FMO DATABASE

FMODB ID: 49V2N

Calculation Name: 3MJG-A-Xray372

Preferred Name: Platelet-derived growth factor subunit B

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJG

Chain ID: A

ChEMBL ID: CHEMBL3108633

UniProt ID: P01127

Base Structure: X-ray

Registration Date: 2023-09-19

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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-625811.945349
FMO2-HF: Nuclear repulsion	585138.901449
FMO2-HF: Total energy	-40673.0439
FMO2-MP2: Total energy	-40785.645479

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:6:THR)

Summations of interaction energy for fragment #1(A:6:THR)

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.
-0.925	1.16	0.072	-0.81	-1.347	0

Interaction energy analysis for fragmet #1(A:6:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.033

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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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].
3	A	8	ALA	0	-0.021	-0.004	3.466	-0.828	1.152	0.073	-0.803	-1.250
4	A	9	GLU	-1	-0.897	-0.953	4.589	-0.070	0.035	-0.001	-0.007	-0.097
5	A	10	PRO	0	-0.028	-0.012	7.284	0.004	0.004	0.000	0.000	0.000
6	A	11	ALA	0	0.001	0.001	10.649	0.081	0.081	0.000	0.000	0.000
7	A	12	MET	0	-0.001	0.000	11.823	0.007	0.007	0.000	0.000	0.000
8	A	13	ILE	0	-0.001	0.006	14.459	0.012	0.012	0.000	0.000	0.000
9	A	14	ALA	0	0.002	0.007	17.620	0.027	0.027	0.000	0.000	0.000
10	A	15	GLU	-1	-0.880	-0.959	18.691	0.022	0.022	0.000	0.000	0.000
11	A	16	CYS	0	-0.020	0.017	21.867	0.014	0.014	0.000	0.000	0.000
12	A	17	LYS	1	0.959	0.976	20.407	-0.122	-0.122	0.000	0.000	0.000
13	A	18	THR	0	-0.006	-0.009	25.849	0.000	0.000	0.000	0.000	0.000
14	A	19	ARG	1	0.787	0.882	19.624	-0.077	-0.077	0.000	0.000	0.000
15	A	20	THR	0	0.013	-0.004	24.270	-0.007	-0.007	0.000	0.000	0.000
16	A	21	GLU	-1	-0.937	-0.960	24.297	0.073	0.073	0.000	0.000	0.000
17	A	22	VAL	0	0.009	-0.008	25.996	0.001	0.001	0.000	0.000	0.000
18	A	23	PHE	0	-0.007	0.001	28.508	-0.008	-0.008	0.000	0.000	0.000
19	A	24	GLU	-1	-0.891	-0.962	32.046	0.044	0.044	0.000	0.000	0.000
20	A	25	ILE	0	-0.029	-0.008	33.979	-0.005	-0.005	0.000	0.000	0.000
21	A	26	SER	0	0.056	0.018	37.553	-0.002	-0.002	0.000	0.000	0.000
22	A	27	ARG	1	0.919	0.938	39.147	-0.029	-0.029	0.000	0.000	0.000
23	A	28	ARG	1	0.941	0.986	41.695	-0.021	-0.021	0.000	0.000	0.000
24	A	29	LEU	0	-0.021	-0.024	38.871	-0.002	-0.002	0.000	0.000	0.000
25	A	30	ILE	0	-0.035	-0.007	42.648	0.001	0.001	0.000	0.000	0.000
26	A	31	ASP	-1	-0.811	-0.895	45.799	0.021	0.021	0.000	0.000	0.000
27	A	32	ARG	1	0.923	0.958	44.534	-0.014	-0.014	0.000	0.000	0.000
28	A	33	THR	0	-0.049	-0.030	48.263	-0.002	-0.002	0.000	0.000	0.000
29	A	34	ASN	0	0.059	0.042	50.561	-0.001	-0.001	0.000	0.000	0.000
30	A	35	ALA	0	0.021	0.000	46.814	0.001	0.001	0.000	0.000	0.000
31	A	36	ASN	0	-0.024	-0.008	47.913	0.000	0.000	0.000	0.000	0.000
32	A	37	PHE	0	-0.043	-0.039	45.035	0.001	0.001	0.000	0.000	0.000
33	A	38	LEU	0	0.017	0.017	41.984	0.000	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.022	0.012	39.813	-0.001	-0.001	0.000	0.000	0.000
35	A	40	TRP	0	0.008	0.039	35.892	0.001	0.001	0.000	0.000	0.000
36	A	41	PRO	0	0.036	0.002	35.621	-0.003	-0.003	0.000	0.000	0.000
37	A	42	PRO	0	0.038	0.005	33.899	-0.003	-0.003	0.000	0.000	0.000
38	A	43	CYS	0	-0.030	-0.013	31.612	-0.003	-0.003	0.000	0.000	0.000
39	A	44	VAL	0	-0.030	-0.011	32.667	0.003	0.003	0.000	0.000	0.000
40	A	45	GLU	-1	-0.879	-0.934	26.885	0.127	0.127	0.000	0.000	0.000
41	A	46	VAL	0	-0.066	-0.026	29.652	-0.007	-0.007	0.000	0.000	0.000
42	A	47	GLN	0	0.011	0.028	26.924	0.011	0.011	0.000	0.000	0.000
43	A	48	ARG	1	0.903	0.935	28.112	-0.060	-0.060	0.000	0.000	0.000
44	A	49	CYS	0	-0.073	-0.020	27.247	0.005	0.005	0.000	0.000	0.000
45	A	50	SER	0	0.070	0.050	23.669	0.000	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.026	0.016	21.825	0.006	0.006	0.000	0.000	0.000
47	A	52	CYS	0	-0.079	-0.047	22.370	-0.007	-0.007	0.000	0.000	0.000
48	A	53	CYS	0	-0.013	0.007	24.035	0.006	0.006	0.000	0.000	0.000
49	A	54	ASN	0	0.024	0.012	25.148	-0.001	-0.001	0.000	0.000	0.000
50	A	55	ASN	0	0.012	0.002	26.154	-0.013	-0.013	0.000	0.000	0.000
51	A	56	ARG	1	1.007	0.999	26.320	0.049	0.049	0.000	0.000	0.000
52	A	57	ASN	0	0.006	0.009	30.857	0.003	0.003	0.000	0.000	0.000
53	A	58	VAL	0	0.004	0.001	29.771	0.004	0.004	0.000	0.000	0.000
54	A	59	GLN	0	0.034	0.024	30.317	0.000	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.848	0.911	29.615	-0.003	-0.003	0.000	0.000	0.000
56	A	62	PRO	0	0.045	-0.004	32.651	0.002	0.002	0.000	0.000	0.000
57	A	63	THR	0	-0.063	-0.047	33.818	-0.004	-0.004	0.000	0.000	0.000
58	A	64	GLN	0	0.004	-0.010	35.506	0.002	0.002	0.000	0.000	0.000
59	A	65	VAL	0	0.026	0.033	35.828	0.004	0.004	0.000	0.000	0.000
60	A	66	GLN	0	-0.014	-0.004	37.506	-0.001	-0.001	0.000	0.000	0.000
61	A	67	LEU	0	0.009	0.014	38.541	0.002	0.002	0.000	0.000	0.000
62	A	68	ARG	1	0.894	0.926	35.284	-0.066	-0.066	0.000	0.000	0.000
63	A	69	PRO	0	-0.012	0.011	41.467	0.000	0.000	0.000	0.000	0.000
64	A	70	VAL	0	0.023	0.002	38.742	0.003	0.003	0.000	0.000	0.000
65	A	71	GLN	0	0.018	0.010	42.093	-0.003	-0.003	0.000	0.000	0.000
66	A	72	VAL	0	0.021	0.013	40.285	0.003	0.003	0.000	0.000	0.000
67	A	73	ARG	1	0.878	0.930	42.760	-0.053	-0.053	0.000	0.000	0.000
68	A	74	LYS	1	0.866	0.948	44.066	-0.026	-0.026	0.000	0.000	0.000
69	A	75	ILE	0	-0.045	-0.045	43.678	-0.001	-0.001	0.000	0.000	0.000
70	A	76	GLU	-1	-0.743	-0.854	47.341	0.026	0.026	0.000	0.000	0.000
71	A	77	ILE	0	-0.006	-0.008	48.772	0.001	0.001	0.000	0.000	0.000
72	A	78	VAL	0	0.026	-0.003	51.443	-0.002	-0.002	0.000	0.000	0.000
73	A	79	ARG	1	1.053	1.034	55.018	-0.020	-0.020	0.000	0.000	0.000
74	A	80	LYS	1	0.976	1.008	50.177	-0.032	-0.032	0.000	0.000	0.000
75	A	81	LYS	1	0.909	0.952	51.872	-0.027	-0.027	0.000	0.000	0.000
76	A	82	PRO	0	0.034	0.010	48.796	-0.001	-0.001	0.000	0.000	0.000
77	A	83	ILE	0	-0.029	-0.023	51.083	0.000	0.000	0.000	0.000	0.000
78	A	84	PHE	0	0.001	-0.003	46.679	0.001	0.001	0.000	0.000	0.000
79	A	85	LYS	1	0.889	0.938	49.095	-0.028	-0.028	0.000	0.000	0.000
80	A	86	LYS	1	0.905	0.950	47.864	-0.042	-0.042	0.000	0.000	0.000
81	A	87	ALA	0	0.028	0.017	46.236	-0.002	-0.002	0.000	0.000	0.000
82	A	88	THR	0	-0.008	0.003	45.366	0.003	0.003	0.000	0.000	0.000
83	A	89	VAL	0	-0.008	0.006	40.363	-0.002	-0.002	0.000	0.000	0.000
84	A	90	THR	0	0.013	-0.007	41.727	0.002	0.002	0.000	0.000	0.000
85	A	91	LEU	0	-0.009	0.012	35.873	-0.001	-0.001	0.000	0.000	0.000
86	A	92	GLU	-1	-0.862	-0.923	36.109	0.035	0.035	0.000	0.000	0.000
87	A	93	ASP	-1	-0.765	-0.852	33.479	0.072	0.072	0.000	0.000	0.000
88	A	94	HIS	0	-0.028	-0.034	31.368	-0.003	-0.003	0.000	0.000	0.000
89	A	95	LEU	0	0.004	-0.012	32.148	0.006	0.006	0.000	0.000	0.000
90	A	96	ALA	0	0.004	0.002	31.207	0.004	0.004	0.000	0.000	0.000
91	A	98	LYS	1	0.991	1.004	30.522	-0.018	-0.018	0.000	0.000	0.000
92	A	100	GLU	-1	-0.876	-0.932	30.777	0.009	0.009	0.000	0.000	0.000
93	A	101	THR	0	0.029	0.004	34.154	-0.004	-0.004	0.000	0.000	0.000
94	A	102	VAL	0	-0.032	-0.013	34.493	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:THR)