FMO DATABASE

FMODB ID: 827JY

Calculation Name: 1V7M-V-Xray372

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: 2023-03-13

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1266686.405108
FMO2-HF: Nuclear repulsion	1211342.013624
FMO2-HF: Total energy	-55344.391484
FMO2-MP2: Total energy	-55504.141605

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:151:CYS)

Summations of interaction energy for fragment #1(V:151:CYS)

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.
-22.606	-11.854	10.919	-8.198	-13.476	0.018

Interaction energy analysis for fragmet #1(V:151:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : 0.019

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	V	9	LEU	0	0.025	0.016	2.601	-10.820	-6.004	0.417	-2.305	-2.929	-0.003
4	V	10	ARG	1	0.943	0.965	4.913	2.509	2.654	-0.002	-0.005	-0.139	0.000
5	V	11	VAL	0	0.005	-0.007	2.189	-3.308	-1.284	3.728	-1.624	-4.128	0.014
6	V	12	LEU	0	0.061	0.036	5.489	0.300	0.407	-0.002	-0.003	-0.102	0.000
7	V	13	SER	0	0.026	0.003	7.626	0.240	0.240	0.000	0.000	0.000	0.000
8	V	14	LYS	1	0.860	0.930	8.716	-0.309	-0.309	0.000	0.000	0.000	0.000
9	V	15	LEU	0	0.068	0.055	6.100	0.086	0.086	0.000	0.000	0.000	0.000
10	V	16	LEU	0	0.080	0.024	9.364	-0.041	-0.041	0.000	0.000	0.000	0.000
11	V	17	ARG	1	0.893	1.006	12.516	-0.099	-0.099	0.000	0.000	0.000	0.000
12	V	18	ASP	-1	-0.914	-0.959	11.960	0.879	0.879	0.000	0.000	0.000	0.000
13	V	19	SER	0	-0.102	-0.103	13.375	-0.016	-0.016	0.000	0.000	0.000	0.000
14	V	20	HIS	0	0.039	0.011	15.169	-0.066	-0.066	0.000	0.000	0.000	0.000
15	V	21	VAL	0	-0.037	-0.015	17.879	0.004	0.004	0.000	0.000	0.000	0.000
16	V	22	LEU	0	0.012	0.031	15.871	-0.014	-0.014	0.000	0.000	0.000	0.000
17	V	23	HIS	0	0.003	0.004	19.365	-0.024	-0.024	0.000	0.000	0.000	0.000
18	V	24	SER	0	-0.061	-0.059	21.257	-0.017	-0.017	0.000	0.000	0.000	0.000
19	V	25	ARG	1	0.944	0.969	20.912	-0.440	-0.440	0.000	0.000	0.000	0.000
20	V	26	LEU	0	-0.023	-0.006	24.325	0.014	0.014	0.000	0.000	0.000	0.000
21	V	27	SER	0	0.012	0.006	26.070	-0.014	-0.014	0.000	0.000	0.000	0.000
22	V	28	GLN	0	-0.035	-0.019	27.107	-0.025	-0.025	0.000	0.000	0.000	0.000
23	V	29	CYS	0	-0.026	0.003	27.582	0.033	0.033	0.000	0.000	0.000	0.000
24	V	30	PRO	0	0.027	0.020	30.463	-0.011	-0.011	0.000	0.000	0.000	0.000
25	V	31	GLU	-1	-0.932	-0.967	33.716	0.177	0.177	0.000	0.000	0.000	0.000
26	V	32	VAL	0	-0.039	-0.006	29.292	0.017	0.017	0.000	0.000	0.000	0.000
27	V	33	HIS	0	0.021	-0.003	31.843	-0.025	-0.025	0.000	0.000	0.000	0.000
28	V	34	PRO	0	-0.053	-0.037	30.680	0.018	0.018	0.000	0.000	0.000	0.000
29	V	35	LEU	0	-0.040	-0.006	26.089	-0.003	-0.003	0.000	0.000	0.000	0.000
30	V	36	PRO	0	0.007	0.010	30.654	-0.020	-0.020	0.000	0.000	0.000	0.000
31	V	37	THR	0	0.000	-0.006	30.458	-0.013	-0.013	0.000	0.000	0.000	0.000
32	V	38	PRO	0	-0.057	-0.039	29.880	0.012	0.012	0.000	0.000	0.000	0.000
33	V	39	VAL	0	0.020	0.021	23.711	0.008	0.008	0.000	0.000	0.000	0.000
34	V	40	LEU	0	0.005	0.003	24.293	-0.025	-0.025	0.000	0.000	0.000	0.000
35	V	41	LEU	0	-0.043	-0.016	20.374	0.051	0.051	0.000	0.000	0.000	0.000
36	V	42	PRO	0	0.009	-0.005	16.801	-0.050	-0.050	0.000	0.000	0.000	0.000
37	V	43	ALA	0	0.016	0.011	19.515	-0.033	-0.033	0.000	0.000	0.000	0.000
38	V	44	VAL	0	0.015	0.015	20.621	-0.036	-0.036	0.000	0.000	0.000	0.000
39	V	45	ASP	-1	-0.977	-0.980	21.461	-0.328	-0.328	0.000	0.000	0.000	0.000
40	V	46	PHE	0	-0.012	-0.025	18.531	-0.059	-0.059	0.000	0.000	0.000	0.000
41	V	47	SER	0	0.015	0.002	22.238	-0.010	-0.010	0.000	0.000	0.000	0.000
42	V	48	LEU	0	-0.002	-0.001	16.809	0.009	0.009	0.000	0.000	0.000	0.000
43	V	49	GLY	0	0.015	0.012	19.233	-0.093	-0.093	0.000	0.000	0.000	0.000
44	V	50	GLU	-1	-0.892	-0.948	21.032	-0.472	-0.472	0.000	0.000	0.000	0.000
45	V	51	TRP	0	-0.001	-0.004	12.174	-0.051	-0.051	0.000	0.000	0.000	0.000
46	V	52	LYS	1	0.914	0.949	14.229	1.541	1.541	0.000	0.000	0.000	0.000
47	V	53	THR	0	-0.015	-0.018	17.034	-0.096	-0.096	0.000	0.000	0.000	0.000
48	V	54	GLN	0	-0.018	0.006	17.737	0.032	0.032	0.000	0.000	0.000	0.000
49	V	55	MET	0	0.060	0.017	16.217	-0.171	-0.171	0.000	0.000	0.000	0.000
50	V	56	GLU	-1	-0.912	-0.985	9.710	-2.897	-2.897	0.000	0.000	0.000	0.000
51	V	57	GLU	-1	-0.878	-0.926	10.906	-0.761	-0.761	0.000	0.000	0.000	0.000
52	V	58	THR	0	-0.007	0.010	12.132	0.139	0.139	0.000	0.000	0.000	0.000
53	V	59	LYS	1	0.882	0.979	12.016	1.525	1.525	0.000	0.000	0.000	0.000
54	V	60	ALA	0	0.036	0.003	8.524	0.059	0.059	0.000	0.000	0.000	0.000
55	V	61	GLN	0	-0.006	-0.013	10.340	0.501	0.501	0.000	0.000	0.000	0.000
56	V	62	ASP	-1	-0.872	-0.947	12.937	-0.219	-0.219	0.000	0.000	0.000	0.000
57	V	63	ILE	0	-0.078	-0.035	9.916	0.096	0.096	0.000	0.000	0.000	0.000
58	V	64	LEU	0	0.006	0.031	9.827	0.191	0.191	0.000	0.000	0.000	0.000
59	V	65	GLY	0	0.087	0.058	11.635	0.109	0.109	0.000	0.000	0.000	0.000
60	V	66	ALA	0	-0.010	-0.012	14.553	-0.002	-0.002	0.000	0.000	0.000	0.000
61	V	67	VAL	0	-0.060	-0.044	9.975	-0.004	-0.004	0.000	0.000	0.000	0.000
62	V	68	THR	0	-0.031	-0.038	13.173	0.130	0.130	0.000	0.000	0.000	0.000
63	V	69	LEU	0	0.030	0.017	14.962	-0.017	-0.017	0.000	0.000	0.000	0.000
64	V	70	LEU	0	0.012	0.017	13.469	-0.012	-0.012	0.000	0.000	0.000	0.000
65	V	71	LEU	0	-0.068	-0.022	13.197	0.002	0.002	0.000	0.000	0.000	0.000
66	V	72	GLU	-1	-0.891	-0.957	15.819	0.473	0.473	0.000	0.000	0.000	0.000
67	V	73	GLY	0	0.025	0.010	19.163	-0.045	-0.045	0.000	0.000	0.000	0.000
68	V	74	VAL	0	-0.094	-0.063	16.772	-0.025	-0.025	0.000	0.000	0.000	0.000
69	V	75	MET	0	-0.043	-0.026	18.576	-0.007	-0.007	0.000	0.000	0.000	0.000
70	V	76	ALA	0	0.064	0.042	21.211	-0.025	-0.025	0.000	0.000	0.000	0.000
71	V	77	ALA	0	0.003	0.007	23.784	-0.036	-0.036	0.000	0.000	0.000	0.000
72	V	78	ARG	1	0.898	0.946	20.758	-0.613	-0.613	0.000	0.000	0.000	0.000
73	V	79	GLY	0	-0.005	0.007	24.622	0.006	0.006	0.000	0.000	0.000	0.000
74	V	80	GLN	0	-0.003	0.009	26.846	-0.038	-0.038	0.000	0.000	0.000	0.000
75	V	81	LEU	0	-0.061	-0.029	26.879	-0.024	-0.024	0.000	0.000	0.000	0.000
76	V	82	GLY	0	0.056	0.037	28.787	0.024	0.024	0.000	0.000	0.000	0.000
77	V	83	PRO	0	-0.005	-0.031	28.919	0.013	0.013	0.000	0.000	0.000	0.000
78	V	84	THR	0	-0.010	-0.006	28.355	0.020	0.020	0.000	0.000	0.000	0.000
79	V	86	LEU	0	0.078	0.030	24.976	0.030	0.030	0.000	0.000	0.000	0.000
80	V	87	SER	0	0.009	0.015	24.209	0.049	0.049	0.000	0.000	0.000	0.000
81	V	88	SER	0	-0.048	-0.005	23.038	0.057	0.057	0.000	0.000	0.000	0.000
82	V	89	LEU	0	0.027	-0.001	21.188	0.060	0.060	0.000	0.000	0.000	0.000
83	V	90	LEU	0	0.017	0.013	19.803	0.061	0.061	0.000	0.000	0.000	0.000
84	V	91	GLY	0	-0.073	-0.050	18.930	0.006	0.006	0.000	0.000	0.000	0.000
85	V	92	GLN	0	0.061	0.026	16.307	0.103	0.103	0.000	0.000	0.000	0.000
86	V	93	LEU	0	0.010	0.010	14.652	0.111	0.111	0.000	0.000	0.000	0.000
87	V	94	SER	0	0.034	0.012	13.679	0.067	0.067	0.000	0.000	0.000	0.000
88	V	95	GLY	0	-0.011	0.000	12.692	0.151	0.151	0.000	0.000	0.000	0.000
89	V	96	GLN	0	-0.001	-0.013	10.100	0.197	0.197	0.000	0.000	0.000	0.000
90	V	97	VAL	0	0.002	-0.008	8.964	0.221	0.221	0.000	0.000	0.000	0.000
91	V	98	ARG	1	0.963	0.974	9.279	-1.167	-1.167	0.000	0.000	0.000	0.000
92	V	99	LEU	0	-0.007	0.018	5.237	0.433	0.433	0.000	0.000	0.000	0.000
93	V	100	LEU	0	-0.015	-0.002	4.615	0.340	0.427	-0.002	-0.006	-0.080	0.000
94	V	101	LEU	0	-0.006	0.001	5.917	0.656	0.656	0.000	0.000	0.000	0.000
95	V	102	GLY	0	0.019	0.014	6.263	0.011	0.011	0.000	0.000	0.000	0.000
96	V	103	ALA	0	-0.031	-0.016	1.993	0.272	-1.737	6.737	-1.918	-2.809	0.012
97	V	104	LEU	0	0.021	0.004	3.634	1.454	2.020	0.022	-0.073	-0.515	0.000
98	V	105	GLN	0	0.078	0.029	5.985	-1.132	-1.132	0.000	0.000	0.000	0.000
99	V	106	SER	0	-0.065	-0.019	4.932	-1.138	-1.138	0.000	0.000	0.000	0.000
100	V	107	LEU	0	-0.035	-0.018	3.720	-1.875	-1.260	0.006	-0.135	-0.486	0.001
101	V	108	LEU	0	0.008	-0.001	5.582	-1.130	-1.122	-0.002	0.000	-0.007	0.000
102	V	109	GLY	0	-0.006	0.018	8.965	-0.341	-0.341	0.000	0.000	0.000	0.000
103	V	110	THR	0	-0.030	-0.029	11.029	-0.158	-0.158	0.000	0.000	0.000	0.000
104	V	111	GLN	0	-0.080	-0.044	11.645	0.147	0.147	0.000	0.000	0.000	0.000
105	V	112	LEU	0	-0.011	-0.003	13.399	-0.155	-0.155	0.000	0.000	0.000	0.000
106	V	113	PRO	0	0.005	-0.004	15.831	0.075	0.075	0.000	0.000	0.000	0.000
107	V	114	PRO	0	0.042	0.027	17.939	-0.003	-0.003	0.000	0.000	0.000	0.000
108	V	115	GLN	0	-0.035	-0.014	19.067	-0.064	-0.064	0.000	0.000	0.000	0.000
109	V	116	GLY	0	0.046	0.028	19.520	-0.006	-0.006	0.000	0.000	0.000	0.000
110	V	117	ARG	1	0.927	0.959	21.214	0.261	0.261	0.000	0.000	0.000	0.000
111	V	118	THR	0	0.013	0.000	22.510	-0.001	-0.001	0.000	0.000	0.000	0.000
112	V	119	THR	0	-0.009	0.006	24.664	-0.025	-0.025	0.000	0.000	0.000	0.000
113	V	120	ALA	0	0.017	0.003	25.603	0.032	0.032	0.000	0.000	0.000	0.000
114	V	121	HIS	0	-0.008	-0.012	25.066	-0.036	-0.036	0.000	0.000	0.000	0.000
115	V	122	LYS	1	1.004	0.999	27.551	-0.101	-0.101	0.000	0.000	0.000	0.000
116	V	123	ASP	-1	-0.828	-0.929	28.183	0.119	0.119	0.000	0.000	0.000	0.000
117	V	124	PRO	0	0.038	0.020	25.336	0.007	0.007	0.000	0.000	0.000	0.000
118	V	125	ASN	0	0.015	0.009	23.600	0.022	0.022	0.000	0.000	0.000	0.000
119	V	126	ALA	0	0.048	0.021	22.901	-0.001	-0.001	0.000	0.000	0.000	0.000
120	V	127	ILE	0	0.029	0.001	20.086	-0.005	-0.005	0.000	0.000	0.000	0.000
121	V	128	PHE	0	-0.051	-0.027	18.818	0.045	0.045	0.000	0.000	0.000	0.000
122	V	129	LEU	0	-0.007	0.013	18.630	-0.016	-0.016	0.000	0.000	0.000	0.000
123	V	130	SER	0	0.054	0.028	18.623	-0.032	-0.032	0.000	0.000	0.000	0.000
124	V	131	PHE	0	0.022	0.019	10.138	-0.048	-0.048	0.000	0.000	0.000	0.000
125	V	132	GLN	0	0.016	-0.010	14.208	-0.118	-0.118	0.000	0.000	0.000	0.000
126	V	133	HIS	0	-0.031	-0.013	15.474	-0.083	-0.083	0.000	0.000	0.000	0.000
127	V	134	LEU	0	0.043	0.016	13.195	-0.147	-0.147	0.000	0.000	0.000	0.000
128	V	135	LEU	0	-0.052	-0.025	9.455	-0.208	-0.208	0.000	0.000	0.000	0.000
129	V	136	ARG	1	0.924	0.961	12.145	0.169	0.169	0.000	0.000	0.000	0.000
130	V	137	GLY	0	0.004	0.009	14.550	-0.127	-0.127	0.000	0.000	0.000	0.000
131	V	138	LYS	1	0.941	0.982	12.936	0.146	0.146	0.000	0.000	0.000	0.000
132	V	139	VAL	0	0.073	0.041	7.697	-0.219	-0.219	0.000	0.000	0.000	0.000
133	V	140	ARG	1	0.969	0.997	8.683	1.239	1.239	0.000	0.000	0.000	0.000
134	V	141	PHE	0	-0.038	-0.042	10.539	-0.421	-0.421	0.000	0.000	0.000	0.000
135	V	142	LEU	0	-0.024	-0.005	6.894	0.232	0.232	0.000	0.000	0.000	0.000
136	V	143	MET	0	-0.012	0.001	4.216	-2.096	-1.921	-0.001	-0.037	-0.137	0.000
137	V	144	LEU	0	-0.025	-0.007	7.136	-0.452	-0.452	0.000	0.000	0.000	0.000
138	V	145	VAL	0	-0.041	-0.010	9.608	0.329	0.329	0.000	0.000	0.000	0.000
139	V	146	GLY	0	0.017	0.014	9.603	0.040	0.040	0.000	0.000	0.000	0.000
140	V	147	GLY	0	0.012	0.012	5.874	-1.364	-1.364	0.000	0.000	0.000	0.000
141	V	148	SER	0	0.035	0.023	6.520	0.173	0.173	0.000	0.000	0.000	0.000
142	V	149	THR	0	-0.074	-0.052	3.261	-5.056	-0.838	0.018	-2.092	-2.144	-0.006

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Interactive mode: IFIE and PIEDA for fragment #1(V:151:CYS)