FMO DATABASE

FMODB ID: J3YM9

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	OptAll
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	-1272186.639553
FMO2-HF: Nuclear repulsion	1216839.454008
FMO2-HF: Total energy	-55347.185546
FMO2-MP2: Total energy	-55506.710859

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.
-20.498	-7.343	8.04	-7.956	-13.241	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 : 0.035 / q_NPA : 0.054

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	0.056	0.019	3.243	-4.891	0.226	0.337	-2.427	-3.026	0.004
4	V	10	ARG	1	0.841	0.910	5.091	0.998	1.135	-0.002	-0.003	-0.132	0.000
5	V	11	VAL	0	0.019	0.005	2.607	-3.097	-0.735	1.891	-1.111	-3.142	0.009
6	V	12	LEU	0	0.033	0.026	5.608	-0.012	0.071	-0.002	-0.002	-0.080	0.000
7	V	13	SER	0	0.001	-0.008	7.376	0.000	0.000	0.000	0.000	0.000	0.000
8	V	14	LYS	1	0.783	0.873	8.771	-0.833	-0.833	0.000	0.000	0.000	0.000
9	V	15	LEU	0	0.045	0.034	6.380	-0.057	-0.057	0.000	0.000	0.000	0.000
10	V	16	LEU	0	0.010	0.004	9.416	-0.094	-0.094	0.000	0.000	0.000	0.000
11	V	17	ARG	1	0.910	0.980	12.417	-0.272	-0.272	0.000	0.000	0.000	0.000
12	V	18	ASP	-1	-0.784	-0.888	12.265	0.783	0.783	0.000	0.000	0.000	0.000
13	V	19	SER	0	-0.035	-0.029	13.001	-0.046	-0.046	0.000	0.000	0.000	0.000
14	V	20	HIS	0	0.062	0.032	14.779	-0.065	-0.065	0.000	0.000	0.000	0.000
15	V	21	VAL	0	-0.014	-0.001	17.415	-0.022	-0.022	0.000	0.000	0.000	0.000
16	V	22	LEU	0	-0.039	-0.010	15.300	-0.009	-0.009	0.000	0.000	0.000	0.000
17	V	23	HIS	0	0.014	-0.006	18.911	-0.021	-0.021	0.000	0.000	0.000	0.000
18	V	24	SER	0	-0.055	-0.038	20.863	-0.025	-0.025	0.000	0.000	0.000	0.000
19	V	25	ARG	1	0.885	0.937	19.624	-0.462	-0.462	0.000	0.000	0.000	0.000
20	V	26	LEU	0	-0.003	0.001	23.931	0.006	0.006	0.000	0.000	0.000	0.000
21	V	27	SER	0	0.004	-0.007	25.707	-0.010	-0.010	0.000	0.000	0.000	0.000
22	V	28	GLN	0	-0.005	0.007	26.967	-0.018	-0.018	0.000	0.000	0.000	0.000
23	V	29	CYS	0	-0.057	-0.020	27.471	0.047	0.047	0.000	0.000	0.000	0.000
24	V	30	PRO	0	0.054	0.026	30.070	-0.012	-0.012	0.000	0.000	0.000	0.000
25	V	31	GLU	-1	-0.910	-0.967	32.906	0.180	0.180	0.000	0.000	0.000	0.000
26	V	32	VAL	0	-0.027	-0.006	28.781	0.013	0.013	0.000	0.000	0.000	0.000
27	V	33	HIS	0	-0.039	-0.019	31.341	-0.021	-0.021	0.000	0.000	0.000	0.000
28	V	34	PRO	0	-0.049	-0.033	30.309	0.018	0.018	0.000	0.000	0.000	0.000
29	V	35	LEU	0	0.013	0.022	25.643	-0.001	-0.001	0.000	0.000	0.000	0.000
30	V	36	PRO	0	0.038	0.033	30.327	-0.020	-0.020	0.000	0.000	0.000	0.000
31	V	37	THR	0	0.008	-0.002	30.511	-0.023	-0.023	0.000	0.000	0.000	0.000
32	V	38	PRO	0	-0.055	-0.034	29.535	0.013	0.013	0.000	0.000	0.000	0.000
33	V	39	VAL	0	0.005	0.012	23.324	0.011	0.011	0.000	0.000	0.000	0.000
34	V	40	LEU	0	0.006	0.004	23.912	-0.024	-0.024	0.000	0.000	0.000	0.000
35	V	41	LEU	0	-0.014	-0.004	20.235	0.053	0.053	0.000	0.000	0.000	0.000
36	V	42	PRO	0	0.025	0.003	16.363	-0.047	-0.047	0.000	0.000	0.000	0.000
37	V	43	ALA	0	0.004	0.009	19.350	-0.016	-0.016	0.000	0.000	0.000	0.000
38	V	44	VAL	0	0.006	0.007	19.944	-0.031	-0.031	0.000	0.000	0.000	0.000
39	V	45	ASP	-1	-0.880	-0.927	21.530	-0.259	-0.259	0.000	0.000	0.000	0.000
40	V	46	PHE	0	0.008	-0.033	19.442	-0.034	-0.034	0.000	0.000	0.000	0.000
41	V	47	SER	0	0.024	0.016	22.636	-0.008	-0.008	0.000	0.000	0.000	0.000
42	V	48	LEU	0	-0.044	-0.021	16.813	-0.012	-0.012	0.000	0.000	0.000	0.000
43	V	49	GLY	0	0.015	0.017	19.322	-0.072	-0.072	0.000	0.000	0.000	0.000
44	V	50	GLU	-1	-0.773	-0.890	21.083	-0.389	-0.389	0.000	0.000	0.000	0.000
45	V	51	TRP	0	-0.025	-0.020	12.032	-0.088	-0.088	0.000	0.000	0.000	0.000
46	V	52	LYS	1	0.774	0.889	12.839	1.568	1.568	0.000	0.000	0.000	0.000
47	V	53	THR	0	-0.046	-0.031	17.384	-0.068	-0.068	0.000	0.000	0.000	0.000
48	V	54	GLN	0	-0.006	0.007	17.263	0.016	0.016	0.000	0.000	0.000	0.000
49	V	55	MET	0	0.061	0.023	16.057	-0.157	-0.157	0.000	0.000	0.000	0.000
50	V	56	GLU	-1	-0.753	-0.891	10.865	-1.834	-1.834	0.000	0.000	0.000	0.000
51	V	57	GLU	-1	-0.867	-0.926	10.729	-0.632	-0.632	0.000	0.000	0.000	0.000
52	V	58	THR	0	0.044	0.019	11.812	0.165	0.165	0.000	0.000	0.000	0.000
53	V	59	LYS	1	0.814	0.923	12.221	1.246	1.246	0.000	0.000	0.000	0.000
54	V	60	ALA	0	0.023	0.001	8.145	0.036	0.036	0.000	0.000	0.000	0.000
55	V	61	GLN	0	-0.025	-0.023	9.867	0.531	0.531	0.000	0.000	0.000	0.000
56	V	62	ASP	-1	-0.817	-0.895	12.682	-0.144	-0.144	0.000	0.000	0.000	0.000
57	V	63	ILE	0	-0.083	-0.039	9.634	0.104	0.104	0.000	0.000	0.000	0.000
58	V	64	LEU	0	0.020	0.021	9.687	0.212	0.212	0.000	0.000	0.000	0.000
59	V	65	GLY	0	0.065	0.051	11.569	0.092	0.092	0.000	0.000	0.000	0.000
60	V	66	ALA	0	0.021	0.011	14.597	0.027	0.027	0.000	0.000	0.000	0.000
61	V	67	VAL	0	-0.030	-0.035	9.394	0.000	0.000	0.000	0.000	0.000	0.000
62	V	68	THR	0	-0.008	-0.018	12.776	0.138	0.138	0.000	0.000	0.000	0.000
63	V	69	LEU	0	0.010	0.009	14.639	-0.024	-0.024	0.000	0.000	0.000	0.000
64	V	70	LEU	0	-0.034	-0.005	13.048	-0.033	-0.033	0.000	0.000	0.000	0.000
65	V	71	LEU	0	-0.042	-0.017	12.721	-0.010	-0.010	0.000	0.000	0.000	0.000
66	V	72	GLU	-1	-0.885	-0.950	15.719	0.474	0.474	0.000	0.000	0.000	0.000
67	V	73	GLY	0	0.062	0.027	19.181	-0.045	-0.045	0.000	0.000	0.000	0.000
68	V	74	VAL	0	-0.044	-0.039	16.525	-0.038	-0.038	0.000	0.000	0.000	0.000
69	V	75	MET	0	-0.054	-0.031	18.528	0.003	0.003	0.000	0.000	0.000	0.000
70	V	76	ALA	0	0.043	0.023	21.048	-0.035	-0.035	0.000	0.000	0.000	0.000
71	V	77	ALA	0	-0.015	0.001	22.783	-0.041	-0.041	0.000	0.000	0.000	0.000
72	V	78	ARG	1	0.827	0.900	21.221	-0.580	-0.580	0.000	0.000	0.000	0.000
73	V	79	GLY	0	0.001	0.005	24.320	-0.002	-0.002	0.000	0.000	0.000	0.000
74	V	80	GLN	0	-0.010	-0.001	26.461	-0.045	-0.045	0.000	0.000	0.000	0.000
75	V	81	LEU	0	-0.053	-0.019	26.329	-0.025	-0.025	0.000	0.000	0.000	0.000
76	V	82	GLY	0	0.068	0.038	28.733	0.020	0.020	0.000	0.000	0.000	0.000
77	V	83	PRO	0	0.009	-0.016	28.801	0.013	0.013	0.000	0.000	0.000	0.000
78	V	84	THR	0	-0.015	0.010	28.792	0.003	0.003	0.000	0.000	0.000	0.000
79	V	86	LEU	0	0.066	0.032	24.845	0.031	0.031	0.000	0.000	0.000	0.000
80	V	87	SER	0	0.060	0.028	24.285	0.044	0.044	0.000	0.000	0.000	0.000
81	V	88	SER	0	-0.004	0.008	22.983	0.066	0.066	0.000	0.000	0.000	0.000
82	V	89	LEU	0	0.004	0.012	20.928	0.065	0.065	0.000	0.000	0.000	0.000
83	V	90	LEU	0	-0.003	-0.005	19.634	0.056	0.056	0.000	0.000	0.000	0.000
84	V	91	GLY	0	-0.003	-0.010	18.794	0.008	0.008	0.000	0.000	0.000	0.000
85	V	92	GLN	0	0.009	0.007	16.773	0.084	0.084	0.000	0.000	0.000	0.000
86	V	93	LEU	0	0.004	0.012	14.740	0.114	0.114	0.000	0.000	0.000	0.000
87	V	94	SER	0	0.054	0.009	13.799	0.063	0.063	0.000	0.000	0.000	0.000
88	V	95	GLY	0	-0.004	0.009	12.651	0.144	0.144	0.000	0.000	0.000	0.000
89	V	96	GLN	0	-0.003	-0.007	9.944	0.258	0.258	0.000	0.000	0.000	0.000
90	V	97	VAL	0	0.026	0.010	8.729	0.200	0.200	0.000	0.000	0.000	0.000
91	V	98	ARG	1	0.960	0.980	9.112	-1.017	-1.017	0.000	0.000	0.000	0.000
92	V	99	LEU	0	-0.003	0.007	5.447	0.455	0.455	0.000	0.000	0.000	0.000
93	V	100	LEU	0	-0.032	-0.003	4.558	0.464	0.566	-0.001	-0.008	-0.092	0.000
94	V	101	LEU	0	0.031	0.013	5.576	0.705	0.705	0.000	0.000	0.000	0.000
95	V	102	GLY	0	-0.016	-0.001	6.428	0.074	0.074	0.000	0.000	0.000	0.000
96	V	103	ALA	0	0.001	0.001	1.821	-2.259	-2.118	5.784	-2.679	-3.246	0.006
97	V	104	LEU	0	-0.001	-0.002	3.561	0.770	1.337	0.021	-0.067	-0.522	0.000
98	V	105	GLN	0	0.031	0.005	5.888	-1.346	-1.346	0.000	0.000	0.000	0.000
99	V	106	SER	0	-0.024	-0.008	4.812	-0.980	-0.807	-0.001	-0.003	-0.170	0.000
100	V	107	LEU	0	-0.096	-0.038	3.296	-2.151	-1.890	0.003	0.370	-0.634	0.002
101	V	108	LEU	0	-0.003	-0.012	5.490	-1.336	-1.333	-0.002	0.000	-0.002	0.000
102	V	109	GLY	0	0.005	0.025	8.765	-0.361	-0.361	0.000	0.000	0.000	0.000
103	V	110	THR	0	-0.027	-0.018	10.798	-0.187	-0.187	0.000	0.000	0.000	0.000
104	V	111	GLN	0	-0.057	-0.031	11.402	0.162	0.162	0.000	0.000	0.000	0.000
105	V	112	LEU	0	0.022	0.005	12.909	-0.173	-0.173	0.000	0.000	0.000	0.000
106	V	113	PRO	0	0.007	0.000	15.671	0.078	0.078	0.000	0.000	0.000	0.000
107	V	114	PRO	0	0.016	0.012	17.668	0.004	0.004	0.000	0.000	0.000	0.000
108	V	115	GLN	0	-0.039	-0.021	18.384	-0.092	-0.092	0.000	0.000	0.000	0.000
109	V	116	GLY	0	0.056	0.030	18.733	0.018	0.018	0.000	0.000	0.000	0.000
110	V	117	ARG	1	0.763	0.864	20.578	0.203	0.203	0.000	0.000	0.000	0.000
111	V	118	THR	0	-0.010	-0.008	21.562	0.014	0.014	0.000	0.000	0.000	0.000
112	V	119	THR	0	-0.012	-0.017	23.714	-0.032	-0.032	0.000	0.000	0.000	0.000
113	V	120	ALA	0	0.013	0.010	24.937	0.033	0.033	0.000	0.000	0.000	0.000
114	V	121	HIS	0	0.003	0.012	24.817	-0.027	-0.027	0.000	0.000	0.000	0.000
115	V	122	LYS	1	0.904	0.927	27.549	-0.146	-0.146	0.000	0.000	0.000	0.000
116	V	123	ASP	-1	-0.781	-0.869	26.681	0.171	0.171	0.000	0.000	0.000	0.000
117	V	124	PRO	0	0.053	0.018	24.695	0.013	0.013	0.000	0.000	0.000	0.000
118	V	125	ASN	0	-0.010	-0.009	23.017	0.033	0.033	0.000	0.000	0.000	0.000
119	V	126	ALA	0	0.035	0.012	22.189	0.007	0.007	0.000	0.000	0.000	0.000
120	V	127	ILE	0	0.020	0.027	19.409	-0.001	-0.001	0.000	0.000	0.000	0.000
121	V	128	PHE	0	0.010	0.000	18.077	0.059	0.059	0.000	0.000	0.000	0.000
122	V	129	LEU	0	-0.031	-0.002	17.704	0.001	0.001	0.000	0.000	0.000	0.000
123	V	130	SER	0	0.020	-0.012	18.231	-0.020	-0.020	0.000	0.000	0.000	0.000
124	V	131	PHE	0	0.010	0.005	10.067	-0.022	-0.022	0.000	0.000	0.000	0.000
125	V	132	GLN	0	-0.028	-0.029	13.662	-0.074	-0.074	0.000	0.000	0.000	0.000
126	V	133	HIS	0	-0.022	0.000	14.933	-0.065	-0.065	0.000	0.000	0.000	0.000
127	V	134	LEU	0	0.057	0.026	12.669	-0.125	-0.125	0.000	0.000	0.000	0.000
128	V	135	LEU	0	-0.035	-0.009	8.760	-0.165	-0.165	0.000	0.000	0.000	0.000
129	V	136	ARG	1	0.858	0.906	11.734	-0.104	-0.104	0.000	0.000	0.000	0.000
130	V	137	GLY	0	0.025	0.018	14.789	-0.136	-0.136	0.000	0.000	0.000	0.000
131	V	138	LYS	1	0.932	0.973	13.049	0.143	0.143	0.000	0.000	0.000	0.000
132	V	139	VAL	0	0.057	0.024	7.408	-0.222	-0.222	0.000	0.000	0.000	0.000
133	V	140	ARG	1	0.981	1.000	8.796	0.494	0.494	0.000	0.000	0.000	0.000
134	V	141	PHE	0	-0.042	-0.035	10.829	-0.352	-0.352	0.000	0.000	0.000	0.000
135	V	142	LEU	0	-0.029	-0.001	6.480	0.148	0.148	0.000	0.000	0.000	0.000
136	V	143	MET	0	-0.036	-0.013	4.250	-1.011	-0.873	-0.002	-0.006	-0.130	0.000
137	V	144	LEU	0	-0.037	-0.015	7.572	-0.249	-0.249	0.000	0.000	0.000	0.000
138	V	145	VAL	0	-0.020	-0.001	9.125	0.233	0.233	0.000	0.000	0.000	0.000
139	V	146	GLY	0	0.010	0.023	9.228	0.161	0.161	0.000	0.000	0.000	0.000
140	V	147	GLY	0	0.008	-0.005	6.030	-1.442	-1.442	0.000	0.000	0.000	0.000
141	V	148	SER	0	0.022	0.015	5.801	0.249	0.249	0.000	0.000	0.000	0.000
142	V	149	THR	0	-0.064	-0.032	3.515	-4.294	-0.223	0.014	-2.020	-2.065	-0.003

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