0.000	0.000
17	A	38	ILE	0	-0.017	0.004	23.579	0.149	0.149	0.000	0.000	0.000	0.000
18	A	39	HIS	0	-0.059	-0.042	27.541	-0.374	-0.374	0.000	0.000	0.000	0.000
19	A	40	SER	0	-0.036	-0.035	28.066	-0.246	-0.246	0.000	0.000	0.000	0.000
20	A	41	ILE	0	0.010	-0.006	22.874	0.430	0.430	0.000	0.000	0.000	0.000
21	A	42	ARG	1	0.962	0.990	24.258	-9.861	-9.861	0.000	0.000	0.000	0.000
22	A	43	ASP	-1	-0.833	-0.884	25.244	11.127	11.127	0.000	0.000	0.000	0.000
23	A	44	LEU	0	0.018	0.007	19.658	0.381	0.381	0.000	0.000	0.000	0.000
24	A	45	GLN	0	-0.042	-0.042	20.641	0.151	0.151	0.000	0.000	0.000	0.000
25	A	46	ARG	1	1.047	1.030	20.801	-10.986	-10.986	0.000	0.000	0.000	0.000
26	A	47	LEU	0	-0.158	-0.076	21.857	0.088	0.088	0.000	0.000	0.000	0.000
27	A	48	LEU	0	-0.098	-0.055	16.573	0.683	0.683	0.000	0.000	0.000	0.000
28	A	49	GLU	-1	-0.734	-0.835	17.759	16.259	16.259	0.000	0.000	0.000	0.000
29	A	50	ILE	0	-0.045	-0.025	15.547	1.107	1.107	0.000	0.000	0.000	0.000
30	A	51	ASP	-1	-0.895	-0.923	17.934	14.302	14.302	0.000	0.000	0.000	0.000
31	A	52	SER	0	-0.083	-0.052	20.250	-0.123	-0.123	0.000	0.000	0.000	0.000
32	A	53	VAL	0	0.003	0.005	15.236	0.417	0.417	0.000	0.000	0.000	0.000
33	A	83	ARG	1	1.010	0.994	24.608	-11.128	-11.128	0.000	0.000	0.000	0.000
34	A	84	ARG	1	0.999	0.977	23.709	-11.679	-11.679	0.000	0.000	0.000	0.000
35	A	85	LYS	1	0.905	0.956	27.697	-9.244	-9.244	0.000	0.000	0.000	0.000
36	A	86	ARG	1	0.996	1.001	31.401	-8.636	-8.636	0.000	0.000	0.000	0.000
37	A	87	SER	0	0.063	0.010	34.101	-0.104	-0.104	0.000	0.000	0.000	0.000
38	A	88	ILE	0	-0.051	0.003	29.454	-0.090	-0.090	0.000	0.000	0.000	0.000
39	A	89	GLU	-1	-0.947	-0.967	31.931	8.790	8.790	0.000	0.000	0.000	0.000
40	A	90	GLU	-1	-0.882	-0.931	27.860	11.154	11.154	0.000	0.000	0.000	0.000
41	A	91	ALA	0	0.013	0.005	27.294	-0.273	-0.273	0.000	0.000	0.000	0.000
42	A	92	VAL	0	0.043	0.017	29.056	0.205	0.205	0.000	0.000	0.000	0.000
43	A	93	PRO	0	0.013	0.016	27.955	-0.079	-0.079	0.000	0.000	0.000	0.000
44	A	94	ALA	0	0.000	0.005	29.741	-0.359	-0.359	0.000	0.000	0.000	0.000
45	A	95	VAL	0	0.050	0.005	30.907	0.148	0.148	0.000	0.000	0.000	0.000
46	A	96	CYS	0	-0.002	0.016	27.547	-0.447	-0.447	0.000	0.000	0.000	0.000
47	A	97	LYS	1	0.966	0.985	32.950	-7.967	-7.967	0.000	0.000	0.000	0.000
48	A	98	THR	0	0.042	0.021	36.568	0.075	0.075	0.000	0.000	0.000	0.000
49	A	99	ARG	1	0.765	0.867	34.473	-8.499	-8.499	0.000	0.000	0.000	0.000
50	A	100	THR	0	-0.033	-0.023	40.138	0.061	0.061	0.000	0.000	0.000	0.000
51	A	101	VAL	0	-0.005	0.007	37.448	0.122	0.122	0.000	0.000	0.000	0.000
52	A	102	ILE	0	0.024	-0.001	40.740	-0.154	-0.154	0.000	0.000	0.000	0.000
53	A	103	TYR	0	-0.025	-0.008	41.398	0.177	0.177	0.000	0.000	0.000	0.000
54	A	104	GLU	-1	-0.894	-0.952	43.149	6.509	6.509	0.000	0.000	0.000	0.000
55	A	105	ILE	0	-0.050	-0.030	44.981	0.042	0.042	0.000	0.000	0.000	0.000
56	A	106	PRO	0	0.019	0.007	44.014	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	107	ARG	1	0.985	0.983	46.162	-5.925	-5.925	0.000	0.000	0.000	0.000
58	A	108	SER	0	0.034	0.014	45.289	-0.118	-0.118	0.000	0.000	0.000	0.000
59	A	109	GLN	0	-0.021	-0.014	47.359	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	110	VAL	0	-0.066	-0.028	49.202	-0.102	-0.102	0.000	0.000	0.000	0.000
61	A	111	ASP	-1	-0.829	-0.913	52.145	5.213	5.213	0.000	0.000	0.000	0.000
62	A	112	PRO	0	0.016	0.011	49.762	0.036	0.036	0.000	0.000	0.000	0.000
63	A	113	THR	0	-0.041	-0.023	51.149	0.020	0.020	0.000	0.000	0.000	0.000
64	A	114	SER	0	-0.018	0.000	53.887	0.016	0.016	0.000	0.000	0.000	0.000
65	A	115	ALA	0	0.061	0.023	52.211	0.076	0.076	0.000	0.000	0.000	0.000
66	A	116	ASN	0	-0.091	-0.045	53.737	0.047	0.047	0.000	0.000	0.000	0.000
67	A	117	PHE	0	-0.034	-0.021	52.516	-0.109	-0.109	0.000	0.000	0.000	0.000
68	A	118	LEU	0	-0.015	0.004	54.908	0.100	0.100	0.000	0.000	0.000	0.000
69	A	119	ILE	0	0.040	0.023	50.562	-0.084	-0.084	0.000	0.000	0.000	0.000
70	A	120	TRP	0	0.009	0.022	53.809	0.052	0.052	0.000	0.000	0.000	0.000
71	A	121	PRO	0	0.043	0.019	52.340	-0.090	-0.090	0.000	0.000	0.000	0.000
72	A	122	PRO	0	0.027	-0.003	49.573	0.025	0.025	0.000	0.000	0.000	0.000
73	A	123	CYS	0	-0.001	0.004	46.209	0.117	0.117	0.000	0.000	0.000	0.000
74	A	124	VAL	0	-0.019	-0.003	46.837	-0.140	-0.140	0.000	0.000	0.000	0.000
75	A	125	GLU	-1	-0.862	-0.909	45.304	6.629	6.629	0.000	0.000	0.000	0.000
76	A	126	VAL	0	-0.047	-0.030	42.358	-0.109	-0.109	0.000	0.000	0.000	0.000
77	A	127	LYS	1	0.922	0.954	42.416	-6.571	-6.571	0.000	0.000	0.000	0.000
78	A	128	ARG	1	0.889	0.937	37.565	-7.406	-7.406	0.000	0.000	0.000	0.000
79	A	129	CYS	0	-0.058	0.007	34.751	-0.048	-0.048	0.000	0.000	0.000	0.000
80	A	130	THR	0	0.029	0.016	33.427	0.099	0.099	0.000	0.000	0.000	0.000
81	A	131	GLY	0	0.027	0.006	31.399	-0.108	-0.108	0.000	0.000	0.000	0.000
82	A	132	CYS	0	-0.063	-0.034	26.051	0.080	0.080	0.000	0.000	0.000	0.000
83	A	133	CYS	0	-0.016	0.019	25.593	-0.297	-0.297	0.000	0.000	0.000	0.000
84	A	134	ASN	0	-0.020	-0.024	23.732	-0.097	-0.097	0.000	0.000	0.000	0.000
85	A	135	THR	0	0.010	0.022	19.691	0.289	0.289	0.000	0.000	0.000	0.000
86	A	136	SER	0	0.051	0.009	19.298	-0.291	-0.291	0.000	0.000	0.000	0.000
87	A	137	SER	0	0.002	0.014	19.034	-0.440	-0.440	0.000	0.000	0.000	0.000
88	A	138	VAL	0	-0.020	-0.001	20.958	-0.419	-0.419	0.000	0.000	0.000	0.000
89	A	139	LYS	1	0.937	0.961	24.415	-11.371	-11.371	0.000	0.000	0.000	0.000
90	A	141	GLN	0	0.021	0.000	30.607	0.009	0.009	0.000	0.000	0.000	0.000
91	A	142	PRO	0	0.037	-0.005	33.154	-0.059	-0.059	0.000	0.000	0.000	0.000
92	A	143	SER	0	-0.030	-0.044	36.955	0.081	0.081	0.000	0.000	0.000	0.000
93	A	144	ARG	1	0.821	0.882	38.893	-7.169	-7.169	0.000	0.000	0.000	0.000
94	A	145	VAL	0	0.009	0.002	40.065	0.075	0.075	0.000	0.000	0.000	0.000
95	A	146	HIS	0	-0.008	-0.004	42.987	-0.081	-0.081	0.000	0.000	0.000	0.000
96	A	147	HIS	0	0.009	0.000	42.775	-0.072	-0.072	0.000	0.000	0.000	0.000
97	A	148	ARG	1	0.846	0.896	47.547	-6.278	-6.278	0.000	0.000	0.000	0.000
98	A	149	SER	0	-0.021	-0.038	50.008	0.111	0.111	0.000	0.000	0.000	0.000
99	A	150	VAL	0	-0.012	0.002	51.392	-0.071	-0.071	0.000	0.000	0.000	0.000
100	A	151	LYS	1	0.841	0.907	53.952	-4.922	-4.922	0.000	0.000	0.000	0.000
101	A	152	VAL	0	0.009	0.016	52.313	0.008	0.008	0.000	0.000	0.000	0.000
102	A	153	ALA	0	-0.018	-0.016	55.726	-0.079	-0.079	0.000	0.000	0.000	0.000
103	A	154	LYS	1	0.843	0.934	56.325	-5.121	-5.121	0.000	0.000	0.000	0.000
104	A	155	VAL	0	-0.016	-0.029	58.106	-0.108	-0.108	0.000	0.000	0.000	0.000
105	A	156	GLU	-1	-0.776	-0.875	59.288	5.045	5.045	0.000	0.000	0.000	0.000
106	A	157	TYR	0	0.013	-0.010	61.539	-0.068	-0.068	0.000	0.000	0.000	0.000
107	A	158	VAL	0	-0.003	0.015	64.646	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	159	ARG	1	1.002	1.006	66.521	-4.291	-4.291	0.000	0.000	0.000	0.000
109	A	160	LYS	1	1.003	1.005	67.943	-4.236	-4.236	0.000	0.000	0.000	0.000
110	A	161	LYS	1	0.939	0.944	68.932	-4.129	-4.129	0.000	0.000	0.000	0.000
111	A	162	PRO	0	0.059	0.037	65.895	0.037	0.037	0.000	0.000	0.000	0.000
112	A	163	LYS	1	0.871	0.944	64.794	-4.506	-4.506	0.000	0.000	0.000	0.000
113	A	164	LEU	0	0.049	0.023	61.622	0.067	0.067	0.000	0.000	0.000	0.000
114	A	165	LYS	1	0.876	0.931	60.339	-4.958	-4.958	0.000	0.000	0.000	0.000
115	A	166	GLU	-1	-0.794	-0.888	59.628	4.991	4.991	0.000	0.000	0.000	0.000
116	A	167	VAL	0	-0.005	0.002	54.396	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	168	GLN	0	0.005	0.013	54.058	0.125	0.125	0.000	0.000	0.000	0.000
118	A	169	VAL	0	0.017	0.008	48.932	0.056	0.056	0.000	0.000	0.000	0.000
119	A	170	ARG	1	0.936	0.973	47.382	-6.045	-6.045	0.000	0.000	0.000	0.000
120	A	171	LEU	0	-0.017	0.005	46.013	0.101	0.101	0.000	0.000	0.000	0.000
121	A	172	GLU	-1	-0.784	-0.887	39.702	7.359	7.359	0.000	0.000	0.000	0.000
122	A	173	GLU	-1	-0.815	-0.866	42.876	6.549	6.549	0.000	0.000	0.000	0.000
123	A	174	HIS	0	0.000	-0.014	36.910	0.089	0.089	0.000	0.000	0.000	0.000
124	A	175	LEU	0	-0.034	-0.029	41.496	-0.059	-0.059	0.000	0.000	0.000	0.000
125	A	176	GLU	-1	-0.802	-0.845	39.730	7.322	7.322	0.000	0.000	0.000	0.000
126	A	178	ALA	0	0.058	0.030	33.972	-0.040	-0.040	0.000	0.000	0.000	0.000
127	A	180	ALA	0	0.018	0.012	27.059	0.100	0.100	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:GLU)