FMO DATABASE

FMODB ID: N1GVQ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-861060.000234
FMO2-HF: Nuclear repulsion	811375.425556
FMO2-HF: Total energy	-49684.574678
FMO2-MP2: Total energy	-49825.547131

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.
-1.005	0.466	-0.002	-0.578	-0.891	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 : -0.021 / q_NPA : -0.027

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	-0.041	-0.020	3.310	-2.024	-0.609	-0.001	-0.575	-0.839	0.001
4	X	26	PRO	0	0.092	0.053	5.108	-0.640	-0.584	-0.001	-0.003	-0.052	0.000
5	X	27	ARG	1	0.985	0.986	8.109	0.875	0.875	0.000	0.000	0.000	0.000
6	X	28	GLU	-1	-0.873	-0.939	9.634	-0.094	-0.094	0.000	0.000	0.000	0.000
7	X	29	VAL	0	0.049	0.029	8.561	0.075	0.075	0.000	0.000	0.000	0.000
8	X	30	ILE	0	0.004	0.003	5.767	0.094	0.094	0.000	0.000	0.000	0.000
9	X	31	GLU	-1	-0.927	-0.983	10.171	-0.354	-0.354	0.000	0.000	0.000	0.000
10	X	32	ARG	1	0.941	0.982	13.299	0.100	0.100	0.000	0.000	0.000	0.000
11	X	33	LEU	0	0.016	0.031	10.461	0.020	0.020	0.000	0.000	0.000	0.000
12	X	34	ALA	0	-0.040	-0.009	13.977	0.024	0.024	0.000	0.000	0.000	0.000
13	X	35	ARG	1	0.835	0.934	15.537	0.237	0.237	0.000	0.000	0.000	0.000
14	X	36	SER	0	-0.027	-0.057	17.623	0.017	0.017	0.000	0.000	0.000	0.000
15	X	37	GLN	0	-0.023	-0.007	19.510	0.005	0.005	0.000	0.000	0.000	0.000
16	X	38	ILE	0	0.001	-0.002	16.073	0.008	0.008	0.000	0.000	0.000	0.000
17	X	39	HIS	0	-0.047	-0.034	20.318	-0.002	-0.002	0.000	0.000	0.000	0.000
18	X	40	SER	0	-0.004	0.006	21.863	0.003	0.003	0.000	0.000	0.000	0.000
19	X	41	ILE	0	0.004	-0.005	18.650	0.002	0.002	0.000	0.000	0.000	0.000
20	X	42	ARG	1	0.900	0.920	19.713	-0.046	-0.046	0.000	0.000	0.000	0.000
21	X	43	ASP	-1	-0.873	-0.939	21.414	0.030	0.030	0.000	0.000	0.000	0.000
22	X	44	LEU	0	-0.048	-0.039	14.083	-0.007	-0.007	0.000	0.000	0.000	0.000
23	X	45	GLN	0	0.017	0.016	16.721	-0.003	-0.003	0.000	0.000	0.000	0.000
24	X	46	ARG	0	0.151	0.114	18.017	-0.002	-0.002	0.000	0.000	0.000	0.000
25	X	47	LEU	0	-0.091	-0.028	17.916	-0.004	-0.004	0.000	0.000	0.000	0.000
26	X	48	LEU	0	-0.150	-0.071	11.753	-0.020	-0.020	0.000	0.000	0.000	0.000
27	X	49	GLU	-1	-0.984	-1.000	15.453	0.137	0.137	0.000	0.000	0.000	0.000
28	X	88	ILE	0	0.018	0.012	26.439	0.002	0.002	0.000	0.000	0.000	0.000
29	X	89	GLU	-1	-0.999	-1.003	27.966	0.048	0.048	0.000	0.000	0.000	0.000
30	X	90	GLU	-1	-0.841	-0.914	22.769	0.089	0.089	0.000	0.000	0.000	0.000
31	X	91	ALA	0	-0.025	-0.017	21.390	-0.009	-0.009	0.000	0.000	0.000	0.000
32	X	92	VAL	0	0.049	0.024	23.032	0.000	0.000	0.000	0.000	0.000	0.000
33	X	93	PRO	0	-0.001	0.012	20.573	-0.004	-0.004	0.000	0.000	0.000	0.000
34	X	94	ALA	0	0.002	-0.006	22.337	-0.005	-0.005	0.000	0.000	0.000	0.000
35	X	95	VAL	0	0.066	0.017	22.679	-0.008	-0.008	0.000	0.000	0.000	0.000
36	X	96	CYS	0	-0.004	0.020	19.144	0.007	0.007	0.000	0.000	0.000	0.000
37	X	97	LYS	1	0.964	0.979	24.560	0.019	0.019	0.000	0.000	0.000	0.000
38	X	98	THR	0	0.047	0.019	28.242	-0.002	-0.002	0.000	0.000	0.000	0.000
39	X	99	ARG	1	0.752	0.863	26.400	0.029	0.029	0.000	0.000	0.000	0.000
40	X	100	THR	0	0.060	0.003	31.942	-0.003	-0.003	0.000	0.000	0.000	0.000
41	X	101	VAL	0	-0.023	0.006	29.840	0.002	0.002	0.000	0.000	0.000	0.000
42	X	102	ILE	0	0.050	0.015	33.136	0.000	0.000	0.000	0.000	0.000	0.000
43	X	103	TYR	0	-0.023	-0.013	34.010	-0.002	-0.002	0.000	0.000	0.000	0.000
44	X	104	GLU	-1	-0.897	-0.965	35.840	-0.016	-0.016	0.000	0.000	0.000	0.000
45	X	105	ILE	0	-0.055	-0.022	37.733	-0.003	-0.003	0.000	0.000	0.000	0.000
46	X	106	PRO	0	0.036	0.019	37.327	0.001	0.001	0.000	0.000	0.000	0.000
47	X	107	ARG	1	0.989	0.987	39.708	0.016	0.016	0.000	0.000	0.000	0.000
48	X	108	SER	0	0.048	0.025	38.976	0.001	0.001	0.000	0.000	0.000	0.000
49	X	109	GLN	0	-0.005	0.002	39.956	-0.001	-0.001	0.000	0.000	0.000	0.000
50	X	110	VAL	0	-0.059	-0.032	42.581	0.001	0.001	0.000	0.000	0.000	0.000
51	X	111	ASP	-1	-0.835	-0.912	45.623	-0.019	-0.019	0.000	0.000	0.000	0.000
52	X	112	PRO	0	-0.031	-0.006	43.353	0.001	0.001	0.000	0.000	0.000	0.000
53	X	113	THR	0	-0.074	-0.022	44.990	0.000	0.000	0.000	0.000	0.000	0.000
54	X	114	SER	0	-0.040	-0.053	47.327	0.002	0.002	0.000	0.000	0.000	0.000
55	X	115	ALA	0	0.045	0.014	45.630	-0.001	-0.001	0.000	0.000	0.000	0.000
56	X	116	ASN	0	-0.025	0.001	47.348	0.000	0.000	0.000	0.000	0.000	0.000
57	X	117	PHE	0	-0.041	-0.020	46.112	0.001	0.001	0.000	0.000	0.000	0.000
58	X	118	LEU	0	0.008	-0.012	47.257	0.000	0.000	0.000	0.000	0.000	0.000
59	X	119	ILE	0	0.007	0.016	43.928	0.000	0.000	0.000	0.000	0.000	0.000
60	X	120	TRP	0	-0.017	0.024	46.801	0.000	0.000	0.000	0.000	0.000	0.000
61	X	121	PRO	0	0.050	0.014	45.017	0.000	0.000	0.000	0.000	0.000	0.000
62	X	122	PRO	0	0.029	0.002	42.576	-0.001	-0.001	0.000	0.000	0.000	0.000
63	X	123	CYS	0	-0.025	-0.010	39.041	-0.001	-0.001	0.000	0.000	0.000	0.000
64	X	124	VAL	0	-0.006	0.002	39.365	0.001	0.001	0.000	0.000	0.000	0.000
65	X	125	GLU	-1	-0.914	-0.943	37.714	-0.014	-0.014	0.000	0.000	0.000	0.000
66	X	126	VAL	0	-0.036	-0.009	34.164	-0.001	-0.001	0.000	0.000	0.000	0.000
67	X	127	LYS	1	0.870	0.943	34.217	0.022	0.022	0.000	0.000	0.000	0.000
68	X	128	ARG	1	0.912	0.944	29.683	0.042	0.042	0.000	0.000	0.000	0.000
69	X	129	CYS	0	-0.050	0.012	26.561	0.003	0.003	0.000	0.000	0.000	0.000
70	X	130	THR	0	0.009	0.011	25.302	0.000	0.000	0.000	0.000	0.000	0.000
71	X	131	GLY	0	0.042	0.016	23.322	0.002	0.002	0.000	0.000	0.000	0.000
72	X	132	CYS	0	-0.040	-0.028	17.797	-0.006	-0.006	0.000	0.000	0.000	0.000
73	X	133	CYS	0	-0.014	0.015	17.309	0.011	0.011	0.000	0.000	0.000	0.000
74	X	134	ASN	0	-0.003	0.002	15.580	0.005	0.005	0.000	0.000	0.000	0.000
75	X	135	THR	0	0.029	0.029	11.076	0.027	0.027	0.000	0.000	0.000	0.000
76	X	136	SER	0	0.052	0.009	10.602	0.001	0.001	0.000	0.000	0.000	0.000
77	X	137	SER	0	-0.046	-0.016	10.946	0.020	0.020	0.000	0.000	0.000	0.000
78	X	138	VAL	0	-0.043	-0.017	12.731	0.007	0.007	0.000	0.000	0.000	0.000
79	X	139	LYS	1	0.925	0.967	16.309	0.250	0.250	0.000	0.000	0.000	0.000
80	X	141	GLN	0	0.017	-0.003	22.425	0.008	0.008	0.000	0.000	0.000	0.000
81	X	142	PRO	0	0.047	-0.008	24.914	0.005	0.005	0.000	0.000	0.000	0.000
82	X	143	SER	0	-0.014	-0.019	28.716	-0.005	-0.005	0.000	0.000	0.000	0.000
83	X	144	ARG	1	0.867	0.914	30.639	0.046	0.046	0.000	0.000	0.000	0.000
84	X	145	VAL	0	0.006	0.010	32.857	0.002	0.002	0.000	0.000	0.000	0.000
85	X	146	HIS	0	-0.014	-0.001	34.928	0.001	0.001	0.000	0.000	0.000	0.000
86	X	147	HIS	0	-0.017	-0.016	35.566	0.001	0.001	0.000	0.000	0.000	0.000
87	X	148	ARG	1	0.908	0.957	39.964	0.028	0.028	0.000	0.000	0.000	0.000
88	X	149	SER	0	-0.005	-0.005	42.828	-0.001	-0.001	0.000	0.000	0.000	0.000
89	X	150	VAL	0	-0.024	-0.001	44.146	0.001	0.001	0.000	0.000	0.000	0.000
90	X	151	LYS	1	0.863	0.924	46.765	0.014	0.014	0.000	0.000	0.000	0.000
91	X	152	VAL	0	-0.001	0.018	45.318	0.001	0.001	0.000	0.000	0.000	0.000
92	X	153	ALA	0	-0.001	-0.014	48.725	0.000	0.000	0.000	0.000	0.000	0.000
93	X	154	LYS	1	0.890	0.967	49.933	0.017	0.017	0.000	0.000	0.000	0.000
94	X	155	VAL	0	0.007	-0.021	51.363	0.001	0.001	0.000	0.000	0.000	0.000
95	X	156	GLU	-1	-0.862	-0.944	52.392	-0.014	-0.014	0.000	0.000	0.000	0.000
96	X	157	TYR	0	0.047	0.010	54.819	0.000	0.000	0.000	0.000	0.000	0.000
97	X	158	VAL	0	-0.021	-0.008	57.816	0.000	0.000	0.000	0.000	0.000	0.000
98	X	159	ARG	1	0.997	0.985	60.367	0.009	0.009	0.000	0.000	0.000	0.000
99	X	160	LYS	1	0.964	0.976	61.864	0.005	0.005	0.000	0.000	0.000	0.000
100	X	161	LYS	1	0.958	0.982	62.583	0.007	0.007	0.000	0.000	0.000	0.000
101	X	162	PRO	0	0.015	0.044	58.908	-0.001	-0.001	0.000	0.000	0.000	0.000
102	X	163	LYS	1	0.930	0.964	57.379	0.012	0.012	0.000	0.000	0.000	0.000
103	X	164	LEU	0	0.039	0.012	54.776	0.000	0.000	0.000	0.000	0.000	0.000
104	X	165	LYS	1	0.947	0.990	53.812	0.016	0.016	0.000	0.000	0.000	0.000
105	X	166	GLU	-1	-0.815	-0.910	52.811	-0.015	-0.015	0.000	0.000	0.000	0.000
106	X	167	VAL	0	-0.025	-0.011	47.961	0.000	0.000	0.000	0.000	0.000	0.000
107	X	168	GLN	0	0.027	0.014	47.127	0.000	0.000	0.000	0.000	0.000	0.000
108	X	169	VAL	0	0.005	0.002	42.133	-0.001	-0.001	0.000	0.000	0.000	0.000
109	X	170	ARG	1	0.933	0.958	37.871	0.043	0.043	0.000	0.000	0.000	0.000
110	X	171	LEU	0	-0.008	0.003	39.103	-0.001	-0.001	0.000	0.000	0.000	0.000
111	X	172	GLU	-1	-0.848	-0.938	32.296	-0.057	-0.057	0.000	0.000	0.000	0.000
112	X	173	GLU	-1	-0.831	-0.902	35.261	-0.027	-0.027	0.000	0.000	0.000	0.000
113	X	174	HIS	0	0.016	0.001	28.843	-0.002	-0.002	0.000	0.000	0.000	0.000
114	X	175	LEU	0	-0.047	-0.031	33.447	0.004	0.004	0.000	0.000	0.000	0.000
115	X	176	GLU	-1	-0.850	-0.901	31.959	-0.045	-0.045	0.000	0.000	0.000	0.000
116	X	178	ALA	0	0.027	0.015	25.623	0.004	0.004	0.000	0.000	0.000	0.000
117	X	180	ALA	0	0.038	0.026	21.086	-0.004	-0.004	0.000	0.000	0.000	0.000
118	X	181	THR	0	0.016	0.000	16.851	-0.002	-0.002	0.000	0.000	0.000	0.000

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