Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: R8K58

Calculation Name: 1KF9-C-Xray372

Preferred Name: Growth hormone receptor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1KF9

Chain ID: C

ChEMBL ID: CHEMBL1976

UniProt ID: P10912

Base Structure: X-ray

Registration Date: 2023-09-23

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1938873.38363
FMO2-HF: Nuclear repulsion 1862813.860918
FMO2-HF: Total energy -76059.522712
FMO2-MP2: Total energy -76279.15216


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(C:533:PRO)


Summations of interaction energy for fragment #1(C:533:PRO)
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.
-5.572-0.0594.073-3.246-6.337-0.008
Interaction energy analysis for fragmet #1(C:533:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / 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   
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].
3C535PHE00.0550.0393.694-0.7381.592-0.040-1.065-1.2250.000
4C536THR0-0.094-0.0586.225-0.663-0.6630.0000.0000.0000.000
5C537LYS10.8840.9348.364-0.357-0.3570.0000.0000.0000.000
6C538CYS0-0.092-0.02710.9620.0420.0420.0000.0000.0000.000
7C539ARG10.7700.84114.000-0.236-0.2360.0000.0000.0000.000
8C540SER0-0.021-0.03217.5580.0150.0150.0000.0000.0000.000
9C541PRO0-0.028-0.01220.777-0.018-0.0180.0000.0000.0000.000
10C542GLU-1-0.691-0.85623.1830.1660.1660.0000.0000.0000.000
11C543ARG10.8110.90224.730-0.121-0.1210.0000.0000.0000.000
12C544GLU-1-0.927-0.94525.7130.1200.1200.0000.0000.0000.000
13C545THR0-0.106-0.08622.3100.0160.0160.0000.0000.0000.000
14C546PHE00.0190.01015.972-0.007-0.0070.0000.0000.0000.000
15C547SER00.0230.02715.0540.0190.0190.0000.0000.0000.000
16C549HIS00.1060.0679.4090.0770.0770.0000.0000.0000.000
17C550TRP00.006-0.0154.040-0.0030.3390.001-0.054-0.2890.000
18C551THR0-0.0060.0192.290-2.790-1.7722.586-1.301-2.302-0.013
19C564ILE0-0.0060.0052.565-1.095-0.3791.005-0.412-1.3080.001
20C565GLN0-0.030-0.0366.0920.0290.0290.0000.0000.0000.000
21C566LEU0-0.0190.0038.0010.4440.4440.0000.0000.0000.000
22C567PHE00.0200.00710.400-0.216-0.2160.0000.0000.0000.000
23C568TYR0-0.027-0.02612.6430.0410.0410.0000.0000.0000.000
24C569THR00.0180.00215.357-0.056-0.0560.0000.0000.0000.000
25C570ARG10.9440.96718.409-0.213-0.2130.0000.0000.0000.000
26C571ARG10.9690.96218.942-0.197-0.1970.0000.0000.0000.000
27C572ASN00.0350.02424.304-0.010-0.0100.0000.0000.0000.000
28C573THR0-0.010-0.00526.927-0.004-0.0040.0000.0000.0000.000
29C574GLN00.005-0.01125.0440.0130.0130.0000.0000.0000.000
30C575GLU-1-0.819-0.89828.5110.0790.0790.0000.0000.0000.000
31C576TRP0-0.034-0.03927.5670.0090.0090.0000.0000.0000.000
32C577THR0-0.104-0.04822.6680.0060.0060.0000.0000.0000.000
33C578GLN00.0020.00618.6760.0230.0230.0000.0000.0000.000
34C579GLU-1-0.832-0.88820.7460.2240.2240.0000.0000.0000.000
35C580TRP0-0.022-0.01213.6970.0440.0440.0000.0000.0000.000
36C581LYS10.8370.90617.453-0.279-0.2790.0000.0000.0000.000
37C582GLU-1-0.765-0.84113.5810.6060.6060.0000.0000.0000.000
38C583CYS0-0.118-0.01311.125-0.133-0.1330.0000.0000.0000.000
39C584PRO0-0.004-0.00515.297-0.027-0.0270.0000.0000.0000.000
40C585ASP-1-0.809-0.88017.1200.2730.2730.0000.0000.0000.000
41C586TYR0-0.007-0.04810.7330.1410.1410.0000.0000.0000.000
42C587VAL00.0200.03514.1680.0150.0150.0000.0000.0000.000
43C588SER0-0.015-0.03916.904-0.018-0.0180.0000.0000.0000.000
44C589ALA0-0.064-0.02215.424-0.031-0.0310.0000.0000.0000.000
45C590GLY0-0.0340.00715.1060.0190.0190.0000.0000.0000.000
46C591GLU-1-0.843-0.94011.0680.4950.4950.0000.0000.0000.000
47C592ASN0-0.134-0.0625.9450.2110.2110.0000.0000.0000.000
48C593SER00.022-0.0368.8470.1370.1370.0000.0000.0000.000
49C595TYR00.031-0.00213.304-0.036-0.0360.0000.0000.0000.000
50C596PHE0-0.018-0.01814.6290.0000.0000.0000.0000.0000.000
51C597ASN00.0980.06519.543-0.019-0.0190.0000.0000.0000.000
52C598SER00.0870.02723.2010.0100.0100.0000.0000.0000.000
53C599SER0-0.085-0.04524.967-0.007-0.0070.0000.0000.0000.000
54C600PHE00.0060.00221.351-0.001-0.0010.0000.0000.0000.000
55C601THR0-0.0630.00922.2890.0270.0270.0000.0000.0000.000
56C602SER00.0120.01723.838-0.020-0.0200.0000.0000.0000.000
57C603ILE0-0.001-0.01024.7960.0140.0140.0000.0000.0000.000
58C604TRP0-0.0010.00626.796-0.001-0.0010.0000.0000.0000.000
59C605ILE0-0.029-0.00324.252-0.003-0.0030.0000.0000.0000.000
60C606PRO00.003-0.00321.0810.0150.0150.0000.0000.0000.000
61C607TYR0-0.038-0.05417.367-0.001-0.0010.0000.0000.0000.000
62C608CYS0-0.169-0.08211.7850.0180.0180.0000.0000.0000.000
63C609ILE0-0.001-0.00510.679-0.003-0.0030.0000.0000.0000.000
64C610LYS10.8970.9399.036-0.420-0.4200.0000.0000.0000.000
65C611LEU0-0.016-0.0063.146-1.232-0.1250.521-0.414-1.2130.004
66C621LYS10.9761.00710.522-0.338-0.3380.0000.0000.0000.000
67C623PHE00.0140.00414.028-0.024-0.0240.0000.0000.0000.000
68C624SER00.047-0.00418.139-0.002-0.0020.0000.0000.0000.000
69C625VAL00.0300.01120.972-0.001-0.0010.0000.0000.0000.000
70C626ASP-1-0.700-0.84121.9840.1200.1200.0000.0000.0000.000
71C627GLU-1-0.901-0.91719.8710.1630.1630.0000.0000.0000.000
72C628ILE0-0.113-0.03916.682-0.003-0.0030.0000.0000.0000.000
73C629VAL00.0440.04419.5230.0180.0180.0000.0000.0000.000
74C630GLN0-0.005-0.00918.3290.0010.0010.0000.0000.0000.000
75C631PRO00.0490.06322.6020.0150.0150.0000.0000.0000.000
76C632ASP-1-0.800-0.87323.3690.1340.1340.0000.0000.0000.000
77C633PRO00.0210.00625.058-0.004-0.0040.0000.0000.0000.000
78C634PRO0-0.066-0.01827.9820.0020.0020.0000.0000.0000.000
79C635ILE00.0240.00031.412-0.002-0.0020.0000.0000.0000.000
80C636ALA00.007-0.01033.670-0.002-0.0020.0000.0000.0000.000
81C637LEU00.0230.02834.029-0.002-0.0020.0000.0000.0000.000
82C638ASN0-0.016-0.01637.865-0.003-0.0030.0000.0000.0000.000
83C639TRP00.0330.01641.3150.0010.0010.0000.0000.0000.000
84C640THR0-0.0190.00044.2120.0010.0010.0000.0000.0000.000
85C641LEU00.0350.03047.9180.0000.0000.0000.0000.0000.000
86C642LEU0-0.0450.00549.2100.0010.0010.0000.0000.0000.000
87C643ASN0-0.007-0.03352.2080.0000.0000.0000.0000.0000.000
88C644VAL00.0080.00353.7550.0000.0000.0000.0000.0000.000
89C645SER0-0.0230.00455.3740.0000.0000.0000.0000.0000.000
90C646LEU00.0970.02957.3140.0000.0000.0000.0000.0000.000
91C647THR0-0.079-0.03258.8850.0000.0000.0000.0000.0000.000
92C648GLY00.0220.00757.540-0.001-0.0010.0000.0000.0000.000
93C649ILE0-0.011-0.00853.8020.0000.0000.0000.0000.0000.000
94C650HIS00.0220.02950.792-0.001-0.0010.0000.0000.0000.000
95C651ALA00.0270.01750.3030.0000.0000.0000.0000.0000.000
96C652ASP-1-0.842-0.89449.1440.0100.0100.0000.0000.0000.000
97C653ILE00.014-0.00943.7640.0000.0000.0000.0000.0000.000
98C654GLN00.0150.00245.4110.0020.0020.0000.0000.0000.000
99C655VAL0-0.008-0.00739.3030.0000.0000.0000.0000.0000.000
100C656ARG10.8910.92641.648-0.025-0.0250.0000.0000.0000.000
101C657TRP0-0.038-0.02335.523-0.002-0.0020.0000.0000.0000.000
102C658GLU-1-0.894-0.95036.4350.0480.0480.0000.0000.0000.000
103C659ALA0-0.002-0.00233.8910.0010.0010.0000.0000.0000.000
104C660PRO00.0120.00728.912-0.001-0.0010.0000.0000.0000.000
105C661ARG11.0131.01030.953-0.062-0.0620.0000.0000.0000.000
106C662ASN0-0.052-0.02925.646-0.010-0.0100.0000.0000.0000.000
107C663ALA0-0.037-0.03029.8790.0040.0040.0000.0000.0000.000
108C664ASP-1-0.848-0.92231.2340.0870.0870.0000.0000.0000.000
109C665ILE00.0380.02233.801-0.001-0.0010.0000.0000.0000.000
110C666GLN0-0.053-0.04437.348-0.001-0.0010.0000.0000.0000.000
111C667LYS10.7500.87331.780-0.107-0.1070.0000.0000.0000.000
112C668GLY00.0560.05135.692-0.002-0.0020.0000.0000.0000.000
113C669TRP0-0.050-0.05329.996-0.004-0.0040.0000.0000.0000.000
114C670MET00.0230.04526.5620.0040.0040.0000.0000.0000.000
115C671VAL0-0.030-0.00531.587-0.006-0.0060.0000.0000.0000.000
116C672LEU0-0.004-0.01829.4490.0030.0030.0000.0000.0000.000
117C673GLU-1-0.823-0.89031.9730.0510.0510.0000.0000.0000.000
118C674TYR0-0.008-0.03332.3330.0060.0060.0000.0000.0000.000
119C675GLU-1-0.766-0.84931.4020.0240.0240.0000.0000.0000.000
120C676LEU00.0040.01232.9260.0010.0010.0000.0000.0000.000
121C677GLN0-0.004-0.02730.728-0.002-0.0020.0000.0000.0000.000
122C678TYR00.0350.00335.0660.0010.0010.0000.0000.0000.000
123C679LYS10.8090.91434.3120.0030.0030.0000.0000.0000.000
124C680GLU-1-0.760-0.86038.456-0.004-0.0040.0000.0000.0000.000
125C681VAL00.0570.01838.463-0.001-0.0010.0000.0000.0000.000
126C682ASN0-0.074-0.05637.884-0.003-0.0030.0000.0000.0000.000
127C683GLU-1-0.845-0.89238.437-0.004-0.0040.0000.0000.0000.000
128C684THR00.004-0.00933.815-0.001-0.0010.0000.0000.0000.000
129C685LYS10.8950.93430.4820.0200.0200.0000.0000.0000.000
130C686TRP00.0260.00431.5200.0020.0020.0000.0000.0000.000
131C687LYS10.8340.93535.103-0.002-0.0020.0000.0000.0000.000
132C688MET0-0.027-0.02232.6470.0020.0020.0000.0000.0000.000
133C689MET0-0.0060.00835.813-0.002-0.0020.0000.0000.0000.000
134C690ASP-1-0.899-0.94636.2850.0200.0200.0000.0000.0000.000
135C691PRO0-0.047-0.02533.9070.0010.0010.0000.0000.0000.000
136C692ILE00.0100.02636.0520.0000.0000.0000.0000.0000.000
137C693LEU00.028-0.00936.8300.0040.0040.0000.0000.0000.000
138C694THR0-0.061-0.02138.6510.0020.0020.0000.0000.0000.000
139C695THR00.0050.00037.4320.0010.0010.0000.0000.0000.000
140C696SER0-0.012-0.03339.546-0.001-0.0010.0000.0000.0000.000
141C697VAL0-0.0120.01239.9160.0000.0000.0000.0000.0000.000
142C698PRO0-0.0200.00142.9770.0000.0000.0000.0000.0000.000
143C699VAL00.0130.01941.6010.0000.0000.0000.0000.0000.000
144C700TYR00.016-0.01444.5970.0000.0000.0000.0000.0000.000
145C701SER0-0.042-0.02746.784-0.001-0.0010.0000.0000.0000.000
146C702LEU0-0.0080.01743.829-0.001-0.0010.0000.0000.0000.000
147C703LYS10.8750.90647.540-0.001-0.0010.0000.0000.0000.000
148C704VAL00.0370.00748.5390.0000.0000.0000.0000.0000.000
149C705ASP-1-0.925-0.95250.3680.0000.0000.0000.0000.0000.000
150C706LYS10.7510.86945.0390.0040.0040.0000.0000.0000.000
151C707GLU-1-0.861-0.92441.8460.0050.0050.0000.0000.0000.000
152C708TYR0-0.035-0.01941.021-0.002-0.0020.0000.0000.0000.000
153C709GLU-1-0.827-0.91334.8450.0030.0030.0000.0000.0000.000
154C710VAL0-0.026-0.03336.711-0.001-0.0010.0000.0000.0000.000
155C711ARG10.8690.96828.180-0.014-0.0140.0000.0000.0000.000
156C712VAL00.0100.00632.468-0.002-0.0020.0000.0000.0000.000
157C713ARG10.8070.90026.551-0.032-0.0320.0000.0000.0000.000
158C714SER00.0180.00028.275-0.001-0.0010.0000.0000.0000.000
159C715LYS10.8640.90427.005-0.061-0.0610.0000.0000.0000.000
160C716GLN00.0870.03427.436-0.008-0.0080.0000.0000.0000.000
161C717ARG10.9460.98229.405-0.066-0.0660.0000.0000.0000.000
162C718ASN0-0.080-0.05130.8590.0010.0010.0000.0000.0000.000
163C719SER0-0.033-0.02627.1340.0000.0000.0000.0000.0000.000
164C720GLY00.0590.05923.265-0.002-0.0020.0000.0000.0000.000
165C721ASN0-0.068-0.05020.620-0.003-0.0030.0000.0000.0000.000
166C722TYR0-0.037-0.02924.0670.0050.0050.0000.0000.0000.000
167C723GLY00.0070.01823.1120.0090.0090.0000.0000.0000.000
168C724GLU-1-0.927-0.97521.0880.0430.0430.0000.0000.0000.000
169C725PHE0-0.046-0.03824.269-0.001-0.0010.0000.0000.0000.000
170C726SER00.0230.02027.4650.0020.0020.0000.0000.0000.000
171C727GLU-1-0.937-0.96429.9610.0310.0310.0000.0000.0000.000
172C728VAL0-0.067-0.04531.3630.0000.0000.0000.0000.0000.000
173C729LEU0-0.0120.01433.6950.0000.0000.0000.0000.0000.000
174C730TYR00.0250.01234.927-0.001-0.0010.0000.0000.0000.000
175C731VAL0-0.051-0.03639.7270.0010.0010.0000.0000.0000.000
176C732THR00.0570.02543.058-0.001-0.0010.0000.0000.0000.000
177C733LEU0-0.040-0.00746.2540.0010.0010.0000.0000.0000.000
178C734PRO00.0140.01649.327-0.001-0.0010.0000.0000.0000.000