FMO DATABASE

FMODB ID: 7JRJK

Calculation Name: 1V7M-V-Xray308

Preferred Name: Thrombopoietin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1V7M

Chain ID: V

ChEMBL ID: CHEMBL1293256

UniProt ID: P40225

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1273783.49755
FMO2-HF: Nuclear repulsion	1218268.233027
FMO2-HF: Total energy	-55515.264523
FMO2-MP2: Total energy	-55675.548604

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(V:6:ACE )

Summations of interaction energy for fragment #1(V:6:ACE )

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.
1.948	2.806	-0.005	-0.438	-0.415	0

Interaction energy analysis for fragmet #1(V:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.010

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].
3	V	8	ASP	-1	-0.856	-0.923	3.857	-0.099	0.759	-0.005	-0.438	-0.415
4	V	9	LEU	0	0.032	0.018	7.341	0.111	0.111	0.000	0.000	0.000
5	V	10	ARG	1	0.940	0.963	10.140	0.677	0.677	0.000	0.000	0.000
6	V	11	VAL	0	-0.009	-0.006	8.195	0.026	0.026	0.000	0.000	0.000
7	V	12	LEU	0	0.063	0.036	11.349	0.072	0.072	0.000	0.000	0.000
8	V	13	SER	0	0.023	0.002	14.305	0.046	0.046	0.000	0.000	0.000
9	V	14	LYS	1	0.865	0.932	14.175	0.354	0.354	0.000	0.000	0.000
10	V	15	LEU	0	0.067	0.054	14.473	0.025	0.025	0.000	0.000	0.000
11	V	16	LEU	0	0.074	0.022	16.679	0.037	0.037	0.000	0.000	0.000
12	V	17	ARG	1	0.896	1.009	19.024	0.220	0.220	0.000	0.000	0.000
13	V	18	ASP	-1	-0.910	-0.957	18.870	-0.255	-0.255	0.000	0.000	0.000
14	V	19	SER	0	-0.102	-0.103	20.842	0.019	0.019	0.000	0.000	0.000
15	V	20	HIS	0	0.035	0.008	22.750	0.022	0.022	0.000	0.000	0.000
16	V	21	VAL	0	-0.036	-0.014	24.104	0.011	0.011	0.000	0.000	0.000
17	V	22	LEU	0	0.011	0.031	23.666	0.011	0.011	0.000	0.000	0.000
18	V	23	HIS	0	0.004	0.004	27.215	0.005	0.005	0.000	0.000	0.000
19	V	24	SER	0	-0.061	-0.059	29.131	0.008	0.008	0.000	0.000	0.000
20	V	25	ARG	1	0.943	0.969	27.227	0.122	0.122	0.000	0.000	0.000
21	V	26	LEU	0	-0.022	-0.005	32.200	0.004	0.004	0.000	0.000	0.000
22	V	27	SER	0	0.014	0.007	34.155	0.004	0.004	0.000	0.000	0.000
23	V	28	GLN	0	-0.037	-0.020	33.902	0.005	0.005	0.000	0.000	0.000
24	V	85	CYS	0	-0.024	0.001	35.451	-0.002	-0.002	0.000	0.000	0.000
25	V	30	PRO	0	0.027	0.020	38.427	0.001	0.001	0.000	0.000	0.000
26	V	31	GLU	-1	-0.932	-0.967	41.966	-0.039	-0.039	0.000	0.000	0.000
27	V	32	VAL	0	-0.038	-0.005	37.745	-0.001	-0.001	0.000	0.000	0.000
28	V	33	HIS	0	0.019	-0.004	40.495	0.001	0.001	0.000	0.000	0.000
29	V	34	PRO	0	-0.052	-0.037	39.746	-0.002	-0.002	0.000	0.000	0.000
30	V	35	LEU	0	-0.042	-0.007	35.256	0.002	0.002	0.000	0.000	0.000
31	V	36	PRO	0	0.008	0.011	39.788	0.002	0.002	0.000	0.000	0.000
32	V	37	THR	0	-0.002	-0.008	39.529	0.003	0.003	0.000	0.000	0.000
33	V	38	PRO	0	-0.054	-0.037	39.034	-0.003	-0.003	0.000	0.000	0.000
34	V	39	VAL	0	0.019	0.020	32.850	0.002	0.002	0.000	0.000	0.000
35	V	40	LEU	0	0.004	0.003	33.155	-0.001	-0.001	0.000	0.000	0.000
36	V	41	LEU	0	-0.041	-0.014	29.535	-0.005	-0.005	0.000	0.000	0.000
37	V	42	PRO	0	0.007	-0.007	25.683	0.005	0.005	0.000	0.000	0.000
38	V	43	ALA	0	0.002	0.003	28.123	-0.005	-0.005	0.000	0.000	0.000
39	V	44	VAL	0	0.017	0.017	28.999	-0.003	-0.003	0.000	0.000	0.000
40	V	45	ASP	-1	-0.974	-0.979	30.143	-0.035	-0.035	0.000	0.000	0.000
41	V	46	PHE	0	-0.009	-0.023	26.780	-0.004	-0.004	0.000	0.000	0.000
42	V	47	SER	0	0.014	0.001	30.960	0.002	0.002	0.000	0.000	0.000
43	V	48	LEU	0	0.000	0.000	25.570	0.003	0.003	0.000	0.000	0.000
44	V	49	GLY	0	0.015	0.013	27.892	0.001	0.001	0.000	0.000	0.000
45	V	50	GLU	-1	-0.892	-0.949	29.467	-0.010	-0.010	0.000	0.000	0.000
46	V	51	TRP	0	-0.009	-0.004	21.001	0.002	0.002	0.000	0.000	0.000
47	V	52	LYS	1	0.915	0.950	21.937	0.009	0.009	0.000	0.000	0.000
48	V	53	THR	0	-0.017	-0.019	25.145	0.004	0.004	0.000	0.000	0.000
49	V	54	GLN	0	-0.018	0.006	26.021	0.007	0.007	0.000	0.000	0.000
50	V	55	MET	0	0.059	0.016	23.117	0.001	0.001	0.000	0.000	0.000
51	V	56	GLU	-1	-0.910	-0.984	16.668	0.032	0.032	0.000	0.000	0.000
52	V	57	GLU	-1	-0.878	-0.927	17.288	0.085	0.085	0.000	0.000	0.000
53	V	58	THR	0	-0.007	0.010	19.215	-0.009	-0.009	0.000	0.000	0.000
54	V	59	LYS	1	0.881	0.980	20.413	-0.001	-0.001	0.000	0.000	0.000
55	V	60	ALA	0	0.043	0.006	16.503	-0.016	-0.016	0.000	0.000	0.000
56	V	61	GLN	0	-0.007	-0.014	18.554	-0.005	-0.005	0.000	0.000	0.000
57	V	62	ASP	-1	-0.873	-0.947	20.792	-0.013	-0.013	0.000	0.000	0.000
58	V	63	ILE	0	-0.066	-0.034	18.487	-0.009	-0.009	0.000	0.000	0.000
59	V	64	LEU	0	0.005	0.031	17.376	-0.012	-0.012	0.000	0.000	0.000
60	V	65	GLY	0	0.090	0.061	19.793	-0.005	-0.005	0.000	0.000	0.000
61	V	66	ALA	0	-0.011	-0.013	22.868	-0.002	-0.002	0.000	0.000	0.000
62	V	67	VAL	0	-0.062	-0.046	18.787	-0.007	-0.007	0.000	0.000	0.000
63	V	68	THR	0	-0.028	-0.036	21.884	-0.006	-0.006	0.000	0.000	0.000
64	V	69	LEU	0	0.028	0.016	23.342	0.000	0.000	0.000	0.000	0.000
65	V	70	LEU	0	0.014	0.016	22.623	-0.001	-0.001	0.000	0.000	0.000
66	V	71	LEU	0	-0.068	-0.021	21.704	-0.002	-0.002	0.000	0.000	0.000
67	V	72	GLU	-1	-0.893	-0.957	24.757	-0.037	-0.037	0.000	0.000	0.000
68	V	73	GLY	0	0.022	0.008	27.894	0.004	0.004	0.000	0.000	0.000
69	V	74	VAL	0	-0.092	-0.062	25.860	0.001	0.001	0.000	0.000	0.000
70	V	75	MET	0	-0.044	-0.026	27.256	-0.001	-0.001	0.000	0.000	0.000
71	V	76	ALA	0	0.065	0.043	29.950	0.003	0.003	0.000	0.000	0.000
72	V	77	ALA	0	0.006	0.007	32.792	0.003	0.003	0.000	0.000	0.000
73	V	78	ARG	1	0.897	0.946	28.994	0.077	0.077	0.000	0.000	0.000
74	V	79	GLY	0	-0.009	0.007	33.395	0.001	0.001	0.000	0.000	0.000
75	V	80	GLN	0	-0.002	0.009	35.477	0.004	0.004	0.000	0.000	0.000
76	V	81	LEU	0	-0.062	-0.029	35.778	0.001	0.001	0.000	0.000	0.000
77	V	82	GLY	0	0.058	0.036	37.271	-0.001	-0.001	0.000	0.000	0.000
78	V	83	PRO	0	-0.006	-0.031	36.868	-0.003	-0.003	0.000	0.000	0.000
79	V	84	THR	0	-0.013	-0.006	36.703	-0.004	-0.004	0.000	0.000	0.000
80	V	86	LEU	0	0.078	0.031	33.720	-0.006	-0.006	0.000	0.000	0.000
81	V	87	SER	0	0.008	0.015	32.650	-0.007	-0.007	0.000	0.000	0.000
82	V	88	SER	0	-0.045	-0.003	31.355	-0.006	-0.006	0.000	0.000	0.000
83	V	89	LEU	0	0.029	-0.001	29.100	-0.008	-0.008	0.000	0.000	0.000
84	V	90	LEU	0	0.016	0.014	28.102	-0.010	-0.010	0.000	0.000	0.000
85	V	91	GLY	0	-0.072	-0.051	27.312	0.006	0.006	0.000	0.000	0.000
86	V	92	GLN	0	0.060	0.026	24.054	-0.010	-0.010	0.000	0.000	0.000
87	V	93	LEU	0	0.008	0.010	22.766	-0.019	-0.019	0.000	0.000	0.000
88	V	94	SER	0	0.033	0.011	22.455	-0.010	-0.010	0.000	0.000	0.000
89	V	95	GLY	0	-0.007	0.001	20.566	-0.005	-0.005	0.000	0.000	0.000
90	V	96	GLN	0	-0.002	-0.013	18.472	-0.030	-0.030	0.000	0.000	0.000
91	V	97	VAL	0	-0.004	-0.010	17.865	-0.018	-0.018	0.000	0.000	0.000
92	V	98	ARG	1	0.964	0.974	18.085	0.113	0.113	0.000	0.000	0.000
93	V	99	LEU	0	-0.005	0.018	13.297	-0.007	-0.007	0.000	0.000	0.000
94	V	100	LEU	0	-0.011	-0.001	13.413	-0.016	-0.016	0.000	0.000	0.000
95	V	101	LEU	0	-0.009	0.000	14.588	0.009	0.009	0.000	0.000	0.000
96	V	102	GLY	0	0.018	0.014	13.441	0.029	0.029	0.000	0.000	0.000
97	V	103	ALA	0	-0.022	-0.014	10.159	0.023	0.023	0.000	0.000	0.000
98	V	104	LEU	0	0.014	0.000	11.090	0.052	0.052	0.000	0.000	0.000
99	V	105	GLN	0	0.072	0.026	13.827	0.038	0.038	0.000	0.000	0.000
100	V	106	SER	0	-0.061	-0.016	8.823	0.060	0.060	0.000	0.000	0.000
101	V	107	LEU	0	-0.036	-0.017	10.535	0.055	0.055	0.000	0.000	0.000
102	V	108	LEU	0	0.006	-0.002	11.352	0.030	0.030	0.000	0.000	0.000
103	V	109	GLY	0	-0.005	0.019	14.101	0.010	0.010	0.000	0.000	0.000
104	V	110	THR	0	-0.031	-0.030	15.505	-0.004	-0.004	0.000	0.000	0.000
105	V	111	GLN	0	-0.079	-0.045	17.895	-0.007	-0.007	0.000	0.000	0.000
106	V	112	LEU	0	-0.012	-0.003	20.263	0.009	0.009	0.000	0.000	0.000
107	V	113	PRO	0	0.005	-0.004	22.942	-0.007	-0.007	0.000	0.000	0.000
108	V	114	PRO	0	0.041	0.028	25.671	-0.003	-0.003	0.000	0.000	0.000
109	V	115	GLN	0	-0.033	-0.012	27.137	0.004	0.004	0.000	0.000	0.000
110	V	116	GLY	0	0.047	0.028	27.799	-0.005	-0.005	0.000	0.000	0.000
111	V	117	ARG	1	0.930	0.960	29.570	0.022	0.022	0.000	0.000	0.000
112	V	118	THR	0	0.020	0.006	31.053	-0.003	-0.003	0.000	0.000	0.000
113	V	119	THR	0	-0.025	-0.006	33.199	0.002	0.002	0.000	0.000	0.000
114	V	120	ALA	0	0.027	0.005	34.517	-0.002	-0.002	0.000	0.000	0.000
115	V	121	HIS	0	0.004	-0.003	34.096	0.000	0.000	0.000	0.000	0.000
116	V	122	LYS	1	0.990	0.992	36.733	0.032	0.032	0.000	0.000	0.000
117	V	123	ASP	-1	-0.812	-0.920	37.217	-0.056	-0.056	0.000	0.000	0.000
118	V	124	PRO	0	0.029	0.014	34.421	-0.003	-0.003	0.000	0.000	0.000
119	V	125	ASN	0	0.011	0.007	32.609	-0.009	-0.009	0.000	0.000	0.000
120	V	126	ALA	0	0.062	0.028	31.728	-0.006	-0.006	0.000	0.000	0.000
121	V	127	ILE	0	0.025	-0.001	29.250	-0.002	-0.002	0.000	0.000	0.000
122	V	128	PHE	0	-0.053	-0.028	27.674	-0.008	-0.008	0.000	0.000	0.000
123	V	129	LEU	0	-0.008	0.013	27.316	-0.009	-0.009	0.000	0.000	0.000
124	V	130	SER	0	0.049	0.024	27.211	-0.005	-0.005	0.000	0.000	0.000
125	V	131	PHE	0	0.024	0.020	19.060	-0.004	-0.004	0.000	0.000	0.000
126	V	132	GLN	0	0.016	-0.010	22.839	-0.009	-0.009	0.000	0.000	0.000
127	V	133	HIS	0	-0.030	-0.013	23.532	-0.008	-0.008	0.000	0.000	0.000
128	V	134	LEU	0	0.042	0.015	21.667	0.001	0.001	0.000	0.000	0.000
129	V	135	LEU	0	-0.053	-0.025	17.828	-0.004	-0.004	0.000	0.000	0.000
130	V	136	ARG	1	0.924	0.962	19.673	0.106	0.106	0.000	0.000	0.000
131	V	137	GLY	0	0.007	0.009	22.327	0.007	0.007	0.000	0.000	0.000
132	V	138	LYS	1	0.941	0.981	21.444	0.038	0.038	0.000	0.000	0.000
133	V	139	VAL	0	0.061	0.037	16.103	0.004	0.004	0.000	0.000	0.000
134	V	140	ARG	1	0.970	0.998	17.099	0.157	0.157	0.000	0.000	0.000
135	V	141	PHE	0	-0.037	-0.041	18.464	0.003	0.003	0.000	0.000	0.000
136	V	142	LEU	0	-0.026	-0.005	15.677	0.014	0.014	0.000	0.000	0.000
137	V	143	MET	0	-0.009	0.000	12.145	-0.028	-0.028	0.000	0.000	0.000
138	V	144	LEU	0	-0.029	-0.008	14.359	-0.001	-0.001	0.000	0.000	0.000
139	V	145	VAL	0	-0.037	-0.009	16.850	0.007	0.007	0.000	0.000	0.000
140	V	146	GLY	0	0.018	0.015	14.311	0.026	0.026	0.000	0.000	0.000
141	V	147	GLY	0	0.013	0.012	12.023	-0.035	-0.035	0.000	0.000	0.000
142	V	148	SER	0	0.036	0.024	10.933	0.051	0.051	0.000	0.000	0.000
143	V	149	THR	0	-0.080	-0.054	5.692	0.038	0.038	0.000	0.000	0.000
144	V	150	LEU	0	0.058	0.011	7.528	-0.044	-0.044	0.000	0.000	0.000
145	V	152	NME	0	0.029	0.032	6.683	-0.021	-0.021	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(V:6:ACE )