FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: GY9K1

Calculation Name: 4A9A-C-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4A9A

Chain ID: C

ChEMBL ID:

UniProt ID: P39729

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -595184.744802
FMO2-HF: Nuclear repulsion 553604.195612
FMO2-HF: Total energy -41580.54919
FMO2-MP2: Total energy -41703.443533


3D Structure Molmil
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:214:LEU)


Summations of interaction energy for fragment #1(C:214:LEU)
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.
-3.879-8.83114.055-5.4-3.701-0.05
Interaction energy analysis for fragmet #1(C:214:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.011
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].
4C215GLU-1-0.932-0.8811.771-5.451-11.53114.059-4.832-3.146-0.052
5C216LYS00.158-0.0733.716-1.018-0.119-0.005-0.546-0.3480.002
6C216LYS10.7331.0017.9121.3031.3030.0000.0000.0000.000
7C217GLN00.102-0.1126.0170.1990.1990.0000.0000.0000.000
8C217GLN0-0.0440.1353.9090.3940.6230.001-0.022-0.2070.000
9C218PRO0-0.029-0.0956.6970.3080.3080.0000.0000.0000.000
10C219LYS00.1030.03110.166-0.096-0.0960.0000.0000.0000.000
11C219LYS10.8541.05411.5370.7640.7640.0000.0000.0000.000
12C220ILE00.060-0.10612.5020.0170.0170.0000.0000.0000.000
13C220ILE0-0.0320.11212.231-0.003-0.0030.0000.0000.0000.000
14C221THR0-0.002-0.12214.562-0.012-0.0120.0000.0000.0000.000
15C221THR0-0.0440.06118.8180.0170.0170.0000.0000.0000.000
16C222LEU00.139-0.11217.316-0.028-0.0280.0000.0000.0000.000
17C222LEU0-0.1140.12119.2770.0010.0010.0000.0000.0000.000
18C223GLU00.015-0.14619.2510.0070.0070.0000.0000.0000.000
19C223GLU-1-0.845-0.78521.710-0.234-0.2340.0000.0000.0000.000
20C224GLU00.135-0.10917.5300.0310.0310.0000.0000.0000.000
21C224GLU-1-0.874-0.74216.618-0.407-0.4070.0000.0000.0000.000
22C225PHE00.137-0.07715.9350.0000.0000.0000.0000.0000.000
23C225PHE0-0.1470.05114.5070.0040.0040.0000.0000.0000.000
24C226ILE0-0.010-0.13316.8670.0080.0080.0000.0000.0000.000
25C226ILE0-0.0830.10520.5880.0030.0030.0000.0000.0000.000
26C227GLU00.054-0.12720.2520.0180.0180.0000.0000.0000.000
27C227GLU-1-1.016-0.83521.479-0.178-0.1780.0000.0000.0000.000
28C228THR0-0.037-0.12318.4410.0270.0270.0000.0000.0000.000
29C228THR0-0.0410.06717.820-0.014-0.0140.0000.0000.0000.000
30C229GLU00.065-0.11414.2730.0380.0380.0000.0000.0000.000
31C229GLU-1-0.988-0.84112.509-0.500-0.5000.0000.0000.0000.000
32C230ARG00.119-0.13714.293-0.004-0.0040.0000.0000.0000.000
33C230ARG10.8291.10116.7580.1490.1490.0000.0000.0000.000
34C231GLY0-0.057-0.12716.0890.0310.0310.0000.0000.0000.000
35C232LYS00.1120.00714.1020.0420.0420.0000.0000.0000.000
36C232LYS10.8331.06412.4490.3540.3540.0000.0000.0000.000
37C233LEU0-0.002-0.11413.6630.0320.0320.0000.0000.0000.000
38C233LEU0-0.0920.10110.9780.0030.0030.0000.0000.0000.000
39C234ASP00.176-0.09114.516-0.007-0.0070.0000.0000.0000.000
40C234ASP-1-0.916-0.80215.7990.0710.0710.0000.0000.0000.000
41C235LYS00.073-0.12916.5560.0150.0150.0000.0000.0000.000
42C235LYS10.8961.08319.4840.0470.0470.0000.0000.0000.000
43C236SER0-0.036-0.09718.930-0.003-0.0030.0000.0000.0000.000
44C236SER0-0.0390.07419.9530.0060.0060.0000.0000.0000.000
45C237LYS00.047-0.12315.8220.0130.0130.0000.0000.0000.000
46C237LYS10.8741.09115.170-0.167-0.1670.0000.0000.0000.000
47C238LEU00.040-0.08915.2850.0380.0380.0000.0000.0000.000
48C238LEU0-0.0910.10214.487-0.007-0.0070.0000.0000.0000.000
49C239THR00.056-0.11415.2990.0120.0120.0000.0000.0000.000
50C239THR0-0.0300.10414.7510.0140.0140.0000.0000.0000.000
51C240PRO0-0.030-0.09216.671-0.030-0.0300.0000.0000.0000.000
52C241ILE00.1340.02018.9870.0260.0260.0000.0000.0000.000
53C241ILE0-0.0570.13117.321-0.003-0.0030.0000.0000.0000.000
54C242THR00.054-0.08719.703-0.015-0.0150.0000.0000.0000.000
55C242THR0-0.0250.06421.9810.0030.0030.0000.0000.0000.000
56C243ILE00.129-0.08021.410-0.001-0.0010.0000.0000.0000.000
57C243ILE0-0.0280.13225.0660.0010.0010.0000.0000.0000.000
58C244ALA00.089-0.10622.392-0.003-0.0030.0000.0000.0000.000
59C244ALA0-0.0610.12822.8090.0010.0010.0000.0000.0000.000
60C245ASN00.090-0.11718.6350.0170.0170.0000.0000.0000.000
61C245ASN0-0.1480.07317.6930.0220.0220.0000.0000.0000.000
62C246PHE00.133-0.08517.2490.0170.0170.0000.0000.0000.000
63C246PHE0-0.0660.10217.826-0.004-0.0040.0000.0000.0000.000
64C247ALA00.093-0.10517.910-0.008-0.0080.0000.0000.0000.000
65C247ALA0-0.0640.12721.4460.0000.0000.0000.0000.0000.000
66C248GLN00.053-0.10317.456-0.006-0.0060.0000.0000.0000.000
67C248GLN0-0.0930.10214.392-0.020-0.0200.0000.0000.0000.000
68C249TRP00.130-0.10013.7620.0510.0510.0000.0000.0000.000
69C249TRP0-0.0980.10511.0530.0070.0070.0000.0000.0000.000
70C250LYS00.093-0.11914.021-0.012-0.0120.0000.0000.0000.000
71C250LYS10.8591.08717.5840.0510.0510.0000.0000.0000.000
72C251LYS00.063-0.09716.515-0.027-0.0270.0000.0000.0000.000
73C251LYS10.8601.07716.927-0.272-0.2720.0000.0000.0000.000
74C252ASP00.127-0.13912.667-0.026-0.0260.0000.0000.0000.000
75C252ASP-1-0.960-0.80011.7260.4370.4370.0000.0000.0000.000
76C253HIS00.094-0.09712.3370.0100.0100.0000.0000.0000.000
77C253HIS0-0.1330.07911.738-0.011-0.0110.0000.0000.0000.000
78C254VAL00.020-0.13313.373-0.044-0.0440.0000.0000.0000.000
79C254VAL0-0.0680.10617.604-0.004-0.0040.0000.0000.0000.000
80C255ILE00.103-0.09815.550-0.045-0.0450.0000.0000.0000.000
81C255ILE0-0.0580.12414.5330.0050.0050.0000.0000.0000.000
82C256ALA00.104-0.11611.3900.0340.0340.0000.0000.0000.000
83C256ALA0-0.0530.13510.827-0.011-0.0110.0000.0000.0000.000
84C257LYS00.018-0.12612.736-0.043-0.0430.0000.0000.0000.000
85C257LYS10.8891.07814.6250.1520.1520.0000.0000.0000.000
86C258ILE00.103-0.06715.291-0.032-0.0320.0000.0000.0000.000
87C258ILE0-0.0820.10617.7860.0030.0030.0000.0000.0000.000
88C259ASN00.055-0.09914.308-0.024-0.0240.0000.0000.0000.000
89C259ASN0-0.0880.07713.231-0.015-0.0150.0000.0000.0000.000
90C260ALA00.121-0.11514.3180.0160.0160.0000.0000.0000.000
91C260ALA0-0.0750.11513.313-0.017-0.0170.0000.0000.0000.000
92C261GLU00.074-0.12614.937-0.028-0.0280.0000.0000.0000.000
93C261GLU-1-0.922-0.78919.081-0.087-0.0870.0000.0000.0000.000
94C262LYS00.132-0.09018.411-0.012-0.0120.0000.0000.0000.000
95C262LYS10.8481.08917.941-0.086-0.0860.0000.0000.0000.000
96C263LYS00.085-0.07616.4240.0100.0100.0000.0000.0000.000
97C263LYS10.8221.03812.3120.1190.1190.0000.0000.0000.000
98C264LEU00.053-0.12017.886-0.003-0.0030.0000.0000.0000.000
99C264LEU0-0.0380.13617.639-0.005-0.0050.0000.0000.0000.000
100C265SER00.046-0.10119.894-0.008-0.0080.0000.0000.0000.000
101C265SER0-0.0350.05521.7990.0050.0050.0000.0000.0000.000
102C266SER0-0.007-0.07221.7500.0020.0020.0000.0000.0000.000
103C266SER0-0.0280.05721.4140.0020.0020.0000.0000.0000.000
104C267LYS00.001-0.09322.2430.0090.0090.0000.0000.0000.000
105C267LYS10.8021.03417.5760.0900.0900.0000.0000.0000.000
106C268ARG00.086-0.06023.473-0.007-0.0070.0000.0000.0000.000
107C268ARG10.7511.02123.5980.0640.0640.0000.0000.0000.000
108C269LYS00.091-0.12625.6230.0100.0100.0000.0000.0000.000
109C269LYS10.8991.08729.8550.0640.0640.0000.0000.0000.000
110C270PRO0-0.007-0.08429.314-0.002-0.0020.0000.0000.0000.000
111C271THR00.0540.01130.959-0.003-0.0030.0000.0000.0000.000
112C271THR0-0.0300.08430.3490.0020.0020.0000.0000.0000.000
113C272GLY00.053-0.07132.8570.0040.0040.0000.0000.0000.000
114C273ARG00.1960.03335.2570.0040.0040.0000.0000.0000.000
115C273ARG10.8531.08031.9460.0190.0190.0000.0000.0000.000
116C274GLU00.090-0.11832.3410.0050.0050.0000.0000.0000.000
117C274GLU-1-0.962-0.84929.167-0.040-0.0400.0000.0000.0000.000
118C275ILE00.005-0.09733.7420.0050.0050.0000.0000.0000.000
119C275ILE0-0.0510.08934.7400.0000.0000.0000.0000.0000.000
120C276ILE00.084-0.08136.2750.0030.0030.0000.0000.0000.000
121C276ILE0-0.0570.10939.1240.0000.0000.0000.0000.0000.000
122C277LEU00.118-0.09436.0180.0020.0020.0000.0000.0000.000
123C277LEU0-0.0990.07533.9820.0000.0000.0000.0000.0000.000
124C278LYS00.079-0.05636.3630.0040.0040.0000.0000.0000.000
125C278LYS10.8441.02431.3280.0180.0180.0000.0000.0000.000
126C279MET00.138-0.06936.9430.0030.0030.0000.0000.0000.000
127C279MET0-0.1390.06539.717-0.002-0.0020.0000.0000.0000.000
128C280SER00.061-0.02040.1360.0010.0010.0000.0000.0000.000
129C280SER0-0.1150.00840.0980.0010.0010.0000.0000.0000.000
130C281ALA00.102-0.06838.2300.0010.0010.0000.0000.0000.000
131C281ALA0-0.1270.06437.7030.0000.0000.0000.0000.0000.000
132C282GLU0-0.113-0.13339.7220.0040.0040.0000.0000.0000.000
133C282GLU-1-0.935-0.95939.3580.0000.0000.0000.0000.0000.000
134C302ALA00.175-0.00655.206-0.001-0.0010.0000.0000.0000.000
135C302ALA0-0.1300.09656.2850.0000.0000.0000.0000.0000.000
136C303TRP00.047-0.10554.5490.0010.0010.0000.0000.0000.000
137C303TRP0-0.1300.08253.846-0.001-0.0010.0000.0000.0000.000
138C304ASP00.103-0.11354.037-0.001-0.0010.0000.0000.0000.000
139C304ASP-1-0.919-0.79556.152-0.014-0.0140.0000.0000.0000.000
140C305LEU00.087-0.09952.4820.0000.0000.0000.0000.0000.000
141C305LEU0-0.1020.09049.7680.0000.0000.0000.0000.0000.000
142C306THR00.005-0.10652.830-0.001-0.0010.0000.0000.0000.000
143C306THR00.0140.08453.5480.0000.0000.0000.0000.0000.000
144C307GLU00.209-0.05453.5220.0000.0000.0000.0000.0000.000
145C307GLU-1-0.980-0.84557.252-0.015-0.0150.0000.0000.0000.000
146C308PHE00.029-0.10353.7120.0000.0000.0000.0000.0000.000
147C308PHE0-0.0940.09353.0810.0000.0000.0000.0000.0000.000
148C309THR00.030-0.07149.821-0.001-0.0010.0000.0000.0000.000
149C309THR0-0.1210.01348.8740.0000.0000.0000.0000.0000.000
150C310ASP00.020-0.15649.906-0.001-0.0010.0000.0000.0000.000
151C310ASP-1-0.942-0.81352.383-0.015-0.0150.0000.0000.0000.000
152C311ALA00.093-0.12051.3980.0000.0000.0000.0000.0000.000
153C311ALA0-0.0630.13153.6830.0000.0000.0000.0000.0000.000
154C312LEU00.092-0.10349.0260.0000.0000.0000.0000.0000.000
155C312LEU0-0.1190.10445.7990.0000.0000.0000.0000.0000.000
156C313LYS00.116-0.06646.637-0.002-0.0020.0000.0000.0000.000
157C313LYS10.8191.04046.4020.0200.0200.0000.0000.0000.000
158C314LYS00.089-0.07447.5340.0000.0000.0000.0000.0000.000
159C314LYS10.8641.05151.7980.0170.0170.0000.0000.0000.000
160C315ALA00.088-0.10849.6960.0010.0010.0000.0000.0000.000
161C315ALA0-0.0960.10049.7980.0000.0000.0000.0000.0000.000
162C316ASP00.056-0.10545.4050.0000.0000.0000.0000.0000.000
163C316ASP-1-1.038-0.89143.164-0.034-0.0340.0000.0000.0000.000
164C317HIS0-0.003-0.08744.955-0.002-0.0020.0000.0000.0000.000
165C317HIS10.7230.97041.9180.0250.0250.0000.0000.0000.000
166C318GLN00.152-0.07446.3250.0010.0010.0000.0000.0000.000
167C318GLN0-0.1480.06949.8310.0010.0010.0000.0000.0000.000
168C319ASP00.038-0.10647.2690.0020.0020.0000.0000.0000.000
169C319ASP-1-0.958-0.84246.659-0.027-0.0270.0000.0000.0000.000
170C320ASP00.089-0.13444.040-0.002-0.0020.0000.0000.0000.000
171C320ASP-1-0.895-0.77343.565-0.025-0.0250.0000.0000.0000.000
172C321GLY0-0.072-0.13043.8670.0000.0000.0000.0000.0000.000
173C322GLY0-0.073-0.04144.6220.0010.0010.0000.0000.0000.000
174C323ILE00.046-0.04940.883-0.002-0.0020.0000.0000.0000.000
175C323ILE0-0.0280.15239.465-0.001-0.0010.0000.0000.0000.000
176C324LYS00.083-0.09637.3620.0030.0030.0000.0000.0000.000
177C324LYS10.7270.98432.9560.0330.0330.0000.0000.0000.000
178C325ASP00.067-0.15336.967-0.005-0.0050.0000.0000.0000.000
179C325ASP-1-0.920-0.76536.863-0.027-0.0270.0000.0000.0000.000
180C326TYR00.013-0.12032.4020.0050.0050.0000.0000.0000.000
181C326TYR0-0.1080.08431.046-0.001-0.0010.0000.0000.0000.000
182C327GLY00.066-0.07032.3480.0020.0020.0000.0000.0000.000
183C328ASP00.014-0.03731.545-0.006-0.0060.0000.0000.0000.000
184C328ASP-1-0.877-0.77030.673-0.014-0.0140.0000.0000.0000.000
185C329GLY0-0.043-0.11428.476-0.005-0.0050.0000.0000.0000.000
186C330SER0-0.003-0.02026.745-0.007-0.0070.0000.0000.0000.000
187C330SER0-0.0890.02827.4670.0050.0050.0000.0000.0000.000
188C331ASN0-0.071-0.11826.542-0.001-0.0010.0000.0000.0000.000
189C331ASN0-0.1110.05826.7950.0040.0040.0000.0000.0000.000
190C332PRO00.093-0.06226.4960.0020.0020.0000.0000.0000.000
191C333THR00.0260.00029.1080.0020.0020.0000.0000.0000.000
192C333THR00.0330.09731.820-0.001-0.0010.0000.0000.0000.000
193C334PHE0-0.025-0.07431.385-0.003-0.0030.0000.0000.0000.000
194C334PHE0-0.0920.08827.614-0.001-0.0010.0000.0000.0000.000
195C335ASP00.234-0.09532.633-0.002-0.0020.0000.0000.0000.000
196C335ASP-1-1.009-0.84336.454-0.008-0.0080.0000.0000.0000.000
197C336ILE00.014-0.12336.144-0.002-0.0020.0000.0000.0000.000
198C336ILE0-0.0480.12035.3130.0000.0000.0000.0000.0000.000
199C337LYS00.029-0.09638.2850.0030.0030.0000.0000.0000.000
200C337LYS10.9121.07740.7630.0180.0180.0000.0000.0000.000
201C338LYS0-0.014-0.10841.918-0.001-0.0010.0000.0000.0000.000
202C338LYS11.0281.01744.8020.0190.0190.0000.0000.0000.000