FMO DATABASE

FMODB ID: 22KKR

Calculation Name: 4D3C-A-Xray321

Preferred Name: Hepatocyte growth factor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4D3C

Chain ID: A

ChEMBL ID: CHEMBL5479

UniProt ID: P14210

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1322564.426329
FMO2-HF: Nuclear repulsion	1262229.989675
FMO2-HF: Total energy	-60334.436654
FMO2-MP2: Total energy	-60502.975967

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:36:ACE )

Summations of interaction energy for fragment #1(A:36: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.
2.441	3.174	-0.005	-0.34	-0.388	0

Interaction energy analysis for fragmet #1(A:36:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.001

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	A	38	THR	0	0.091	0.009	3.875	1.043	1.776	-0.005	-0.340	-0.388
4	A	39	ILE	0	-0.031	-0.020	7.007	0.329	0.329	0.000	0.000	0.000
5	A	40	HIS	0	0.010	0.005	6.432	0.266	0.266	0.000	0.000	0.000
6	A	41	GLU	-1	-0.965	-0.966	7.687	-0.085	-0.085	0.000	0.000	0.000
7	A	42	PHE	0	-0.032	-0.022	11.106	0.046	0.046	0.000	0.000	0.000
8	A	43	LYS	1	0.896	0.957	14.389	0.111	0.111	0.000	0.000	0.000
9	A	44	LYS	1	0.949	0.975	16.471	0.256	0.256	0.000	0.000	0.000
10	A	45	SER	0	0.039	0.023	18.405	0.017	0.017	0.000	0.000	0.000
11	A	46	ALA	0	-0.018	-0.025	21.782	-0.012	-0.012	0.000	0.000	0.000
12	A	47	LYS	1	0.958	0.989	22.629	0.123	0.123	0.000	0.000	0.000
13	A	48	THR	0	0.053	0.008	24.028	0.009	0.009	0.000	0.000	0.000
14	A	49	NME	0	-0.014	0.017	24.606	-0.011	-0.011	0.000	0.000	0.000
15	A	66	ACE	0	0.039	-0.015	14.287	0.011	0.011	0.000	0.000	0.000
16	A	67	ALA	0	0.012	-0.010	12.635	0.006	0.006	0.000	0.000	0.000
17	A	68	ASP	-1	-0.743	-0.891	7.506	-1.582	-1.582	0.000	0.000	0.000
18	A	69	GLN	0	-0.089	-0.040	8.778	-0.037	-0.037	0.000	0.000	0.000
19	A	96	CYS	0	-0.077	-0.052	10.630	0.070	0.070	0.000	0.000	0.000
20	A	71	ALA	0	0.108	0.075	9.686	0.085	0.085	0.000	0.000	0.000
21	A	72	ASN	0	0.045	0.098	5.813	-0.043	-0.043	0.000	0.000	0.000
22	A	73	ARG	1	0.880	0.925	8.414	0.626	0.626	0.000	0.000	0.000
23	A	84	CYS	0	-0.125	-0.033	11.702	0.093	0.093	0.000	0.000	0.000
24	A	75	THR	0	0.034	-0.030	8.367	0.035	0.035	0.000	0.000	0.000
25	A	76	ARG	1	0.923	0.960	6.168	0.169	0.169	0.000	0.000	0.000
26	A	77	ASN	0	0.053	0.037	11.321	0.036	0.036	0.000	0.000	0.000
27	A	78	LYS	1	0.952	0.986	12.786	0.226	0.226	0.000	0.000	0.000
28	A	79	GLY	0	-0.009	-0.011	14.871	-0.022	-0.022	0.000	0.000	0.000
29	A	80	LEU	0	-0.042	-0.012	16.246	-0.006	-0.006	0.000	0.000	0.000
30	A	81	PRO	0	0.020	0.013	19.590	0.012	0.012	0.000	0.000	0.000
31	A	82	PHE	0	0.030	0.010	20.236	0.008	0.008	0.000	0.000	0.000
32	A	83	THR	0	0.043	0.018	18.363	-0.005	-0.005	0.000	0.000	0.000
33	A	85	LYS	1	0.910	0.980	17.064	0.065	0.065	0.000	0.000	0.000
34	A	86	ALA	0	0.005	0.005	18.488	-0.008	-0.008	0.000	0.000	0.000
35	A	87	PHE	0	0.003	-0.006	13.614	-0.009	-0.009	0.000	0.000	0.000
36	A	88	VAL	0	0.035	0.037	18.631	0.000	0.000	0.000	0.000	0.000
37	A	89	PHE	0	-0.012	-0.002	16.483	-0.019	-0.019	0.000	0.000	0.000
38	A	90	ASH	0	0.058	0.020	18.514	0.011	0.011	0.000	0.000	0.000
39	A	91	LYS	1	0.840	0.948	18.695	0.277	0.277	0.000	0.000	0.000
40	A	92	ALA	0	0.065	0.046	23.653	0.010	0.010	0.000	0.000	0.000
41	A	93	ARG	1	0.932	0.946	23.730	0.136	0.136	0.000	0.000	0.000
42	A	94	LYS	1	0.977	1.003	23.236	0.140	0.140	0.000	0.000	0.000
43	A	95	GLN	0	0.050	0.028	17.118	-0.047	-0.047	0.000	0.000	0.000
44	A	97	LEU	0	-0.025	-0.005	18.406	0.020	0.020	0.000	0.000	0.000
45	A	98	TRP	0	0.001	-0.016	14.406	0.012	0.012	0.000	0.000	0.000
46	A	99	PHE	0	0.047	0.018	19.603	0.015	0.015	0.000	0.000	0.000
47	A	100	PRO	0	0.002	0.036	20.679	-0.009	-0.009	0.000	0.000	0.000
48	A	101	PHE	0	0.003	-0.040	22.945	0.013	0.013	0.000	0.000	0.000
49	A	102	ASN	0	0.060	0.032	22.247	-0.006	-0.006	0.000	0.000	0.000
50	A	103	SER	0	-0.033	-0.003	24.041	0.012	0.012	0.000	0.000	0.000
51	A	104	MET	0	-0.046	-0.019	24.670	0.008	0.008	0.000	0.000	0.000
52	A	105	SER	0	-0.105	-0.055	27.699	0.007	0.007	0.000	0.000	0.000
53	A	106	NME	0	0.053	0.033	29.483	-0.001	-0.001	0.000	0.000	0.000
54	A	116	ACE	0	0.026	-0.020	23.584	0.001	0.001	0.000	0.000	0.000
55	A	117	ASH	0	-0.114	-0.048	19.216	0.008	0.008	0.000	0.000	0.000
56	A	118	LEU	0	0.040	0.024	20.219	-0.019	-0.019	0.000	0.000	0.000
57	A	119	TYR	0	0.011	0.010	15.089	-0.013	-0.013	0.000	0.000	0.000
58	A	120	GLU	-1	-0.847	-0.935	17.819	-0.134	-0.134	0.000	0.000	0.000
59	A	121	ASN	0	0.061	0.023	14.268	0.001	0.001	0.000	0.000	0.000
60	A	122	LYS	1	0.968	0.971	14.845	0.116	0.116	0.000	0.000	0.000
61	A	123	ASP	-1	-0.855	-0.903	15.401	-0.033	-0.033	0.000	0.000	0.000
62	A	124	TYR	0	-0.087	-0.056	18.229	0.013	0.013	0.000	0.000	0.000
63	A	125	ILE	0	-0.056	-0.033	20.347	-0.004	-0.004	0.000	0.000	0.000
64	A	126	ARG	1	0.894	0.943	22.229	0.032	0.032	0.000	0.000	0.000
65	A	127	ASN	0	-0.015	0.003	21.005	-0.002	-0.002	0.000	0.000	0.000
66	A	206	CYS	0	0.005	0.003	24.272	0.007	0.007	0.000	0.000	0.000
67	A	129	ILE	0	-0.038	-0.026	27.901	-0.007	-0.007	0.000	0.000	0.000
68	A	130	ILE	0	0.035	-0.011	31.389	0.003	0.003	0.000	0.000	0.000
69	A	131	GLY	0	0.021	0.011	35.028	0.000	0.000	0.000	0.000	0.000
70	A	132	LYS	1	0.986	1.013	36.912	0.015	0.015	0.000	0.000	0.000
71	A	133	GLY	0	0.025	0.015	33.663	-0.001	-0.001	0.000	0.000	0.000
72	A	134	GLY	0	0.025	0.009	33.568	-0.002	-0.002	0.000	0.000	0.000
73	A	135	SER	0	-0.063	-0.053	32.470	-0.003	-0.003	0.000	0.000	0.000
74	A	136	TYR	0	0.077	0.049	24.736	-0.007	-0.007	0.000	0.000	0.000
75	A	137	LYS	1	0.908	0.956	25.889	0.054	0.054	0.000	0.000	0.000
76	A	138	GLY	0	0.053	0.036	23.038	-0.010	-0.010	0.000	0.000	0.000
77	A	139	THR	0	0.024	-0.012	18.893	-0.004	-0.004	0.000	0.000	0.000
78	A	140	VAL	0	-0.014	0.010	21.052	-0.003	-0.003	0.000	0.000	0.000
79	A	141	SER	0	0.021	0.009	21.170	-0.002	-0.002	0.000	0.000	0.000
80	A	142	ILE	0	-0.012	-0.007	21.872	0.001	0.001	0.000	0.000	0.000
81	A	143	THR	0	0.024	0.020	25.492	0.000	0.000	0.000	0.000	0.000
82	A	144	LYS	1	1.001	1.005	28.442	-0.001	-0.001	0.000	0.000	0.000
83	A	145	SER	0	-0.016	0.005	30.816	0.004	0.004	0.000	0.000	0.000
84	A	146	GLY	0	0.002	0.000	27.163	0.003	0.003	0.000	0.000	0.000
85	A	147	ILE	0	-0.037	-0.026	26.893	-0.001	-0.001	0.000	0.000	0.000
86	A	148	LYS	1	0.968	0.987	21.763	0.048	0.048	0.000	0.000	0.000
87	A	189	CYS	0	-0.025	-0.026	25.910	-0.004	-0.004	0.000	0.000	0.000
88	A	150	GLN	0	0.009	-0.001	26.554	-0.001	-0.001	0.000	0.000	0.000
89	A	151	PRO	0	-0.052	-0.044	26.304	-0.001	-0.001	0.000	0.000	0.000
90	A	152	TRP	0	0.015	0.010	28.110	0.006	0.006	0.000	0.000	0.000
91	A	153	SER	0	-0.055	-0.032	28.570	0.003	0.003	0.000	0.000	0.000
92	A	154	SER	0	-0.038	-0.008	30.182	0.002	0.002	0.000	0.000	0.000
93	A	155	MET	0	-0.007	0.004	32.000	0.001	0.001	0.000	0.000	0.000
94	A	156	ILE	0	0.015	0.040	33.165	0.004	0.004	0.000	0.000	0.000
95	A	157	PRO	0	0.009	-0.022	31.913	-0.004	-0.004	0.000	0.000	0.000
96	A	158	HIS	1	0.816	0.931	33.983	0.025	0.025	0.000	0.000	0.000
97	A	159	GLU	-1	-0.821	-0.899	36.026	-0.029	-0.029	0.000	0.000	0.000
98	A	160	HIS	0	0.000	-0.015	34.197	0.005	0.005	0.000	0.000	0.000
99	A	161	SER	0	0.031	0.024	38.865	-0.002	-0.002	0.000	0.000	0.000
100	A	162	PHE	0	-0.013	-0.027	35.469	0.001	0.001	0.000	0.000	0.000
101	A	163	LEU	0	0.067	0.037	34.976	-0.004	-0.004	0.000	0.000	0.000
102	A	164	PRO	0	0.073	0.015	31.924	0.002	0.002	0.000	0.000	0.000
103	A	165	SER	0	-0.058	-0.023	34.414	0.000	0.000	0.000	0.000	0.000
104	A	166	SER	0	-0.030	-0.010	37.548	0.002	0.002	0.000	0.000	0.000
105	A	167	TYR	0	-0.015	0.015	35.765	0.004	0.004	0.000	0.000	0.000
106	A	168	ARG	1	1.021	1.015	34.774	0.048	0.048	0.000	0.000	0.000
107	A	169	GLY	0	0.007	0.004	32.548	0.003	0.003	0.000	0.000	0.000
108	A	170	LYS	1	0.910	0.949	32.327	0.037	0.037	0.000	0.000	0.000
109	A	171	ASP	-1	-0.883	-0.918	26.576	-0.086	-0.086	0.000	0.000	0.000
110	A	172	LEU	0	0.029	0.041	29.070	0.002	0.002	0.000	0.000	0.000
111	A	173	GLN	0	0.011	-0.010	25.306	0.003	0.003	0.000	0.000	0.000
112	A	174	GLU	-1	-0.924	-0.964	21.878	-0.121	-0.121	0.000	0.000	0.000
113	A	175	ASN	0	0.002	0.007	22.909	-0.001	-0.001	0.000	0.000	0.000
114	A	176	TYR	0	-0.006	-0.004	20.672	0.002	0.002	0.000	0.000	0.000
115	A	201	CYS	0	-0.015	-0.011	25.460	0.004	0.004	0.000	0.000	0.000
116	A	178	ARG	1	0.709	0.824	25.292	0.058	0.058	0.000	0.000	0.000
117	A	179	ASN	0	0.043	0.049	30.938	0.003	0.003	0.000	0.000	0.000
118	A	180	PRO	0	-0.022	-0.021	34.197	0.000	0.000	0.000	0.000	0.000
119	A	181	ARG	1	0.907	0.930	36.202	0.027	0.027	0.000	0.000	0.000
120	A	182	GLY	0	-0.027	0.007	38.121	0.002	0.002	0.000	0.000	0.000
121	A	183	GLU	-1	-0.936	-0.979	38.526	-0.017	-0.017	0.000	0.000	0.000
122	A	184	GLU	-1	-0.868	-0.960	39.117	-0.011	-0.011	0.000	0.000	0.000
123	A	185	GLY	0	0.001	0.018	38.441	0.001	0.001	0.000	0.000	0.000
124	A	186	GLY	0	0.038	0.032	35.110	0.001	0.001	0.000	0.000	0.000
125	A	187	PRO	0	-0.120	-0.079	30.709	-0.002	-0.002	0.000	0.000	0.000
126	A	188	TRP	0	0.066	0.045	32.309	0.002	0.002	0.000	0.000	0.000
127	A	190	PHE	0	0.014	0.003	31.362	0.005	0.005	0.000	0.000	0.000
128	A	191	THR	0	-0.002	-0.025	30.516	-0.003	-0.003	0.000	0.000	0.000
129	A	192	SER	0	-0.048	-0.036	28.103	-0.001	-0.001	0.000	0.000	0.000
130	A	193	ASN	0	0.067	0.022	30.234	0.000	0.000	0.000	0.000	0.000
131	A	194	PRO	0	0.011	-0.017	32.948	-0.001	-0.001	0.000	0.000	0.000
132	A	195	GLU	-1	-0.926	-0.951	36.152	-0.005	-0.005	0.000	0.000	0.000
133	A	196	VAL	0	0.022	0.031	35.011	0.000	0.000	0.000	0.000	0.000
134	A	197	ARG	1	0.881	0.962	35.542	0.021	0.021	0.000	0.000	0.000
135	A	198	TYR	0	-0.022	-0.030	34.795	-0.003	-0.003	0.000	0.000	0.000
136	A	199	GLU	-1	-0.807	-0.914	32.987	-0.001	-0.001	0.000	0.000	0.000
137	A	200	VAL	0	0.010	0.003	32.993	-0.004	-0.004	0.000	0.000	0.000
138	A	202	ASP	-1	-0.921	-0.948	29.104	0.006	0.006	0.000	0.000	0.000
139	A	203	ILE	0	-0.069	-0.040	26.355	-0.002	-0.002	0.000	0.000	0.000
140	A	204	PRO	0	0.092	0.060	27.007	-0.001	-0.001	0.000	0.000	0.000
141	A	205	GLN	0	-0.017	-0.012	29.434	-0.007	-0.007	0.000	0.000	0.000
142	A	207	SER	0	0.009	0.004	31.299	0.002	0.002	0.000	0.000	0.000
143	A	208	GLU	-1	-0.928	-0.955	31.941	0.006	0.006	0.000	0.000	0.000
144	A	209	NME	0	-0.011	0.007	30.696	0.003	0.003	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:36:ACE )